Genomics Exam Review
Course Introduction
Genomics is the comprehensive study of the structure, function, evolution, mapping, and editing of genomes, which are the complete set of DNA within a single cell of an organism. This course introduces students to the fundamental concepts and technologies in genomics, including DNA sequencing, genome assembly and annotation, comparative genomics, functional genomics, and the application of bioinformatics tools. Emphasis is placed on understanding how genomic data is generated, analyzed, and interpreted, as well as exploring its impact on fields such as medicine, agriculture, and evolutionary biology. Through hands-on exercises and case studies, students gain practical experience in analyzing genomic datasets and learn about current advances and ethical considerations in the field.
Recommended Textbook
Introduction to Genetic Analysis 11th Edition by Anthony J.F. Griffiths
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Chapter 1: The Genetics Revolution
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Sample Questions
Q1) 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
Q2) A sample of normal double-stranded DNA was found to have a guanine content of 18%.What is the expected proportion of adenine?
A)9%
B)32%
C)36%
D)68%
E)82%
Answer: B
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Page 3
Chapter 2: Single-Gene Inheritance
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Sample Questions
Q1) What is the maximum number of heterozygous genotypes that could be produced by monohybrid self?
A)1 B)2
C)3
D)4
E)6
Answer: A
Q2) A dominant gene b<sup>+</sup> is responsible for the wild-type body color of Drosophila;its recessive allele b produces black body color.A testcross of a heterozygous b<sup>+</sup>/b female by a black b/b male gave 52 black and 58 wild-type progeny.If a black female from these progeny were crossed with a wild-type brother,what phenotypic ratios would be expected in their offspring?
A)All males will be wild type,and all females will be black.
B)All progeny will be black.
C)All progeny will be wild type.
D)75% will be wild type,25% will be black.
E)50% will be wild type,50% will be black.
Answer: E
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Page 4
Chapter 3: Independent Assortment of Genes
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Sample Questions
Q1) Several pairs of light brown hamsters with identical genotypes were mated.Altogether,the F<sub>1</sub> was comprised of 143 individuals: 62 light brown,41 brown,38 beige (very,very light brown),1 dark brown,and 1 white.What mode of inheritance of the phenotype "fur color" could most easily explain these results?
Answer: Polygenic inheritance: The different phenotypes can be considered as different "degrees of brownness" and could be explained by a system of two genes with two alleles each that work in an equal and additive manner.The parents would be A/a;B/b.A cross between two such individuals would produce a ratio of 1:4:6:4:1 in terms of "doses" if we consider the dominant alleles are "functioning" and the recessive ones as "non-functioning," in terms of producing pigment.
Q2) Which of the following is/are TRUE with respect to haploid and diploid cells?
A)Following DNA replication,haploid cells become diploid.
B)In diploid cells,meiosis I results in the formation of two haploid cells.
C)In haploid cells,condensed chromosomes have an "I" shape,while in diploid cells they have an "X" shape.
D)In haploid cells meiosis is simpler,owing to unpaired chromosomes.
E)The process of meiosis is identical in haploid and diploid cells.
Answer: B
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Chapter 4: Mapping Eukaryote Chromosomes by
Recombination
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Sample Questions
Q1) The maize genes sh and bz are linked,40 map units apart.If a plant sh<sup>+</sup>bz/sh bz<sup>+</sup> is selfed,what proportion of the progeny will be sh bz/sh bz?
A)0.04
B)0.10
C)0.20
D)0.40
E)0.50
Q2) Neurospora loci d and f are located on the same chromosome.The d locus always segregates at M<sub>I</sub>,while the e locus segregates at M<sub>II</sub> at a frequency of 10%.Assuming complete interference,the distance between loci d and f is:
A)5 map units.
B)10 map units.
C)20 map units.
D)40 map units.
E)45 map units.
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Chapter 5: The Genetics of Bacteria and Their Viruses
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Sample Questions
Q1) A strain of E.coli has the genotype (and phenotype)leu<sup>-</sup> lac<sup>-</sup>.This notation means that this strain if bacteria is unable to:
A)metabolize the amino acid leucine and synthesize the sugar lactose.
B)utilize the amino acid leucine and synthesize the sugar lactose.
C)utilize the amino acid leucine and the sugar lactose.
D)synthesize the amino acid leucine and utilize the sugar lactose.
E)synthesize the amino acid leucine and the sugar lactose.
Q2) A permissive bacterial strain is simultaneously infected with two strains of T4-like phage.One phage strain has the genotype a<sup>-</sup>b<sup>+</sup>,while the other is a<sup>+</sup>b<sup>-</sup>.If the map distance between markers a and b is about 10 map units,what proportion of the progeny phages are expected to have the genotype a<sup>+</sup>b<sup>+</sup>?
A)about 1/20
B)about 1/10
C)about 4/10
D)about 4/5
E)about 9/10
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Page 7
Chapter 6: Gene Interaction
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Sample Questions
Q1) Two new mutant lines of a flowering plant have been obtained; one breeds true for blue flower color and the other breeds true for red flower color (wild-type flower color is purple). Consider the following crosses.
1. blue \(\times\) purple \(\rightarrow F _ { 1 }\) all purple \(\rightarrow F _ { 2 } 75 \%\) purple; \(25 \%\) blue
2. red \(\times\) purple \(\rightarrow \mathrm { F } _ { 1 }\) all purple \(\rightarrow \mathrm { F } _ { 2 } 75 \%\) purple; \(25 \%\) red
3. red \(\times\) blue \(\rightarrow F _ { 1 }\) all purple
If the red pigment is a precursor of the purple pigment,the blue pigment is a precursor of the red pigment,and a colorless compound is the precursor of the blue pigment in a linear biosynthetic pathway controlling flower color,what phenotypic ratios do you expect in the F<sub>2</sub> of cross 3?
A)3 purple : 1 white (colorless)
B)9 purple : 3 blue : 3 red : 1 white (colorless)
C)9 purple : 4 blue : 3 red
D)9 purple : 7 white (colorless)
E)12 purple : 3 blue : 1 white (colorless)
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Page 8
Chapter 7: Dna: Structure and Replication
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Q1) The number of proteins in the prokaryotic replisome is 13,while the number in a eukaryotic cell is 27.What are important protein components of the replisome in general? Why might a eukaryotic cell have more components?
Q2) Erwin Chargaff provided experimental data (Chargaff's rules)that helped Watson and Crick to gain important insight into the structure of DNA.What did Chargaff determine,and what did it mean to Watson?
Q3) Which statement below best describes the situation between nucleotides on opposite strands in a DNA molecule?
A)A-T and C-G bonding between opposite strands involves two hydrogen bonds for either pair.
B)A-T and C-G bonding between opposite strands involves three hydrogen bonds for either pair.
C)A-T bonding between opposite strands involves two hydrogen bonds,whereas G-C bonding between strands involves three hydrogen bonds.
D)A-T bonding between opposite strands involves three hydrogen bonds,whereas G-C bonding between strands involves two hydrogen bonds.
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Page 9
Chapter 8: Rna: Transcription and Processing
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Sample Questions
Q1) A major difference between eukaryotes and prokaryotes is that eukaryotes have a nucleus,whereas prokaryotes do not.Discuss the impact of having a nucleus on the creation of mature mRNA.
Q2) Following splicing,the conserved adenosine nucleotide within the intron displays an unusual array of bonds,including:
A)a phosphate attached to the 4-carbon of the adenine nitrogenous base.
B)phosphodiester bonds attached at three places on the ribose (2 ,3 ,5 ).
C)additional methyl (-CH<sub>3</sub>)groups added to the adenine.
D)a DNA strand attached to the spliced RNA.
E)attachment to an arginine amino acid.
Q3) Name the three major modifications of mRNA in eukaryotes before it is transported to the cytoplasm.In addition,tell why each of the modifications is necessary.
Q4) In what cellular compartment are introns removed from pre-mRNA to make mature mRNA?
A)cytoplasm
B)endoplasmic reticulum
C)nucleus
D)mitochondria
E)Golgi apparatus
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Chapter 9: Proteins and Their Synthesis
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Sample Questions
Q1) You believe you created a protein translation machine that operates outside of the cell.If you combine the "translation machine" with an mRNA and charged tRNAs,a protein product is generated.However,as you do additional experiments,you find that though the correct amino acids are joined together,the protein is nonfunctional.What might be missing in your system,causing these synthesized proteins to lack activity?
Q2) Which of the following are types of posttranslational processing that will not occur in a prokaryote?
A)addition of a phosphate group
B)removal of a phosphate group
C)addition of a co-factor
D)cleavage of a mitochondrial targeting sequence
E)None of the answer options are correct.
Q3) The "wobble" base is less important than the other two nucleotides in a codon and is found:
A)at the 5 end of the RNA codon's sense strand.
B)at the 3 end of the mRNA codon's antisense strand.
C)at the 3 end of the tRNA anticodon.
D)at the 5 end of the tRNA anticodon.
E)within a tRNA hairpin loop structure.
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Page 11
Chapter 10: Gene Isolation and Manipulation
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Sample Questions
Q1) Assume that a cosmid will carry inserts of about 50 kb and that cosmids are used to clone a 3 Mb (megabase)genome.Assuming you are particularly lucky and have no duplication in your library,what is the smallest number of cosmid clones you would need for a "complete" genomic library?
A)3000 clones
B)600 clones
C)300 clones
D)60 clones
E)30 clones
Q2) Transgenic plants can be generated using T-DNA plasmid carrying a gene of interest.To get the DNA into the plant cells,the researchers:
A)use a syringe needle to inject the DNA into pollen before fertilization.
B)use a syringe needle to inject the DNA into groups of cells in the plant's root tissue.
C)co-cultivate bacteria with T-DNA and plant cells,resulting in DNA transfer.
D)add a mild detergent to cultures of plant cells to open holes in the cell wall.
E)remove the plant cell's normal DNA and replace it with the T-DNA.
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Chapter 11: Regulation of Gene Expression in Bacteria and Their Viruses
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Q1) 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.
Q2) The order of the structural genes controlling the trp operon is:
A)trpE,trpD,trpC,trpB,trpA.
B)trpA,trpC,trpB,trpD,trpE.
C)trpE,trpD,trpC,trpA trpB.
D)trpA,trpB,trpC,trpD,trpE.
E)None of the answer options are correct.
Q3) Which of the following is an example of a cis-acting element?
A)\(\beta\)-galactosidase
B)operator site
C)lacI repressor protein
D)lactose
E)permease
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Chapter 12: Regulation of Gene Expression in Eukaryotes
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Q1) Compared to heterochromatin,euchromatin is:
A)rich in genes and comprised of densely packed nucleosomes.
B)poor in genes and comprised of densely packed nucleosomes.
C)rich in genes and comprised of loosely packed nucleosomes.
D)poor in genes and comprised of loosely packed nucleosomes.
E)rich in genes and completely lacking nucleosomes.
Q2) Regions of a chromosome that are packaged in less-condensed chromatin are known as:
A)homochromatin.
B)heterochromatin.
C)euchromatin.
D)epichromatin.
E)hyperchromatin.
Q3) Methylation of H3 lysine residue 4:
A)is associated with activation of gene expression.
B)is associated with repression of gene expression.
C)has no effect on gene expression.
D)creates binding sites for other gene repressors.
E)None of the answer options are correct.
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Page 14
Chapter 13: The Genetic Control of Development
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Sample Questions
Q1) A morphogen is a molecule that induces:
A)cells to undergo cellular division.
B)cells to increase in size.
C)various responses in surrounding tissue in a non-concentration-dependent manner.
D)various responses in surrounding tissue in a concentration-dependent manner.
E)None of the answer options are correct.
Q2) In Drosophila melanogaster,Hox genes are:
A)clustered into operons.
B)clustered in one large gene complex.
C)clustered together in two gene complexes.
D)clustered together in three gene complexes.
E)evenly distributed throughout the genome.
Q3) In homeotic mutants:
A)one body structure is missing.
B)one body structure has been changed into another.
C)one body structure has been duplicated.
D)one body structure has significantly increased in size.
E)the organism is infertile.
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15
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) Which of the following statements is/are TRUE about reverse genetics?
A)Reverse genetics analysis starts with an altered phenotype in an organism.
B)Reverse genetics analysis starts with a known DNA sequence,mRNA,or protein.
C)Reverse genetics can be performed by random mutagenesis,targeted mutagenesis,or by phenocopying.
D)All of the answer options are correct.
E)Reverse genetics analysis starts with a known DNA sequence,mRNA,or protein,and it can be performed by random mutagenesis,targeted mutagenesis,or by phenocopying.
Q3) Describe the information content of a genome.
Q4) Please list three (3)approaches to reverse genetics.
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Page 16
Chapter 15: The Dynamic Genome: Transposable Elements
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Q1) Transposable elements that are comprised of DNA transposons are known as:
A)class 1 elements.
B)class 2 elements.
C)class 3 elements.
D)alpha elements.
E)D elements.
Q2) Which of the following statements is/are TRUE about the miniature inverted repeat transposable elements (MITEs)?
A)MITEs are examples of retrotransposons.
B)MITEs are examples of DNA transposons.
C)MITEs can attain very high copy numbers in humans.
D)MITEs contain transposase gene.
E)None of the answer options are correct.
Q3) Transposable elements that transpose via an RNA intermediate is known as:
A)class 1 elements.
B)class 2 elements.
C)class 3 elements.
D)alpha elements.
E)D elements.
Q4) Compare and contrast autonomous and nonautonomous transposable elements.
Page 17
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Chapter 16: Mutation, Repair, and Recombination
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Q1) A small (one base pair)insertion in the middle of the coding region of a gene will cause a:
A)synonymous mutation.
B)silent mutation.
C)nonsense mutation.
D)missense mutation.
E)frameshift mutation.
Q2) Crossing over is a very precise process.Why is it important that the process of crossing over is so precise? What impact would there be if it were not precise? Draw a picture depicting an imprecise crossover and show the result of this imprecise event.
Q3) A mouse is homozygous for a transversion that eliminated the splice site between the first exon and the first intron of gene "G." The resulting mutant mRNA is longer than the wild type,but the protein that it encodes is much shorter than its wild-type counterpart.Provide a logical and plausible explanation for these observations.
Q4) Photoreactivation repair is effective only in the presence of visible light.What other repair mechanism is available to repair pyrimidine dimers if visible light was not available? Describe the steps of this mechanism.
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18
Chapter 17: Large-Scale Chromosomal Changes
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Sample Questions
Q1) In an animal bearing the heterozygous inversion ABCDE[*]FGHI / ABGF[*]EDCHI,in one meiocyte,a crossover occurred between the D and E loci and another crossover occurred between the F and G loci.The two crossovers involved the same two chromatids.What will be the proportion of abnormal meiotic products from that meiosis? (Note: [*] = centromere.)
A)0%
B)25%
C)50%
D)100%
E)It depends on the distance between D and E and between F and G.
Q2) A triploid with 5 chromosomes in each set (3n = 15)is discovered.What is the probability of a meiosis in which all univalents pass to the same pole?
A)1/5
B)1/10
C)1/15
D)1/16
E)1/25
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Chapter 18: Population Genetics
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Sample Questions
Q1) What group of organisms has,overall,the highest genetic diversity?
A)humans
B)invertebrates
C)plants
D)vertebrates other than humans
E)unicellular eukaryotes
Q2) In a tropical human population in Hardy-Weinberg equilibrium for an autosomal locus determining presence/absence of pigment in the skin,the frequency of albinism (aa)is 1 in 10,000.The frequency of heterozygotes is approximately:
A)1 in 25.
B)1 in 50.
C)1 in 75.
D)1 in 100.
E)1 in 1000.
Q3) In a Pygmy group in central Africa,the frequencies of alleles determining the ABO blood groups were estimated as 0.2 for I<sup>A</sup>,0.1 for I<sup>B</sup>,and 0.7 for i.Assuming random mating with respect to blood group,determine the expected frequencies of the blood types A,B,AB,and O.
Q4) How is the genetic composition of a population defined?
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Chapter 19: The Inheritance of Complex Traits
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Q1) The mean weight in a population of fruit flies (Drosophila melanogaster)grown in identical conditions is 1.10 mg,and the standard deviation is 0.05.The heaviest fly in this population weighs 1.30 mg.The genetic deviation of this individual is:
A)0.05 mg.
B)0.15 mg.
C)0.20 mg.
D)0.84 mg.
E)It is impossible to determine based on these data.
Q2) Presume that the number of leaves in clovers is controlled by the combined actions of two genes,A and B,with no contributions from the environment.A/A results in four leaves,A/a in three leaves,and a/a in two leaves.Moreover,the genotypes B/B and B/b result in one additional leaf (b/b has no effect on leaf number). a)Based on the above information:
A)A has an additive mode of action and B has a dominant mode of action.
B)A has a dominant mode of action and B has an additive mode of action.
C)both A and B have a dominant mode of action.
D)both A and B have an additive mode of action.
E)the respective modes of action of A and B cannot be determined.
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Chapter 20: Evolution of Genes and Traits
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Q1) In what way can synonymous mutations still have a selective component?
Q2) Which of the following are requirements for evolution by natural selection?
I environmental change
II differential survival and reproduction
III heritability of phenotypic variation
IV variation in phenotype
V sexual reproduction
A)II,III,V
B)II,III,IV
C)I,II,IV
D)III,IV,V
E)II,IV,V
Q3) Which of the following reduce heterozygosity?
A)migration
B)directional selection
C)large population size
D)balancing selection
E)mutation
Q4) How will pleiotropy affect selection at particular loci?
Q5) What is meant by the phrase,"The force of selection is myopic."?
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