
Course Introduction
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Course Introduction
Molecular Biology explores the molecular mechanisms that govern the structure, function, and regulation of the genetic material within living cells. This course covers the central dogma of molecular biology, including DNA replication, transcription, and translation, as well as gene expression, regulation, and mutation. Students will also examine molecular techniques such as PCR, gel electrophoresis, and cloning, and their applications in research, medicine, and biotechnology. The course emphasizes developing a strong conceptual understanding of molecular processes as they relate to cellular function and genetic inheritance.
Recommended Textbook
iGenetics A Molecular Approach 3rd Edition by Peter J. Russell
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Q1) What are the differences between eukaryotes and prokaryotes?
Answer: Eukaryotes possess a nucleus that is separated from the rest of the cell by a double-layered nuclear membrane.Prokaryotes lack a nucleus.Prokaryotes also lack all membrane-bound organelles,such as mitochondria,endoplasmic reticula,and Golgi bodies.Such organelles are present in eukaryotes.Prokaryotes are generally also much smaller than eukaryotes,and are usually unicellular.
Q2) Why are genetic databases so important to the study of modern genetics?
Answer: The available information about the genetics of a large number of organisms has increased dramatically in the past few years.As a result,it has become impossible to study,learn,and remember all of it.All this information needs to be stored in such a way that it may be accessed and searched easily.This is done in computer databases that have assumed enormous importance in the study of genetics.
Q3) Genetics is central to biology because genes and their functions form the basis of all life processes.
A)True
B)False
Answer: True
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Q1) The genome of the T-even family of bacteriophage consists of single-stranded RNA.
A)True
B)False
Answer: False
Q2) Which form of DNA is a left-handed double helix?
A)A-DNA
B)B-DNA
C)L-DNA
D)R-DNA
E)Z-DNA
Answer: E
Q3) Who used radioactively labeled T2 bacteriophage to confirm the identity of the transforming principle?
A)Griffith
B)Hershey and Chase
C)Avery
D)Gierer and Schramm
E)Beadle and Tatum
Answer: B
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Q1) A cross is made between yeast cells with different alleles for a set of linked genes: pr<sup>+q</sup> × p<sup>+rq+</sup>.The resulting tetrads show a 3:1 ratio for r<sup>+ </sup>to r instead of the expected 2:2 ratio.Can you explain how this could have occurred?
Answer: Gene conversion by a mismatch repair mechanism could have caused this deviation from expected ratios.During pairing of homologous chromosomes in meiosis,recombination between the two inner chromatids occurred,resulting in heteroduplex (mismatched)DNA strands.Both mismatches were repaired by excision and DNA synthesis to match the parent DNA with the r<sup>+</sup> allele.
Q2) During replication,the direction of synthesis of new DNA from the leading and lagging strands is
A)5' to 3' only.
B)3' to 5' only.
C)from left to right only.
D)both 5' to 3' and 3' to 5'.
E)different,depending on whether the cell is prokaryotic or eukaryotic.
Answer: A
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Q1) Albinism is caused by an inborn error of metabolism.
A)True
B)False
Q2) How do scientists,lacking the ability to make controlled genetic crosses in humans,study the inheritance of and give genetic counseling on human genetic disorders?
Q3) Normal and sickle-cell hemoglobin molecules differ
A)in the number of amino acids in each molecule.
B)by a single DNA point mutation that leads to the substitution of one amino acid for another.
C)in the number and orientation of the amino acid chains attached to the heme portion of each molecule.
D)in the number of oxygen molecules that can be carried by each molecule.
E)by the type of bone marrow that produces them.
Q4) A carrier for a disease
A)is homozygous for the dominant mutation.
B)is homozygous for the recessive mutation.
C)is heterozygous for the dominant mutation.
D)is heterozygous for the recessive mutation
E)is hemizygous for any mutation.
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Q1) During transcription,the synthesis of the mRNA strand proceeds in which direction?
A)5' to 3' only
B)3' to 5' only
C)Both 5' to 3' and 3' to 5'
D)Either 5' to 3' or 3' to 5'
E)First 5' to 3',and then 3' to 5'
Q2) Posttranscriptional insertion or deletion of nucleotides that is absent in the DNA template is called
A)RNA splicing.
B)RNA editing.
C)RNA processing.
D)RNA capping.
E)RNA modification.
Q3) How does the rate of initiation of transcription relate to the similarity of the promoter region to the consensus sequence?
Q4) The sequence of a template strand of DNA is 3'-CATTACGCTT-5'.What is the sequence of the corresponding mRNA?
Q5) Describe the structure and organization of the rDNA repeat unit in eukaryotes.
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Q1) Protein synthesis begins when ribosomes bind to the UGA codon.
A)True
B)False
Q2) Describe a cell-free protein synthesizing system with which you could determine unambiguously which codons specify which amino acids.
Q3) With absolutely no exception,all organisms use the same genetic code for the production of proteins.
A)True
B)False
Q4) How can a carrot plant express a bacterial gene?
A)Because the bacterial gene hijacks the carrot's cellular machinery
B)Because the genetic code is the same in both organisms
C)Because of the wobble phenomenon
D)Because of the degeneracy of the genetic code
E)A carrot cannot express a bacterial gene.
Q5) Describe and differentiate among the primary,secondary,and tertiary structures of a protein.To which kinds of interactions can each of these stages be ascribed?
Q6) Why is methionine the first amino acid to be added to every polypeptide chain?
Q7) When does quaternary structure occur?
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Q1) The codon 5'-AAA-3' codes for the amino acid lysine.Which of the following mutations in this codon is a neutral mutation?
A)5'-ATA-3' to isoleucine
B)5'-AGA-3' to arginine
C)5'-AAG-3' to lysine
D)5'-CAA-3' to glutamine
E)5'-AAC-3' to asparagine
Q2) A transposon may carry genes for proteins that enable their transposition as well as genes for other functions such as drug resistance.
A)True
B)False
Q3) A tumor suppressor gene is cloned and mutagenized in vitro,then injected into mouse embryos to create knockout mice.How could you identify the heterozygous knockout mice and create mice susceptible to tumors?
Q4) For a particular gene,if one gene in a million experiences a mutation each generation,what is its mutation frequency?
Q5) How can PCR be used to induce site-specific mutations in DNA?
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Q6) Explain what a mutator gene is and give an example.
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Q1) What advantage do cDNA libraries have over genomic libraries?
Q2) Describe the basic approach to shotgun genome sequencing.
Q3) It is not always easy to locate or identify genes based on cDNA.How is this problem created by the differences between cDNA and DNA with respect to a given gene?
Q4) Describe a DNA microarray setup for assaying mutations associated with a hypothetical genetic disease.
Q5) Plasmid
A)Eukaryotic cloning vector
B)Molecule used in DNA sequencing
C)Origin of replication
D)Small circular fragment of DNA
E)Endonuclease isolated from bacteria
Q6) YAC
A)Eukaryotic cloning vector
B)Molecule used in DNA sequencing
C)Origin of replication
D)Small circular fragment of DNA
E)Endonuclease isolated from bacteria
Q7) What problem does this result in?

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Q1) The genome of cancer cells tends to become unstable.
A)True B)False
Q2) What is one advantage that an RNAi screen may have over a screen for gene knockouts?
Q3) The FOXP2 protein appears to play a critical role in brain size regulation.
A)True
B)False
Q4) After how many PCR cycles,starting from a single starting molecule,will fragments consisting of only the target DNA (the DNA between the primers)be generated?
Q5) How do we know that some of the microbes in our gut are beneficial to us?
Q6) A genomic region can rapidly become very common in a population due to A)positive selection.
B)negative selection.
C)specific selection.
D)linkage equilibrium.
E)homologous recombination.
Q7) Calculate the number of copies that would be produced from a single starting molecule after 10 rounds of PCR.
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Q1) Two STR loci were determined to have the following allele frequencies in the general population:
\[\begin{array} { l l l }
& \text { STR A } & \text { STR B } \\
\text { Alleles: } & \text { 1A: } 0.1 & \text { 1B: } 0.4 \\ & 2 \mathrm {~A} : 0.55 & 2 \mathrm {~B} : 0.4 \\ & 3 \mathrm {~A} : 0.25 & \text { 3B: } 0.2 \\ & 4 \mathrm {~A} : 0.1 & \end{array}\]
A suspect in a criminal trial was genetically tested for these loci and was found to have the genotype (1A,1A)for STR A and (2B,2B)for STR B-homozygous for both loci.What is the probability that a randomly sampled person from this population would also have this genotype?
Q2) Briefly explain how Ti plasmids induce crown gall (tumor)growth in plants parasitized by Agrobacterium tumefaciens,highlighting the specific properties that make this plasmid so useful in biotechnology.
Q3) How has the Bt protein been used to increase insect-resistance in plants?
Q4) Study of P elements in Drosophila has shown that gene regulation can be accomplished by differential mRNA transcript processing.Explain.
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Q1) A dihybrid cross yields 320 F<sub>2</sub> offspring.How many are expected to resemble the homozygous recessive parental?
A)10
B)16
C)20
D)60
E)180
Q2) Speculate on the molecular basis for dominance and recessiveness,using flower color as an example,where red is dominant over white.
Q3) Net or overall probabilities are obtained by multiplying separate independent probabilities.This is formally known as
A)the sum rule.
B)the chi-square test.
C)the product rule.
D)the sign test.
E)the probability rule.
Q4) The phenotype determines the genotype.
A)True
B)False
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Q1) Chromosomes with only one arm are known as A)metacentric.
B)submetacentric.
C)acrocentric.
D)telocentric.
E)acentric.
Q2) Red-green color blindness in humans is an X-linked recessive trait.What will the progeny ratios be if a carrier female is mated with a normal male?
A)All the sons will be color blind; all the daughters will be normal.
B)All the sons and half the daughters will be color blind.
C)Half the sons will be color blind; all the daughters will be carriers.
D)Half the sons will be color blind; half the daughters will be carriers.
E)All the sons and all the daughters will be normal.
Q3) Cells obtained from a Triplo-X woman would contain ________ Barr bodies.

Q4) What is the connection between the work of Mary Lyon and Murray Barr?
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Q1) What is the cause of Tay-Sachs disease?
Q2) Mutants that make up a complementation group complement each other.
A)True
B)False
Q3) Phenylketonuria (PKU)is an example of a phenotype that is solely influenced by genes.
A)True
B)False
Q4) The 9:6:1 F<sub>2</sub> ratio found in fruit shape in summer squash is a deviation from an expected Mendelian ratio.What does this represent?
Q5) Which of the following will result in modifications to the expected Mendelian ratios?
A)Epistasis
B)Incomplete dominance
C)Incomplete penetrance
D)Gene interaction
E)All of these
Q6) An allele that exhibits incomplete dominance is usually haplosufficient.
A)True
B)False
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Q1) Explain how Curt Stern showed,using evidence from Drosophila,that genetic recombination is associated with the physical exchange of parts between homologous chromosomes.
Q2) A DNA mutation that gives a distinguishable phenotype for a chromosome or gene is a
A)recessive allele.
B)lethal mutation.
C)parental type.
D)linkage group.
E)genetic marker.
Q3) If two genes are not linked,then the expected phenotypic ratio resulting from a testcross is
A)9:3:3:1.
B)1:2:1.
C)3:1.
D)1:1:1:1.
E)1:1.
Q4) What is the difference in the likelihood of linkage between two genes with a lod score of 2 and two genes with a lod score of 3?
Q5) What does the chi-square test tell us about the linkage of two genes?
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Q1) The E.coli chromosome is
A)linear.
B)circular.
C)single-stranded.
D)less than a megabase in length.
E)compartmentalized within an intracellular membrane.
Q2) Cotransductants can be detected when the transduced genes are
A)closely linked.
B)far apart on the same chromosome.
C)on different chromosomes.
D)mutant.
E)Both B and D
Q3) Minimal media is
A)growth media used in the smallest volume in which cells can grow.
B)growth media designed to minimize the growth of contaminants.
C)growth media that contains the minimal nutritional requirements for normal cells.
D)a way to visualize new mutations in a minimum amount of time.
E)used to reveal only mutant cell colonies against a dark background.
Q4) What are temperate bacteriophages?
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Q1) How does a Philadelphia chromosome occur,and what condition does it cause?
Q2) A(n)________ inversion includes the centromere.
A)concentric
B)pericentric
C)paracentric
D)epicentric
E)chromocentric
Q3) In some fruit flies,an inversion involving the white-eyed locus (w)moves the w<sup>+</sup>gene from one end of the X chromosome to a location nearer to the centromere.Flies with a w<sup>+</sup> or w<sup>+</sup>/w genotype are normally expected to have red eyes.However,in flies with the inversion,the eyes are mottled red and white.Explain why.
Q4) Most monoploid individuals do not survive because
A)they do not have the appropriate gene dosages. B)their cells cannot divide properly.
C)recessive lethal mutations cannot be masked by dominant alleles. D)they have missing genes.
E)they have only one sex chromosome.
Q5) How is hybrid sterility overcome in allopolyploid plants?
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Q1) The enzyme transacetylase is responsible for uptake of lactose.
A)True
B)False
Q2) The structural genes in the lac operon are transcribed into a single polycistronic mRNA molecule.
A)True
B)False
Q3) Give an overview of the mechanism by which ultraviolet radiation induces the lytic pathway in lambda phage.
Q4) The genetic switch for the infection pathways of lambda phage is controlled by two regulatory proteins: ________ and ________.
A)lambda repressor,Cro
B)lambda repressor,permease
C)excisionase,integrase
D)recA,Cro
E)lyase,lysogenase
Q5) A constitutive gene is a gene that is occasionally expressed.
A)True
B)False
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Q1) Insect growth and metamorphosis is controlled by the steroid hormones ecdysone and juvenile hormone (JH).In insects like butterflies and moths that have a distinct larval (juvenile)and adult stage,the relative amount of JH determines whether the insect molts to the next juvenile stage or switches to become an adult.Can you think of a way to use this hormonal system to control caterpillar agricultural pests?
Q2) Which of the following secondary structures may be a DNA-binding domain?
A)Zinc finger
B)Leucine zipper
C)Helix-turn-helix
D)A and B only
E)A,B,and C
Q3) In genetic imprinting,expression depends on the parent of origin of a given allele.How might imprinting affect the expression of a hypothetical autosomal disease that expresses in dominant fashion and recessive fashion,and how might imprinting be detected?
Q4) Describe how siRNA functions in regulation of expression and how this can be used as a tool in genetic research.
Q5) What are some advantages and disadvantages of arranging gene clusters into operons?
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Q1) The X-controlling element gene is
A)SRY.
B)XIC.
C)Xce.
D)MATa.
E)Xist.
Q2) ________ cells may differentiate into any cell or tissue type.
A)Pluripotent
B)Omnipotent
C)Totipotent
D)Hyperpotent
E)Potent
Q3) If cell and tissue differentiation is controlled genetically,how can environmental factors play a role in determining the final phenotype?
Q4) No human cells lose all of their DNA during differentiation.
A)True
B)False
Q5) Can you think of a specific example in which multiple genome datasets would be useful in the study of morphogenesis?
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Q1) Metastatic cancer is
A)terminally differentiated.
B)malignant.
C)invasive.
D)B and C only
E)A,B,and C
Q2) Small DNA tumor viruses such as SV40 and HPV have viral oncogenes that are not homologs of host cell genes.Some of these novel viral oncogenes make proteins that exert their tumorigenic effect by
A)binding to and inactivating pRB.
B)making Gag,Pol and Env proteins more active.
C)causing cellular proto-oncogenes to mutate into oncogenes.
D)causing apoptosis in target tissues.
E)inactivating the immune system.
Q3) The products of tumor suppressor genes stimulate cell proliferation,while the products of proto-oncogenes inhibit cell proliferation.
A)True
B)False
Q4) List the ways in which proto-oncogenes may be converted to oncogenes.
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Q1) Two neighboring Caribbean islands harbor iguana populations.One island (island A)has a total iguana population of 800,while the other (island B)has a population less than half that size,numbering 250.On island A,the frequency of an allele p is estimated at 0.75,while this same allele is present at a frequency of 0.90 on island B.During a hurricane tracking across the islands,a group of about 100 iguanas get rafted from island A to island B.What effect does this have on the frequency of allele p on island B?
Q2) The genetic variation between human "races," such as Africans and Europeans,is greater than the variation within a single race.
A)True
B)False
Q3) What is the observed genotypic frequency of Aa individuals?
A)0.144 B)0.72

Q4) Show algebraically that under Hardy-Weinberg equilibrium, allele frequencies will not change from one generation to another.
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Q1) Narrow-sense heritability for a trait can be obtained from a regression of midparent value on offspring value.
A)True
B)False
Q2) Which of the following problems might arise in a statistical study as a result of a population sample of inadequate size?
A)A non-representative sample
B)Sampling error
C)A non-random sample
D)A sample drawn from a biased subset of data points
E)All of these
Q3) In parent-offspring regression,the average value of the parents is termed the
A)mean parental value.
B)parental average.
C)midparent value.
D)median parental value.
E)modal parental value.
Q4) Define,in your own words,the biological meaning of heritability.
Q5) Distinguish between polygenic and multifactorial traits.
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Q1) One of the lines of evidence supporting the theory that modern humans originated in Africa is that the modern-day human population of Africa contains the greatest diversity of genetic variants of any human population.Why is this consistent with the idea that humans first evolved in Africa?
Q2) Nonsynonymous substitutions
A)do not lead to amino acid change.
B)lead to amino acid change.
C)refer to substitutions in unrelated lineages.
D)affect only certain amino acids.
E)lead to transversions.
Q3) Codon bias suggests that
A)some codons evolved earlier than others.
B)not all nonsynonymous substitutions are neutral.
C)some codons are selectively favored over others.
D)small fitness effects can make a large difference over time.
E)some tRNAs are more abundant than others.
Q4) Humans have an extremely high level of genetic similarity,with greater than 99% sequence identity across populations.Yet,many people appear very different phenotypically.How do you reconcile these observations?
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