Concepts of Genetics, 12E William S Klug Test Bank

Concepts of Genetics, 12E

By William S Klug

Email: richard@qwconsultancy.com

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) In the 1600s, William Harvey studied reproduction and development. What is the term given to 1) _______ the theory that states that an organism develops from the fertilized egg by a succession of developmental events that lead to an adult?

A) sequential pattern formation B) epigenesis C) equational transformation D) preformation E) transduction

2) What is the term given to the theory that states that the fertilized egg contains a complete

2) _______

miniature adult?

A) conjugation B) cell theory C) preformation D) transduction E) transformation

3) What is the term given to the theory that put forth the idea that living organisms could arise by

3) _______

incubating nonliving components?

A) spontaneous generation B) natural selection C) preformation D) collective combination E) evolution

4) What is a homunculus?

A) the intermediate stage of the DNA after CRISPR-Cas treatment B) during development sometimes a growing individual's cell can become mutated and one

4) _______

part of the child has different characteristics than the other C) a sperm or egg containing a miniature adult, perfect in size and proportion D) when the mitochondrion grows in size before splitting into two via fission E) a large cyst or growth on a plant due to viral infection

5) Who, along with Alfred Wallace, formulated the theory of natural selection?

A) Charles Darwin B) James Watson C) William Harvey D) Louis Pasteur E) Gregor Mendel

5) _______

6) Who was the Augustinian monk that conducted a decade of experiments on the garden pea,

6) _______

eventually showing that traits are passed from parents to offspring in predictable ways?

A) Gregor Mendel B) Hippocrates C) Francis Crick D) Aristotle

E) Alfred Wallace 7) In many species, there are two representatives of each chromosome. In such species, the

7) _______

characteristic number of chromosomes is called the ________ number. It is usually symbolized as ________.

A) monoploid; n B) diploid; 2n C) diploid; n D) haploid; n E) haploid; 2n

8) Genetics is the study of ________.

A) mutation and recession B) inheritance and variation C) replication and recombination D) transcription and translation E) diploid and haploid

8) _______

9) Early in the twentieth century, Walter Sutton and Theodor Boveri noted that the behavior of

9) _______

chromosomes during meiosis is identical to the behavior of genes during gamete formation.

They proposed that genes are carried on chromosomes, which led to the basis of the ________.

A) Law of Segregation B) Chromosome Theory of Inheritance C) Law of Independent Assortment D) First Law of Thermodynamics E) Chromosomal Maintenance Theory

10) What is a mutation?

A) an inherited change in a DNA sequence B) an inherited change in DNA sequences that is the source of all genetic variation C) a change in DNA that leads to death D) the source of all genetic variation E) an inherited changed in DNA sequence that is always bad for an organism

10) ______

11) Which of the following is TRUE about alleles?

A) The phenotype of the individual will always indicate with certainty the alleles of the

11) ______

individual.

B) Alleles come in two forms, the good form and the bad form.

C) Individuals carry both forms of each allele.

D) An allele is a variant form of a gene.

E) An individual will only carry one version of an allele.

12) Until the mid-1940s, many scientists considered proteins to be the likely candidates for the genetic material. Which of the following characteristics led scientist to believe DNA was NOT the genetic material?

A) DNA is more stable than protein.

B) DNA is less abundant than protein.

C) Protein can fold into may shapes.

D) DNA has less variation than protein.

E) DNA is less abundant than protein and DNA has less variation than protein.

12) ______

13) Name the individual who, while working with the garden pea in the mid-1850s, demonstrated

13) ______

quantitative patterns of heredity and developed a theory involving the behavior of hereditary factors.

A) Theodor Boveri B) George Wallace C) Walter Sutton D) Barbara McClintock E) Gregor Mendel

14) Which of the following is the subdiscipline of biology concerned with the study of heredity and

14) ______

variation at the molecular, cellular, developmental, organismal, and populational levels?

A) molecular biology B) biochemistry C) genetics D) cell biology E) cytogenetics

15) Which of the following is an example of natural selection?

A) bacteria can be effectively killed by treatment with bleach B) a bird's beak is able to effectively crack the seeds it encounters C) sometime during human's life they break a bone and it heals D) human beings develop freckles from being out in the sun E) depending on the food a turtle eats, it shell may grow faster or slower

15) ______

16) What term is used to describe the fact that different genes in an organism often provide

16) ______

differences in observable features?

A) genotype B) natural selection C) inheritance D) alleles E) phenotype

17) Which of the following is an example of heredity?

A) Doberman pinschers and boxers have similar body shapes.

B) Flying squirrels have a different mechanism of flight than mosquitos.

C) Both moths and birds have wings and can fly.

D) Flies and molluscs both have eyes.

E) Dalmation dogs all have spots.

17) ______

18) Which of the following is NOT an example of variation?

A) giraffes have not been seen in an albino form B) cats can have long or short fur C) both monocotyledons and dicotyledons perform the dark reaction D) a child does not have her mother's hair color E) lobsters can come in many colors including blue, read, and brown

18) ______

19) What would happen if, during meiosis, the chromosome number was not halved before egg

19) ______

and sperm formation?

A) the spindle would be compromised B) n would become halved C) each offspring would have different phenotypes than their parents

D) nothing E) in each successive generation, the offspring would double their chromosome number 20) Alternative forms of a gene are called ________.

A) alleles B) genotypes C) meiotic products D) mutants E) phenotypes

20) ______

21) The various characteristics of organisms that result from their genetic makeup are collectively

21) ______

referred to as an organism's ________.

A) phenotype B) proteome C) alleles D) genotype E) genome

22) Name the substance that serves as the hereditary material in eukaryotes and prokaryotes.

A) lipid B) DNA or deoxyribonucleic acid C) carbohydrate D) protein E) RNA or ribonucleic acid

22) ______

23) Which of the following contains all the others?

A) DNA strand B) hydrogen bond C) double helix D) sugar E) nucleotide

23) ______

24) A fundamental property of DNA's nitrogenous bases that is necessary for the double-stranded

24) ______

nature of its structure is ________.

A) ring structure B) anti-parallel C) deoxyribose versus ribose D) complementarity E) sugar phosphate backbone

25) Which of the following is the function of DNA? A) DNA is required when cells are using their ribosomes to translate a protein.

B) DNA is involved in the expression of stored genetic information.

C) DNA is used structurally to hold the nucleus together.

D) DNA serves to hold the information for protein, lipid, and carbohydrate storage.

E) DNA is responsible for the storage and replication of genetic information.

25) ______

26) Which of the following molecules serves the function to express the genetic material by being

26) ______

translated to protein?

A) RNA B) carbohydrate

C) lipid D) DNA E) cholesterol 27) Name the bases in DNA and their pairing specificities.

A) adenine:guanine, thymine:cytosine B) adenine:cytosine, guanine:uracil C) adenine:guanine, guanine:uracil D) adenine:thymine, guanine:cytosine E) adenine:uracil, guanine:cytosine

27) ______

28) The ________ consists of a linear series of three adjacent nucleotides present in mRNA

28) ______

molecules.

A) law of segregation B) messenger RNA C) genetic code D) chromosomal theory of inheritance E) Watson—Crick base pairing

29) Which of the following processes describes the formation of a complementary RNA molecule?

A) transcription B) replication C) translation D) mutation E) mosaicism

29) ______

30) If a scientist changed a cell's ionic composition and complementarity between DNA strands

30) ______

could no longer occur, what would the scientist first detect?

A) cell membranes would become less permeable B) DNA strands become shorter C) DNA becomes single stranded D) RNA would start binding to DNA E) ribosomes would move into the nucleus

31) Reference is often made to adapter molecules when describing protein synthesis in that they

31) ______

allow amino acids to associate with nucleic acids. To what class of molecules does this term refer?

A) protein B) DNA C) tRNA D) amino acids E) mRNA

32) Given that DNA is the genetic material in prokaryotes and eukaryotes, what other general structures (macromolecules) and substances made by the cell are associated with the expression of that genetic material?

A) lipids and carbohydrates B) RNA (messenger, ribosomal, and transfer), ribosomes, enzymes, and proteins C) DNA and protein D) DNA and RNA E) chromosomes

32) ______

33) Which of the following are true about codons?

A) They are complementary to DNA and are a two-nucleotide code for an amino acid.

B) They are complementary to DNA and specify amino acids at the ribosome.

C) They are placed at random in the RNA. D) They are complementary to RNA and specify amino acids at the ribosome.

E) They are a circular series of nucleotide triplets.

33) ______

34) What is another term for a biological catalyst?

A) enzyme B) protein C) codon

34) ______ D) lipid

E) ribosome

35) A protein's shape and chemical behavior are determined by ________.

A) the type of cell in which it resides B) the environment of an organism C) its linear sequence of amino acids D) the cholesterol makeup of the lipid membrane E) the cell's age

35) ______

36) Once a protein is made, its biochemical or structural properties play a role in producing

36) ______

________.

A) DNA B) chromosome C) phenotype D) genotype E) mutant

37) When mutation alters a gene, it may modify or even eliminate the encoded protein's usual

37) ______

________ and cause an altered ________.

A) structure; genotype B) function; phenotype C) ribosome; phenotype D) function; genotype E) cell type; genotype

38) Recombinant DNA technology is dependent on a particular class of enzymes, known as

38) ______

________ that cuts DNA at specific nucleotide sequences.

A) recombinant DNA technology B) restriction enzymes C) vectors D) clones E) genomes

39) What represents an organism's genome?

A) the nuclear and mitochondrial DNAs B) all the protein in a cell C) all the RNA in a cell D) a catalog of mutations in a cell E) an organism's genome can be defined as the complete haploid nuclear DNA content of an

39) ______

organism.

40) A ________ is an organism produced by biotechnology that involves the transfer of hereditary

trait s

across species.

40)

____ __

A) transgenic organism B) vector C) mutant D) frankenfood E) clone 41) What term is applied to a variety of projects whereby genome sequences are deposited in

41) ______

databases for research purposes?

A) proteomics B) genomics C) bioinformatics D) genetics E) cloning

42) Organisms that are well understood from a scientific standpoint and are often used in basic

42) ______

biological research are often called ________.

A) vectors B) model organisms C) clones D) restriction enzymes E) recombinant DNA technology

43) ________ is a discipline involved in the development of both hardware and software for processing, storing, and retrieving nucleotide and protein data.

A) Proteomics B) Bioinformatics C) Cloning D) Recombinant DNA technology E) Genomics

43) ______

1) B 2) C 3) A 4) C 5) A 6) A 7) B 8) B 9) B 10) B 11) D 12) E 13) E 14) C 15) B 16) E 17) E 18) C 19) E 20) A 21) A 22) B 23) C 24) D 25) E 26) A 27) D 28) C 29) A 30) C 31) C 32) B 33) B 34) A 35) C 36) C 37) B 38) B 39) E 40) A 41) B 42) B 43) B

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Living organisms are categorized into two major groups based on the presence or absence of a 1) _______ nucleus. What group is defined by the presence of a nucleus?

A) prokaryotic organism B) eukaryotic organism C) virus D) mitochondrial organism E) bacterium

2) What is the name of the membranous structure that compartmentalizes the cytoplasm of

2) _______

eukaryotic organisms?

A) ribosome B) nucleoid C) cytosol D) endoplasmic reticulum E) mitochondria

3) You have identified a mutant in human cells that when shifted to 37°C, the microfilaments

3) _______

depolymerize (fall apart). Which of the following would be true about this mutant at 37°C? A) The cells would no longer be able to produce ATP. B) The endoplasmic reticulum could still import polypeptides but could no longer synthesize lipids.

C) The sister chromatids would no longer be attached to each other.

D) The cells would change shape.

E) The mitochondria would no longer work.

4) Name two cellular organelles, each containing genetic material, which are involved in either

4) _______

photosynthesis or respiration.

A) lysosome and chloroplast B) chloroplasts and mitochondria C) rough and smooth endoplasmic reticula D) peroxisomes and mitochondria E) chloroplast and endoplasmic reticulum

5) The nucleolus organizer region (NOR) is responsible for production of what type of cell

5) _______

structure?

A) ribosome B) chromatids C) mitochondria D) endoplasmic reticulum E) nucleolus

6) The diploid chromosome number of an organism is usually represented as 2n. Humans have a

6) _______

diploid chromosome number of 46. What would be the expected haploid chromosome number in a human?

A) 16 B) 24 C) 92 D) 23 E) 12

7) Which chromosome has a telomere but the p arm is much shorter than the q arm?

7) _______

A) submetacentric B) sex chromosome C) acrocentric D) metacentric E) telocentric 8) Which of the following is true about sex-determining chromosomes?

A) They are independent during meiosis.

B) They are always metacentric.

C) They do not participate in meiosis.

D) They act like homologous chromosomes during meiosis so each gamete will get one sex

8) _______

chromosome.

E) They have the same gene configuration and same loci.

9) What significant genetic function occurs in the S phase of the cell cycle?

A) cytokinesis B) DNA synthesis C) karyokinesis D) centromere division E) chromosome condensation

9) _______

10) During interphase of the cell cycle, ________.

A) RNA replicates B) sister chromatids move to opposite poles C) DNA content essentially doubles

10) ______

D) the nuclear membrane disappears E) DNA recombines 11) The house fly, Musca domestica, has a haploid chromosome number of 6. How many chromatids should be present in a diploid, somatic, metaphase cell?

A) 6 B) 12 C) 3

D) 18

E) 24

12) How many haploid sets of chromosomes are present in a diploid individual cell with a chromosome number of 32?

A) 16 B) 2

C) 32

D) 1

11) ______

12) ______

E) 8

13) How many haploid sets of chromosomes are present in an individual cell that is pentaploid

13) ______

(5n)?

A) 3 B) 4 C) 2 D) 5 E) It is impossible to tell with the information given.

14) You may have heard through various media of an animal alleged to be the hybrid of a rabbit

14) ______

and a cat. Given that the cat (Felis domesticus) has a diploid chromosome number of 38 and a rabbit (Oryctolagus cuniculus) has a diploid chromosome number of 44, what would be the expected chromosome number in the somatic tissues of this alleged hybrid?

A) 38 B) 44 C) 82 D) 41 E) 40

15) Which of the follow could occur if a cell cycle checkpoint was missed?

15) ______

A) Cohesin could not function correctly.

B) An unreplicated chromosome could be put through mitosis.

C) The spindle apparatus would not form.

D) DNA would mutate during G2.

E) The cell cycle would be arrested until the error could be corrected.

16) In which stage of the cell cycle is G0 located?

A) S B) G1 C) G2

16) ______ D) anaphase

E) M

17) When cells withdraw from the continuous cell cycle and enter a "quiescent" phase, they are said to be in what stage?

A) G0

B) G1

C) M

D) S

17) ______

E) G2

18) A typical G1 nucleus is 2n and contains 2C (two complements) of DNA. Which of the

18) ______

following is true?

A) A cell in prophase is 2n and contains 2n of DNA. B) A prophase cell is 4n and contains 4C of DNA. C) A cell in G2 is 4n and contains 2C of DNA. D) A cell in metaphase is 2n and contains 2C of DNA. E) A cell in prophase is 2n and contains 4C of DNA.

19) Which part of interphase does DNA duplication take place?

A) S B) G1 C) M D) G0

19) ______ E) G2

20) The centromere of a chromosome separates during ________.

A) telophase B) interphase C) anaphase D) prophase E) prometaphase

20) ______

21) Normal diploid somatic (body) cells of the mosquito Culex pipiens contain six chromosomes.

21) ______

Assuming that all nuclear DNA is restricted to chromosomes and that the amount of nuclear DNA essentially doubles during the S phase of interphase, how much nuclear DNA would be present in metaphase I of mitosis? Note: Assume that the G1 nucleus of a mosquito cell contains 3.0 × 10-12 grams of DNA. A) 1.5 × 10−12 g

B) 3.0 × 10−12 g C) 12 × 10−12 g D) 6.0 × 10−12 g E) 0.75 × 10−12 g 22) If a typical somatic cell has 64 chromosomes, how many chromosomes are expected in each gamete of that organism?

A) 32 B) 128

C) 8

D) 64

E) 16

23) In an organism with 60 chromosomes, how many bivalents would be expected to form during meiosis?

A) 30

B) 240

C) 15

D) 60

22) ______

23) ______

E) 120

24) The ant, Myrmecia pilosula, is found in Australia and is named bulldog because of its aggressive

behavior. It

is 24) particularl y interestin g because it carries all its genetic informatio n in a single pair of chromoso mes. In other words, 2n = 2. (Males are haploid and have just one chromoso me.)

Which of the following figures would most likely represent a correct configurat ion of chromoso mes in a metaphas e I cell of a female?

A)

B)

____ __

C)

D)

E)

25) A G1 somatic cell nucleus in a female diploid Myrmecia pilosula (bulldog ant) contains 2

25) ______

picograms of DNA. How much DNA would be expected in a metaphase I cell of a female?

A) 16 picograms B) 8 picograms C) 4 picograms D) 32 picograms E) Not enough information is provided to answer the question.

26) Myrmecia pilosula (the bulldog ant) actually consists of several virtually identical, closely related

26) ______

species, with females having chromosome numbers of 18, 20, 32, 48, 60, 62, and 64. Assume one crossed a female of species (A) with 32 chromosomes and a male of species (B) with 9 chromosomes (males are haploid, and each gamete contains the n complement). How many chromosomes would one expect in the body (somatic) cells of the female offspring?

A) 4.5 B) 9 C) 41 D) 32 E) 25

27) What is the outcome of synapsis, a significant event in meiosis?

A) side-by-side alignment of homologous chromosomes B) monad movement to opposite poles C) dyad formation D) side-by-side alignment of nonhomologous chromosomes

27) ______

E) chiasma segregation 28) Which of the following is true about the second meiotic division?

A) The products are four identical gametes.

B) Synapsis occurring in the second meiotic division.

C) Sister chromatids are pulling apart.

D) Homologous chromosomes are pulling apart.

E) Nondisjunction would lead to extra bivalents forming.

28) ______

29) Which if the following is not a source of genetic variation in meiosis?

A) law of independent assortment B) the random lining up of chromosomes on the metaphase plate C) polar body formation D) tetrad formation E) crossing over

29) ______

30) The accompanying sketch depicts a cell from an organism in which 2n = 2 and each

30) ______

chromosome is metacentric.

Which of the following is the correct stage for this sketch?

A) anaphase of meiosis II B) anaphase of meiosis I C) telophase of meiosis II D) anaphase of mitosis E) telophase of mitosis

31) Given that each G1 nucleus from this organism contains 16 picograms of DNA, how many

31) ______

picograms of chromosomal DNA would you expect in the cell shown below?

A) 16

B) 4

C) 32

D) 2

E) 8

32) The horse (Equus caballus) has 32 pairs of chromosomes, whereas the donkey (Equus asinus) has

31

pairs

____ __

of 32) chromoso mes. How many chromoso mes would be expected in the somatic tissue of a mule, which is a hybrid of these two animals?

A) 126

B) 62

C) 64

D) 63

E) 60

33) Which of the following are the areas where chromatids intertwine during meiosis?

A) synapsis B) nondisjunction C) chiasma D) tetrad E) bivalent

33) ______

34) After meiosis II, ________ would be formed.

A) dyads B) chiasma C) tetrads

34) ______ D) monads

E) synapsis

35) Which of the following would occur if there was no chiasma formation in prophase I? A) All gametes would have the same phenotype.

B) In a heterozygote, there would only be a 2:2 formation after meiosis II, never a 1:1:1:1.

C) All gametes would have the same genotype.

D) In a heterozygote, there would only be a 1:1:1:1 formation after meiosis II, never a 2:2.

E) Mosaic chromosomes would form.

35) ______

36) Which term describes meiosis I? A) equinational B) confrontational C) multiplicative D) reducational E) middling

36) ______

37) Which if the following is true?

A) A chromosome always contains the same number of chromatids, regardless of phase of

37) ______

the mitotic or meiotic cell cycle.

B) A chromosome may contain one or two chromatids in different phases of the mitotic or meiotic cell cycle.

C) Cells are 4n after S phase.

D) Cells are considered to be 2n after meiosis I. E) Sister chromatids in mitosis are not identical.

38) If a typical G1 nucleus contains 2C (two complements) of DNA, a gamete that is haploid (n)

cont ains

________ of DNA.

____ __

38) A) 0.5C

B) 2C

C) 3C

D) 4C

E) 1C 39) ______

39) During meiosis, chromosome number reduction takes place in ________.

A) anaphase I B) prophase I C) metaphase I D) telophase II E) anaphase II 40) A bivalent at prophase I contains ________ chromatids.

A) three B) eight C) one

40) ______ D) four

E) two

41) The meiotic cell cycle involves ________ number of cell division(s) and ________ number of DNA replication(s).

A) two; two

B) two; one

C) one; two

D) two; zero

E) one; one 42) ______

42) An organism with a haploid number of 10 will produce ________ combinations of chromosomes at the end of meiosis.

A) 32 B) 1024

C) 10

D) 100

41) ______

E) 10,000

43) An organism with a diploid chromosome number of 46 will produce ________ combinations of

43) ______

chromosomes at the end of meiosis.

A) 8388608 B) 46 C) 23 D) 7.04 × 1013

E) 529 44) The stage at which "sister chromatids go to opposite poles" immediately follows which of the

44) ______

stages listed below?

A) mitotic metaphase B) metaphase of meiosis I C) metaphase of meiosis II D) A and B E) A and C

45) Drosophila melanogaster, the fruit fly, has a 2n chromosome number of 8. Assuming that a

45) ______

somatic G2 nucleus from one of the individuals in this scenario contains about 8.0 picograms of DNA, how much nuclear DNA would you expect in a fly egg?

A) 8 pg B) 4 pg C) 2 pg D) 16 pg E) 1 pg

46) In a healthy female, how many secondary oocytes would be expected to form from 100 primary

46) ______

oocytes? How many first polar bodies would be expected from 100 primary oocytes?

A) 200; 300 B) 100; 100 C) 200; 50 D) 100; 50 E) 50; 50

47) In a healthy male, how many sperm cells would be expected to be formed from (a) 400 primary spermatocytes? (b) 400 secondary spermatocytes?

A) (a) 800; (b) 800 B) (a) 400; (b) 400

47) ______

C) (a) 100; (b) 800 D) (a) 1600; (b) 800 E) (a) 1600; (b) 1600 48) There is about as much nuclear DNA in a primary spermatocyte as in ________ spermatids.

A) 3 B) 4 C) 1 D) 0.5 E) 2

48) ______

49) List, in order of appearance, all the cell types expected to be formed during spermatogenesis.

A) primary spermatocyte, secondary spermatocyte, spermatozoa, spermatid, spermatogonia B) primary spermatocyte, secondary spermatocyte, spermatid, spermatozoa, spermatogonia C) spermatozoa, spermatid, spermatogonia , primary spermatocyte, secondary spermatocyte D) spermatogonia, spermatozoa, spermatid, primary spermatocyte, secondary spermatocyte E) spermatogonia, primary spermatocyte, secondary spermatocyte, spermatid, spermatozoa

49) ______

50) List, in order of appearance, all the cell types expected to be formed during oogenesis.

A) primary oocyte, secondary oocyte and first polar body, second polar body, ootid,

50) ______

oogonium B) oogonium, primary oocyte, secondary oocyte and first polar body, ootid and second polar body C) primary oocyte, secondary oocyte and first polar body, ootid, second polar body, oogonium D) oogonium, primary oocyte, second polar body and ootid, secondary oocyte and first polar body E) primary oocyte, secondary oocyte and first polar body, oogonium, second polar body and ootid

51) In plants, which stage is haploid?

A) spermatozoa B) polar body C) sporophyte D) germ cell E) gametophyte

51) ______

52) Which of the following is diploid?

A) zygote B) gametophyte C) megaspore D) egg E) sperm

52) ______

53) Electron microscopy of metaphase chromosomes demonstrated various degrees of coiling.

53) ______

What was the name of the model that depicted this process?

A) chromatid folding B) packing C) condensation D) folded-fiber E) double-stranded

54) During the transition from interphase to metaphase chromosome, the DNA undergoes how much compaction?

A) 10 fold

B) 5000 fold

C) 500 fold

D) 2 fold

E) 50 fold

54) ______

1) B 2) D 3) D 4) B 5) A 6) D 7) C 8) D 9) B 10) C 11) E 12) B 13) D 14) D 15) B 16) B 17) A 18) E 19) A 20) C 21) D 22) A 23) A 24) D 25) C 26) E 27) A 28) C 29) C 30) A 31) A 32) D 33) C 34) D 35) B 36) D 37) A 38) E 39) A 40) D 41) B 42) B 43) A 44) E 45) B 46) B 47) D 48) B 49) E 50) B

51) E 52) A 53) D 54) B

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Name the single individual whose work in the mid-1800s contributed to our understanding of 1) _______ the particulate nature of inheritance as well as the basic genetic transmission patterns. With what organism did this person work?

A) Calvin Bridges; Drosophila B) Thomas Hunt Morgan; Drosophila C) George Beadle; Neurospora D) Boris Ephrussi; Ephestia E) Gregor Mendel; Pisum sativum

2) A recessive allele in dogs causes white spots. If two solid colored dogs are mated and produce a

2) _______

spotted offspring, what is the percentage chance their next puppy would be solid colored?

A) 75% B) about 90% C) 25% D) about 66% E) 50%

3) Polydactyly is expressed when an individual has extra fingers and/or toes. Assume that a man

3) _______

with six fingers on each hand and six toes on each foot marries a woman with a normal number of digits. Having extra digits is caused by a dominant allele. The couple has a son with normal hands and feet, but the couple's second child has extra digits. What is the probability that their next child will have polydactyly?

A) 7/16 B) 1/2 C) 1/32 D) 1/8 E) 3/4

4) Tightly curled or wooly hair is caused by a dominant gene in humans. If a heterozygous

4) _______

curly-haired person marries a person with straight hair, what percentage of their offspring would be expected to have straight hair?

A) 75% curly B) 25% curly C) 100% straight D) 50% straight E) It is impossible to predict the outcome.

5) You have identified a plant in your garden with a new flower color. You want to determine if

5) _______

this phenotype is dominant or recessive. Which cross would tell you this?

A) selfing the plant B) sequencing the DNA for the trait C) crossing the new plant to one you know has the dominant trait D) crossing the plant to one you know has the recessive trait E) crossing the plant to a plant of the same type of any color

6) Which types of phenotypic ratios are likely to occur in crosses when dealing with a single gene pair for which all the genotypic combinations are of equal viability?

A) 1:2:1, 3:1 B) 9:3:3:1, 27:9:9:9:3:3:3:1 C) 2:3, 1:2 D) 1:4:6:4:1, 1:1:1:1

6) _______

E) 12:3:1, 9:7 7) Assume that a black guinea pig crossed with an albino guinea pig produced 5 black offspring.

7) _______

When the albino was crossed with a second black guinea pig, 4 black and 3 albino offspring were produced. What genetic explanation would apply to these data?

A) albino = dominant; black = recessive B) albino = recessive; black = dominant C) albino = recessive; black = recessive D) albino = dominant; black = incompletely dominant E) albino and black = codominant

8) The process that leads to development haploid gamete is best described as ________.

A) replication B) Mendelian inheritance C) segregation D) dominance or recessiveness E) independent assortment

8) _______

9) Mendel crossed two pea plants with round seeds. All seeds of the offspring were round. He

9) _______

then crossed a plant with round seeds to a plant with wrinkled seeds and all offspring had wrinkled seeds. Which of the following is true?

A) wrinkled is dominant B) the trait does not breed true C) round is dominant D) a mutation occurred E) the plants he used were not true breeding

10) A cross between two individuals with different phenotypes that resulted in approximately 50%

10) ______

of each type of offspring would indicate the cross was ________.

A) true dominant to a heterozygous dominant B) a heterozygous dominant crossed to a homozygous recessive C) a homozygous recessive crossed to a heterozygous recessive D) true breeding dominant to recessive E) a heterozygous dominant crossed to a heterozygous recessive

11) Mendel's Law of Segregation is supported by a ________ testcross ratio.

A) 3:2 B) 3:1 C) 1:1 D) 5:2

11) ______ E) 2:1

12) To test Mendel's Law of Segregation, the experimenter needs ________.

A) a minimum of two contrasting forms of a gene B) at least 500 offspring to count C) access to several generations of data D) a DNA sequencing apparatus E) the ability to perform a test cross

12) ______

13) If an F2 generation from a self-cross always yields offspring in a 3:1 phenotypic ratio, which of

13) ______

the following P crosses could have occurred?

A) aa × Aa B) Aa × AA C) aa × aa

D) AA × AA

E) AA × aa

14) Assuming complete dominance, a phenotypic ratio of ________ is expected from a monohybrid sib or self-cross.

14) ______

A) 3:2

B) 5:2

C) 2:1

D) 3:1

E) 1:1

15) Assume that you have a garden and some pea plants have solid leaves and others have striped

15) ______

leaves. You conduct a series of crosses [(a) through (e)] and obtain the results given in the table.

Define gene symbols and give the possible genotypes of the parents of cross E.

A) striped is dominant to solid SS × ss B) striped is dominant to solid Ss × ss C) solid is dominant to striped Ss × ss D) solid is dominant to striped Ss × Ss E) solid is dominant to striped SS × ss 16) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene. Two

16) ______

parents with normal pigmentation have an albino child. What is the probability that their next child will be albino?

A) 1/16 B) 1/4 C) 1/3 D) 3/4 E) 1/2

17) Dentinogenesis imperfecta is a rare, autosomal, dominantly inherited disease of the teeth that

17) ______

occurs in about one in 8000 people. The teeth are somewhat brown in color, and the crowns wear down rapidly. Assume that a male with dentinogenesis imperfecta and no family history of the disease marries a woman with normal teeth. What is the probability that their first child will have dentinogenesis imperfecta?

A) 1/2 B) 3/4 C) 100% D) 1/4 E) 1/8

18) Mendel indicated that traits were made up of unit factors. Today, we call unit factors

18) ______

________.

A) alleles B) phenotypes C) genotypes D) genes E) characters

19) Assuming a typical monohybrid cross in which one allele is completely dominant to the other, what ratio is expected if the F1s are crossed?

A) 2:1 B) 1:1 C) 3:2

D) 4:3

19) ______

E) 3:1

20) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene. Two

20) ______

parents with normal pigmentation have an albino child. What is the probability that their next child will be wild type?

A) 3/16 B) 3/4 C) 0% D) 1/2 E) 1/8

21) The autosomal (not X-linked) gene for brachydactyly, short fingers, is dominant to normal

fing er

____ __

length.

21) Assume that a female with brachydac tyly in the heterozyg ous condition is married to a man with normal fingers.

What is the probabilit y that their first child will have brachydac tyly?

A) 1/8

B) 2/3

C) 1/2

D) 3/4

E) 1/4

22) Tightly curled hair is caused by a dominant autosomal gene in humans. If a heterozygous

22) ______

curly-haired person marries a person with straight hair, what phenotypes (and in what proportions) are expected in the offspring?

A) 3 curly : 1 straight B) 1 curly : 3 straight C) 2 curly : 1 straight D) 1 curly : 1 straight E) 1 curly : 2 straight

23) A certain type of congenital deafness in humans is caused by a rare autosomal dominant gene.

23) ______

In a mating involving a deaf man and a deaf woman, could all the children have normal hearing?

A) No, because it is dominant. Children always get the dominant alleles.

B) Yes, because traits assort independently.

C) No, because children favor their parents.

D) Yes, assuming that the parents are heterozygotes (because the gene is rare), it is possible that all of the children could have normal hearing.

E) Yes, because it must be recessive if it's rare.

24) A certain type of congenital deafness in humans is caused by a rare autosomal recessive gene.

In a mating involving a deaf man and a deaf woman, could some of the children have normal hearing?

A) No, traits get passed down from father to child and the father is deaf.

B) Yes, because it's rare.

C) Yes, because traits assort independently.

D) No, since the gene in question is recessive, both of the parents are homozygous and one

24) ______

would not

expect normal hearing in the offspring.

E) No, because the parents would teach their children sign language.

25) What are two typical testcross ratios?

A) 1:1 and 1:1:1:1 B) 1:1 and 9:3:3:1

25) ______ C) 3:1 and 1:1:1:1

D) 3:1 and 9:3:3:1

26) Which types of phenotypic ratios are likely to occur in crosses when dealing with two gene pairs for which all the genotypic combinations are of equal viability?

A) 6:6:2 B) 1:2:1, 3:1 C) 12:2:2 D) 9:3:3:1

26) ______

E) 2:3, 1:2

27) Which of the following describes the product law?

A) The probabilities of two events occurring in a specific sequence are the product of their

27) ______

individual probabilities squared.

B) The product of the sum of the probabilities of two simultaneous events describes the ability of those two events to occur together.

C) The probability of two or more independent events occurring simultaneously is equal to the sum of their individual probabilities.

D) The probability of two or more independent events occurring simultaneously is equal to the product of their individual probabilities.

E) The probably of two linked events occurring simultaneously is equal to the probabilities of each individual event.

28) Which types of phenotypic ratios are likely to occur in testcrosses when dealing with two gene

28) ______

pairs for which all the genotypic combinations are of equal viability?

A) 1:2:1, 3:1 B) 12:3:1, 9:7 C) 1:1:1:1 D) 9:3:3:1, 27:9:9:9:3:3:3:1 E) 2:3, 1:2

29) The phenotype of vestigial (short) wings (vg) in Drosophila melanogaster is caused by a recessive

29) ______

mutant gene that independently assorts with a recessive gene for hairy (h) body. Assume that a cross is made between a fly with normal wings and a hairy body and a fly with vestigial wings and normal body hair. The wild-type F1 flies were crossed among each other to produce 1024 offspring. Which phenotypes would you expect among the 1024 offspring, and how many of each phenotype would you expect?

A) Phenotypes: wild, vestigial, hairy, and vestigial hairy; Numbers expected: wild (576), vestigial (192), hairy (192), and vestigial hairy (64).

B) All vestigial hairy.

C) Phenotypes: wild, vestigial, hairy, and vestigial hairy; Numbers expected: wild (192), vestigial (256), hairy (64), and vestigial hairy (192).

D) Phenotypes: wild, vestigial, hairy, and vestigial hairy; Numbers expected: wild (256), vestigial (256), hairy (256), and vestigial hairy (256).

E) All wild type.

30) Which phenotypic ratio is likely to occur in crosses of two completely dominant, independently segregating gene pairs when both parents are fully heterozygous?

A) 9:3:3:1 B) 3:1 C) 3:2:3:1 D) 2:4:6:8

31) What is segregation?

A) Fertilization is random.

B) Genes lie on chromosomes.

30) ______

E) 1:1:1:1 31) ______

C) During gamete formation, allele pairs are separated to form haploid gametes.

D) Chromosomes can swap information during meiosis.

E) During gamete formation, segregating pairs of unit factors assort independently of each other.

32) What is independent assortment?

A) During gamete formation, segregating pairs of unit factors assort independently of each

32) ______

other.

B) During gamete formation, allele pairs are separated to form haploid gametes.

C) Fertilization is random.

D) Chromosomes can swap information during meiosis.

E) Genes lie on chromosomes.

33) Under what conditions does one expect a 9:3:3:1 ratio?

A) dihybrid test cross (F2) with independently assorting, completely dominant genes B) monohybrid test cross (F2) with independently assorting, completely dominant genes C) monohybrid cross (F2) with independently assorting, completely dominant genes D) dihybrid cross (F1) with independently assorting, completely dominant genes E) dihybrid cross (F2) with independently assorting, completely dominant genes

33) ______

34) Under what conditions does one expect a 1:1:1:1 ratio?

A) AaBb × aabb B) AaBb × AaBb C) AAbb × aaBB D) Aabb × AABB E) AABB × aabb

34) ______

35) What conditions are likely to apply if the progeny from the cross AaBb × AaBb appear in the

35) ______

9:3:3:1 ratio?

A) dihybrid test cross B) complete dominance, independent assortment, and no gene interaction C) dihybrid cross with incomplete dominance D) incomplete segregation and complete dominance E) gene interaction and independent assortment

36) Which types of phenotypic ratios are likely to occur in crosses when dealing with three gene

36) ______

pairs for which all the genotypic combinations are of equal viability?

A) 2:3, 1:2 B) 1:2:1, 3:1 C) 1:4:6:4:1, 1:1:1:1 D) 27:9:9:9:3:3:3:1 E) 12:3:1, 9:7

37) According to Mendel's model, because of the ________ of chromosomes during meiosis, all possible combinations of gametes will be formed in equal frequency.

A) law of segregation B) independent assortment C) the product rule D) chromosomal theory of inheritance E) law of unit factors

37) ______

38) How many kinds of gametes will be expected from an individual with the genotype PpCcTTRr? A) 16 B) 2 C) 8 D) 4 E) 1

38) ______

39) For the purposes of this question, assume that being Rh+ is a consequence of D and that Rh−

39) ______

individuals are dd. The ability to taste phenylthiocarbamide (PTC) is determined by the gene symbolized T (tt are nontasters). A female whose mother was Rh− has the MN blood group, is Rh+ and a nontaster of PTC, and is married to a man who is MM, Rh −, and a nontaster. Assume that all the loci discussed in this problem are autosomal and independently assorting. Which of the following is NOT a possible genotype of the children?

A) MNDdtt B) MNddtt C) MNDDtt D) MMDdtt E) MMddtt

40) ______

40) Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is self-fertilized. If the capital letters represent dominant, independently assorting alleles. How many different genotypes will occur in the F2?

A) 32 B) 243 C) 25 D) 64 E) 1024

41) ______

41) Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is self-fertilized. If the capital letters represent dominant, independently assorting alleles. What proportion of the F2 genotypes will be recessive for all five loci?

A) 1/64 B) 1/16 C) 1/1024 D) 1/243 E) 1/256

42) Assuming independent assortment, what proportion of the offspring of the cross AaBbCcDd × AabbCCdd will have the aabbccdd genotype?

A) 0% B) 1/512 C) 1/256

D) 1/64

E) 1/1024

43) How many different kinds of gametes can be produced by an individual with the genotype AABbCCddEeFf? A) 16

B) 64

C) 8

D) 4

42) ______

43) ______

E) 32

44) Which of the following represents the trihybrid ratio if AaBbCc is selfed?

A) 9:3:3:1 B) 18:12:15:9:9:3:3:1 C) 27:9:9:9:3:3:3:1 D) 16:9:9:6:6:3:3:1 E) 1:1:1:1:1:1:1:1

44) ______

45) Assuming no crossing over between the gene in question and the centromere, when do alleles

45) ______

segregate during meiosis?

A) anaphase II B) anaphase I C) interphase D) prophase II E) prophase I

46) According to Charles Darwin and Alfred Wallace, variations followed a more continuous pattern. According to Mendel's model, variation due to dominance-recessive relationships followed a more ________ form.

A) smooth B) discontinuous C) transferred D) abstract

46) ______

E) normalized 47) Which of the following groups of scientists were influential around the year 1900 in setting the

47) ______

stage for our present understanding of transmission genetics?

A) Watson, Crick, Wilkins, and Franklin B) Darwin, Mendel, and Lamarck C) Hippocrates, Aristotle, and Kölreuter D) Beadle, Tatum, and Lederberg E) de Vries, Correns, Tschermak, Sutton, and Boveri

48) The number of possible gametes, each with different chromosome compositions, is 2n, where n

48) ______

equals ________.

A) the haploid number B) the number of genes C) the diploid number D) the number of offspring E) the number of alleles

49) What meiotic process, relative to the number of chromosomes of a given species, accounts for a

49) ______

significant amount of genetic variation in gametes?

A) independent assortment of chromosomes B) pairing of homologous chromosomes C) trivalent formation D) formation of the meiotic spindle during chromosome segregation E) bivalent formation

50) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene (a). Two

50) ______

parents with normal pigmentation have an albino child. What is the probability that their next child will be an albino girl?

A) 1/8 B) 3/4 C) 1/2 D) 1/3 E) 1/4

51) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene (a). Two

51) ______

parents with normal pigmentation have an albino child. What is the probability that their next three children will be albino?

A) 1/4 B) 1/64 C) 3/4 D) 0% E) 1/8

52) Dentinogenesis imperfecta is a rare, autosomal, dominantly inherited disease of the teeth that

52) ______

occurs in about one in 8000 people (Witkop 1957). The teeth are somewhat brown in color, and the crowns wear down rapidly. Assume that a male with dentinogenesis imperfecta and no family history of the disease marries a woman with normal teeth. What is the probability that their first two children will have dentinogenesis imperfecta?

A) 1/2 B) 1/8 C) 100% D) 1/4 E) 3/4

53) Dentinogenesis imperfecta is a rare, autosomal, dominantly inherited disease of the teeth that

53) ______

occurs in about one in 8000 people (Witkop 1957). The teeth are somewhat brown in color, and the crowns wear down rapidly. Assume that a male with dentinogenesis imperfecta and no family history of the disease marries a woman with normal teeth. What is the probability that their first child will be a girl with dentinogenesis imperfecta?

A) 100% B) 1/8 C) 3/4 D) 1/4 E) 1/2

54) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene. Two parents with normal pigmentation have an albino child. What is the probability that their next

chil will be d a wild

type girl?

____ __

54) A) 0%

B) 1/4

C) 3/8

D) 3/4

E) 1/2

55) Albinism, lack of pigmentation in humans, results from an autosomal recessive gene. Two

55) ______

parents with normal pigmentation have an albino child. What is the probability that their next three children will be wild type?

A) 3/64 B) 1/32 C) 1/4 D) 3/8 E) 0%

56) The autosomal (not X-linked) gene for brachydactyly, short fingers, is dominant to normal

56) ______

finger length. Assume that a female with brachydactyly in the heterozygous condition is married to a man with normal fingers. What is the probability that their first two children will have brachydactyly?

A) 2/3 B) 1/4 C) 1/8 D) 3/4 E) 1/2

57) The autosomal (not X-linked) gene for brachydactyly, short fingers, is dominant to normal

57) ______

finger length. Assume that a female with brachydactyly in the heterozygous condition is married to a man with normal fingers. What is the probability that their first child will be a brachydactylous girl?

A) 3/4 B) 1/4 C) 1/2 D) 2/3 E) 1/8

58) For which of the following questions would you use the sum law?

A) determining the change of rolling a 5 on a ten-sided die B) determining the chance of pulling either a club or a heart from a deck of cards C) determining the chance of pulling an ace from a deck of cards D) determining the chance of having a tall plant with purple flowers E) determining the chance of having a baby girl

58) ______

59) The Chi-square test involves a statistical comparison between measured (observed) and

59) ______

predicted (expected) values. One generally determines degrees of freedom as ________.

A) one less than the number of classes being compared B) the sum of the two categories C) ten minus the sum of the two categories D) the number of categories being compared E) one more than the number of classes being compared

60) In what ways is sample size related to statistical testing?

A) By increasing sample size, one decreases the reliability of the statistical test and increases

60) ______

the likelihood of erroneous conclusions from chance fluctuations in the data.

B) The larger the sample size is, the more likely you are to introduce errors into your data.

C) By increasing sample size, one increases the reliability of the statistical test and increases the likelihood of erroneous conclusions from chance fluctuations in the data.

D) By increasing sample size, one increases the reliability of the statistical test and decreases the likelihood of erroneous conclusions from chance fluctuations in the data.

E) There is no correlation.

61) In a Chi-square analysis, what general condition causes one to reject (fail to accept) the null hypothesis?

A) when observed >> expected B) usually when the probability value is less than 0.005 C) usually when the probability value is less than 0.5 D) when observed = expected

61) ______

E) usually when the probability value is less than 0.05 62) If one is testing a goodness of fit to a 9:3:3:1 ratio, how many degrees of freedom would be associated with the Chi-square analysis?

A) 1 B) 2

C) 3

D) 4

62) ______

E) 5

63) Which of the following is true?

A) With the test of a 3:1 ratio, there are three degrees of freedom.

B) Assume that a Chi-square test was conducted to test the goodness of fit to a 3:1 ratio and

63) ______

that a Chi-square value of 2.62 was obtained. The null hypothesis should be accepted.

C) Assume that a Chi-square test was conducted to test the goodness of fit to a 9:3:3:1 ratio and a Chi-square value of 10.62 was obtained. The null hypothesis should be accepted.

D) The large the Chi-square value, the more likely your results are real.

E) Assume that a Chi-square test provided a probability value of 0.02. The null hypothesis should be accepted.

64) In a Chi-square test, as the value of the χ2 increases, the likelihood of rejecting the null

64) ______

hypothesis ________.

A) increases B) is doubled C) increases by a factor of 10 D) stays the same E) decreases

65) In studies of human genetics, usually a single individual brings the condition to the attention of

65) ______

a scientist or physician. When pedigrees are developed to illustrate transmission of the trait, what term does one use to refer to this individual?

A) proband B) mutant C) cousin D) F1 B E) child

66) Which of the following best describes the relationship at the molecular level between mutant alleles and phenotype?

A) A mutant allele will cause only one phenotype.

B) A mutant allele will cause the wild-type protein not to be made.

C) The wild-type allele is always dominant.

D) Mutant alleles will only cause problems when seen in the homozygous form, no matter the gene affected.

E) A mutant allele can have different effects depending on the gene product's function.

66) ______

1) E 2) A 3) B 4) D 5) D 6) A 7) B 8) C 9) A 10) B 11) C 12) A 13) E 14) D 15) C 16) A 17) A 18) A 19) E 20) A 21) C 22) D 23) D 24) D 25) A 26) D 27) D 28) C 29) A 30) A 31) C 32) A 33) E 34) A 35) B 36) D 37) B 38) C 39) C 40) B 41) D 42) A 43) C 44) C 45) B 46) B 47) E 48) A 49) A 50) A

51) B 52) D 53) D 54) C 55) A 56) B 57) B 58) B 59) A 60) D 61) E 62) C 63) B 64) A 65) A 66) E

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) A mutation in a gene often results in a reduction of the product of that gene. The term for this 1) _______ type of mutation is ________.

A) multiple allelism B) loss of function or null (in the case of complete loss) C) incomplete dominance D) gain of function E) codominance

2) Which mutations are generally dominant since one copy in a diploid organism is sufficient to

2) _______

alter the normal phenotype?

A) gain of function B) loss of function C) neutral D) null E) conditional

3) Assume that a mutation occurs in the gene responsible for the production of hexosaminidase A,

3) _______

such that only about 50% of the enzyme activity is found in the heterozygote compared with a homozygous normal individual. If heterozygotes are phenotypically normal, we would say that the mutant allele is ________ to its normal allele.

A) dominant B) epistatic C) gain of function D) auxotrophic E) recessive

4) What is the most prevalent form of an allele called?

A) normal B) dominant C) recessive

4) _______ D) neutral

E) wild type

5) Which of the following is true?

A) A neutral mutation leads to a phenotype that can help or hurt the organism depending on

5) _______

the environment.

B) A mutation in the DNA can be observed at the macroscopic level even if there's no change in phenotype.

C) Each biochemical pathway is governed by one gene.

D) A neutral mutation leads to no discernable phenotype.

E) A neutral allele leads to a change in function in a protein that neither harms nor helps an organism.

6) Typically, when one wishes to represent a gene, the symbol used is ________.

A) in all upper case letters B) underlined C) in italics D) in all lowercase letters E) in bold print

6) _______

7) With incomplete dominance, a likely ratio resulting from a monohybrid cross would be

________.

7)

_______ A) 3:3

B) 3:1

C) 1:2:1

D) 1:2:2:4

E) 9:3:3:1

8) Assume that a dihybrid cross (AaBb × AaBb) is made in which the gene loci are autosomal,

8) _______

independently assorting, and incompletely dominant. What phenotypic ratio would you expect from such a cross?

A) 2:2:2:2:2:2:2:2 B) 1:2:1:2:4:2:1:2:1 C) 1:2:1:2:2:2:1:4:1 D) 2:1:1:2:2:1:4:2:2 E) 1:2:2:1:4:2:1:2:1

9) Assume that a cross is made between two organisms that are both heterozygous for a gene that

9) _______

shows incomplete dominance. What phenotypic and genotypic ratios are expected in the offspring?

A) phenotypic 1:1:1:1; genotypic 1:2:1 B) phenotypic 3:1; genotypic 1:2:1 C) phenotypic 1:2:1; genotypic 1:1:1:1 D) phenotypic 1:2:1; genotypic 1:3 E) phenotypic 1:2:1; genotypic 1:2:1

10) Assume that a dihybrid cross is made in which the genes' loci are autosomal, independently

10) ______

assorting, and incompletely dominant. How many different phenotypes are expected in the offspring?

A) 4 B) 9 C) 6 D) 12 E) 2

11) A ________ ratio indicates incomplete dominance.

A) 3:1 B) 1:2:1 C) 1:1:1:1

11) ______ D) 2:2:2

E) 9:7

12) The trait of medium-sized leaves in iris is determined by the genetic condition PP′. Plants with

12) ______

large leaves are PP, whereas plants with small leaves are P′P′. A cross is made between two plants each with medium-sized leaves. What is the term for this allelic relationship?

A) epistasis B) positional effect C) multiple alleles D) codominance E) incomplete dominance

13) The trait of medium-sized leaves in iris is determined by the genetic condition PP′. Plants with

13) ______

large leaves are PP, whereas plants with small leaves are P′P′. A cross is made between two plants each with medium-sized leaves. If they produce 80 seedlings, what would be the expected phenotypes, and in what numbers would they be expected?

A) 20 (large leaves), 20 (medium leaves), 40 (small leaves) B) 40 (large leaves), 0 (medium leaves), 40 (small leaves) C) 40 (large leaves), 40 (medium leaves), 0 (small leaves) D) 10 (large leaves), 60 (medium leaves), 10 (small leaves) E) 20 (large leaves), 40 (medium leaves), 20 (small leaves)

14) The trait for medium-sized leaves in iris is determined by the genetic condition PP′. Plants with large leaves are PP, whereas plants with small leaves are P′P′. The trait for red flowers is controlled by the genes RR, pink by RR′, and white by R′R′. A cross is made between two plants each with medium-sized leaves and pink flowers. If they produce 320 seedlings, what would be

the notype expe s, and cted in phe what

____ __

numbers 14) would they be expected?

Assume no linkage.

A) 20 large, red; 40 medium, red; 20 small, red; 80 large, pink; 40 medium, pink; 40 small, pink; 20 large, white; 40 medium, white; 20 small, white B) 40 large, red; 20 medium, red; 40 small, red; 20 large, pink; 80 medium, pink; 20 small, pink; 40 large, white; 20 medium, white; 40 small, white C) 80 large, red; 40 medium, red; 20 small, red; 40 large, pink; 20 medium, pink; 40 small, pink; 20 large, white; 40 medium, white; 20 small, white D) 35 large, red; 35 medium, red; 35 small, red; 35 large, pink; 35 medium, pink; 35 small, pink; 35 large, white; 35 medium, white; 35 small, white E) 20 large, red; 40 medium, red; 20 small, red; 40 large, pink; 80 medium, pink; 40 small, pink; 20 large, white; 40 medium, white; 20 small, white

15) The following coat colors are known to be determined by alleles at one locus in horses:

15) ______

palomino = golden coat with lighter mane and tail cremello = almost white chestnut = brown The following table gives ratios obtained in matings of the above varieties: Cross 1 2 3 4

Parents cremello x cremello chestnut x chestnut cremello x chestnut palomino x palomino

Offspring all cremello all chestnut all palomino 1/4 = chestnut 1/2 = palomino 1/4 cremello

Assign gene symbols for the genetic control of coat color on the basis of these data.

A) C1C1 = palomino, C2C2 = chestnut, C1C2 = cremello

B) C1C1 = cremello, C2C2 = chestnut, C1C2 = palomino C) C1C1 = palomino, C2C2 = cremello, C1C2 = chestnut D) C1C1 = chestnut, C2C2 = cremello, C1C2 = palomino E) C1C1 = chestnut, C2C2 = palomino, C1C2 = cremello 16) Which of the following statements is true?

A) Even in a seemingly clear-cut example of complete dominance, at the protein or enzyme

16) ______

level, one can detect about half the activity or gene product.

B) The threshold effect is only seen in incomplete dominance, not in codominance.

C) An individual won't show incomplete dominance if one allele is a loss of function allele.

D) In the threshold effect, one would expect the gain of function mutant to be recessive.

E) With both incomplete dominance and codominance, one expects heterozygous and homozygous classes to be phenotypically identical.

17) Which of the following is an example of codominance?

A) flowers of a certain plant can come in purple, blue, or yellow

17) ______

B) there are many possible mutations that lead to white eyes in flies C) in roan cattle, you can see a mix or both red and white furs D) a certain plant can have jagged, rough, or smooth edges on its leaves E) a scorpion's venom is more potent when it's younger 18) What is the blood type of individuals who cannot add the terminal sugar to the H substance?

A) Bombay phenotype B) B C) AB D) A E) O

18) ______

19) A situation in which there are more than two alternative forms of a given gene would be called

19) ______

________.

A) hemizygosity B) multiple alleles C) alternation of generations D) incomplete dominance E) codominance

20) In mice, there is a set of multiple alleles of a gene for coat color. Four of those alleles are as

20) ______

follows: C = full color (wild type) cch = chinchilla cd = dilution c = albino Given that the gene locus is not sex-linked and that each allele is dominant to those lower in the list, give the phenotypic ratios expected from the following cross. wild (heterozygous for dilution) × chinchilla (heterozygous for albino) A) 1 full color : 1 chinchilla : 2 dilution : 1 albino B) 2 full color : 1 chinchilla : 1 dilution C) 2 full color : 2 chinchilla : 1 dilution D) 1 chinchilla : 2 dilution : 1 albino E) 1 full color : 1 chinchilla : 1 dilution : 1 albino

21) In mice, there is a set of multiple alleles of a gene for coat color. Four of those alleles are as follows: C = full color (wild type) cch = chinchilla cd = dilution c = albino Given that the gene locus is not sex-linked and that each allele is dominant to those lower in the list, give the phenotypic ratios expected from the following cross. chinchilla (heterozygous for albino) × albino A) 1 chinchilla : 2 albino B) 1 full color : 1 chinchilla : 1 albino C) 1 chinchilla :1 albino D) 2 chinchilla : 1 albino E) 1 dilution : 1 chinchilla : 1 albino

21) ______

22) In a mating between individuals with the genotypes IAi × ii, what percentage of the offspring are expected to have the O blood type?

A) 100% B) 75%

C) 0%

D) 25%

E) 50%

23) In a mating between individuals with the genotypes IAIB × ii, what percentage of the offspring are expected to have the O blood type?

A) 100% B) 50%

C) 75%

D) 0%

22) ______

23) ______

E) 25%

24) With ________, there will be more than two genetic alternatives for a given locus.

A) multiple alleles B) codominance C) incomplete dominance D) epistasis E) gain of function mutant

24) ______

25) The ABO blood group locus in humans provides an example of ________.

A) epistasis B) auxotrophy C) conditional alleles D) multiple alleles E) incomplete dominance

25) ______

26) What would be a typical phenotypic monohybrid ratio in which a lethal allele is involved?

A) 6:2:3:1 B) 3:1 C) 9:3:3:1 D) 2:1 E) 13:5

26) ______

27) Achondroplasia is a form of human dwarfism. If two individuals with achondroplasia have

27) ______

children with the following ratio, 2 dwarf to 1 wild type, what is the means of inheritance of this phenotype?

A) epistasis B) simple dominance C) simple recessive D) recessive lethal E) dominant lethal

28) An allele of RNA polymerase in Drosophila demonstrates a recessive lethal inheritance pattern.

28) ______

Which of the following is true?

A) Homozygous recessive offspring will never be seen.

B) Two homozygous recessive parents will have 100% homozygous offspring.

C) The threshold effect is not seen in recessive lethality.

D) Homozygous lethal genes will always demonstrate a gain of function pattern.

E) Two heterozygotes will have offspring with a 2:1 pattern.

29) A snapdragon plant has red, pink, or white flowers, inherited in an incomplete dominance pattern. It can come in tall or dwarf (homozygous recessive) varieties. What is the ratio expected if you cross a pink tall (heterozygous) plant with a pink short plant?

A) 3 red tall : 3 red short : 1 white tall : 1 white short B) 2 red tall : 2 red short : 1 pink tall : 1 pink short : 1 white tall : 1 white short C) 1 red tall : 1 red short : 1 pink tall : 1 pink short : 1 white tall : 1 white short D) 2 red tall : 1 red short : 1 pink tall : 1 pink short : 2 white tall : 1 white short E) 1 red tall : 1 red short : 2 pink tall : 2 pink short : 1 white tall : 1 white short

29) ______

30) Rabbits can come in an allelic series where brown > himilayan > chinchilla > albino, where >

30) ______

means dominant over. They also can come in long (recessive) and short fur. You wish to obtain rabbit babies that are albino with long fur. Which of the following crosses would you do?

A) albino with long fur × homozygous himilayan with short fur (heterozygote) B) homozygous brown with long fur × albino with short fur (heterozygote) C) albino with long fur × albino with short fur (homozygous) D) chinchilla heterozygous with albino with short fur (heterozygous) × brown heterozygous with albino with long fur E) albino with long fur × brown chinchilla heterozygote with long fur

31) What term is used to express the idea that several genes exert influence over the same

31) ______

characteristic?

A) transformation B) coextension C) terminal interaction D) gene interaction E) co-adhesion

32) A condition in which one gene pair masks the expression of a nonallelic gene pair is called

32) ______

________.

A) recessiveness B) dominance C) epistasis D) additive alleles E) codominance

33) Typical ratios resulting from epistatic interactions in dihybrid crosses would be ________.

A) 1:2:2:4:1:2:1:2:1, 1:2:1 B) 3:1, 1:1 C) 9:3:3:1, 1:2:1 D) 1:1:1:1, 1:4:6:4:1 E) 9:3:4, 9:7

33) ______

34) A mutant gene that produces brown eyes (bw) is located on chromosome #2 of Drosophila

34) ______

melanogaster, whereas a mutant gene producing bright red eyes, scarlet (st), is located on chromosome #3. Phenotypically, wild-type flies (with dull red eyes), whose mothers had brown eyes and whose fathers had scarlet eyes, were mated. The 800 offspring possessed the following phenotypes: wild type (dull red), white, scarlet (bright red), and brown. Most of the 800 offspring had wild-type eyes, whereas those with white eyes were the least frequent.

From the information presented above, how many white-eyed flies would you expect in the F2 generation?

A) 450

B) 50

C) 350

D) 200

E) 150

35) In the mouse, gene A allows pigmentation to be deposited in the individual coat hairs; its allele a prevents such deposition of pigment, resulting in an albino. Gene B gives agouti (wild-type fur); its allele b gives black fur. What would the expected ratio of the progeny be in a cross of a doubly heterozygous agouti mouse mated with a doubly homozygous recessive white mouse?

A) 3 (agouti) :4 (black) : 9 (albino) B) 1 (agouti) :1 (black) : 2 (albino) C) 1 (agouti) :1 (black) :1 (albino)

35) ______

D) 9 (black) : 27(albino) E) 9 (agouti) :3 (black) : 4 (albino) 36) Which of the following statements is false?

A) Epistasis would not be expected to occur in a biochemical pathway.

B) Epistasis refers to a gene (or genes) of one pair masking the expression of a gene (or

36) ______

genes) at a different locus.

C) When an allele is dominant, the heterozygous combination is the same phenotypically as one of the homozygotes.

D) Dominance refers to the form of expression of a gene in relation to its allele (or alleles).

E) Epistasis is a nonallelic interaction; dominance is an allelic interaction.

37) ______

37) The following F2 results occur from a typical dihybrid cross: purple: white: white: white:

A_B_ aaB_ A_bb aabb

9/16 3/16 3/16 1/1

If a double heterozygote (AaBb) is crossed with a fully recessive organism (aabb), what phenotypic ratio is expected in the offspring?

A) 9 purple : 7 white B) 1 purple : 3 white C) 1 purple : 1 white D) 3 purple : 1 white E) 12 purple : 4 white

38) Many of the color varieties of summer squash are determined by several interacting loci: AA or

38) ______

Aa gives white, aaBB or aaBb gives yellow, and aabb produces green. Assume that two fully heterozygous plants are crossed. Give the phenotypes (with frequencies) of the offspring.

A) 12 white : 3 yellow : 1 green B) 3 white : 9 yellow : 4 green C) 4 white :9 yellow : 3 green D) 12 white : 1 yellow : 3 green E) 9 white : 3 yellow : 4 green

39) Which of the following ratio is not likely to occur in crosses (F2) when one is dealing with two interacting, epistatic gene pairs?

A) 3:1 B) 9:7

C) 15:1

D) 12:3:1

39) ______

E) 9:3:4

40) Assume that a dihybrid F2 ratio, resulting from epistasis, was 9:3:4. If a double heterozygote

40) ______

was crossed with the fully recessive type, what phenotypic ratio is expected among the offspring?

A) 9:3:4 B) 12: 3: 1 C) 1:2:1 D) 1:1:1 E) 1:1:2

41) Assume that a dihybrid F2 ratio, resulting from epistasis, was 15:1. If a double heterozygote

41) ______

was crossed with the fully recessive type, what phenotypic ratio is expected among the offspring?

A) 1:3 B) 1:2 C) 5:7 D) 1:1 E) 3:1

42) Comb shape in chickens represents one of the classic examples of gene interaction. Two gene pairs interact to influence the shape of the comb. The genes for rose comb (R) and pea comb (P)

toge produc ther e

walnut 42) comb. The fully homozygo us recessive condition (rrpp) produces the single comb.

Assume that a rose-comb chicken is crossed with a walnut-co mb chicken and the following offspring are produced: 17 walnut, 16 rose, 7 pea, and 6 single.

What are the probable genotypes of the parents?

____ __

A) Rrpp × RrPp B) RRPP × Rrpp C) rrpp × RrPp D) rrPP × RRpp E) RrPp × RRPP 43) Many of the color varieties of summer squash are determined by several interacting loci: AA or

43) ______

Aa gives white, aaBB or aaBb gives yellow, and aabb produces green. Crosses among heterozygotes give a 12:3:1 ratio. What type of gene interaction would account for these results?

A) epistasis B) complementation C) multiple alleles D) conditional lethal E) incomplete dominance

44) A particular cross gives a modified dihybrid ratio of 9:7. What phenotypic ratio would you expect in a testcross of the fully heterozygous F1 crossed with the fully recessive type?

44) ______

A) 2:1

B) 1:3

C) 1:1

D) 2:3

E) 3:1

45) When two squash plants with disc-shaped fruit are crossed, depending on the genotype of the

45) ______

parents, disc, sphere, and long fruits may be seen in the offspring. This is an example of ________.

A) dominant lethal B) heterogenous trait C) epistasis D) complementation E) two gene interaction with novel phenotypes

46) What is a heterogenous trait?

A) a trait in which different sexes have different manifestations of severity B) a trait in which many genes can potentially be mutated to lead to the same phenotype C) a trait in which offspring show a more severe phenotype depending on which parent

46) ______

donates the allele

D) a trait that differs, but not based on environmental conditions E) a trait in which the phenotype differs based on the environment 47) Alleles that are masked by an epistatic locus are said to be ________ to the genes at that locus.

A) hypostatic B) auxotrophic C) functional D) complementary E) conditional

47) ______

48) Multiple mutations that are found to be present in a single gene are said to belong to the same

48) ______

________ group.

A) phenotypic B) expression C) allelic D) complementation E) transfer

49) Which of the following crosses would indicate that the mutants were in the same

49) ______

complementation group?

A) pink eye fly × pink eye fly -> all white eye offspring B) red eye fly × red eye fly -> 3 : 1 ratio C) pink eye fly × pink eye fly -> pink eye fly D) pink eye fly × pink eye fly -> purple eye flies E) pink eye fly × white eye fly -> all white eyes

50) What is the term for a gene mutation that leads to a myriad of disparate effects?

A) lethal allele B) multiple allele C) pleiotropy D) expressivity E) complementation

50) ______

51) With which of the following would hemizygosity most likely be associated?

A) X-linked inheritance

51) ______

B) codominance C) sex-limited inheritance D) incomplete dominance E) trihybrid crosses 52) Because of the mechanism of sex determination, males of many species can be neither

52) ______

homozygous nor heterozygous. Such males are said to be ________.

A) recessive B) complementary C) dominant D) hemizygous E) None of the answers listed are correct.

53) The white-eyed gene in Drosophila is recessive and sex-linked. Assume that a white-eyed female

53) ______

is mated to a wild-type male. What would be the phenotypes of the offspring?

A) females wild type, males white eyed B) all white eyed C) females half wild type, half white eyed; males white eyed D) all wild type E) females white eyed; males wild type

54) Two forms of hemophilia are determined by genes on the X chromosome in humans. Assume

54) ______

that a phenotypically normal woman whose father had hemophilia is married to a normal man.

What is the probability that their first son will have hemophilia?

A) 100% B) zero C) 1/2 D) 1/3 E) 1/4

55) Two forms of hemophilia are determined by genes on the X chromosome in humans. Assume

55) ______

that a phenotypically normal woman whose father had hemophilia is married to a normal man.

What is the probability that their first daughter will have hemophilia?

A) 100% B) 1/4 C) zero D) 1/2 E) 1/3

56) The deficiency of the enzyme glucose-6-phosphate dehydrogenase (G6PD) is inherited as a

56) ______

recessive gene on the X chromosome in humans. A phenotypically normal woman (whose father had G6PD) is married to a normal man. What fraction of their sons would be expected to have G6PD? A) 1/3 B) 1/2 C) zero D) 1/4 E) 100%

57) A cross was made between homozygous wild-type female Drosophila and yellow-bodied male Drosophila. All of the resulting offspring were phenotypically wild type. Offspring of the F 2 generation had the following phenotypes: Sex male male female

Phenotype Number wild 96 yellow 99 wild 197

Based on this information, how is the yellow allele inherited?

A) recessive, X linked B) sex-influenced inheritance C) dominant, autosomal D) dominant, X linked E) recessive, autosomal

57) ______

58) If an X-linked disorder is lethal to the affected individual prior to the age at which one reaches

58) ______

reproductive maturation, the lethality will be expressed only in males. Why is this so?

A) At the cellular level, the protein will work less well in the male's cells.

B) Because it's sex-limited inheritance, females do not demonstrate the phenotype.

C) This is not true. We will see the lethality in females as well.

D) As it's a lethal allele, it will kill the homozygous recessive first. These are the males.

E) The only sources of the lethal allele in the population are heterozygous females who are "carriers" and do not express the disorder.

59) The accompanying figure is a pedigree of a fairly common human hereditary trait in which the

59) ______

boxes represent males and the circles represent females. Shading symbolizes the abnormal phenotype.

Given that one gene pair is involved, what is the inheritance pattern?

A) dominant, X linked B) sex-influenced inheritance C) recessive, autosomal D) recessive, X linked E) dominant, autosomal

60) The genes for zeste eyes and forked bristles are located on the X chromosome in Drosophila

60) ______

melanogaster. Both genes are recessive. A cross is made between a zeste-eyed female and a forked-bristled male. If 200 offspring from this cross were obtained, what is the expected offspring's phenotype and sex?

A) 50 wild female, 50 forked female; 50 zeste forked male, 50 zeste male B) all wild type C) 100 forked female; 100 zeste male D) 100 zeste female; 100 zeste forked male E) 100 wild female; 100 zeste male

61) Which of the following is true about X-linkage?

A) X linkage demonstrates that only the wild-type allele is the dominant allele.

B) One result of X-linkage is a crisscross pattern of inheritance in which sons express

61) ______

recessive genes of their fathers and daughters express recessive genes of their mothers.

C) Females will only express dominant alleles.

D) One result of X-linkage is a crisscross pattern of inheritance in which daughters express recessive genes of their fathers and sons express recessive genes of their mothers.

E) Males are more liable to express recessive alleles as they are hemizygous.

62) What is a significant difference between X-linked and sex-influenced inheritances?

A) Sex-influenced inheritance requires epistasis. X-linked inheritance does not.

B) X-linked inheritance affects females and sex-influenced inheritance affects males.

62) ______

C) X-limited inheritance is only recessive. Sex-influenced inheritance can be recessive or dominant.

D) There are no differences. They are the same.

E) In X-linked inheritance, the gene in question is on the X chromosome; in sex-influenced inheritance, the gene is autosomal.

63) Name three modes of inheritance that are influenced by the sex of individuals.

A) sex-influenced, epistasis, sex-limited B) epistasis, conditional alleles, expressivity C) X-linked, sex-influenced, sex-limited D) penetrance, X-limited inheritance, X-linked inheritance E) conditional alleles, sex-limited, X-linked

63) ______

64) Which of the following is an example of sex-limited inheritance?

A) beard formation in humans B) hemophilia C) cat fur length D) human baldness E) hair color in humans

64) ______

65) A ________ is one whose expression is influenced by some environmental condition.

A) conditional mutant B) multiple allele C) positional effect D) expressive allele E) X-linked allele

65) ______

66) Which of the following statements is true?

A) The term expressivity defines the percentage of individuals who show at least some degree

66) ______

of expression of a mutant genotype.

B) Genomic imprinting occurs when one allele converts another.

C) Penetrance specifically refers to the expression of lethal genes in heterozygotes.

D) Genomic anticipation refers to observations that a genetic disorder occurs at an earlier age in successive generations, whereas genetic imprinting occurs when gene expression varies depending on parental origin.

E) Expressivity is the term used to describe the balanced genetic output from a hemizygous condition.

1) B 2) A 3) E 4) E 5) D 6) C 7) C 8) B 9) E 10) B 11) B 12) E 13) E 14) E 15) B 16) A 17) C 18) E 19) B 20) B 21) C 22) E 23) D 24) A 25) D 26) D 27) E 28) A 29) E 30) D 31) D 32) C 33) E 34) B 35) B 36) A 37) B 38) A 39) A 40) E 41) E 42) A 43) A 44) B 45) E 46) B 47) A 48) D 49) C 50) C

51) A 52) D 53) A 54) C 55) C 56) B 57) A 58) E 59) C 60) E 61) E 62) E 63) C 64) A 65) A 66) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) What term is applied when two genes fail to assort independently, that is, they tend to 1) _______ segregate together during gamete formation?

A) discontinuous inheritance B) linkage C) Mendelian inheritance D) dominance and/or recessiveness E) tetrad analysis

2) Which of the following statements is true?

A) The chromosomal theory of inheritance denotes that linked alleles will never be

2) _______

separated.

B) If two gene loci are on nonhomologous chromosomes, genes at these loci are expected to assort independently.

C) Linkage without crossing over leads to all recombinant chromosomes.

D) The linkage ratio is best seen in genes on nonhomologous chromosomes.

E) A centromere and its surrounding genes constitute a linkage group.

3) A ________ is all the genes on a single chromosome.

A) chromosomal conglomeration B) recombination group C) linkage group D) gene loci line E) genetic allele formation

3) _______

4) If complete linkage occurs, we expect ________.

A) a 9:3:3:1 ratio in the F2 B) a 1:1:1:1 ratio in the test cross C) to see all four types of offspring D) to see only parental phenotypes in the F2 of the appropriate test cross E) to see only recombinant phenotypes in the F2 of the appropriate test cross

4) _______

5) Assume that a cross is made between AaBb and aabb plants and that the offspring fall into

5) _______

approximately equal numbers of the following groups: AaBb, Aabb, aaBb, aabb. These results are consistent with which of the following?

A) alternation of generations B) independent assortment C) hemizygosity D) complete linkage E) incomplete dominance

6) Which of the following scenarios would erroneously lead you to believe two genes reside on different chromosomes when they in fact are on the same chromosome?

A) the genes are very close together on the chromosome, such that there is never a crossover between them B) the genes are very far apart on the same chromosome, such that there is never a crossover between them

6) _______

C) a mating between consanguineous individuals D) the genes are very far apart on the same chromosome, such that there is always a crossover between them

E) too large a sample size 7) Assume that a cross is made between AaBb and aabb plants and that the offspring occur in the

7) _______

following numbers: 106 AaBb, 48 Aabb, 52 aaBb, 94 aabb. These results are consistent with which of the following?

A) linkage with 50% crossing over B) linkage with approximately 33 map units between the two gene loci C) independent assortment D) sex-linked inheritance with 30% crossing over E) 100% recombination

8) Who was the student in Morgan's laboratory who first realized that the sequence of genes could

8) _______

be determined by Morgan's proposal that two genes located relatively close to each other are less likely to form chiasma between them than if the two genes were relatively far apart?

A) Thomas Hunt B) Gregor Mendel C) A. H. Sturtevant D) Barbara McClintock E) Charles Darwin

9) At what stage of the meiotic cell cycle and during what chromosomal configuration does

9) _______

crossing over occur?

A) during synapsis in prometaphase B) during synapsis at the four-strand stage of meiosis C) at the four-strand stage of meiosis, after synapsis of homologous chromosomes, and before the end of prophase I D) in S phase of meiosis E) during bivalent formation, after synapsis of homologous chromosomes, and before the end of prophase I

10) Below is a diagram during crossing over. Describe the outcome.

10) ______

A) segregation of alleles (A and a) during meiosis II B) a 1:1 ratio C) formation of parental alleles only D) segregation of alleles (A and a) during meiosis I E) offspring will not look like either parent 11) What is the relationship between the degree of crossing over and the distance between two

genes?

11)

______ A) It is direct: as the distance decreases, the frequency of recombination increases.

B) It is direct: as the distance increases, the frequency of recombination increases.

C) It is indirect: as the distance decreases, the frequency of recombination doubles.

D) It is indirect: as the distance increases, the frequency of recombination doubles.

E) There is no correlation.

12) Assume that there are 12 map units between two loci in the mouse and that you are able to

12) ______

microscopically observe meiotic chromosomes in this organism. If you examined 200 primary oocytes, in how many would you expect to see a chiasma between the two loci mentioned above?

A) 96 B) 24 C) 6 D) 48 E) 12

13) The cross GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge

13) ______

103. From these data, one can conclude that ________.

A) the G and E loci are segregating independently B) the G and E loci assort independently C) the G and E loci reside on the same chromosome over 50 map units apart D) the G and E loci are linked E) the G and E loci show complete linkage

14) The cross GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge

14) ______

103. From these data one can conclude that ________.

A) the recombinant progeny are GE/ge and GE/ge B) the recombinant progeny are GE/GE and ge/ge C) the recombinant progeny are gE/GE and GE/ge D) the recombinant progeny are gE/ge and Ge/ge E) the recombinant progeny are Ge/Ge and gE/gE

15) Choose the true statement below.

A) When two genes are over 50 map units apart, a crossover would theoretically occur 0% of

15) ______

the time.

B) When two genes are over 50 map units apart, a crossover can theoretically occur 100% of the time.

C) Linkage (viewed from results of typical crosses) always occurs when two loci are on the same chromosome.

D) A single crossover on a chromosome will always yield the recombinant phenotype of the genes you are interested in.

E) The percentage of tetrads involved in exchange between two genes is equal to the number of recombinant progeny seen.

16) The cross GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge

16) ______

103. From these data, one can conclude that there are ________ map units between the G and E loci.

A) 25 B) 15 C) 5 D) 10 E) 20

17) The genes for purple eyes and curved wings are approximately 21 map units apart on chromosome II in Drosophila. Assume that a purple-eyed female was mated to a curved wing male and that the resulting F1 phenotypically wild-type females were mated to purple, curved males. Of 1000 offspring, what would be the expected number of flies with purple eyes and curved wings?

A) 105 B) 540 C) 210 D) 790 E) 395

17) ______

18) Phenotypically wild-type F1 female Drosophila, whose mothers had light eyes (lt) and fathers

18) ______

had straw (stw) bristles, produced the following offspring when crossed to homozygous light-straw males: Phenotype light-straw wild-type light straw

Number 22 18 970 970 Total: 2000

Compute the map distance between the light and straw loci.

A) 98 map units B) 8 map units C) 4 map units D) 12 map units E) 2 map units

19) Assume that the genes for tan body and bare wings are 15 map units apart on chromosome II in

19) ______

Drosophila. Assume also that a tan-bodied, bare-winged female was mated to a wild-type male and that the resulting F1 phenotypically wild-type females were mated to tan-bodied, bare-winged males. Of 1000 offspring, what would be the expected of wild-type offspring, and in what numbers would they be expected?

A) 8 B) 75 C) 50 D) 350 E) 425

20) Assume that investigators crossed a strain of flies carrying the dominant eye mutation Lobe on

20) ______

the second chromosome with a strain homozygous for the second chromosome recessive mutations smooth abdomen and straw body. The F1 Lobe females were then backcrossed with homozygous smooth abdomen, straw body males, and the following phenotypes were observed: smooth abdomen, straw body Lobe smooth abdomen, Lobe straw body smooth abdomen Lobe, straw body

820 780 42 58 148 152

Give the gene order of these three loci.

A) smooth, Lobe, straw B) Lobe, straw, smooth C) Lobe, smooth, straw D) smooth, straw, Lobe E) it is impossible to tell

21) Assume that investigators crossed a strain of flies carrying the dominant eye mutation Lobe on the second chromosome with a strain homozygous for the second chromosome recessive mutations smooth abdomen and straw body. The F1 Lobe females were then backcrossed with homozygous smooth abdomen, straw body males, and the following phenotypes were observed:

straw smo body oth Lobe abd smoot ome h n, abdom

en, Lobe straw body smooth abdomen Lobe, straw body

21)

____ __

42 58 148

152

What is the coefficient of coincidenc e?

A) 0.75

B) 0.25

C) zero

D) 0.33

E) 0.5

22) Assume that investigators crossed a strain of flies carrying the dominant eye mutation Lobe on

22) ______

the second chromosome with a strain homozygous for the second chromosome recessive mutations smooth abdomen and straw body. The F1 Lobe females were then backcrossed with homozygous smooth abdomen, straw body males, and the following phenotypes were observed: smooth abdomen, straw body Lobe smooth abdomen, Lobe straw body smooth abdomen Lobe, straw body

820 780 42 58 148 152

Give the map units between Lobe and straw.

A) 10 B) 20 C) 7.5

D) 5

E) 15

23) In Drosophila, assume that the gene for scute bristles (s) is located at map position 0.0 and that

23) ______

the gene for ruby eyes (r) is at position 15.0. Both genes are located on the X chromosome and are recessive to their wild-type alleles. A cross is made between scute-bristled females and ruby-eyed males. Phenotypically wild-type F1 females were then mated to homozygous double mutant males, and 1000 offspring were produced. Give the frequency of scute expected.

A) 425 B) 360 C) 500 D) 75 E) 250

24) Assume that a cross is made between AaBb and aabb plants and that the offspring occur in the

24) ______

following numbers: 106 AaBb, 48 Aabb, 52 aaBb, 94 aabb. These results are consistent with which scenario described?

A) The genes are unlinked.

B) There is a very high coefficient of coincidence.

C) In the AaBb parent, the dominant alleles are on one homolog and the recessive alleles are on the other.

D) In the AaBb parent, each homolog has one dominant allele and one recessive allele.

E) It is impossible to tell.

25) In the fruit fly, Drosophila melanogaster, a spineless (no wing bristles) female fly is mated to a male that is claret (dark eyes) and hairless (no thoracic bristles). Phenotypically wild-type F1

fem progen ale y were

____ __

mated to 25) fully homozygo us (mutant) males, and the following progeny (1000 total) were observed: Phenotype s spineless wild claret, spineless claret claret, hairless hairless, claret, spineless hairless hairless, spineless

Number Observed 321 38 130 18 309

32 140 12

What is the gene order?

A) hairless, spineless, claret B) claret, spineless, hairless C) it is impossible to tell D) claret, hairless, spineless E) spineless, claret, hairless 26) In the fruit fly, Drosophila melanogaster, a spineless (no wing bristles) female fly is mated to a male that is claret (dark eyes) and hairless (no thoracic bristles). Phenotypically wild-type F1 female progeny were mated to fully homozygous (mutant) males, and the following progeny (1000 total) were observed: Phenotypes spineless wild claret, spineless claret claret, hairless hairless, claret, spineless hairless

Number Observed 321 38 130 18 309 32 140

hairl n ess, hairles spin s and eless spinele ss?

Wha t are the map dista nces bet wee

26)

______ A) 50

B) 45

C) 10

D) 30

E) 40

27) Three loci, mitochondrial malate dehydrogenase that forms a and b (MDHa, MDHb), glucuronidase

27) ______

that forms 1 and 2 (GUS1, GUS2), and a histone gene that forms + and − (H+, H−), are located on chromosome #7 in humans. Assume that the MDH locus is at position 35, GUS at position 45, and H at position 75. A female whose mother was homozygous for MDHa, GUS2, and H+ and whose father was homozygous for MDHb, GUS1, and H− produces a sample of 1000 egg cells.

Give the expected numbers of the MDHa GUS2 H− cells she would produce. Assume no chromosomal interference.

A) 0 B) 15 C) 135 D) 235 E) 315

28) In a three-point mapping experiment, which class do you expect to find the least?

A) recombinant B) single crossover C) parental D) noncrossover E) double crossover

28) ______

29) In a three-point mapping experiment, how many different genotypic classes are expected?

A) 1 B) 2 C) 0 D) 8 E) 4

29) ______

30) The phenomenon in which one crossover decreases the likelihood of crossovers in nearby

30) ______

regions is called ________.

A) reciprocal genetic exchange B) mitotic recombination C) negative interference D) positive interference E) chiasma

31) Assume that two genes are 80 map units apart on chromosome II of Drosophila and that a cross

31) ______

is made between a doubly heterozygous female and a homozygous recessive male. What percent recombination would be expected in the offspring of this type of cross?

A) 80 B) 5 C) 50 D) 30 E) 100

32) Which of the following is an example of positive interference?

A) A crossover in one region inhibits crossovers in nearby regions.

B) A single crossover stimulates further recombination.

C) Crossovers will not occur near centromeres.

D) Double crossovers do not occur.

E) An actively transcribed gene is less likely to undergo crossover than a quiescent one.

32) ______

33) Which of the following best describes why mapping is most accurate when genes are close

33) ______

together on a chromosome?

A) Double crossover events yield a result that looks the same as one crossover in a two gene mapping experiment and this throws off the calculations.

B) This is not true; relative distance of two loci on a chromosome has no effect on accuracy of mapping.

C) This is not true; mapping genes is most accurate when genes are far away from each other.

D) Double crossover events yield a result that looks the same as no crossover in a two gene

mapping

experiment and this throws off the calculations.

E) The centromere gets in the way.

34) The coefficient of coincidence reflects the frequency of observed double crossovers compared to

34) ______

the frequency of expected double crossovers. What is the relationship between the coefficient of coincidence and interference?

A) Interference equals the coefficient of coincidence.

B) Interference is recombinants minus nonrecombinants.

C) Interference is one minus the coefficient of coincidence.

D) Interference is the inverse square of the coefficient of coincidence.

E) Interference equals the coefficient of coincidence divided by the map units calculated.

35) If interference is complete, what would be the frequency of double crossovers?

A) 0.75 B) 2 C) 1 D) 0

35) ______ E) 0.25

36) ________ occurs when a crossover in one region of a chromosome reduces crossovers in nearby

36) ______

regions.

A) Negative interference B) Positive interference C) Triple crossover D) Negative supercoiling E) Coefficient of coincidence

37) What two terms apply to the fusion of cultured human and mouse cells that produces cell lines

37) ______

that are useful in assigning a gene to a particular human chromosome?

A) forward and reverse B) single and double C) heterokaryon and synkaryon D) positive and negative E) lod score and pod score

38) What is a lod score?

A) determination of how often double crossovers occur B) a calculation to show how much interference is occurring in crossover formation C) determination of how often a gene mapping experiment gives the correct results D) determination of the probability that two traits are linked by analyzing pedigrees E) a method using cell fusion to determine on which chromosome a gene resides

38) ______

39) Methods for determining the linkage group and genetic map in humans involve which of the

39) ______

following?

A) tetrad analysis and bromodeoxyuridine B) twin spots and tetrad analysis C) chiasma-type and classical analyses D) DNA markers E) zygotene and pachytene DNA syntheses

40) What relatively recent scientific advancement has made mapping by linkage or classical genetic mapping approaches virtually obsolete?

A) positive interference B) negative interference C) the inclusion of the X and Y chromosomes in SNP experiments

40) ______

D) the genome sequence of a species E) the use of synteny 41) What is a physical map of a chromosome?

A) identification of the length of the chromosome by comparing it to known chromosomes B) description of the base pair difference between two loci C) determination of how far apart genes are my recombination mapping D) determination of where the centromere lies E) determination of the p and q arm length

41) ______

42) Based on the classic experiments of Creighton and McClintock with maize, crossing over

42) ______

involves a physical exchange between chromatids. What particular chromosomal characteristic allowed their experiments to succeed?

A) colored bands along the lengths of a chromosome B) a missing chromosome C) a chromosome with a unique cytological marker D) three chromosomes with identical structure E) an extra chromosome

43) Sister chromatid exchanges increase in frequency in the presence of X-rays, certain viruses,

43) ______

ultraviolet light, and certain chemical mutagens. In what autosomal recessive disorder is there known to be an increase in sister chromatid exchanges?

A) cystic fibrosis B) Harlequin syndrome C) Huntington's disease D) achondroplasia E) Bloom syndrome

44) Which of the following statements is true?

A) Crossing over has a cytological basis.

B) Exchanges occur between homologous chromosomes, but never between sister chromatids.

C) Sister chromatid exchange would mutate one strand of DNA. D) Sister chromatid exchange would lead to a reshuffling of alleles.

E) Harlequin chromosomes are a result of homologous recombination.

44) ______

1) B 2) B 3) C 4) D 5) B 6) D 7) B 8) C 9) C 10) A 11) B 12) D 13) D 14) D 15) B 16) E 17) E 18) E 19) E 20) A 21) C 22) E 23) A 24) C 25) D 26) C 27) C 28) E 29) D 30) D 31) C 32) A 33) D 34) C 35) D 36) B 37) C 38) D 39) D 40) D 41) B 42) C 43) B 44) A

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Max Delbrück presented the first evidence that bacteria are capable of spontaneous mutation.

1) _______ What is the name of the test that Delbrück used to demonstrate this phenomenon?

A) logarithmic test B) fluctuation test C) prototrophic test D) auxotrophic test E) lag test

2) ________ are bacteria that can grow on minimal medium and are assumed to be wild type.

A) Prototrophs B) Mutants C) F+ cells D) Hfr E) Auxotrophs

2) _______

3) ________ have lost, through ________, the ability to grow on minimal medium.

A) prototrophs; mutation B) mutants; adaptation C) auxotrophs; mutation D) prototrophs; adaptation E) auxotrophs; adaptation

3) _______

4) What is the adaptation hypothesis?

A) The phage mutates to infect bacteria more effectively.

B) The phage and bacteria both mutate so the phage becomes less virulent.

C) The phage mutates so it can't infect bacteria any longer.

D) The bacteria will mutate so it can become an auxotroph.

E) The phage stimulates the bacteria to mutate to become immune to the phage.

4) _______

5) In which phase of the bacterial cell cycle do the cells grow most quickly?

A) lag B) fluctuation C) stationary D) log E) adaptation

5) _______

6) Analyze the following growth of a bacterial colony.

the W bacteriu hat m? is the ge not yp e of

Medium Complete with glucose Complete with lactose (no glucose) Minimal Minimal media plus biotin, threonine, leucine, methionine, and lactose Minimal media plus biotin, leucine, and glucose Minimal media plus threonine, leucine, and lactose Minimal media plus leucine, methionine, and glucose

Growth Yes Yes No Yes No No Yes

6)

_______

A) bio+, leu+, lac− B) bio+, thr+, leu+, met+ C) leu+, met+, lac− D) leu+, met+, lac+ E) bio+, thr+, lac− 7) Which of the following is true about the interrupted mating technique?

A) Time of contact is not applicable to this protocol.

B) Donor will pass only beneficial genes to the recipient.

C) The recipient bacterium will choose the best genes.

D) Genes are transferred from the donor to recipient in a linear fashion based upon time of

7) _______

contact.

E) Genes will be passed from the centromere.

8) Jacob, Wollman, and others developed a linkage map of E. coli that is based on time. What form

8) _______

of recombination is involved in generating a linkage map based on time?

A) adaptation B) time of transfer C) conjugation D) transformation E) transduction

9) Assume that the gene trpA in an auxotrophic strain of E. coli is located at 27 minutes, whereas

9) _______

the gene pyrE is located at 81 minutes.

Present an experimental scheme that would allow you to convert one of the auxotrophic strains to a prototrophic strain.

A) Hfr (auxotroph) × F− (auxotroph)

B) F+ (wild type) × F− (auxotroph) C) Hfr (wild type) × F− (auxotroph) D) Hfr (auxotroph) × F− (wild type) E) F+ (auxotroph) × F− (wild type) 10) ________ bacteria contain an F factor or plasmid that is capable of initiating conjugation.

10) ______

________ bacteria contain an F plasmid that possesses a portion of the bacterial chromosome.

A) F−; F+

B) Merozygotes; F− C) F+; Merozygotes D) F−; Hfr E) F+; Hfr 11) Describing bacterial conjugation, which of the following matings is most likely to result in a change from F- to F+?

A) donor Hfr recipient FB) donor F− recipient Hfr C) donor Hfr recipient F+ D) donor F− recipient F+ E) donor F+ recipient F−

11) ______

12) What is a form of recombination in bacteria that involves the F plasmid?

A) transformation B) conjugation C) transduction D) fluctuation E) adaptation

12) ______

13) How do different strains of E. coli can reveal different linkage arrangements of genes in Hfr

13) ______

crosses?

A) Different strains may have different F factors and therefore different initiation points for chromosome transfer.

B) They do not. All Hfr strains are identical.

C) In different Hfr strains, different genes will be transferred based on where the centromere resides.

D) In different Hfr strains, genes can be in different order on the chromosome.

E) Hfr strains will demonstrate different areas of recombination, due to dominance and recessiveness of genes.

14) Which of the following is true about a merozygote?

A) Merozygotes were crucial to our understanding of the formation of the sex pilus.

B) A conjugation with an Hfr donor will never produce a merozygote.

C) It is formed from an Hfr to F+ cross.

D) It can spontaneously form from an Hfr cell.

E) A merozygote can form if an F factor carries chromosomal DNA and is injected into an F −

14) ______

cell.

15) In a bacterial cross in which the donor (Hfr) is a+b+ and the recipient strain (F−) is a−b−, it is

15) ______

expected that recombinant bacteria ________.

A) will be a mixture of a+b+, a−b−, and a−b+

B) will be a mixture of a+b+ and a−b− C) will be a mixture of a+b+, a−b−, a+b−, and a−b+ D) will all remain a−b− E) will all be a+b+ 16) ________ can initiate chromosome transfer from one E. coli to another.

A) A temperate phage B) An Hfr cell C) A plasmid D) An F− cell E) An F+ cell

16) ______

17) The interrupted mating technique was used with a series of Hfr strains and the following

17) ______

results were obtained.

1) LQRYX 2) QLPZ 3) BTZP 4) LPZTB 5) PLQRY What is the order of the genes?

A) BTPZLQRYX

B) PZTBXYRQL C) XYRPZTBQL D) XYRQLPZTB E) RLQZTBXYP 18) Once an exogenous (foreign) piece of DNA is in the bacterial cell, it is incorporated into the

18) ______

bacterial genome through ________.

A) transformation B) crossing-over (recombination) C) transduction D) DNA replication E) conjugation

19) Name the general category into which double-stranded circular extrachromosomal DNA

19) ______

elements such as F factors, ColE1, and R would fall.

A) r-determinant B) plasmid C) capsid D) partial diploid E) plaque

20) What is an R plasmid?

A) They are the plasmids that carry the F factor.

B) They are a plasmid that can exist in the chromosome or outside the chromosome.

C) It is an F factor that has picked up part of a bacterial genome.

D) They function in bacterial recombination.

E) They carry a gene for resistance to an environmental attribute, such as heavy metals, and

20) ______

genes for the transfer of the plasmid.

21) ________ can exist integrated into the bacterial chromosome or as an autonomous plasmid unit

21) ______

in the cytosol.

A) R factor B) F′ plasmid C) Episomes D) Col plasmid E) Temperate phages

22) What are the general structural features of a prokaryotic plasmid?

A) circular double-stranded DNA in the cytosol B) made of protein and existing in the cytosol C) circular double-stranded DNA in the nucleus D) linear double-stranded DNA integrated into the chromosome E) proteins on the bacterial chromosome

22) ______

23) Bacteria that are in a particular physiological state to become transformed are called ________.

A) competent B) resistant C) episomal D) temperate E) transformable

23) ______

24) After transformation, heteroduplex formation, and resolution, the resulting daughter cells are

24) ______

________.

A) both transformed B) one transformed and one nontransformed C) both have plasmids D) both wild type E) both mutant

25) What is meant by the term cotransformation?

A) An F− cell can become F+ several times in a life cycle.

B) Several pieces of DNA can form heteroduplexes in a cell.

C) More than one phage infects a bacterial cell.

D) A cell can pick up more than one F factor.

E) Cotransformation occurs when several linked genes are transformed simultaneously.

25) ______

26) Bacteriophages engage in two interactive cycles with bacteria. What are these cycles?

A) lytic and lysogenic B) heteroduplex and homoduplex C) insertion and replication D) negative and positive E) auxotrophic and prototrophic

26) ______

27) A bacteriophage that is capable of entering either a lytic or a lysogenic cycle is called a(n)

27) ______

________.

A) temperate bacteriophage B) virulent bacteriophage C) plaque-forming unit D) episome E) plasmid

28) The clearing made by bacteriophages in a "lawn" of bacteria on an agar plate is called a

28) ______

________.

A) lysogenic zone B) clear zone C) prophage D) host range E) plaque

29) Temperate phages are those that can enter either the ________ or the ________ cycle.

A) functional; nonfunctional B) lytic; lysogenic C) former; nonformer D) virulent; avirulent E) complementing; competing

29) ______

30) What is the process by which a temperate bacteriophage infects a bacterial cell and

30) ______

subsequently integrates its chromosome into the bacterial chromosome?

A) lysis B) transduction C) transformation D) lysogeny

E) temperate 31) Which of the following is a possible outcome of the lysogenic cycle?

A) bacterial cell lysis, prophage formation and propagation, and bacterial fission are all

31) ______

possible outcomes of the lysogenic cycle

B) prophage formation and propagation C) bacterial fission D) prophage formation E) bacterial cell lysis 32) Which of the following occurs during cell lysis?

A) lysogeny B) episome propagation C) prophage formation D) binary fission E) plaque formation

32) ______

33) Which of the following is an episome?

A) lytic phage B) F factor C) F factor and temperate phage D) temperate and lytic phages E) temperate phage

33) ______

34) What is the first step in phage formation inside the bacterial cell?

A) tail fibers are added B) tail formation C) adherence to the pilus D) lysis E) DNA packaging as the viral heads assemble

34) ______

35) When a bacteriophage genome incorporates itself into the chromosome of the host, that phage

35) ______

genome is referred to as a(n) ________.

A) T4 phage B) temperate phage C) prophage D) episome E) lytic phage

36) Assume that one counted 67 plaques on a bacterial plate where 0.1 ml of a 10 −5 dilution of

36) ______

phage was added to bacterial culture. What is the initial concentration of the undiluted phage?

A) 6.7 × 107 pfu/ml (pfu = plaque-forming units)

B) 0.1 × 105 pfu/ml C) 67 pfu/ml D) 6.7 × 105 pfu/ml E) 6.7 × 10−5 pfu/ml 37) What is a bacteriophage?

A) a virus that exclusively undergoes the lysogenic cycle B) a bacterium that infects a virus C) a virus that exclusively undergoes the lytic cycle

37) ______

D) a bacterium that infects other bacteria E) a virus that has a bacterium as its host 38) What is a plaque composed of?

A) bacteriophage and dead bacteria B) bacteriophage and agar C) lysed bacteria, phage, and agar D) live bacteria and bacteriophage E) lysed bacteria

38) ______

39) Which of the following statements is false?

A) A bacteriophage that can only undergo lysis is called a virulent phage.

B) A symbiotic relationship between a phage and a bacterium apparently occurs in the

39) ______

process of lysogeny.

C) Lysogeny is a process that occurs during transformation and conjugation.

D) A prophage can exist in a quiescent state in the bacterial chromosome.

E) Viral genomes comprise only genes for viral structure and assembly.

40) Transduction is a form of recombination in bacteria that involves ________.

A) physical contact between the bacteria involved B) bacteriophages C) 5-bromouracil D) plasmids E) fertility factors

40) ______

41) Name two forms of recombination in bacteria.

A) conjugation and transduction B) mixed and generalized C) insertion and replication D) auxotrophic and prototrophic E) lytic and lysogenic

41) ______

42) If two different auxotrophic strains are placed in a liquid medium culture tube, prototrophic

42) ______

strains can sometimes be subsequently recovered. Choose the mechanism below that would not allow this genetic change.

A) reverse mutation B) transformation C) genetic suppression D) conjugation E) transduction

43) A form of bacterial recombination that involves a viral intermediate is called ________.

A) transformation B) plaque assay C) transduction D) conjugation E) competency

43) ______

44) ________ is most likely associated with transduction.

A) Plasmid ColE B) Lysogeny

44) ______

C) Conjugation D) factor E) Transformation 45) ________ of genes is an indication that the genes are linked.

A) Cotransduction B) Conjugation C) Reversion D) Recombination E) Transformation

45) ______

46) Viral mutations and variants are often categorized by changes in ________.

A) host range and/or plaque morphology B) plaque morphology C) host range D) viral size E) capsid shape

46) ______

47) In a mixed infection experiment, you study two plaque phenotypes of large (l+) versus small

47) ______

(l−) and bumpy (b+) versus smooth (b−). You mix small (l− b+) with smooth (l+ b−) and identify 50 small, smooth and 47 large, bumpy. How far apart are the genes?

A) 490 B) 1000 C) 99 D) 49 E) There is not enough information to calculate the distance.

48) ______

48) In a mixed infection experiment, the results of an h+r and hr+ cross are as follows.

Genotype h+r hr+ h+r+ hr

Number of plaques 42 34 12 12

How far apart are these two genes?

A) 8 B) 48

C) 2

D) 24

E) 12

49) To produce recombinants in phage ________.

A) two crossovers are required B) one crossover is required C) a bacterial cell must be competent D) the F factor must be present E) phage recombinants do not occur

49) ______

50) In Seymour Benzer's studies, if he mixed two RII phage together (co-infection studies in K12)

50) ______

and the resulting phage always failed to lyse K12 ________.

A) the two mutants were in different cistrons B) the two mutants complemented each other C) the two mutants were in the same cistron D) the two mutants failed to infect bacteria

E) the two mutants represented mutations in both A and B

1) B 2) A 3) C 4) E 5) D 6) D 7) D 8) C 9) C 10) C 11) E 12) B 13) A 14) E 15) A 16) B 17) D 18) B 19) B 20) E 21) C 22) A 23) A 24) A 25) E 26) A 27) A 28) E 29) B 30) D 31) A 32) E 33) C 34) E 35) C 36) A 37) E 38) C 39) C 40) B 41) A 42) E 43) C 44) B 45) A 46) A 47) D 48) E 49) E 50) C

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) The Protenor mode of sex determination is the ________.

1) _______ A) scheme based on F plasmids inserted into the FMR-1 gene B) hermaphroditic scheme C) scheme based on single translocations in the X chromosome D) XO/YY scheme E) XX/XO scheme 2) The Lygaeus mode of sex determination is the ________.

A) scheme based on single translocations in the X chromosome B) XX/XO scheme C) XO/YY scheme D) XY/XX scheme E) hermaphroditic scheme

2) _______

3) The sex of birds, some insects, and other organisms is determined by a ZW chromosomal

3) _______

arrangement in which the males have like sex chromosomes (ZZ) and females are ZW (similar to XY in humans). Assume that a recessive lethal allele on the Z chromosome causes death of an embryo in birds. What sex ratio would result in the offspring if a cross were made between a male heterozygous for the lethal allele and a normal female?

A) 4:1 male to female B) 3:1 male to female C) 2:1 male to female D) 1:2 male to female E) 1:1 male to female

4) In humans, the male is the ________ sex.

A) homogametic B) homomorphic C) heteromorphic D) heterogametic E) monogametic

4) _______

5) In humans, the genetic basis for determining the sex "male" is accomplished by the presence of

5) _______

________.

A) a portion of the Y chromosome B) one X chromosome C) sets of autosomes D) high levels of estrogen E) multiple alleles scattered throughout the autosomes F) a balance between the number of X chromosomes and the number of haploid

6) Jacobs syndrome in humans, which is manifested by a higher than average stature and potential behavioral problems, is caused by which chromosomal condition?

A) 45, X B) triploidy C) 47, XYY D) 47, 21+

7) Which of the following human genetic conditions is missing a chromosome?

6) _______

E) 47, XXY 7) _______

A) XXXX syndrome B) Down's syndrome C) Jacob syndrome D) Klinefelter syndrome E) Turner syndrome 8) Individuals have been identified who have two different karyotypes, such as 45, X/46, XY or 45,

8) _______

X/46, XX. Such individuals are called ________.

A) homogametic B) heteromorphic C) mosaics D) heterogametes E) trisomic

9) Which of the following karyotypes would lead to male characteristics in humans?

A) XXY B) XYY C) XO D) XO and XYY E) XXY and XYY

9) _______

10) A small part of the human Y chromosome contains the gene that is responsible for determining

10) ______

maleness. What is the name of this gene?

A) Dax B) medulla C) Xist

D) SRY

E) NRY

11) Under what condition might a human female have the XY sex chromosome complement?

A) She has an XX chromosome and a Y chromosome.

B) The X chromosome has a mutation such that it is able to overpower the Y chromosome.

C) This female would have one complete X chromosome and a Y chromosome that lacks

11) ______

SRY.

D) This is not possible.

E) The Y chromosome has an active Xist gene on it.

12) Klinefelter and Turner syndromes have how many chromosomes, respectively?

A) 45, 47 B) 47, 46 C) 46, 46 D) 46, 45

12) ______ E) 47, 45

13) Which region(s) of the X chromosome recombine during meiosis?

A) the heterochromain B) the pseudoautosomal regions C) the centromere D) the male-specific region of the Y E) SRY

13) ______

14) What does the nonrecombining region of the Y contain?

A) the genes that have homologues on the X chromosome B) SRY C) the centromere D) A, B, and C E) B and C

14) ______

15) A color-blind woman with Turner syndrome (XO) has a father who is color blind. Given that

the gene

for the 15) color-blin d condition is recessive and X-linked, provide a likely explanatio n for the origin of the color-blin d and cytogeneti c conditions in the woman.

____ __

A) no abnormalities had to occur to produce this daughter B) nondisjunction in the other in meiosis I or II C) nondisjunction in the mother in meiosis I and in the father in meiosis II D) nondisjunction in the father at meiosis I E) nondisjunction in the father in meiosis I or II 16) Although triple-X human females typically have normal offspring, what kinds of gametes, with respect to the X chromosomes, would you expect from such XXX females? Which of the following is an example of metaphase of meiosis I?

A)

B)

C)

16) ______

D)

E)

17) A recessive gene for red-green color blindness is located on the X chromosome in humans.

17) ______

Assume that a woman with normal vision (her father is color blind) marries a color-blind male.

What is the likelihood that this couple's first son will be color blind?

A) 100% B) 75% C) 0% D) 25% E) 50%

18) One form of hemophilia is caused by a sex-linked recessive gene. Assume that a man with

18) ______

hemophilia marries a phenotypically normal woman whose father had hemophilia. What is the probability that they will have a daughter with hemophilia? (Note: In this problem, you must include the probability of having a daughter in your computation of the final probability.)

A) 1/16 B) 1/4 C) 1/2 D) 1/8 E) 3/4

19) One form of hemophilia is caused by a sex-linked recessive gene. Assume that a man with

19) ______

hemophilia marries a phenotypically normal woman whose father had hemophilia. What is the probability that their first son will have hemophilia?

A) 1/8 B) 1/2 C) 1/4 D) 1/16 E) 3/4

20) Assume that a man who carries an X-linked gene has children. Assuming normal meiosis and

20) ______

random combination of gametes, the man would pass this gene to ________.

A) all of his daughters B) all of his sons C) all of his children D) half of his sons E) half of his daughters

21) Glucose-6-phosphate dehydrogenase (G6PD) deficiency is inherited as an X-linked recessive

21) ______

gene in humans. A woman whose father suffered from G6PD marries a normal man. What percentage of their sons is expected to be G6PD? A) 100% B) 50% C) 0% D) 25% E) 75%

22) The accompanying figure is a pedigree of a fairly common human hereditary trait; the boxes represent males and the circles represent females. Filled in symbols indicate the abnormal phenotype. Given that one gene pair is involved, what is the inheritance pattern of the trait?

22)

______

A) X-linked recessive B) X-linked dominant C) autosomal recessive D) autosomal dominant E) epistasis 23) Which of the following statements below is false?

A) Normally in humans, females are carriers of X-linked recessive traits if they are

23) ______

heterozygous.

B) Normally in humans, a male that is carrying an X-linked dominant trait will pass it to all his daughters.

C) At meiosis I, the X and Y chromosomes line up as if they were homologs.

D) Normally in humans, all the sons of a male showing an X-linked phenotype will inherit the trait.

E) Normally in humans, all the sons of a female homozygous for an X-linked recessive gene will inherit that trait.

24) What is the ratio of male to female conceptions in a population called?

A) primary sex ratio B) anomalous gender reorder calculation C) secondary sex ratio D) gender order E) conception birth order number

24) ______

25) For an individual with the XXY chromosomal composition, the expected number of Barr bodies

25) ______

in interphase cells is ________.

A) one B) zero

C) three

D) variable

E) two

26) A color-blind, chromatin-positive male child (one Barr body) has a maternal grandfather who

26) ______

was color blind. The boy's mother and father are phenotypically normal. What needed to occur to have this genetic outcome?

A) The chromosomal doubling effect of meiosis II occurred in the father.

B) The mother must be heterozygous and underwent nondisjunction at meiosis I. C) The mother must be heterozygous and underwent nondisjunction at meiosis II. D) Nondisjunction in meiosis I of the father occurred.

E) The mother is homozygous recessive and underwent nondisjunction in meiosis I or II.

27) A cross is made between a female calico cat and a male cat having the gene for black fur on his X chromosome. What fraction of the offspring would one expect to be calico?

A) 2/3 B) 1/2 C) 1/4 D) 3/4

27) ______

E) none

28) What region is the major control center of X inactivation in mammals?

A) MSY B) SRY C) NRY D) Xic E) Barr Body

28) ______

29) How many Barr bodies would one expect to see in cells of Turner syndrome females and

29) ______

Klinefelter syndrome males?

A) zero and one

B) one and zero C) one and one D) zero and two E) zero and zero 30) X-linked genes in female mammals often demonstrate ________.

A) nonrecombination during meiosis B) incomplete dominance C) phenotypic mosaicism D) heterochromatin formation E) underrepresentation in the genome

30) ______

31) Dosage compensation in mammals typically involves the random inactivation of one of the two

31) ______

X chromosomes relatively early in development. Such X chromosome inactivation often leads to phenotypic mosaicism. Assume that black fur in cats is due to the X-linked recessive gene b, whereas its dominant allele B produces yellow fur. A Bb heterozygote is a mosaic called "tortoise shell" or "calico." A mating between a black male and a calico female occurred. Give the phenotypes of the offspring.

A) calico females and yellow males B) calico females, yellow females, black males, and yellow males C) all calico regardless of sex D) calico females, black females, yellow makes, and black males E) all black regardless of sex

32) Where is the general location of a Barr body?

A) in the nucleolus B) stuck in a nuclear pore C) attached to the nuclear envelope D) adjacent to the Y chromosome E) attached to the other X chromosome

32) ______

33) Which of the following statements is false?

A) A typical XX human female has one Barr body.

B) An individual with Turner Syndrome has no Barr bodies.

C) An individual with Klinefelter syndrome generally has one Barr body.

D) In a cell with X chromosomes lacking the XIC, there is still X inactivation.

E) Dosage compensation is accomplished in humans by inactivation of the Y chromosome.

33) ______

34) Which of the following is not a tenant of the Lyon hypothesis?

A) X inactivation of descendant cells is the same as the progenitor cell.

B) initial X inactivation is random.

C) X inactivation occurs on the maternal X chromosome.

D) X inactivation is passed down during mitosis.

E) X inactivation occurs early in development.

34) ______

35) In Drosophila, sex is determined by a balance between the number of haploid sets of autosomes

35) ______

and the number of ________.

A) nucleolar organizers B) centromeres C) telomeres D) Y chromosomes

E) X chromosomes 36) Assume that you are told that a particular organism, Drosophila, has the XO chromosome

36) ______

complement. You are also told that the autosomal complement is a normal 2n. You know that in humans the XO complement is female determining. Would you be correct in assuming that the Drosophila sex for XO is also female? Choose the answer that includes the correct explanation.

A) No, sex determination in Drosophila is dependent on the presence or absence of the Y chromosome.

B) No, it takes two X chromosomes to produce a female in humans and a Y chromosome to produce a male in Drosophila.

C) Yes, the presence of an X chromosome determines a female in both organisms.

D) Yes, because sex determination in humans and insects is essentially the same.

E) No, the chromosomal basis for sex determination in Drosophila is based on the balance between the number of X chromosomes and haploid sets of autosomes.

37) What are the sex-chromosome constitution (X and Y chromosomes) of the inviable offspring

37) ______

resulting from a cross between a white-eyed female (Xw XwY) and a wild-type male (normal chromosome complement) in Drosophila melanogaster?

A) XwXwY and YY

B) YY and XwYY C) X+XwY and X+XwXw D) X+XwXw and YY E) X+Y 38) In Drosophila, an individual female fly was observed to be of the XXY chromosome complement

38) ______

(normal autosomal complement) and to have white eyes as contrasted with the normal red eye color of wild type. The female's father had red eyes, and the mother had white eyes. Knowing that white eyes are X-linked and recessive, present an explanation for the genetic and chromosomal constitution of the XXY, white-eyed individual.

A) nondisjunction in meiosis II of father B) nondisjunction in meiosis I of mother C) nondisjunction in meiosis I of mother and meiosis II of father D) nondisjunction in either meiosis I or meiosis II of the mother E) nondisjunction in meiosis II of mother

39) In Drosophila, an individual female fly was observed to be of the XXY chromosome complement

39) ______

(normal autosomal complement) and to have white eyes as contrasted with the normal red eye color of wild type. The female's mother and father had red eyes. The mother, however, was heterozygous for the gene for white eyes. Knowing that white eyes are X-linked and recessive, present an explanation for the genetic and chromosomal constitution of the XXY, white-eyed individual.

A) nondisjunction in meiosis I of the mother B) nondisjunction in meiosis I of both the mother and father C) nondisjunction in meiosis I of the father D) nondisjunction in meiosis II of the mother E) nondisjunction in meiosis I or II in father

40) Which of the following statements is true regarding Drosophila?

A) The ratio of X to Y chromosomes determines fly sex.

B) The Y chromosome determines male flies.

40) ______

C) The ratio of autosomes to fly Y and X chromosomes determines fly sex.

D) The Y chromosome plays no role in fly sex determination or fly reproduction.

E) The Y chromosome plays no role on fly sex determination but does contain genes for fly reproduction.

41) Give the sex of the following Drosophila assuming that the autosomes are present in the normal

41) ______

number. XO; XY; XXY. Answers are in order (respectively).

A) female; male; female B) female; male; male C) male; male; female D) male; male; male E) male; female; female

42) Give the sex of the following people assuming that the autosomes are present in the normal

42) ______

number. XO; XY; XXY. Answers are in order (respectively).

A) female; male; female B) male; female; female C) female; male; male D) male; male; female E) male; male; male

43) Assuming a normal number of autosomes, what would be the sex of the following: XXY mouse,

43) ______

XXY Drosophila?

A) male and male, respectively B) female and male, respectively C) male and female, respectively D) both neuter E) female and female, respectively

44) Data produced by C. Bridges in the early part of this century indicate that sex in Drosophila is

44) ______

determined by ________.

A) the number of Y chromosomes B) the number of X chromosomes C) a balance between the number of X chromosomes and the number of haploid sets of autosomes D) the SRY gene E) the ratio of X to Y chromosomes

45) In Drosophila, the sex of a fly with the karyotype ________ is male.

A) XXX:2A B) XX:2A C) XXY:2A D) XYY:4A

45) ______ E) XO:2A

46) In Drosophila, the female is the ________ sex.

A) mosaic B) genic balance C) isogametic D) heterogametic E) homogametic

46) ______

47) In ________, sex is determined by the ratio of the number of X chromosomes to the number of

47) ______

haploid sets of autosomes.

A) Drosophila B) humans

C) C. elegans D) reptiles E) Drosophila and C. elegans 48) Genotypic sex determination does not in ________.

A) flies B) birds C) round worms D) reptiles E) mammals

48) ______

1) E 2) D 3) C 4) D 5) A 6) E 7) E 8) C 9) E 10) D 11) C 12) E 13) B 14) E 15) B 16) E 17) E 18) B 19) B 20) A 21) B 22) C 23) D 24) A 25) A 26) C 27) C 28) D 29) A 30) C 31) D 32) C 33) E 34) C 35) E 36) E 37) D 38) D 39) D 40) E 41) C 42) A 43) C 44) C 45) E 46) E 47) E 48) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) The condition that exists when an organism gains or loses one or more chromosomes but not a 1) _______ complete haploid set is known as ________.

A) aneuploidy B) trisomy C) triploidy D) euploidy E) polyploidy

2) Having a complete set or sets of chromosomes is called ________.

A) diploid B) aneuploidy C) euploid D) ploidy E) monoploid

2) _______

3) ________ is viewed as a major cause of aneuploidy.

A) Segmental deletions B) Nondisjunction C) X-ray mutations D) Colchicine treatment E) Heat treatment

3) _______

4) Trisomy 21, or Down syndrome, occurs when there is a normal diploid chromosomal

4) _______

complement but one (extra) chromosome 21. Although fertility is reduced in both sexes, females have higher fertility rates than males. Van Dyke et al. (1995; Down Syndrome Research and Practice 3(2): 65—69) summarize data involving children born of Down syndrome individuals. Assume that children are born to a female with Down syndrome and a normal 46-chromosome male. What proportion of the offspring would be expected to have Down syndrome?

A) None of the offspring would be expected to have Down syndrome.

B) One-third of the offspring would be expected to have Down syndrome.

C) All the children would be expected to have Down syndrome.

D) Two-thirds of the offspring would be expected to have Down syndrome.

E) One-half of the offspring would be expected to have Down syndrome.

5) Trisomy 21, or Down syndrome, occurs when there is a normal diploid chromosomal complement but one (extra) chromosome 21. While there is reduced fertility in both sexes, females have higher fertility than males. Van Dyke et al. (1995; Down Syndrome Research and Practice 3(2): 65-69) summarize data involving children born of Down syndrome individuals.

Given the fact that conceptuses with 48 chromosomes (four #21 chromosomes) are not likely to survive early development, what percentage of surviving offspring would be expected to have Down syndrome if both parents have Down syndrome?

A) One-third of the surviving offspring would be expected to have Down syndrome.

B) One-half of the surviving offspring would be expected to have Down syndrome.

C) Two-thirds of the surviving offspring would be expected to have Down syndrome.

D) None of the surviving offspring would be expected to have Down syndrome.

E) All the children would be expected to have Down syndrome.

5) _______

6) What explanation is generally given for lethality of monosomic individuals?

A) Cells count the number of chromosomes they have and will undergo apoptosis when the

6) _______

chromosome number is incorrect.

B) Monosomic chromosomes cannot undergo mitosis correctly.

C) The loss of a single chromosome is not generally lethal, unless the individual is inbred.

D) The gametes of monosomic individuals cannot undergo meiosis, and this is lethal.

E) Monosomy may unmask recessive lethals that are tolerated in heterozygotes carrying the wild-type allele.

7) What is the leading cause of Down syndrome?

A) The nondisjunctional event that produces Down syndrome occurs more frequently

7) _______

during oogenesis in women older than age 35.

B) In older females, chromosome 21 is duplicated leading to abnormal egg formation.

C) In older parents, there is egg/sperm incompatibility leading to duplication of chromosome 21.

D) In men over 25, sperm formation is impaired and produces monosomic children.

E) Aberrant implantation in the uterus leads to developmental problems in the fetus.

8) What experiment led to the identification of the DSCR (Down Syndrome Critical Region)?

A) a mouse model was developed lacking the DSCR B) an extra DSCR was injected into yeast cells C) a mouse model was developed trisomic for the DSCR D) cancer cells were sequenced to identify the VEGF gene E) transgenic humans were developed that had a duplicated DSCR

8) _______

9) Name two methods used in genetic prenatal diagnostic testing in humans.

A) chorionic villus sampling and cellular mitotic analysis B) whole genome sequencing and PCR C) amniocentesis and DSCR D) amniocentesis and NIPGD E) amniocentesis and fetal uterine physiology compatibility test

9) _______

10) Haploinsufficiency refers to ________.

A) the process by which a single gene will cause a cascading effect on a genome's phenotype B) the condition whereby a single chromosome is insufficient to sustain life C) the genetic predisposition for some genes to come in only one copy in the genome D) the condition whereby a single cell is insufficient to divide to cause cancer E) a state of being whereby a single gene is sufficient to cause several phenotypes

10) ______

11) Given that a human normally contains 46 chromosomes, give the chromosome number for each

11) ______

of the following conditions: Turner syndrome (female, no Barr bodies) Klinefelter syndrome (male, one Barr body) A) 45, 46 B) 47, 45 C) 47, 47

D) 46, 47

E) 45, 47

12) Given that a human normally contains 46 chromosomes, give the chromosome number for each of the following conditions: Triploid Trisomy 13 A) 138, 47 B) 96, 47

C) 138, 45

D) 69, 47

E) 69, 45

12) ______

13) Assume that a species has a diploid chromosome number of 24. The term applied to an

13) ______

individual with 25 chromosomes would be ________.

A) trisomy B) aneuploidy C) euploid D) triploid E) aneuploidy and trisomy

14) An individual with Patau syndrome would be ________.

A) termed a euploid B) termed a triploid C) said to have a trisomy D) termed a haploid E) said to have a monosomy

14) ______

15) Noninvasive prenatal genetic diagnosis is sometimes preferred to amniocentesis because

15) ______

________.

A) the mother does not have to be present B) it requires less technical time of a research lab C) it gives more precise results D) it gives quicker results E) it requires only a blood draw from the mother

16) A child is born with Turner's syndrome and she is red green color blind (recessive X-linked).

16) ______

Her father is red green color blind as well and her mother is homozygous dominant for color sight. What had to happen in order for this child to be born with this chromosomal complement?

A) nondisjunction in meiosis II of the father B) nondisjunction in either meiosis I or meiosis II of the mother C) nondisjunction in meiosis II of the mother D) nondisjunction in either meiosis I or meiosis II of the father E) nondisjunction in meiosis I of the father

17) A son is born with Kleinfelter's syndrome and hemophilia. His father was normal and his

17) ______

mother was a carrier for the recessive X-linked blood clotting disorder. What occurred in meiosis to produce this genetic outcome?

A) nondisjunction in meiosis II of the mother B) nondisjunction in meiosis II of the father C) nondisjunction in meiosis I of the father D) nondisjunction in either meiosis I or meiosis II of the mother E) nondisjunction in meiosis I of the mother

18) What is the outcome of nondisjunction in meiosis I? A) a resultant gamete that may harbor from one chromosome both sister chromatids or none

18) ______

at all B) a resultant gamete that may harbor from one chromosome both homologs from one parent or none at all C) a resultant gamete that is devoid of all chromosomes D) a resultant gamete that is triploid E) four gametes that are all trisomic

19) An expected meiotic pairing configuration in a ________ would be a trivalent.

19) ______

A) monosomic individual B) diploid C) monoploid D) trisomic individual E) triploid 20) Name the polyploid condition that is formed from the addition of an extra set of chromosomes

20) ______

identical to the normal diploid complement of the same species.

A) alloeuploidy, assuming the normal chromosome complement is diploid B) autotetraploidy, assuming the normal chromosome complement is haploid C) autooctoploidyploidy, assuming the normal chromosome complement is haploid D) autotetraploidy, assuming the normal chromosome complement is diploid E) allotetraploidy, assuming the normal chromosome complement is diploid

21) Colchicine is an alkaloid derived from plants. What is its effect on chromosome behavior?

A) By blocking DNA replication, chromosomes do not undergo meiosis I and instead all

21) ______

gametes suffer from aneuploidy.

B) By interfering with spindle formation, replicated chromosomes fail to migrate to the poles at anaphase; thus, sister chromatids end up in the same nucleus.

C) By blocking DNA replication, chromosomes do not undergo meiosis II and instead half the gametes are empty.

D) By interfering with spindle formation, replicated chromosomes fail to migrate to the poles at anaphase; thus, homologous chromosomes end up in the same nucleus.

E) By blocking DNA replication, chromosomes fail to migrate to the poles at anaphase; thus, homologous chromosomes end up in the same nucleus.

22) Doubling the chromosomes of a sterile species hybrid with colchicine or cold shock is a method

22) ______

used to produce a fertile species hybrid called a ________.

A) allopolyploid B) (amphidiploid) C) autoallopolyploid D) autoploid E) triploid

23) Assume that an organism has a diploid chromosome number of 14. There would be ________ chromosomes in a tetraploid.

A) 14 B) 28

C) 56

D) 104

23) ______

E) 42

24) An ________ may arise when three sperm cells are involved in fertilization of a single egg.

A) autotriploid B) aneuploidy C) allotriploid D) autotetraploid E) allotetraploid

24) ______

25) Assume that an organism has a haploid chromosome number of 7. There would be ________

25) ______

chromosomes in a monoploid individual of that species.

A) 28 B) 42 C) 3.5

D) 7

E) 14

26) Assume that a species has a diploid chromosome number of 24. The term applied to an individual with 36 chromosomes would be ________.

A) allopolyploid

26) ______

B) triploid C) monoploid D) tetraploid E) aneuploidy 27) Which of the following is an example of an endopolyploid?

A) one chromosome is lost during cell division B) an individual suffers from a trisomy C) two diploid mate and produce a tetraploid D) an egg has complete nondisjunction and the resultant offspring is triploid E) cells lining the gut of mosquito larvae attain 16n ploidy

27) ______

28) How do deletions and translocations in chromosomes often occur?

A) during meiosis I, sister chromatid exchange leads to abnormalities B) when cells undergo meiosis II, chromosomes naturally break when sister chromatids are

28) ______

being pulled apart

C) chromosomes will fuse telomere to telomere D) chromosomes will break and the sticky ends will rejoin E) colchicine treatment causes chromosomal rearrangements 29) The condition known as cri-du-chat syndrome in humans has a genetic constitution designated

29) ______

as ________.

A) triploidy B) heteroplasmy C) trisomy D) 45, X E) 46, 5p-

30) What is formed when meiosis occurs in an individual who is heterozygous for an intercalary

30) ______

deletion?

A) a trifecta chromosomal cross B) a terminal loop C) a compensation loop D) a translocation E) a translocation cross

31) The chromosomal aberration that causes cri-du-chat syndrome can be referred to as a(n)

31) ______

________.

A) simple translocation B) inversion C) reciprocal translocation D) segmental deletion E) duplication

32) Provide an example of gene redundancy that occurs in both eukaryotes and prokaryotes.

A) centromeres B) rDNA C) cell wall proteins D) spindle fiber protein genes E) CNV

32) ______

33) Describe double Bar mutations in Drosophila melanogaster.

A) large deletion in the X chromosome B) an X chromosome with two duplications of the 16A region C) a female fly with only one X chromosome D) duplications in a portion of the X chromosome E) an inversion heterozygote of the X chromosome

33) ______

34) Gene amplification is the basis for ________.

A) a segmental deletion B) bar-eyed flies C) the nucleolar organizing region D) formation of the translocation cross E) interstitial deletions

34) ______

35) What error of meiosis leads to both a duplication and a deletion?

A) replication cross formation B) D loop formation C) unequal crossing over D) X-ray chromosomal breakage E) replication errors

35) ______

36) Which of the following is not a potential outcome of a gene duplication?

A) they may result in gene redundancy B) they may result in providing the raw material for evolution C) they may lead to the development of gene families D) they may lead to translocation cross formation during synapsis E) they may produce phenotypic variation

36) ______

37) What is NOT a potential consequence of a copy number variation?

A) phenotypic consequences that track with the number of each gene B) loss of function at multiple loci C) higher protein levels of specific genes D) none E) phenotypic consequences leading to enhanced ability to fight infection

37) ______

38) A chromosome without a centromere is ________.

A) acentric B) dicentric C) pericentric D) paracentric E) segmental

38) ______

39) A ________ inversion is one whose breakpoints do not flank the centromere.

A) segmental B) dicentric C) acentric D) paracentric E) pericentric

39) ______

40) Inversion heterokaryotypes are often characterized as having reduced crossing over and

inve n rsio hetero

reduced fertility. Assume that you were examining a strain of organisms you knew to be

karyotype 40) s and saw a relatively high number of double chromatid bridges extending between anaphase I nuclei, as indicated in the following drawing.

What is the product of this type of inversion loop?

A) two chromosomes with deletions and two with duplications B) four wild-type chromosomes C) two acentric fragments and two dicentric chromosomes D) two chromosomes with deletions and two acentric fragments E) one acentric fragment, one dicentric chromosome, and two wild-type chromosomes 41) What type of chromosomal configuration does the following diagram illustrate?

____ __

41)

____ __

A) inversion (paracentric) heterozygote B) inversion (paracentric) homozygote C) simple translocation heterozygote D) inversion (paricentric) heterozygote E) reciprocal translocation heterozygote 42) What is a potentially evolutionary advantage of inversion heterozygosity?

A) haploinsufficiency does not occur in inversion heterozygotes B) if a favorable complement of alleles occurs in an inversion heterozygote, they will not be

42) ______

disrupted by crossing over C) inversion loops stimulate favorable allele combinations D) there is none E) enhanced genetic variation in the offspring

43) Although the most frequent forms of Down syndrome are caused by a random error,

43) ______

nondisjunction of chromosome 21, Down syndrome occasionally runs in families. The cause of this form of familial Down syndrome is ________.

A) a chromosomal aberration involving chromosome 1 B) a maternal age effect C) a translocation between chromosome 21 and a member of the D chromosome group D) an inversion involving chromosome 21 E) too many X chromosomes

44) Which of the following statements is TRUE? A) Inversions and translocations are without evolutionary significance.

B) In general, inversion and translocation heterozygotes are as fertile as organisms whose

44) ______

chromosomes are in the standard arrangement.

C) Individuals with familial Down syndrome are trisomic and have 47 chromosomes.

D) Familial Down syndrome is caused by a translocation involving chromosome 21.

E) Translocations may be pericentric or paracentric.

45) A genomic condition that may be responsible for some forms of fragile X syndrome, as well as

45) ______

Huntington disease, involves ________.

A) plasmids inserted into the FMR-1 gene B) single translocations in the X chromosome C) various lengths of trinucleotide repeats D) multiple breakpoints fairly evenly dispersed along the X chromosome E) multiple inversions in the X chromosome

46) Genetic anticipation is best described as ________.

46) ______

A) trinucleotide repeats form fragile sites B) trinucleotide repeats increase in future generations C) the G2 gap before meiosis D) the phenomenon by which synapsis is delayed due to translocation cross formation E) cells stop during the cell cycle to check for DNA damage or acentric fragments 47) Recently, a gene located on chromosome 3 in humans, FHIT, has been shown to be associated

47) ______

with the significant human malady known as ________.

A) "mad-cow" disease B) XYY/XY mosaicism C) Huntington disease D) Klinefelter syndrome E) cancer

48) What is a fragile site?

A) an area around the centromere prone to inversion due to gene duplications B) the telomere of a chromosome can fall off due to spindle malfunctions during meiosis C) a structural component of a chromosome due to the nucleotide sequence to it that leads to a high percentage of chromosomal breakage D) a site in a chromosome prone to duplication, such as the bar gene E) a structural component of a chromosome due to proteins bound to it that leads to a high percentage of chromosomal breakage

48) ______

1) A 2) C 3) B 4) E 5) C 6) E 7) A 8) C 9) D 10) B 11) E 12) D 13) E 14) C 15) E 16) B 17) A 18) A 19) E 20) D 21) B 22) B 23) B 24) D 25) D 26) B 27) E 28) D 29) E 30) C 31) D 32) B 33) B 34) C 35) C 36) D 37) B 38) A 39) D 40) C 41) A 42) B 43) C 44) D 45) C 46) B 47) E 48) C

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) What is the name of a form of extrachromosomal inheritance that is due to transmission of 1) _______ symbiotic or parasitic microorganisms?

A) pathogenic paternal transfer B) infectious heredity C) uniparental genome transfer D) microbial genomic transfer E) organellar inheritance

2) Forms of inheritance that do not follow typical Mendelian patterns and that appear to be more

2) _______

influenced by the parent contributing the most cytoplasm to the embryo are grouped under the general heading of ________.

A) suppressive inheritance B) extrachromosomal inheritance C) neo-Mendelian inheritance D) sex-linked inheritance E) dominance and/or recessiveness

3) Which of the following organelles are involved in the general category of organelle heredity?

A) factors and episomes B) mitochondria and chloroplasts C) lysosomes and peroxisomes D) Golgi apparatus and rough endoplasmic reticulum E) Golgi apparatus and nuclei

3) _______

4) To which of the following does the term heteroplasmy refer?

A) a circumstance that is homologous to incomplete dominance B) conditions in which the germ plasm is a mixture of dominant and recessive genes C) various stages of development of mitochondria and chloroplasts D) cells with a variable mixture of normal and abnormal organellar genomes E) heterozygous individuals with more than one gene pair involved

4) _______

5) The plant coleus has three distinct leaf color phenotypes: green, white, and variegated (white

5) _______

and green mixed) the crosses are made as follows: female variegated leaves × male green leaves gives offspring with all variegated leaves female green leaves × male with white leaves gives offspring with all green leaves female with white leaves × male with variegated leaves gives offspring with all white leaves This is an example of ________.

A) maternal effect B) Mendelian inheritance C) genomic imprinting D) X-linked recessive disorder E) cytoplasmic inheritance

6) ________ phenotypes are passed equally to offspring by both males and females.

A) Autosomal dominant

6) _______

B) X-linked dominant C) X-linked recessive D) Autosomal recessive E) Mitochondrial 7) Which of the following matings indicates that a Chlamydomonas mutant with photosynthetic

7) _______

defects (that resulted from a deficiency in chloroplast translation) is located on the chloroplast genome?

A) mt+ photo+ × mt− photo− yields all str−

B) mt+ photo− × mt− photo+ yields all str− C) mt+ photo− × mt− photo+ yields mt+ photo− and mt− photo+ D) mt+ photo− × mt− photo+ yields mt+ photo+ and mt− photo− E) a petite × alpha wild type yields all petite 8) Why is variegation in four o'clock plants determined by the phenotype of the ovule source?

A) Recessive genes demonstrating variegation come from the ovule.

B) The ovule nuclear genome contains the genes for leaf coloration.

C) Dominant genes demonstrating variegation come from the ovule.

D) The chloroplasts determine the leaf coloration, and the chloroplasts are inherited through

8) _______

the ovule.

E) The mitochondria determine the leaf coloration, and the mitochondria are inherited through the ovule.

9) In what way do segregational petite mutations differ from neutral petites?

A) Segregational petites follow Mendelian inheritance as a result of the influence of nuclear

9) _______

genes; neutral petites, when crossed to wild type, produce only wild-type, normal-sized colonies.

B) When a segregational petite is crossed to a wild-type cell, all offspring are petite.

However, when a neutral petite is crossed to a wild-type cell, all offspring are wild type.

C) When a neutral petite is crossed to a segregational petite, all offspring are neutral petites.

D) Neutral petites follow Mendelian inheritance as a result of the influence of nuclear genes; segregational petites, when crossed to wild type, produce only wild-type, normal-sized colonies.

E) Neutral petites are dominant and segregational petites are recessive mitochondrial genes.

10) What is the expression pattern of dominant-negative mutations in petite strains of yeast?

A) Expression of wild-type mitochondria is enhanced.

B) Mitochondrial membranes become hyperpolarized.

C) The function of wild-type mitochondria is suppressed.

D) Expression of mutant mitochondria resembles expression of wild-type mitochondria.

E) Mitochondria show enhanced capacity of oxidative phosphorylation.

10) ______

11) In Neurospora crassa, a mutation called poky (phenotype is slow growth) is passed down

11) ______

cytoplasmically. Which cross below is not consistent this type of inheritance?

A) female wild type × male wild type yields half poky B) female wild type × male wild type yields all wild type C) female poky × male wild type yields all poky D) female poky × male poky yields all poky E) female wild type × male poky yields all wild type

12) The inheritance of the petite phenotype in Saccharomyces cerevisiae is complicated by an

inter action

____ __

of 12) mitochon drial and nuclear genes.

Which of the following is a false statement about petites in S. cerevisiae?

A) Both nuclear and cytoplasmic (mitochondrial) genes contribute to the petite phenotype in some cases.

B) Segregational petites are characterized by mutations in the nuclear genome.

C) Suppressive petites are characterized by mitochondria lacking most of its DNA. D) Neutral petites, when crossed to wild type, yield wild-type mitochondrial function.

E) The three categories of petites are segregational, neutral, and suppressive.

13) You discover a new alien race that you decide to call the PAMMARIANS. They are different

13) ______

from us in that they have three sexes, called Q, R, and S. All three sexes must fuse their gametes to form a new PAMMARIAN (and you thought dating on the Earth was hard!). They have nuclear DNA and extrachromosomal organelles, similar to mitochondria, called MITOCHLORIANS, which have their own DNA. The R gender is like human females (they donate the cytoplasm during the mating). Q and S do NOT donate cytoplasm during mating, like human males. Which of the following is TRUE? A) In a mating, if only the Q gender individual has a mitochlorian DNA mutation that causes a phenotype, the offspring will have NO mitochlorian mutant phenotype.

B) In a mating, if the S and Q genders have a mitochlorian DNA mutation, the offspring will be mutant as well.

C) In a mating, if only the S gender individual has a mitochlorian DNA mutation that causes a phenotype, the offspring WILL HAVE a mitochlorian mutant phenotype.

D) In a mating, if only the Q gender individual has a mitochlorian DNA mutation that causes a phenotype, the offspring WILL HAVE a mitochlorian mutant phenotype.

E) In a mating, if only the R gender individual has a mitochlorian DNA mutation that causes a phenotype, the offspring will have NO mitochlorian mutant phenotype.

14) In organelle heredity, which of the following is TRUE? A) In a reciprocal cross, the offspring will always have the phenotype that the mother (egg)

14) ______

has.

B) In a reciprocal cross, the offspring will have different phenotypes depending on which phenotype the father has.

C) In a reciprocal cross, the offspring will have the phenotype of the mother's genotype.

D) In a reciprocal cross, the imprinted gene will always come from the mother.

E) In a reciprocal cross, the offspring will have varied phenotypes depending on which X chromosome is converted into a Barr body.

15) Inheritance of the green and white patches phenotype in Mirabilis jalapa (four o'clock) is an example of ________.

A) maternal influence

15) ______

B) maternal effect C) reciprocal cytoplasmic inheritance D) infectious heredity E) organelle heredity 16) An example of ________ involves pigmentation in Mirabilis jalapa.

A) maternal effect B) X-linked recessive C) gene dosage effect D) nucleolar inheritance E) organelle heredity

16) ______

17) In aerobically cultured yeast, you isolate a petite mutant. You believe it is a suppressive

17) ______

mutant. Which cross would you do below to determine that it is indeed suppressive?

A) wild type × wild type yields petite B) petite × petite yields half petite and half wild type C) petite × wild type yields all petites D) petite × petite yields all petite E) petite × wild type yields half petite and half wild type

18) In what way do mitochondrial mutations influence phenotype?

A) Cells with mutated mitochondrial DNA cannot undergo anaphase.

B) They affect the production of ribosomes and protein synthesis.

C) They affect the production of ATP generated through cellular respiration.

D) They cause the nuclear DNA to segregate ineffectively.

E) Mutated mitochondrial DNA has no effect on phenotypes.

18) ______

19) Which three classes of macromolecules are encoded by mtDNA? A) proteins, transfer RNAs, and ribosomal RNA B) carbohydrates, enzymes, and proteins C) photosystem I, photosystem II, and tRNA D) transfer RNA, ribosomal RNA, and nuclear RNA E) lipids, carbohydrates, and nucleic acids

19) ______

20) The endosymbiont theory is support by several lines of evidence one of which is ________.

A) mitochondria, chloroplast, and bacteria all have circular chromosomes B) the chloroplast genome resembles the genome of the mitochondria C) both mitochondria and peroxisomes have circular chromosomes D) both bacteria and lysosomes have degradative enzymes E) both mitochondria and chloroplasts generate ATP

20) ______

21) One explanation for organelle inheritance of disease phenotypes is that ________.

A) chloroplasts, for example, are completely dependent on the nuclear genome for

21) ______

components B) organelles such as mitochondria are always wild type C) mitochondria and chloroplasts have DNA that is subject to mutation D) mitochondria and chloroplasts lack DNA and are therefore dependent on the maternal cytoplasmic contributions E) None of the answers listed are correct.

22) Approximately one in 5000 humans either have a mitochondrial DNA disorder or are at risk for

developing

such a 22) disorder.

What future approach involving nuclear transplant ation might be available to treat mtDNA-b ased human disorders?

____ __

A) mitochondrial replacement therapy B) mitochondrial activation C) mitochondrial suppression D) nuclear disintegration E) nuclear activation 23) Through the study of mitochondrial disorders, scientists have suggested a link between the

23) ______

decline of mitochondrial function and aging. What process appears to be involved in this suspected phenomenon?

A) recombination among mtDNAs of different mitochondria B) accumulation of mutations in the mtDNA C) decline of mutations in the nuclear genome D) accumulation of sporadic mutations in the nuclear genome E) recombination of mtDNA and nuclear DNA

24) Which criterion below does not indicate that a human disorder may be attributable to

24) ______

genetically altered mitochondria?

A) deficiency in ability to generate ATP B) documentation of a specific mitochondrial genetic mutation C) deficiency in some bioenergetic functions of mitochondria D) passed down more readily to male offspring E) maternal rather than Mendelian inheritance pattern

25) Describe the molecular and transmission characteristics of Leber's hereditary optic neuropathy

25) ______

(LHON).

A) cytoplasmic inheritance, which includes cpDNA lesions B) maternal inheritance, which includes mtDNA lesions C) X-linked recessive D) cytoplasmic inheritance, which includes mtDNA lesions E) dominant maternal inheritance

26) Name two human disorders that appear to be transmitted extrachromosomally.

A) Duchenne muscular dystrophy and Down syndrome B) reactive oxygen syndrome and myoclonic epilepsy and ragged red fiber disease C) myoclonic epilepsy and ragged red fiber disease and Leber's hereditary optic neuropathy D) poky chromosome syndrome and kidney cancer

26) ______

E) cri-du-chat syndrome and Leber's hereditary optic neuropathy 27) Kearns-Sayre syndrome (KSS) results in progressive loss of vision and hearing, as well as heart

27) ______

defects. What is the genetic basis for this disease?

A) Reactive oxygen species mutate DNA. B) ATP builds up and runs the electron transport chain backwards.

C) Too much sunlight damages mtDNA. D) Deletions occur in mtDNA, and the proportion of defective mtDNAs increases as the severity of the symptoms increases.

E) Ageing shortens the telomeres of the mitochondrial DNA.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

28) The genes for light eyes (lt; light) and straw bristles (stw; straw) are tightly linked on 28) ____________ chromosome 2 in Drosophila melanogaster. The Malpighian tubes of lt larvae and adults are maternally affected in that Malpighian tubes of lt/lt organisms, whose mothers were lt+/lt and have more yellow pigment than those from lt/lt mothers. There is no maternal effect associated with the straw locus. Give the phenotypes of the offspring from the following crosses.

Cross #1: Cross #2: Cross #3:

Female lt stw/lt stw lt+ stw/lt stw lt+ stw+/lt stw

Male lt+stw+/lt stw lt stw+/lt stw lt stw/lt stw

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

29) Direction of shell coiling in Lymnaea peregra is strongly and most directly influenced by 29) ______ ________.

A) the genotype of the embryo itself B) the genotype of the mother C) the phenotype of the mother D) the phenotype of the father E) the genotype of the father

30) Direction of shell coiling in the snail Lymnaea peregra is conditioned by a form of

30) ______

extrachromosomal inheritance known as ________.

A) sex-linked inheritance B) maternal effect C) epistasis D) independent assortment E) heteroplasmy

31) The maternal effect in Lymnaea is such that the genotype of the egg determines the direction of shell coiling regardless of the genotype of the offspring. Apparently, the cause of this spectacular maternal effect results from ________.

A) colicins "poisoning" one of the cleavage centers B) genophores present in the egg cytoplasm C) allelic substitution as demonstrated from RNA injection experiments D) the F factor exerting its influence on the centrosome E) orientation of the spindle apparatus in early cleavage

31) ______

32) Molecular/structural orientations (gradients) in an egg are thought to play a significant role in

32) ______

development. What is the origin of such gradients?

A) The side facing up has the lowest concentration of molecules.

B) Where the sperm penetrated the egg is the area of highest concentration.

C) When an egg is fertilized, the gradient is set up based on the side of the egg on which the most mitochondria reside.

D) During early development, the nucleus is placed into position of the highest concentration.

E) During formation of the egg, nutritional as well as informational molecules (RNAs) are placed in appropriate positions for the development of the embryo.

33) Molecular/structural orientations (gradients) in an egg are thought to play a significant role in

33) ______

development. What evidence indicates that the maternal genotype is involved in providing such gradients?

A) Results (non-Mendelian) indicate that the direction of shell coiling in snails is determined by the genotype of the mother, not the genotype of the zygote.

B) Results indicate that the snail shell coiling is passed exclusively from the mother.

C) The snail's father's genotype dictates the next generation's phenotype.

D) The snail shell coiling depends on the genotype of the mother and the offspring.

E) Snail shell's coil based on environmental conditions.

34) Axis development is determined by a MATERNAL EFFECT gene in Drosophila. A dominant

34) ______

Bicoid allele is required to set up the correct axis development in flies. bb (two loss of function alleles) is LETHAL in this MATERNAL EFFECT gene.

A female Drosophila named Eustacia had all dead offspring. What is Eustacia's GENOTYPE? A) Bb or bb B) BB or Bb C) Bb D) bb E) BB

35) In MATERNAL EFFECT, which of the following is TRUE? A) In a reciprocal cross, the offspring's genotype and phenotype are the same as the

35) ______

mother's.

B) The mother's phenotype is the offspring's phenotype.

C) In a reciprocal cross, only the father's alleles are expressed.

D) The mother's genotype is the offspring's phenotype.

E) In a reciprocal cross, the grandfather's alleles have the most influence.

36) Which of the following is false?

A) It is safe to say that a maternal effect is caused by the genotype, not the phenotype, of the

36) ______

parent producing the egg.

B) In a reciprocal cross, if an offspring has the mother's phenotype for both crosses, cytoplasmic inheritance is responsible.

C) In maternal effect, an offspring will have the genotype of their mother.

D) The direction of shell coiling in Lymnaea peregra is influenced by the orientation of the first cleavage division.

E) When a maternal effect gene is seen, the offspring will demonstrate the phenotype of the mother's genotype.

37) Snail shell coiling is determined by a MATERNAL EFFECT gene. Snail shells can have either a right-handed (dextral) coiling or a left-handed (sinistral) coiling. Dextral (D) is completely dominant to sinistral (d). Answer the following questions based upon this information. A sinistral female snail named Eustacia has offspring that are all dextral.

What is the Eustacia's GENOTYPE?

37) ______

A) dd B) Dd or dd C) DD D) Dd E) DD or Dd

1) B 2) B 3) B 4) D 5) E 6) A 7) B 8) D 9) A 10) C 11) A 12) C 13) A 14) A 15) E 16) E 17) C 18) C 19) A 20) A 21) C 22) A 23) B 24) D 25) D 26) C 27) D 28) Cross #1: Cross #2: Cross #3:

29) B 30) B 31) E 32) E 33) A 34) D 35) D 36) C 37) D

1/2 light Malpighian tubes, straw bristles, 1/2 wild type more pigmented Malpighian tubes, 1/2 straw bristles more pigmented Malpighian tubes, 1/2 straw bristles

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) The Central Dogma specifies that the information in ________.

1) _______ A) RNA is copied into a DNA molecule during transcription, and the information in that DNA molecule is used to make a protein during translation B) protein is copied into an RNA molecule during translation, and the information in that RNA molecule is used to make DNA during transcription C) DNA is copied directly into a protein D) DNA is copied into an RNA molecule during translation, and the information in that RNA molecule is used to make a protein during transcription E) DNA is copied into an RNA molecule during transcription, and the information in that RNA molecule is used to make a protein during translation

2) A particular ________ carry the information for making a particular protein, but ________ can

2) _______

be used to make any protein.

A) ribosome and mRNA; a gene and a tRNA B) gene and ribosome; a tRNA and an mRNA C) tRNA and ribosome; a gene and an mRNA D) gene and tRNA; a ribosome and an mRNA E) gene and mRNA; a ribosome and a tRNA

3) Match the function of DNA on the left with the appropriate description on the right. i. expression ii. variation iii. replication iv. storage

3) _______

a. stable maintenance and passage of information b. duplication of genetic material c. potential for alteration d. production of a phenotype

Which of the choices below is correct?

A) i = b; ii = d; iii = a; iv = c B) i = d; ii = c; iii = b; iv = a C) i = d; ii = b; iii = c; iv = a D) i = c; ii = a; iii = b; iv = d E) i = d; ii = b; iii = a; iv = c

4) In the mid-1940s, genetic information was known to consist of ________.

A) nucleic acid and lipid B) lipid and protein C) carbohydrate and nucleic acid D) nucleic acid and protein E) protein and carbohydrate

4) _______

5) Who discovered that DNA was the genetic material (or "transforming principle") that could

5) _______

convert nonvirulent R-type Diplococcus pneumoniae bacterium to the virulent S-type?

A) Frederick Griffith B) Watson, Crick, Wilkins, and Franklin C) Avery, MacLeod, and McCarty D) Erwin Chargaff E) Hershey and Chase

6) The classic Hershey and Chase (1952) experiment that offered evidence in support of DNA

6) _______

being the genetic material in bacteriophages made use of which of the following labeled component(s)?

A) nitrogen and oxygen B) tritium C) hydrogen D) oxygen and phosphorus E) phosphorus and sulfur

7) In the classic experiment conducted by Hershey and Chase, why was the pellet radioactive in

7) _______

the centrifuge tube that contained bacteria with viruses?

A) The radioactive protein coats of the viruses were in the pellet.

B) The radioactive viruses were in the pellet, and the bacteria were in the supernatant.

C) The bacteria were in the pellet, and many contained the radioactive viral DNA. D) The radioactive viruses (coats plus DNA) were in the pellet.

E) The bacteria were in the pellet, and they had incorporated radioactive proteins into their cell membranes.

8) When a protoplast is infected by only the nucleic acid component of a virus, the infection is

8) _______

referred to as ________.

A) transduction B) transfection C) recombination D) transformation E) lysis

9) Genetic functions in a eukaryote can be observed in ________.

A) mitchondria and chloroplasts B) mitchondria C) chloroplasts, mitchondria, and the nucleus D) the nucleus E) chloroplasts

9) _______

10) If protein were the genetic principle and not nucleic acid, significant mutagenic effects would

10) ______

be detected at ________.

A) 300 nm B) 280 nm

C) 320 nm

D) 240 nm

E) 260 nm

11) Reverse transcriptase is an enzyme found in association with retroviral activity. It has the

11) ______

property of ________.

A) most lysozymes B) requiring no template C) synthesis of DNA from an RNA template D) translation E) synthesis of RNA from a DNA template

12) What are the two major components of the tobacco mosaic virus?

A) lipids and nucleic acids B) RNA and DNA C) RNA and protein D) carbohydrates and nucleic acids

12) ______

E) DNA and protein 13) The figure below shows a representative dinucleotide:

13) ______

This figure represents ________, and the arrow is closest to the ________ end.

A) DNA; 3' B) RNA; 5' C) RNA; 3' D) DNA; 5'

14) The figure below shows a representative dinucleotide:

14) ______

Spleen diesterase is an enzyme that breaks the covalent bond that connects the phosphate to the 5' carbon. If the dinucleotide is digested with spleen diesterase, to which base and to which carbon on the sugar is the phosphate now attached?

A) A; 3' B) T; 3' C) T; 5' D) A; 5'

15) The covalent linkage between the monomers in a dinucleotide is a(n) ________.

A) phosphodiester bond B) peptide bond C) ester bond D) disulfide bond E) ionic bond

15) ______

16) The basic structure of a nucleotide includes ________.

A) base, sugar, and phosphate

16) ______

B) amino acids C) mRNA, rRNA, and tRNA D) phosphorus and sulfur E) tryptophan and leucine 17) Regarding the structure of DNA, the covalently arranged combination of a deoxyribose and a

17) ______

nitrogenous base would be called a(n) ________.

A) nucleotide B) oligonucleotide C) nucleoside monophosphate D) ribonucleotide E) nucleoside

18) The figure below is a nucleotide:

18) ______

If you were told that this molecule could be found in either DNA or RNA, depending on the identity of the chemical groups labeled (X) and (Y), the nitrogen-containing ring structure would have to be ________.

A) guanine B) uracil C) thymine D) cytosine E) adenine

19) The figure below is a nucleotide:

chemic If al this group mol labeled ecul (X) e would wer be e ______ foun __ and d in the a chemic DN al A group chai labeled n, (Y) the would

be ________.

____ __

19) A) H; OH

B) OH; OH

C) OH; H

D) H; H

20) The figure below is a nucleotide:

20) ______

If this molecule were found in an RNA chain, the chemical group labeled (X) would be ________ and the chemical group labeled (Y) would be ________.

A) OH; H B) H; H C) OH; OH D) H; OH

21) Any two nucleic acid fragments will spontaneously hybridize if they encounter each other as

21) ______

long as they are ________ and ________.

A) identical; compatible B) transcribed; translated C) primed; replicated D) DNA; RNA E) complementary; antiparallel

22) Considering the structure of double-stranded DNA, which kind(s) of bonds hold one

22) ______

complementary strand to the other?

A) hydrogen B) disulfide C) ionic D) van der Waals E) covalent

23) The base content of a sample of nucleic acid is as follows: A = 31%, G = 31%, T = 19%, C = 19%.

23) ______

What conclusion should be drawn from this information?

A) The purine/pyrimidine ratio in this molecule fits Chargaff's data.

B) This nucleic acid is double-stranded DNA. C) The strands in this molecule are parallel rather than antiparallel.

D) This nucleic acid is made of RNA. E) This nucleic acid is single-stranded DNA.

24) The two DNA chains in a double helix ________.

24) ______

A) are parallel to each other in 5' to 3' directionality B) have identical base sequences C) wind around each other in such a way that purines are always opposite pyrimidines and vice versa D) are held together due to the charges of their phosphate groups E) have an overall diameter of 2 μm

25) If 15% of the nitrogenous bases in a sample of DNA from a particular organism are thymine, what percentage should be cytosine?

A) 15% B) 40%

C) 30%

D) 35%

25) ______

E) 70%

26) In an analysis of the nucleotide composition of double-stranded DNA to see which bases are

26) ______

equivalent in concentration, which of the following would be true?

A) A + C = G + T B) A = G and C = T C) A + T = G + C D) G = T E) A = C

27) In base pair between a guanine and a cytosine, ________ hydrogen bonds form between a

27) ______

partially positive hydrogen on the guanine and a more electronegative atom on the cytosine.

A) 2 B) 0 C) 3 D) 1 E) 4

28) The most specific name for an incoming monomer about to be incorporated into a DNA chain is

28) ______

________.

A) nucleoside monophosphate B) deoxyribonucleoside triphosphate C) nucleotide D) deoxyribonucleoside E) ribonucleoside diphosphate

29) Which of the following clusters of terms accurately describes DNA as it is generally viewed to

29) ______

exist in prokaryotes and eukaryotes?

A) double-stranded, parallel, (A + T)/C + G) = 1.0, (A + G)/(C + T) = 1.0 B) double-stranded, antiparallel, (A + T)/C + G) = variable, (A + G)/(C+ T) = 1.0 C) double-stranded, parallel, (A + T)/C + G) = variable, (A + G)/(C + T) = 1.0 D) double-stranded, antiparallel, (A + T)/C + G) = variable, (A + G)/(C + T) = variable E) single-stranded, antiparallel, (A + T)/C + G) = 1.0, (A + G)/(C + T) = 1.0

30) The form of DNA that is observed to adopt a left-handed helix is ________.

A) D-DNA B) Z-DNA C) C-DNA D) A-DNA

30) ______ E) P-DNA

31) The form of DNA that is believed to be most biologically significant is ________.

A) A-DNA B) B-DNA C) Z-DNA D) E-DNA E) D-DNA

31) ______

32) Compared with B-DNA, A-DNA is ________ compact, has ________ base pairs per turn, and is

32) ______

a ________ helix.

A) more; fewer; left-handed B) less; more; right-handed C) more; fewer; right-handed D) less; fewer; left-handed E) more; more; right-handed

33) Arrange the principal forms of RNA in order of abundance from LEAST abundant to MOST

33) ______

abundant.

A) tRNA, mRNA, rRNA B) tRNA, rRNA, mRNA C) rRNA, tRNA, mRNA D) mRNA, rRNA, tRNA E) mRNA, tRNA, rRNA

34) When calculating a molecule's Svedberg coefficient, the rate of sedimentation is affected by the

34) ______

molecule's ________.

A) mass B) shape C) size D) size and shape E) mass, size, and shape

35) Which type of rRNA can be found in both prokaryotes and eukaryotes?

A) 23S B) 5S C) 18S D) 16S

35) ______ E) 5.8S

36) Some forms of genetic regulation can be facilitated by ________.

A) lncRNA B) siRNA C) miRNA D) lncRNA and siRNA E) miRNA, siRNA, and lncRNA

36) ______

37) FISH can be used to determine the ________.

A) chromosomal location of specific genetic information B) difference between A-form and B-form DNAs C) melting temperature of a fragment of DNA D) difference in lengths between two fragments of DNA E) locations of major and minor grooves in a double helix

37) ______

38) The figure below represents an aqueous solution of four identical DNA double helices in pure

38) ______

water:

Which one of the following figures represents the state of the DNA molecules at the melting temperature (Tm)?

A)

B)

C)

D)

E)

39) Consider the following two statements about DNA melting temperature: 1) The melting temperature of a sample of DNA is the temperature at which 50% of the double helices in the sample have completely denatured.

2)

ecule with A 53% mol G—C

____ __

base pairs 39) would have a higher melting temperatu re than a molecule of equivalent length with 53% A—T base pairs.

Determine which one of the statement s below is CORREC T.

A) Statement 1) is false; statement 2) is true.

C) Statement 1) and statement 2) are true.

B) Statement 1) is true; statement 2) is false.

D) Statement 1) and statement 2) are false.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

40) Explain the tetranucleotide hypothesis and its relationship to the substance referred to as 40) ____________ nuclein.

41) Briefly define transformation and describe the relationship between the phenomenon of

41) ____________

transformation and the discovery that DNA is the genetic material in bacteria.

42) Explain why the distribution of protein and nucleic acid in a eukaryotic cell favors

42) ____________

nucleic acid as the genetic material.

43) Identify the nitrogenous bases and pentose sugars in DNA and RNA.

43) ____________

44) What is the difference between a polynucleotide and an oligonucleotide?

44) ____________

45) What does it mean for a double helix of DNA to be antiparallel and complementary?

45) ____________

46) Why would D-DNA and E-DNA be unlikely to be found in the genomes of living

46) ____________

organisms?

47) Compare and contrast the principal types of RNA in terms of their cellular roles,

47) ____________

relative abundance, and variation in length.

48) How do urea and NaCl influence temperature-induced DNA melting?

48) ____________

49) Explain the technique of electrophoretic separation of DNA fragments.

49) ____________

50) You determine the sequence of an isolated gene, and wish to find its location in the genome. Propose a procedure using fluorescence to locate your gene of interest.

50) ____________

1) E 2) E 3) E 4) D 5) C 6) E 7) C 8) B 9) C 10) B 11) C 12) C 13) A 14) A 15) A 16) A 17) E 18) D 19) C 20) C 21) E 22) A 23) E 24) C 25) D 26) A 27) A 28) B 29) B 30) B 31) B 32) C 33) E 34) D 35) B 36) E 37) A 38) E 39) A 40) In the 1860s, Friedrich Miescher isolated an acidic substance (called nuclein) from cell nuclei, which turned out to be deoxyribonucleic acid. Although DNA was found to be present in chromosomes, it fell out of favor as the presumptive genetic material because of the incorrect hypothesis that DNA was a molecule of repeating units of four nucleotides, called the tetranucleotide hypothesis.

41) Transformation is the process whereby one organism is genetically altered by exposure to DNA from another organism. Since DNA can carry heritable "traits" from one organism to another, it must be the genetic material.

42) DNA is found where primary genetic functions occur; protein is found everywhere.

43) DNA has deoxyribose as the sugar in its nucleotides. The purines that are found in DNA are adenine and guanine, and the pyrimidines found in DNA are thymine and cytosine. RNA has ribose as the sugar in its nucleotides. The purines that are found in RNA are adenine and guanine, and the pyrimidines found in RNA are uracil and cytosine.

44) Polynucleotides are polymers longer than 30 nucleotides; oligonucleotides are approximately 4-30 nucleotides in length.

45) When the two strands in double-stranded DNA associate with each other, one strand runs 5' to 3' in one direction, the other strand runs in the same plane, but with a 3' to 5' orientation (antiparallel). Hydrogen bonding between strands occurs between adenines and thymines, and between cytosines and guanines, which are in turn called complementary base pairs.

46) They only occur in helices lacking guanine, and it is exceptionally unlikely to find an organism that has no guanine.

47) rRNA is the most abundant, serves a structural and functional role in a ribosome, and can be found in six widely different lengths. tRNAs are the next most abundant, carry amino acids to ribosomes for incorporation into proteins, and exhibit a narrow range of sizes. mRNAs are the least abundant, provide a blueprint for translation, and have the widest range of lengths observed.

48) Urea competes for hydrogen bonds; thus, the bases pair with the urea rather than with each other. This weakens the complementary associations that are required to hold the DNA helix together; thus, less heat is required for melting. The sodium of sodium chloride associates with and neutralizes the strong negative charges on the phosphates. The phosphates do not repel each other with the sodium ion present; thus, the double-stranded structure requires more energy to melt.

49) A mixture of different sized DNA molecules are subjected to an electric field, and migrate through a semisolid matrix such that smaller fragments travel further in the matrix. Also see Figure 10.18.

50) A single-stranded probe molecule could be synthesized, which is complementary to one strand of your gene and labeled with a fluorescent marker. Mitotic cells could then be immobilized and their chromosomes denatured, followed by introduction of labeled probe. After hybridization, the fluorescent label is detected, identifying the chromosome and location of the gene of interest.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Which of the following terms accurately describes the replication of DNA in vivo?

1) _______ A) dispersive B) semidiscontinuous C) nonreciprocal D) conservative E) nonlinear 2) After ONE round of DNA replication in Meselson and Stahl's classic experiment, ________.

A) the semiconservative model was conclusively proven to be the accurate model B) the conservative model was conclusively proven to be an inaccurate model C) both the conservative and the semiconservative models were still possibilities D) all three models of replication were still possibilities E) the dispersive model was conclusively proven to be an inaccurate model

2) _______

3) DNA replication proceeds ________.

A) progressively B) dispersively C) semiconservatively D) unidirectionally E) discontinuously

3) _______

4) If DNA replication were fully conservative, how many intact parental double helices would

4) _______

have been detected in Meselson and Stahl's experiment after three rounds of replication?

A) 3 B) 7 C) 8 D) 1 E) 0

5) The amount of DNA that is replicated from a single origin of replication is referred to as a(n)

5) _______

________.

A) primer B) fork C) replicon D) ori E) Okazaki fragment

6) Which DNA Polymerase III subunit is not part of the clamp loading assembly?

A) θ B) ν C) γ D) χ

6) _______ E) δ

7) DNA replication occurs by adding ________.

A) NTPs to the 3′ end of the daughter strand B) dNTPs to the 3′ end of the daughter strand C) dNTPs to the 3′ end of the template strand D) dNTPs to the 5′ end of the template strand E) NTPs to the 5′ end of the daughter strand

7) _______

8) DNA polymerase III adds nucleotides ________.

A) to the 3′ end of the RNA primer B) in the place of the primer RNA after it is removed

8) _______

C) to both ends of the RNA primer D) to internal sites in the DNA template E) to the 5′ end of the RNA primer 9) DNA polymerase I is thought to add nucleotides ________.

A) in a 5′ to 5′ direction B) in the place of the primer RNA after it is removed C) to the 5′ end of the primer D) on single-stranded templates without need for an RNA primer E) to the 3′ end of the primer

9) _______

10) Which terms accurately reflect the nature of replication of the chromosome in E. coli?

A) multirepliconic and telomeric B) unidirectional and reciprocal C) bidirectional and multirepliconic D) unidirectional and fixed point of initiation E) bidirectional and fixed point of initiation

10) ______

11) Which cluster of terms accurately reflects the nature of DNA replication in prokaryotes?

A) fixed point of initiation, bidirectional, conservative B) fixed point of initiation, bidirectional, semiconservative C) fixed point of initiation, unidirectional, conservative D) random point of initiation, unidirectional, semiconservative E) random point of initiation, bidirectional, semiconservative

11) ______

12) Which of the following statements about the oriC region in E. coli is incorrect?

A) It is directly recognized and bound by DNA helicase.

B) It is rich in AT base pairs.

C) It is 245 base pairs in length.

D) It includes five repeating sequences of 9 base pairs.

E) It includes three repeating sequences of 13 base pairs.

12) ______

13) The protein responsible for the initial step in unwinding the DNA helix during replication of

13) ______

the bacterial chromosome is coded for by the ________ gene.

A) dnaA B) polB C) polA

D) dnaE

E) gyrA

14) If E. coli DNA polymerase III was able to initiate DNA synthesis opposite a single-stranded

14) ______

template, which molecule(s) would no longer be essential?

A) DNA ligase B) DNA polymerase I C) DNA gyrase D) single-stranded binding proteins E) helicase

15) The discontinuous aspect of replication of DNA in vivo is caused by ________.

A) sister-chromatid exchanges B) the 5′ to 3′ polarity restriction C) trinucleotide repeats D) topoisomerases cutting the DNA in a random fashion E) polymerase slippage

15) ______

16) Given the accompanying diagram, assume that a G1 chromosome (left) underwent one round

16) ______

of replication in 3H-thymidine and the metaphase chromosome (right) had both chromatids labeled. Which of the following replicative models (conservative, dispersive, semiconservative) could be eliminated by this observation?

A) dispersive B) conservative C) semiconservative D) conservative and dispersive E) semiconservative and dispersive 17) During DNA replication, ________ are 1000-2000 nucleotide long strands synthesized on the

17) ______

________ strand to maintain the ________ of replication.

A) primers; leading; discontinuity B) Okazaki fragments; lagging; bidirectionality C) Okazaki fragments; leading, accuracy D) Okazaki fragments; leading; semidiscontinuity E) primers, lagging; continuity

18) As unwinding of the helix occurs during DNA replication, tension referred to as ________ is

18) ______

created ahead of the replication fork. This tension is relieved by the action of ________.

A) processivity; DNA gyrase B) supercoiling; DNA helicase C) supercoiling; single-stranded binding proteins D) supercoiling; DNA gyrase E) processivity; primase

19) Which of the following statement about DNA replication in E. coli is correct?

A) Single-stranded binding proteins are only required on the leading strand.

B) There are two molecules of DNA polymerase III per replication fork.

C) Only the lagging strand needs to be primed.

D) DNA polymerase I follows closely behind DNA helicase in the replication fork.

E) There are two molecules of DNA helicase per replication fork.

19) ______

20) The protein product of the E. coli dnaE gene is a component of ________.

A) DNA ligase B) DNA polymerase I C) DNA polymerase III D) primase E) DNA helicase

20) ______

21) The activity of ________ would be quickly undone in the absence of single-stranded binding

21) ______

protein.

A) primase B) DNA polymerase III C) DNA helicase D) DNA polymerase I E) DNA ligase

22) DNA replication in eukaryotes ________.

A) initiates at multiple origins B) takes place multiple times per cell cycle C) synthesizes DNA approximately 25 times faster than in prokaryotes D) occurs without the need of a primer E) utilizes a single type of DNA polymerase

22) ______

23) Chromatin is defined as ________.

A) DNA complexed with protein B) a catalytic molecule with a protein component and an RNA component C) supercoiled loops of bacterial DNA D) hybrid molecules of DNA and RNA E) genetic material found only in mitochondria

23) ______

24) Assembly of new nucleosomes is carried out by complexes abbreviated ________.

A) TLS B) DSB C) CAF D) SSB E) TERC

24) ______

25) Which eukaryotic DNA polymerase would least likely be involved in repair?

A) β B) δ C) γ D) α

25) ______ E) ε

26) Structures located at the ends of eukaryotic chromosomes are called ________.

A) recessive mutations B) permissive mutations C) centromeres D) telomeres E) telomerases

26) ______

27) Telomerase reads ________ as a template and synthesizes ________ as a product.

A) DNA; DNA B) DNA; protein C) DNA; RNA D) RNA; DNA E) RNA; RNA

27) ______

28) The process of making DNA from an RNA template is referred to as ________.

A) reverse transcription B) recombination C) transversion D) translation E) transcription

28) ______

29) Telomerase adds nucleotides to the ________.

A) 3′ end of the parental strand

29) ______ B) 5′ end of the daughter strand

C) 3′ end of the daughter strand

D) 5′ end of the parental strand

30) A molecule that possesses both a protein component and an RNA component is referred to as a

30) ______

________.

A) polymerase B) tetramer C) dimer D) ribonucleoprotein E) holoenzyme

31) Which of the following is not an essential step in homologous recombination?

A) endonuclease nicking B) duplex separation C) exonuclease degradation D) strand displacement E) branch migration

31) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

32) The Meselson and Stahl's experiment provided conclusive evidence for the 32) ____________ semiconservative replication of DNA in E. coli. What pattern of bands would occur in a CsCl gradient for conservative replication?

33) Briefly describe what is meant by the term autoradiography and identify a classic

33) ____________

experiment that used autoradiography to determine the replicative nature of DNA in eukaryotes.

34) Compare and contrast DNA Polymerases I, II, and III in E. coli. What capabilities are

34) ____________

shared, and which are exclusive to only one type of polymerase?

35) Explain why DNA primers can be used in in vitro DNA synthesis reactions, but not in

35) ____________

vivo.

36) DNA replication in vivo requires a primer with a free 3′ end. What molecular species

36) ____________

provides this 3′ end, and how is it provided?

37) Why does DNA replication have to be semidiscontinuous in order to be bidirectional?

37) ____________

38) Explain the need for, and action of, DNA gyrase in bacterial DNA replication.

38) ____________

39) A drug is added to a culture of E. coli cells that inhibit DNA gyrase. Predict the effect

39) ____________

of this drug on DNA replication in the affected cells.

40) Describe the benefit to researchers of conditional mutants.

40) ____________

41) What is meant by a gene knockout?

41) ____________

42) Compare and contrast DNA replication in prokaryotes and eukaryotes.

42) ____________

43) What is the name of the replication unit in prokaryotes, and how does it differ in

43) ____________

eukaryotes?

44) What is meant by processivity of a DNA-synthesizing enzyme?

44) ____________

45) Compare the rate of DNA replication in prokaryotes and eukaryotes.

45) ____________

46) Describe the DNA base sequence arrangement at the end of the Tetrahymena

46) ____________

chromosome and the resolution of DNA replication at the end of a linear DNA strand.

47) Describe a somewhat extraordinary finding related to the Tetrahymena telomerase

47) ____________

enzyme.

48) Why are bacteria not dependent on telomerase for complete DNA replication?

48) ____________

49) What is meant by homologous recombination?

49) ____________

50) Describe two processes for which recombination is essential.

50) ____________

1) B 2) B 3) C 4) D 5) C 6) A 7) B 8) A 9) B 10) E 11) B 12) A 13) A 14) B 15) B 16) B 17) B 18) D 19) B 20) C 21) C 22) A 23) A 24) C 25) D 26) D 27) D 28) A 29) A 30) D 31) C 32) After one generation in the 14N, there would be two bands, one heavy and one light (no intermediate). After the second generation in the 14N, there would also be two bands, one heavy and one light (no intermediate).

33) Autoradiography is a technique that allows an isotope to be detected within a cell; the Taylor, Woods, and Hughes (1957) experiment used 3H-thymidine.

34) None of the polymerases are able to initiate chain synthesis, but all are able to extend an existing fragment in the 5′ to 3′ direction. All three possess proofreading ability (3′ to 5′ exonuclease), but only DNA polymerase I possesses primer removal ability (5′ to 3′ exonuclease).

35) The need for the primer is to provide a 3′ OH group to which DNA-synthesizing enzymes can add new nucleotides. In an in vitro reaction, provided the template sequence is known, complementary single-stranded DNA primers can be synthesized and included in the reaction.

36) The free 3′ end is provided by an RNA primer; it is provided by the enzymatic activity of RNA primase.

37) The requirement of synthesis to be 5′ to 3′, and the antiparallel nature of double-stranded DNA, means that in both replication forks one of the stands must be made in fragments directed back toward the origin of replication.

38) DNA helicase induces supercoiling (tension) in the parental DNA as it processes. DNA gyrase relieves this tension so that replication fork progression can continue without grinding to a halt.

39) Without DNA gyrase to relieve the supercoiling of the DNA induced by DNA helicase, the tension in the closed circle of DNA would cause replication machinery to stall, preventing replication from completing and preventing the cells from dividing.

40) Many mutations that would be interesting to study are lethal. Conditional mutations allow researchers to observe wild-type behavior under permissive conditions, and loss-of-function effects under restrictive conditions.

41) The designed loss of a specific gene in order to study its function. This is often accomplished in the context of a conditional knockout, where the gene is affected in some tissue types but not others, allowing genes to be studied for which complete loss would be lethal.

42) Eukaryotic DNA is replicated in a manner very similar to that in E. coli: bidirectional, continuous on one strand and discontinuous on the other, and similar requirements for synthesis. However, in eukaryotes, Okazaki fragments are about one-tenth the size of those in bacteria. Different portions of the chromosome (euchromatin, heterochromatin) replicate at different times. There are multiple replication origins in eukaryotic chromosomes.

43) replicon; one replicon in prokaryotes, multiple replicons in eukaryotes 44) The strength of the association between the enzyme and its substrate, and thus the length of DNA that is synthesized before the enzyme dissociates from the template.

45) Eukaryotic DNA polymerases synthesize DNA at a rate 25 times slower (about 2000 nucleotides per minute) than do prokaryotes.

46) Telomeres terminate in a 5′-TTGGGG-3′ sequence, and telomerase is capable of adding repeats to the ends, thus allowing the completion of replication without leaving a gap and shortening the chromosome following each replication.

47) The enzyme contains a short piece of RNA that is essential for its catalytic activity.

48) Telomerase allows for the accurate replication of linear DNA molecules, and bacteria typically possess circular chromosomes.

49) Genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology.

50) The exchange of genetic information during meiosis, and the repair of double-stranded breaks in DNA molecules.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Viral chromosomes exist in a variety of conformations and can be made up of ________.

1) _______ A) RNA only B) DNA only C) protein- or lipid-coding sequences D) DNA, RNA, or protein E) DNA or RNA 2) In E. coli, the genetic material is composed of ________.

A) RNA and protein B) circular, double-stranded DNA C) circular, double-stranded RNA D) linear, double-stranded DNA E) polypeptide chains

2) _______

3) This figure represents supercoiled, circular, double-stranded DNA:

3) _______

If this molecule of DNA originated as a linear molecule with a linking number (L) of 30, which was then circularized and unwound, the L for the unwound circular molecule would be ________.

A) 20 B) 32 C) 28 D) 30 E) 18

4) Type I topoisomerases differ from type II topoisomerases in that the type I enzymes ________.

A) induce negative supercoiling B) ligate fragments of DNA that have been hydrolyzed C) decrease the linking number (L) of a double helix D) cleave one strand of a double helix E) cleave both strands of a double helix

4) _______

5) If relaxed circular DNA is designated (R), supercoiled circular DNA is designated (S), and

5) _______

linear DNA is designated (L), arrange these conformations in order of increasing rate of sedimentation during centrifugation.

A) (S), (L), (R) B) (L), (R), (S) C) (L), (S), (R) D) (S), (R), (L) E) (R), (S), (L)

6) In which of the following ways do polytene chromosomes differ from other chromosomes?

A) Polytene chromosomes are replicated but not separated.

B) Polytene chromosomes are multiple copies of identical single-stranded DNA. C) Polytene chromosomes can only be found in bacteria.

D) Polytene chromosomes are separated but not replicated.

6) _______

E) Polytene chromosomes represent uncoiled versions of meiotic chromosomes.

7) The condensed areas in polytene and lampbrush chromosomes are referred to as ________.

A) chiasmata B) chromatids C) puffs D) chromomeres E) centromeres

7) _______

8) Which statement about lampbrush chromosomes is incorrect?

A) The loops consist of two DNA helices, whereas the axis consists of a single DNA helix.

B) More DNA is looped out from the axis than is required for a single gene.

C) They are meiotic chromosomes.

D) Instead of being condensed, they are extended.

E) Looped out regions are active in RNA synthesis.

8) _______

9) Eukaryotic chromosomes contain two general domains that relate to the degree of

9) _______

condensation. These two regions are ________.

A) called heterochromatin and euchromatin B) void of introns C) uniform in the genetic information they contain D) each void of typical protein-coding sequences of DNA E) separated by large stretches of repetitive DNA

10) Chromatin of eukaryotes is organized into repeating interactions with protein octamers called

10) ______

nucleosomes. Nucleosomes are composed of which class of molecules?

A) histones B) nonhistone chromosomal proteins C) lipids D) H1 histones E) glycoproteins

11) The condition that some organisms contain much larger amounts of DNA than are apparently

11) ______

"needed" and that some relatively closely related organisms may have vastly different amounts of DNA is more typical in ________.

A) prokaryotes than in eukaryotes B) the alphoid rather than the diploid family C) viruses than in bacteria D) eukaryotes than in prokaryotes E) RNA viruses than in DNA viruses

12) In human chromosomes, satellite DNA sequences of about 170 base pairs in length are present

12) ______

in tandem arrays of up to 1 million base pairs. Found mainly in centromere regions, these DNA sequences are called ________.

A) telomeres B) primers C) alphoid families D) telomere-associated sequences E) euchromatic regions

13) In addition to highly repetitive and unique DNA sequences, a third category of DNA sequences

exist s.

What is it called, and what types of elements are involved in it?

____ __

13)

A) dominant DNA; euchromatin and heterochromatin B) multiple gene family DNA; hemoglobin and 5.0S RNA C) moderately repetitive DNA; SINEs, LINEs, and VNTRs D) permissive DNA; centromeres and heterochromatin E) composite DNA; telomeres and heterochromatin 14) Chromosomal regions that represent evolutionary vestiges of duplicated copies of genes that

14) ______

have underdone sufficient mutations to render them untranscribable are called ________.

A) LINEs B) alleles C) pseudogenes D) satellites E) transposons

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) A particular variant of the lambda bacteriophage has a DNA double-stranded genome 15) ____________ of 51,365 base pairs. How long would this DNA be?

16) List several configurations that characterize different viral chromosomes.

16) ____________

17) Describe the chromosomal conformations of φX174 and polyomaviruses.

17) ____________

18) Explain how linear DNA can be supercoiled.

18) ____________

19) What is the relationship between topoisomers?

19) ____________

20) How was it experimentally determined that "puffs" are transcriptionally active?

20) ____________

21) How does a polytene chromosome differ from a typical eukaryotic chromosome?

21) ____________

22) Although mutations have been observed in many different genes, they have not been

22) ____________

isolated in histones. Why does this seem reasonable? If one wanted to produce antibodies to histones, would it be an easy task? Explain your answer.

23) What is unusual about the amino acid composition of histones? How is the function of

23) ____________

histones related to the amino acid composition? Of which histones are nucleosomes composed?

24) Describe the basic structure of a nucleosome. What is the role of histone H1?

24) ____________

25) Compare and contrast the chromosome structure of viruses, bacteria, and eukaryotes.

25) ____________

26) List the components of a nucleosome.

26) ____________

27) What similarities do bacterial chromosomes have with eukaryotic chromosomes?

27) ____________

28) What are histones, and how are they arranged in nucleosomes?

28) ____________

29) When native chromatin is digested with micrococcal nuclease, what significant result

29) ____________

occurs?

30) In the formation of nucleosomes, one histone class, H1, is not directly involved, yet it

30) ____________

does associate with DNA to form higher level chromosomal structures. Where does this histone (H1) associate?

31) What are minisatellites and microsatellites?

31) ____________

32) Briefly state what is meant by repetitive DNA.

32) ____________

33) What is meant by SINE in terms of chromosome structure? By LINE? Why are they

33) ____________

called "repetitive"?

34) How do VNTRs relate to DNA fingerprinting?

34) ____________

35) Approximately how much of the mammalian genome is composed of repetitive DNA?

35) ____________

36) Briefly describe the makeup of VNTRs (variable number tandem repeats).

36) ____________

37) In instances in the eukaryotic genome, DNA sequences represent evolutionary vestiges

37) ____________

of duplicated copies of genes. What are such regions called and what are their characteristics?

1) E 2) B 3) C 4) E 5) B 6) A 7) D 8) A 9) A 10) A 11) D 12) C 13) C 14) C 15) One base pair is 0.34 nm; therefore, 51,365 bp × 0.34 nm/bp = 17,464 nm or 17.46 μm.

16) DNA (single- and double-stranded), RNA (single- and double-stranded), linear, circular 17) single-stranded DNA, circular; double-stranded DNA, circular, respectively 18) In eukaryotes with linear chromosomes, regions of DNA can be supercoiled if their ends are anchored to chromatin proteins that serve as a structural framework, or lattice.

19) They are molecules of DNA that differ in their linking numbers (L) but are otherwise identical.

20) Puffs actively incorporate radioactively labeled RNA precursors during autoradiography assays. Bands that are not extended into puffs incorporate fewer radioactive precursors or none at all.

21) Polytene chromosomes are found in a variety of tissues in the larvae of some flies and several species of protozoans and plants. A polytene chromosome contains banding patterns and is large because of repeated replications of DNA without nuclear division.

22) Histones represent one of the most conserved molecules in nature because they are involved in a fundamental and important function relating to chromosome structure. Mutations are probably lethal. As all antibody-producing organisms have essentially the same histones, it would be difficult to find an organism that produces histone antibodies, for to do so would be self-destructive.

23) Histones contain large amounts of positively charged amino acids such as lysine and arginine. Thus, they can bind electrostatically to the negatively charged phosphate groups of nucleotides. Nucleosomes are composed of all histones except H1.

24) Nucleosomes are composed of four different histone molecules, each of which exists twice, thus forming an octamer. Histone H1 is between nucleosomes and is associated with linker DNA. 25) The amount of DNA per structure (virus particle, bacterium, or cell) increases as one goes from viruses to eukaryotic cells. Viral chromosomes may be composed of single-stranded or double-stranded RNA or DNA, whereas bacterial and eukaryotic DNA is double-stranded. Bacterial DNA is considered to be a covalently closed circle; the "global" structure of eukaryotic chromosomes is uncertain. Although some proteins are associated with viral and bacterial DNAs, the regularly spaced histones of eukaryotic chromosomes are unique.

26) Histones H2A, H2B, H3, and H4 exist as two types of tetramers: (H2A)2 + (H2B)2 and (H3)2 + (H4)2.

27) Both have double-stranded DNA and several types of proteins associated with that DNA (nucleosomes in eukaryotes and HU and H1 proteins in bacteria).

28) Histones include five main classes of relatively small basic proteins containing relatively large amounts of lysine and arginine. Nucleosomes are made of two each of four types of histones.

29) DNA fragments of approximately 200 base pairs in length are formed.

30) in the spaces between nucleosome and DNA complexes 31) Both are highly repetitive, relatively short DNA sequences.

32) DNA is present in repeated sequences—(GACAT)n, for example.

33) SINE = short interspersed elements, a moderately repetitive sequence class; LINE = long interspersed elements.

Multiple copies exist–up to 900,000 Alu, sequences, for example.

34) VNTRs are variable number tandem repeats of 15-100 base pairs long that vary among individuals. Because each

non-t win individual has a different VNTR pattern, identity of individuals is unique.

35) About 5-10% of a mammalian genome is highly repetitive; about 30% is moderately repetitive.

36) VNTRs are repeating DNA sequences of about 15-100 base pairs long that are found within and between genes.

These sequences may be repeated to give regions 1000-5000 bp in length. They are dispersed throughout the genome.

37) Pseudogenes are duplicated copies of genes that have undergone considerable mutation and share some homology to the original gene.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Which of the following is true regarding the genetic code?

1) _______ A) The genetic code is overlapping.

B) The genetic code has three start codons and one stop codon.

C) The genetic code is ambiguous.

D) The genetic code is considered to not be universal.

E) The genetic code is degenerate.

2) If there were 75 naturally occurring amino acids then what is the smallest codon size?

A) 1 B) 2 C) 3 D) 4 E) 5

2) _______

3) When scientists were attempting to determine the structure of the genetic code, Crick and

3) _______

coworkers found that when three base additions or three base deletions occurred in a single gene, the wild-type phenotype was sometimes restored. These data supported the hypothesis that ________.

A) there are three amino acids per base B) the code contains internal punctuation C) the code is triplet D) the code is overlapping E) AUG is the initiating triplet

4) The experiments that deciphered the genetic code used an enzyme called polynucleotide

4) _______

phosphorylase. If researchers added this enzyme to a large quantity of only guanine (G) ribonucleoside diphosphates then a RNA molecule would be produced that would code for which amino acid?

A) proline (pro) B) glycine (gly) C) phenylalanine (phe) D) lysine (lys) E) arginine (arg)

5) In 1964, Nirenberg and Leder used the triplet binding assay to determine specific codon

5) _______

assignments. A complex of which of the following components was trapped in the nitrocellulose filter?

A) uncharged tRNAs and ribosomes B) ribosomes and DNA C) free tRNAs D) sense and antisense strands of DNA E) charged tRNA, RNA triplet, and ribosome

6) What is the name given to the three bases in a messenger RNA that bind to the anticodon of tRNA to specify an amino acid placement in a protein?

A) codon B) wobble C) procodon

D) rho

E) cistron

7) What is the initiator triplet in both bacteria and eukaryotes? What amino acid is recruited by this triplet?

A) UAA, UGA, or UAG; no amino acid called in B) AUG; arginine

6) _______

7) _______

C) UAA, UGA, or UAG; arginine D) AUG; methionine E) UAA, UGA, or UAG; methionine 8) Due to the wobble hypothesis, which position in the codon, if changed to a different nucleotide,

8) _______

would be least likely to cause a change in the amino acid encoded?

A) third nucleotide of the codon B) second nucleotide of the codon C) first nucleotide of the codon D) any nucleotide of the codon.

E) Either the first or second nucleotide of the codon.

9) A particular mRNA is 300 nucleotides long. If a mutation in the middle of the sequence

9) _______

changed a codon from a AAA to a UAA then what would be a reasonable prediction?

A) The protein coded by this mRNA would be longer.

B) The protein coded by this mRNA would kill the cell.

C) The protein coded by this mRNA would be shorter.

D) The protein coded by this mRNA would not form due to a failure in initiation.

E) The protein coded by this mRNA would be the same size.

10) The genetic code is fairly consistent among all organisms. The term often used to describe such

10) ______

consistency in the code is ________.

A) universal B) overlapping C) trans-specific D) exceptional E) None of the above

11) The nuclear genetic code is considered universal with a few exceptions. Some of these

11) ______

exceptions are found when comparing the nuclear genetic code of humans to what?

A) human mitochondrial genetic code B) angiosperm's genetic code C) acterial genetic code D) phage M2 genetic code E) chimpanzee's genetic code

12) The finding that some phage genes have multiple initiation sites is evidence against what

12) ______

characteristic of the genetic code?

A) The genetic code is a triplet code.

B) The genetic code is universal.

C) The genetic code is commaless.

D) The genetic code is nonoverlapping.

E) The genetic code is unambiguous.

13) The relationship among a gene, a messenger RNA, and a protein is that ________.

A) genes make mRNA, which then make proteins B) genes make proteins, which then make mRNA C) proteins make mRNA, which then make genes D) mRNAs make genes, which then make proteins E) mRNAs make proteins, which then make genes

13) ______

14) Which of the following bacterial RNA polymerase subunits is found in the holoenzyme, but not

14) ______

the core enzyme?

A) β (beta) B) α (alpha) C) ω (omega) D) σ (sigma) E) β′ (beta prime)

15) An mRNA that is being produced comes off of the ________.

A) coding strand in both bacteria and eukaryotes B) template strand in bacteria and the coding strand in eukaryotes C) coding or template strand in both bacteria and eukaryotes depending upon the species D) coding strand in bacteria and the template strand in eukaryotes E) template strand in both bacteria and eukaryotes

15) ______

16) When considering the initiation of transcription, one often finds consensus sequences located in

16) ______

the region of the DNA where RNA polymerase(s) binds. Which of the following is a common consensus sequence?

A) satellite DNAs B) TTTTAAAA C) any trinucleotide repeats D) GGTTC E) TATAAT

17) A mutation in a particular bacterial gene prevents the formation of a hairpin loop. This is most

17) ______

likely to affect which part of transcription?

A) This mutation will affect termination.

B) This mutation will not affect any aspect of transcription in bacteria.

C) This mutation will affect elongation.

D) This mutation will affect initiation, elongation, and termination.

E) This mutation will affect initiation.

18) Eukaryotic transcription is different than bacterial transcription because eukaryotic

18) ______

transcription ________.

A) does not require the mRNA to be modified B) does not require general transcription factors to initiate transcription C) requires the uncoiling of the chromatin fiber D) occurs in the cytoplasm E) only requires one RNA polymerase

19) Which transcription factor binds directly to the TATA-box sequence?

A) TFIIB B) TFIIA C) TFIIC D) TFIID E) enhancers

19) ______

20) A mutation of what type of sequence is predicted to have the greatest effect on the rate of

20) ______

transcription?

A) silencer B) termination sequence

C) proximal-promoter element D) enhancer E) core promoter 21) Which mRNA modification is likely absent if the mRNA is degrading prematurely from the 5′

21) ______

end of the mRNA? A) removal of introns B) addition of the 3′ polyadenylated tail C) addition of the 7-methylguanosine cap to the 5′ end D) RNA editing E) splicing together of exons

22) It has been recently determined that the gene for Duchenne muscular dystrophy (DMD) is

22) ______

more than 2000 kb (kilobases) in length; however, the mRNA produced by this gene is only about 14 kb long. What is a likely cause of this discrepancy?

A) There are more amino acids coded for by the DNA than by the mRNA. B) The exons have been spliced out during mRNA processing.

C) When the mRNA is produced, it is highly folded and therefore less long.

D) The DNA represents a double-stranded structure, whereas the RNA is single-stranded.

E) The introns have been spliced out during mRNA processing.

23) An intron is a section of ________.

A) RNA that is removed during RNA processing B) the transfer RNA (tRNA) that binds to mRNA codon C) the carbohydrate that serves as a signal for RNA transport D) protein that is clipped out posttranslationally E) DNA that is removed during DNA processing

23) ______

24) If one compares the base sequences of related genes from different species, one is likely to find

24) ______

that corresponding ________ are usually conserved, but the sequences of ________ are much less well conserved.

A) chaperons; exons B) exons; introns C) introns; chaperons D) introns; exons E) introns; proteins

25) In which cellular organelle do the three posttranscriptional modifications often seen in the

25) ______

maturation of mRNA in eukaryotes occur?

A) cytoplasm B) lysosome C) nucleus D) Golgi E) mitochondrion

26) Which of the following intron groups is matched appropriately with a true statement?

A) Spliceosomal introns are removed using the catalytic ability of the intron itself.

B) Group I introns are removed from rRNAs that are found in mitochondria and chloroplasts.

C) Group II introns are removed from mRNA in mammals.

D) Spliceosomal introns are removed using large protein-based enzyme complexes.

26) ______

E) Group I introns are removed from rRNAs using large protein-based enzyme complexes.

27) The type of RNA modification that requires guide RNAs is ________.

A) addition of the 7-methylguanosine cap to the 5′ end B) addition of the 3′ polyadenylated tail C) RNA editing D) removal of introns E) splicing together of exons

27) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

28) Describe the direction of information flow in living systems. Use appropriate, scientific 28) ____________ terms in your description.

29) Sidney Brenner argued that the code was nonoverlapping because he considered that

29) ____________

coding restrictions would occur if it were overlapping. A second major argument against an overlapping code involved the effect of a single nucleotide change. In an overlapping code, how many adjacent amino acids would be affected by a single nucleotide change? In a nonoverlapping code, how many amino acid(s) would be affected?

30) From the late 1950s to the mid-1960s, numerous experiments using in vitro cell-free

30) ____________

systems provided information on the nature of the genetic code. Briefly explain how the use of polynucleotide phosphorylase and the triplet binding assay were used to decipher the genetic code and why the triplet binding assay was more precise.

31) Suppose that in the use of polynucleotide phosphorylase, nucleotides A and C are

31) ____________

added in a ratio of 1A:5C. What is the probability that an AAA sequence will occur?

32) "Breaking the genetic code" has been referred to as one of the most significant scientific

32) ____________

achievements in modern times. Describe (in outline or brief statement form) the procedures used to break the code.

33) Reading the RNA sequences in a 5′ to 3′ direction, a base at the first position of an

33) ____________

anticodon on the tRNA would pair with a base at the ________ position of the mRNA.

34) Explain the "wobble hypothesis" and why it allows a single tRNA to recognize more

34) ____________

than one codon.

35) A particular mRNA makes a protein that has a unformylated methionine as its first

35) ____________

amino acid. Did this mRNA come from a bacterial or a eukaryotic cell? Explain.

36) Write a sequence of mRNA that codes for five amino acids and the mRNA should

36) ____________

contain proper punctuation and polarity.

37) There is some indication that the code is in some way ordered; a certain pattern exists.

37) ____________

Describe an observation that supports this view.

38) The finding that virtually all organisms use the same genetic code provides the basis for declaring that the code is universal. Name at least two exceptions to such universality.

38) ____________

39) In the context of molecular genetics, how does one reconcile the terms overlapping genes

39) ____________

and nonoverlapping code?

40) What are three observations that suggested eukaryotic RNA was an intermediate

40) ____________

between DNA and protein.

41) Describe the effects of mutating a sigma factor gene in bacteria.

41) ____________

42) In a particular bacterial mutant, a specific gene is not producing a mRNA or the

42) ____________

corresponding protein. Researchers sequence the gene and determine that there are no mutations in the coding portion of the gene. What could explain these observations?

43) Describe how rho-dependent termination occurs in bacteria.

43) ____________

44) Describe a difference between the RNA polymerases of eukaryotes and prokaryotes.

44) ____________

45) In eukaryotes, which three factors appear to encourage the specific association of RNA

45) ____________

polymerase(s) to a specific region of DNA?

46) What are four ways that mRNA can be modified?

46) ____________

47) List four possible reasons that explain the importance of introns.

47) ____________

48) What is meant by the term heterogeneous nuclear RNA (hnRNA)?

48) ____________

49) A researcher is looking at a cellular sample using an electron microscope. They observe

49) ____________

that while mRNA is being transcribed from the DNA that ribosomes are binding to the mRNA to make proteins. Is this sample from a bacterial or a eukaryotic cell?

1) E 2) D 3) C 4) B 5) E 6) A 7) D 8) A 9) C 10) A 11) A 12) D 13) A 14) D 15) E 16) E 17) C 18) C 19) D 20) E 21) C 22) E 23) A 24) B 25) C 26) D 27) C 28) DNA is replicated and passed to offspring through a variety of reproductive processes. Information contained in the base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.

29) two; one 30) Use of polynucleotide phosphorylase for the random assembly of nucleotides provided for the assembly of RNA homopolymers and random heteropolymers, which when placed in the cell-free protein-synthesizing system, provided products (polypeptide chains) for analysis. The triplet binding assay along with the use of repeating copolymers were used to verify information provided earlier and to establish the ordered codon assignments.

31) 1/6 × 1/6 × 1/6 = 1/216 32) (a) use of polynucleotide phosphorylase for the production of synthetic "mRNAs" (b) introduction of synthetic mRNAs into the cell-free protein-synthesizing system (c) frameshift mutations in the rII region of T4 phage to show code is triplet and degenerate (d) triplet binding assay to produce mRNA–tRNA-ribosome complex (e) development of regular copolymers for use in the cell-free protein-synthesizing system 33) third 34) The relaxed pairing at the third position of the codon and the first position of the anticodon are less constrained and do not need to follow the traditional base pair rules. This allows for a single tRNA to recognize multiple codons.

35) Eukaryotic cell. Eukaryotic mRNA code for proteins starts with an unformylated methionine whereas bacterial mRNA code for proteins starts with a formylated methionine.

36) 5′ AUG (any four amino acid coding codons) and (UAA, UGA, or UAG) 3′ 37) Certain amino acids may be grouped according to the middle base; for example, U or C in the second position often specifies hydrophobic amino acids. Also, codons with the same two starting letters frequently encode the

same amino acid.

38) mitchondrial DNA; Mycoplasma capricolum; some protozoans 39) The genetic code contains codons that are nonoverlapping; however, overlapping genes are observed in some viruses in which, due to differential use of AUG to initiate translation, the same mRNA can yield different protein products.

40) (1) DNA is found in the nucleus and protein synthesis occurs in the cytoplasm, (2) RNA is synthesized in the nucleus and has a chemical similarity to DNA, and (3) RNA is transported out of the nucleus and into the cytoplasm where protein translation occurs.

41) The core RNA polymerase enzyme will form. Since there are more than one sigma factor genes, by mutating a single sigma factor gene there will be some holoenzymes that will not form which will affect specific gene transcription.

42) One of the two consensus sequences are likely mutated. Either the Pribnow box (TATAAT) or the −35 sequence (TTGACA).

43) A bacterial protein called rho factor binds to an mRNA at the rut site. It moves along the mRNA in a 5′-to-3′ direction chasing after the RNA polymerase. When it reaches the hairpin loop it removes it and then proceeds to break through the hydrogen bonds holding the RNA-DNA together, which successfully removes the RNA polymerase.

44) In eukaryotes, three polymerases (I, II, and III) have been identified; only one has been described in prokaryotes.

45) promoters, enhancers, and transcription factors 46) (1) Adding a modified guanine to the 5′ end, (2) adding a polyadenylation tail to the 3′ end, (3) splicing of introns, and (4) RNA editing.

47) (1) introns allow for alternative splicing, (2) exon shuffling, which can aid in evolution of new genes, (3) the intron can be a microRNA itself that can regulated gene expression, and (4) introns can contain enhancer and silencer sequences that aid in gene regulation.

48) pre-mRNA, primary transcripts before processing in eukaryotes 49) Bacteria. Since bacteria lack a nucleus, the ribosomes can bind to the mRNA as it's being synthesized and initiate translation.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) A bacterium's large subunit is 60S and its small subunit is 40S. What is the size of the ribosome 1) _______ containing both subunits?

A) 70S B) 100S

C) 80S

D) 120S

E) 20S

2) Which of the following is true regarding the tRNA structure?

A) The nucleotides found in a tRNA molecule can only be adenine, uracil, guanine, and

2) _______

cytosine.

B) The anticodon is found at the 3′ end of the tRNA molecule.

C) A tRNA molecule that has an amino acid attached to it is called a charged tRNA. D) An amino acid binds to the 5′ end of the tRNA molecule.

E) The tRNA binds to an mRNA's codon at the variable loop.

3) If humans had 25 amino acids instead of 20 amino acids then how many aminoacyl tRNA synthetases would humans have?

A) 4 B) 75

C) 3

D) 25

3) _______

E) 20

4) During initiation in bacterial translation, a particular mutation causes the premature binding of

4) _______

the large ribosome subunit to the small ribosome subunit. Which component of initiation is not working properly?

A) Ribosome's E site B) IF2 C) IF1 D) IF3 E) Shine-Dalgarno sequence on the mRNA

5) A mutation in EF-Tu would have a DIRECT effect on which part of translation?

A) The next tRNA would not be able to enter the A site of the ribosome.

B) The polypeptide would form, but translation termination would be blocked.

C) The peptide bond formation would be blocked.

D) Translocation would be directly blocked.

E) The small and large subunits would not bind.

5) _______

6) What signals termination of translation in bacteria?

A) EF-Tu and EF-G B) the stop amino acid is attached to the growing peptide chain C) RF1 and RF2 D) a tRNA specific to the stop codon enters the ribosome's A site E) ribozymes

6) _______

7) A protein is 300 amino acids long. Which of the following could be the number of total

7) _______

nucleotides in the section of DNA that codes for this protein? (Remember: DNA is double-stranded.)

A) 300 B) 1800 C) 900 D) 100 E) 3

8) The term peptidyl transferase relates to ________.

A) 5′ capping of mRNA

8) _______

B) elongation factors binding to the large ribosomal subunit C) peptide bond formation during protein synthesis D) discontinuous strand replication E) base additions during mRNA synthesis 9) X-ray crystallography has revealed and confirmed many details about the ribosome. All of the

9) _______

following are such details, EXCEPT ________.

A) rRNA in the ribosome is in direct contact with the different loops of the tRNA molecule B) the ribosome is a dynamic structure that changes during its different functional states C) the distance the tRNA must travel between the E, P, and A sites is considered to be relatively short D) the wobble hypothesis is further supported E) rRNAs are more likely than proteins to be the catalytic molecule of the ribosome

10) Translation in bacterial and eukaryotic cells has many similarities, but there are also several key

10) ______

differences. Which of the following is one of those differences that is seen in eukaryotes?

A) Translation and transcription are coupled.

B) Eukartyotic mRNA contains a Shine—Dalgarno sequence that increases the efficiency of translation.

C) Eukaryotes only require one release factor that recognizes all three stop codons.

D) Eukaryotic ribosomes are smaller with fewer proteins and RNA molecules.

E) Eukaryotes use the 5′ G-cap and Poly-A-tail on their mRNAs to initiate translation.

11) The one-gene:one-enzyme hypothesis emerged from work on which two organisms?

A) Neurospora and Drosophila B) E. coli and humans C) Drosophila and humans D) E. coli and yeast E) All of the answers listed are correct.

11) ______

12) By their experimentation using the Neurospora fungus, Beadle and Tatum were able to propose

12) ______

the far-reaching hypothesis that ________.

A) several different enzymes may be involved in the same step in a biochemical pathway B) genetic recombination occurred in Neurospora C) prototrophs will grow only if provided with nutritional supplements D) more than one codon can specify a given amino acid E) the role of a specific gene is to produce a specific enzyme

13) A researcher is studying the synthesis of a specific amino acid found in Neurospora. She knows that the pathway begins with a precursor that is converted into the amino acid with two known intermediates (Substance Blue and Substance Green). She accurately predicts that this amino acid synthesis pathway is catalyzed by three enzymes, (I, II, and III). She subsequently identifies three mutants that she calls Mutant I, Mutant II, and Mutant III. With the information about the mutants below place the enzymes in the order that the enzymes act in this pathway.

(Note: the numbers I, II, and III don't necessarily indicate the order in which the enzymes appear.)

Mutant I (only Enzyme I is mutated) is unable to synthesize the amino acid even if she provided the mutant with both Substance Blue and Substance Green.

Mutant II (only Enzyme II is mutated) is able to synthesize the amino acid if she provided the mutant with Substance Blue or Substance Green.

Mutant III (only Enzyme III is mutated) is able to make the amino acid if she provided the

mut the ant mutant with with Subs only tanc Substa e nce Gree Blue. n, but not if she prov ided

13)

______ A) II, III, I B) III, II, I C) II, I, III D) I, II, III E) III, I, II F) More than one codon can specify a given amino acid.

14) The β chain of adult hemoglobin is composed of 146 amino acids of a known sequence. In

14) ______

comparing the normal β chain with the β chain in sickle-cell hemoglobin, what alteration is one likely to find?

A) glutamic acid replacing valine in the first position B) trinucleotide repeats C) valine instead of glutamic acid in the sixth position D) extensive amino acid substitutions E) frameshift substitutions

15) Often point mutations can cause a protein to be made that differs in just one amino acid. Which

15) ______

of the following changes is most likely to cause the greatest change in protein function?

A) a mutation that replaces an asparagine with a glutamine B) a mutation that replaces a valine with an isoleucine C) a mutation that replaces a proline with an aspartic acid D) a mutation that replaces a glutamic acid with an aspartic acid E) a mutation that replaces a serine with a cysteine

16) The primary structure of a protein is determined by ________.

A) covalent bonds formed between fibroin residues B) a series of helical domains C) the sequence of amino acids D) pleated sheets E) hydrogen bonds formed between the components of the peptide linkage

16) ______

17) The protein shown below provides an example of which level of protein folding?

17)

______

A) tertiary B) pentenary C) primary D) quaternary E) secondary 18) Side groups of amino acids are typically classified under which of the following?

A) polar, nonpolar B) primary, secondary C) long, short D) linear, circular E) alpha, omega

18) ______

19) All of the following are examples of posttranslational modifications, EXCEPT________.

A) Polypeptide chains can be cleaved to produce a shorter and functional polypeptide.

B) Polypeptides can be degraded and then reassembled to produce entirely different

19) ______

sequenced polypeptides.

C) Prosthetic groups, such as metals or vitamins, can be added.

D) Individual amino acid residues are sometimes modified, such as adding a phosphates, acetyl, or methyl groups can be added.

E) The N-terminal amino acid is often removed or modified.

20) What is the name of the protein that helps fold other proteins into their final and functional

20) ______

form?

A) collagen B) ubiquitin C) proteasomes D) chaperone E) flippase 21) Creutzfeldt-Jakob, Huntington, Alzheimer, and Parkinson disease are all characterized with

21) ______

which part of protein synthesis?

A) elongation B) termination C) initiation D) N-terminal modification E) protein folding

22) Which protein class directly controls many of the metabolic reactions within a cell?

A) hydrophilic proteins B) repressor proteins C) operator proteins D) structural proteins E) enzymes

22) ______

23) Modular portions of a protein that fold into stable conformations with specific functional

23) ______

capabilities are referred to as ________.

A) protein subunits B) protein domains C) protein secondary structures D) protein quaternary structures

E) protein chaperones SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

24) Describe the structure of a tRNA molecule. Your answer should include a list of five 24) ____________ important sites on the tRNA and two reasons why tRNA's modified bases are important.

25) Assume that a base addition occurs early in the coding region of a gene. Is the protein

25) ____________

product of this gene expected to have MORE or FEWER altered amino acids compared with the original gene with a base deletion late in the coding region? Explain.

26) The accompanying drawing represents simultaneous transcription and translation in E.

26) ____________

coli. The direction of the RNA polymerase is given by the arrow.

(a) Is the letter A nearer the 5′ or the 3′ end of the molecule? (b) Is the letter B nearer the 5′ or the 3′ end of the molecule? (c) Is the letter C nearer the 5′ or the 3′ end of the tRNA molecule? (d) What is the "S" value for the large rRNA that is closest to the letter D? (e) Which terminus (N or C) of the growing polypeptide chain is nearer to the letter E?

27) Consider the roles of IF1, IF2, and IF3 during translation. Predict what the effect would

27) ____________

be if IF1, IF2, and IF3 were mutated.

28) Three major types of RNAs are mRNA, rRNA, and tRNA. For each of the conditions

28) ____________

below, predict the consequences in terms of the population of proteins being synthesized in a particular cell and the effects on individual proteins. (a) An acridine dye—induced mutation (adds or deletes single bases in DNA) leads to an mRNA for one protein-producing gene. The condition is heterozygous in the involved cell. (b) A deletion (homozygous) that removes approximately half of the rRNA genes.

29) What are polyribosomes and why are they important?

29) ____________

30) Provide five reasons why translation is more complex in eukaryotes compared to

30) ____________

bacteria.

31) Explain why a eukaryotic mRNA that has begun to be degraded from the 3' end, but

31) ____________

still has its complete coding region intact is not efficiently translated.

32) ____________

32) Given the accompanying table: Supplement Strain A Strain B Strain C Strain D

1 + + + -

2 + + -

3 + + + +

4 + -

Where numbers 1 through 4 indicate four supplements that must be added to sustain growth of the organism. Determine a possible metabolic pathway that would give the results seen for the four mutant strains, A through D.

33) The following table presents the effect of different media on the growth response of

33) ____________

tryptophan mutations in Salmonella typhimurium (+ = growth, - = no growth).

Strain trp-8 trp-2 trp-3 trp-1

No Supplement -

Medium Supplement with ICP AA IN TRY + + + + + + + + + +

(a) Construct the biochemical pathway for the compounds IGP, AA, IN, and TRY based on these data. (b) Place strains of bacteria (mutations) in the appropriate steps in the pathway. (c) In bacteria it is often possible to make partial diploid strains. Assume that a diploid strain was made containing the complete genomes of the trp-2 and trp-1 strains.

Would this diploid strain be able to grow on the unsupplemented medium? Explain your answer.

34) The problem below relates to the synthesis of several intermediates in the citric acid

34) ____________

cycle, which is essential in the production of ATP through aerobic respiration. A set of experimental results relating the growth (+) of Neurospora on several media is given in the table. Based on the information provided, present the biochemical pathway for the substances oxaloacetate, fumarate, malate, and succinate, and the locations of the metabolic blocks produced by the various strains.

35) Much has been learned about the relationship between genes and gene products through the use of the mold Neurospora. What specific attributes make Neurospora a

goo organism for d such studies?

35)

____________

36) Nutritional mutants in Neurospora can be "cured" by treating the medium with

36) ____________

substances in the defective metabolic pathway. What determines whether the mutant strain (auxotroph) is "cured" by a particular substance?

37) Sickle-cell anemia is caused when one nucleotide is changed to another nucleotide in

37) ____________

the hemoglobin gene. How does this one small change cause the life-threatening disease of sickle-cell anemia?

38) Sickle-cell anemia is caused by a mutation that changes the second nucleotide of the

38) ____________

codon from GAG to GUG. This results in a change of the amino acid from glutamic acid to valine. If the mutation affected the third nucleotide of the codon and changed GAG to GAU then the amino acid would change from a glutamic acid to aspartic acid.

Would you predict this change to have the same effect?

39) In what ways do the amino acid side chains interact to influence protein function?

39) ____________

40) Below are several phenomena relating to protein structure. Clearly describe each

40) ____________

phenomenon, the conditions under which each occurs, and the probable influence each has on protein structure. (a) hydrophobic interactions (b) hydrogen bonds (c) disulfide bridges

41) Assuming that an amino acid sequence is 250 amino acids long, how many different

41) ____________

molecules, each with a unique sequence, could be formed?

42) Regarding the protein structure, how are β-pleated sheets arranged and stabilized?

42) ____________

43) Considering the types of side chains on amino acids and their relationship to protein

43) ____________

structure, where are the amino acids with hydrophobic side chains most likely to be located?

44) List at least three posttranslational modifications known to occur as a newly

44) ____________

synthesized protein matures.

45) The diseases bovine spongiform encephalopathy and Creutzfeldt—Jakob disease are

45) ____________

caused by what kind of protein? How does this protein cause these diseases?

46) Which class of protein functions primarily by lowering the energy of activation during a reaction?

46) ____________

1) C 2) C 3) D 4) D 5) A 6) C 7) B 8) C 9) C 10) E 11) A 12) E 13) A 14) C 15) C 16) C 17) D 18) A 19) B 20) D 21) E 22) E 23) B 24) The five sites are amino acid binding site, ΤψC stem, variable loop, anticodon stem, D stem, and acceptor stem.

The modified bases are important in conferring structural stability and play a role in hydroben bonding between tRNA and mRNA, which helps explain the wobble effect.

25) Since an addition or deletion of a base pair would change every codon after the addition or deletion, then adding a base early in the coding region would change more amino acids than deleting a base later in the coding region.

26) (a) 3′, (b) 5′, (c) 3′, (d) 23S, (e) N 27) If IF1 was mutated then the second tRNA would bind prematurely to the A site. If IF2 was mutated then the fMET tRNA would not be transferred to the P site of the small ribosome subunit. If IF3 was mutated then the large ribosomal subunit would prematurely bind to the small subunit.

28) (a) Population of proteins: Half of the protein products of that gene will be defective, and the other half will be normal. Individual protein: The protein should show multiple amino acid substitutions "downstream" from the point of the mutation. If a nonsense triplet is introduced, the protein will be shortened in the substituted region. (b) Population of proteins: There would be an overall reduction in protein synthesis. Individual proteins: All of the proteins would be made in their normal form but at reduced levels.

29) Polyribosomes are clusters of ribosomes held together on an mRNA molecule. This allows for multiple proteins to be synthesized from a single mRNA before it is degraded. This is particularly important in bacteria since they don't protect their mRNA. 30) There are several possible answers, but could include the following reasons. (1) In eukaryotes, mRNA needs to be transported out of the nucleus prior to it being translated. (2) Eukaryotic ribosomes are larger and are composed of more proteins and rRNA molecules. (3) Translation initiation in bacteria requires the mRNA contain the Shine—Dalgarno sequence. However, in eukaryotes, a more complex initiation process is needed that requires the 5'-G cap and the 3'-poly-A tail. (4) Translation initiation in eukaryotes requires many more initiation factors. (5) There are two tRNAs for methionine in eukaryotes: one for the initiating AUG codon and a different one used for all other AUG codons. (6) Termination in eukaryotes uses one of three possible Release Factors (one for each stop codon) while bacteria have a total of two release factors.

31) Eukaryotic translation uses a closed-loop process where the 5' G cap and the 3' poly A-tail of the mRNA loop around and interact with the ribosome to initiate translation. If the 3' poly-A tail has begun to degrade then translation will not efficiently be initiated.

32) X →

+→ 4 → +→ 2 → +→1 → +→ 3 ↑ ↑ ↑ ↑ C B A D 33) (a) →+→>AA→+→>IGP→+→>IN→+→?Try →+→>AA→+→>IGP→+→IN→+→Try ↑ ↑ ↑ ↑ (b) 8 2 3 1 (c) Yes, complementation will occur because the trp-2 strain is also trp-1+ and the trp-1 strain is also trp-2+.

34) succinate →+→ fumarate →+→ malate →+→ oxaloacetate ↑ ↑ ↑ l41 l62 l36 35) Knowledge of its biochemistry; its haploid ascospores; relative ease of isolating nutritional mutations 36) The substance needs to be added after the metabolic block in the biochemical pathway.

37) Substituting this one nucleotide changes the amino acid from glutamic acid codon to valine. Glutamic acid is a polar negatively charged amino acid whereas valine is a nonpolar. Even though it is only a single base change, the result is a major change in the amino acid that allows the hemoglobin protein to stick to other hemoglobin proteins that results in the sickling of the red blood cell.

38) A change in one polar-charged amino acid to another polar-charged amino acid would be predicted to have less of a phenotype compared to a mutation that resulted in a change from a polar-charged amino acid to a nonpolar amino acid. Changes to the third nucleotide of a codon are often less damaging than changes to the first or second nucleotide.

39) Higher-level folding of proteins is dependent on a variety of interactions (ionic, covalent, hydrogen, hydrophobic, hydrophilic, etc.), which determine the functional three-dimensional structure of proteins.

40) (a) Hydrophobic interactions: These are nonpolar side chains of amino acids that tend to associate to form hydrophobic clusters usually away from the protein surface. (b) Hydrogen bonds: Such bonds may occur between the components of the peptide bond, the side chains, or a combination of the two. They are responsible for helical and pleated sheet structures of proteins. (c) Disulfide bridges: Such bonds are formed between two cysteine side chains and, because of their covalent nature, represent relatively strong attractive forces between different (sometimes distant) regions of proteins.

41) 20250

42) Several chains run in parallel or antiparallel fashion stabilized by hydrogen bonds formed between components of the peptide linkage.

43) Away from the water environment and in the interior portion of the molecule 44) N-terminal removal or modification of an amino acid, modification of some amino acids, addition of carbohydrate side chains, trimming of polypeptide chains, removal of signal sequences, addition of metals 45) These diseases are caused by the prion protein. The healthy prion (PrPC) is characterized by the secondary structure of alpha helices whereas the diseased prion (PrPSc) is characterized by the secondary structure of beta sheets.

46) Enzymes

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) In bacteria and eukaryotes, a mutation is when ________.

1) _______ A) the amino acid sequence in a protein molecule is directly changed B) DNA is unable to be replicated C) the nucleotide sequence in a DNA molecule is directly changed D) the nucleotide sequence in an mRNA molecule is directly changed E) the expression of a gene changes without the DNA sequence being changed 2) A mutation that changes an amino acid-coding codon to a stop codon is classified as what kind

2) _______

of codon?

A) neutral B) conditional C) silent D) nonsense E) missense

3) Which of the following mutations would be classified as a transversion?

A) CGA to GCT B) CGA to a CCA C) CGA to a CGT D) CGA to a CGU E) CGA to a GGA

3) _______

4) A geneticist is studying a particular Drosophila mutant that produces a phenotype of "no wing"

4) _______

due to a mutation in a gene called wingless. She takes the mutant wingless and mutagenizes it.

She hypothesizes that any fly that emerges with wings will be due to the original mutated gene reverting back to the wild-type allele. From this study, she identifies a fly that now has wings.

When she sequences the wingless gene, she discovers that the original mutation is still there, and there are no other mutations in the wingless gene. However, a second gene at a separate locus is mutated. The second mutation is best classified as a(n) ________.

A) haploinsufficiency mutation B) intergenic suppressor mutation C) conditional mutation D) null mutation E) intragenic suppressor mutation

5) Germ cell mutations ________.

A) affect somatic cell function in the current generation B) are usually found in every cell of the next generation C) are the cause of testicular cancer D) are only seen in females E) are of no consequence to the next generation

5) _______

6) A class of mutations that results in multiple contiguous amino acid changes in proteins is likely

6) _______

to be which of the following?

A) transversion B) recombinant

C) transition D) base analog E) frameshift 7) Mutations that arise in nature, from no particular artificial agent, are called ________.

A) spontaneous mutations B) nutritional mutations C) chromosomal losses D) cosmic mutations E) induced mutations

7) _______

8) At what stage is a mutation predicted to have the effect?

A) after birth but before puberty B) after the age of 60 C) during early embryonic development D) shortly after birth E) after puberty

8) _______

9) From the Luria-Delbruck fluctuation test, when would mutations arise in yeast cells to allow for

9) _______

survival in the presence of toxic levels of hydrogen peroxide?

A) Mutations are random and would have appeared prior to being exposed to hydrogen peroxide.

B) Mutations are adaptive and would have appeared immediately in response to the hydrogen peroxide.

C) Mutations are adaptive and would have appeared after most of the cells died in the presence of hydrogen peroxide.

D) Mutations are random but would not have formed until after the hydrogen peroxide was introduced.

E) Mutations are adaptive and would have formed prior to being exposed to hydrogen peroxide.

10) Tautomeric shifts ________.

A) are likely to cause frameshifts B) allow purines to bind to purines C) can cause missense mutations due to mispairings D) allow pyrimidines to bind to pyrimidines E) are known to cause insertion or deletion mutations

10) ______

11) Which of the following two mutagens that would be classified as base analogs?

A) acridine orange and proflavine B) ethylmethane sulfonate and ethylmethylketone peroxide C) ultraviolet light and cosmic radiation D) hydroxyurea and peroxidase E) 5-Bromouracil and 2-amino purine

11) ______

12) Which f the following mutagens is matched correctly with its action?

A) acetaldehyde is a free radicle B) 5-Bromouracil is an alkylating agent C) mustard gasses are base analogs D) ethidium bromide is an intercalating agent E) 2-Amino purine is an adduct-forming agent

12) ______

13) Thymine dimers form when ________.

A) two thymines adjacent to each other are deleted from the DNA sequence B) two thymines on the same strand and adjacent to each other bind together C) two thymines are inserted into a DNA sequence D) two thymines on separate strands of DNA bind to together E) two thymines on the same strand but not adjacent to each other bind together

13) ______

14) Which of the following diseases are caused by an expansion of trinucleotide repeats?

A) cystic fibrosis B) achondroplasia C) Marfan's syndrome D) beta-thalassemia E) fragile X syndrome

14) ______

15) Adenine methylase is an enzyme used during mismatch repair (MMR). It helps determine

15) ______

which strand needs to be repaired by discriminating between template and new DNA strand. If this enzyme is mutated, how would MMR be affected?

A) MMR would be hindered because both strands would be unmethylated and both would appear as template DNA strands.

B) MMR would be hindered because both strands would be overmethylated and both would appear as template DNA strands and it would not be possible to determine which strand has the mutation.

C) MMR would be hindered because both strands would be unmethylated and both would appear as new DNA strands and it would not be able to determine which strand has the error.

D) MMR would not be hindered because adenine methylase is not directly involved in MMR. E) MMR would be hindered because both strands would be overmethylated and both would appear as new DNA strands and it would not be able to determine which strand has the error.

16) One would predict that bacteria that lack the enzyme photolyase would be more sensitive to

16) ______

what kind of mutagen?

A) base analog B) alkylating agents C) UV light D) reactive oxygen species E) intercalating agents

17) Which repair mechanism is most likely affected if the enzyme DNA glycosylase is not

17) ______

functioning properly?

A) double-strand break repair B) photoreactivation repair C) nucleotide excision repair D) SOS repair E) base excision repair

18) Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at "normal" rates. Such individuals are likely to suffer from ________.

A) xeroderma pigmentosum

18) ______

B) SCID C) muscular dystrophy D) phenylketonuria E) Huntington disease 19) During the Ames test, his− bacteria are exposed to a chemical. If the bacteria remains his+, then

19) ______

what can we say about the chemical?

A) The chemical is certainly a cancer-causing chemical.

B) The chemical is safe to consume and is not likely a mutagen.

C) The chemical is not safe to consume even though it is not likely a mutagen.

D) The chemical is not safe to consume because it is likely a mutagen.

E) The chemical is safe to consume even though it is likely a mutagen.

20) Transposons, or jumping genes, are DNA elements that move within the genome. In which

20) ______

organismic groups are transposons found?

A) ancient bacteria B) bacteria C) eukaryotes D) mammals E) all organismic groups

21) All insertion sequences (IS elements) contain two structural elements that are essential for their

21) ______

movement. What are these two elements?

A) integrase and oncogenes B) integrase and pseudogenes C) transposase and inverted terminal repeats D) transposase and oncogenes E) proto-oncogenes and oncogenes

22) Some bacterial transposons, known as Tn elements, are larger than insertion sequences (IS

22) ______

elements) and contain protein-coding genes that have human health significance. What might such a bacterial transposon contain?

A) proto-oncogene B) pseudogene C) drug resistance D) dissociation element E) oncogene

23) Barbara McClintock discovered mobile elements in corn by analyzing the genetic behavior of

23) ______

two elements, Ds and Ac. The interplay between these two elements has become one of the most interesting stories of discovery in the field of genetics. How do Ds and Ac interact?

A) While Ds moves only if Ac is present in the genome, Ac is capable of autonomous movement.

B) Both elements can move only within chromosome 9.

C) Ds causes a deletion next to the insertion site of Ac. D) Ac causes a deletion next to the insertion site of Ds. E) The movement of Ac is dependent on two forms of Ds.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

24) Compare and contrast between the following types of mutations: missense, nonsense, 24) ____________ silent, and neutral.

25) A heterozygote could have a variety of phenotypes depending on whether or not the

25) ____________

mutation is recessive, dominant, or haploinsufficient. In this example, the gene A is necessary to form a tail in mice. If the mouse is a heterozygote (A/a), then what would you predict the phenotype to be if the mutation was recessive, dominant, or haploinsufficient.

26) Three major types of RNAs are mRNA, rRNA, and tRNA. For each of the conditions

26) ____________

below, predict the consequences in terms of the population of proteins being synthesized in a particular cell. What qualitative and quantitative changes, if any, are expected in the individual protein involved (if one is involved) and in the population of proteins produced in that cell? a) A frameshift mutation in mRNA. The condition is heterozygous in the involved cell. b) A deletion (homozygous) that removes approximately half of the rRNA genes.

27) Assume that a new mutation occurs in the germ line of an individual. What finding

27) ____________

would suggest that the new mutation is dominant rather than recessive?

28) How was it determined that X-rays are mutagenic?

28) ____________

29) Explain the effects of a somatic mutation on the individuals and their offspring if the

29) ____________

mutation is recessive or dominant.

30) In a survey of 240,000 human births, six achondroplastic births were recorded to

30) ____________

parents who were unaffected. Given that this form of dwarfism is caused by a fully penetrant, dominant, autosomal gene, what is the mutation rate?

31) DNA may be damaged from the by-products of normal cellular aerobic respiration.

31) ____________

Name three of these electrophilic oxidants that are generally classified as reactive oxidants.

32) Describe the mutagenic action of the following two mutagens: 5-bromouracil and

32) ____________

ultraviolet light.

33) Some mutagens cause genetic changes that can be "corrected" by reexposing cells to the

33) ____________

same mutagen. Other mutagens do not behave in this way. Provide one example of each of these two types of agents and describe the mutational changes caused in DNA. Explain why some mutagens behave in one way, whereas others do not.

34) Considering the electromagnetic spectrum, identify likely mutagens from the following

34) ____________

list: radio waves, microwaves, infrared, ultraviolet, X-rays, gamma rays, and cosmic rays.

35) In World War I, mustard gas was used as a chemical weapon, and at a high dose, it

35) ____________

would cause death. However, it is now known to be a chemical mutagen. Explain how those who came in contact with mustard gas and survived have an increase chance of developing mutations.

36) Three human disorders—fragile X syndrome, myotonic dystrophy, and Huntington's disease–are conceptually linked by a common mode of molecular upset. Describe the phenomena that link these disorders.

36) ____________

37) What is meant by the term photoreactivation repair?

37) ____________

38) Describe the action of the enzyme transposase.

38) ____________

39) How were insertion sequences (IS elements) first discovered?

39) ____________

40) What are LINES?

40) ____________

1) C 2) D 3) C 4) B 5) B 6) E 7) A 8) C 9) A 10) C 11) E 12) D 13) B 14) E 15) C 16) C 17) E 18) A 19) D 20) E 21) C 22) C 23) A 24) All of these mutations base substitutions (or point mutation); however, their effects are different. Missense mutations change one amino acid to another amino acid; nonsense mutations change an amino acid-coding codon to a stop codon; silent mutations change an amino acid-coding codon to a codon that codes for the same amino acid (due to the degeneracy of the genetic code); and a neutral mutation changes a codon to a different amino acid, but it has no effect on the protein's function.

25) If the mutation is recessive, then the phenotype should be similar to wild type, and tail development should be unaffected. If the mutation is dominant, then the A/a mouse would likely have no tail. If the mutation is haploinsufficient, then one might predict an abnormal tail (perhaps shorter or misshaped).

26) (a) Population of proteins: Half of the protein products of that gene will be defective, and the other half will be normal. Individual protein: The protein should show multiple amino acid substitutions "downstream" from the point of the mutation. If a nonsense triplet is introduced, the protein would be shortened in the substituted region. (b) Population of proteins: There would be an overall reduction in protein synthesis. Individual protein: All of the proteins would be made in their normal form, but at reduced levels.

27) If the new mutation is dominant and passed to the next generation, it would be expressed. New recessive mutations are not normally expressed in the next generation unless, through a combination with a like mutation from the other parent, they are homozygous.

28) H. J. Muller determined that a direct relationship occurred between X-linked recessive lethals and X-ray dose in Drosophila.

29) Somatic cell mutations can only affect the individuals they occur in and will not affect their offspring. Whether or not the mutation affects the individuals can vary depending upon whether or not the mutation is recessive or dominant. If the mutation is recessive, then it is less likely to affect the individuals unless the wild-type allele also becomes mutated or if the recessive mutation occurs on a male's X-chromosome. If the mutation is dominant, then it is more likely to affect the individuals. However, even dominant mutations' phenotypes may have less impact due to the thousands of other cells in the tissue that remain unmutated. It should be noted that an accumulation of several mutations in a single cell could lead to diseases such as cancer.

30) 6/(4.8 × 105)

31) Superoxides (O2−), hydroxyl radicals (∙OH), and hydrogen peroxide (H2O2)

32) The mutagen 5-bromouracil is an analog of thymine, which anomalously pairs with guanine. Ultraviolet light causes thymine dimers.

33) Mutagens that cause base substitutions are "corrected" by mutagens of the same class (nitrous acid, 2-aminopurine, and 5-bromouracil). Frameshift mutations are "corrected" by the same class of frameshift mutagens, but not by mutagens that cause base substitutions. X-rays cause major structural changes in chromosomes (deletions, translocations, etc.) and are not "corrected" by any mutagen, including X-rays.

34) ultraviolet, X-rays, gamma rays, and cosmic rays 35) Mustard gas is an alkylating agent that donates an alkyl group to an amino or keto group on nucleotides. This causes mismatch pairing and increases transition mutations.

36) All three are caused by disparate genes, but each gene was found to contain repeats of a unique trinucleotide sequence. In addition, the number of repeats may increase in each subsequent generation (genetic anticipation).

37) Photoreactivation repair, discovered in 1949, is a process described in E. coli in which UV-induced DNA damage can be partially reversed if cells are briefly exposed to light in the blue range of the visible spectrum.

38) Transposase makes staggered cuts in chromosomal DNA, into or out of which an IS element can insert.

39) IS elements were first discovered during the analysis of mutations in the gal operon of E. coli.

40) LINES are long interspersed elements that are plentiful in the human genome.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) What term would be applied to a regulatory condition that occurs when a protein is associated 1) _______ with a particular section of DNA and greatly reduces transcription?

A) positive control B) induction C) stimulation D) negative control E) activation

2) Enzymes that are continuously produced are said to have a(n) ________ expression.

A) repressible B) inducible C) positive D) constitutive E) negative

2) _______

3) What term refers to clusters of bacterial genes that are under the control of a single regulatory

3) _______

region?

A) attenuation B) operon C) prototroph D) allosteric E) autotroph

4) In the lac operon, the product of structural gene lacZ is capable of ________.

A) splitting the linkage of lactose to produce glucose and galactose B) binding to the operator of the lac operon C) forming lactose from two glucose molecules D) transporting lactose into the cell E) forming ATP from pyruvate

4) _______

5) If lactose is accumulating outside of E. coli and is unable to enter, then which structural gene of

5) _______

the lac operon is most likely mutated?

A) lacX B) lacY

C) lacI

D) lacA

E) lacZ

6) To translate the three enzymes of the lac operon, ________ mRNA molecule(s) is/are transcribed.

A) 1

B) 0

C) 4

D) 3

6) _______

E) 2

7) lacI codes for a(n) ________, and when lacI is mutated, the lac operon is ________.

A) activator; never expressed B) repressor; never expressed C) activator; constitutively expressed D) structural gene; never expressed E) repressor; constitutively expressed

7) _______

8) Which binds to the operator of the lac operon?

8) _______

A) lactose B) permease C) beta galactosidase D) repressor E) activator 9) A protein, like the lac repressor, is said to be ________ because when it binds lactose, it

9) _______

structurally changes and its chemical activity also changes.

A) allosteric B) multimeric C) enzymatic D) digestive E) structural

10) Some lac operon mutations allow for beta galactosidase to be expressed constitutively even in

10) ______

the absence of lactose. Which of the following lac genotypes would allow for this constitutive expression?

A) Is P+ O+ Z+ Y+ A+

B) I+ P+ Oc Z+ Y+ A+ C) I+ P+ O+ Z+ Y+ A+ D) I+ P+ O+ Z- Y+ A+ E) I+ P- O+ Z+ Y+ A+ 11) Which of the following terms best characterizes catabolite repression associated with the lac

11) ______

operon in E. coli?

A) constitutive B) inducible system C) negative control D) repressible system E) positive control

12) What is the name of the molecule that binds to CAP to activate transcription of the lac operon?

A) glucose B) ATP C) galactose D) lactose E) cAMP

12) ______

13) When both lactose and glucose are available to E. coli, which part of the lac operon regulation

13) ______

assures that glucose will be metabolized first?

A) Permease allows lactose to enter the cell when lactose enters the cell.

B) CAP binds to cAMP and then to the promoter only in the presence of low glucose.

C) The repressor binds to the operator in the absence of lactose.

D) RNA polymerase transcribes the lac operon to make a single RNA molecule.

E) The repressor cannot bind to the operator in the presence of lactose.

14) Through genetic analysis, Jacob and Manod were able to make predictions about the lac

14) ______

operon. However, which of the following techniques confirmed their predictions?

A) PCR B) crystal structure analysis C) CRISPR D) recombinant DNA technology E) DNA sequencing

15) When referring to attenuation in regulation of the trp operon, it would be safe to say that when

ther e are

____ __

high 15) levels of tryptopha n available to the organism, ________.

A) translational termination is likely B) ribosomes are stalling during translation of the attenuator region C) the trp operon is being transcribed at relatively high levels D) tryptophan is inactivating the repressor protein E) transcriptional termination is likely 16) ______

16) Genetic regulation in bacteria can involve alterations in RNA secondary structure. What phenomenon occurs in the trp operon that involves such alterations?

A) capping B) polyadenylation of the 3′ end of the mRNAs C) intron processing D) transcription E) attenuation

17) ______

17) Usually, bacteria only make tryptophan when tryptophan is absent or available in low concentration. However, a particular bacterial mutation makes tryptophan all the time whether or not tryptophan is present. What could explain this phenotype?

A) the terminator hairpin is unable to form B) trpA is mutated C) the antiterminator hairpin is unable to form D) trpD is mutated E) trpE is mutated

18) What two important domains within a riboswitch involve the ligand-binding site?

A) B site and C site B) A site and B site C) alpha and beta D) conformation and anticonformation E) aptamer and expression platform

18) ______

19) Small noncoding RNAs regulate gene expression in bacteria by ________.

A) activating translation B) by both inhibiting and activating translation C) repressing transcription D) inhibiting translation E) activating transcription

19) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

20) Compare and contrast positive and negative controls of gene expression in bacteria.

20) ____________ 21) Present an overview of bacterial gene regulation in terms of growth efficiency.

21) ____________

22) In the accompanying diagram, what type of control, positive or negative, is operating?

22) ____________

The oval structure is RNA polymerase.

23) Certain mutations in the regulator gene of the lac system in E. coli result in maximal

23) ____________

synthesis of the lac proteins (β-galactosidase, etc.) even in the absence of the inducer (lactose). Provide an explanation for this observation.

24) Present a detailed description of the actions of the regulatory proteins in inducible and

24) ____________

repressible enzyme systems.

25) (a) Describe by labeled diagram the structural components of the lac operon in E. coli.

25) ____________

(b) State the function of the lac regulator gene. (c) State the function of β-galactosidase in the lac system. (d) Show by diagram the manner in which lactose brings about transcription of the three structural genes of the lac operon. (e) Explain why certain mutations in the regulator gene (I−) of the lac system result in maximal synthesis of β-galactosidase, permease, and transacetylase even in the absence of the inducer (lactose).

26) The table below lists several genotypes associated with the lac operon in E. coli. For

26) ____________

each, indicate with a "+" or a "−" whether functional β-galactosidase would be expected to be produced at induced levels.

Genotype (a) I + O + Z +/F'I - O + Z+ (b) I - Oc Z +/F'I - O + Z(c ) Is Oc Z+/F'I + O + Z+ (d) I - O + Z + /F'I - O + Z+

β-galactosidase production No Lactose With Lactose

I+ = wild-type repressor I- = mutant repressor (unable to bind to the operator) Is = mutant repressor (insensitive to lactose) O+ = wild-type operator Oc = constitutive operator (insensitive to repressor)

27) The accompanying table lists several genotypes associated with the lac operon in E. coli. For each, indicate with a "+" or a "−" whether β-galactosidase would be expected to

be duced at pro induced levels.

27) Genotype (a) I + O + Z +/F'I + O + Z+ (b) I - Oc Z -/F'I - Oc + Z(c ) I - Oc Z+/F'I - O + Z+ (d) Is Oc Z- /F'Is O + Z+

β-galactosidase production No Lactose With Lactose

____ ____ ____

I+ = wild-type repressor I- = mutant repressor (unable to bind to the operator) Is = mutant repressor (insensitiv e to lactose) O+ = wild-type operator Oc = constitutiv e operator (insensitiv e to repressor)

28) Describe what is meant by a gratuitous inducer. Give an example.

28) ____________

29) When lactose is first introduced into the medium, the lac operon is not induced and

29) ____________

thus permease isn't induced. How it is possible for lactose to enter the cell before the lac operon is induced?

30) A constitutive mutation in the lac operon may be of several types. Name two types of

30) ____________

constitutive mutations and explain why they are constitutive.

31) What is the function of the lacY gene in the lac operon?

31) ____________

32) Explain why lacOc mutations are cis-acting while lacI mutations can be trans-acting.

32) ____________

33) What experimental results would indicate that the mutation lacIs is dominant to lacI+?

33) ____________

34) The cAMP-CAP complex and RNA polymerase bind more efficiently to the lac operon

34) ____________

together than either does alone. What term is applied to this increased efficiency of binding?

35) Describe the positive control exerted by the catabolite-activating protein (CAP).

35) ____________

Include a description of catabolite repression.

36) The catabolite repression system in E. coli essentially represses the lac operon when

36) ____________

glucose is present. What evolutionary advantage would favor evolution of such a system?

37) Regarding the trp operon, trpR− maps to a considerable distance from the structural

37) ____________

genes. The mutation either inhibits the interaction with tryptophan or inhibits repressor formation entirely. In the presence of tryptophan in the medium, would you expect the trp operon to be transcriptionally active? Explain.

38) What is an allosteric molecule?

38) ____________

39) State whether the following statement is true or false, then give your reasoning. The

39) ____________

terminating "hairpin" loop occurs in the trp operon when sufficient tryptophan is present.

40) Monod discovered that if tryptophan is present in relatively high quantities in the

40) ____________

growth medium, the enzymes necessary for its synthesis are repressed. How does this occur?

41) Explain how small noncoding RNAs (sRNAs) can function as both a negative regulator and a positive regulator.

41) ____________

1) D 2) D 3) B 4) A 5) B 6) A 7) E 8) D 9) A 10) B 11) E 12) E 13) B 14) B 15) E 16) E 17) A 18) E 19) B 20) Both forms of control result from an interaction of a molecule (usually considered to be a protein) with the genetic material (either RNA or DNA). Positive control results when the interaction stimulates transcription, whereas negative control occurs when the interaction inhibits transcription.

21) Genetic systems have evolved that allow for "in-house" production of growth substances when not supplied in the environment or when in full supply. When needed substances are in full supply, such genetic systems are repressed.

22) Positive 23) There has been a mutation in the gene that produces the repressor so that it can't bind to the operator (a mutation in the repressor that prevents lactose binding would have the opposite effect), or the operator is mutated so that it will not interact with the repressor.

24) Inducible system: The repressor is normally active, but the inducer inactivates the repressor. Repressible system: The repressor is inactive, but is activated by the corepressor. Active repressors turn off transcription.

25) (a) See appropriate diagrams in the text. (b) The regulator gene produces a repressor protein that interacts with the operator to shut off transcription. In the presence of lactose, the repressor protein does not interact with the operator. (c) β-Galactosidase cleaves the lactose sugar into its components, glucose and galactose. (d) See appropriate diagrams in the text. (e) Such mutations provide modified proteins that are unable to associate with the operator to shut off transcription. − + (b) + + 26) (a) (c) + + (d) + + − + 27) (a) (b) − − (c) + + (d) − − 28) A gratuitous inducer is a chemical analog of a natural inducer. It serves as an inducer but is not a substrate for the reactions related to the natural inducer. Isopropylthiogalactoside (IPTG) is a gratuitous inducer of the lactose operon.

29) While the lac operon is not induced yet, there is low level expression most of the time which allows a small amount of permease to be expressed. This allows lactose to enter the cell at low levels until the lac operon is needed for full induction.

30) lacI− is a lac operon constitutive mutation because it is unable to bind to the operator DNA. If it can't bind, then the operon will not be inhibited. Similarly, the lacOc mutation causes a constitutive expression of the lac operon genes.

This is se the lacOc mutation removes the operator and without an operator the operon cannot be turned off. becau 31) The lacY gene codes for permease, a membrane-bound protein that transports lactose into the bacterial cell.

32) The operator region does not produce a diffusible product, whereas the lacI gene does.

33) In lacIs / lacI+ partial diploids, the lac operon is in a repressed state in the presence of lactose.

34) Cooperative binding 35) Regarding regulation of the lac operon, in the absence of glucose, CAP (dependent on cAMP and adenyl cyclase) binds to the CAP site and facilitates transcription (positive control). Transcription of the operon is inhibited in the presence of glucose (catabolite repression).

36) Glucose can enter glycolysis "as is," whereas lactose must first be split into glucose and galactose. To do so, the energy-requiring synthesis of β-galactosidase is required. It is more energy efficient to burn glucose than lactose.

37) With either of the two scenarios mentioned in the problem, the absence of repressor function in a repressible system means that there would be no repression of the operon. The operon would be transcriptionally active.

38) One that can change in shape and chemical activity while interacting with other molecules.

39) True; the hairpin loop terminates transcription because when tryptophan is present, it is energetically favorable to prevent more of its synthesis.

40) Attenuation occurs in which transcription of the operon is terminated.

41) sRNAs can negatively regulate translation by binding to ribosome-binding sequences of mRNA. This blocks the ability for ribosomes to bind to and initiate translation. sRNAs can positively regulate translation by disrupting hairpin loops that usually cover and inhibit the ribosome-binding sequence. However, unmasking this area, the ribosomes are free to bind and activate translation.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Gene regulation in eukaryotes is more complicated than bacterial gene regulation. Which of the 1) _______ following describes a gene regulation event that occurs in eukaryotes but not in bacteria?

A) In eukaryotes, mRNA degrades quickly compared to bacterial mRNA that is more stable.

B) In eukaryotes, transcription and translation occur in the same cellular compartment.

C) In eukaryotes, mRNA does not need to be modified.

D) In eukaryotes, proteins are post-translationally modified, whereas bacterial proteins are never post-translationally modified.

E) In eukaryotes, histones must be added or removed to regulate gene expression.

2) The nuclear regions that contain RNA polymerase and transcription regulatory molecules that

2) _______

help compartmentalize eukaryotic regulation are called ________.

A) nucleosomes B) transcription factories C) histones D) chromosome territories E) interchromatin compartments

3) In a particular organism, there are two similar genes called YFG1 and YFG2. YFG1 is expressed

3) _______

in the liver and not in the pancreas, and YFG2 is expressed in the pancreas but not the liver.

Neither YFG1 nor YFG2 is expressed in the heart. Based on these observations, which of the following is most true?

A) Neither YFG1 nor YFG2 isolated from any tissue (the liver, the pancreas, and the heart) would be DNase I sensitive.

B) The YFG1 gene isolated from the pancreas and the YFG2 gene isolated from the liver would be DNase I sensitive.

C) Both YFG1 and YFG2 genes isolated from any tissue (the liver, the pancreas, and the heart) would be DNase I sensitive.

D) Both YFG1 and YFG2 genes isolated from the heart would be DNase I sensitive.

E) The YFG1 gene isolated from the liver and YFG2 gene isolated from the pancreas would be DNase I sensitive.

4) Which of the following is true about histone acetyltransferase (HAT)?

A) HATs will make the chromatin more compacted and less available to transcription

4) _______

regulatory proteins.

B) HATs have an overall effect of increasing the positive charges on DNA. C) HATs are usually linked to increasing gene expression.

D) HATs will add acetyl groups to DNA. E) HATs will remove acetyl groups from histone proteins.

5) DNA is methylated on which nucleotides?

A) uracil B) thymine C) guanine

5) _______ D) adenine

E) cytosine

6) If a promoter region is mutated in such a way that it can no longer be methylated, what would the most likely effect be?

A) The gene linked to the promoter would be expressed at regular levels.

B) The gene linked to that promoter would be over expressed.

C) The gene linked to the promoter would still be expressed, but the protein should contain

6) _______

different amino acids.

D) The gene linked to that promoter would not undergo replication.

E) The gene linked to the promoter would be under expressed.

7) Considering the location of genes in the interphase nucleus, certain chromosomal territories

7) _______

appear to exist. Specifically, ________.

A) even-numbered chromosomes are located in the interior of the nucleus, whereas odd-numbered chromosomes are located peripherally B) large chromosomes are more likely to be located in the center of the nucleus C) gene-poor regions of chromosomes are located outside the nucleus, whereas gene-rich regions are located inside the nucleus D) each chromosome appears to occupy a discrete domain E) small chromosomes are more likely to be located in the center of the nucleus

8) Which of the following would be an example of a cis acting eukaryotic gene regulatory

8) _______

element?

A) RNA polymerase B) metallothionein C) TATA binding protein D) general transcription factors E) enhancer

9) A regulatory sequence of DNA that is 10,000 base pairs away from the gene it regulates is

9) _______

mutated. The result is that the gene being regulated is now expressed at a higher rate compared to when this regulatory sequence was not mutated. What would this sequence of DNA best be called?

A) zinc finger motif B) insulator C) activator protein D) enhancer E) silencer

10) What is the general position of the consensus sequence called the GC box? What is its sequence?

A) terminator; CAAT B) promoter; GGGCGG C) attenuator; GGGCGG D) terminator; GGGCGG E) promoter; CAAT

10) ______

11) Which process seems to be the most similar between eukaryotic and prokaryotic genetic

11) ______

regulations?

A) transcriptional regulation B) 5'-capping regulation C) poly(A) tail addition D) intron/exon shuffling E) RNA splicing regulation

12) Which of the following clusters of terms apply when addressing enhancers or silencers as elements associated with eukaryotic genetic regulation?

A) cis-acting, variable orientation, variable position B) cis-acting, variable position, fixed orientation C) trans- and cis-acting, variable position

12) ______

D) trans-acting, fixed position, fixed orientation E) cis-acting, fixed position, fixed orientation 13) Two modular elements that appear as consensus sequences upstream from RNA polymerase II

13) ______

transcription start sites are ________.

A) enhancers and telomeres B) microsatellites and transposons C) rDNA and nucleolar organizers D) TTAA and CCTT E) TATA and CAAT

14) Which of the following is a functional domain that is found in eukaryotic transcription factors

14) ______

and bacteria?

A) basic leucine zipper motif B) basic leucine zipper and zinc finger motifs C) zinc finger motif D) basic leucine zipper, zinc finger, and helix-turn-helix motifs E) helix-turn-helix motif

15) What type of DNA sequence a repressor protein be expected to bind?

A) enhancer B) TATA Box C) GC Box D) insulator E) silencer

15) ______

16) The pre-initiation complex (PIC) contains several proteins. What would be the direct

16) ______

consequence be if PIC failed to form?

A) Translation would not be initiated.

B) mRNA splicing would not be initiated.

C) Replication would not be initiated.

D) Transcription would not be initiated.

E) Protein would not fold properly.

17) In what way do upstream activator sequences (UASs), regulatory sequences in yeast, differ

17) ______

from enhancers and silencers?

A) UASs function in the middle of transcription units.

B) UASs function only downstream.

C) UASs function only upstream.

D) UASs can function only in the 5'→ 3' direction.

E) Enhancers function only downstream.

18) The GAL gene system in yeast is used to metabolize galactose. In the presence of galactose, the

18) ______

GAL genes are expressed; however, in the absence of galactose, the GAL genes are repressed. A yeast mutant is discovered that continuously expresses the GAL genes in the presence or absence of galactose. Which GAL gene is likely mutated?

A) GAL1 B) GAL4 C) GAL 10 D) GAL3 E) GAL180

19) UASs (upstream activating sequences) are DNase hypersensitive. This means that ________.

A) more than one strand of DNA exists in each UAS B) each UAS is likely to be single stranded

19) ______

C) any given UAS is composed of a double-stranded site with a bound repressor D) a UAS is constitutively open E) each UAS has more histone-binding sites than non-UAS sites 20) The ENCODE Project's goal was to identify all functional DNA sequences within the human

20) ______

genome. Which of the following is a finding from ENCODE? A) ENCODE determined that approximately 15% of the human genome codes for a protein.

B) ENCODE was able to determine that each enhancer exerts its regulatory function on only a single gene.

C) ENCODE determined that approximately 25% of the human genome has some sort of biochemical function.

D) ENCODE was able to determine that 75% of the genome is transcribed in at least one cell type.

E) ENCODE was able to classify that a large part of the human genome is "Junk DNA."

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

21) Explain five ways that eukaryotic gene regulation is more complex than bacterial gene 21) ____________ regulation?

22) List at least three levels or types of genetic regulation in eukaryotes.

22) ____________

23) Describe how the presence or absence of nucleosomes influences gene transcription.

23) ____________

24) Approximately 5% of the cytosine residues are methylated in the genome of any given

24) ____________

eukaryote. In what way is DNA methylation related to genetic regulation?

25) In what way 5'-azacytidine can influence transcription?

25) ____________

26) In what way 5'-azacytidine is used (experimentally) in the treatment of sickle-cell

26) ____________

anemia?

27) Some diseases are linked to the under or over expression of specific genes. A particular

27) ____________

cancer is characterized by the overexpression of a gene. Do you predict the histones associated with this gene to be acetylated? Describe why this would lead to increased gene expression and how histone acetyl transfer (HAT) and histone deacetylase (HDAC) could be involved.

28) Enhancers are said to be cis-acting. What is meant by cis-acting, and what are

28) ____________

enhancers?

29) Describe three characteristics of enhancers and silencers.

29) ____________

30) Describe the difference between a focused promoter and a dispersed promoter.

30) ____________

31) Describe the function and general natures of promoters in eukaryotes. Include the three

31) ____________

different parts of the promoter and their positions from the 5' end of a eukaryotic gene.

32) Mutations in the promoter region of the β-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, and TATA box), does transcription usually increase or decrease? Explain.

32) ____________

33) On a specific chromosome, an enhancer helps activate the expression of Gene A, but

33) ____________

not Gene B, which is equally close to the enhancer. A mutant is identified where this enhancer is now activating the expression of both Gene A and Gene B. Explain what has likely been mutated.

34) Transcription factors are important molecules that regulate gene activity in eukaryotes.

34) ____________

What are the two general classes of transcription factors that exist in eukaryotes?

Describe where they bind and what their effects are.

35) Explain why a transcription factor must have at least two functional domains.

35) ____________

36) The human metallothionein IIA gene (hMTIIA) is transcriptionally regulated through

36) ____________

the interplay of regulatory elements and transcription factors. What is the function of this gene, and how is it regulated by environmental circumstances?

37) What are zinc finger motifs, and why are they frequently encountered in descriptions

37) ____________

of genetic regulation in eukaryotes?

38) What is meant by the term helix-turn-helix (HTH)?

38) ____________

39) Describe the ENCODE project and list five of their findings.

39) ____________

1) E 2) B 3) D 4) C 5) E 6) B 7) D 8) E 9) E 10) B 11) A 12) A 13) E 14) E 15) E 16) D 17) C 18) E 19) D 20) D 21) (1) Eukaryotes have histones, whereas bacteria don't have histones and these histones have to be removed to turn on gene expression. (2) Eukaryotes have a nucleus and therefore transcription occurs in the nucleus and translation occurs in the cytoplasm, whereas bacterial transcription and translation are coupled in the cytoplasm.

(3) mRNAs in eukaryotes are processed (splice, poly-adenylated, and addition of modified guanine) before they are translated, whereas bacterial mRNA are not processed in a similar way. (4) mRNA in eukaryotes is typically much longer lived, whereas bacterial mRNAs are degraded shortly after they are transcribed. (5) Eukaryotes have a larger array of post-translational mechanisms than bacteria.

22) Transcriptional regulation, DNA methylation, posttranscriptional regulation, and posttranslational regulation.

23) The binding of transcription factors requires accessing nucleosomal DNA. When nucleosomes are tightly associated with the DNA transcription, proteins can't access the DNA; however, when nucleosomes are loosely associated with the DNA, then the DNA transcription proteins have easier access to the DNA. To turn genes on and off, the nucleosomes need to modulate from being on or off the DNA. 24) There is an inverse relationship between the degree of methylation of eukaryotic DNA and the degree of gene expression.

25) Nitrogen is at the 5' position of 5'-azacytidine. The base can be incorporated into DNA in place of cytidine, but it cannot be methylated. Under methylation of the CG dinucleotide increases transcription.

26) The use of 5'-azacytidine reduces the amount of methylation in certain hemoglobin genes and enhances expression (transcription).

27) One would predict that since this gene is overexpressed that the histones are acetylated. Therefore, HAT is working or perhaps over active and HDAC is not working properly. When histones are acetylated, the histones will relax their association with the DNA allowing the gene to be more likely expressed.

28) Cis-acting means that the genes under control must be in the same chromosome as the cis-acting element.

Enhancers are sections of DNA that activate transcription of other sections of DNA on the chromosome.

29) Position need not be fixed. Orientation may be inverted without significant effect. They can regulate other genes when inserted. They can act at a great distance from the promoter.

30) A focused promoter specifies transcription initiation at a single specific nucleotide, whereas a dispersed promoter directs the initiation of transcription from a number of weak transcription start sites spread over a fairly wide region (50-100 nucleotides).

31) Promoter regions are necessary for the initiation of transcription. Promoters that interact with RNA polymerase II are usually located within 100 bp upstream of a gene and usually contain a TATA box (-25 to -30) and a CAAT box (-70 to -80).

32) Transcription should decrease because by changing these modular elements, the general transcription factors cannot bind efficiently or recruit RNA polymerase.

33) Gene A is activated by the enhancer but not Gene B due to an insulator sequence that allows the enhancer to only activate Gene A and prevents activation of Gene B. However, in this mutant, the insulator is mutated and can no longer block the activation of Gene B by the enhancer and thus both Genes A and B are activated by this enhancer.

34) General transcription factors assemble at promoter regions adjacent to the site of transcription. They are typically important in basal levels of transcription. The other class includes activators and repressors that bind at more distant regions called enhancer and repressor sequences, respectively. Activators and repressors are responsible for increased regulation and are often important in tissue specific and developmental regulation.

35) Transcription factors are modular proteins with at least two functional domains: one binds to DNA in promoters and enhancers, and the other activates transcription.

36) The gene hMTIIA produces a protein that binds to heavy metals and protects cells from their toxicity. The gene is transcribed at low levels in all cells but is induced to express at high levels in cells exposed to heavy metals.

37) Zinc fingers consist of amino acid sequences containing two cysteine and two histidine residues at repeating intervals. Interspersed cysteine and histidine residues covalently bind zinc atoms, folding the amino acids into loops (zinc fingers). They are one of the major groups of eukaryotic transcription factors.

38) A geometric conformation is formed by two adjacent alpha helices separated by a "turn" of several amino acids.

Such motifs bind to the major grooves of DNA and interact with the DNA backbone.

39) The ENCODE project stands for Encyclopedia of DNA Elements. The project set out to identify all functional DNA sequences that are found in the human genome. They have made several discoveries including: (1) < 2% of the human genome codes for proteins, (2) >80% of the genome has some sort of biochemical activity, (3) enhancers can regulated several different promoters for different genes, (4) about 75% of the human genome is transcribe in one cell or another, and (5) identify many diseases that are linked to nonprotein coding portions of the gene.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Which of the following is the most common type of alternative splicing in animals and involves 1) _______ making mRNA molecules that lack a complete exon?

A) alternative promoters B) cassette exons C) alternative splice site D) mutually exclusive exons E) intron retention

2) In a eukaryote, what is the best way to compare the number of genes in a genome to the

2) _______

number of proteins that the genome can produce and why?

A) The number of proteins is usually fewer than the number of genes due to alternate splicing.

B) The number of proteins is usually fewer than the number of genes due to histone modification.

C) The number of proteins is usually greater than the number of genes due to histone modification.

D) The number of proteins is equivalent to the number of genes due to alternative splicing.

E) The number of proteins is usually greater than the number of genes due to alternate splicing.

3) Mutations that affect SR proteins will have what kind of effect on gene expression?

A) General transcription factors will be unable to bind to promoters.

B) RNA polymerase will be unable to terminate transcription.

C) Ribosomes will not be able to bind to mRNA molecules in the cytoplasm.

D) Polyadenylation at the 3' end will be blocked.

E) Splicing of the mRNA will not be activated.

3) _______

4) Having two copies of the X-chromosome gene, ________, initiates the female sex-determining

4) _______

pathway by which gene regulatory mechanism?

A) DSX; alternative splicing B) TRA; alternative splicing C) DSX; alternative polyadenylation D) SXL; alternative splicing E) SXL; alternative polyadenylation

5) Which of the following statements is predicted if a population of fruit flies were fed a chemical

5) _______

that blocked the function of the SXL protein?

A) The mRNA produced from the doublesex (dsx) gene would not be spliced.

B) The transformer (tra) gene would be maximally expressed.

C) The progeny in the next generation would be predominantly male.

D) The progeny in the next generation would be predominantly female.

E) The progeny in the next generation would be approximately 50% male and 50% female.

6) The human disease spinomuscular atrophy is caused by a failure of which posttranscription regulatory mechanism?

A) alternative splicing B) mRNA surveillance

6) _______

C) RNA interference D) translation initiation E) alternative polyadenylation 7) In regards to mRNA stability, what is the effect of decapping enzymes?

A) The polyadenylation of mRNAs is stabilized allowing mRNAs to be protected at the 3'

7) _______

end.

B) The m7G cap of mRNAs is removed causing mRNAs to be degraded from the 5' end.

C) The m7G cap of mRNAs is stabilized allowing mRNAs to be protected at the 5' end.

D) The polyadenylation of mRNAs is removed and mRNAs are degraded from the 3' end.

E) The splicing of mRNAs is blocked, which destabilizes mRNAs. 8) ________ are cytoplasmic structures that will aggregate mRNA molecules for either

8) _______

degradation or later translation.

A) Ribosomes B) Mitochondria C) Proteasomes D) Processing bodies E) Golgi apparatus

9) Adenosine—uridine-rich elements are ________.

A) trans-acting elements that bind to mRNA to recruit ribosomes to mRNA for translation

9) _______

initiation B) cis-acting elements that recruit RNA-binding proteins to mRNA to either degrade or stabilize the mRNAs C) trans-acting elements that block mRNA splicing D) cis-acting elements where ribosomes bind to in order to initiate translation E) trans-acting elements that bind to mRNA to either degrade or stabilize mRNA

10) mRNA surveillance mechanisms are necessary ________.

A) to measure the concentration of mRNAs in the cytoplasm B) for polyadenylation at the 3' end of mRNA C) to recruit general transcription factors to the promoter D) in determining which alternative splice site should be used E) to eliminate mRNAs with a premature stop codon

10) ______

11) A researcher is studying plant development. She isolates a mutant and discovers that the piece

11) ______

of DNA that is mutated does not code for a protein. However, this piece of DNA is complimentary to a gene known to function in early embryonic plant development. The mutant she identified most likely functions as a(n) ________.

A) ribosomal RNA (rRNA) B) microRNA (miRNA) C) transfer RNA (tRNA) D) intron E) general transcription factor known to regulate many different genes

12) If the protein Dicer is not functioning, then which kind of posttranscriptional gene regulation is most likely affected?

A) alternative adenylation B) alternative splicing C) microRNA (miRNA) and small interfering RNA (siRNA)

12) ______

D) only microRNA (miRNA), but not small interfering RNA (siRNA) E) small interfering RNA (siRNA) 13) microRNA (miRNA) and small interfering RNA (siRNA) use a similar process and proteins to

13) ______

regulate gene expression. Which of the following is more commonly associated with the miRNA pathway?

A) The protein complex RISC is found in the miRNA pathway but not the siRNA pathway.

B) The protein Dicer is found in the miRNA pathway but not the siRNA pathway.

C) In animals, the miRNA pathway usually leads to mRNA degradation, and in the siRNA pathway, the mRNA is not degraded.

D) The protein Drosha is found in the miRNA pathway but not the siRNA pathway.

E) The protein AGO is found in the miRNA pathway but not the siRNA pathway.

14) The discovery of RNA interference (RNAi) led to its use in biotechnology and medicine. All of

14) ______

the following are examples of how RNAi could be used in biotechnology or medicine, EXCEPT ________.

A) to treat a disease characterized by a gene that is not expressed B) to treat a disease characterized by the normal expression of a mutated gene C) to study loss-of-function phenotypes of specific genes in a model research organism D) to treat a disease characterized by the overexpression of a nonmutated gene E) to treat a disease characterized by the buildup of a specific protein

15) Which of the following statements is most true regarding long noncoding RNAs (lncRNAs)?

A) lncRNAs are characteristically about the same size as sncRNAs. B) lncRNAs do not contain a 5' guanine cap or a 3' poly-A-tail.

C) Some lncRNAs regulate alternative splicing.

D) lncRNAs act only as posttranscriptional regulators and never as pretranscription

15) ______

regulators.

E) Some lncRNAs will decrease the activity of miRNAs. 16) A long poly-A-tail is necessary to initiate translation. Which protein binds directly to eIF4E to

16) ______

inhibit translation initiation?

A) poly-A polymerase B) PABP C) maskin D) CPEB E) PARN

17) A particular fibroblast mutation fails to move to the site of infection. It is discovered that this

17) ______

mutation causes a particular protein to be absent, which leads to premature actin mRNA translation. Which protein is most likely absent due to the mutation?

A) ZBP1 (zip code-binding protein) B) CPEB C) poly-A polymerase D) general transcription factor E) Src

18) What posttranslational modification occurs on the protein CPEB to initiate mRNA translation?

A) glycosylation B) phosphorylation C) ubiquitination D) methylation

18) ______

E) acetylation 19) What is the general name of enzymes that add phosphate groups to protein targets?

A) ligases B) proteases C) phosphatases D) acetylases E) kinases

19) ______

20) Which protein modification is most closely linked to protein degradation?

A) ubiquitination B) phosphorylation C) glycosylation D) methylation E) acetylation

20) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

21) What is the general gene regulation mechanism that "cassette exons" and "intron 21) ____________ retention" are involved with? Explain their differences in regards to which kinds of organism use each and how each is different in what they do.

22) Mutating the gene Transformer (tra) in Drosophila that is chromosomally XX leads to the

22) ____________

development of only males. Explain.

23) List three general pathways in which eukaryotic mRNA is typically degraded in

23) ____________

eukaryotes.

24) What is nonsense-mediated decay, why is it important, and what is a proposed

24) ____________

mechanism as to how it works?

25) Cancer is caused by many different types of gene mutations. Some mutations are in

25) ____________

proto-oncogenes, which lead to overexpression of the genes, and other mutations are in tumor suppressor genes, which lead to under expression or no expression in these genes. Which kinds of gene mutations would RNA interference (RNAi) be better at treating? Explain.

26) What are two features of circular RNAs (cirRNAs) that limit their ability to be

26) ____________

degraded?

27) Describe how cells control the size of the poly-A tail on mRNA molecules in order to

27) ____________

regulate translation initiation. Next explain how a kinase inhibitor could decrease gene expression in regards to polyadenylation? Your answer should include the following proteins in your answer: Maskin, PARN, CPEB, eIF4E, eIF4G, and Poly-A polymerase.

28) Compare and contrast kinases and phosphatases.

28) ____________

29) A particular mutant was found that produced a protein that was longer lived than its

29) ____________

normal protein. Upon sequencing the mutant, the researcher discovered that specific lysine amino acids had been changed to arginines. Propose a model of what this mutation caused to allow the proteins to be longer lived.

1) B 2) E 3) E 4) D 5) C 6) A 7) B 8) D 9) B 10) E 11) B 12) C 13) D 14) A 15) E 16) C 17) A 18) B 19) E 20) A 21) They are different types of alternative splicing. Cassette exons is a method used mainly by animals, and intron retention is used mainly by plants, fungi, and protozoa. Cassette exons achieves alternative splicing by excluding one or more exons from the mature mRNA. Intron retention achieves alternative splicing by including introns into the mature mRNA (this can lead to novel functions or no function in the mature protein).

22) In nonmutated fertilized eggs that are supposed to develop into females (XX), the two copies of SXL causes the expression of tra, which then leads to an alternative splicing pathway of the dsx gene that induces female development. However, even though sxl is present at levels to cause female development (because of the two X chromosomes), only males form because the SXL target is tra. If tra is not expressed or mutated, then males will form due to the alternative splicing of dsx that leads to male development.

23) Deadenylation-dependent decay, decapping, and nonsense-mediated decay 24) Nonsense-mediated decay is a type of RNA surveillance that identifies mRNA with premature stop codons and eliminates them. Nonsense-mediated decays are important because mRNAs with premature stop codons will usually make nonfunctional proteins that could be harmful or it's just a waste of cellular energy to make a protein that is not functional. How the cell identifies this nonsense-containing mRNAs is not yet known, but a model is that the cell can recognize such mRNAs due to the large distance between the poly-A tail and the stop codon (usually this distance is relatively short).

25) RNAi would be better at treating proto-oncogene mutations as RNAi will bind to overexpressed mRNA molecules and degrade them. Tumor suppressor gene mutations lead to fewer mRNA molecules, so RNAi would just make the situation worse by degrading the few tumor suppressor mRNAs that remain.

26) Circular RNAs are closed and thus lack a 5' end or 3' end, so they cannot be degraded by nucleases from either end.

27) Typically, an mRNA cannot initiate translation unless it has a sufficiently long poly-A tail at the 3' end of the mRNA. To inhibit translation initiation, a protein called CPEB binds to the CPE sequence on the mRNA. This will then bring in an enzyme called PARN. PARN is a ribonuclease that shortens the poly-A tail. In addition, CPEB also recruits the protein called Maskin. Maskin binds to the translation initiation factor called eIF4E. This prevents eIF4E from binding to eIF4G, which now blocks initiation. Together this keeps the 3' poly-A tail short and blocks the interaction of the two IF proteins. To initiate translation, the protein CPEB gets phosphorylated by a specific kinase. This causes a conformational change that excludes both Maskin and PARN. With these two proteins gone, now the poly-A tail can extend and eIF4E and eIF4G can interact with each other to initiate translation.

If a kinase inhibitor was introduced, then CPEB would not be phosphorylated, so no conformational change would occur, and the Maskin and PARN would be able to continue to exert their inhibitory effect on translation

initiati on.

28) Both are enzymes involved in posttranslational modifications involving phosphate groups. These modifications typically activate or deactivate enzyme functions. Kinases add a phosphate group and phosphatases remove phosphate groups.

29) Proteins are often targeted for degradation by ligating ubiquitin molecules to a protein at their lysine amino acids.

As this protein is longer lived and has fewer lysines, then it is reasonable to predict that the mutation prevents ubiquitination at these specific sites that causes it to evade being degraded.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) ________ is the study of phenomena and mechanisms that cause chromosome-associated 1) _______ heritable changes to gene expression that are not dependent on changes in DNA sequence.

A) Transmission genetics B) Population genetics C) Preformation D) Mutagenesis E) Epigenetics

2) All of the following are epigenetic mechanisms, EXCEPT ________.

A) changing gene expression by adding and removing methyl groups to DNA B) changing gene expression by adding and removing chemical groups to histone proteins C) changing gene expression by changing the nucleotide sequence through mutation D) changing gene expression by the use of small noncoding RNAs E) changing gene expression by the use of long noncoding RNAs

2) _______

3) Which of the following is the most common place to find DNA methylation?

A) on cytosines when adjacent to other cytosines B) on cytosines when adjacent to guanines C) on guanines when adjacent to cytosines D) on cytosines when they are base paired to guanines E) on guanines when adjacent to other guanines

3) _______

4) In terms of epigenetics, how the promoter would be described for a gene that is not expressed

4) _______

in lung tissue but is expressed in heart tissue?

A) In lung cells, the cytosines of the promoter would be hypomethylated, and would be hypermethylated in heart cells.

B) In lung cells, the guanines in the promoter would be hypomethylated, but would be hypermethylated in heart cells.

C) In lung cells, the cytosines of the promoter would be hypermethylated, and would be hypomethylated in heart cells.

D) In lung cells, the guanines in the promoter would be hypermethylated, and would be hypomethylated in heart cells.

E) The promoters should appear the same in both types of cells, but the mRNA produced would be hypermethylated more in lung cells compared to heart cells.

5) Which DNA methyltransferase (DNMT) is important in maintaining DNA methylation patterns

5) _______

during DNA replication?

A) DNMT3a B) DNMT3b C) DNMT1 D) DNMT2 E) DNMT 1 and DNMT3a

6) The sum of histone modifications and their interactions is called the ________.

A) genetic code B) histone code C) protein code

6) _______

D) transcription code E) expression code 7) Different modification of the histone have different effects on gene expression. For instance, the

7) _______

ninth amino acid of histone 3 is a lysine (H3K9) can be acetylated once or methylated up to three times. Which of the following is true regarding H3K9 modification?

A) If H3K9 is acetylated, then the gene will be repressed.

B) If H3K9 has a single methyl group, then the gene will be repressed.

C) If H3K9 has three methyl groups, then the gene will be repressed.

D) If H3K9 has three methyl groups, it is maximally activated compared to only having one methyl group.

E) If H3K9 has two methyl groups, then the gene will be activated.

8) Long noncoding RNAs that partially overlap protein-coding genes and are transcribed in the

8) _______

opposite direction are best classified as ________.

A) bidirectional lncRNA genes B) microRNAs C) antisense lncRNA genes D) piwi interacting RNAs E) intronic lncRNA genes

9) A particular small noncoding RNA that is linked to spermatogenesis is most likely classified as

9) _______

what kind of noncoding RNA? A) bidirectional lncRNAs B) microRNAs C) antisense lncRNAs D) short interfering RNAs E) piwi-interacting RNAs

10) Which of the following is an example of genomic imprinting in humans?

A) A random pattern of autosomal allele inactivation is observed.

B) The maternal and paternal alleles of a gene pair are both expressed.

C) Human males have only one Y-chromosome and one X-chromosome.

D) One of the two X-chromosomes in females is randomly expressed and the other is

10) ______

repressed.

E) In some allele pairs, only the paternal sourced allele is expressed, and in others, only the maternal sourced allele is expressed.

11) Which of the following genotypes would most likely lead to a low birth weight and a small

11) ______

placenta?

A) Igf2+/Igf2- where the mutated Igf2- allele comes from the maternal source.

B) Igf2+/Igf2+ where neither maternal nor paternal allele is mutated.

C) Igf2+/Igf2- and it doesn't matter which parental source the mutated Igf2- comes from.

D) Igf2+/Igf2- where the mutated Igf2- allele comes from the paternal source.

E) Igf2+/Igf2- but only in female progeny as the Igf2 gene is on the X-chromosome.

12) What is the name of the DNA region that controls the expression of a cluster of genes through methylation?

A) imprinting control regions B) promoters C) epimutations D) enhancers

12) ______

E) insulators 13) Prader-Willi (PW) and Angelman syndromes (AS) are imprinting disorders of the same region

13) ______

on chromosome 15. Normally, the genes associated with PW are ________ imprinted (silenced), and the one gene associated with AS is ________ imprinted (silenced).

A) maternally; paternally B) maternally; randomly C) paternally; maternally D) randomly; paternally E) paternally; paternally

14) In humans, the number of genes that are imprinted is less than 1%. These imprinted genes are

14) ______

usually associated with ________.

A) brain function B) DNA replication C) apoptosis D) growth regulation E) metabolic pathways

15) Which of the following statements is most true regarding X-inactivation?

A) When a cell divides, the inactive X-chromosome remains inactive in the newly formed

15) ______

cell.

B) X-inactivation is caused primarily by the expression of several small noncoding RNAs (sncRNA).

C) X-inactivation results in repressing the expression of approximately 75% of the genes on the X-chromosome.

D) X-inactivation is more common in males than females.

E) X-chromosomes that remain active are called Barr bodies.

16) In terms of overall methylation, what is the most accurate way to describe the genomes of

16) ______

cancer cells?

A) Cancer cells have an overall hypermethylated genome compared to healthy cells.

B) Cancer cells have an overall hypomethylated genome compared to healthy cells.

C) Cancer cells have equivalent methylated genomes compared to healthy cells.

D) A few types of cancers are have hypomethylated genomes, but it is not common in most types of cancers.

E) A few types of cancers are have hypermethylated genomes, but it is not common in most types of cancers.

17) About 5% of those with Rubinstein-Taybi syndrome develops cancer as a result to decreased

17) ______

gene expression. This is directly linked to abnormal histone modification caused by a dysfunctional enzyme. What enzyme is this?

A) histone acetylase (HAT) B) BRCA1 C) histone deacetyltransferase (HDAC) D) DNA methyltransferase (DMT) E) No enzyme could cause this as cancer is caused only by direct DNA mutations.

18) Which of the following statements is the most accurate in regards to mice pups who receive less maternal nurturing?

A) As adults they have high levels of glucocorticoid receptor expression.

B) As adults they have increased promoter methylation.

18) ______

C) As adults they are more likely to nurture their offspring.

D) As adults their brains are heavily mutated.

E) As adults they have increased ability to adapt to stress.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

19) List the three major epigenetic mechanisms.

19) ____________ 20) Compare and contrast DNMT1, DNMT3a, and DNMT3b in regards to what they do,

20) ____________

when they act, and how they affect gene transcription.

21) Using the histone code different histone modifications follow a particular

21) ____________

nomenclature. Describe the histone with this code: H3K27me3 and what is the effect of this histone modification?

22) Describe the four types of long noncoding RNAs (lncRNA).

22) ____________

23) Consider the genes IGF2 and H19 and the imprinting control region (ICR) between

23) ____________

them. If the paternal ICR region was mutated in such a way that it could not be methylated but the maternal ICR was not mutated, how would that effect growth? In your explanation describe the expression of IGF2 and H19 from both the maternal and paternal alleles.

24) Explain the roles of XIST and TSIX during X-inactivation in females.

24) ____________

25) Is there a risk for epigenetic linked diseases in using artificial reproductive technologies

25) ____________

(ART) such as in vitro fertilization?

26) Even though cancer genomes are overall hypomethylated, explain why some genes are

26) ____________

hypermethylated in cancer cells.

27) Explain how HATs and HDACs can lead to the formation of cancer.

27) ____________

28) Based on rat studies that show how maternal nurturing helps offspring respond better

28) ____________

to stress propose a model to help explain why human children who are abused have a higher suicide rate.

29) What are the two goals of the NIH Roadmap Epigenomics Project?

29) ____________

30) The data from the NIH Roadmap Epigenomics Project are classified into which five

30) ____________

categories?

1) E 2) C 3) B 4) C 5) C 6) B 7) C 8) C 9) E 10) E 11) D 12) A 13) A 14) D 15) A 16) B 17) A 18) B 19) (1) Addition or removal of methyl groups from DNA, (2) chromatin remodeling by adding and removing chemical groups from histone proteins, and (3) regulation of gene expression by noncoding RNA molecules.

20) DNMT1, DNMT3a, and DNMT3b are DNA methyltransferases and all add methyl groups to cytosines that are typically adjacent to guanines (CG). Promoters that get methylated will usually decrease gene expression. DNMT1 is primarily responsible for maintaining methylation patterns as DNA is being replicated and DNMT3a and DNMT3b are responsible for establishing the original methylation patterns.

21) The lysine at position 27 on histone 3 has three methyl groups. The effect of this modification is linked to gene repression.

22) (1) Antisense lncRNA partially overlap protein-coding genes and are transcribed in the opposite direction of the protein-coding gene. (2) Intronic lncRNA genes are located within introns, and their transcription does not overlap with the adjacent exon. (3) Bidirectional lncRNA genes use the promoter of a protein-coding gene but are transcribed in the opposite direction. (4) Intergenic lncRNA genes are discrete transcription units located outside the protein-coding region.

23) There would be reduced growth and a smaller placenta. The maternal copy of ICR is usually not methylated and so would remain unmethylated allowing for the expression of the maternal H19. Expressed H19 produces a noncoding RNA that suppresses IGF2. Typically, the paternal copy of ICR is hypermethylated so that H19 is not expressed and thus IGF2 can be expressed. In this mutant, the ICR is unable to be methylated and thus H19 will be expressed and then the resulting noncoding RNA will repress the IGF2. This would result in the repression of both maternal and paternal copies of IGF2 and will result in slower growth of the fetus and placenta.

24) Both XIST and TSIX are long noncoding RNAs (lncRNA). XIST is expressed from the X-chromosome to be inactivated. The XIST lncRNA will repress the genes on the inactivated X-chromosomes. The TSIX is expressed from the X-chromosome that is to remain active. When TSIX is expressed, its lncRNA will repress the XIST. 25) Yes. There is an increase in imprinting errors, and maternal specific methylation is reduced when using ART. Some examples are an increase in Beckwith—Wiedemann syndrome, Angelman syndrome, and Prader-Willi syndrome.

26) Hypermethylation of promoters will lead to reduced expression of those genes. Some genes such as cell cycle stop and DNA repair genes need to be expressed. When they aren't expressed, this can lead to cancer.

Hypermethylation will reduce their expression.

27) HATs usually lead to gene expression, and HDACs usually lead to gene repression. In cancer cells if HATs are mutated, then genes that are normally expressed to prevent cancer are now repressed, which can lead to cancer. In addition, in cancer cells if HDACs are mutated, then genes that are normally inactive to suppress cancer will now be expressed leading to cancer.

28) From rat studies, it could be proposed that human children that are abused will have decreased histone acetylation

and sed DNA methylation associated with the genes for glucocorticoid receptors. These receptors in the hypothalamic increa region of the brain are important in mediating stress.

29) The goals are to (1) provide a set of at least 1000 reference epigenomes in a range of cell types from healthy and diseased individuals and (2) delineate the epigenetic differences in healthy and diseased states.

30) (1) Histone modifications, (2) DNA methylation, (3) open and closed chromatin configurations, (4) expression levels of protein-coding genes, and (5) expression profiles for small nuclear RNAs such as miRNA.

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Recombinant DNA technologies are methods used to do which of the following?

1) _______ A) integrate DNA in computers to make them faster B) manipulate DNA for the study of specific sequences C) combine chromosomes to make them easier to study D) join together DNA molecules from the same source E) induce homologous recombination inside a cell 2) Cloned DNA is useful in studying which area(s) of genetic manipulation?

A) learning about translation of a gene B) learning about the structure and organization of DNA C) learning about introns D) determining size of an organism's genome E) producing commercial products

2) _______

3) A restriction enzyme that uses a six (6) base recognition sequence will cut DNA, on average,

3) _______

every ________ bases, if all four nucleotides are present in equal proportions.

A) 500 B) 5000 C) 1296 D) 4096

E) 256

4) Recognition sequences for restriction enzymes possess the unique quality of being the same

4) _______

when read 5′ to 3′ on either strand. What is this property called?

A) consensus sequence B) origin sequence C) recombination sequence D) palindromic sequence E) gene sequence

5) When choosing a restriction enzyme for use in recombinant DNA technologies, it is often

5) _______

preferred that the enzyme generate cohesive, or "sticky," ends. Why is this preferred?

A) The sticky ends prevent the DNA from re-annealing to any DNA. B) The sticky ends have hydrogen bonds that help re-anneal the cut DNA. C) The sticky ends do not have hydrogen bonds to help in re-annealing the cut DNA. D) The sticky ends make the DNA bind tighter to any cut DNA. E) The sticky ends stick to the purification medium making the fragments easier to purify.

6) Assume that a plasmid (circular) is 2800 base pairs in length and has restriction sites for EcoRI

6) _______

at the following locations: 400, 700, 1400, and 2600. Give the expected sizes of the restriction fragments following complete digestion with EcoRI. A) 300, 700, 2200 B) 700, 400, 1400, 2600 C) 300, 600, 700, 1200 D) 200, 400, 700, 1200 E) 400, 1200, 1600

7) DNA ligase ________.

A) adds bases into a growing DNA molecule B) cuts the DNA to produce sticky or blunt ends

7) _______

C) removes bases from a DNA molecule D) reconnects the phosphodiester linkage between bases on the same strand of DNA E) reconnects the bases together between the DNA strands 8) Transformation of cells using the technique of heat shock requires which of the following?

A) the use of calcium and brief exposure to elevated temperature B) the use of zinc ions C) the use of calcium ions D) brief electric shock E) brief exposure to elevated temperature

8) _______

9) A plasmid contains a multiple cloning site inside the coding region of the lacZ gene and also

9) _______

contains an ampicillin resistance gene at a separate locus. When cells are transformed with a successfully recombinant plasmid containing a piece of DNA cloned into the multiple cloning site, what color will the colonies be when grown on an agar plate containing ampicillin and X-gal?

A) blue B) clear C) white D) green E) colonies will not grow

10) There are multiple cloning vector types in modern recombinant DNA technology ranging from

10) ______

plasmids to viral vectors. Which vector type is most useful when cloning an insert of approximately 500kb?

A) bacterial artificial chromosome B) bacterial plasmid C) human artificial chromosome D) viral vector E) yeast artificial chromosome

11) Restriction mapping is used to characterize cloned DNA. What does a restriction map tell the

11) ______

researcher about the cloned DNA? A) The restricted conditions under which the organism can grow.

B) The size of the genome the cloned DNA was isolated from.

C) The number of sites and distance between them for the specific restriction enzyme.

D) The distances between restriction sites for the specific restriction enzyme.

E) The number of restriction sites for the specific restriction enzyme.

12) If one wishes to clone a gene using typical restriction endonucleases, how does the restriction

12) ______

endonuclease identify the appropriate cut sites in the genome?

A) The endonuclease identifies its specific recognition sequence.

B) The endonuclease cuts randomly in the genome.

C) The endonuclease recognizes the gene of interest.

D) The endonuclease cannot identify the cut sites.

13) The following are four processes common to most cloning experiments: i) transforming bacteria ii) plating bacteria on selective medium iii) cutting DNA with restriction endonucleases iv) ligating DNA fragments

Plac this list e the in the com order pon in ents which of they

____ __

would 13) most likely occur during a cloning experimen t.

A) iii, iv, i, ii

B) ii, i, iv, iii

C) iv, i, iii, ii

D) i, ii, iii, iv

E) ii, iii, i, iv

14) What is necessary to generate a genomic DNA library?

A) A single fragment that contains at least one copy of the DNA sequence in the organism's

14) ______

genome.

B) Many overlapping fragments of the genome with at least one copy of every DNA sequence in the organism's genome.

C) Many fragments of the genome with at least one copy of every DNA sequence in the organism's genome.

D) Many overlapping fragments of the genome with at least one copy of every DNA sequence in the organism.

E) Many fragments of the genome with at least one copy of every DNA sequence in the organism.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) When generating a cDNA library, one may get different sequences returned if samples 15) ____________ are taken at different times. Why is this the case?

16) What is the most serious drawback to using library screening to study genetics?

16) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

17) Which of the following best describes a cloning vector?

17) ______ A) The fragment of DNA encoding a gene of interest.

B) The direction in which DNA is cloned.

C) A DNA molecule that accepts DNA fragments and replicates the fragment in a host.

D) A DNA molecule that accepts DNA fragments and degrades them in a host.

18) A scientist is troubleshooting the synthesis of a cDNA library. The scientist performs both a

18) ______

Northern and a Southern blot. The Northern blot demonstrated the presence of RNA while the Southern blot indicated that no cDNA was present in the sample. What is likely to be the cause of the failed synthesis of the cDNA library?

A) defective reverse transcriptase B) temperature too cold for annealing C) proper primers D) too many dNTPs

19) The genomics era began with the development of which of the following?

A) whole-transcriptome sequencing B) PCR C) third-generation sequencing D) whole-genome sequencing

19) ______

20) A probe with the sequence 5'-A-T-G-C-C-A-G-T-3' will serve as a probe for which sequence?

A) 3'-A-C-T-G-G-C-A-T-3' B) 3'-T-A-C-G-G-T-C-A-5' C) 3'-A-T-G-C-C-A-G-T-5' D) 3'-T-G-S-C-C-G-T-A-5'

20) ______

21) Genomic libraries are constructed from the fragments generated from a ________ digest.

A) random B) incomplete C) complete D) gene specific

21) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

22) The development of polymerase chain reaction (PCR) was a watershed event in 22) ____________ recombinant DNA technology. What are two characteristics of PCR that make it such an important development?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

23) During the hybridization/annealing phase of a PCR reaction, the primers bind to the target 23) ______ DNA sequence at a specific temperature. What effect would an increase in the GC content of the primer have on the optimal temperature for annealing the primer to a target DNA sequence?

A) the annealing temperature would increase B) the annealing temperature would decrease C) the annealing temperature would remain the same

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

24) Briefly explain the three major steps in the polymerase chain reaction.

24) ____________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

25) RT-PCR (reverse transcription-polymerase chain reaction) can be used to compare gene 25) ______ expression levels during an organism's response to the environment. A scientist monitoring a tetracycline resistance gene will see what response in the expression when the organism is challenged?

A) increased gene expression B) no change in gene expression C) decreased gene expression

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

26) Why are DNA binding dyes such as SYBR green integral to the technique of qPCR? 26) ____________ 27) In a PCR, the polymerase adds nucleotides to the 3'-hydroxyl of the terminal nucleotide

27) ____________

of each primer. Briefly describe how this results in the amplification of the single region of interest in the genome.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

28) What is the order of the three main steps in a PCR? 28) ______ A) denaturation, elongation, annealing primers B) denaturation, annealing primers, elongation C) elongation, annealing primers, denaturation D) annealing primers, denaturation, elongation 29) A PCR was designed to clone a DNA sequence of 1.5 kb. When the products were run on an agarose gel, there was a smear of bands ranging from 1.5 kb to 6 kb. Which of the following is a reason for this result?

29) ______

A) the polymerase overran the reverse primer B) the polymerase denatured C) the thermocycler malfunctioned D) one of the primers did not bind SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

30) Assume that you have cut λ DNA with the restriction enzyme HindIII. You separate the 30) ____________ fragments on an agarose gel and stain the DNA with ethidium bromide. You notice that the intensity of the stain is less in the bands that have migrated closer to the "+" pole. Give an explanation for this finding.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

31) Due to single nucleotide polymorphisms (SNPs), all humans have a slightly different 31) ______ nucleotide sequence for their genome. Restriction mapping is used in forensic sciences to match DNA evidence to a potential suspect of a crime. How does restriction mapping reduce the likelihood of misidentifying a suspect?

A) SNPs only add new restriction sites to the genome resulting in a unique "fingerprint" for each person B) SNPs only remove restriction sites from the genome resulting in a unique "fingerprint" for each person C) SNPs change the genes that are expressed D) SNPs add and remove restriction sites resulting in a unique "fingerprint" for each person

32) Nucleic acid blotting is commonly used in molecular biology. Northern blotting is used to

32) ______

detect the presence of which type of nucleic acid?

A) deoxyribonucleic acids B) transfer ribonucleic acids C) unnatural nucleic acids D) ribonucleic acids E) triphosphate nucleic acids

33) Fluorescence in situ hybridization is another way to visualize the presence of a nucleotide

33) ______

sequence. Which of the following is an advantage of FISH over Northern and Southern blots?

A) Blotting is not used in FISH. B) Fluorophores are not used in Northern or Southern blots.

C) There are no advantages to FISH over Northern and Southern blots.

D) Probes are not needed in FISH.

34) When a 5-kb circular plasmid is digested with a restriction enzyme that has three recognition sites on the plasmid, how many bands can be visualized on an agarose gel?

A) 1 B) 2 C) 3

34) ______

D) 4

35) Spectral karyotypes take advantage of which of the following?

A) Probes can be made with different radioactive isotopes.

B) Chromosomes can be labeled with different radioactive isotopes.

C) Probes can be labeled with different color fluorophores.

D) Chromosomes are different colors under a microscope.

35) ______

36) Agarose gels separate DNA fragments based on what property?

A) amount of agarose in the DNA

36) ______

B) charge of the DNA molecule C) size of the fragment D) amount of adenine bases in the sequence 37) What is the main purpose of a DNA probe?

A) cuts DNA targets C) hybridizes to a target sequence

37) ______ B) extend the growing polynucleotide D) binds to proteins

38) Next-generation sequencing takes advantage of the concept of sequencing-by-synthesis. What

38) ______

is sequence-by-synthesis?

A) The use of a single polymerase in a nanopore that reports on a single molecule of synthesized DNA. B) The use of firefly luciferase and pyrophosphate to report on nucleotide incorporation.

C) The use of PCR to incorporate ddNTPs, followed by electrophoresis.

D) The use of a multiwell system and microfluidics to detect incorporated nucleotides at each base.

39) Third-generation sequencing strategies are based on which of the following?

A) sequencing multiple strands of DNA with different sequences to generate a library B) sequencing DNA using PCR C) sequencing a single strand of DNA D) sequencing an ensemble of DNA strands with the same sequence

39) ______

40) Sanger sequencing is based on the order in which ddNTPs are added to a growing

40) ______

polynucleotide. Why are ddNTPs integral to the Sanger sequencing method?

A) They have a 2′ hydroxyl that allows for extension of the polynucleotide.

B) They have a 3′ hydroxyl that allows for extension of the polynucleotide.

C) They do not have a 3′ hydroxyl, which does not allow the extension of the polynucleotide.

D) They do not have a 2′ hydroxyl, which does not allow the extension of the polynucleotide.

41) High throughput sequencing takes advantage of automated reading of sequencing data. Which

41) ______

of the following assists in automating the sequencing readout?

A) radioactive dNTPs B) fluorescently tagged dNTPs C) fluorescently tagged ddNTPs D) radioactive ddNTPs

42) When performing a sequencing reaction using Sanger sequencing, which ddNTPs must be

42) ______

included in the reaction?

A) ddATP B) ddCTP C) ddTTP D) ddGTP E) all four ddNTPs must be present

43) ddATP, ddTTP, ddCTP, and ddGTP are labeled with red, green, yellow, and blue fluorescent

43) ______

dyes, respectively. A five-base read from a sequencing reaction produced the following color sequence, read by the computer: red, yellow, yellow, green, green. What is the sequence of the template DNA? A) TGGAA B) TTCCA C) AAGGT D) ACCTT

44) What is the function of a ddNTP in DNA sequencing?

A) termination of DNA synthesis B) provide a 3′ hydroxyl for continued elongation

44) ______

C) enhancing the processivity of the polymerase D) methylation of guanine 45) Which of the following describes a "knock-out" organism?

A) An organism that is negative for alleles coding a gene of interest.

B) An organism that is capable of out-competing another organism.

C) An organism that is positive for alleles coding a gene of interest.

D) An organism that loses consciousness randomly.

45) ______

46) A knock-out mouse is made with respect to the PFKL gene, and this mouse is now described as

46) ______

which of the following?

A) a loss-of-function PFKL mouse B) a retention-of-function PFKL mouse C) a gain-of-function PFKL mouse D) an enhancement-of-function PFKL mouse

47) The generation of a knock-out organism generally requires all the following EXCEPT ________.

A) embryonic stem cells B) a targeting vector C) a selectable marker D) knowledge of the target sequence E) knowledge of the sequence product

47) ______

48) Conditional knock-out organisms provide which advantage over full knock-out organisms?

A) They allow scientists to turn the gene off at any time during the organism's development.

B) They allow scientists to render the organism unconscious at any time.

C) They allow scientists to study genome size.

D) They allow scientists to turn on the gene at any time during the organism's development.

48) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

49) Transgenic animals are useful in studying the effects of a gene product on the 49) ____________ organism's phenotype. Briefly describe how you would study the effect of overexpression of a pancreatic enzyme using a transgenic animal.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

50) Protospacer adjacent motifs, PAMs, allow bacteria to do which of the following?

50) ______ A) recognize and digest foreign DNA B) recognize proper spacing for bacterial transcription initiation C) recognize and integrate foreign DNA D) recognize and digest their own DNA 51) Which of the following is not a common system for generating knock-out organisms?

A) homologous recombination B) transformation C) CRSPR-CAS D) cre-lox

51) ______

52) The CRISPR-Cas system of gene editing is based on what naturally occurring biological

52) ______

process?

A) viral defense against eukaryotic defenses B) viral defense against bacterial defenses

C) bacterial defense against viral infection D) eukaryotic defense against viral infection

1) B 2) E 3) D 4) D 5) B 6) C 7) D 8) A 9) C 10) E 11) C 12) A 13) A 14) B 15) The cDNA library uses reverse transcriptase to copy mRNA present in the cell to DNA. If cellular conditions change over time the genes being expressed could change as well resulting in a change in the mRNA present when samples are taken. This would result in a different cDNA library being generated.

16) The sequence of the gene must be known in order to design probes to locate the gene in the library.

17) C 18) A 19) D 20) B 21) A 22) One advantage of PCR over bacterial cloning is that exponentially more DNA clones can be made in a shorter time frame. A second advantage is the cost reduction in generating cloned DNA through the use of thermostable Taq polymerase.

23) A 24) The first step is denaturation of the target DNA molecule by exposure to high temperature. The second step is annealing of primers to the target DNA. The third step is the synthesis of the target DNA sequence by a thermostable DNA polymerase.

25) A 26) The SYBR green dye binds double-stranded DNA. As more DNA is synthesized in the qPCR reaction, the light emitted by SYBR green increases in proportion to the amount of DNA present. This is what allows real-time quantification of the DNA. 27) The primers are used to initiate DNA synthesis by the polymerase and the antiparallel nature of the DNA ensures that the region between the primers is replicated while the region outside the primers is not.

28) B 29) D 30) Since the smaller fragments migrate toward the "+" pole, away from the origin, they bind less stain than the larger fragments near the origin.

31) D 32) D 33) A 34) C 35) C 36) C 37) C 38) D 39) C 40) C 41) C

42) E 43) D 44) A 45) A 46) A 47) E 48) A 49) The gene of interest can be inserted into the organism's genome under the regulation of a pancreas-specific promoter. This will cause the enzyme to be overproduced in the pancreatic tissue, potentially resulting in a changed phenotype.

50) A 51) B 52) C

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) A newly sequenced gene is cloned and expressed in a bacterial cell. The bioinformatics 1) _______ databases suggest that this gene produces an enzyme that catalyzes the conversion of carbon dioxide to bicarbonate. After weeks of experiments, a scientist determined the enzyme has a completely different function. This is an example of ________.

A) incorrect enzyme experiments B) incorrect qPCR C) incorrect BLAST parameters D) incorrect annotation E) incorrect sequencing

2) Which E-value represents the highest probability of a BLAST result not being chance?

A) 1 B) 0.01 C) 1 × 10-3 D) 1 × 10-4 E) 0.1

2) _______

3) How many potential reading frames are there in a 1500-bp segment of double-stranded DNA? A) 4 B) 6 C) 2 D) 1 E) 5

3) _______

4) A new gene is discovered during the sequencing of a bacterial genome. After a BLAST analysis,

4) _______

the new gene aligns with a known sequence from the same bacterium. The sequence identity is 95%. Which of the following statements best describes the relationship of the newly discovered gene and the known gene?

A) It is a paralog to the known gene and is a result of a recent gene duplication.

B) It is an ortholog to the known gene and is a result of a recent gene duplication.

C) It is a paralog to the known gene and is a result of an older gene duplication.

D) It is an ortholog to the known gene and is a result of an older gene duplication.

5) The Human Genome Project, which got under way in 1990, is an international effort to

5) _______

________.

A) collect samples of cells from all parts of the world in order to preserve human genetic diversity B) determine the base sequence of the human genome and to identify all the genes within C) collect plant seeds in order to reduce the impact of human activity on plant extinction D) clone deleterious genes from humans and study their mode of action E) clone beneficial genes from humans for eventual use in gene therapy

6) The sequencing of the human genome lead to the realization that chromosome 19 contains

6) _______

many genes while chromosomes 13 and Y contain relatively few. This finding implies what about the density of genes in a genome?

A) Genes are not uniformly distributed and appear in clusters separated by large noncoding regions.

B) Genes have no organization and randomly appear throughout the genome and chromosomes.

C) Genes are uniformly distributed throughout the genome.

D) Genes are uniformly distributed on chromosomes but not through the entire genome.

7) Under the umbrella of the Human Genome Project, a program was set up to involve scientists, health professionals, policy makers, and the public in formulating policy and legislation related to the application of human genomic information. What is it called?

7) _______

A) HGPC (Human Genome Project Consortium) B) WGS (Whole Genome Systems) C) ELSI (Ethical, Legal, and Social Implications) D) HGSI (Human Genome Sequencing Initiative) 8) What is one cause for the 21,000 protein encoding sequences in the human genome producing

8) _______

between 200,000 and 1 million different proteins?

A) CRISPR-Cas systems B) restriction enzymes C) CNVs D) alternative splicing E) SNPs

9) Numerous scientists around the world have proposed to sequence 10,000 vertebrate genomes

9) _______

in five years. What is the name of this plan?

A) 10K or Bust B) Bigger Than Life Plan C) Vertebrate Beginnings D) Vertebrate Enlightenment E) Genome 10K

10) Compared with eukaryotic chromosomes, bacterial chromosomes are ________.

A) large, triple-helix, Z-DNA, organized in single gene units with introns B) large, mainly organized in single-gene transcription units without introns C) small, mainly organized in single-gene transcription units with introns D) large, mainly organized in polygenic transcription units without introns E) small, with high gene density

10) ______

11) Compared with prokaryotic chromosomes, eukaryotic chromosomes are ________.

A) small, mainly organized in polygenic transcription units without introns B) small, mainly organized in single-gene transcription units with introns C) large, mainly organized in polygenic transcription units without introns D) large, linear, less densely packed with protein-coding genes, mainly organized in

11) ______

single-gene units with introns

E) large, mainly organized in single-gene transcription units without introns 12) Most of the bacterial genomes described in the text have fewer than ________.

A) 500 genes B) 50 genes C) 10,000 genes D) 5000 base pairs E) 10,000 base pairs

12) ______

13) A bacterial polygenic transcription unit ________.

A) is void of start (AUG) and termination (UAA, UGA, UAG) triplets B) is capped at the 5′ end and carries a poly-A tail at the 3′ end C) contains information for one protein product D) contains information for more than one protein product E) None of the answers listed is correct.

13) ______

14) What is the typical gene density per kilobase in prokaryotes?

14) ______

A) 1200

B) 1

C) 12

D) 426,000

E) 3000

15) In general, the organization of genes in bacteria is different from that in eukaryotes. In E. coli,

15) ______

approximately 27 percent of all genes are organized into contiguous, functionally related units containing multiple genes under coordinated control that are transcribed as a single unit. Such contiguous gene families are called ________.

A) contigs B) proteomes C) transcriptomes D) pseudogenes E) operons

16) Which of the following is not an emerging "-omics" field?

A) metagenomics B) pharmacogenomics C) transcriptomics D) chromosomics E) glycomics

16) ______

17) Personal genome sequencing assists with the recognition and determination of what?

A) silent mutations in the genome B) locations for introns C) somatic genome mosaicism D) inheritable diseases and their alleles

17) ______

18) Somatic genome mosaicism is best described as ________.

A) differences in gen location in the genome B) differences in proteins expressed between cells of an organism C) differences in genome sequence between cells of an organism due to errors incurred

18) ______

during division

D) differences in genome sequence between cells of an organism due to errors in sequencing SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

19) Describe the difference between whole-genome sequencing and whole-exome 19) ____________ sequencing.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

20) The project seeking to determine transcriptional start sites, promoters, enhancers, and other 20) ______ functional elements of the genome is called ________.

A) NCBI B) NIH C) ENCODE D) PANTHER E) LUMINA

21) Nutrigenomics is the study of ________.

A) the relationship between diet and the genome B) the effect of genomics on dietary desires C) the vitamins and minerals in the genome D) the effect of nutrition on genome sequences

21) ______

22) Several years ago, scientists compared the genome of a wooly mammoth to that of an African

22) ______

elephant and found them to be 98.5% identical. This is an example of what type of "-omics"?

A) space-age genomics B) extinctomics C) exomics D) stone-age genomics E) proteomics

23) One major difference between prokaryotic and eukaryotic genes is that eukaryotic genes can

23) ______

contain internal sequences, called ________, which get removed in the mature message.

A) exteins B) splice-outs C) introns D) exons E) inteins

24) The dog (Canis familiaris) genome has recently been sequenced. About how many of the dog's genes are shared with humans?

A) ~75% B) ~50%

C) >95%

D) <25%

25) Aligning genome sequences from different organisms to determine their evolutionary history is referred to as ________.

A) evogenomics C) metagenomics

24) ______

25) ______

B) stone-age genomics D) comparative genomics

26) The advent of genomic sequencing and annotations using bioinformatics has led to the

26) ______

realization that some of the long-held beliefs about prokaryotic genome structure were incorrect. Which of the following has not been refuted by modern bioinformatic discoveries?

A) Bacterial genomes are always smaller than eukaryotic genomes.

B) All bacterial genomes are circular.

C) Prokaryote genomes do not contain introns.

D) Prokaryotes have a single chromosome.

27) Which of the following is a major contributor to variation in gene density in eukaryotes?

A) restriction sites B) heterochromatin C) repetitive sequences D) transposons

27) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

28) Describe how comparative genomics is aiding in the discovery and treatment of human 28) ____________ disease.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

29) The genome of the domesticated dog, Canis familiaris, was sequenced in 2005. Using the dog as 29) ______ a model system provides insight into which of the following human disease states?

A) behavioral conditions (i.e., obsessive-compulsive disorders) B) aneuploidies C) multifactorial diseases D) aneuploidies, multifactorial diseases, and behavioral conditions

30) Genomes from several primates have been sequenced and annotated. These primates range

fromchimp

anzee to 30) Rhesus monkey to Neandert hal and modern humans.

What is the advantage of having so many primate sequences available to researcher s?

____ __

A) Comparative genomics allows for determining evolutionary trends.

B) The primate sequences can be compared to learn about dietary trends.

C) The primate sequences can be compared to learn about social behavior.

D) Phenotypes can be determined from the genomes.

31) With the rise of drug-resistant bacteria in hospitals there has been an effort to develop new

31) ______

antibiotics as well as novel methods to combat resistant infections. The sequencing of entire communities of organisms including environmental samples has led to the discovery of millions of uncharacterized bacteria that could provide new drugs. This sequencing method is called ________.

A) biome genomics B) whole-community sequencing environmental genomics C) D) shotgun genomics

32) A microbiome is essential for human infant development. Where does an infant obtain the

32) ______

origins of its microbiome?

A) the hospital B) the infant has a microbiome at conception C) the father D) the mother

33) The data from metagenomic experiments is commonly displayed in a Venn diagram where

33) ______

there is overlap between datasets that suggest correlation with disease states. If a patient exhibits genomic sequences from multiple overlapping regions of the diagram what happens to their predisposition to the disease?

A) It stays the same.

B) It goes down.

C) It goes up.

D) Genetics do not play a role in disease predisposition.

34) Transcriptomics is ________.

A) determining phenotype B) measuring how much DNA is in the genome C) determining epigenetic markers D) the quantification of gene expression

34) ______

35) Transcriptomics requires the isolation of RNA to generate sequence data. If a scientist wants to

35) ______

use next-generation sequencing to perform their experiment which of the following is necessary?

A) euchromatin B) reverse transcriptase C) protein quantification D) heterochromatin

36) DNA microarray analysis is excellent for ________.

A) studying all of a sample's unexpressed genes simultaneously B) studying one gene's expression very closely C) studying all of a sample's expressed genes simultaneously D) studying all of a sample's genes simultaneously

36) ______

37) A drawback to using microarrays is ________.

A) the spots are very tiny B) researcher-made arrays have high variability C) commercial microarrays have high variability in quality D) the arrays do not cover enough of the genome

37) ______

38) Using RNA-seq generates data in situ. What does RNA-seq not provide data for?

A) gene expression levels B) location of transcript in the genome amount of protein produced by RNA C) D) sequence of the RNA

38) ______

39) Proteomics is the "-omics" study of proteins, investigating the complete set of proteins in a cell.

39) ______

What does proteomics provide data on?

A) the similarity between genes coding for a protein B) the gene sequence for the protein C) amount of protein in a cell D) posttranslational modification to proteins

40) ______

40) A common first separation technique in 2D gels is isoelectric focusing. What property is isoelectric focusing taking advantage of?

A) the pH at which the overall charge is zero B) amino acid content C) charge D) size

41) Proteins separated on 2D gels provide information on their pH and size but not their identity.

41) ______

MALDI-mass spectrometry provides this missing information by which of the following?

A) generating a gene "fingerprint" for the protein B) generating a m/z ratio "fingerprint" for the protein C) generating a sequence "fingerprint" for the protein D) generating sequence data for the protein

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

42) MALDI-mass spectrometry was used to identify a protein from preserved T. rex 42) ____________ samples. Briefly describe how this was done.

43) Describe the similarities between sequencing a protein and sequencing a genome.

43) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

44) What does MALDI stand for?

44) ______ Matrix-Assisted Ligand Desorption Ionization A) B) Maser-Assisted Ligand Desorption Ionization C) Maser-Assisted Laser Desorption Ionization D) Matrix-Assisted Laser Desorption Ionization

1) D 2) D 3) B 4) A 5) B 6) A 7) C 8) D 9) E 10) E 11) D 12) C 13) D 14) B 15) E 16) D 17) C 18) C 19) Whole-genome sequencing sequences the entire genome of an organism. Whole-exome sequencing generates deeper reads of only the exons of an organism's genome.

20) C 21) A 22) D 23) C 24) A 25) D 26) C 27) C 28) Comparative genomics is revealing orthologous genes in lower eukaryotes that provide opportunity to study disease states without the threat to human life.

29) D 30) A 31) C 32) D 33) C 34) D 35) B 36) C 37) B 38) C 39) D 40) A 41) B 42) The T. rex sample was believed to be collagen. A synthetic collagen was made and examined using MALDI-mass spectrometry. This generated a "fingerprint" for collagen. The T. rex sample was then examined with MALDI-mass spectrometry. The "fingerprints" matched, confirming the T. rex sample was collagen.

43) Similar to genome sequencing protein sequences are broken up into smaller strings then overlapping regions are stitched together, similar to contigs until the entire sequence is known.

44) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Biotechnology is commonly used to produce transgenic plants and animals that are then 1) _______ harvested for useful products. This process is commonly referred to as which of the following?

A) tuna farming B) culturing C) animal farming D) biopharming E) genetic production

2) Mastitis in cows results in infected mammary glands. The use of biotechnologies to introduce

2) _______

the antibiotic gene lysostaphin from Stpahylococcus simulans is an example of generating what type of animal?

A) a synthetic animal B) a conditional knock-out animal a transgenic animal C) D) a knock-out animal

3) RFLPs can be used to identify point mutations through which of the following mechanisms?

A) The mutation can occur outside of a restriction site causing a change in the cutting

3) _______

pattern for restriction enzymes.

B) The mutation can occur in a restriction site, causing a change in the cutting pattern for restriction enzymes.

C) The mutation can occur causing a shortening of the mRNA that is then compared to wild type.

D) The mutation can be silent in the coding for protein resulting in a different amino acid being inserted.

4) SNPs are characterized by being ________.

A) highly heterogeneous with variable amino acid substitutions B) lethal genes with small noteworthy transcribed regions C) homogeneous with various nucleotides transcribed repeatedly D) variable in the population with variable base sequences E) highly uniform in the population with variable numbers of tandem repeats

4) _______

5) A DNA microarray (also called a DNA chip) can be used to ________.

A) detect RFLPs B) determine protein translation levels C) generate mutations in the gene of interest D) detect mutations that may indicate a risk of disease

5) _______

6) Probes that bind under very stringent hybridization conditions resulting in the differential

6) _______

binding over one nucleotide are called ________.

A) allele-specific oligonucleotides (ASOs) B) generation-specific probes C) microsatellites D) short, variable repeats E) VNTRs

7) Which of the following best describes the term edible vaccine?

A) A recombinant organism that expresses the vaccine in a consumable portion of the

7) _______

organism.

B) A vaccine that can be eaten by a human and alter the genome.

C) Part of a recombinant organism that the vaccine can be purified from.

D) A DNA that a human can eat and relies on the human cells to generate the vaccine.

8) Generally, vaccines are used to stimulate the immune system by providing antigens of potential

8) _______

pathogens. What is the typical composition of a vaccine?

A) naked DNA B) RNA from bacteria genes encoding for virulence factors C) D) inactivated or attenuated viruses

9) A transgenic organism is one in which ________.

A) DNA from a different organism is introduced to produce a more resilient bacterium B) its genes have transferred to new chromosomes C) DNA from a different organism is introduced to produce a biopharmaceutical D) a naturally occurring plasmid has been transferred through natural means

9) _______

10) Selective breeding has been used for centuries to ________.

A) enhance growth and yield from domesticated plants and animals B) train crops to grow in more favorable environments C) remove favorable traits from plants and animals D) ensure purity of genetic lines

10) ______

11) As proof of a functional synthetic genome the JCVI conducted ________ to demonstrate that

11) ______

JCVI-syn1.0 was a functional genome.

A) gene editing C) genome transplantation

B) whole genome sequencing D) homologous recombination

12) Using single-cell RNA sequencing a clinician can now determine ________ in one experiment

12) ______

instead of two?

A) gene expression and protein levels associated with those genes B) whether the organism is transgenic or not C) ratio of genes present to the expression levels of those genes D) heterozygosity

13) Personal genomics has led to the discovery of many new genes associated with disease states.

13) ______

Studies on autism spectrum disorder have revealed how many genes to have an impact on the disease state?

A) 1 B) 63 C) >100 D) 5

14) Which of the following is not an application of RFLPs? A) paternity testing B) proteomics C) forensic science D) evolutionary biology

14) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) Genome-wide association studies are identifying many genes that may affect disease 15) ____________ risk. Describe how GWAS is used to determine if a mutation or gene may be a risk factor for disease.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

16) One procedure that has greatly enhanced prenatal screening is ________.

A) fetal blood sampling B) RNA-seq C) GWAS D) chorionic villus sampling

16) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

17) Describe how microarrays have led to improved diagnosis of two types of diffuse large 17) ____________ B-cell lymphomas.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

18) The CJVI undertook a comparison between M. genitalium and Haemophilus influenzae in an effort 18) ______ to determine what?

A) the core set of genes needed for M. genitalium to infect humans B) the core set of genes that cause H. influenzae virulence C) the core set of genes needed for understanding life D) the core set of genes needed to sustain life

19) One possible use of synthetic biology is bioremediation; this application is best described as

19) ______

________.

A) transplanting a completely synthesized genome into a host that can then use genes to process the pollutant B) collecting pollutants and subjecting naturally occurring organisms to extreme levels to force evolution to process the pollutant C) isolating bacteria from polluted areas and adjusting their genome to process the pollutant D) synthesizing an entire organism that can process the pollutant

20) Synthetic biologists are creating gene clusters that have logic functions and memory called ________.

A) genetic computers C) synthetic gene circuits

20) ______

B) synthetic genes D) organic computers

21) The organization founded to ensure privacy and fairness in the interpretation of genetic

21) ______

information is called ________.

A) ELSI, Ethical, Legal, and Social Implications B) ELISA, Ethical Listing in Sequence Association C) CJVI, Craig J. Venter Institute D) GWAS, genome-wide associated sequences

22) In the past decades, direct-to-consumer (DTC) genetic tests have become widespread. Which U. S. federal agency is responsible for the future regulation of these tests?

A) FDA B) FBI C) EPA

22) ______

D) DEA

23) In 2010, the American Civil Liberties Union filed suit against Myriad Genetics. The court ruled

23) ______

in favor of the ACLU. What precedent did this court case set with regard to biotechnologies?

A) confirmed that human genes can be patented B) confirmed human genes cannot be patented C) confirmed that any gene-related biotechnologies cannot be patented D) confirmed that synthetic genes cannot be patented

24) There is a fear that preconception genetic testing may lead to "designer babies." What historical practice comes to mind regarding the production of such babies?

24) ______

A) eugenics

B) gene editing

C) gene driving

D) inbreeding

25) With the multitudes of genetic tests and bioinformatic databases available to clinicians and

25) ______

researchers, diagnosis via genetic information is becoming more common. Which of the following is a major concern with regard to genetic testing?

A) There are genetic tests for diseases that currently have no treatment.

B) Genetic discrimination is easy to define and prevent.

C) A negative result in a genetic test means a person will never get the disease.

D) Parents and clinicians will use prenatal genome sequencing in a responsible manner.

26) Due to the relatively unregulated environment that genomic information is being collected in, which of the following is not a concern?

A) variability of handling protocols C) variability in the genomes sequenced

26) ______

B) confidentiality of genetic information D) variability in data collection methods

27) Currently, the most common method of vaccination is injection. Modern biotechnology is likely

27) ______

to make injection less common through the development of ________.

A) fusion proteins B) biopharming C) edible vaccines D) gene editing

28) There are several problems associated with the use of new GMOs. One of which is ________.

A) the yields from the genetic modification may not be useful in the field B) the ecological impact is largely unknown C) the ecological impact is well known D) the GMO could prove dangerous for human consumption

28) ______

29) To fight the recent outbreak of Zika virus in the Americas, scientists took advantage of

29) ______

________ to force a gene to be passed on to progeny that resulted in short-lived offspring that did not reach maturity.

A) DNA vaccines B) CRISPR-Cas C) gene drive D) selective breeding

30) The use of ASOs in the process of in vitro fertilization to determine the genetic risk factors present is called ________.

A) RFLP analysis C) next-generation sequencing

30) ______

B) genome scanning D) preimplantation genetic diagnosis

31) Evolving genome sequencing methods continue to be used in ever more time-sensitive

31) ______

situations. Which of the following is an emerging situation in which the CDC is using WGS, NGS, and TGS? A) pathogen identification B) tracking impact of pathogens on host genomes C) isolating pathogens after they have spread D) vaccine generation

32) The incorporation of a heavy metal inducible promoter in front of RFP in the transgenic animal GloFish is an example of what?

A) an in vitro assay for water contamination by heavy metals B) a bioassay for water contamination by heavy metals C) a transgenic fish that glows under UV light when heavy metals are absent D) a transgenic animal sold as a gimmick

32) ______

33) What is the ultimate goal of the Human Genome Project?

A) to rid the human population of genetic disease B) to understand all of the proteins generated in a cell C) to map all the genes in the genome so they can be edited with CRISPR-cas D) to better understand the genes and regulatory elements of the genome

33) ______

34) The incorporation of the lacZ gene into the JCVI-syn1.0 genome was used as an indicator for

34) ______

successful transplantation because ________.

A) the original genome of M. mycoides contained lacZ B) the M. capricolum genome did not include lacZ C) tetracycline resistance is conferred by lacZ D) tetracycline resistance is a selective marker

35) The CJVI has identified approximately 473 genes make up the core set of genes for prokaryotes.

35) ______

What did their findings suggest is the core set of genes in the human genome?

A) about 2000 B) about 500 C) about 20,000 D) about 1000

36) Current DTC genetic tests provide all of the following EXCEPT ________.

A) an overwhelming amount of information regarding an individual's genetic risk factors B) allele-specific information with regard to an individual's genome C) a reliable substitute for a trained healthcare professional D) information regarding risk factors for disease states

36) ______

1) D 2) C 3) B 4) D 5) D 6) A 7) A 8) D 9) C 10) A 11) C 12) C 13) C 14) B 15) The genomes of several hundred to several thousand diseased individuals are subject to individual genome sequencing as well as several thousand of non-diseased individuals. The genomes are then compared to determine if there are patterns or associations between certain genes and the disease state. This does not mean a carrier of the correlated gene will develop the disease, just that there is a risk factor.

16) D 17) Diffuse large B-cell lymphoma patients predominantly fell into two groups. One responded well to chemotherapy while the second group responded poorly. Previously there was no way to know which group the patient fell into before treatment. Gene-expression microarrays demonstrated that there are different gene-expression patterns between the two groups and can be used to spare patients whose cancer would not respond well to chemotherapy and the horrendous side effects of the treatment.

18) D 19) A 20) C 21) A 22) A 23) B 24) A 25) A 26) C 27) C 28) B 29) C 30) D 31) A 32) B 33) D 34) B 35) A 36) C

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Which term refers to the regulatory events that establish a specific pattern of gene activity and 1) _______ developmental fate for a given cell?

A) gradient regulated B) determination C) differentiation D) attenuation E) lysogen

2) Which general genetic process is believed to account for the variety of cellular structures and

2) _______

functions in eukaryotic cells?

A) negative control exclusively B) maternal environmental activities C) variable gene activity D) intron processing E) RNA processing

3) Immediately after fertilization of a Drosophila egg, the zygote nucleus undergoes a series of

3) _______

divisions. Subsequent nuclear migration generates a(n) ________.

A) cleavage nucleus B) syncytium C) zygote D) homeodomain E) maternal effect

4) In what order do the segmentation genes function in Drosophilia?

A) gap, pair-rule, segment-polarity B) segmentational, helical, spherical C) gap, segment-polarity, pair-rule D) transdeterminal, gap, pair-rule E) pair-rule, transdeterminal, gap

4) _______

5) Mutations that eliminate a contiguous region in the Drosophila embryo's segmentation pattern

5) _______

are called ________.

A) compartment genes B) segment genes C) homeodomains D) linkage genes E) gap genes

6) Which of the following is a fundamental characteristic of the Notch pathway?

A) It allows mRNAs to accumulate in the posterior portion of the Drosophila embryo.

B) It directs mRNAs to antisense systems in the posterior portion of all organisms.

C) It works through direct cell-to-cell contact.

D) It works through nuclear signals involving the lac operon.

E) It provides symmetry to plant flowers.

6) _______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

7) Provide an explanation of the differences between differentiation and determination.

7) _____________ Provide examples of each process and indicate how each is involved in development.

8) How does determination relate temporally to differentiation?

8) _____________

9) Describe the difference between a totipotent cell and a pluripotent cell.

9) _____________

10) Provide a brief description of the variable gene activity hypothesis as it relates to

10) ____________

development. What information is often provided in support of this hypothesis?

11) Design an experiment that would allow you to determine if a particular nucleus in a

11) ____________

Drosophila embryo is capable of directing development of an entire new fly.

12) It is often said that development is a two-step process. What two steps are likely to be

12) ____________

referred to here?

13) What kinds of general observations cause one to conclude that development is the

13) ____________

result of variable gene activity?

14) Three investigators–Nüsslein-Volhard, Wieschaus, and Lewis–won the Nobel Prize for

14) ____________

physiology and medicine in 1995 for work they did in 1970 with Drosophila. Briefly describe their findings.

15) Maternal effects are cases of extrachromosomal inheritance in which the genotype of

15) ____________

the mother influences the phenotype of her immediate offspring in a non-Mendelian manner. Provide a rationale for the molecular basis of a maternal effect.

16) Experiments involving nuclear transplantation in amphibians indicate that nuclei

16) ____________

derived from blastula are more likely to support development of complete and normal adults compared with those derived from later stages of development. What do these experiments tell us about the process of development?

17) Which functions earlier in development: maternal-effect genes or zygotic genes?

17) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

18) In Drosophila, which type of genes are controlled by maternal gene products laid down in 18) ______ gradients in the egg?

A) gap genes B) segment polarity genes C) pair-rule genes D) all genes are controlled by maternal gene products

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

19) In most species the expression of Hox genes is colinear with the anterior to posterior 19) ____________ organization of the organism. Describe what this means.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

20) Arabidopsis thaliana has homologous gene clusters to the Hox genes found in Drosophila. What are these master regulatory clusters called?

A) MRCs C) CURLY LEAF genes

20) ______

B) MADS-box proteins D) Hox genes 21) ______

21) Flowers that develop in Arabidopsis originate from concentric rings of cells. What class of gene(s) is responsible for the development of sepals?

A) A and B genes B) A genes C) B and C genes

D) C genes

22) C. elegans is used as a model organism in the study of the Notch signaling pathway. What is the

22) ______

method communication between cells in the Notch signaling pathway?

A) direct cell-to-cell contact through transmembrane proteins B) release of extracellular signals to be detected by neighboring cells C) cells do not communicate using the Notch signaling pathway D) electrical propagation of signals across small gaps

23) ______

23) A gene that specifies the fate of a particular anatomical segment in Drosophila is called a(n) ________.

A) MADS genes C) selector gene

B) silent gene D) determinant genes

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

24) Which class of genes controls the developmental identity of segments along the 24) ____________ anterior—posterior axis?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

25) Mutations in the selector genes sometimes form structures in the wrong segment, transforming 25) ______ the antenna of a fly into a leg, for example. What are such mutations called?

A) homologous mutations B) lethal mutations C) homeotic mutations D) silent mutations

26) Over the course of evolution, humans have obtained four Hox gene clusters due to duplication.

26) ______

The presence of multiple Hox gene clusters suggests what?

A) All four clusters are active and represent the added complexity of vertebrate development.

B) Only two of the clusters are active and represent the added complexity of vertebrate development.

C) Three of the four clusters are silent and have no effect on development.

D) Only one of the clusters is silent since it would result in Drosophila development not vertebrate.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

27) It is presently believed that the asymmetric distribution of substances in the egg, 27) ____________ positioned by the mother, is responsible for establishing the determined state. Which general term describes such molecular positioning?

28) What is the significance of the homeodomain?

28) ____________

29) From a human developmental standpoint, what is the significance of Hox genes?

29) ____________

30) The bicoid gene of Drosophila generates embryos with two posterior regions. What is the

30) ____________

likely aspect of embryonic development that the bicoid gene probably controls?

31) Give a brief definition of a homeobox.

31) ____________

32) During development, many genes act in such a way as to decrease the number of

32) ____________

alternative developmental pathways that a cell can follow. Usually there are two alternative developmental paths for a cell to follow. What is the term given to genes that act in this fashion?

33) What significant conclusion has the classic work on the eyeless and Pax6 genes provided

33) ____________

in terms of developmental mechanisms?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

34) The process whereby a cell's eventual developmental fate is set is called ________.

34) ______ A) differentiation B) determination C) embryogenisis D) notching 35) The process whereby a cell's determined state is expressed is called ________.

A) differentiation B) determination C) notching D) embryogenisis

35) ______

36) A mutation seen in Drosophila is found to cause antennae to grow on the abdomen of the flies.

36) ______

What type of mutation is this likely to represent?

A) evolutionary mutation C) lethal mutation

B) silent mutation D) homeotic mutation

37) Which of the following is not a set of master regulatory genes that control homeobox genes during development?

A) Hox

B) Polycomb

37) ______

C) CURLY LEAF

38) After fertilization of an egg the totipotent cell divides and the cells begin to specialize. These

38) ______

30—40 cells are called ________ and are pluripotent.

A) T cells B) germ line cells embryonic stem cells C) D) somatic cells

39) A homeobox gene is one that produces a ________.

A) transcription factor that strips methylation from the entire genome B) maternal transcription factors C) repetitive nucleotide sequence such as VNTR D) 60 amino acid DNA binding domain

39) ______

40) Development of the anchor cell in the vulva in the nematode C. elegans is the result of ________.

A) stochastically increased production of the LIN-12 protein B) specific upregulation of the LIN-12 protein C) specific upregulation of the Delta protein D) stochastically increased production of Delta protein

40) ______

41) Caenorhabditis elegans is extremely useful as an experimental model system due to all of the

41) ______

following EXCEPT ________.

A) its genetics are well known B) adults contain a small, fixed number of cells

C) its genome has been sequenced D) it is highly variable in size and shape making it good for evo-devo studies

1) B 2) C 3) B 4) A 5) E 6) C 7) Determination is the early commitment of a cell to an eventual developmental fate. Differentiation is the set of functional and structural changes associated with the expression of that developmental fate. When nuclei of the developing Drosophila embryo reach the blastoderm stage, they become determined. Differentiation of the cells in Drosophila occurs during metamorphosis. Development, therefore, probably depends first on the determination of cells, then on the differentiation of cells.

8) Determination occurs when a cell's developmental fate is set, whereas differentiation is the expression of that determined state. Determination occurs before differentiation.

9) Totipotent cells are capable of becoming any type of cell in the mature organism. Pluripotent cells are capable of becoming any cell in the organism with the exception of placental and embryonic cell types.

10) Since all cells apparently have the same genetic information, yet may differ structurally and functionally, the variable gene activity hypothesis suggests that differential gene transcription (genetic regulation) accounts for such cellular diversity.

11) Experiments in support of such genomic equivalence include the following: the observation that chromosome number and structure do not consistently change in different cells of an organism, nuclear transplantation in amphibians, and the presence of genes but no gene products in some tissues (hemoglobin, for example). For the Drosophila experiment, one could do nuclear transplantation similar to the classic experiments in amphibians and recent experiments in mammals or transplant a cell from embryos of one genotype to the posterior end of the early embryos of another genotype. The transplanted cells would be reprogrammed into germ cells by the posterior P granules. The transplant can be detected in the next generation by the recognizable different phenotypes due to different genotypes of the donor and recipient.

12) determination and differentiation 13) Individual cells of multicellular organisms produce different gene products, and each apparently has an equal genomic complement.

14) They identified and characterized a number of maternal-effect and zygotic genes that control pattern formation in Drosophila.

15) During development of the egg, females provide numerous nutritional and informational substances, which direct and support early embryonic development. These substances are often in the form of transcription factors, receptors, mRNA, and proteins, although other substances are also likely (substrates and products).

16) Development occurs as a series of cascades, with early genes influencing late genes, at times with stability. Such progressive determination, if stable, may be irreversible and fail to support development of an entire organism from a single cell. A number of epigenetic factors such as chromatin remodeling and DNA methylation are also likely to come into play.

17) maternal-effect genes

18) A 19) Hox genes expressed at the anterior of the organism are located at the 3′ end of the gene cluster. Those expressed in the posterior are transcribed form the 5′ end of the cluster.

20) B 21) B 22) A 23) C 24) Homeotic genes 25) C 26) A 27) maternally constructed molecular gradients 28) The homeodomain is a highly conserved protein of 60 amino acids found in a variety of organisms, which, in

conju nction with other factors, is thought to play a role in DNA binding and transcriptional activation.

29) Hox genes are highly conserved among all organisms with bilateral symmetry. The arrangement and expression pattern of Hox genes establish anterior/posterior development in mammals. Some limb malformations in humans are caused by mutations in Hox genes.

30) Anterior—posterior polarity 31) a highly conserved genetic element that encodes a 60 amino acid sequence with DNA-binding characteristics 32) binary switch genes 33) Some vertebrate versions of binary switch genes are capable of triggering developmentally significant processes across broad evolutionary distances. Such genes are therefore related evolutionarily.

34) B 35) A 36) D 37) A 38) C 39) D 40) D 41) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Driver mutations provide a growth advantage to a tumor cell. Which type of mutation is 1) _______ known to accumulate in cancer cells but has no direct contribution to the cancer phenotype?

A) insignificant mutations B) indirect mutations C) carrier mutations D) alteration mutations E) passenger mutations

2) Which of the following general mechanisms appear to be involved in the formation of cancer

2) _______

cells?

A) transdetermination, mutation, allosteric interactions B) inversions, operon formation, methylation C) RNA failure, DNA phosphorylation, phosphorylation of adenyl cyclase D) genomic instability, DNA repair failure, chromatin modifications E) suppression, tabulation, projection 3) What is the name of the protein that combines with cyclins to exert local control of the cell

3) _______

cycle?

A) hexokinase B) ATPase C) cyclin-dependent kinase D) phosphatase E) integrase

4) Which of the following proteins function as a cell-cycle regulator and transcription factor that

4) _______

can result in cell death (apoptosis) to a damaged cell?

A) phosphokinase B) cyclin C) p34 D) p102 E) p53

5) Mutations in the ras gene family induce normally quiescent cells to proceed into the replication

5) _______

cycle. This converts the ras gene from a ________ gene to a ________ gene.

A) tumor suppressor; proto-oncogene B) mutant; oncogene C) proto-oncogene; oncogene D) pseudooncogene; proto-oncogene E) oncogene; proto-oncogene

6) Mutant versions of genes that are normally involved in promoting the development of cancer are known as ________.

A) malignant genes B) tumor suppressors C) proto-oncogenes D) attenuators

6) _______

E) oncogenes 7) In sporadic cases of retinoblastoma, only two gene mutations are thought to be necessary in the

7) _______

same cell for a tumor to develop. This happens when an organism inherits a mutant allele and a wild-type allele forms the parents. When the wild-type allele is mutated, resulting in tumorigenesis, this process is called, ________.

A) loss of heterozygosity B) recombination C) attenuation D) metastasizing E) gain of heterozygosity

8) What is the name of the protein that appears to regulate the entry of cells into an S phase? This

8) _______

protein is also known as the "guardian of the genome."

A) phosphokinase B) p102 C) cyclin D) p34 E) p53

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

9) Provide a definition of cancer at the genetic level.

9) _____________ 10) Briefly describe what a passenger mutation is with respect to cancer genetics.

10) ____________

11) Chronic myelogenous leukemia appears to be associated with a chromosomal

11) ____________

rearrangement. How is a chromosomal rearrangement responsible for this disease?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

12) Signal transduction is best described as ________.

12) ______ A) communication between nuclei of two organisms B) transmission of signals external to the cell to the nucleus C) transmission of signals from cancer cells to normal cells D) communication between cells through physical interaction SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

13) Why do cancer researchers study molecular events associated with mitosis?

13) ____________ 14) What is the significance of CDK/cyclin interactions with respect to cancer cell

14) ____________

proliferation?

15) A loss-of-function mutation in BAX proteins could eliminate apoptotic response in cell.

15) ____________

Describe why this type of mutation is a passenger mutation and not a driver mutation.

16) Describe why cancer cells are more susceptible to chemotherapies and radiation

16) ____________

therapies than normal cells.

17) Which three stages or transitions in the cell cycle seem to serve as points of control (checkpoints)?

17) ____________

18) Describe how tumor-suppressor genes keep cells in check.

18) ____________

19) Name two of the classes of proteins that combine to directly control progression

19) ____________

through the cell cycle.

20) Describe the general relationship that may exist between mutations and cancer.

20) ____________

21) Chronic myelogenous leukemia is a cancer found in white blood cells. What is its

21) ____________

supposed genetic basis of this disease?

22) Describe the normal function of a tumor-suppressor gene.

22) ____________

23) Describe the cellular and molecular function of the ras gene family and the

23) ____________

consequences of mutations in ras.

24) Describe three genetic mechanisms whereby proto-oncogenes can become

24) ____________

overexpressed.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

25) What is the name of a normal gene that serves to promote cellular division?

25) ______ oncogene proto-oncogene A) B) C) cancer gene D) post-oncogene 26) Which category of genetic changes does not lead to the formation of oncogenes?

A) translocations B) correct DNA repair C) copy number changes D) point mutations

26) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

27) Describe the molecular nature of mutation, as related to cancer, in a ras gene.

27) ____________ 28) Briefly describe the following types of genes: tumor-suppressor gene, proto-oncogene, and

28) ____________

oncogene.

29) Much has been written about p53 in terms of cancer biology. What is p53, and what is

29) ____________

its significance?

30) What are two properties that various types of cancer cells share?

30) ____________

31) Most p53 mutations that result in cancer are a result of loss of function in p53. Describe

31) ____________

one method through which a gain-of-function mutation in p53 could cause cancer.

32) Most cancers arise due to mutations in somatic cells, if someone has a predisposition to

32) ____________

cancer, what genetic circumstance likely exists?

33) In what way can loss of heterozygosity lead to cancer?

33) ____________

34) The genetic difference between familial retinoblastoma and sporadic retinoblastoma

34) ____________

appears to be based on those with the familial form starting out being ________, whereas those with the sporadic form start out being ________.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

35) Most cancer-causing animal viruses are RNA viruses called ________.

35) ______ A) retroviruses B) DNA viruses C) classic viruses D) neoviruses SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

36) In what way might a virus contribute to cancer formation?

36) ____________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

37) All of these are known to cause cancer EXCEPT ________.

37) ______ A) chronic infections B) some viruses DNA repair C) D) radiation SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

38) Provide a simple definition of a carcinogen.

38) ____________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

39) As more is learned about cancer, it has become clear that cancer, with few exceptions, ________. 39) ______ A) has no genetic basis B) is only dependent on the inherited genetics C) is 100% dependent on inherited genetics D) is a result of genetics and environmental factors 40) Many of the known cancers are a result of ________.

A) the genetic instability of the human genome B) the genetic stability of the human genome C) the non-carcinogenic nature of our environment D) exercising regularly

40) ______

41) Any agent that causes damage to DNA is a potential ________.

A) proto-oncogene B) pollutant carcinogen C) D) oncogene

41) ______

42) All of the following are checkpoints in the cell cycle EXCEPT ________.

A) M B) G1/S C) G2/M

42) ______ D) M/G1

43) The gene p53 is called the ________ because it corrects mutations in the spindle apparatus before nondisjunction can occur.

A) guardian of the genome C) M phase checkpoint monitor

43) ______

B) tumor-suppressor monitor D) S phase checkpoint monitor

44) A tumor-suppressor gene normally functions to ________.

A) suppress cell division B) induce cell division C) create mutations forming cancer cells D) repair cancer cells

44) ______

45) Which virus type results in the immediate onset of cancer phenotype upon infection of a host?

45) ______

A) adenovirus C) acute transforming retrovirus

B) retrovirus D) lentivirus

46) When considered as a root cause for cancer, which of the following is linked to at least 17 types of human cancer?

A) smoking C) not exercising regularly

46) ______

B) eating a high-fat diet D) eating a low-fat diet

47) Examined cancer cells from the lungs of smokers demonstrate which of the following?

A) unregulated methylation patterns B) the occurrence of tumor-suppressor mutations is less in the lung than the throat C) mutation rates that are similar to those in a smoker's heart D) normal mutation rates compared to non-smokers

47) ______

48) A retrovirus uses ________ to make a DNA copy of RNA. A) reverse transcriptase B) ras proteins C) CDKs D) cyclins

48) ______

1) E 2) D 3) C 4) E 5) C 6) E 7) A 8) E 9) Cancer is a genetic disorder that can result from mutation of a given gene or genes, which may produce a defective gene product or a change in the timing or amount of gene expression. Such mutations alter cell-cycle control. Some cancers show familial distributions.

10) A passenger mutation is a genetic alteration that does not result in a tumor. It is a mutation that confers a selective advantage to tumorigenesis in the presence of an oncogene.

11) Joining of chromosomes 9 and 22 through translocation generates a hybrid gene bcr/c-abl that produces a protein that is inappropriately active and causes the disease.

12) B 13) While mitosis is a basic process related to genetic and general biological studies, it is also a significant event in the cell cycle. The cell cycle is regulated by a variety of gene products, which, when altered by mutation, may lead to cancer.

14) Many CDK/cyclin interactions serve as checkpoints for progression through the cell cycle. In cancerous cells mutations either CDK or its partner cyclin could deregulate key checkpoints resulting in cancer cell proliferation.

15) The loss of function of the apoptotic genes are a passenger mutation as they do not contribute to tumorigenesis but confer a selective advantage by eliminating the apoptotic defense mechanism.

16) Cancer cells suffer from mutations that affect DNA repair enzymes and are constantly proliferating resulting in a much higher mutation accumulation rate that could lead to apoptotic response or necrosis. Normal cells are nonproliferating and have functional DNA repair mechanisms that prevent their apoptotic response.

17) G1/S, G2/M, M 18) Tumor-suppressor genes generate gene products that regulate cell cycle checkpoints and may initiate apoptosis.

When these genes suffer mutations their ability to regulate cell cycle and apoptosis is lost resulting in tumrigenesis.

19) CDK and cyclins 20) Control of the cell cycle is dependent on a variety of gene-produced proteins such as kinases and cyclins as well as other related factors. Mutations in genes that encode these proteins may disrupt normal cell-cycle control. The G1 checkpoint is altered in some forms of cancer, and mutant cyclins have been shown to be related to a gene product that is overexpressed in some forms of leukemia. Nonmutant genes often suppress the formation of cancer by exerting control over the cell cycle. When mutated, such control may be lost.

21) CML is the result of a specific translocation between chromosome 9 and 22. The C-ABL gene from chromosome 9 is translocated next to the BCR gene on chromosome 22. This results in a fusion protein being expressed. The new chromosomal construct is called the Philadelphia chromosome.

22) A tumor-suppressor gene is a gene whose normal function is to suppress cell division. When mutant, cell division control is lost and a cancer may form.

23) The ras gene family encodes a protein that is involved with signal transduction in the cell membrane. Point mutations may cause changes in function that promote abnormal signaling, thus stimulating uncontrolled cell growth.

24) Mutations can occur which cause an enhancement of the promoter or other upstream regulatory signals.

25) B 26) B 27) The ras gene family encodes a protein of 189 amino acids, which is involved with signal transduction in the cell membrane. Point mutations may cause changes in function to allow signals to enter the cell abnormally, thus stimulating uncontrolled cell growth.

28) Tumor-suppressor genes normally function to inactivate or repress cell division. Proto-oncogenes normally

functi on to promote cell division, whereas oncogenes are mutant forms of proto-oncogenes.

29) Mutations in the p53 gene are important in the development of a number of cancers. It is a tumor-suppressor gene that normally functions to control the transition from late G1 to S phase. The product of p53 has DNA-binding properties.

30) uncontrolled proliferation and accumulation of somatic mutations 31) The gain-of-function mutation in p53 could result in the overproduction of chromatin-remodeling enzymes. The improper expression of these enzymes would likely result in misexpression of other genes and could lead to tumorigenesis.

32) a germ-line mutation in a proto-oncogene or tumor suppressor, which is inherited 33) Loss of heterozygosity occurs when a cancer-producing gene that exists in the heterozygous state becomes exposed through deletion, mutation, recombination, or chromosomal aberration. Such a gene now is either homozygous or hemizygous.

34) heterozygous for the retinoblastoma gene; homozygous normal

35) A 36) Proviral DNA may integrate near a proto-oncogene and alter its expression, thus generating an oncogene, or it may bring in an oncogene during an infection. In either case, the cell cycle can be upregulated by a virus.

37) C 38) a cancer-causing agent 39) D 40) A 41) C 42) D 43) A 44) A 45) C 46) A 47) A 48) A

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Meristic traits are characterized by having phenotypes that are described by ________.

1) _______ A) irrational numbers B) imaginary numbers C) prime numbers D) complex numbers E) whole numbers 2) _______

2) Quantitative inheritance involves the interaction of a number of gene loci. The pattern of genetic transmission typical of quantitative inheritance is ________.

A) continuous variation of phenotypic expression B) typical of Mendelian inheritance C) usually a pattern that clearly reflects dominance and recessiveness D) discontinuous distributions such as 3:1 E) a 9:3:3:1 ratio

3) Assume that a cross is made between tall and dwarf tobacco plants. The F 1 generation showed

3) _______

intermediate height, while the F2 generation showed a distribution of height ranging from tall to dwarf, like the original parents, and many heights between the extremes. These data are consistent with which one of the following modes of inheritance?

A) hemizygosity B) incomplete dominance C) multiple-factor inheritance D) alternation of generations E) codominance

4) Bell-shaped distributions produced by plotting results of F2 and F3 crosses are typical of which

4) _______

type of inheritance?

A) multiple-factor inheritance B) hemizygosity C) alternation of generations D) incomplete dominance E) codominance

5) When multiple genes contribute to the expression of a phenotype they are called ________.

A) nonadditive alleles B) additive alleles C) heterozygous alleles D) homozygous alleles E) concordant alleles

5) _______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

6) Continuous inheritance is often related to the term quantitative inheritance. Why? 6) _____________ 7) The 9:3:3:1 ratio is typical of a dihybrid cross in which complete dominance and independent assortment occur. What is the dihybrid ratio with independent assortment

of lygenes? po

7)

_____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

8) How many gene pairs are involved in generating a typical 1:4:6:4:1 ratio?

8) _______ 4 6 2 3 A) B) C) D) 9) When a trait is polygenic, but has a small number of discrete classes, it is said to be a(n)

9) _______

________ trait.

A) qualitative B) continuous C) meristic D) oncogenic E) threshold

10) In the early part of the twentieth century, Nilsson-Ehle and others described experiments

10) ______

showing that multiple loci may be involved in the inheritance of certain traits. Such patterns are often called ________.

A) threshold traits B) indeterminate traits C) continuous traits D) polygenic traits

11) Assume that you are studying a trait determined by a number of polygenes. If there are seven phenotypic categories, how many genes are probably involved?

A) 4 B) 2 C) 3

D) 7

12) Polygenic traits often demonstrate a ________ distribution when the phenotypes from a proper sample are represented in a histogram.

A) binomial B) normal

C) uniform

11) ______

12) ______

D) Poisson

13) If the proportion of F2 individuals resembling either of the two most extreme phenotypes (the

13) ______

parental phenotypes) can be determined, what formula can be applied to determine the number of gene pairs involved?

A) =

B) s =

where n is the number of gene pairs) where s is the number of gene pairs)

C) 2n + 1 (where n is the number of gene pairs) D) 1/4n (where n is the number of gene pairs) 14) What formula can be used to determine the number of categories (phenotypes) possible in the

14) ______

F2 results of a polygenic system?

A) s =

where s is the number of gene pairs) 2n + 1 (where n is the number of gene pairs) B) C) 1/4n (where n is the number of gene pairs)

D) =

where n is the number of gene pairs

15) Assume that in the F2 of a series of crosses, 1/64 of the offspring resemble one of the parents (P).

How many gene pairs are involved in producing these results?

A) 3 B) 64 C) 16 D) 6

E) 32

15) ______

16) Assume that four polygenic gene pairs are involved in determining phenotypes of F 2. How many phenotypic classes are expected?

A) 9 B) 4

C) 8

D) 16

17) What is the term given to a random subset of individuals who are selected for measurement in a particular study?

A) representatives C) sample

17) ______

B) placebos D) controls 18) ______

18) Which of the following is not a statistical value often used to represent a sample when evaluating QTLs? A) mode C) mean

16) ______

B) variance D) standard deviation

19) Given the following numbers, calculate the mean: 10, 12, 14, 16, 18.

A) 18 B) 13 C) 14

19) ______ D) 10

20) s2 = S (Xi − X)2/n − 1 is the formula for calculating which statistical value?

A) covariance B) standard deviation C) mean D) variance

20) ______

21) To estimate how much the means of a variety of like samples drawn from the same population

21) ______

might vary, what statistic is often used?

A) standard error of the mean C) relative error of the mean

B) variance of the mean D) standard deviation of the mean

22) Which statistical value is used to represent the linkage of the increase in one measurement to the increase in a second measurement?

A) standard deviation C) variance

23) Identical twins are ________.

A) hemizygotic B) dizygotic

22) ______

B) correlation coefficient D) covariance 23) ______ C) homozygotic

D) monozygotic

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

24) Define the term broad-sense heritability (H2). What is implied by a relatively high value 24) ____________ of H2? Express aspects of broad-sense heritability in equation form.

25) If one is attempting to determine the influence of genes or the environment on

25) ____________

phenotypic variation, inbred strains with individuals of a relatively homogeneous or constant genetic background are often used. Variation observed between different inbred strains reared in a constant or homogeneous environment would likely be caused by genetic factors. What would be the source of variation observed among members of the same inbred strain reared under various environmental conditions?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

26) What is the formal expression used to examine the relative importance of genetic versus 26) ______ environmental factors?

A) genotype-by-environment interaction variance VP = VG + VE + VG*E B) correlation coefficient s = C) narrow-sense heritability index (h2) = VA/VP D) broad-sense heritability index (H2) = VG/VP SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

27) We often refer to the host of genetic factors in the genome that have an influence on a 27) ____________ particular gene's expression as its genetic background. What influence does genetic background have over the phenotype of the organism?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

28) Which of the following is not a component of phenotypic variance?

28) ______ environmental variance A) B) the interaction between genetics and environment C) the covariance D) genetic variance SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

29) Interpret the meaning of an H2 (broad-sense heritability) value that approaches 1.0.

29) ____________ 30) Interpret the meaning of an H2 (broad-sense heritability) value that approaches 0.0.

30) ____________

31) Provide a brief definition of the term interactive variance.

31) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

32) Which statement best describes h2 (narrow-sense heritability)?

32) ______ A) The proportion of phenotypic variance due to additive genotypic variance alone.

B) The genotypic variance due to additive action of various QTLs. C) It measures the contribution genotypic variance to total phenotypic variance.

D) The deviation from additive components when they behave epistatically.

33) Which value of narrow-sense heritability (h2) indicates a selection will have a significant impact in altering the initial population?

A) 99 B) 0.20

C) 20

33) ______

D) 0.99

34) What is the name of the process of selecting a specific group of organisms from an initially

34) ______

heterogeneous population for future breeding purposes?

A) natural selection B) diversity selection C) artificial selection D) exclusive selection

35) Which of the following mammalian traits exhibits a relatively low h2 value?

A) milk yield in cattle B) litter size in mice C) tail length in mice D) birth weight in cattle

35) ______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

36) What is meant by the term heritability? Describe the components of heritability and

36) ____________

provide a brief explanation of each. Of what interest is heritability to animal and plant breeders?

37) As used in twin studies in mammals, distinguish between the terms concordant and

37) ____________

discordant.

38) Describe the value of using twins in the study of questions relating to the relative

38) ____________

impact of heredity versus environment.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

39) Which human trait would be expected to have high concordance?

39) ______ weight hair length A) B) C) eye color D) contracting measles SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

40) Individuals with the same genetic background and a high degree of homozygosity are 40) ____________ said to be isogenic. Of what value are isogenic strains in genetic studies?

41) How would the use of a large series of monozygotic and dizygotic twins enhance

41) ____________

studies on the genetic basis of human behavior?

42) Typically, one thinks of identical (MZ) twins being genetically identical. However,

42) ____________

genomic differences do exist between MZ twins by epigenetic processes. What are epigenetic processes?

43) What are QTLs?

43) ____________

44) In the analysis of quantitative traits, positions on chromosomes called quantitative trait

44) ____________

loci (QTLs) are often discussed. In the same context, restriction fragment length polymorphisms (RFLPs) are also discussed. What is the relationship between QTLs and RFLPs?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

45) A "marker" in a genetic sense usually represents a site along a chromosome where a specific 45) ______ nucleotide sequence exists. What specific phrase is used when such markers are identified by restriction endonucleases and a particular set of DNA fragments is generated?

A) RFLP B) expression QTL C) restriction site D) QTL

46) Expression QTL mapping allows researchers to characterize ________.

A) loci that encode phenotypes B) loci that control gene expression C) loci that modify the rate of protein translation D) loci that have high mutating rates

46) ______

47) Polygenes are involved in determining ________.

A) traits that are strictly determined by environmental factors B) traits that have a distinct all or none phenotype

47) ______

C) traits that are strictly determined by genetic variance D) continuously varying traits 48) Which theory suggests that many factors or genes contribute to the phenotype in a cumulative or quantitative manner?

A) heritability theory C) multiple factor hypothesis

B) threshold gene theory D) additive gene theory

49) ________ alleles are those that are not epistatic over nonallelic genes that influence the same phenotypic characteristic.

A) Discontinuous

B) Additive

C) Nonadditive

51) ______

B) skin color D) general body structure

52) Concordance refers to the frequency with which members of a twin pair express a ________ trait.

A) similar

50) ______

B) genetic factors D) epigenetic regulation

51) Which trait is probably not caused primarily by genes that behave codominantly or epistatically?

A) eye color C) height

49) ______

D) Threshold

50) Heritability is a measure of the degree to which the phenotypic variation of a given trait is due to ________.

A) environmental factors C) somatic mutations

48) ______

B) different

C) mutated

D) unrelated

52) ______

1) E 2) A 3) C 4) A 5) B 6) In continuous inheritance, we consider each involved locus as having a quantitative input on the production of a single characteristic of the phenotype. In addition, although it may not always be the case, we would consider each gene product to be qualitatively similar.

7) 1:4:6:4:1

8) C 9) E 10) D 11) C 12) B 13) D 14) B 15) A 16) A 17) C 18) A 19) C 20) D 21) A 22) B 23) D 24) Broad-sense heritability (H2) refers to the degree to which phenotypic variation is due to genetic factors. A very high value of H2 indicates that the environment had a relatively low impact on phenotypic variation. VP = VE + VG + VGE. 25) Nongenetic factors generally categorized as "environmental" components

26) D 27) Genetic background reflects all of the epigenetic influences exerted on a single or a set of genes that directly impact the observed phenotype.

28) C 29) Almost all the phenotypic variation is determined by genotype differences and environmental factors have little to no effect.

30) Almost all the phenotypic variation is determined by the environment.

31) Interactive variance occurs when two or more loci behave epistatically.

32) A 33) D 34) C 35) B 36) Heritability refers to the degree to which observed phenotypic variation for a given trait is inherited. Components include environmental variance, genetic variance, and interaction between the two. From information on heritability, breeders can determine the degree of improvement to expect from selective breeding.

37) Concordant refers to a given trait expressed similarly between twins; discordant refers to a case in which one member of the twin pair expresses the trait but the other does not.

38) Monozygotic twins are derived from the splitting of a single fertilized egg and are therefore of identical genetic makeup. When such twins are raised in the same versus different settings, an estimate of relative hereditary and environmental influences can often be made.

39) C

40) Because the genetic background is the same (or at least very similar), phenotypic variation must be due to nongenetic factors.

41) Monozygotic twins are genetically identical, and when reared under the same versus different environments, one can estimate the degree to which variation in behavior is determined by heredity. Dizygotic twins are genetically different but by having the same intrauterine and developing environment (if being reared in the same household), one can again estimate the influence of heredity on behavioral traits.

42) Epigenetic processes involve the chemical modification of DNA and associated histones.

43) QTLs are quantitative trait loci and refer to genes controlling the expression of quantitative traits.

44) In many organisms, traditional genetic markers are not available for the mapping of regions of chromosomes containing genes responsible for determining quantitative trait loci (QTLs). DNA polymorphisms generate molecular markers RFLPs, which can serve as reference points in mapping QTLs.

45) A 46) B 47) D 48) C 49) B 50) B 51) A 52) A

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) What is the term given to a group of individuals belonging to the same species that live in a 1) _______ defined geographic area that actually or potentially interbreed?

A) hybrid vigor B) population C) cytogenetics D) consanguinity E) genetics

2) What term is given to the total genetic information carried by all members of a population?

A) genome B) gene pool C) race D) breeding unit E) chromosome complement

2) _______

3) A number of mechanisms operate to maintain genetic diversity in a population. Why is such

3) _______

diversity favored?

A) Diversity leads to inbreeding advantages.

B) Greater genetic diversity increases the chances of haploidy.

C) Genetic diversity helps populations avoid diploidy.

D) Genetic diversity may better adapt a population to inevitable changes in the environment.

E) Homozygosity is an evolutionary advantage.

4) In a population of 100 individuals, 49% are of the NN blood type. What percentage is expected

4) _______

to be MN assuming Hardy-Weinberg equilibrium conditions?

A) 9% B) 42% C) 21% D) 51% E) There is insufficient information to answer this question.

5) Albinism is an autosomal recessive trait in humans. Assume that there are 100 albinos (aa) in a

5) _______

population of 1 million. How many individuals would be expected to be homozygous normal (AA) under equilibrium conditions?

A) 999,900 B) 980,100 C) 10,000 D) 19,800 E) 100

6) Which method is often used to analyze proteins and nucleic acids by physical separation when

6) _______

estimating genetic variation in populations?

A) centrifugation B) fluorometry C) in situ hybridization D) absorption spectrophotometry E) electrophoresis

7) In small isolated populations, gene frequencies can fluctuate considerably. The term that applies to this circumstance is ________.

7) _______

A) allelic separation B) stabilizing selection C) genetic isolation D) natural selection E) genetic drift 8) Which general term is used to group various biological and behavioral properties of organisms

8) _______

that act to prevent or reduce interbreeding?

A) phyletic evolution B) allopatric speciation C) inbreeding D) reproductive isolating mechanisms E) genetic divergence

9) _______

9) Assume that a trait is caused by the homozygous state of a gene that is recessive and autosomal. Nine percent of the individuals in a given population express the phenotype caused by this gene. What percentage of the individuals would be heterozygous for the gene? Assume that the population is in Hardy-Weinberg equilibrium.

A) 9% B) 58% C) 42% D) 91%

10) Which assumption pertains to a population in a Hardy-Weinberg equilibrium?

A) a small population B) a selectively mating population C) no migration, mutation or, genetic drift D) a selective advantage of one genotype

10) ______

11) Assume that in a Hardy-Weinberg population, 9% of the individuals are of the homozygous

11) ______

recessive phenotype. What percentage are homozygous dominant?

A) 49% B) 9% C) 91%

D) 51% 12) ______

12) In a population that meets the Hardy-Weinberg equilibrium assumptions, 81% of the individuals are homozygous for a recessive allele. What percentage of the individuals would be expected to be heterozygous for this locus in the next generation?

A) 72% B) 81% C) 19% D) 18%

13) In a population of cattle, the following color distribution was noted: 36% red (RR), 48% roan

13) ______

(Rr), and 16% white (rr). This population is in a Hardy-Weinberg equilibrium. What will be the distribution of genotypes in the next generation if the Hardy-Weinberg assumptions are met?

A) 30% red; 50% roan; 20% white B) 40% red; 40% roan; 20% white C) 36% red; 48% roan; 16% white D) 30% red; 60% roan; 10% white

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

14) In a population of 10,000 individuals, where 3600 are MM, 1600 are Mm, and 4800 are 14) ____________ mm, what are the frequencies of the M alleles and the m alleles?

15) What is meant by the equation p + q = 1.0?

15) ____________

16) What does the variable 2pq represent?

16) ____________

17) Assuming that p = 0.3 for a population in Hardy-Weinberg equilibrium, what would be

17) ____________

the expected frequency of heterozygotes for the involved allelic pair?

18) Give a brief definition of the term genetic equilibrium.

18) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

19) A certain form of albinism in humans is recessive and autosomal. Assume that 1% of the 19) ______ individuals in a given population are albino. Assuming that the population is in Hardy-Weinberg equilibrium, what percentage of the individuals in this population is expected to be heterozygous?

A) 9% B) 99% C) 18% D) 82%

20) Which of the following does not change gene frequencies in populations?

A) selection B) diet C) migration

20) ______ D) mutation

21) Which factor contributes to the phenomenon of natural selection?

A) genetic homogeneity in a population B) lack of competition in mating C) competition for survival D) underpopulation

21) ______

22) Selection that favors the middle phenotype and selects against the extreme phenotypes is said

22) ______

to be ________.

A) stabilizing selection C) directional selection

B) disruptive selection D) diselection

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

23) One of the Hardy-Weinberg assumptions states that all genotypes in the population are 23) ____________ free of selective advantage. What influence might a selective advantage of a genotype have on a Hardy-Weinberg equilibrium?

24) Mutation and migration introduce new alleles into populations. What is the most likely

24) ____________

principal force that will shift allelic frequencies within large populations?

25) Which term is given to the measure of the proportion of offspring that a particular

25) ____________

phenotype will contribute to the next generation?

26) Briefly describe how the founder effect can impact the allelic frequencies in a

26) ____________

population.

27) Which would change allele frequencies more quickly: selection against a dominant

27) ____________

allele or selection against a recessive allele?

28) Which natural factors affect changes in genetic variation?

28) ____________

29) Suppose that a given gene undergoes a mutation to a dominant allele such that 2 out of

29) ____________

100,000 offspring exhibit the new mutant phenotype. Assuming that these offspring are heterozygous, what is the mutation rate for the gene?

30) Migration occurs when individuals move between populations. Considering a single

30) ____________

pair of alleles, A and a, what formula is used to indicate the new frequency of A in one generation of migration?

31) One of the Hardy-Weinberg assumptions states that the population is infinitely large.

What influence might a small population size have on a Hardy-Weinberg equilibrium?

31) ____________

32) What are the genetic consequences of inbreeding?

32) ____________

33) In zoo animals, inbreeding often occurs because of a lack of a sufficient pool of

33) ____________

breeding individuals. Under such conditions, what two characteristics are often exhibited among inbred organisms?

34) Two species that have experienced several thousand years of isolation from one

34) ____________

another are now incapable of producing viable offspring despite mating efforts. What type of reproductive isolating mechanism developed between the two species?

35) Provide a general definition for the term speciation.

35) ____________

36) What single event is probably common to all occurrences of speciation?

36) ____________

37) Define the term fitness.

37) ____________

38) Present a rationale for using DNA sequence polymorphisms as an index of genetic

38) ____________

diversity.

39) Why is mitochondrial DNA often used in construction of phylogenetic trees?

39) ____________

40) What type of evolutionary information can be gained by examining the DNA sequence

40) ____________

of a gene for a protein such as cytochrome c?

41) Cytochrome c is a respiratory pigment found in the mitochondria of eukaryotes.

41) ____________

Compared with some other proteins, it has changed very slowly over long periods of time. Why?

42) What are phylogenetic trees?

42) ____________

43) Would one expect a linear relationship between DNA sequence divergence and

43) ____________

phylogenetic distance? Why or why not?

44) What information have the results of mitochondrial DNA analysis offered concerning

44) ____________

the phylogenetic relationships between Neanderthals and modern humans?

45) In the evolutionary sense, what is meant by the term molecular clock?

45) ____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

46) In the case of complete dominance in a population in equilibrium, we cannot tell which 46) ______ individuals are homozygous dominants and which are heterozygous, what information is needed to determine the frequency of homozygous dominant and heterozygous genotypes?

A) the mutation rate in the population B) the frequency of heterozygous recessive genotype C) the size of the sample population D) the frequency of homozygous recessive genotype

47) Given an inheritance pattern of incomplete dominance and 81 flowers that are red (R1R1), 18 flowers that are pink (R1R2), and 1 flower that is white (R2R2), what is the frequency of the R1 allele?

47) ______

A) 0.2

B) 0.1

C) 0.9

D) 0.8

48) For a given locus, in a population with two alternative alleles, the allele frequencies p + q = ________.

A) 100

B) 1.0

C) 0

48) ______

D) p × q

49) If a gene has three alleles in a population, their frequencies must add up to ________.

A) 1.5 B) 1.0 C) 0 D) 3.0

49) ______

50) Directional selection generates a phenotypic shift ________.

A) toward both extremes of the phenotype B) toward the mean of the extremes of the phenotype C) away from either extreme of the phenotype D) toward an extreme of the phenotype

50) ______

51) Natural selection occurs when there is nonrandom elimination of genotypes from a population

51) ______

due to ________.

A) differences in viability or reproductive success B) similarities in viability or reproductive success C) decreased predation D) differences in reproductive isolation mechanisms

52) What is the differential reproduction of genotypes, resulting from their variable fitness?

A) genetic drift B) evolution C) discrimination D) selection

52) ______

53) What is regarded as a strong evolutionary mechanism for changing allelic frequencies?

A) selection B) mutations C) recombination D) migration

53) ______

54) Genetic drift is primarily associated with what size breeding populations?

A) very large B) mid-sized C) very small D) Genetic drift has the same effect on all population sizes.

54) ______

55) Genetic drift arises from all the following EXCEPT ________.

A) mutations B) a genetic bottleneck C) a small breeding population D) a founder effect

55) ______

56) Inbreeding will change ________.

A) mating isolation mechanism C) diet

56) ______ B) species D) gene frequencies

57) Evolution is dependent on ________ in the evolving population.

A) equilibrium B) constant gene frequencies C) genetic diversity D) inbreeding

57) ______

58) Conservation of amino acid sequence among distantly related groups of organisms is

58) ______

suggestive of a(n) ________.

A) important function for that sequence B) intrinsic resistance to mutations in that sequence C) lack of selective pressure on that sequence

D) lack of common ancestor

1) B 2) B 3) D 4) B 5) B 6) E 7) E 8) D 9) C 10) C 11) A 12) D 13) C 14) M = 0.6; m = 0.4 15) The sum of the relevant individual alleles in a population is equal to 100% of those alleles.

16) the expected frequency of heterozygotes in a population in Hardy—Weinberg equilibrium 17) 0.42 18) a condition for a population in which the frequency of given alleles remain constant from generation to generation 19) C 20) B 21) C 22) A 23) Certain alleles will reach the next generation on a nonrandom basis, thus upsetting the equilibrium.

24) natural selection 25) fitness 26) The founder effect generates an increase in recessive allelic frequencies by having an individual carrier found an isolated population with minimal migration effects. This preserves the frequency of recessive alleles.

27) selection against a dominant allele 28) Chromosomal assortment and crossing over reshuffle combinations of mutations at different loci; forces such as selection, genetic drift, and migration can increase or decrease the frequencies of mutant alleles in populations.

29) 1/100,000 30) pi' = (1 - m)pi + mpm

31) Sampling error would cause random and possibly significant fluctuations in determination of gene frequencies.

32) For a given allele, inbreeding increases the proportion of homozygotes in a population.

33) higher frequency of aberrant phenotypes and higher mortality rates 34) postzygotic mechanisms 35) The process of splitting a genetically homogeneous population into two or more populations that undergo genetic differentiation and eventual reproductive isolation.

36) The generation of reproductive isolating mechanisms–geographic, behavioral, physiological, and mechanical–provides common factors in the speciation process.

37) Fitness is a measure of the proportion of offspring that a particular phenotype will contribute to the next generation.

38) It is natural to expect that the forces that bring about speciation are dependent upon reproductive isolation. As groups of organisms become reproductively isolated (whether through development of geographic or genetic barriers), it is natural to expect that through the accumulation of mutations, DNA sequences will diverge. It is also natural to expect that some DNA sequences will diverge more rapidly than others and that some differences in DNA sequences may be more evolutionarily important than others. Therefore, while there may be a general relationship between genetic diversity and evolutionary (phylogenetic) diversity, it is likely that there are exceptions.

39) Mitochondrial DNA evolves relatively quickly, so that if a "fast clock" is needed to estimate relatively short

evolut time periods, mitochondrial DNA can be especially useful. Also, it is not subject to recombination, so the separate ionary mitochondrial genetic lineages remain distinct with little mixing.

40) Cytochrome c is a respiratory pigment found in the mitochondria of eukaryotes. Because of its vital role in aerobic metabolism, it has evolved very slowly. Differences signify vast evolutionary distances.

41) It serves a vital function; therefore, any changes in amino acid sequence are usually strongly selected against.

42) diagrammatic representations of evolutionary relationships among organisms 43) Not necessarily, because some sections of DNA evolve more slowly if they code for products that serve important cellular functions, whereas other sections without such constraints evolve more quickly.

44) Although Neanderthals and humans share a common ancestor, Neanderthals were a separate hominid line and probably did not contribute mitochondrial genes to H. sapiens.

45) Molecular clocks are amino acid or nucleic acid sequences in which evolutionary changes accumulate over time.

Ideally, such changes accumulate at a constant rate, so that the degree of differentiation is correlated to the length of time of divergence.

46) D 47) C 48) B 49) B 50) D 51) A 52) D 53) A 54) C 55) A 56) D 57) C 58) A

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) CRISPR-Cas functions in bacteria to ________.

1) _______ A) code for restriction enzymes B) edit genomes C) replicate viral DNA D) fight viruses 2) Mechanisms of adaptive immunity include ________.

A) restriction enzymes B) learning from past exposures C) blocking phage adsorption D) blocking phage DNA insertion

2) _______

3) cas genes code for a variety of proteins, including ________.

A) lysozymes B) RNases C) crRNAs D) polysaccharides

3) _______

4) Which of the following is the correct order of steps for the CRISPR-Cas mechanism?

A) cleavage, target interference, biogenesis B) transcription, cleavage, spacer acquisition C) spacer acquisition, biogenesis, target interference D) target interference, transcription, biogenesis

4) _______

5) Type II CRISPR-Cas systems are the most widely used systems because ________.

A) they were discovered first B) they use a nuclease complex C) Streptococcus pyogenes is an important research organism D) they only require a single protein, Cas9

5) _______

6) Which of the following is required to efficiently target DNA in vitro using CRISPER-Cas9?

A) tRNA B) native crRNA C) target RNA D) Cas9

6) _______

7) Genome editing is based on ________.

A) methylating specific DNA sequences with specific proteins B) transcribing specific DNA sequences with specific proteins C) targeting and manipulating specific DNA sequences with specific nucleases D) acetylating specific DNA sequences with specific nucleases

7) _______

8) Which of the following is a pathway available to cells to repair double-stranded DNA breaks?

A) nonhomologous directed repair B) nonhomologous end-joining C) homologous end-joining D) homologous directed end joining

8) _______

9) The promiscuity of the CRISPER-Cas9 system likely benefits bacteria by ________.

A) enabling faster search of large genomes B) continuing the evolutionary process C) increasing the safety of medical applications D) facilitating defense against new viral attacks

9) _______

10) The primary benefit of CRISPR-Cas over TALENs and ZFNs is ________.

A) the specificity of the nuclease B) the speed of the process

10) ______

C) the cost D) the ability of Cas9 to bind engineered sgRNA 11) A strategy to induce random indels in a target sequence might use ________.

A) NHEJ to ligate fragments B) HDR to match damaged and undamaged chromosomes C) NHEJ and Cas9 D) HDR and a donor template

11) ______

12) Reverse genetics is a strategy with which researchers ________.

A) delete a genome and investigate the function of plasmids B) turn on a gene and monitor the effects C) delete genes and monitor the effects D) investigate the function of proteins

12) ______

13) dCas9 is a useful tool in the CRISPER-Cas toolkit because it can ________.

A) deactivate the transcription of a gene B) fluoresce and help researchers locate target sequences C) bind DNA, but it cannot cut DNA D) bind DNA, but it cannot travel down the template strand

13) ______

14) All of the following are challenges in gene therapy EXCEPT ________.

A) designing a strategy B) unknown cell types unknown specific mutations C) D) inaccessible tissues

14) ______

15) Examples of modifications to Cas9 include all of the following EXCEPT ________.

A) fluorescent proteins B) promotor domains C) epigenetic modifiers D) repression domains

15) ______

16) The primary value of the CRISPER-Cas system in biotechnology is ________.

A) simple modifications of genomes B) addition of random indels C) rapid and cost-effective production of genetically modified organisms D) the removal of ineffective genes

16) ______

17) Applications of CRISPER-Cas in biotechnology include all of the following EXCEPT ________.

A) engineering pigs that are resistance to PRRS B) modulating epigenetic regulation C) increasing drought resistance of crops D) creating bioreactors to manufacture human proteins

17) ______

18) An advantage of base editor technology is that ________.

A) uracil is more specific than cytosine and enables greater fidelity B) DNA is not cut, so there are no indels C) specific basic sequences are edited, leading to a more specific product D) the hybrid protein changes A to T for greater variability

18) ______

19) A major limitation of CRISPER-Cas to treat human disease in vivo is modifying millions of cells.

19) ______

What are the characteristics of successful delivery vehicles?

A) They induce an immune response.

B) They bind to target proteins.

C) They are carried by erythrocytes.

D) They are encapsulated in target cells (via endosomes).

20) A strategy to reduce off target effects of the CRISPER-Cas system is to limit homology with other regions of the genome. This principle capitalizes on the specificity of which step of the mechanism?

A) spacer acquisition B) crRNA biogenesis C) leader sequence determination D) target interference

20) ______

1) D 2) B 3) B 4) C 5) D 6) D 7) C 8) B 9) D 10) D 11) A 12) C 13) C 14) A 15) B 16) C 17) B 18) B 19) D 20) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) VNTRs are useful in DNA forensics because ________.

1) _______ A) the VNTRs have very little variation in length B) the VNTRs have exactly the same sequence between people C) the VNTRs act as an identifier for a group of individuals D) the number of VNTRs varies between people SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

2) Justify the FBI's use of only 20 short tandem repeats (STRs) as their core set of STRs for 2) _____________ forensic analysis.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

3) The development of which biotechnology revolutionized the field of DNA forensics?

3) _______ A) Sanger sequencing B) GWAS C) capillary electrophoresis D) PCR SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

4) Present evidence supporting the argument that Y chromosome STR profiling is not 4) _____________ sufficient for proper DNA profiling.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

5) Mitochondrial DNA profiling is useful in developing DNA profiles from samples that are in 5) _______ less than ideal condition. What is a major limitation of using mitochondrial DNA profiling?

A) It is possible to differentiate between maternal relatives.

B) It is present in high copy number.

C) It is useful in identifying victims of disasters when relatives are available for reference.

D) It is not possible to differentiate between maternal relatives.

6) Single-nucleotide polymorphisms (SNPs) are being used more and more in forensic analysis yet

6) _______

have not been fully embraced. However, SNPs have found an exemplary use in which of the following fields?

A) evolution studies B) VNTR copy number studies protein stability studies C) D) epigenetic regulation studies

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

7) DNA phenotyping represents an emerging technology that uses SNPs to determine 7) _____________ physical features. Describe why DNA phenotyping faces skepticism in court rooms and from other scientists with regard to its accuracy.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

8) DNA phenotyping poses several concerns as an emerging technology. Which of the following is 8) _______ not a concern with DNA phenotyping?

A) intellectual property of the company's methodologies B) its ability to help identify missing persons C) racial profiling D) privacy violations SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

9) Provide support for using the product rule in generating a high confidence that an 9) _____________ individual has a unique DNA profile using multiple STRs.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

10) Which of the following contribute to an increased probability of a random match of a DNA 10) ______ profile in a population?

A) a population containing limited VNTR variation B) a random population with many relatives C) a population with inbreeding D) a population with a small number of identical twins

11) CODIS (Combined DNA Index System) is a database that contains DNA profiles from all of the following EXCEPT ________.

A) crime scene evidence C) people convicted of certain crimes

11) ______

B) public servants D) unidentified remains

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

12) There are several concerns with using DNA profiling in forensics with the advent of 12) ____________ cheaper synthesis methods for DNA. Propose a mechanism to determine if crime scene evidence is natural or synthetic.

13) Why does DNA profiling pose potential ethical problems when a partial match occurs

13) ____________

in CODIS?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

14) When using DNA profiling in prosecuting criminal cases, lawyers must be very thorough in 14) ______ their investigation of the DNA evidence. Which of the following could cause issues with the DNA evidence presented in a court case?

A) deference B) transference C) recombination D) quantity

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) Explain why Identical twins can have the same STRs in a DNA profile yet still exhibit 15) ____________ differing phenotypes.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

16) Using the values in TABLE ST 2.2; what is the expected genotype frequency for the two loci 16) ______ profile consisting of D8S1179 and D5S818?

A) 0.019 B) 0.001936

C) 0.102

D) 0.000421

17) STRs are repeated elements in the genome. They have ________ nucleotides per repeat

com pared

____ __

to VNTRs. 17)

A) fewer C) precisely two times the number

B) the same number D) more

18) One of the advantages of STR profiling over VNTR profiling is that ________.

A) STRs are not variable in the number of repeats, whereas VNTRs are B) STRs are variable in the number of repeats, whereas VNTRs are not C) it presents more variable sequences reducing false positive matches D) it requires much less DNA because PCR can be used to amplify small samples

18) ______

19) Mitochondrial DNA profiling is used to trace the maternal side of family trees. Why is this

19) ______

done using mtDNA? A) The mtDNA is supplied to the zygote only from the egg.

B) The mtDNA undergoes recombination allowing allelic mixture.

C) The mtDNA only comes from the father so all differences are from the mother.

D) The mtDNA under low selective pressure mutates readily.

20) Mitochondrial DNA profiling is primarily used to differentiate ________.

A) unrelated individuals B) mothers and sons C) mothers from daughters D) siblings

20) ______

1) D 2) By characterizing 20 STRs, the analysis covers over two billion combinations even if each STR only exhibits four alleles each. This is highly unlikely as STRs vary in repeats from 7 to 40 times.

3) D 4) Y chromosomal STR profiling is not sufficient for DNA profiling as it only focuses on the Y chromosome of individuals. As Y chromosomes do not undergo recombination, they are directly inherited from father to son and as such, all males of the same patrilineage will be identified by the same STR pattern.

5) D 6) A 7) DNA phenotyping faces scrutiny and skepticism due to its reliance on multiple genes as well as multiple SNPs in those genes to provide a rather low probability of a correct identification.

8) B 9) The product rule states that the probability of an individual having certain alleles in a population is the result of the product of each of the individual allelic frequencies in the population. As such, one STR locus with two alleles at a frequency of 0.361 and 0.141 would have a 10% chance of being unique in a population. However, by examining a second locus containing one allele at a frequency of 0.243, we can demonstrate that the likelihood of an individual having both STRs is ~0.6%.

10) C 11) B 12) Testing evidence for methylation patterns and comparing those patterns to those seen in natural DNA samples.

13) A partial match in CODIS could lead investigating agencies to focus on family members of the partial match. The ethical issue arises when it is considered right to suspect someone of a crime based on his or her DNA.

14) B 15) While the DNA sequence of identical twins is the same, there is evidence that environmental factors affect the epigenetic regulation of genes that could result in differing phenotypes.

16) B 17) A 18) D 19) A 20) A

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Precision medicine is ________.

1) _______ A) an approach that applies precise treatment to a large population B) an approach that maximizes the cost/benefit to a sizable population of patients C) an approach that uses "-omics" data to determine treatment for large populations D) an approach that uses individual and molecular information to direct treatment 2) _______

2) Personalized medicine is ________.

A) a subset of precision medicine B) based on an average of molecular profiles C) involves screening drugs on individual patients D) used to design treatments for multiple patients

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

3) Mutations in the proteins that are involved in drug metabolism are of immense 3) _____________ importance in personalized medicine. Explain how being aware of mutations in the gene CYP2D6 can affect a physician's treatment plan for an individual.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

4) Using "-omics" data prior to designing a treatment for patients is the goal of ________.

4) _______ A) precision medicine B) neopharmaceuticals C) next generation medicine D) classic medicine 5) _______

5) Targeted drugs are therapeutics designed to ________.

A) treat only one person B) treat a large class of diseases C) treat a specific disease based on the efficacy of the drug in a large population D) treat a specific disease based on the efficacy of the drug in a small population

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

6) One method for determining if a targeted drug will be effective is to perform a FISH 6) _____________ assay on a biopsy of the diseased tissue. How does FISH demonstrate potential efficacy of the drug?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

7) Immunotherapies seek to take advantage of ________ in treating cancers.

7) _______ a patient's own cancer cells a patient's own immune system A) B) C) a patient's own SNPs D) a patient's own genome SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question. in vidual.

8) A patient suffering from an unknown cancer is being treated with standard chemotherapy. Describe how personalized medicine could potentially help treat this

di

8)

_____________

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

9) Neoantigens are ________.

9) _______ mutations that are silent A) B) mutations that result in cancer C) mutated proteins expressed in the cytosol of cancer cells D) mutated proteins expressed on the outer membrane of cancer cells SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

10) Cancer cells have developed a mechanism to repress T cell response to neoantigens.

10) ____________ Present a method that would allow restoration of the T cell response when the response is halted at a checkpoint.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

11) In order to take advantage of adoptive cell therapies, the tumor must be biopsied and the tumor 11) ______ infiltrating leukocytes are ________ for reactivity and then cultured ________ prior to being reinfused into the patient.

A) screened; in vivo B) screened; in vitro C) mutated; in vitro D) mutated; in vivo

12) One method to target the immune system of a patient to a cancer cell that it is nonresponsive to is the use of ________.

A) WGS

B) CARs

C) VNTRs

12) ______

D) SNPs

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

13) Chimeric antigen receptors are engineered surface receptors on autologous T cells.

13) ____________ Describe how CARs provide a method of targeting cancer cells.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

14) Which of the following is not a side effect of current CAR T cell therapies?

14) ______ A) headaches B) inflammatory response C) neurotoxicity D) eventual tumor resistance SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) The age of precision medicine comes with many legal and ethical issues. Evaluate the 15) ____________ current hurdles to personalized medicine becoming common place.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

16) In future, medical schools will have to adapt their education to include ________ to better equip 16) ______ physicians to interpret precision medicine data.

A) pharmacology B) biochemistry

C) anatomy

D) bioinformatics

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

17) Describe the structural differences between endogenous T cell receptors and CAR T cell

17) ____________

receptors.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

18) All of the following are ways tumors avoid immune response EXCEPT ________.

18) ______ A) the use of checkpoint molecules B) the use of endocytosis to destroy T cells C) the presence of regulatory T cells D) abnormal expression of MHC 19) Adoptive cell transfer uses autologous cells. What does autologous cells?

A) cells are taken from the patient, augmented, and then reinfused to the patient B) cells are taken from a donor other than the patient C) cells that are automatically expressing chimeric receptors D) automatically made

19) ______

20) Immune system cells that are responsible for the recognizing neoantigens and targeting tumors

20) ______

are called ________.

A) regulatory T cells C) monocytes

B) tumor-infiltrating lymphocytes D) macrophages

1) D 2) A 3) CYP2D6 is involved in the metabolism of a significant number of current pharmaceuticals. Mutations in CYP2D6 can result in altered metabolism rates for the drugs. A physician that is aware of the mutations and their affect on drug metabolism will be able to adjust the dosage so as to avoid over/under dosing of the patient.

4) A 5) D 6) A FISH assay determines the copy number of the gene for which the fluorescent probe was designed to target. If the target gene is present in a higher than normal copy number, the drug target is likely to be expressed at high levels as well. This suggests that the drug target is present and will respond to the targeted therapeutic.

7) B 8) By sequencing the entire exome of the patient, mutations in coding regions can be identified. These mutations can then be compared to databases that contain drugs and their targets. If the mutated genes determined in the whole genome sequencing show up in the drug database, a potential therapeutic has been found.

9) C 10) To restore T cell function when the response is halted at a checkpoint, one would design a checkpoint inhibitor.

This will prevent the cancer cell from suppressing the T cell response at the checkpoint.

11) B 12) B 13) CARs allow the engineered targeting of cancer cells by recombinantly expressing genetically engineered cell surface receptors that are designed to activate T cells upon binding neoantigens on the cancer cell surface.

14) A 15) There are several hurdles that precision medicine must overcome to be more accessible. One is the logistics of storing and readily accessing the medical records and genomic information of patients. Very few hospitals and practitioners currently have the information technology to handle the data. Second is the legal and ethical issues that surround patient confidentiality and the sharing of records to improve the accuracy and usefulness of precision medicine.

16) D 17) Endogenous T cell receptors are very complex and contain multiple transmembrane domains and signaling domains. They also have invariant domains as well as the variant domains that bind antigens. CAR T cell receptors are much simpler; comprised of a signaling domain a single transmembrane domain and two variable domains connected with a linker sequence.

18) B 19) A 20) B

Exam Name___________________________________ SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

1) Describe the difference between genetically modified (GM) food and foods that are 1) _____________ selectively breed for over centuries.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

2) When GMOs are generated through the transfer of genetic material across species, the GMO is 2) _______ said to be ________.

A) exogenic

B) isogenic

C) transgenic

D) cisgenic

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

3) Describe how genetically modifying plants could provide farmers with a boost in 3) _____________ productivity of their crops.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

4) What is a major concern surrounding GMOs that critics cite as an argument against GMOs? 4) _______ A) They could escape containment and breed with non-GMOs and create unregulated hybrids.

B) They could escape containment and produce even more useful genetic variants.

C) They could escape containment and outcompete non-GMOs resulting in extinction of the GMO. D) They could escape containment and pollute other gene pools.

5) Bt crops are an insect-resistant GM plant. Bt crops are used mainly because the cry proteins,

5) _______

which confer the insecticidal properties, are shown to ________.

A) break down slowly in sunlight B) only target a few pest species C) pollute the ground water D) have few negative effects on humans

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

6) Genetic modification of rice to generate beta-carotene in the endosperm has great 6) _____________ potential to alleviate vitamin A deficiency in third-world countries. However, there is still much controversy surrounding its growth. Provide supporting arguments for the planting and consumption of Golden Rice 2.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

7) Current methods used in the generation of GM plants are still in development. The chance of a 7) _______ productive GM plant being generated by biolistic methods is dependent on ________.

A) random mutations making a proper promoter B) being infected by a particular bacterium C) integration of the Ti plasmid D) in vitro cells taking up DNA-coated gold beads

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

8) Selection of a successfully transformed plant cell requires several steps including

8) _____________

growth in a selective media, checking for the gene of interest, and checking for phenotype. Propose a method of detecting a transfected gene's presence in a developing organism.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

9) The use of a positive selection marker in the development of Golden Rice 2 allowed the 9) _______ transgenic plants to grow on ________, which is usually unusable by plants.

A) xylose 6-phosphate B) fructose 6-phosphate C) mannose 6-phosphate D) glucose 6-phosphate

10) The use of beta-glucuronidase (GUS) in the generation of Roundup-Ready soybeans is an example of a ________.

A) herbicide resistance C) agrobacterium resistance

B) positive marker D) negative marker

11) Predict the phenotype of the following gene construct if it is successfully transfected into plant cells. Promoter- GUS- PFK1 A) green precipitate C) white precipitate

11) ______

B) blue precipitate D) no precipitate

12) Which method would best meet the need in generating GM plants if food crops were threatened by invasive insect species?

A) selective breeding C) biolistic methods

10) ______

12) ______

B) CRSPR-cas D) agrobacterium-mediated technology

13) Gene-edited organisms are seeing much less regulatory oversight than transgenic organisms.

13) ______

Why is this the case?

A) Transgenic organisms are more complicated and require more testing.

B) The gene-edited organisms have no foreign DNA in them and do not fall under current regulatory statutes.

C) The gene-edited organisms are safer.

D) Transgenic organisms are simpler than gene-edited organisms and have more regulations because of it.

14) GM foods are controversial for many reasons. Which of the following does not represent a

14) ______

controversy between advocates and critics of GM foods?

A) GM foods increase yields on farm land.

B) GM foods cause disease in consumers.

C) GM foods have an unknown impact on the environment.

D) GM foods have an unknown impact on consumers.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

15) Why should GM foods be considered on a case-by-case basis instead of making general 15) ____________ statements about all GM foods?

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

16) GM foods are considered safe by advocates who cite ________.

16) ______ 20 years of consumption with no reliable correlation to disease or adverse effects A)

B) robust toxicity testing that is done in humans shows no adverse effects C) the GM food is exactly the same as the non-GM food D) the lack of reliable data due to relaxed governmental oversight 17) Critics of GM foods often cite the ________ as reason to be skeptical of the safety of GM foods.

A) the in depth testing of DNA that makes it through the food refinement process B) vast number of studies conducted on the consumption of GM foods C) fact that most GM foods are not directly consumed by humans D) the extreme governmental oversight of GM food production

17) ______

18) The future of GM organisms is encouraging. A project is underway to produce a GM chicken

18) ______

that is incapable of ________.

A) regulating the number of eggs laid B) spreading avian influenza C) contracting avian influenza D) reproducing but containing twice as much breast meat

19) Why is the cassava plant difficult to engineer without the help of modern biotechnology?

A) The plant is integral to African agriculture and is already optimized.

B) The plant has a very low mutation rate.

C) The plant does not undergo recombination events, which limits genetic drift.

D) The plant is long lived making selective breeding ineffective.

19) ______

20) GM plants that are in various developmental pipelines include those that are ________.

A) incapable of recombination B) tolerant of radiation exposure C) tolerant of heavy metals D) tolerant of increased salinity

20) ______

1) GM foods are modified using biotechnology as opposed to non-GM foods, which are grown and mated selectively for many generations to promote desired phenotypes.

2) C 3) Modifying the genome of crops planted by the farmer to have favorable traits such as improved yield, improved drought tolerance, and herbicide resistance would increase the farmers' productivity.

4) A 5) D 6) The GM food crop Golden Rice 2 could alleviate the vitamin A deficiencies found in over 1590 million children, 19 million pregnant women, and almost 500,000 children. The Golden Rice 2 GMO is grown on the same land as non-GMO rice and can be made sterile to prevent the GMO from reproducing out of control.

7) D 8) PCR primers that specifically target the gene of interest can be designed and the genomic DNA isolated from the GM plant used as the template for PCR. If the gene is present in the genome, a PCR product will be formed.

9) C 10) B 11) B 12) B 13) B 14) A 15) Each GM food is developed for a specific purpose. Each one contains different genes from different organisms and it is possible that those genes result in different phenotypes in varying host organisms. Therefore, one cannot make blanket statements about GMOs when each is a unique creation.

16) A 17) C 18) B 19) D 20) D

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Gene therapy strives to ________.

1) _______ A) provide new gene sequences to make people stronger B) mitigate the symptoms of a disease state C) cut out defective genes D) cure the disease state 2) Gene therapy is ________.

A) capable of treating diseases associated with an unknown gene B) not a good candidate for cancer therapeutics C) able to treat any type of cell no matter where it is in the body D) an example of translational medicine

2) _______

3) Minimizing off-target effects of gene therapy is a concern with ________.

A) in vivo gene therapy B) autologous gene therapy C) the use of adenovirus therapy D) ex vivo gene therapy

3) _______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

4) A patient experiencing a disease state due to a gene deletion was treated with 4) _____________ adenovirus gene therapy. The gene therapy was successful and the gene deletion was corrected. However, the patient began to develop cancer not long after the gene therapy. Develop a theory as to why the cancer presented so rapidly after gene therapy.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

5) Lentiviral vectors are preferred over adenoviral vectors because ________.

5) _______ A) the inserted DNA forms episomes, which prevent insertion mutations B) the lentivirus cannot infect nondividing cells C) they do not have to be engineered by taking out their replicative genes D) the inserted DNA cannot be reproduced when cells divide 6) Viral vectors are not the only method being studied for gene therapy purposes. Which of the

6) _______

following is a nonviral delivery method for gene therapy?

A) electrically stimulating cells to take up DNA B) gene pills C) DNA bound to the surface of liposomes D) DNA covered with protein

7) Hematopoietic stem cells (HSCs) are particularly useful in gene therapy because ________.

A) they are short lived in vitro B) they differentiate into all tissue types C) they are easy to obtain from patients D) they are useable across many patients without rejection fears

7) _______

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

8) Treatment of ADA-SCID is often considered the first success for gene therapy. Ashanti

8) _____________

DeSilva is a young girl that suffered from an autosomal form of SCID and was treated using retroviral gene therapy. Explain why the treatment is not an undisputed success.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

9) Despite the promise of gene therapy treating disease, there were two major setbacks to clinical 9) _______ trials. This setbacks brought to light the disadvantages of using retroviral vectors for gene therapy, which include ________.

A) certain viral vectors do not insert in important genes of the host B) controlled insertion of the therapeutic gene in the host genome C) the viral vector will not impact the host D) the unknown response of a patient to the retroviral vector

10) ______

10) Gene therapy to treat Leber congenital amaurosis has recently shown some promise in revitalizing the gene therapy field. This is due in large part to injecting adeno-associated virus loaded with RPE65 just under the retina. What does the product of gene RPE65 do?

A) metabolizes retinal B) metabolizes cone cell waste C) metabolizes retinol D) metabolizes rod cell waste

11) ______

11) A serious concern about gene therapies and their commercialization is ________.

A) the lack of individuals treatable with the drug B) the ease of achieving regulatory approval C) their cost to the consumer D) their speedy development process

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

12) ZFNs and TALENs have high specificity for their target cleavage site. How is this 12) ____________ specificity achieved?

13) With gene therapy being at the cutting edge of medical technologies, it is not surprising

13) ____________

that serendipitous treatments are discovered. Explain how treating an HIV-positive patient with stem cells from an HIV-resistant donor cured him or her of HIV while targeting his or her acute myeloid leukemia.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

14) The use of CRISPR-cas has revolutionized the gene therapy field. One of the first uses of 14) ______ CRISPR-cas to edit genes in vivo was done at MIT. What disease did they cure?

A) B-thalassemia B) type 1 tyrosinemia C) RDEB D) HIV

15) CTL019 was the first gene edited CAR T cell therapy approved by the FDA. Initial treatments of

15) ______

patients with CTL019 demonstrated over ________ remission rate after the first treatment.

Exemplifying the power of gene editing in treating acute lymphoblastic leukemia.

A) 99% B) 90% C) 95% D) 80%

16) The gene PD-1 plays an important role in immune response to tumor cells. How would using gene editing to knock out this gene help T cells recognize and kill cancer cells?

A) PD-1 will not be expressed on the cancer cell surface. This prevents T cell recognition.

B) PD-1 will be expressed in the cytosol of the cancer cell. This protects PD-1 from the T cell.

16) ______

C) PD-1 will be expressed in the cytosol of the T cell. This protects PD-1 from cancer cells.

D) PD-1 will not be expressed on the T cell surface. This circumvents one line of the cancer cells defense.

17) What is the target of the first CRISPR-cas gene editing in humans?

A) FUH B) COL7A1 C) CAR T cells

17) ______ D) PD-1

18) In 2015, a group of Chinese researchers used CRISPR-cas gene editing to edit the HBB gene in

18) ______

86 human embryos. What were the conclusions form this study?

A) 71 of the 86 embryos contained the desired gene edit.

B) CRISPR-cas is safe for use in human patients.

C) CRISPR-cas was not ready for use in human patients.

D) CRISPR-cas gene editing had no negative effects on the surviving embryos.

19) One gene therapy that does not rely on gene editing is RNA interference. This therapy uses ________ to interfere with expression of proteins at the translational level.

A) tRNA B) mtRNA C) miRNA

19) ______

D) mRNA

20) Which gene therapy is currently approved in the United States?

A) germ-line gene therapy B) somatic gene therapy C) enhancement gene therapy D) stem cell gene therapy

20) ______

1) D 2) D 3) A 4) The cancer is most likely a direct result of the gene therapy. The use of adenovirus as a gene therapy vector results in the therapeutic gene inserting at random into the host cell genome. In this case, the therapeutic gene most likely inserted into the host genome in such a way as to be tumorigenic.

5) A 6) B 7) C 8) While Ashanti's immune system was bolstered by the gene therapy, she also received regular injections of adenosine deaminase enzyme. This made it unclear whether the adenosine deaminase found in her system was due to the active gene delivered by the gene therapy or the injections of purified adenosine deaminase.

9) D 10) C 11) C 12) Both ZFNs and TALENs require dimerization to work. This means that each monomer must recognize and bind its target sequence and be close enough for dimerization to occur. ZFNs have a spacing of 5-7 nucleotides, whereas TALENs have a spacing of about 13 base pairs.

13) Using mutant CCR5 T cells in the stem cell transplant to treat Timothy Brown's leukemia, the HIV was not capable of spreading to the new T cells. This resulted in the decline of HIV-positive T cells and the eventual curing of his or her HIV.

14) B 15) D 16) D 17) D 18) C 19) C 20) B

Exam Name___________________________________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Neurogenetics is ________.

1) _______ A) the study of genes associated with the formation of neurons B) the study of genetics that makes human brains unique C) the study of the genetic basis for neurodegenerative disease D) the study of the protein basis for neurodegenerative disease 2) _______

2) Huntington's disease (HD) is the model neurodegenerative disease because ________.

A) it is monogenic B) only a few analytical approaches have been used to study it C) it does not have a defined set of symptoms and disease progression D) it is not 100% penetrant

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

3) HD was the first example of complete dominance in human inheritance. Describe the 3) _____________ impact this has on inheriting the disease state.

4) Huntington's observations of the disease that later took his name were published prior

4) _____________

to the rediscovery of Gregor Mendel's work on inheritance. Support the argument that Huntington was describing a phenotype with complete dominance.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

5) Early mapping of the HD gene was done using ________.

5) _______ A) RFLP mapping B) SNP mapping C) northern blotting D) WGS 6) After James Gusella's first attempt to link the RFLP marker to HD failed, he used a new RFLP

6) _______

marker on ________ to determine if there was linkage of disease phenotype to the new G8 marker.

A) a small Venezuelan population that has HD B) a large Venezuelan population that has HD C) a specific subset of an American HD family D) the same population of HD patients as his first experiment

7) The second study by Gusella demonstrated four haplotypes for HD based on the restriction

7) _______

enzyme HindIII. Which haplotype demonstrated linkage to the disease phenotype?

A) A B) B C) C D) D

8) The success of Gusella, Wexler, and their colleagues in mapping both the G8 marker and HD

8) _______

gene to chromosome 4 launched a new branch of genetics called ________.

A) personalized medicine B) genomics reverse genetics C) D) neurogenetics

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

9) Explain how the use of sequencing technologies finally brought the search for the HD

9) _____________

gene to a close as reported by the Huntington's Disease Collaborative Research Group.

10) Since the discovery of the HTT gene, genetic testing for the number of CAG repeats has

10) ____________

been developed. However, there are serious ethical questions raised by the prospect of prenatal testing as well as the testing of minors. Develop an argument for why minors should not be tested for HD unless they demonstrate juvenile HD symptoms.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

11) HD is known as a polyQ disease. How does "polyQ" relate to HD? 11) ______ A) There are many Q nucleotides added to the HTT gene in the disease state.

B) There are many trinucleotide repeats, which are called "Qs" in the disease state.

C) There are many Q amino acids added to the huntingtin protein in the disease state.

D) There are many CAG repeats, which code for glutamic acid residues in the disease state.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

12) Why does the mHTT gene have such wide-ranging effects in the disease state?

12) ____________ MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

13) The favored model organism for studying the development of HD is ________.

13) ______ A) H. sapiens B) D. C) M. musculus D) C. elegans melanogaster

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

14) An important study of HD conducted by A. Yamamoto demonstrated that turning off 14) ____________ the HTT gene early in the progression of the disease results in the aggregates being degraded and prevention of the disease. Explain how Yamamoto designed his experiment.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

15) Gene silencing has been effective in mouse models of HD that are heterozygous for the mHTT 15) ______ gene. The results are promising as ________.

A) the study demonstrated the ZFN only targeted the mHTT allele and left the normal HTT expression level unchanged B) the injection into both sides of the mouse brain resulted in reduced mHTT C) the injection into one side of the mouse brain affected both sides of the brain D) both mHTT and HTT were down regulated

16) Researcher Xiao-Jiang Li has used ________ to edit the exon of hua mutant HTT allele in mice.

16) ______

Three weeks after the injection of therapeutic into the brain the mice demonstrated a reduction in protein aggregates.

A) TALENs B) CRISPR-cas C) ZFNs D) lentiviral transfection

17) HD heredity seems to increase if a father inherits the mutant allele from his mother. This is most likely caused by ________.

A) selection B) segregation

C) imprinting

D) recombination

17) ______

18) Other neurodegenerative diseases also function through aggregation of misfolded proteins.

18) ______

However, the initial protein aggregates are different in each disease. Work on HD may still be vital to treating other diseases as ________.

A) the method of aggregation is the same in all neurodegenerative disease B) not all neurodegenerative disease spread C) the method of disaggregation is similar in all neurodegenerative disease D) other neurodegenerative diseases use axonal transport to spread to unaffected cells

19) How do Parkinson's causing aggregates enter unaffected cells?

A) endocytosis B) exocytosis C) alpha-synuclein aggregates cannot enter unaffected cells D) phagocytosis

19) ______

20) How does the development of protein aggregates in Huntington's disease bring about dementia

20) ______

in patients?

A) disruption of the neuronal connection of the entire central nervous system B) disruption of neuronal connection between the caudate region and the frontal lobe C) disruption of the neuronal connection to the frontal lobe resulting in brain weight gain of ~30% D) disruption of neuronal connection between the medulla and the caudate region

1) C 2) A 3) As HD exhibits complete dominance in the inheritance pattern, it does not matter if the individual is heterozygous or homozygous for the mutant allele. The disease will develop and progress regardless of the number of mutant alleles present.

4) Huntington wrote that "when either or both parents have shown manifestations of the disease…the offspring almost invariably suffer from the disease." This describes a situation where one parent does not carry the mutant allele and the other could be heterozygous; thus implying that the heterozygous parent passes the mutant allele to the offspring, which in turn suffer from the disease with only one mutant allele in their genotype. The presentation of the disease with only one mutant allele in the genotype is complete dominance.

5) A 6) B 7) C 8) C 9) Sequencing of the contigs that covered the end of Chromosome 4 that had been previously identified as the location of the HD locus revealed an "interesting contig" that contained a CAG repeat sequence. The population of individuals without HD had 17 alleles with CAG repeats varying from 11 to 34 copies. HD individuals had alleles with 42—66 repeats of the CAG trinucleotide. HD was known to be a trinucleotide repeat disease and the research group proposed HTT as the gene responsible for HD and named its gene product huntingtin.

10) minors should not be tested for HD because there is currently not cure or preventative for the disease. This will have a direct impact on their quality of life as they will have to live with the knowledge that they will develop HD. In addition, minors may be denied health coverage based on their genetic test results. This is a continuing ethical dilemma for genetic testing.

11) C 12) The mHTT causes a wide range of disease phenotypes because of the ubiquitous nature of huntingtin. Huntingtin is pivotal in protein-protein interactions and is found in almost all cellular compartments from nucleus to mitochondria and cytosol. When mHTT begins to aggregate, it results in the disruption of many cellular processes giving rise to the multitude of disease phenotypes.

13) C 14) Yamamoto cloned the mHTT gene behind an inducible promoter that responded to doxycycline. When the mice were fed water containing doxycycline, the mHTT gene was turned on and disease progression commenced. When doxycycline was removed from the water, the mHTT gene was turned off and disease progression halted.

Yamamoto monitored the aggregates of mHTT and determined that if the gene expression was arrested early enough, the disease state could be reversed by normal cellular functions.

15) A 16) B 17) C 18) D 19) A 20) B