Exam 1

Question 1

Modern genetics and genomic analyses have benefited enormously from technical advances,
especially since the 1970s. Among these advances are:
A. the “rediscovery” of Darwin and application of his laws to artificial selection experiments
B. identification of RNA as the genetic message
C. elucidation of the genetic code
D. methods for targeted genome editing
E. all of the above

Answer 1

D. methods for targeted genome editing

Question 2

Which of the following is consistent with the “RNA World” hypothesis (i.e., that RNA was the
ancestral genetic material)?
A. the widespread occurrence of self-replicating RNAs
B. the ability of RNAs with modified bases to catalyze small peptides
C. the abundance of adenine and uracil dimers in pre-biotic times
D. the relatively simple components that make up ribonucleotides
E. the simplicity of modern ribosomes

Answer 2

B. the ability of RNAs with modified bases to catalyze small peptides

Question 3

Complete the statement: Deoxyribonucleotides are composed of a phosphate backbone, …
A. … a deoxyribose sugar, a nitrogenous base, and are bound together by phosphodiester bonds.
B. … a deoxyribose sugar, a nitrogenous base, and are bound together by non-covalent hydrogen bonds.
C. … a ribose sugar, a nitrogenous base, and are bound together by phosphodiester bonds.
D. … a deoxyribose sugar, a nitrogenous base, and are bound together by covalent hydrogen bonds.
E. … a dideoxyribose sugar, a nitrogenous base, and are bound together by non-covalent hydrogen bonds

Answer 3

A. … a deoxyribose sugar, a nitrogenous base, and are bound together by phosphodiester bonds.

Question 4

Which of the following is essential for natural selection to occur?
A. there must be multiple traits targeted
B. there must be a consistent relationship between an individual’s value of a trait and its survival or reproductive success
C. there must be a long period of time during which selective factors can act
D. traits must be continuous rather than discrete
E. the population must be small enough for adequate inbreeding to occur

Answer 4

B. there must be a consistent relationship between an individual’s value of a trait and its survival or reproductive success

Question 5

Since the inception of DNA sequencing, the amount of raw sequence data that can be generated by
a sequencing instrument per “run” has increased by:
A. less than 2-fold
B. less than 20-fold
C. less than 200-fold
D. less than 2000-fold
E. none of the above

Answer 5

E. none of the above

Question 6

According to NASA (1979), “life…
A. …is currently complex and so must have originated with simpler RNA.”
B. …is unlikely to have evolved by Darwinian selection.”
C. …is a self-sustaining system capable of Darwinian selection.”
D. …is defined by Darwinian selection and so must only be terrestrial.”
E. …is a self-sustaining system that guides the production of new variation.”

Answer 6

C. …is a self-sustaining system capable of Darwinian selection.”

Question 7

During transcription, the Mediator complex functions primarily to
A. bridge distant activators to the pre-initiation complex
B. disassemble nucleosomes as RNA polymerase reads the template strand
C. melt DNA strands apart within the transcription “bubble”
D. allow for ribosome assembly upstream of ATG
E. none of the above

Answer 7

A. bridge distant activators to the pre-initiation complex

Question 8

An important pathological role for aberrant histone modification in a pediatric glioma is suggested
by:
A. consistent methylation of histone H3 lysine 27 across patients
B. the ubiquity of histone 3 defects across sites of tumor spread, consistent with an early step in oncogenesis
C. recurrent mutations in histone 3 genes across patients that change lysine-27 to methionine
D. both A and B
E. both B and C

Answer 8

E. both B and C

Question 9

The genetic code
A. has overlapping codons
B. is degenerate
C. often results in functional proteins when 2 nucleotides are inserted and 1 nucleotide is deleted
D. reads 3’ to 5’ on the mature mRNA
E. none of the above

Answer 9

B. is degenerate

Question 10

Which of the following statements is true about cis-regulatory elements
A. they consist of short, invariant sequences shared between genes
B. they contain primarily sense codons
C. they encode both activator and repressor proteins
D. they can be found within intronic sequence
E. they are localized only within the promoter itself

Answer 10

D. they can be found within intronic sequence

Question 11

The stop codon of a typical eukaryotic protein-coding gene marks…
A. the end of the gene
B. the place where transcription starts
C. the place where transcription ends
D. the final codon before an untranslated region is transcribed
E. the final frameshift in the coding sequence

Answer 11

D. the final codon before an untranslated region is transcribed

Question 12

Sequencing of the human genome revealed
A. just under 2,000,000 genes, similar to what had been predicted theoretically
B. just over 40,000 genes, similar to what had been predicted theoretically
C. gene bodies as large as 2,000,000 bp
D. as many as 20,000 exons per gene
E. as few as 2000 non-coding genes

Answer 12

B. just over 40,000 genes, similar to what had been predicted theoretically

Question 13

Pioneer transcription factors differ from most transcription factors in being able to
A. reprogram states of cellular differentiation
B. access their binding sites despite close associations between DNA and nucleosomes
C. initiate chromatin remodeling
D. all of the above
E. none of the above

Answer 13

D. all of the above

Question 14

Malaria resistance in some individuals is conferred by a T-to-C mutation…
A. in the upstream coding sequence of Duffy antigen/chemokine receptor (DARC)
B. in a trans regulatory element of DARC
C. that impairs binding of a GATA transcription factor
D. that enhances binding of a transcriptional repressor
E. in the 5’ UTR sequence of DARC

Answer 14

C. that impairs binding of a GATA transcription factor

Question 15

Mature mRNA includes a polyA tail that represents
A. a post-transcriptional modification
B. a polyT segment in the template strand of DNA
C. an important site of preinitiation complex assembly
D. the most 5’ portion of the primary transcript
E. sequence coding for the carboxy terminal poly-lysine region of most proteins

Answer 15

A. a post-transcriptional modification

Question 16

The eukaryotic preinitation complex
A. can interact with core promoter sequence motifs including the TATA box and Initator
B. can assemble at enhancer elements distant from the gene body
C. transcribes DNA in the 5’ to 3’ direction
D. both A and B
E. both A and C

Answer 16

D. both A and B

Question 17

Mendel’s Law of Independent Assortment accurately describes
A. the reason some alleles are recessive
B. the segregation of alleles at genes not physically linked to one another
C. why the two alleles of a gene are incorporated independently into gametes
D. the molecular nature of genes and alleles
E. the reason that parental traits seem to blend together in offspring

Answer 17

B. the segregation of alleles at genes not physically linked to one another

Question 18

Once the preinitiation complex has assembled and transcription begins, RNA polymerase II
A. immediately advances to the transcription terminator signal, at which point another RNA
polymerase II begins transcription
B. stops for as long as splicing requires
C. pauses after an initial period of elongation comprising up to ~60 nucleotides
D. interacts directly with transcription factors at distant cis regulatory elements
E. hands-off transcription to either RNA polymerase I or RNA polymerase III, depending on the
gene

Answer 18

C. pauses after an initial period of elongation comprising up to ~60 nucleotides

Question 19

How do histone acetyl transferase (HAT) enzymes promote gene expression?
A. by adding acetyl groups to core promoter nucleotides, thereby enhancing RNA polymerase II
binding efficiency
B. by adding acetyl groups to specific amino acids in histone tails, reducing the affinity of nucleosomes for DNA
C. by acetylating the growing primary RNA transcript, allowing for increased stability and protein synthesis
D. by binding to cis regulatory elements distant from the gene body, thereby acting as a transcription factors
E. by sliding nucleosomes to new positions along the DNA molecule

Answer 19

B. by adding acetyl groups to specific amino acids in histone tails, reducing the affinity of nucleosomes for DNA

Question 20

Dapi is an example of:
A. a plant defense chemical
B. a chemical used to visualize protein by fluorescence
C. a DNA minor groove intercalator
D. both A and B
E. both A and C

Answer 20

C. a DNA minor groove intercalator

Question 21

Splicing depends critically on recognition of the following sites:
A. 5’ splice acceptor (GU), branch, and 3’ splice donor (AG)
B. 5’ splice donor (GU), branch, and 3’ splice acceptor (AG)
C. 5’ splice acceptor (AG), branch, and 3’ splice donor (GU)
D. 5’ splice donor (AG), branch, and 3’ splice acceptor (GU)
E. none of the above

Answer 21

B. 5’ splice donor (GU), branch, and 3’ splice acceptor (AG)

Question 22

Gene bodies sometimes overlap because
A. cis regulatory elements can be far from the coding sequence itself
B. transposable elements normally copy gene coding sequences “in frame”
C. exons and introns can be templated on different strands of DNA
D. genes frequently share a basal promoter
E. alternative splicing allows single primary transcripts to encode >1 polypeptide from >1 gene

Answer 22

C. exons and introns can be templated on different strands of DNA

Question 23

During transcription, RNA polymerase II reads
A. the RNA-like strand in the 5’ to 3’ direction
B. the RNA-like strand in the 3’ to 5’ direction
C. the template strand in the 5’ to 3’ direction
D. the template strand in the 3’ to 5’ direction
E. none of the above

Answer 23

D. the template strand in the 3’ to 5’ direction

Question 24

Kary Mullis played an important role in developing PCR. He demonstrated that
A. ribonucleotides are required as primers for extension
B. DNA strands can be ligated back together for uninterrupted priming
C. oligonucleotide primer binding during denaturation allowed for subsequent product extension
D. new strands extended during the annealing phase increase exponentially
E. none of the above

Answer 24

E. none of the above

Question 25

Thyroid hormone nuclear receptors are examples of transcription factors
A. with DNA methylase activity
B. requiring proteolytic cleavage for translocation from cytoplasm to nucleus
C. able to switch between repressive and activating states
D. able to acetylate histones
E. with similarity to linker histones

Answer 25

C. able to switch between repressive and activating states

Question 26

Which of the following would you expect to be more common in heterochromatin as opposed to
euchromatin?
A. methylated DNA
B. active RNA pol II
C. acetylated histones
D. HAT proteins
E. Mediator complexes

Answer 26

A. methylated DNA

Question 27

What is true about cis-regulatory elements?
A. they code for activator and repressor proteins
B. they are localized only 5’ to the proximal promoter
C. they can be thousands of bases from the transcriptional start site
D. they are often translated at the same time as the RNA itself
E. they are small, invariant sequence motifs often shared between genes

Answer 27

C. they can be thousands of bases from the transcriptional start site

Question 28

In DNA…
A. guanine and cytosine are purines that bind to one another covalently
B. thymine and cytosine are pyrimidines that bind to one another non-covalently
C. adenine is a purine, thymine is a pyrimidine and they bond to one another covalently
D. guanine is a purine, thymine is a pyrimidine and they bond to one another non-covalently
E. guanine is a purine, cytosine is a pyrimidine and they bond to one another non-covalently

Answer 28

E. guanine is a purine, cytosine is a pyrimidine and they bond to one another non-covalently

Question 29

Which of the following statements best represents Mendel’s Law of Segregation?
A. Alleles for different traits segregate independently during gamete formation.
B. Alleles for a single trait segregate into different gametes during meiosis.
C. Homologous chromosomes separate during mitosis.
D. Dominant alleles always segregate into the same gamete.
E. Recessive alleles are more likely to segregate during fertilization.

Answer 29

B. Alleles for a single trait segregate into different gametes during meiosis.

Question 30

Which of the following best describes the most important finding of Frederick Griffith’s
experiments in which he injected Pneumococcus bacteria into mice?
A. Virulent bacteria caused pneumonia in mice.
B. Virulent bacteria were transformed into non-virulent bacteria when co-injected with cell
components from heat-killed non-virulent bacteria
C. Non-virulent bacteria transformed into virulent bacteria when injected with cell
components from heat-killed virulent bacteria.
D. The immune system of mice was responsible for bacterial transformation, whether towards
virulence or non-virulence.
E. Protein was identified as the genetic material responsible for transformation between virulence
states.

Answer 30

C. Non-virulent bacteria transformed into virulent bacteria when injected with cell