Genomics Exam Preparation Guide
Course Introduction
Genomics is the study of the structure, function, evolution, and mapping of genomes, which are the complete set of DNA within a single cell of an organism. This course explores the principles and techniques used to analyze entire genomes, including sequencing technologies, bioinformatics tools, and comparative genomics. Students will learn how genomic data is generated, managed, and interpreted, and will examine applications in areas such as medicine, agriculture, and evolutionary biology. Emphasis is placed on the role of genomics in understanding genetic variation, gene expression, and the molecular basis of disease.
Recommended Textbook
Molecular Biology 2nd Edition by David P. Clark
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26 Chapters
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276 Flashcards
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Chapter 1: Cells and Organisms
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Q1) Which of the following is not common to all cells?
A)ribosomes
B)plasma membrane
C)nucleus
D)cytosol
Answer: C
Q2) The process of duplicating DNA prior to cell division is called .
A)DNA replication
B)transcription
C)translation
D)gene expression
Answer: A
Q3) DNA replication occurs in all organisms.
A)True
B)False
Answer: True
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Chapter 2: Basic Genetics
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Q1) A triploid organism would have copies of all genes.
A)0
B)1
C)2
D)3
Answer: D
Q2) A allele determines the phenotype even when only one copy is present.
A)dominant
B)recessive
C)codominant
D)homozygous
Answer: A
Q3) Homologous chromosomes contain the same genes for the same traits at the same loci.
A)True
B)False
Answer: True
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Page 4
Chapter 3: DNA, RNA, and Protein
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Q1) Given the following sequence,which of the following is the complementary DNA strand?
5'-CCTAGAAACTG-3'
A)5'-CCTAGAAACTG-3'
B)5'-GGATCTTTGAC-5'
C)3'-GGATCTTTGAC-5'
D)3'-CAGTTTCTAGG-3'
Answer: C
Q2) Which of the following is not correctly paired?
A)adenine:thymine
B)guanine:cytosine
C)adenine:uracil
D)guanine:adenine
Answer: D
Q3) During DNA base pairing,which of the following would be incorrectly paired?
A)guanine:cytosine
B)adenine:thymine
C)purine:purine
D)purine:pyrimindine
Answer: C
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Chapter 4: Genes, genomes, and DNA
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Q1) Type II topoisomerases .
A)break both strands of DNA
B)include DNA gyrase,for example
C)change the linking number in steps of two
D)are all of the above
Q2) Homologous chromosomes .
A)are the same length
B)have the same genes at the same loci
C)pair up during cell division
D)are all of the above.
Q3) Compared to the other answers listed,which is the least compacted structure?
A)DNA double helix
B)chromatid
C)30 nm fiber
D)nucleosome
Q4) Topoisomerases .
A)are antibiotics that kill bacterial cells
B)bend DNA
C)change the level of supercoiling in DNA
D)repair DNA
6
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Chapter 5: Manipulation of Nucleic Acids
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Q1) By what technique can individual DNA molecules be visualized?
A)electron microscopy and metal shadowing
B)light microscopy only
C)agarose gel electrophoresis
D)Northern blot
Q2) FISH allows DNA or RNA to be visualized in its natural location.
A)True
B)False
Q3) Agarose gel electrophoresis allows the separation of DNA based upon A)charge
B)base composition
C)size
D)pH
Q4) At which wavelength do the bases of DNA and RNA nucleotides absorb the most light?
A)200 nm
B)260 nm
C)280 nm
D)300 nm
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Chapter 6: Polymerase Chain Reaction
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Q1) Which of the following uses an RNA template during the technique?
A)TA cloning
B)RAPD
C)Inverse PCR
D)RT-PCR
Q2) During which step in PCR does synthesis occur?
A)Denaturation
B)Annealing
C)Elongation
D)Termination
Q3) RNA can be synthesized in PCR if RNA polymerase and RNA nucleotides are used in place of DNA polymerase and DNA nucleotides,respectively.
A)True
B)False
Q4) In real time PCR,the presence of double-stranded DNA is detected by
A)fluorescence of SYBR Green
B)luminescence of SYBER Green
C)quenching of SYBR Green fluorescence
D)rapid decrease in the amount of SYBR Green fluorescence
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Chapter 7: Recombinant DNA Technology
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Q1) Which of the following cloning vectors carries the largest insert relative to the others in the answer choices?
A)BACs
B)cosmids
C)PACs
D)plasmids
Q2) Why must a shuttle vector possess two origins of replication instead of one?
A)Shuttle vectors must replicate in multiple hosts with each host requiring a different origin.
B)Shuttle vectors must be able to replicate from two different origins of replication depending upon the specific growth conditions.
C)Shuttle vectors only have one origin of replication,not two.
D)Shuttle vectors use one origin for replication and the other origin for shuttling recombinant DNA into new hosts.
Q3) A collection of cloned DNA fragments is called a .
A)consortium
B)chromosomal database
C)chromosome library
D)gene library
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Page 9
Chapter 8: DNA Sequencing
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Q1) DNA moves across nanopore detectors because .
A)an electrical charge is applied
B)there is a high concentration of salt on one side of the channel
C)there is a difference in pH across the membrane
D)it is physically pulled across by enzymes
Q2) Which sequencing method would work best for determining the sequence of a single DNA molecule?
A)pyrosequencing
B)third generation sequencing
C)second generation sequencing
D)chain termination sequencing
Q3) Dideoxy nucleotides are missing a 3' hydroxyl.
A)True
B)False
Q4) All of the following are second generation sequencing methods except .
A)454 sequencing
B)Illumina/Solexa sequencing
C)SOLiD/Applied Biosystems method
D)Pyrosequencing
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Chapter 9: Genomics Systems Biology
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Q1) Genes in the family are of particular interest due to their pharmaceuticals.
A)cytochrome P450
B)CYP2D6
C)Glutathione S-transferease
D)SNP
Q2) The genomes of some plants and a few protozoa have more genes than humans.
A)True
B)False
Q3) Which of the following makes up more percentage of the human genome than the others listed in the answer choices?
A)protein coding genes
B)LINEs
C)heterochromatin
D)introns
Q4) Sequence tagged sites are needed when genomes .
A)contain mostly coding sequence
B)contain mostly non-coding sequence
C)are very tiny
D)have many repetitive sequences
Page 11
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Chapter 10: Cell Division and DNA Replication
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Q1) During which phase of the cell cycle is DNA replicated?
A)mitosis
B)S-phase
C)G1
D)G2
Q2) The process of does not use mitosis.
A)gamete formation
B)embryogenesis
C)asexual reproduction
D)tissue repair/wound healing
Q3) Origins are replication are .
A)GC-rich
B)AT-rich
C)runs of adenine residues
D)heavily methylated
Q4) DNA is duplicated during mitosis.
A)True
B)False
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Chapter 11: Transcription of Genes
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Q1) Large ribosomal RNAs are transcribed by .
A)RNA polymerase I
B)RNA polymerase II
C)RNA polymerase III
D)None of the above
Q2) The is the site on the DNA where RNA polymerase binds to initiate transcription.
A)promoter
B)enhancer
C)5' UTR
D)origin
Q3) The eukaryotic promoter recognized by RNA polymerase II contains three regions.Which of the following is not part of the trio?
A)TATA box
B)upstream elements
C)initiator box
D)Enhancer
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Chapter 12: Processing of RNA
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Sample Questions
Q1) Which modified nucleotide base is part of the 5' cap on eukaryotic mRNAs?
A)cytosine
B)guanine
C)adenine
D)uracil
Q2) Some pre-rRNAs are processed to generate mature rRNA and tRNA.
A)True
B)False
Q3) Multiple messenger RNAs can be generated from the same gene by selecting
A)an alternative promoter when available
B)a different location for the addition of the polyA)tail
C)and splicing different exon cassettes
D)all of the above
Q4) In bacteria, is involved in processing tRNAs.
A)ribonuclease P
B)ribonuclease H
C)ribonuclease D
D)ribonuclease E/F
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Chapter 13: Protein Synthesis
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Sample Questions
Q1) The enzyme that links the appropriate amino acid to the acceptor stem of specific tRNAs is called .
A)aminoacyl tRNA synthetase
B)ribosomes
C)ribozymes
D)ribonuclease P
Q2) How many different types of amino acids are there in proteins?
A)1
B)3
C)20
D)50
Q3) The type of covalent bond that forms between adjacent protein monomers is called a .
A)beta-linkage
B)phosphodiester bond
C)peptide bond
D)glycosidic bond
Q4) The anticodon of the tRNA is complementary to the codon on mRNA.
A)True
B)False
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Chapter 14: Protein Structure and Function
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Q1) Dissociation refers to the loss of structure of proteins.
A)primary
B)secondary
C)tertiary
D)quaternary
Q2) The binding of a regulatory molecule to an allosteric site on a protein that results in the inhibition of the protein is an example of .
A)non-competitive inhibition
B)allosteric activation
C)competitive inhibition
D)positive regulation
Q3) All of the following are functions of proteins except .
A)defense
B)structural support
C)energy production
D)major plasma membrane component
Q4) Polar amino acids are hydrophilic and would be located on the exterior of proteins.
A)True
B)False
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Chapter 15: Proteomics
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Q1) Why might proteins be tagged?
A)purification
B)identification
C)anchoring
D)all of the above
Q2) Which method allows a researcher to find a gene based upon the protein that it encodes?
A)Co-immunoprecipitation
B)Phage display
C)RT-PCR
D)Intein trapping
Q3) What is the proteome?
A)The total set of proteins in the cell at any given point.
B)The number of genes that are expressed in a specific growth condition.
C)The total set of proteins encoded by the organism's genome.
D)The number of expressed genes.
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Chapter 16: Regulation of Transcription in Prokaryotes
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Q1) Some nucleotides are involved in transcriptional regulation.
A)True
B)False
Q2) Which of the following is an example of negative regulation?
A)A gene is switched on in the presence of an activator.
B)A gene is de-repressed.
C)A gene is induced.
D)A gene is switched off by a repressor protein.
Q3) Autoregulation occurs when .
A)IPTG binds to LacI
B)allo-lactose binds to LacI
C)a repressor binds to its own gene to prevent transcription
D)CRP binds to cAMP and the the lac operon
Q4) All of the following are associated with two-component regulatory systems except
A)gratuitous inducer
B)phosphorelay
C)DNA binding regulator
D)sensor kinase
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Chapter 17: Regulation of Transcription in Eukaryotes
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Q1) Housekeeping genes are always .
A)off until needed
B)on
C)induced
D)repressed
Q2) Xist is .
A)a gene encoding an untranslated RNA involved in X-inactivation
B)the heterochromatin of inactivated X chromosomes
C)is a gene that is only found on active X chromosomes
D)helps inactivate the X chromosome of males
Q3) In eukaryotes,negative regulation occurs by .
A)obstructing RNA polymerase II
B)interfering with activators
C)interfering with repressors
D)binding of repressors to operators
Q4) Acetylated histones .
A)form highly condensed heterochromatin
B)are a target of proteases
C)never occurs
D)allow nucleosomes to be less aggregated
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Chapter 18: Regulation at the RNA Level
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Q1) Riboswitches .
A)can bind small molecules
B)are useful in translational control
C)are found on the 5' end of the mRNA
D)are all of the above
Q2) Which statement is false?
A)Nucleases are not part of the RNAi scenario.
B)Some small RNAs help stabilize the mRNA and protect it from degradation.
C)RNAi is a form of gene silencing that involves degradation of target RNAs.
D)Riboswitches bind small molecules.
Q3) Proteins that prevent translation of mRNA are called .
A)nucleases
B)translational repressors
C)proteases
D)mRNA silencers
Q4) Which nuclease is responsible for generating siRNA?
A)Ribonuclease P
B)Dicer
C)Slicer
D)RISC
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Chapter 19: Analysis of Gene Expression
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Q1) Levels of transcription for a specific gene are measured using all of the following except .
A)quantitative PCR
B)reporter genes
C)primer extension
D)DNA microarrays
Q2) Microarrays and SAGE have the ability to monitor .
A)large numbers of mRNAs simultaneously
B)small numbers of specific mRNAs
C)proteins expressed under a given condition
D)the binding of a protein to a DNA or RNA molecule
Q3) Which of the following techniques would not be useful for determining the number of mRNA copies present in a cell?
A)SAGE
B)DNA microarrays
C)Quantitative PCR
D)Primer extension
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Chapter 20: Plasmids
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Q1) Transferable plasmids use as a form of replication during transfer.
A)bidirectional replication
B)rolling circle replication
C)conservative
D)none of the above
Q2) Which family of plasmids carries genes for antibiotic resistance?
A)R-plasmids
B)F-plasmids
C)P-plasmids
D)X-plasmids
Q3) Bidirectional replication for F-plasmids occurs at the .
A)origin of vegetative replication
B)origin of transfer
C)origin of chromosomal replication
D)linear ends
Q4) The Ti-plasmid was used as the platform for genetically engineering plants.
A)True
B)False
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Page 22
Chapter 21: Viruses
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Q1) Which of the following is not a viral genome arrangement?
A)double-stranded DNA
B)single-stranded DNA
C)positive single-stranded RNA
D)negative double-stranded RNA
Q2) Enveloped viruses only infect .
A)plants
B)bacteria
C)animals
D)yeast
Q3) The early genes of viruses are transcribed by .
A)host RNA polymerase
B)viral RNA polymerase
C)DNA polymerase
D)rolling circle replication
Q4) The largest virus is .
A)herpesvirus
B)poxvirus
C)mimivirus
D)HIV
Page 23
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Chapter 22: Mobile DNA
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Q1) All transposons have all of the following characteristics except .
A)the gene for transposase
B)inverted repeats
C)resolvase
D)antibiotic resistance genes
Q2) Resolvase is needed for .
A)conservative transposition
B)replicative transposition
C)simple transposons
D)retrotransposons
Q3) Internal resolution sites of complex transposons are recognized by .
A)Dicer
B)cointegrase
C)recombinase
D)resolvase
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Chapter 23: Mutations and Repair
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Q1) Spontaneous mutations occur .
A)from errors in replication
B)when organisms grow at high temperatures
C)in the presence of mutagens
D)from ultraviolet radiation
Q2) A mutation changes the coding sequence of the gene by inserting single base pair.
A)nonsense
B)silent
C)frameshift
D)reversion
Q3) In some repair mechanisms,the parental DNA strand is used as a guide for repairing mistakes made in the newly synthesized DNA strand.The cell is able to distinguish the parental strand from the new strand because immediately following replication,the DNA is .
A)fully methylated
B)still single-stranded
C)hemi-methylated
D)non-methylated
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Chapter 24: Recombination
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Q1) Homologous recombination is .
A)the exchange of DNA between similar sequences
B)the exchange of DNA between dissimilar sequences
C)the formation of a heteroduplex
D)the removal of a holiday junction
Q2) Mutations in RAD genes cause .
A)recombination to occur randomly
B)radiation sensitivity
C)excessive recombination events during meiosis
D)a decline in gamete production
Q3) Which of the following proteins is required for lambda integration in the genome of Escherichia coli?
A)transposase
B)resolvase
C)Int protein
D)Xis protein
Q4) A heteroduplex is a double helix with two strands from different DNA or RNA molecules.
A)True
B)False
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Chapter 25: Bacterial Genetics
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Q1) In order for cells to take up naked DNA,they must be .
A)dead
B)actively replicating
C)competent
D)weak
Q2) Hfr strains have an integrated .
A)F plasmid
B)R plasmid
C)prophage
D)lysogen
Q3) A prophage .
A)only occurs when a viral genome is integrated into the host genome
B)is replicated along with host cell DNA
C)occurs in the lysogenic life cycle of viruses.
D)all of the above
Q4) DNA transfer that occurs via a virus is called .
A)transfection
B)conjugation
C)transduction
D)transformation
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Chapter 26: Molecular Evolution
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Q1) Gene duplication generates new genes with novel roles.
A)True
B)False
Q2) The transfer of genetic information from one species to another species is called
A)recombination
B)vertical gene transfer
C)horizontal gene transfer
D)conjugation
Q3) Evolution relies upon .
A)mutations made in somatic cells only
B)mutations occurring in gametes
C)mutations that result in altered protein function of somatic cells
D)mutations in mRNA only
Q4) The African Eve hypothesis is based on .
A)Y chromosome analysis
B)identification of junk DNA sequences
C)mitochondrial DNA sequences
D)ribosomal RNA sequencing
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