exam 2
You perform DNA replication in a test tube (in vitro) using a single-stranded linear DNA as the template and the appropriate DNA primer. From the list below, identify the proteins that are required for one round of replication. a.) DNA polymerase b.) primase c.) ligase d.) helicase e.) all of the proteins listed
a.) DNA polymerase
Which is a characteristic of E. coli DNA polymerases? a.) DNA polymerase III functions as a holoenzyme that polymerizes DNA with high processivity b.) DNA polymerase I functions as a core enzyme that clamps around the DNA c.) DNA polymerase III functions as a single polypeptide chain that can form phosphodiester bonds d.) DNA polymerase I functions as a multimeric protein that participates in DNA repair
a.) DNA polymerase III functions as a holoenzyme that polymerizes DNA with high processivity
Which of the following is/are false about DNA replication? Select ALL that apply. a.) in bidirectional replication both strands are replicated but in unidirectional replication, only one strand is replicated b.) in unidirectional replication there is only one replication fork whereas in bidirectional replication there are two c.) DNA replication of most bacterial genomes is unidirectional d.) in unidirectional replication there is only one replication eye whereas in bidirectional replication there are two
a.) in bidirectional replication both strands are replicated but in unidirectional replication, only one strand is replicated c.) DNA replication of most bacterial genomes is unidirectional d.) in unidirectional replication there is only one replication eye whereas in bidirectional replication there are two
The figure above represents DNA replication in E. coli. The darkest portions of nucleic acids are newly synthesized DNA, mid-shaded portions represent templates and the lightest portions were synthesized "first". Which of the following is true about the protein found at position #3? Select all that apply a.) it has DNA polymerase activity b.) it has 3'-5' exonuclease activity c.) it is an RNA polymerase d.) it is an RNA polymerase e.) it has endonuclease activity f.) It has 5'-3' exonuclease activity g.) it has topoisomerase activity
a.) it has DNA polymerase activity b.) it has 3'-5' exonuclease activity f.) It has 5'-3' exonuclease activity
The figure above represents DNA replication in E. coli. The darkest portions of nucleic acids are newly synthesized DNA, mid-shaded portions represent templates and the lightest portions were synthesized "first". Which of the following is/are true about the homohexameric proteins represented at position #5? Select all that apply a.) it is a helicase b.) it moves on the leading strand c.) it moves on the leading strand template d.) it moves on the lagging strand template e.) it has ATPase activity f.) it moves on the lagging strand g.) it moves in a 5' to 3' direction
a.) it is a helicase d.) it moves on the lagging strand template e.) it has ATPase activity g.) it moves in a 5' to 3' direction
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 the newly-made strand from the parental strand b.) it must be able to distinguish which chain is of the right polarity c.) it must be able to distinguish which chain possess the right sequence d.) it must be able to distinguish which chain contains more incorrect bases e.) it must be able to distinguish the leading strand from the lagging strand
a.) it must be able to distinguish the newly-made strand from the parental strand
You have discovered a new exo- mutant of DNA polymerase. The enzyme's 3' to 5' exonuclease function has been destroyed. Which of the following properties do you expect the mutant polymerase to have? a.) it will be more likely to generate mismatched base pair b.) it will polymerase in both the 5' to 3' direction and the 3' to 5' direction c.) it will fall off the template more frequently than the normal exo+ polymerase d.) it will polymerase more slowly than the normal exo+ polymerase e.) none of them
a.) it will be more likely to generate mismatched base pair
If DNA polymerase I was mutated so that all its enzymatic activities were inactive, which part of replication would be most affected? a.) processing of Okazaki fragments b.) synthesis of Okazaki fragments c.) adjusting of supercoiling d.) all statements are true e.) all statements are false
a.) processing (joining) of Okazaki fragments
The mechanism of DNA replication is studied in an E. coli replication fork. Which is a characteristic of this replication fork? a.) strand III is a lagging strand template while strand IV is a leading strand template b.) the double-helix containing strands II and IV will form base-pairs using phosphodiester bonds c.) strand I is replicated continuously while strand II is replicated discontinuously d.) the double-helix containing strands I and III must be denatured in order for replication to continue e.) none of the statements is correct
a.) strand III is a lagging strand template while strand IV is a leading strand template
In transcription-coupled repair (TCR), how is the presence of a lesion thought to be detected? a.) the lesion is signaled by a stalled RNA polymerase b.) the lesion is signaled by a stalled DNA polymerase c.) there are special enzymes that scan DNA for such lesions d.) the lesion is signaled by a stalled peptidyl transferase e.) the lesion is detected by single-stranded binding proteins
a.) the lesion is signaled by a stalled RNA polymerase
Which mechanism contributes to accuracy during DNA replication in E. coli? a.) the mismatch repair system recognizes an incorrect base-pair and corrects the mistake in the non-methylated strand b.) all DNA polymerases have a 5' to 3' exonuclease activity which can remove incorrect nucleotides during replication c.) using primers increases accuracy because the first nucleotides in a new nucleic acid chain are more likely to be correct d.) none of the above
a.) the mismatch repair system recognizes an incorrect base-pair and corrects the mistake in the non-methylated strand
Which of the following is FALSE about bacterial RNA polymerase catalyzed reactions (synthesis of RNA)? a.) these reactions occur at the catalytic site located in the sigma subunit b.) they require only the core RNA polymerase c.) they can occur in the absence of sigma d.) new nucleotides are always added at the 3' end e.) NTPs act as substrates
a.) these reactions occur at the catalytic site located in the sigma subunit
Transcription involves synthesis of an RNA chain representing one strand of a 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 product is the _______ strand. Select ALL that apply. a.) coding/antisense b.) antisense/coding c.) template/coding d.) nontemplate/coding e.) sense/noncoding f.) nontemplate/sense
b.) antisense/coding c.) template/coding
In higher eukaryotes, many of the Cs followed by Gs in the so called CpG islands are methylated resulting in 5-mC (5-methyl-C). 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.) deamination/NER/insertions b.) deamination/BER/transitions c.) alkylation/BER/transversions d.) deamination/NER/transitions
b.) deamination/BER/transitions
Which is a property of RNA primers in an E. coli replication fork? a.) RNA primers are synthesized and proofread by the primase enzyme b.) each RNA primer is both polymerized and degraded in the 5' to 3' direction c.) RNA primers are synthesized using a DNA template and NDPs d.) all of the above e.) none of the above
b.) each RNA primer is both polymerized and degraded in the 5' to 3' direction
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 at the end of each chromosome d.) extended the leading strand template at the end of each chromosome e.) extend the lagging strand template at the end of each chromosome
b.) extend the lagging strand to the end of each chromosome
How does DNA polymerase discriminate between the insertion of correct and incorrect nucleotides as DNA replication proceeds? a.) incorrect nucleotides repel each other because of their charges b.) if the new "base pair" exhibits improper geometry within the active site the incorrect nucleotide will not be incorporated and will diffuse away c.) correct base pairing of template and the incoming dNTP allows for proper positioning of the substrates within the active site d.) incorrect dNTPs cannot enter the active site
b.) if the new "base pair" exhibits improper geometry within the active site the incorrect nucleotide will not be incorporated and will diffuse away c.) correct base pairing of template and the incoming dNTP allows for proper positioning of the substrates within the active site
Why is an intact (blunt ends) double stranded linear DNA an ineffective template for DNA polymerase? a.) it lacks a 3'-hydroxyl group and a template b.) it has a 3'-hydroxyl group, but lacks a template c.) it has a 3'-hydroxyl group and has a template d.) it lacks a 3'-hydroxyl group but has a template e.) it lacks a 5'-hydroxyl group and a template
b.) it has a 3'-hydroxyl group, but lacks a template
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.) alkylation/transversions b.) oxidation/transversions c.) deamination/transversions d.) alkylation/transitions e.) oxidation/transitions
b.) oxidation/transversions
Photoreactivation refers to what? Select all the apply a.) fixing depurination of DNA b.) reversing UV radiation linking of pyrimidines by photolyases c.) fixing strand nicks/breaks in DNA molecules d.) NER activation by visible light e.) photolyase activation by visible light
b.) reversing UV radiation linking of pyrimidines by photolyases e.) photolyase activation by visible light
The mechanism of DNA replication is studied in an E. coli replication fork. Which is a characteristic of this replication fork? a.) strands I and III will be covalently bonded to each other when replication is completed b.) strands II and IV have an antiparallel orientation as the fork moves to the right c.) strands III and IV will be H-bonded to each other when replication is completed d.) strands I and II have base sequences that are identical to each other e.) none of the statements is correct
b.) strands II and IV have an antiparallel orientation as the fork moves to the right
Which is a property of Okazaki fragments in an E. coli replication fork? a.) Okazaki fragments are polymerized in the 3' to 5' direction by DNA polymerase III b.) an Okazaki fragment for the leading strand is polymerized to a length of 1000-2000 nucleotides c.) an Okazaki fragment for the lagging strand has a base sequence complementary to its template d.) Okazaki fragments are joined together by DNA polymerase I to form a long chain e.) all of the statements f.) none of the statements
c.) an Okazaki fragment for the lagging strand has a base sequence complementary to its template
Which of the following is FALSE about the Ames test? a.) auxotrophic bacterial stains are used to look for revertants b.) chemicals that are genotoxic, at concentrations that are not cytotoxic, result in more colonies than on the control plate c.) chemicals that are genotoxic, at concentrations that are not cytotoxic, result in fewer colonies than on the control plate d.) chemicals that may be converted during the detoxification process to mutagens are treated first with liver extracts e.) mutagens at high concentrations may be cytotoxic and result in fewer colonies than on the control plates (no test chemical present)
c.) chemicals that are genotoxic, at concentrations that are not cytotoxic, result in fewer colonies than on the control plate
How are the ends of the linear eukaryotic chromosome replicated? a.) the ends of the linear chromosomes are maintained by the action of the polymerase enzyme b.) the ends of the linear chromosomes are maintained by the continuous joining of Okazaki fragments c.) the ends of the linear chromosomes are maintained by the activity of the telomerase enzyme d.) the ends of the linear chromosomes are maintained by the formation of a replication fork
c.) the ends of the linear chromosomes are maintained by the activity of the telomerase enzyme
In eukaryotes, the repair of double-stranded breaks is mostly done by ________ and often results in some ___________. a.) NER and often results in some loss of RNA b.) TLS and often results in some loss of DNA c.) BER and often results in some loss of DNA d.) NHEJ and often results in some loss of DNA
d.) NHEJ and often results in some loss of DNA
In eukaryotes, the selection of the origin of replication is mediated by the formation of the pre-replicative complex. It comprises of... a.) ORC and helicase b.) ORC and the initiator protein c.) a helicase loader and a helicase d.) ORC, two helicase loaders, and a helicase
d.) ORC, two helicase loaders, and a helicase
The figure above represents DNA replication in E. coli. The darkest portions of nucleic acids are newly synthesized DNA, mid-shaded portions represent templates and the lightest portions were synthesized "first". Which of the following best described the position or structure located near #1? Select all that apply a.) 3' end b.) lagging strand c.) DNA polymerase d.) RNA primer e.) 5' end
d.) RNA primer e.) 5' end
With respect to the palm domain of the DNA polymerase, which of the following is NOT its property? a.) binds to 2 divalent ions b.) contains primary elements of the catalytic site c.) brings about the environmental changes around 3'-OH of growing DNA strand d.) composed of a special alpha helix called O-helix
d.) composed of a special alpha helix called O-helix
Water can be DNA's "enemy" by participating in all of the following reactions EXCEPT: a.) deamination of adenine, converting it to inosine b.) deamination of 5 methyl Cs, converting them to Ts c.) hydrolysis generating AP sites (abasic) d.) deamination of Ts, converting them to Cs e.) deamination of 5 methyl Cs, converting them to Ts
d.) deamination of Ts, converting them to Cs
Why do eukaryotic nuclear chromosomes have multiple initiation sites (origin of replication) in their DNA unlike bacteria that usually have only one? Select all that apply. a.) prokaryotic cells incorporate nucleotides at much slower rates b.) eukaryotes have more DNA polymerases c.) prokaryotic chromosomes are much more complex structures than eukaryotic ones d.) nuclei of higher organisms can have up to 1000 times the amount of DNA as bacteria e.) eukaryotic Okazaki fragments are ~1/10th the length of prokaryotic ones
d.) nuclei of higher organisms can have up to 1000 times the amount of DNA as bacteria e.) eukaryotic Okazaki fragments are ~1/10th the length of prokaryotic ones
Statement A. In eukaryotes, the pre-replicative complex (pre-RC) can be formed only during G1 but it remains inactive until the onset of the 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) Statement C: ORC in yeast can bind to ARS at any point of the cell cycle a.) all statements: A, B, and C are false b.) only A is true c.) only C is true d.) only B and C are true e.) only B is true f.) only A and C are true g.) all statements: A, B, and C are true h.) only A and B are true
d.) only B and C are true
Statement A: the activation of origins of replication is very similar in all organisms 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 prokaryotic origins of replication, helicases are loaded by helicase loaders directly onto single stranded DNA generated by the initiators a.) both A and B are false b.) only A is true c.) both A and B are true d.) only B is true
d.) only B is true
Concerning the promoters recognized by general sigma factor in E. coli, mutations in the -10 region tend to affect the formation of the ______ complexes and the mutations in the -35 region affect the formation of the _____ complexes. a.) closed/open b.) closed/closed c.) open/open d.) open/closed e.) closed or open depending on gene
d.) open/closed
Which of the following is FALSE about the E. coli general sigma factor (o70)? a.) mutations in sigma may suppress mutations in promoters b.) it contacts promoter directly at -10 and -35 c.) it has several DNA binding domains d.) removal of C-terminus allows sigma (alone) to bind promoters e.) it has a helix turn helix motif
d.) removal of C-terminus allows sigma (alone) to bind promoters
Which of the following is NOT a function of Dna A? a.) replication protein recruitment b.) initiates DNA melting c.) DNA binding d.) synthesis of primer
d.) synthesis of primer
Okazaki's fragments are generated on... a.) the leading strand in a 5' to 3' direction b.) the leading strand in a 3' to 5' directions c.) the lagging strand in the 3' to 5' direction d.) the lagging strand in the 5' to 3' direction
d.) the lagging strand in the 5' to 3' direction
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.) homologous recombination b.) MMR c.) NHEJ d.) NER e.) BER
e.) BER
Which of the following contributes to stabilizing the 2D and/or 3D structures of RNA? Select all that apply. a.) G:U base pairing b.) U:A:U base triplets c.) hydrogen bonding via 2'OH group d.) base stacking e.) G:A base pairing
e.) G:A base pairing
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.) alkylation/transversions b.) oxidation/transitions c.) oxidation/transversions d.) deamination/transversions e.) alkylation/transitions f.) oxidation/deletions or insertions
e.) alkylation/transitions
Which of the following statements is true? a.) DNA polymerase requires a primer to initiate replication b.) polymerization of DNA for both the lagging and the leading strands is in the 5' to 3' direction c.) DNA polymerase moves along the template strand in the 3' to 5' direction d.) none of the above e.) all of the above
e.) all of the above
Which of the following statements about mammalian telomeres is INCORRECT? a.) they may protect the cell from chromosomal fusions b.) they all contain multiple copies of short DNA sequences that is specific for each organism c.) they may protect chromosomes from degradation d.) their length may contribute to the ability of somatic cells to proliferate e.) they can be extended by an enzyme called telomerase that carries a DNA molecule that is complementary to the telomeric repeats
e.) they can be extended by an enzyme called telomerase that carries a DNA molecule that is complementary to the telomeric repeats
Explain why patients with xeroderma pigmentosum are more prone to cancer than the rest of the population. a.) xeroderma pigmentosum patients cannot employ the nucleotide excision repair mechanism. when these patients are exposed to UV light, thymine dimers are formed and they are not able to repair this defect. these dimers distort the structure of DNA and cause them to have a high risk of developing skin cancer b.) xeroderma pigmentosum patients cannot employ the nucleotide excision repair mechanism. when these patients are exposed to UV light, the adjacent adenine forms dimers are formed and they are not able to repair this defect. these dimers distort the structure of DNA and cause them to have a high risk of developing skin cancer c.) xeroderma pigmentosum patients can employ the nucleotide excision repair mechanism. when these patients are exposed to UV light, thymine dimers are formed and they are able to repair this defect. these dimers do not distort the structure of DNA and cause them to have a moderate risk of developing skin cancer d.) xeroderma pigmentosum patients cannot employ the nucleotide excision repair mechanism. when these patients are exposed to UV light, the adjacent thymine cannot form thymine dimers and they are not able to repair this defect. the non-formation of dimers distorts the structure of DNA and they have a high risk of developing skin cancer
a.) xeroderma pigmentosum patients cannot employ the nucleotide excision repair mechanism. when these patients are exposed to UV light, thymine dimers are formed and they are not able to repair this defect. these dimers distort the structure of DNA and cause them to have a high risk of developing skin cancer
There are 11 GATC sequences within oriC which is 245 bp long. Assuming that all bases are present in the same amounts, would would be the (theoretical) APPROXIMATE minimum length of a DNA fragment to find this sequence once if its occurrence was random? a.) 64 b.) 260 c.) 16 d.) 400 e.) 120
b.) 260
TRANSCRIBE the following sequence: 3'- TCTAGGC -5' a.) 5'- CGGAUCU -3' b.) 5'- GCCUAGA -3' c.) 5'- UCUAGGC -3' d.) 5'- AGAUCCG -3' e.) 5'- GCCTAGA -3'
b.) 5'- GCCUAGA -3'
With respect to EUKARYOTIC replication, which of the following proteins are not correctly paired with their function? Pick all that apply. a.) DNA polymerase alpha - synthesis of RNA primer b.) DNA polymerase epsilon - elongation of DNA lagging strand c.) tau protein - connects DNA polymerase cores via clamp loader d.) DNA delta - elongation of DNA leading strand e.) all proteins are correctly paired with their functions
b.) DNA polymerase epsilon - elongation of DNA lagging strand c.) tau protein - connects DNA Polymerase cores via clamp loader d.) DNA delta - elongation of DNA leading strand
Which of the following statements is correct about DNA replication? a.) DNA polymerase reads the template strand in the 5' to 3' direction and adds nucleotides only in the 3' to 5' direction. The leading strand is synthesized in the direction of the replication fork. Replication on the lagging strand occurs in the direction away from the replication fork in long stretches of DNA called Okazaki fragments b.) DNA polymerase reads the template strand in the 3' to 5' direction and adds nucleotides only in the 5' to 3' direction. The leading strand is synthesized in the direction of the replication fork. Replication on the lagging strand occurs in the direction away from the replication fork in short stretches of DNA called Okazaki fragments c.) DNA polymerase reads the template strand in the 5' to 3' direction and adds nucleotides only in the 5' to 3' direction. The leading strand is synthesized in the direction of the replication fork. Replication on the lagging strand occurs in the direction away from the replication fork in short stretches of DNA called Okazaki fragments d.) DNA polymerase reads the template strand in the 3' to 5' direction and adds nucleotides only in the 5' to 3' direction. The leading strand is synthesized in the direction away from the replication fork. Replication on the lagging strand occurs in the direction of the replication fork in short stretches of DNA called Okazaki fragments e.) none of the above
b.) DNA polymerase reads the template strand in the 3' to 5' direction and adds nucleotides only in the 5' to 3' direction. The leading strand is synthesized in the direction of the replication fork. Replication on the lagging strand occurs in the direction away from the replication fork in short stretches of DNA called Okazaki fragments
There are several repair systems in organisms to fix/repair UV radiation damage. Which is/are mechanism(s) utilized in humans? a.) NHEJ b.) NER c.) photoreactivation d.) MMR e.) BER
b.) NER
Which of the following is true about the transcription initiation in E. coli? Select all that apply a.) the core RNA polymerase enzyme binds to and denatures the upstream -35 sequence b.) RNA polymerase holoenzyme binds to different promoters to different extents depending upon the base sequence c.) the specificity for the promoter is determined by the core RNA polymerase d.) the o factor associates with the core RNA polymerase enzyme recognizes and melts an A-T rich sequence in the promoter
b.) RNA polymerase holoenzyme binds to different promoters to different extents depending upon the base sequence d.) the o factor associates with the core RNA polymerase enzyme recognizes and melts an A-T rich sequence
