BIOL 4003 EXAM 2

Which of the following is not one of the four criteria that the genetic material must fulfill to function?

a. store information

b. replication

c. DNA repair

d. transmission

c

You have analyzed the composition of the genetic material in a virus and found the following: 32% adenine, 31% uracil, 18% guanine and 19% cytosine. From this analysis, which of the following is the most likely structure of the viral genome?

a. single-stranded DNA

b. double-stranded DNA

c. single-stranded RNA

d. double-stranded RNA

d

DNA is able to store information because of

a. the 5' to 3' direction of the strands

b. the sequence of the bases

c. the relative locations of the major and minor grooves

d. the spiral, double-helical structure

b

The following question is about DNA replication. In the drawing below, the top strand is the template DNA. After the middle RNA primer (located between the two upward pointing arrows) is removed and the gap is filled with DNA, where does DNA ligase function?

a. on the 5' end of the Okazaki fragment

b. on the 3' end of the Okazaki fragment

c. both arrows

d. neither arrow

b

Two circular DNA molecules are topoisomers of each other; they contain the same amount of DNA. Let's call them DNA-1 and DNA-2. Under the electron microscope, DNA-2 is more compact compared to DNA-1. The level of gene transcription is lower for DNA-1. Which of the following possibilities would best explain these observations?

a. DNA-1 has 4 negative supercoils and DNA-2 has 2 positive supercoils

b. DNA-1 has 4 positive supercoils and DNA-2 has 2 negative supercoils

c. DNA-1 has 2 positive supercoils and DNA-2 has 4 negative supercoils

d. DNA-1 has 2 positive supercoils and DNA-2 has 2 positive supercoils

c

Which of the following is the correct order for the hierarchy of compaction leading to metaphase chromosome?

a. formation of nucleosomes, formation of a 30 fiber, formation of loop domains, further compaction of loop domains

b. formation of nucleosomes, formation of loop domains, further compaction of loop domains, formation of a 30 fiber

c. formation of a 30 fiber, formation of nucleosomes, formation of loop domaines, further compaction of loop domains

d. formation of loop domains, further compaction of loop domains, formation of nucleosomes, formation of a 30 fiber

a

In the lagging strand, DNA is made in the direction _____ the replication fork and is made as _______.

a. toward, one continuous strand

b. away from, one continuous strand

c. toward, Okazaki fragments

d. away from, Okazaki fragments

d

At the E coli origin of replication, the function of DnaA protein is

a. to bind DnaA boxes and separate the AT rich region

b. to coat the DNA to prevent it from re-forming a double helix

c. to promote the binding of DNA polymerase to the origin

d. to promote the methylation of the GATC site

a

A gene encodes a pre-mRNA with 8 axons and 7 introns. A mutation eliminates the 3' splice site from intron 5. What exons would be found in the mRNA after splicing was complete?

a. 1-2-3-4-5-6-7-8

b. 1-2-3-4-6-7-8

c. 1-2-3-4-5-7-8

d. 1-2-3-4-7-8

c

The role of a sigma factor during bacterial transcription is to cause

a. the binding of RNA polymerase to the promoter

b. RNA polymerase to move along the DNA during the elongation stage of transcription

c. rho-dependent termination

d. rho-independent termination

a

consensus sequence

the most commonly occurring bases within a sequence element

A mutation that encodes the lac repressor prevents allolactose from binding to the repressor. Even so, the lac repressor can still bind to the operator site. How would you expect this mutation to affect the regulation of the lac operon?

a. the operon would be turned on in the presence or absence of lactose

b. the operon would be turned off in the presence or absence of lactose

c. the operon would be turned off in the presence of lactose but would be turned on in its absence

d. the operon would be turned on in the presence of lactose but would be turned off in its absence

b

Let's suppose you have isolated a mutant strain of E coli in which the lac operon is constitutively expressed. To understand the nature of this defect, you create a merozygote in which the mutant strain contains an F' factor with a normal lac operon and a normal lacI gene. You then compare the mutant strain and the merozygote with regard to their B-galactosidase activities in the presence and absence of lactose.

a. the mutation is in the lacI gene that encodes the lac repressor and prevents the lac repressor from binding to the operator

b. the mutation is in the lacI gene that encodes the lac repressor and prevents the lac repressor from binding to allolactose, the lac repressor can still bind to the operator site

c. the mutation is in the lacO (operator site) the normal lac repressor does not bend to the mutant repressor

d. the mutation is in the lacO (operator site), the normal lac repressor bends very tightly to the mutant operator

a

For a riboswitch that controls translation, the binding of a small molecule such as TPP controls whether the RNA

a. has an anti terminator or a terminator stem loop

b. has a Shine-Dalgarno antisequestor or the Shine-Dalgarno sequence in a stem loop

c. a degraded 5' end

d. undergoes rho-dependent termination

b

Regulatory transcription factors would not be controlled by which of the following?

a. small effector molecules

b. RNA polymerase II

c. protein-protein interactions

d. covalent modifications

b

Which of the following is not a reason why histones are removed so that eukaryotic genes can be transcribed?

a. so an activator protein can bind to a nucleosome-free region

b. so the pre-initiation complex can bind to a NFR

c. so RNA polymerase can recognize the start codon of the gene

d. so RNA polymerase can slide along the template DNA and make RNA

c

Which of the following does not happen for the glucocorticoid receptor to activate a gene?

a. protein-protein interaction

b. covalent modification of the glucocorticoid receptor

c. the binding of small effector molecules

d. the binding of the glucocorticoid receptor to the DNA

b

Which of the following statements is true?

a. all epigenetic changes are passed from parent to offspring

b. some epigenetic changes involve a change to the DNA sequence

c. epigenetic changes are permanent over the course of many generations

d. some epigenetic changes are caused by environmental factors

d

During XCI in the embryo, where is the Tsix gene expressed?

a. on the Barr body only

b. on the active chromosome only

c. on both

d. on neither

b

An example of an epigenetic change that is programmed during development is

a. genomic imprinting

b. lung cancer caused by an agent in cigarette smoke

c. differences in the coat color of mice carrying the Aw allele

d. the development of queen beens due to royal jelly

a

An anticodon on a tRNA is GUC. Which amino acid would it carry?

a. aspartic acid

b. glutamine

c. leucine

d. valine

b

The genetic code and wobble rules for tRNA-mRNA pairing are shown above. If we assume that the tRNAs do not contain modified bases, what is the minimum number of tRNAs that are needed to recognize all of the arginine codons?

a. 1

b. 2

c. 3

d. 6

c

The genetic code is degenerate. This phenomenon is illustrated by codon(s) for which of the following amino acids?

a. proline

b. arginine

c. valine

d. all of the above

d

A gene that encodes a tRNA changes the anticodon from GAG to CAG. This mutation does not alter which amino acid is attached to the mutant tRNA. What effect would this mutation have on translation?

a. it would have no effect due to the wobble rules

b. it could introduce a leucine where a stop codon occurs

c. it could introduce a leucine where a valine is supposed to be

d. it could introduce a valine where a leucine is supposed to be

c

Based solely on the drawing shown, the ncRNA in part A functions as a

a. guide

b. scaffold

c. decoy

d. blocker

e. ribozyme

a

A mutation changes a valine codon to a histidine codon. This is a

a. silent mutation

b. missense mutation

c. frameshift mutation

d. nonsense mutation

b

A key event that promotes trinucleotide repeat expansion is

a. chromosome breakage

b. the formation of a hairpin

c. the presence of an AT-rich region

d. the presence of a lesion in the DNA

b

According to the Holliday model for homologous recombination, a heteroduplex is formed due to

a. the initial breakage of the DNA at a single location in two different DNA strands

b. the formation of a D-loop

c. the migration of a Holliday junction

d. the resolution of the Holliday junction into two separate DNA molecules

c

Following homologous recombination, gene conversion may occur via

a. mismatch DNA repair

b. mismatch DNA repair or gap synthesis

c. nucleotide excision repair or non homologous end joining

d. nucleotide excision or gap repair synthesis

b

Which of the following proteins is/are needed during some types of retrotransposition, such as the movement of Ty elements in yeast?

a. transposase

b. reverse transcriptase

c. integrase

d. both b and c

d

Which of the following proteins is NEVER needed during retrotransposition?

a. transposase

b. reverse transcriptase

c. integrase

d. all of the above may be needed

a

In the experiment of Avery, McLeod, and McCarty, the addition of RNase and protease to DNA extracts

a. prevented the conversion of type S bacteria to type R bacteria

b. allowed the conversion of type S bacteria into type R bacteria

c. prevented the conversion of type R bacteria into type S bacteria

d. allowed the conversion of type R bacteria into type S bacteria

d

Which of the following would not be found in a strand of DNA?

a. thymine

b. deoxyribose

c. uracil

d. adenine

c

The nucleotides within a single DNA strand are attached together via

a. a covalent bond between a 5' phosphate and a 3' OH group

b. a covalent bond between a 3' phosphate group and a 5' OH group

c. hydrogen bonding between complementary bases

d. both a and c

a

Chargaff's studio of the base compostion of various species provides evidence for

a. a helical structure in DNA

b. the AT/GC rule

c. base stacking

d. the major and minor grooves

b

Which of the following is not a pyramiding?

a. adenine

b. thymine

c. cytosine

d. uracil

a

Which of the following is not found in a bacterial chromosome?

a. many genes

b. one centromere

c. some repetitive sequences

d. one origin of replication

b

Bacterial chromosomes become more compact by

a. binding to histones and DNA supercoiling

b. forming loop domains and DNA supercoiling

c. DNA supercoiling only

d. binding to histones only

b

A chromosome territory region is a region

a. of a chromosome that carries a cluster of genes

b. of a chromosome that has particular sets of DNA-binding proteins

c. in a cell nucleus that is occupied by a single chromosome

d. in a dividing cell where a chromosome will travel via the spindle apparatus

c

When comparing the genome of a simple eukaryote, such as yeast, to a complex eukaryote, such as a plant, why is the plant genome so much larger?

a. the plant genome has more genes and more repetitive DNA

b. the plant genome has more genes and more origins of replication

c. the plant genome has a higher GC content

d. the plant genome has more repetitive DNA and more origins of replication

a

The following statements below concern DNA replication. Only one of them is true. Which is the true statement?

a. DNA double helix does not obey the AT/GC rule.

b. a DNA double helix could contain one strand that is 4 generations older than its complementary strand.

c. A DNA double helix may contain two strands of DNA that were made at the same time

d. A DNA strand can serve as a template strand on only one occasion

b

What are the expected results for the Meselson and Stahl experiment after 5 generations (i.e. 5 rounds of DNA replication in the presence of light nitrogen)? Note: during generation 0, the DNA is all heavy, and subsequent generations only make light DNA.

a. 1/4 half heavy, 3/4 light

b. 1/8 half heavy, 7/8 light

c. 1/16 half-heavy, 15/16 light

d. 1/32 half-heavy, 31/32 light

c

Which of the following is not a function of the DnaA protein at the origin of replication?

a. binds to DnaA boxes

b. facilitates the methylation of GATC sites

c. binds to other DnaA proteins

d. aids in the separation of the AT rich region

b

How many replication forks are formed at an origin of replication?

a. one

b. two

c. four

d. many

b

The two things that DNA polymerase cannot do is to

a. synthesize DNA in the 5' to 3' direction and begin synthesis on a bare template strand

b. synthesize DNA in the 3' to 5' direction and begin synthesis on a bare template strand

c. use an RNA primer and proofread the DNA

d. proofread the DNA and synthesize DNA in the 5' to 3' direction

b

How is a new DNA strand made in the leading strand?

a. DNA is made in the direction toward the replication fork and is made as one continuous strand

b. DNA is made in the direction away from the replication fork and is made as one continuous strand

c. DNA is made in the direction toward the replication fork and is made as Okazaki fragments

d. DNA is made in the direction away from the replication fork and is made as Okazaki fragments

a

During proofreading, DNA polymerase recognizes a base mismatch and

a. removes nucleotides from newly made strand in the 5' to 3' direction

b. removes nucleotides from newly made strand in the 3' to 5' direction

c. removes nucleotides from template strand in the 3' to 5' direction

d. removes nucleotides from the template strand in the 5' to 3' direction

b

Below is a DNA molecule. Which ends are extended by telomerase?

a. both 5' ends

b. both 3' ends

c. the top ends

d. the bottom ends

b

What is not a function of the RNA that is found within telomerase?

a. to bind telomerase to the end of the telomere

b. to act as a primer for DNA synthesis

c. to act as a template for DNA synthesis

d. all of them are functions of the RNA in telomerase

b

A mutation in the lacZ gene alters B-galactosidase so it makes more allolactose compared with a normal B-galactosidase enzyme. How would this mutation affect the expression of the lac operon?

a. the lac operon could not be expressed in the presence of lactose in the environment

b. the lac operon would be constitutively expressed in the absence of lactose

c. it would require less lactose in the environment to express the lac operon

d. it would require more lactose in the environment to express the lac operon

c

With regard to lac operon regulation via catabolite activator protein, which of the following statements is correct?

a. glucose lowers cAMP levels. CAP binds to the DNA when cAMP is bound to CAP.

b. glucose lowers cAMP levels. CAP does not bind to the DNA when cAMP is bound to CAP.

c. glucose raises cAMP levels. CAP binds to the DNA when cAMP is bound to CAP.

d. glucose raises cAMP levels. CAP does not bind to the DNA when cAMP is bound to CAP.

a

A small effector molecule that inhibits transcription binds to a regulatory protein and causes it to not to bind to the DNA. The regulatory protein

a. is a repressor

b. is an activator

c. is neither a repressor or an activator

b

A mutation prevents the lac repressor from recognizing allolactose. In the absence of allolatose, the mutant repressor has the same affinity for the lac operator sites as a normal repressor. How would you expect this mutant repressor to affect regulation of the lac operon? Assume no glucose is present.

a. the operon would be turned on in the presence or absence of lactose in the environment

b. the operon would be turned off in the presence or absence of lactose in the environment

c. the operon would be turned off in the presence of lactose but turned on in lactose

d. the operon would be turned on in the presence of lactose but turned off in its absence

b

For a riboswitch that controls transcription, what is the effect of a regulatory molecule such as TPP?

a. it binds to a repressor and causes the repressor to bind to an operator site

b. it binds to an activator and causes the activator to bind to an operator site

c. it binds to an RNA molecule and causes a change in its conformation

d. it binds directly to the promoter and prevents transcription

c

ATP-dependent chromatin remodeling complexes may

a. alter the locations of nucleosomes

b. evict histones

c. replace standard histones with histone variants

d. do all of the above

d

Which of the following phenomena could you study using ChIp-seq?

a. to see if a regulatory transcription factor binds to mediator and/or TFIID

b. to measure the level of transcription of a given gene in real time

c. to analyze the binding of protein to DNA on a genome-wide scale

d. to determine if a mutation at a regulatory site alters the transcription level of a given gene

c

The ferritin mRNA in mammals is controlled by the iron regulatory protein that binds to an iron response element near the 5' end of the mRNA. What do you expect to happen when iron levels are low?

a. the translation of mRNA would be low

b. the translation of the mRNA would be high

c. IRP would bind to the IRE

d. both a and c

d

Within a eukaryotic genome, where would you expect to find nucleosome-free regions?

a. within both telomeres

b. at the beginning of a gene (at the core promoter)

c. at the end of a gene (at the terminator)

d. b and c

d

Which of the following events need to happen for the glucocorticoid receptor to activate a gene?

a. protein-protein interaction

b. the binding of the glucocorticoid receptor to a GRE

c. the binding of a small effector molecule to the glucocorticoid receptor subunits

d. all of the above need to happen

d

The Avy allele of the agouti gene involves the insertion of a transposable element upstream from the normal agouti promoter. The transposable element carries a promoter that causes the over expression of the agouti gene. Mice carrying this allele tend to have coat colors that are more yellow than mice that don't have this transposable element. If pregnant mice are fed a diet that contains chemical that inhibit DNA methylation, how would you expect that this diet would affect the coat color of offspring carrying the Avy allele?

a. their fur would be more yellow because the gene would be overexpressed

b. their fur would be less yellow because the gene would be underexpressed

c. their fur would be more yellow because the gene would be underexpressed

d. their fur would be less yellow because the gene would be overexpressed

a

Which of the following possibilities explain how PcG complexes are able to silence genes?

a. the compaction of nucleosomes

b. the attachment of ubiquitin to histone proteins

c. the direct inhibition of transcription factors, such as TFIID

d. all of the above

d

Epigenetic changes may

a. be programmed during development

b. be caused by environmental changes

c. involve changes in the DNA sequence of a gene

d. a and b

d

For XCI to occur, where are the Xist and Tsix genes expressed?

a. Xist is expressed only on Xa, and Tsix is expressed only on Xi

b. Xist is expressed only on Xi and Tsix is expressed only on Xa

c. both are only expressed on Xa

d. both are only expressed on Xi

b

Which of the following examples is an epigenetic change that is programmed during development?

a. variation in coat color in mice due to variation in expression of the Avy allele

b. XCI

c. effects of royal jelly on the formation of queen bees

d. effects of cigarette smoke in causing lung cancer

b

In humans, a recent study has shown that maternal anxiety during pregnancy can diminish the methylation of the ICR located at the H19 and ifg2 goes of the embryo and the fetus. how would this affect the expression of the maternal and paternal alleles of ifg2 gene after the baby is born?

a. it would not affect the expression of the paternal allele, but the maternal allele would be overexpressed

b. it would not affect the expression of the maternal allele, but the paternal allele would be overexpressed

c. it would not affect the expression of the paternal allele, but the maternal allele would be inhibited

d. it would not affect the expression of the maternal allele, but the paternal allele would be inhibited

d

Which of the following are components that HOTAIR ncRNA can bind to?

a. PCR2 complex, LSD1 complex, and GA rich regions

b. PCR2 complex, LSD1 complex, and miRNA

c. PCR2 complex, miRNA, and GA rich regions

d. PCR2 complex only

a

The experiments of Fire and Mellow are consistent with the idea that the type of molecule that initiates the process of RNA interference is

a. antisense RNA

b. sense RNA

c. double-stranded RNA

d. ribosomal RNA

c

Which genes of the CRISPR was-9 system are not needed for the expression and interference phases?

a. cas1, cas2

b. cas9

c. tracr

d. crispr

a

Let's suppose that a chemical is a mutagen. If you tested this chemical using the Ames test, there will be _____ colonies on the plates in which the cells had been exposed to the mutagen because the mutagen converts some of the cells from _______.

a. less, + to -

b. more, + to -

c. less, - to +

d. more, - to +

d

A gene exists in two alleles, which we will call B and b. The gene is 1123 bp in length, and the B and b alleles exhibit single base pair differences at six different sites. If gene conversion changed the b allele into the B allele, which mechanism would you favor to explain this conversion?

a. mismatch repair

b. gap repair synthesis

c. nucleotide excision repair

d. direct repair

b

According to the double-strand break model for homologous recombination, what happens right after DNA strand degradation at the double-stranded break site?

a. breakage of DNA strands in the homologous chromosome

b. formation of the D loop

c. the migration of Holliday junction

d. the resolution of the Holliday junction into two separate DNA molecules

b

During homologous recombination, how is a heteroduplex formed?

a. by the initial breakage of the DNA at a single location in two different DNA strands

b. the formation of a D loop

c. the migration of a Holliday junction

d. the resolution of the Holliday junction into two separate DNA molecules

c

Which of the following is a cause of spontaneous mutations?

a. chemotherapy

b. UV light

c. tautomeric shift

d. chemicals

c

Which of the following is/are ways that a retroelement can proliferate?

a. using reverse transcriptase and integrase

b. using transposase

c. target site primed reverse transcription

d. both a and c

d

Why does the movement of retrotransposons produce direct repeats on both sides of the retrotransposon?

a. integrase makes staggered cuts at the new site of insertion

b. the staggered cuts are filled by DNA gap repair synthesis

c. integrase causes one of the two inverted repeats to flip to the opposite direction

d. a and b

d

Which of the following statements regarding retrotransposons is the most accurate?

a. retrotransposons are most abundant in prokaryotic genomes

b. retrotransposons are most abundant in the genomes of simple eukaryotic genomes

c. retrotransposons are most abundant in complex eukaryotic genomes

d. they're rare

c

During nucleotide excision repair, the role of UvrC is to

a. detect DNA lesions

b. make cuts on either side of the lesion

c. remove the damaged strand

d. make a new strand where the damaged strand has been removed

b