Practice Exam 2 Questions

1) The structures best represented by the letter E (black and white portions are? 2) The correct designation for the structure or position labelled A could be?

1) composed of RNA and DNA 2) a primer

Transcribe the following sequence: 5' - TCTAGGC- 3'?

5' - GCCUAGA - 3'

Assume that the following single strand of DNA was synthesized using standard dA TP , dGTP , dCTP , and dTTP precursors; however, the innermost phosphate (alpha phosphate) of all the dGTPs was labeled with 32P. 3'—CT AGT AGCTT A—5' Assume also that the strand was degraded to completion by the enzyme spleen diesterase. Spleen diesterase cleaves DNA at the covalent bond that connects the 5' carbon of the sugar to the phosphate. Which of the resulting nucleotide(s) might now carry the 32P?

C and T

In order to create the replication forks (initiate DNA replication) in E.coli, oriC needs to be "activated". The firststep in this process involves binding of _______ proteins to oriC and melting of short stretch of DNA before other proteins can join the complex. This protein is referred to as the __________. a. DnaX/replicator b. DnaA/initiator c. DnaB/helicase loader d. DnaC/helicase e. DnaD/primase

b. DnaA/initiator

What is the advantage of transcription-coupled repair? a. It allows the cell to do two things at once. b. It ensures that the genes of greatest importance to a particular cell receive the highest priority on the repair list. c. It ensures that the genes with most extensive damage receive the highest priority on the repair list. d. It repairs noncoding sequences preferentially. e. It is the most accurate method of repair.

b. It ensures that the genes of the greatest importance to a particular cell receive the highest priority on the repair list

Which of the following mechanisms can correct and remove/repair pyrimidine dimers in humans? a. photoreactivation b. NER c. translesion synthesis d. all of the above e. b and c only

b. NER

Which of the following is/are true? a. RNAP III can initiate at its promoters in the absence of any additional factors b. RNAP III promoters usually contain positions that lie downstream of the startpoint c. RNAP III functions primarily within the nucleolus d. all of the above e. b. and c. only

b. RNAP II promoters usually contain positions that lie downstream of the start point

Which DNA repair mechanism removes single nucleotides altered by reactive chemicals that may be present in the diet or be produced by metabolism? Such alterations are recognized by enzymes called glycosylases. a. nucleotide excision repair b. base excision repair c. mismatch repair d. double-strand breakage repair e. all of the above

b. base excision repair

There is a large class of DNA polymerases that are specialized for incorporating nucleotides opposite various types of DNA lesions in the template strand. They engage in a type of DNA synthesis called __________. They usually do not possess ______________ activity that is characteristic of most other DNA polymerases. a. translational synthesis/ a helicase b. translesion synthesis/ a 3' to 5' exonuclease c. transdimensional synthesis/ a polymerase d. translesion synthesis/ a ligase e. transliteral synthesis/ a 5' to 3' exonuclease

b. translesion synthesis/ a 3' to 5' exonuclease

DNA is composed of two strands, only one of which typically is used as a template for RNA synthesis. By what mechanism is the correct strand chosen? a. Both strands are tried and the one that works is remembered. b. Only one strand has the start codon. c. The promoter acts to aim (position) the RNA polymerase. d. A start factor informs the system. e. It is chosen randomly.

c. The promoter acts to aim (position) the RNA polymerase

Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA? a. promoter b. "up" element c. intrinsic transcription terminator d. operator e. both c and d

c. intrinsic transcription terminator

Considering a typical prokaryotic or eukaryotic cell what is the most abundant type of RNA? a. mRNA b. tRNA c. rRNA d. miRNA e. snRNA

c. rRNA

Which of the following is not an activity of bacterial core RNA polymerase or any of the eukaryotic RNAPs (I-III)? a. unwinding and rewinding of DNA b. catalyzing addition of ribonucleotides c. recognition of promoters d. holding a newly synthesized portion of RNA product e.holding separated DNA strands

c. recognition of promoters

The best term to describe the extension of the lagging strand template of vertebrate telomeres is? a. DNA replication b. termination c. reverse transcription d. transcription e. reverse replication

c. reverse transcription

Concerning the promoters recognized by general sigma factor (σ70) in E. coli, mutations in the -35 region tend to affect the formation of the _____complexes and the mutations in the -10 region affect the formation of the _____complexes.

closed/ open

8-OxoG may be generated by ______ and this modified base has a tendency to pair with A. Therefore if it is not repaired prior to replication its presence in DNA would lead to _________. a. oxidation/transitions b. deamination/transverison c. alkylation/transitions d. oxidation/transversions e. alkylation/transversions

d. oxidation/transversions

A eukaryotic cell lacking a telomerase activity would a. have a high probability of becoming cancerous. b. not be able to repair Okazaki fragments. c. never be able to divide. d. undergo a reduction in chromosome length during each cell cycle. e. All of the above

d. undergo a reduction in chromosome length during each cell cycle

Which of the following statements about telomerase is incorrect? a. It is a DNA Polymerase that generates a single stranded DNA. b. It is a reverse transcriptase. c. It requires a primer. d. It does not require a template at the end of the chromosome because it carries its own template. e. None of the above.

e. None of the above

Which of the following statements about mammalian telomeres is incorrect? a. They all contain multiple copies of a short DNA sequence that is specific for each organism. b. They may protect chromosomes from degradation. c. They can be extended by an enzyme called telomerase that carries an RNA molecule that is complementary to the telomeric repeats. d. They may protect the cell from chromosomal fusions. e. None of the above.

e. None of the above, they are all correct

What happens when the DNA polymerase on the lagging strand template completes the synthesis of an Okazaki fragment? a. It disengages from the beta clamp. b. It binds more tightly to the beta clamp. c. It cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction closer to the replication fork. d. It cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction farther from the replication fork. e. a and c

e. a and c (It disengages the beta clamp; it cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction closer to the replication fork)

Which of the following could have an effect on initiation of DNA replication in E. coli? a. binding of secA at oriC b. binding of ORC to oriC c. the methylation state at oriC d. all of the above e. a and c only

e. a and c only (binding of secA at oriC and the methylation state at oriC)

Why do eukaryotic cells have multiple initiation sites in their DNA unlike bacteria that usually have only one? a. Cells of higher organisms can have up to 1000 times the amount of DNA as bacteria. b. Prokaryotic cells incorporate nucleotides at much slower rates. c. Eukaryotic Okazaki fragments are ~10X shorter. d. all of the above e. a. and c. only

e. a and c only (more DNA than bacteria; Eukaryotic Okazaki fragments are ~10 times shorter)

Which type of DNA repair involves the preferential repair of strands of genes that are actively serving as templates for RNA synthesis? a. transcription-coupled pathway b. global pathway c. base excision repair d. nucleotide excision repair e. a and d

e. a and d (transcription-coupled pathway and nucleotide excision repair)

Which type of DNA repair involves the preferential repair of strands of genes that are actively serving as templates for RNA synthesis? a. transcription-coupled repair (TCR) b. non-homologous end joining (NHEJ) c. base excision repair (BER) d. nucleotide excision repair (NER) e. a and d only

e. a and d only (Transcription-Coupled Repair and Nucleotide Excision Repair)

The function of eukaryotic telomerase is to a. synthesize DNA primers at the end of each chromosome. b. extend the lagging strand to the end of each chromosome. c. extend the leading strand template at the end of each chromosome. d. extend the leading strand at the end of each chromosomes e. extend the lagging strand template at the end of each chromosome.

e. extend the lagging strand template at the end of each chromosome

An eukaryotic cell lacking a telomerase activity would a. have a high probability of becoming cancerous. b. not be able to repair Okazaki fragments. c. never be able to divide. d. all of the above e. none of the above

e. non of the above

Statement A. In eukaryotes the pre-replicative complex (pre-RC) can be formed only during M but it remainsinactive until the onset of S phase. Statement B. The ability to form pre-RCs or activate them during different stages of the cell cycle is controlled by the level of activity of Cdk (cyclin dependent kinase)

only statement B is true

As replication proceeds, the lagging strand of DNA is looped back on itself so that it has the same orientation as the leading strand template; the looped DNA repeatedly grows and shortens during lagging strand replication. This model is often referred to as the _________.

trombone model

Here is a diagram of DNA replication in E.coli. The darker strands are newly synthesized, #1 points to the new strand in the top duplex and #4 in the bottom duplex. 1) The hexametric protein complex indicated by #5 is a ________. It uses _______ as an energy source. 2) The sliding clamp (beta clamp) would be found associated with structure # ___________ and greatly increases its processivity. 3) #3 indicates __________ that is a single polypeptide protein with several enzymatic activities. One of these activities is a ___________ that could be used in nick translation to label double-stranded DNA molecules. 4) #3 indicates a single polypeptide protein with several enzymatic activities. One of these activities is a _____ that is used for primer removal and the other is _________ used for proofreading 5) The sliding clamp (beta clamp) would be found associated with structure # ___________ and greatly increase its ___________. 6) At which position would you find a topoisomerase? 7) What protein/enzyme that functions at or near every replication fork in E. coli is missing from the diagram?

1) helicase/ ATP 2) 2 3) DNA polymerase I/ 5' to 3' exonuclease activity 4) 5' to 3' exonuclease activity; 3' to 5' exonuclease activity 5) two/ processivity 6) six 7) Primase

RNA polymerase moves along the template strand of DNA in the ____ direction, and adds nucleotides to the ____ end of the growing transcript.

3' to 5'; 3'

Place the steps in base excision repair (BER) in the correct order. 1 -A base is removed by cleavage of glycosidic linkage attaching it to deoxyribose. 2 - Baseless deoxyribose is recognized by AP endo/nuclease that created a nick in one strand. 3 - DNA glycosylase recognizes a specific base. 4 - The nick is sealed by DNA ligase. 5 - DNA polymerase inserts one or several nucleotides using a nick as a primer.

3. DNA glycosylase recognizes a specific base 1. A base is removed by cleavage of glycosidic linkage attaching it to deoxyribose 2. Baseless deoxyribose is recognized by AP endonuclease that created a nick in one strand 5. DNA polymerase inserts one or several nucleotides using a nick as a primer 4. The nick is sealed by DNA ligase

Place the steps in base excision repair (BER) in the correct order. 1 - Damaged base is removed by cleavage of glycosidic linkage attaching it to deoxyribose. 2 - Baseless deoxyribose phosphate in site is excised by a specialized AP endo/exonuclease. 3 - DNA glycosylase recognizes specific altered base. 4 - The strand is sealed by DNA ligase. 5 - Gap is filled by DNA polymerase; it inserts a nucleotide complementary to the undamaged strand.

3. DNA glycosylase recognizes specific altered base 1. Damaged base is removed by cleavage of glycosidic linkage attaching it to deoxyribose 2. Baseless deoxyribose phosphate is site is excised by a specialized AP endo/exonuclease 5. Gap is filled by DNA polymerase; it inserts a nucleotide complementary to the undamaged strand 4. The strand is sealed by DNA ligase

Bacterial RNA polymerase passes through several steps prior to elongation. These steps include 1. release or change of association with sigma, 2. formation of an open binary complex. 3. formation of a closed binary complex. 4. abortive initiation. 5. promoter clearance. The correct sequence of events is:

3. Formation of a closed binary complex 2. Formation of an open binary complex 4. Abortive initiation 1. Release or change of association with sigma 5. Promoter clearance

Statement A. The activation of origins of replication is very similar in all organisms and requires sequence-specific binding of initiator proteins, meting of AT rich region by initiators that is followed by recruitment of replication machinery. Statement B. At all origins of replication helicases are loaded, by helicase loaders, directly onto single stranded DNA generated by the initiators.

Both A and B are FALSE

Statement A. In eukaryotes the pre-replicative complex (pre-RC) can be formed only during G1 but it remains inactive until the onset of S phase. Statement B. The ability to form pre-RCs or to activate them during different stages of the cell cycle is controlled by the level of activity of Cdk (cyclin dependent kinase)

Both A and B are true

Statement A. Prokaryotic intrinsic transcription terminators consist of two features that are both required for termination to occur: a hairpin that is followed by a run of U's Statement B. Eukaryotic RNA Pol. I and III terminate transcription right after specific terminator sequences are transcribed similarly to prokaryotic RNA Pol.

Both A and B are true

Statement A. The activation of origins of replication is very similar in all bacteria and requires sequence-specific binding of initiator proteins, melting of AT rich region by initiators, that is followed by recruitment of replication machinery. Statement B. At all origins of replication helicases are loaded onto DNA by helicase loaders but only in bacteria they are loaded directly onto single stranded DNA that was melted by the initiators.

Both A and B are true

Many of the RNA polymerase II promoters contain ______, an element generally present at a "fixed" distance upstream from startpoint. When present, this element is bound by ________ via its subunit called _________.

TATA box/ TFIID/ TBP

Which of the following statements is false when comparing prokaryotes with eukaryotes? a. The prokaryotic chromosome is usually circular, whereas eukaryotic nuclear chromosomes are linear. b. Prokaryotic chromosomes usually have a single origin of replication, whereas eukaryotic chromosomes have many. c. The rate of elongation during DNA replication is higher in prokaryotes than in eukaryotes. d. Prokaryotes produce longer Okazaki fragments during DNA replication than eukaryotes. e. The ends of eukaryotic and prokaryotic chromosomes comprise telomeres.

The ends of eukaryotic and prokaryotic chromosomes comprise telomeres

Before RNA polymerase II can leave the promoter its CTD needs to be phosphorylated by the _____activity of ___.

kinase/ TFIIH

Many of the RNA polymerase II promoters are TATA-less but they are still recognized by the same specific GTF in a sequence specific manner. These promoters must contain ______ plus DPE or DCE that are all recognized by a _______ subunit of ________.

Inr/TAF/ TFIID

Here is a sketch of a replication bubble, as you might see in E. coli. Arrows inside the bubble indicate the direction of the replication forks. If the arrow outside the bubble (red arrow) represents the 3' end of the strand it is nearest to, where is (are) the most likely place(s) to see the Okazaki fragments?

Positions closest to letters (c) and (a)

In order to create the replication forks (initiate DNA replication) in E.coli, oriC needs to be "activated". The first step in this process involves binding of _______ proteins to oriC and melting of short stretches of DNA before other proteins can join the complex. During DNA replication ________ protein is required only at oriC. a. DnaA b. DnaB c. DnaC d. DnaG e. SSB

a. DnaA

What happens to the core DNA polymerase III (in E.coli) on the lagging strand template when it completes the synthesis of an Okazaki fragment? a. It starts removal of the RNA primer and replaces it with DNA. b. It disengages from the beta clamp c. It begins proofreading the completed Okazaki fragment d. It cycles to the helicase/SSB complex at the replication fork\ e. All of the above

b. It disengages from the beta clamp

Which of the following statements best describes the termination of transcription in prokaryotes? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through an intron, and the splicing machinery causes the polymerase to let go of the transcript. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase.

b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript

One of the RNA polymerase I ancillary factors, SL1, consists of four proteins. One of its component proteins is also required for the initiation by RNA polymerase II and RNA polymerase III as a part of a "positioning" factor. This protein common to all three "positioning" factors is called _______. a. TFIID b. TBP c. TFIIIB d. UBF1 e. PABP

b. TBP

What must the mismatch repair system be able to distinguish in order to tell which nucleotide of a mismatched pair to replace? a. It must be able to distinguish which chain possesses the right sequence. b. It must be able to distinguish the newly made strand from the parental strand. c. It must be able to distinguish which chain is of the right polarity. d. It must be able to distinguish which chain contains more incorrect bases. e. all of the above

b. it must be able to distinguish between the newly made strand and from the parental strand

Assuming there are 9 TCGA sequences within a 600 bp long regulatory region of an eukaryotic gene. How many of these tetramers would you expect to find in a 600 bp sequence anywhere else in the genome assuming that all 4 bases are present in equal proportions? a. most likely none b. maybe 2 c. probably 4 d. more than 5 e. can't predict

b. maybe 2

Extension of the lagging strand template at vertebrate telomeres occurs by a process that could be termed as a. replication b. reverse transcription c. termination d. translation e. transcription

b. reverse transcription

Which of the following is analogous to telomeres? a. the pull tab on a soft drink can b. the two ends of a shoelace c. the central spindle of a CD that fits around while in the case d. the mechanism of a zipper that allows the separated parts to be joined e. the correct letters used to replace errors in a document after they have been deleted in a word processor

b. the two ends of a shoelace

Nick translation where a part of one DNA strand is replaced by a new strand (e.g. incorporating labeled nucleotides to generate radioactive or fluorescent probes) requires the following enzymatic activities: a. DNA polymerase adding new nucleotides to the 5' end and 3' to 5' exonuclease activity for "old" strand degradation b. DNA polymerase adding new nucleotides to the 5' end followed by ligase activity c. DNA polymerase adding new nucleotides to the 3' end and 5' to 3' exonuclease activity for "old" strand degradation d. Primase activity followed by DNA polymerase adding new nucleotides to the 5' end e. DNA polymerase adding new nucleotides to the 3' end and 3' to 5' exonuclease activity for "old" strand degradation

c. DNA polymerase adding new nucleotides to the 3' end and 5' to 3' exonuclease activity for "old" strand

Which of the following is false? a. RNA polymerase I (generally) requires only two ancillary factors for efficient initiation of transcription b. RNA polymerase I requires TBP for initiation of transcription c. RNA polymerase I transcribes 5S rRNA d. RNA polymerase I promoters are bipartite consisting of core promoter and UCE e. None of the above

c. RNA polymerase I transcribes 5S rRNA

Alternative sigma factors are used as a means to regulate gene expression in bacteria. A replacement of one sigma factor for another on bacterial RNA polymerase will enable __________ . a. a promoter to function as a terminator b. a terminator to function as a promoter c. RNA polymerases to initiate transcription using a new (different) set of promoters d. RNA polymerase to read through transcription terminators e. RNA polymerase to terminate at a new set of terminators

c. RNA polymerase to initiate transcription using a new (different) set of promoters

Which of the following statements best describes the termination of transcription in eukaryotes by RNA Pol II? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase, which continues to synthesize more "nonfunctional" RNA. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. It may be a, b or c. depending on a gene.

c. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase, which continues to synthesize more "nonfunctional" RNA

Which of the following is false about the E. coli general sigma factor ( σ70)? a. it contacts promoter directly at -10 and -35 b. mutations in sigma may suppress mutations in promoters c. removal of C-terminus allows sigma (alone) to bind promoters d. It has several DNA binding domains e. none of the above

c. Removal of C-terminus allows sigma (alone) to bind promoters

In transcription-coupled repair (TCR), how is the presence of a lesion thought to be detected? a. There are special enzymes that can scan the DNA for such lesions b. The lesion is signaled by a stalled DNA polymerase c. The lesion is signaled by a stalled RNA polymerase d. The lesion is signaled by a stalled peptidyl transferase e. The lesion is detected by single-stranded binding proteins

c. The lesion is signaled by a stalled RNA polymerase

One of the factors that may affect initiation of DNA replication in E. coli a. the acetylation state of histones at oriC b. the acetylation state of A's at oriC c. the methylation state of A's at oriC d. the methylation state anywhere on the chromosome e. the methylation state of T's at ARS

c. The methylation state of A's at oriC

Which of the following statements about mammalian telomeres is incorrect? a. They all contain multiple copies of a short DNA sequence that is specific for each organism. b. They may protect chromosomes from degradation. c. They can be extended by an enzyme called telomerase that carries a DNA molecule that is complementary to the telomeric repeats d. they may protect the cell from chromosomal fusion e. None of the above

c. They can be extended by an enzyme called telomerase that carries a DNA molecule that is complementary to the telomeric repeats

Which protein/enzyme is used to decatenate E. coli chromosomes after replication? a. DNA pol b. Telomerase c. Topoisomerase d. Ligase e. Helicase

c. Topoisomerase

O6 - methylG may be generated by ______ and this modified base has a tendency to pair with T. Therefore if it is not repaired prior to replication its presence in DNA would lead to _________. a. oxidation/transitions b. deamination/transverions c. alkylation/transitions d. oxidation/deletions or insertions e. alkylation/transversions

c. alkylation/transitions

The function of eukaryotic telomerase is to a. synthesize DNA primers at the end of each chromosome. b. extend the lagging strand to the end of each chromosome. c. extend the lagging strand template at the end of each chromosome. d. finish the synthesis of the leading strand at the end of each chromosomes e. extend the leading strand template at the end of each chromosome.

c. extend the lagging strand template at the end of each chromosome

A specific prokaryotic transcription unit that is 5,000 nucleotides long uses only 1,200 nucleotides to make a protein consisting of 400 amino acids. This is best explained by the fact that a. it may contain several introns that are spliced out b. there is redundancy and ambiguity in the genetic code c. many nucleotides may be present within the 5' and 3' UTR's d. nucleotides break off and are lost during or after the transcription process e. a and c

c. many nucleotides may be present within the 5' and 3' UTR's

The enzyme polynucleotide phosphorylase randomly assembles nucleotides into a polynucleotide polymer. You add polynucleotide phosphorylase to a solution of adenosine triphosphate and guanosine triphosphate. The resulting artificial mRNA molecule would have ____ possible different codons if the code involved three-base sequences and ____ possible different codons if the code involved four-base sequences. a. 16;32 b. 4;8 c. 4;16 d. 8;16 e. 16;64

d. 8; 16

Water can be DNA's "enemy" by participating in all of the following reactions except: a. Hydrolysis generating AP sites (abasic). b. Deamination of Cs converting them to Us. c. Deamination of 5 methyl Cs converting them to Ts. d. Deamination of Ts converting them to Cs e. None of the above

d. Deamination of T's converting them to C's

Which of the following statements about telomerase is incorrect? a. It is a DNA polymerase that generates single-stranded DNA b. It is a reverse transcriptase c. It does not require a primer d. It does not require a template at the end of the chromosome because it carries its own template in the form of RNA e. none the above

d. It does not require a template at the end of the chromosome because it carries its own template in the form of RNA

How does active CRP (or CAP) induce expression of the genes of the lac operon? a. It terminates production of repressor molecules. b. It degrades the substrate lactose. c. It stimulates splicing of the encoded genes. d. It stimulates the binding of RNA polymerase to the promoter. e. It binds steroid hormones and controls translation

d. It stimulates binding of the RNA polymerase to the promoter

Which of the following is characteristic of the lytic cycle? a. Many bacterial cells containing viral DNA are produced. b. Viral DNA is incorporated into the host genome. c. The viral genome replicates without destroying the host. d. New phages are produced and released while killing the host. e. The virus-host relationship usually lasts for generations.

d. New phages are produced and released while killing the host

RNA polymerase and DNA polymerase differ in that a. RNA polymerase uses RNA as a template, and DNA polymerase uses a DNA template. b. RNA polymerase binds to single-stranded DNA, and DNA polymerase binds to double-stranded DNA. c. RNA polymerase is much more accurate than DNA polymerase. d. RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a primer to initiate DNA synthesis. e. RNA polymerase does not need to separate the two strands of DNA in order to synthesize an RNA copy, whereas DNA polymerase must unwind the double helix before it can replicate the DNA.

d. RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a primer to initiate DNA synthesis

If antitermination is utilized to regulate gene expression, this mechanism enables __________. a. promoters to function as a terminator b. terminator to function as a promoter c. RNA polymerases to initiate transcription using a new (different) set of promoters d. RNA polymerases to read through the transcription terminators e. RNA polymerases to terminate at a new set of promoters

d. RNA polymerases to read through the transcription terminators

Individuals with the disorder xeroderma pigmentosum are hypersensitive to sunlight because their cells have an impaired ability to a. replicate DNA by translesion polymerases. b. repair chromosomal breaks. c. correct mismatches generated during replication d. remove pyrimidine dimers by NER pathway

d. Remove pyrimidine dimers by NER pathway

The 5' end of each Okazaki fragment begins with: a. the same RNA primer that began synthesis on the leading strand. b. a DNA primer binding to the template DNA. c. DNA polymerase binding to the template DNA. d. a separate RNA primer. e. a small DNA primer.

d. a separate RNA primer

Transcription involves synthesis of an RNA chain representing one strand ofa DNA duplex. The strand with the complementary sequence to RNA product is the ________ strand and the one that has the "same" sequence as the RNA productis the ________ strand. a. antisense/sense b. noncoding/nontemplate c. template/coding d. all of the above e. only b and c are correct

d. all of the above

Which of the following may contribute to stabilizing the 2D and/or 3D structures of RNA? a. hydrogen bonding via 2'OH group b. base stacking c. G-U base pairing d. all of the above e. a and b only

d. all of the above (hydrogen bonding via 2'OH group base stakcing G-U base pairing)

Which of the following is false about A-form double helices? a. they are left handed with ~ 11 bp/turn b. they are a typical confirmation of all nucleic acids under physiological conditions c. they are never found in nature d. all of the above e. a. and b. only

d. all of the above statements are false about A-form double helices

In higher eukaryotes many of the Cs followed by Gs in the so called CpG islands are methylated resulting in 5-mC. These bases have a tendency to undergo _______ by water giving rise to Ts. If these Ts are not removed prior to replication by _________ they will cause __________. a. alkylation/BER/transversions b. deamination/NER/insertions c. alkylation/ BER/transitions d. deamination/BER/transitions e. deamination/NER/transitions

d. deamination/BER/transitions

Which of the following is most likely to produce a frameshift mutation? a. alkylaing agents b. nitrous acid c. UV radiation d. intercalating agents e. oxidation of a base

d. intercalating agents

Which one of the following is not directly involved in mismatch repair in E.coli? a. MutS b. DNA Polymerase c. MutH endonuclease d. methyltransferase e. exonuclease

d. methyltransferase

In eukaryotic cells, a complex of proteins binds to broken ends (ds breaks) of the DNA duplex and catalyzes a series of reactions that rejoin the broken strands by a process that usually results in some DNA loss. This is an example of what kind of repair? a. nucleotide excision repair b. base excision repair c. homologous recombination d. non homologous end joining e. single-stranded breakage repair

d. non homologous end joining

In eukaryotic cells, a complex of proteins binds to the broken ends (ds breaks) of the DNA duplex and catalyzes a series of reactions that rejoin the broken strands by a process that usually results in some DNA loss. This is an example of what kind of repair? a. nucleotide excision repair b. base excision repair c. homologous recombination d. non homologous end joining e. single-strand breakage repair

d. non-homologous end joining

Which of the following is false when activation of oriC and ARS are compared? a. The initiator that binds to oriC is DnaA and the initiator that binds to ARS is a heterohexamer called ORC. b. In both cases the initiators bind to the cis-acting elements within the origins in a sequence specific manner. c. In both cases binding of the initiators to the origins is required for the recruitment of other proteins that are necessary for the formation of replication forks d. none of the above e. both b and c are false

d. none of the above are false

Which of the following strategies is not used by phages to organize the expression of their genes into regulatory cascades? a. successive alternative sigma factors b. phage specific RNA polymerases c. antitermination proteins d. successive alternative ribosomes e. all of the above may be used by different phages

d. successive alternative ribosomes

Which of the following is false about nuclear genes for the 3 largest rRNAs in higher eukaryotes? a. they are transcribed in the nucleolus b. each "gene" is transcribed into a large precursor RNA that needs to be cut and trimmed to give rise to 3 mature rRNAs c. they are transcribed by RNA Pol I d. they are translated into r-proteins in the cytoplasm e. none of the above is false; all are true

d. they are translated into r-proteins in the cytoplasm

Every organism has several different DNA polymerases. There are several families of DNA polymerases that are involved in __________ which involves addition of nucleotides across abasic sites or damaged/abnormal bases. These enzymes usually not capable of proofreading, which depends on __________ activity. a. translational synthesis/a 3' to 5' exonuclease b. translesion synthesis/a 5' to 3' exonuclease c. translesion synthesis/a ligase d. translesion synthesis/a 3' to 5' exonuclease e. translational synthesis/a 5' to 3' exonuclease

d. tranlesion synthesis/a 3' to 5' exonuclease

Which of the following statements about transcription regulation is incorrect? a. In negative control the default state is "on" unless a repressor binds the operator (n prokaryotes) and turns the gene off. b. The binding of a repressor protein blocks or reduces transcription c. Some repressor proteins require the presence of a corepressor molecule in order to bind an operator d. In positive control the default state is "off" and the transcription is activated to above the basal level only when the activator is bound to its binding element (site). e. In positive control an activator always binds the operator and allows RNA polymerase to initiate transcription

e. In positive control an activator always binds the operator and allows RNA polymerase to initiate transcription.

Which of the following is false about Ames test? a. Mutagens at high concentrations may be cytotoxic and result in fewer colonies than on the control plates (no test chemical present). b. Chemicals that are genotoxic, at concentrations that are not cytotoxic, result in more colonies than on the control plates. c. Auxothrophic bacterial strains are used to look for revertants. d. Chemicals that may be converted during the detoxification process to mutagens are treated 1st with liver extracts. e. None of the above

e. None of the above are false; all are true of Ames Test

If the position of a nucleotide (base) in (or near) a transcription unit is assigned the value of 0 (zero), this base is? a. the startpoint of replication b. the startpoint of transcription c. the startpoint of translation d. the end point of transcription e. none of the above because bases are never assigned a value of 0 (zero)

e. None of the above because bases are never assigned a value of 0 (zero)

Why do eukaryotic cells have multiple initiation sites in their DNA unlike bacteria that usually have only one? a. Cells of higher organisms can have up to 1000 times the amount of DNA as bacteria. b. Eukaryotic cells incorporate nucleotides at much slower rates. c. Eukaryotic DNA sequences are much more complicated. d. Eukaryotic cells have too many DNA polymerases e. a and b

e. a and b (Cells of higher organisms can have up to 1000 times the amount of DNA as bacteria; Eukaryotic cells incorporate nucleotides at much slower rates)

Transcription involves synthesis of an RNA chain representing one strand of a DNA duplex. The strand that has the "same" sequence as the RNA product is the ________ strand and the one with the complementary sequence (to RNA) is the ________ strand a. antisense/sense b. sense/antisense c. coding/template d. nontemplate/noncoding e. both b and c

e. b and c (sense/antisense and coding/template)

Which of the following is false about bacterial RNA polymerase catalyzed reactions (synthesis of RNA)? a. dNTPs act as substrates b. new nucleotides are always added at the 3' end c. these reactions occur at the catalytic site located in the sigma subunit d. they can occur in the absence of sigma e. both a. and c. are false

e. both a and c are false (dNTPs act as substrates= FALSE) (these reactions occur at the catalytic site located in the sigma subunit=FALSE)