Genomics
Chapter Exam Questions
Course Introduction
Genomics is an interdisciplinary course that explores the structure, function, evolution, mapping, and editing of genomes in living organisms. Students will examine how genome sequencing technologies and computational analysis are used to investigate genetic variation and understand complex biological systems. Topics include genome organization, comparative genomics, functional genomics, and applications in medicine, agriculture, and biotechnology. The course emphasizes the ethical, legal, and social implications of genomic research, preparing students to critically evaluate advances in this rapidly evolving field.
Recommended Textbook
Introduction to Genetic Analysis 11th Edition by Anthony J.F. Griffiths
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Page 2
Chapter 1: The Genetics Revolution
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Q1) Which of the following is/are FALSE about genes?
A)Genes are located on chromosomes.
B)Genes come in variants known as alleles.
C)Genes always encode protein products.
D)All of the answer options are correct.
E)None of the answer options are correct.
Answer: C
Q2) Which of the following is a correct representation of the central dogma?
A)RNA DNA protein
B)protein DNA RNA
C)DNA RNA protein
D)DNA protein DNA
E)None of the answer options are correct.
Answer: C
Q3) Explain what it means to say that the genetic code is redundant.How does this redundancy help protect against mutations?
Answer: The genetic code is redundant because some of the amino acids are encoded by more than one triplet (codon).This protects against the effects of mutation since a change in the nucleotide base may not cause a different amino acid to be inserted.
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Chapter 2: Single-Gene Inheritance
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Q1) What is the maximum number of heterozygous genotypes that could be produced by monohybrid self?
D)4
E)6
Answer: A
Q2) Mendel studied the inheritance of phenotypic characters determined by alleles of seven different genes.It is an interesting coincidence that the pea plant has seven pairs of chromosomes (n = 7).What is the probability that,by chance,Mendel's seven genes would each be located on a different chromosome? You may assume that the pea's chromosomes are all the same size.
Answer: 6!/7<sup>6</sup> = 6.12 * 10<sup>-3</sup>
Take each gene in turn.The probability is 1 that the first gene falls on a chromosome.The probability that the second gene falls on any of the remaining six chromosomes is 6/7,the next is 5/7,etc.The overall probability is the product of all these.
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Chapter 3: Independent Assortment of Genes
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Q1) If stem length in a certain species of crops was solely determined by polygenic inheritance,how many different genes would be required in this system to explain the existence of 15 different stem lengths ranging from 15 to 29 cm?
Answer: A system with seven genes and two alleles each work in an equal and additive manner.It can be helpful to start by thinking about how many genes are required for 3,4,5,etc. ,different phenotypes.From there,one will notice that the number of possible phenotypes is always equal to 2x the number of genes + 1.
Q2) Define Mendel's experimental evidence for diploid chromosome content in pea plants.
Answer: Mendel noticed that recessive traits were "hidden" in the F<sub>1</sub> progeny of his monohybrid and dihybrid crosses.When the F<sub>1</sub> plants were selfed,the recessive trait appeared again in the next generation of plants (F<sub>2</sub>).This was reproducible and followed a ratiometric pattern consistent with two genetic determinants (genes)being carried for each trait.
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Chapter 4: Mapping Eukaryote Chromosomes by
Recombination
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Q1) In the cross mt<sup>+</sup>al<sup>+</sup> \(\times\) mt al,the mt locus shows an M<sub>II</sub> frequency of 12%,the al locus an M<sub>II</sub> frequency of 10%.Most asci were parental ditypes.The order of loci is:
A)al - centromere - mt.
B)al - mt - centromere.
C)centromere - al - mt.
D)centromere - mt - al.
E)mt - centromere - al.
Q2) Consider the following experimental results. (M = mapping function and MU = M x 50)
\[\begin{array} { c c c }
\text { OBSERVED RF } & \mathrm { M } & \mathrm { MU } \\
18.5 \% & 0.46 & 23.1 \\ & & \\
6.4 \% & 0.137 & 6.8 \end{array}\]
Based on these results,would you advocate the use of mapping functions? In which situations would you recommend using them?
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Chapter 5: The Genetics of Bacteria and Their Viruses
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Q1) In a generalized transduction experiment,donor E.coli cells have the genotype a<sup>+</sup>c<sup>+</sup>b<sup>-</sup>,and recipient cells have the genotype a<sup>-</sup>c<sup>-</sup>b<sup>+</sup>.Pl-mediated transductants for a<sup>+</sup> were selected,and their total genotypes were determined,with the following results:
\[\begin{array} { l }
\text {Genotype}&\text { Number of progeny}\\
\hline a ^ { + } c ^ { + } b ^ { - } &95 \\
a ^ { + } c ^ { - } b ^ { - } &205\\
a ^ { + } c ^ { + } b ^ { + }& 5 \\
a
^ { + } c ^ { - } b ^ { + } &\underline { 195 } \\ &500 \end{array}\]
a)What is the order of the three genes?
b)What is the cotransduction frequency for:
\(a\) and \(c\) ?
\(a\) and \(b ?\)
\(b\) and \(c ?\)
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Chapter 6: Gene Interaction
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Q1) In sweet peas,the allele C is needed for color expression (c results in white).The precise color expressed is determined by the alleles R (red)and r (blue).A cross between certain red and blue plants resulted in progeny as follows: 3/8 red,3/8 blue,1/4 white.What were the genotypes of the plants crossed?
A)\ C/c;R/r \(\times\) C/C;R/R
B)C/c;R/r \(\times\) C/c;R/r
C)C/c;R/r \(\times\) C/c;r/r
D)C/c;R/r \(\times\) c/c;R/r
E)C/c;r/r \(\times\) C/C;R/r
Q2) On an illegal wolf ranch in Wyoming,cowboys breed gray wolves and sell them illegally.A mutation was identified,generating a beautiful gray "speckled" coat color.The speckled wolves were particularly popular with buyers.The breeders struggled to keep up with demand.They noticed that when two speckled wolves were bred,their pups always contained some normal gray and some speckled gray pups.In one typical season of interbreeding the speckled wolves,they cumulatively generated 82 speckled and 38 gray pups.State a clear genetic explanation for the pattern illustrated.
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Chapter 7: Dna: Structure and Replication
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Q1) Smooth (S)and rough (R)strains of Streptococcus pneumonia are distinct because of their ability to cause illness (death in rodents).This trait is controlled by genes that regulate:
A)the production of a protective polysaccharide coat (capsule)around each cell.
B)the production of lethal toxins.
C)the speed of bacterial growth.
D)the metabolic rate of microbial glycolysis.
E)the bacterial ability to penetrate through the membrane of animal cells.
Q2) If Escherichia coli,grown for a period of time in <sup>15</sup>N,is transferred to <sup>14</sup>N for one generation of DNA replication,the resulting DNA should have <sup>14</sup>N added to all "new" DNA.If conservative replication is occurring,the <sup>14</sup>N-containing "new" DNA will compose:
A)one strand of all bacterial chromosomes.
B)both strands of DNA in half of all bacterial chromosomes.
C)regions dispersed throughout all bacterial DNA.
D)none of the new DNA;it will only be found in the old DNA.
E)All of the answer options are correct.
Q3) Telomeres regulate the replication of the ends of chromosomes in eukaryotes.Why is this structure implicated in human aging?
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Chapter 8: Rna: Transcription and Processing
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Q1) For protein-encoding genes,six general transcription factors (GTFs)function to:
A)identify a gene's promoter,facilitating RNA polymerase II binding.
B)terminate transcription at the end of an open reading frame.
C)assemble the RNA polymerase subunits.
D)arrest DNA replication.
E)recruit the ribosome to newly synthesized RNAs.
Q2) The sigma factor protein's role in transcription in E.coli includes which of the following?
A)forms part of the core enzyme required for transcription initiation
B)helps the holoenzyme to bind to the promoter
C)contributes to the proof reading activity of RNA polymerase
D)plays a role in transcription termination
E)All of the answer options are correct.
Q3) The conserved adenine nucleotide in introns serves as the:
A)site for intron recognition for the spliceosome.
B)branch point for the formation of the intronic "lariat."
C)key point for ribosome assembly and initiation of translation.
D)initial site of intronic RNA digestion and removal.
E)molecular signal for RNA splicing.
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Chapter 9: Proteins and Their Synthesis
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Q1) A tRNA with the anticodon 3 -ACC-5 would carry the amino acid:
A)phenylalanine.
B)tyrosine.
C)serine.
D)threonine.
E)tryptophan.
Q2) You found a mouse gene sequence containing an open reading frame that should produce a 43 kDa protein.You express this protein in cultured mouse cells by transforming the cells with a plasmid bearing your gene of interest.When you isolate proteins from these cells and probe for your protein of interest,you find that the detected protein is 49 kDa.Why might your protein be larger than expected when analyzed by immunoblot?
Q3) Many antibiotics operate by interfering with translation-associated process or other essential cellular functions.How does tetracycline inhibit cellular translation? If tetracycline inhibits such an important process,why is it not lethal to humans when ingested to treat infection?
Q4) Describe how it was determined that the genetic code was not overlapping.What evidence was used to support this?
Q5) Describe the types of RNAs participating in translation.
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Chapter 10: Gene Isolation and Manipulation
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Q1) A linear molecule of DNA 9 kb in length is isolated and mapped using restriction endonucleases EcoRI and HindIII.The fragments generated by the single and double digests are shown below.The numbers refer to the length of fragments in kilobases.
EcoRI: 7 kb,2 kb
HindIII: 5 kb,4 kb
EcoRI + HindIII: 4 kb,3 kb,2 kb
SalI: 8.5 kb,0.5 kb
EcoRI + SalI: 7 kb,1.5 kb,0.5 kb
Construct a restriction map of this linear fragment of DNA.
Q2) This linear vector is comprised of bacteriophage genome components and can carry cloned DNA up to 15 kb in size.
A)pUC19
B)lambda
C)fosmid
D)bacterial artificial chromosome
E)T-vector
Q3) Human insulin can be made purer,and at a lower cost,using recombinant DNA technology.What sort of DNA clone might be ligated into a bacterial expression plasmid to be used in this strategy?
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Page 12
Chapter 11: Regulation of Gene Expression in Bacteria and Their Viruses
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Q1) In Bacillus,the presence of alternate forms of which molecule is responsible for the control of large numbers of genes?
A)DNA dependent RNA polymerase
B)TFII
C) factor
D)Trp repressor
E)Operator protein
Q2) In the presence of the repressor molecule and the absence of free tryptophan,the trp operon is:
A)constitutively transcribed.
B)derepressed.
C)induced.
D)repressed.
E)transcribed but not translated.
Q3) In the bacteriophage \(\lambda\),the mutants cI,cII,and cIII form:
A)form turbid plaques and are able to establish lysogeny.
B)form clear plaques and are unable to establish lysogeny.
C)form turbid plaques and are unable to establish lysogeny.
D)form clear plaques and are able to establish lysogeny.
E)form both clear and turbid plaques.
Page 13
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Chapter 12: Regulation of Gene Expression in Eukaryotes
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Q1) DNA elements that prevent the spreading of heterochromatin into adjacent euchromatic regions are called:
A)enhancer blocking elements.
B)euchromatin buffers.
C)barrier insulators.
D)barrier buffers.
E)barrier-blocking elements.
Q2) The enzyme responsible for removing acetyl groups from histone proteins is called:
A)histone acetylase (HA).
B)histone deacetylase (HDAC).
C)histone acetylmethyltransferase (HAT).
D)histone acetyltransferase (HAT).
E)histone methyltransferase (HMT).
Q3) The miRNA-RISC complex is known to inhibit translation.List several possible mechanisms for translational inhibition mediated by miRNA-RISC.
Q4) Histones are essentially identical in sequence/structure in all eukaryotic organisms from yeast to plants to animals.What does this say about the biophysical properties of DNA-packaging and the evolution of eukaryotic organisms?
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Chapter 13: The Genetic Control of Development
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Q1) Establishment of the dorsal-ventral axis of the Drosophila embryo:
A)involves the production of localized DL mRNA on the ventral side of the developing embryo.
B)occurs via at least two paracrine signals transmitted between the developing oocyte and the surrounding somatic follicle cells.
C)involves the zygotically expressed DL morphogen.
D)depends on the activity of anterior-posterior morphogens,such as BCD or HB-M.
E)None of the answer options are correct.
Q2) The class of genes that affect patterning within each segment is the:
A)maternal-effect genes.
B)gap genes.
C)pair-rule genes.
D)segment polarity genes.
E)Hox genes.
Q3) Homeosis is defined as the failure to:
A)form the correct number of segments.
B)correctly polarize a developing embryo.
C)develop antenna.
D)correctly establish segmental identity.
E)None of the answer options are correct.
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Chapter 14: Genomes and Genomics
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Q1) When comparing different genomes,"synteny" is defined as:
A)the same genes in the same order.
B)the same genes in essentially the same order.
C)the same genes in reverse order.
D)different genes found on similar chromosomes.
E)duplication of entire genomes.
Q2) Genes that have been inherited from a common ancestor are called: A)homologs.
B)orthologs.
C)paralogs.
D)heterologs.
E)alleles.
Q3) Deducing the protein encoding genes from genomic sequences involves: A)ORF detection.
B)direct evidence from cDNA sequences.
C)predictions of binding site.
D)predictions based on codon bias.
E)All of the answer options are correct.
Q4) Describe the information content of a genome.
Q5) Please list three (3)approaches to reverse genetics.
Page 16
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Chapter 15: The Dynamic Genome: Transposable Elements
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Q1) Compare and contrast autonomous and nonautonomous transposable elements.
Q2) Which of the following statements is/are FALSE about Tc1 elements found in C.elegans?
A)Tc1 elements are retrotransposons.
B)Tc1 elements can transpose only in somatic cells.
C)Tc1 elements were used to study the RNAi based silencing mechanisms.
D)Single Tc1 element can trigger the silencing of all copies of Tc1 elements in the C.elegans genome.
E)None of the answer options are correct.
Q3) A corn plant is homozygous for a mutant allele that results in no pigment in the seed (i.e.,white).The mutant is caused by Ds insertion that often exits late in seed development,when there is an active Ac element in the genome.If there is NO active Ac element,the seeds of this plant will be:
A)no pigment (i.e. ,white).
B)pigmented all over.
C)white with small spots of pigment.
D)white with large spots of pigment.
E)weakly pigmented.
Q4) a)What is the C-value paradox?
b)What is the explanation for the C-value paradox?
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Chapter 16: Mutation, Repair, and Recombination
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Q1) E.coli cells that have null mutations in the gene encoding adenine methylase will have:
A)a higher spontaneous mutation rate than wild-type E.coli.
B)the same spontaneous mutation rate as wild-type E.coli.
C)a lower spontaneous mutation rate than wild-type E.coli.
D)more double-strand breaks in their DNA than wild-type E.coli.
E)fewer double-strand breaks in their DNA than wild-type E.coli.
Q2) The spontaneous reversion rate for a chemically induced mutation is 1 × 10<sup>-</sup><sup>8</sup>.For EMS ,the rate is 0.9 × 10<sup>-</sup><sup>8</sup>,and for acridine,it is 2 × 10<sup>-</sup><sup>5</sup>.What change was involved in the original mutation?
A)an AT to CG transversion
B)an AT to GC transition
C)a frameshift mutation
D)a GC to AT transition
E)a GC to TA transversion
Q3) Five different mutations were derived from base pair substitutions at a single codon.In this codon,the mutant alleles had arginine,leucine,glycine,serine,and cysteine.What was the wild-type codon?
Q4) How do mutation and DNA damage differ?
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Chapter 17: Large-Scale Chromosomal Changes
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Q1) A particular hybrid species is defined as 3n = 12.It is discovered that at meiosis,pairing is always univalent + bivalent (never trivalent)in this species.How many bivalents will be present in prophase of meiosis I?
A)2
B)3
C)4
D)8
E)12
Q2) An allotetraploid plant with 2n = 30 is backcrossed to one of its progenitor species that has an n = 8.A sterile progeny is produced.How many chromosomes will this sterile individual possess,and what are the chromosome numbers of the two progenitor species?
Q3) In a triploid of genotype B/b/b,what proportion of gametes will be B?
A)1/6
B)1/4
C)1/3
D)1/2
E)2/3
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Chapter 18: Population Genetics
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Q1) A horticulturist plans to self a plant,then (individually)self each of the F<sub>1</sub> plants,and repeat the same procedure until he obtains a plant that is heterozygous at no more than one gene.If the parental plant has 15,000 genes and is heterozygous for all of them,how many generations will this process take? (For the purposes of this question,count the parental plant as "1 generation.")
A)8 generations
B)15 generations
C)30 generations
D)15,000 generations
E)30,000 generations
Q2) After a thorough analysis of the DNA from 150 university students,a small region of the human X chromosome is found to have three SNP sites.Two of those sites have three different variants,while the third site has four.How many different haplotypes were present in each student's cells?
A)1 or 2
B)3 or 6
C)10 or 20
D)32 or 64
E)It is impossible to determine based on this information alone.
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Chapter 19: The Inheritance of Complex Traits
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Q1) Which of the following has more important value to the plant or animal breeder?
A)broad-sense heritability
B)variance
C)correlation
D)additive deviation
E)dominance deviation
Q2) Imagine that an association mapping study revealed a particular variant of a SNP to be strongly associated with susceptibility to insomnia.From these data,you could infer that:
A)the SNP is closely linked to a locus that plays a role in insomnia.
B)the SNP is located in a gene that determines insomnia.
C)the SNP provides evidence that insomnia is a genetic condition.
D)the variant SNP most likely causes insomnia.
E)the variant SNP plays a role in insomnia.
Q3) In a large flock of turkeys,average body weight is 5.0 kg.In a test to determine if the average weight of the flock can be increased by selective breeding,6.2 kg birds are removed and allowed to interbreed.Their progeny have an average weight of 5.2 kg.Calculate the narrow-sense heritability (h<sup>2</sup>).
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Chapter 20: Evolution of Genes and Traits
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Q1) Which of the following is/are NOT a principle of Darwinian evolution?
A)There is variation in morphology,physiology,and behavior among individuals in a population.
B)Offspring resemble their parents more closely than unrelated individuals.
C)In any given environment,some individuals are more successful at surviving and reproducing than others.
D)Darwinian evolution fully describes where all living things come from.
E)All of the answer options are correct.
Q2) In E.coli,the mutation of beta-lactamase in response to cefotaxime exposure involved five changes in the gene sequence,which can be accomplished through __________ different orderings.
A)16
B)32
C)64
D)120
E)240
Q3) Darwin's theory of evolution was developed around three central principles: the principle of variation,the principle of heredity,and the principle of selection.Define each of these principles,and explain their role in evolution.
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