MCB 250 Exam 2

Take a random sequence of DNA 5' to 3' and translate the putative protein that would result from the reading frame starting with first nucleotide. How often would you expect to find a stop codon in this reading frame? A. 1/4096 codons B. 1/20 codons C. 1/260 codons D. 1/64 codons

B. 1/20 codons

Type I topoisomerases are capable of doing all of the following except: A. Modify DNA topology without using ATP. B. Increase the negative supercoiling of DNA. C. Alter the linking number of a DNA molecule in steps of 1. D. Relax the free energy stored in supercoiling. E. Cleave and reseal phosphodiester bonds in the DNA backbone.

B. Increase the negative supercoiling of DNA.

A point mutation that leads to the production of a full-length protein with one altered amino acid is a: A. Nonsense mutation B. Missense mutation C. Frameshift mutation D. Silent mutation E. Insertion mutation

B. Missense mutation

Which of the following statements regarding the structure of RNA is INCORRECT? A. RNA does not form adenine-thymine (A-T) base pairs. B. RNAs with extended regions of base-pair complementarity adopt a helical form identical to B-type DNA. C. The ribose ring has a hydroxyl (-OH) group on its 2' carbon. D. Bases in RNA can form non-Watson-Crick base pairs. E. Base-pairing between short complementary sequences can fold a single-stranded RNA into a stable 3-dimensional structure.

B. RNAs with extended regions of base-pair complementarity adopt a helical form identical to B-type DNA.

Type II topoisomerases display all of the following characteristics EXCEPT: A. They are found in both E. coli and humans. B. They only introduce supercoiling and cannot relax a covalently closed circular DNA. C. They transiently cleave both strands of the double helix. D. They require ATP to alter the linking number of DNA. E. They alter linking number in increments of 2.

B. They only introduce supercoiling and cannot relax a covalently closed circular DNA.

One common type of DNA mutation is the thymine dimer. These dimers result from: A. incorporation of base analogs. B. exposure to UV radiation. C. spontaneous deamination of thymine. D. exposure to reactive oxygen species. E. errors in DNA replication.

B. exposure to UV radiation.

The nucleolus is the site of: A. Pol II phosphorylation B. rRNA transcription and processing C. Condensed chromatin D. DNA methylation

B. rRNA transcription and processing

A random mutation in the sequence of bacterial ribosome-binding site (RBS) is likely to result in which of the following? A. pausing of the ribosome during elongation B. reduced initiation of translation C. increased Rho-dependent termination D. reduced transcription of the mRNA E. shortening of the peptide as it is being translated

B. reduced initiation of translation

Promoters for E. coli genes that are transcribed by the sigma 70-RNA polymerase holoenzyme can vary, but which of the following is never part of the promoter DNA? A. the -35 element B. the +10 element C. the UP-element D. the -10 element

B. the +10 element

Which protein is specifically required for translocation of a bacterial ribosome along the mRNA? A. the aminoacyl-tRNA synthetase B. the EF-G protein C. the EF-Tu protein D. the Cap-binding protein E. the ribosome releasing factor

B. the EF-G protein

Which enzymatic activity is primarily responsible for the proofreading step of DNA replication? A. 3' to 5' exonuclease activity B. hydrolytic editing C. RNAseH activity D. 5' to 3' exonuclease activity E. tRNA synthetase activity

A. 3' to 5' exonuclease activity

Once elongation is underway, tRNAs involved in the process occupy a series of sites on the complexed ribosome. The occupation of sites occurs in the following order. A. A Site, P Site, E Site B. A Site, P Site, E Site, S Site C. A Site, S Site, E Site D. P Site, E Site, A Site E. S Site, A Site, P Site, E Site

A. A Site, P Site, E Site

Which of the following statements is CORRECT? A. Alternative splicing allows one gene to produce different proteins in different cell types. B. Protein isoforms resulting from alternative splicing have identical amino acid sequences. C. A single pre-mRNA can undergo only two forms of alternative splicing. D. Alternative splicing is a purely random process. E. Alternative splicing cannot alter the exons at the far 5' and 3' ends of the gene.

A. Alternative splicing allows one gene to produce different proteins in different cell types.

In E. coli, DNA polymerases I and III differ in many regards. Which of the following statements is not accurate? A. DNA polymerase I is able to proofread; DNA polymerase III is not. B. DNA polymerase III is responsible for the majority of DNA synthesis in E. coli. C. DNA polymerase I can replace RNA primers with DNA; DNA polymerase III does not. D. DNA polymerase I has 5' to 3' exonuclease activity; DNA polymerase III does not. E. The processivity of DNA synthesis is an order of magnitude greater for DNA polymerase III as compared to DNA polymerase I.

A. DNA polymerase I is able to proofread; DNA polymerase III is not.

In E. coli, the primary component of the mismatch repair system is the protein MutS. How does MutS recognize mismatched base pairs? A. It detects minor distortions in the DNA at the mismatch. B. When mismatched base pairs are transcribed, MutS edits the RNA transcript to correct the mutation. C. It reads the major groove and counts the number of hydrogen bonds to determine if there is correct base pairing. D. It identifies hemimethylated base pairs and methylates the unmodified base. E. It recognizes purine-purine and pyrimidine-pyrimidine mismatches because they are, respectively, longer and shorter than a purine-pyrimidine pair.

A. It detects minor distortions in the DNA at the mismatch.

Which of the following is true of the "end replication problem"? A. It explains why the 5' ends of daughter DNA molecules get shorter each time the DNA replicates. B. It explains why the 3' ends of daughter DNA molecules get shorter each time the DNA replicates. C. It affects only bacterial replication. D. It is solved by the combined action of DNA Pol I and ligase. E. It explains why eukaryotic organisms have fewer genes than they do proteins.

A. It explains why the 5' ends of daughter DNA molecules get shorter each time the DNA replicates.

What is the role of DnaC at oriC? A. Loads Helicase B. Loads SeqA C. Prevents TopoI from relaxing the DNA D. Loads DnaA E. Prevents Dam from acting

A. Loads Helicase

The "+1" for a given gene is defined as: A. The start site of transcription B. The start site of translation C. The start site of DNA replicationI D. The start site of the Chicago Marathon

A. The start site of transcription

What is the primary purpose of RNA splicing? A. To assemble the protein-coding sequences of the gene into a single continuous reading frame. B. To shorten mRNAs so that they can be transported to the cytoplasm for translation. C. To remove untranslated regions (UTRs) from the 5' and 3' ends of the pre-mRNA. D. To cleave the operon transcripts into multiple functional gene products. E. To add capping sequences to the 5' and 3' ends of the mRNA to protect against exonucleases.

A. To assemble the protein-coding sequences of the gene into a single continuous reading frame.

Which of the following reactions with covalently closed, circular DNA (cccDNA) does NOT result in a new linking number? A. incubation with ethidium bromide B. incubation with a type II topoisomerase C. a brief incubation with DNase followed by resealing the breaks in the phosphodiester backbone with another enzyme (DNA ligase) D. incubation with a type I topoisomerase

A. incubation with ethidium bromide

Transfer RNAs (tRNAs) contain a number of unusual bases (not A, U, C or G) that result from post-transcriptional chemical modifications. Which one of the following unusual bases contributes to "wobble" base-pairing between certain pairs of codons and anticodons? A. inosine B. dihydrouridine C. methylguanine D. pseudouridine E. hypoxanthine

A. inosine

Which of the following types of RNA is LEAST stable? A. mRNA B. rRNA C. tRNA

A. mRNA

DNA polymerase ensures that the correct nucleotide is incorporated into the growing strand of DNA by: A. monitoring the ability of the incoming nucleotide to form the appropriate base pair. B. selecting the correct nucleotide in an exonuclease active site in the DNA polymerase. C. incorporating random nucleotides and then subsequently removing the wrong ones. D. specifically allowing only the correct nucleotide to enter the active site.

A. monitoring the ability of the incoming nucleotide to form the appropriate base pair.

Are the 5' splice site and 3' splice site labeled 5' and 3' with respect to the ends of the intron or the ends of the exons? A. the intron B. the exons

A. the intron

A nucleosome forms hydrogen bonds with what part of the DNA? A. with the phosphodiester backbone and with bases via the minor groove B. with the phosphodiester backbone and with bases via the major groove C. only with bases via the major groove D. only with bases via the minor groove

A. with the phosphodiester backbone and with bases via the minor groove

Histones form hydrogen bonds with what part of the DNA? A. with the phosphodiester backbone and with bases via the minor groove B. only with bases via the major groove C. only with bases via the minor groove D. with the phosphodiester backbone and with bases via the major groove

A. with the phosphodiester backbone and with bases via the minor groove

During the process of translation, which component has the responsibility of ensuring that the tRNA is correctly charged, i.e. carries the amino acid that corresponds to its anti-codon? A. the peptidyl transferase center of the ribosome B. the aminoacyl-tRNA synthetase C. the messenger RNA D. the peptidyl-tRNA E. the factor binding center

B. the aminoacyl-tRNA synthetase

The initiation of transcription requires the melting of the DNA double helix, i.e. separating hydrogen-bonded base pairs, around the +1 site. How is this melting accomplished in E. coli? A. DNA helicase first unwinds the double helix around the +1 site. B. Topoisomerase first returns the linking number to Lk0. C. Bases at the promoter region flip outward from the double helix into pockets on the sigma factor. D. RNA polymerase gets the energy to cause separation of strands from ATP hydrolysis. E.DnaA: ATP complexes bind to and twist the double helix at the +1 site.

C. Bases at the promoter region flip outward from the double helix into pockets on the sigma factor.

Which of the following statements regarding Nucleotide excision repair (NER) is INCORRECT? A. Requires Pol I to complete the repair B. NER recognizes helix distortions C. Creates an abasic site as an intermediate in repair D. Requires Ligase to complete the repair E. NER involves the removal and replacement of DNA containing altered bases

C. Creates an abasic site as an intermediate in repair

The 10 nm fiber and the 30 nm fiber are two chromatin structures that differ in width. Which comparison between these two structures is INCORRECT? A. DNA is more heavily compacted in the 30 nm fiber. B. Formation of the 30 nm fibers requires histone protein H1. C. DNA is more accessible to the enzymes that regulate its function in the 30 nm fiber. D. In the 30 nm fiber, more DNA is associated with nucleosomes and the linker DNA is shorter. E. Formation of the 30 nm fiber requires modifications of the tail domains of the core histones.

C. DNA is more accessible to the enzymes that regulate its function in the 30 nm fiber.

DnaA-ATP binds to multiple sites at oriC forming a Nucleoprotein Complex and causing a local region of negative supercoiling. This is analogous to: A. DNA PolIII core B. Single stranded binding protein C. Histones D. Helicase E. Type 2 topoisomerase

C. Histones

The 16S RNA is the primary component of the: A. Large subunit of the ribosome B. Acceptor stem of the tRNA C. Small subunit of the ribosome D. Splicesome E. Enzyme that charges the tRNA

C. Small subunit of the ribosome

The ribosome allows the formation of a new peptide bond once it ensures that: A. The appropriate amino acid is attached to the tRNA B. The mRNA is being translated in the appropriate frame C. The codon-anticodon interaction is correct D. The peptide was initiated on the appropriate start codon E. Rho is not bound to the mRNA

C. The codon-anticodon interaction is correct

Which of the following statements regarding E. coli RNA polymerase is CORRECT? A. Has 5' to 3' exonuclease activity B. Requires helicase to open the DNA for transcription C. The transcription bubble is contained entirely within the polymerase D. Actively prevents dNTPs from entering the active site E. Binds to a clamp for processivity

C. The transcription bubble is contained entirely within the polymerase

How is open complex formation mediated in Pol II transcription initiation? A. Sigma factor melts the DNA B. Pol II doesn't form an open complex C. There is an ATP-dependent helicase in the initiation complex D. Mediator complex melts the DNA

C. There is an ATP-dependent helicase in the initiation complex

For a covalently closed circular double-stranded DNA, the linking number is: A. equal to the number of helical turns in the DNA double helix. B. the number of hydrogen bonds holding the two strands together. C. an invariant topological property of that DNA molecule. D. altered by distorting the shape of the DNA molecule.

C. an invariant topological property of that DNA molecule.

Gyrase is different from other Type II topoisomerases because Gyrase: A. can relax positively supercoiled DNA. B. does not require ATP. C. can introduce negative supercoils into negatively supercoiled DNA. D. has an active site phenylalanine instead of tyrosine.

C. can introduce negative supercoils into negatively supercoiled DNA.

Promoter escape occurs when RNA polymerase enters into which phase of the transcription cycle? A. open complex B. termination C. elongation D. closed complex E. initiation

C. elongation

A mutation in the sequence of prokaryotic DNA encoding the ribosome binding site (RBS) may result in which of the following? A. reduced transcription of the mRNA for the gene in which the mutation occurs B. paused ribosome during elongation C. reduced initiation of translation D. paused RNA polymerase during elongation

C. reduced initiation of translation

Base excision repair: A. occurs only in eukaryotes. B. requires an active site tyrosine. C. replaces bases other than A, T, C or G. D. requires hemimethylated DNA. E. requires gyrase activity.

C. replaces bases other than A, T, C or G.

Which of the following statements is INCORRECT? A. snRNPs are an important component of the spliceosome. B. snRNPs are short nuclear RNAs complexed with splicing proteins. C. snRNPs are an important component of the ribosome. D. Some snRNPs function as ribozymes, i.e. they catalyze chemical reactions in the splicing process. E. snRNPs orchestrate splicing by complementary base pairing with conserved sequences in the mRNA.

C. snRNPs are an important component of the ribosome.

Rho-dependent termination of transcription requires all of the following EXCEPT: A. the six subunits of the Rho protein. B. the absence of ribosomes bound to the transcript. C. the stem-loop secondary structure in the transcript. D. ATP hydrolysis.

C. the stem-loop secondary structure in the transcript.

The genetic code is said to be "degenerate." This indicates that: A. The code does not wear a facemask in public B. There is a tRNA for every codon C. A given codon can designate more than one amino acid D. A single amino acid can be coded for by more than one codon E. There are more than one stop codons

D. A single amino acid can be coded for by more than one codon

One mechanism by which a repressor protein can inhibit transcription in bacteria is by: A. Methylate the -10 sequence B. Bind hemi-methylated DNA C. Inhibiting Rho-dependent termination D. Block binding of RNA Polymerase holoenzyme to the DNA E. Bind the UP element

D. Block binding of RNA Polymerase holoenzyme to the DNA

Methylation and subsequent deamination of cytosine produces what type of mutation after one round of DNA replication? A. G-to-A transition B. C-to-A transversion C. G-to-C transition D. C-to-T transition E. C-to-T transversion

D. C-to-T transition

Which of the following remains associated with the mRNA when it is exported from the nucleus? A. Pol II C-terminal tail B. Poly A polymerase C. U2 snRNA D. Cap binding protein E. 18S rRNA

D. Cap binding protein

You work for a pharmaceutical company and discover a chemical compound with antibiotic properties. When this chemical is added to E. coli, the bacteria stop producing full-length mRNAs and instead accumulate short transcripts of 8-10 nucleotides in length. Which of the following steps in transcription is most likely affected by the drug? A. Binding to the promoter B. Formation of the open complex C. Rho-dependent termination D. Promoter clearance E. Elongation rate of the core polymerase

D. Promoter clearance

In eukaryotes, which RNA polymerase is responsible for transcribing mRNAs? A. RNA polymerase I B. RNA polymerase IV C. RNA polymerase III D. RNA polymerase II E. There is only one RNA polymerase in eukaryotes.

D. RNA polymerase II

In E. coli, ribosomal RNA processing requires: A. A specific mediator B. Specific DNases C. A specific sigma factor D. Specific RNases

D. Specific RNases

Which of the following statements about telomerase is INCORRECT? A. Telomerase has reverse transcriptase activity. B. Telomerase generates a new primer: template junction by providing its own template. C. Telomerase acts to elongate the 3' end of linear DNAs. D. Telomerase replaces the final RNA primer with DNA during DNA replication. E. Telomerase is a ribonucleoprotein.

D. Telomerase replaces the final RNA primer with DNA during DNA replication.

Which of the following statements is NOT true of aminoacyl-tRNA synthetases? A. They activate the amino acid and covalently bond it to the mature tRNA. B. Each member of this protein family is dedicated to one particular amino acid. C. They attach the amino acid to the -CCA at the 3'-end of the mature tRNA. D. They attach the amino acid to the elongating peptide and catalyze translocation. E. They are primarily responsible for the accuracy of mRNA translation.

D. They attach the amino acid to the elongating peptide and catalyze translocation.

What is the role of DNA helicase? A. Relax positive DNA supercoils B. Bind single stranded DNA and keep it from reanealling C. Confer processivity to DNA Pol III D. Unwind the DNA at the replication fork E. Load clamps

D. Unwind the DNA at the replication fork

Mutations that alter the -10 of a given gene away from consensus will likely: A. cause increased scrunching B. enhance termination C. decrease binding of sigma 70 to core polymerase D. decrease transcription initiation E. increase transcription initiation

D. decrease transcription initiation

The functional state of RNA polymerase II is altered by phosphorylation on which region of the protein? A. the alpha subunit B. the mediator complex C. the sigma factor D. the C-terminal tail domain E. the N-terminal tail domain

D. the C-terminal tail domain

A complete ribosome has how many tRNA binding sites? A. 2 B. 1 C. 4 D. 0 E. 3

E. 3

What is the role of SeqA in E. coli? A. Determines which strand of the DNA is replicated B. Binds to Dam methylase to inhibit its function C. Binds to DnaA to prevent it from binding ATP D. Loads Helicase E. Binds hemimethylated Ori to prevent premature initiation

E. Binds hemimethylated Ori to prevent premature initiation

5' Capping and 3' polyadenylation have which of the following in common? A. Both involve unusual linkages between nucleotides B. Both involve template-independent polymerization C. Both involve methylation of nucleotides D. Both involve cleavage of the mRNA at specific sequences E. Both are important for export of the mRNA from the nucleus

E. Both are important for export of the mRNA from the nucleus

Which of the following statements concerning peptide bond formation is CORRECT? A. It directly requires GTP hydrolysis B. It is catalyzed by an enzymatic protein C. The reaction is spontaneous between two free amino acids D. It occurs primary with formyl-methionine E. It involves an amino group attacking a ester bond

E. It involves an amino group attacking a ester bond

In Nature, DNA supercoiling is almost always negative. Why? A. Negative supercoiling keeps DNA from denaturing at high temperatures. B. Negative supercoiling relaxes circular DNAs. C. Negative supercoiling compacts DNA. D. Negative supercoiling is an inherent property of right-'handed helices. E. Negative supercoiling stores energy for cellular processes that require strand separation.

E. Negative supercoiling stores energy for cellular processes that require strand separation.