questions

Telomeres A. Become shorter with age B. Become longer with age C. Stay the same length with age

A. Become shorter with age

You are a DNA-binding protein sampling the genome along the major groove. You come across the chemical signature *AADH*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A G-C B. G-C or C-G C. A-T D. T-A

A. G-C

What method would you use if you wanted to see if two proteins co-localize A. Immunofluorescence B. Immunoprecipitation C. Western blot

A. Immunofluorescence

During initiation of replication, DnaC: binds the origin and forms oligomers. loads DnaB helicase onto each strand to form the prepriming complex. expands the replication bubble, while primase forms RNA primers at each replication fork. directs clamp loading and assembly of one Pol III holoenzyme complex. allows lagging-strand priming and Okazaki fragment synthesis.

Correct: loads DnaB helicase onto each strand to form the prepriming complex.

Which of the following terms is mismatched? template strand: guides the polymerase reaction primer terminus: 3′ end of primer where nucleotides will be added primer strand: contains a free 5′-OH group Okazaki fragment: small DNA fragments primed template: DNA-RNA hybrid formed before strand synthesis

Correct: primer strand: contains a free 5′-OH group

Why is the temperature for the annealing step in PCR lower than the denaturing step? a. The lower temperature causes the template DNA to separate, which allows the primers to bind. b. The lower temperature allows the polymerase to move along the strand, adding new nucleotides. c. The lower temperature allows the primers to bind to the template strands, forming hydrogen bonds. d. The annealing step actually has a higher temperature than the denaturing step. e. The lower temperature inhibits the formation of covalent bonds between the two DNA strands.

c. The lower temperature allows the primers to bind to the template strands, forming hydrogen bonds.

At which point in the cell cycle would a chromosome look like two sister chromatids joined at the center? a. G1 phase b. S phase c. G2 phase d. M phase

d. M phase

The DNA I polymerase reaction is BEST described as: (dNTP)n + dNTP → (dNTP)n + 1 + PPi (dNTP)n + dNTP → (dNTP)n + 1 + PPi (dNDP)n + dNTP → (dNMP)n + 1 + PPi (dNMP)n + dNTP → (dNMP)n + 1 + PPi (dNDP)n + dNTP → (dNTP)n + 1 + PPi

(dNMP)n + dNTP → (dNMP)n + 1 + PPi

In contrast to linear DNA, circular DNA replication typically: A. has a single origin of replication. B. does not produce a replication bubble. C. occurs only at a single replication fork. D. does not produce Okazaki fragments.

A. has a single origin of replication.

The following are commonly used radio-isotpes. With what you already know about the composition of DNA and proteins, which one would you chose for labelling of DNA to discriminate from protein? A. 3H B. 32P C. 35S D. 131I

B. 32P

Okazaki isolated a mutant giving rise to this pattern in the same experimental setup. Which enzyme is most likely affected by the mutation? A. An enzyme making primers B. An enzyme ligating the discontinuous DNA fragments C. An enzyme unwinding the DNA strands D. All of the above

B. An enzyme ligating the discontinuous DNA fragments

You are a DNA-binding protein sampling the genome along the major groove. You come across the chemical signature *HDAA*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A G-C B. C-G C. A-T D. T-A

B. C-G

Suppose you are provided with an actively dividing culture of E. coli bacteria to which radioactive thymine has been added. What would happen if a cell replicates once in the presence of this radioactive base? A. DNA in one daughter cell would be radioactive, but not the other B. DNA in both daughter cells would be radioactive. C. Neither of the daughter cells would be radioactive.

B. DNA in both daughter cells would be radioactive.

You are a DNA-binding protein sampling the genome along the minor groove. You come across the chemical signature *ADA*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A C-G B. G-C or C-G C. A-T D. A-T or T-A

B. G-C or C-G

What type of interaction is directly responsible for the formation of secondary structure? A. Peptide bonds between adjacent amino acids B. Hydrogen bonds between sections of the polypeptide backbone C. Hydrogen bonds between R-groups of amino acids D. Di-sulfide bonds between cysteine residues

B. Hydrogen bonds between sections of the polypeptide backbone

If the Adenine content of the DNA of a particular species was determined to be 27%, what is the Guanine content? A. 73% B. 37% C. 23% D. 36.5%

C. 23%

A DNA molecule consists of a strand of the following sequence: 5'-GAATCGCAT-3'. What will the sequence of the complementary strand be? (Note the polarity) A. 5'-GAATCGCAT-3' B. 3'-GAATCGCAT-5' C. 5'-ATGCGATTC-3' D. 3'-ATGCGATTC-5'

C. 5'-ATGCGATTC-3'

You are a DNA-binding protein sampling the genome along the major groove. You come across the chemical signature *ADAM*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A C-G B. G-C or C-G C. A-T D. A-T or T-A

C. A-T

With respect to the dotted line, in which direction(s) does DNA replication proceed? A.Right B. Left C. Both

C. Both

Which double stranded DNA molecule will denature at the highest temperature? A. AATTCGA B. AATCCGG C. GGAACGG D. CCATGCA

C. GGAACGG

In comparison to the eGFP treated group, mice that were infected with mTERT expressing virus had A. Higher survival rates and higher rates of cancer-related death B. Lower survival rates and higher rates of cancer-related death C. Higher survival rates and similar rates of cancer-related death D. Lower survival rates and similar rates of cancer-related death

C. Higher survival rates and similar rates of cancer-related death

Many signaling and receptor molecules at the cell's surface are embedded in the cell membrane. Which amino acid(s) would be most suitable for insertion into the lipid bilayer? A. acidic B. basic C. Neutral nonpolar D. Neutral polar

C. Neutral nonpolar

At which position in the protein would a change from phenylalanine (non-polar) to glutamine (polar) make the biggest difference? A. On the N-terminus B. On the C-terminus C. On the inside D. On the surface

C. On the inside

Lack of telomerase activity limits what? A. The rate of DNA replication B. The number of replicons that form during replication C. The number of times a cell can divide D. The number of Okazaki fragments that can be linked together

C. The number of times a cell can divide

When you go to the beauty parlor to get a "perm" one of the first steps usually includes treating the hair with a sulfhydryl reducing agent. What is this likely to do to the hair? A. I don't know, I never go to the beauty parlor B. breaks H bonds, but not peptide bonds so hair shape can change C. breaks disulfide bonds between alpha helices so hair shape can change D. breaks bonds at the base of the hair so the hair can change shape

C. breaks disulfide bonds between alpha helices so hair shape can change

Bacteria replicate their chromosome bidirectionally, which means they need only a single replication fork. True False

Correct: False

Because primase cannot copy telomere DNA, there is a problem replicating chromosome ends. True False

Correct: False

Which of the following E. coli DNA polymerases function(s) in the replication of the chromosome? Pol III Pol I Pol IV Pol II and Pol IV Pol II

Correct: Pol III

Which of the following describes the approximate chromosomal location of the termination of replication in bacteria? Termination occurs one-quarter of the way around the chromosome. Termination occurs at oriC once the replication fork has advanced the entire length of chromosome. Termination occurs halfway around the chromosome. Termination is random. The chromosomal location of termination is not known.

Correct: Termination occurs halfway around the chromosome.

All known DNA polymerases extend DNA only in the 5′ to 3′ direction. True False

Correct: True

DNA polymerases can add nucleotides only to an existing DNA strand; therefore a primer containing a 3′OH is required. True False

Correct: True

Telomeres at the end of eukaryotic chromosomes are composed of a short repeating sequence. True False

Correct: True

The end replication problem does not occur in circular DNA. True False

Correct: True

The E. coli Pol III holoenzyme is composed of all the following EXCEPT: clamp loaders (τ complex). δ units within the clamp loader. two ring-shaped β sliding clamps. three Pol III cores. processivity sliders.

Correct: processivity sliders.

You are a DNA-binding protein sampling the genome along the minor groove. You come across the chemical signature *AHA*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A C-G B. G-C or C-G C. A-T D. A-T or T-A

D. A-T or T-A

You are a DNA-binding protein sampling the genome along the major groove. You come across the chemical signature *MADA*. What base pair is this? {A: Hydrogen bond acceptor, D: Hydrogen bond donor H: Hydrogen group M: Methyl group} A C-G B. G-C or C-G C. A-T D. T-A

D. T-A

How did Meselson and Stahl distinguish between semiconservative and conservative replication in their experiment? a. After one round of replication, only mixed DNA molecules were present in the gradient. b. After one round of replication, only heavy DNA molecules were present in the gradient. c. After one round of replication, only mixed DNA strands were present in alkaline gradients. d. After two rounds of replication, only mixed DNA molecules were present in the gradient. e. After two rounds of replication, only heavy DNA strands were present in alkaline gradients.

a. After one round of replication, only mixed DNA molecules were present in the gradient.

A biochemist isolates a peptide hormone with the following sequence: ADSERNCQLVILLAWLPGVKVQCALLDRET Which residues can be connected by a disulfide bond? (Assume the residues are numbered 1 through 30, left to right.) a. C7, C23 b. S3, Q8, Q22 c. C7, Q8, C23, Q22 d. Q8, Q22, K20

a. C7, C23

For a PCR reaction, two primers are used because a. DNA is double stranded. b. DNA polymerase works only in the 5' to 3' direction. c. RNA is single stranded. d. they can then double the speed of the reaction. e. All of the above.

a. DNA is double stranded.

Which of the following is NOT a component of a polymerase chain reaction (PCR)? a. DNA ligase to connect the fragments together b. primers complementary to each end of the sequence to be amplified c. heat stable Taq polymerase d. dNTPs e. DNA containing the sequences to be amplified

a. DNA ligase to connect the fragments together

Which interactions hold the two strands in the DNA double helix together? a. Hydrogen bonding between complementary strands b. Phosphodiester bonds in the backbone c. Hydrophobic stacking d. Peptide bonds

a. Hydrogen bonding between complementary strands

In the central dogma developed by Francis Crick and others, three kinds of RNA play important roles: rRNAs, tRNAs, and mRNAs. Which of the following are characteristic features of *rRNA*? a. Only a few types in a cell; located in ribosomes; sequence highly *conserved* in different life forms; are functional RNAs (do not encode proteins). b. Only a few types in a cell; located in ribosomes; sequence highly variable in different life forms; are functional RNAs (do not encode proteins). c. Only a few types in a cell; located in ribosomes; sequence highly variable with *modified bases*; are functional RNAs (do not encode proteins). d. Only a few types in a cell; located in ribosomes; sequence highly conserved in different life forms; *encode ribosomal proteins*.

a. Only a few types in a cell; located in ribosomes; sequence highly conserved in different life forms; are functional RNAs (do not encode proteins).

True or False: A nucleoside consists of a pentose sugar and base, but not a phosphate group. a. True b. False

a. True

Which of the following statements is NOT correct regarding protein separation techniques? a. Western blotting is a useful technique to isolate proteins for use in downstream assays. b. Size-exclusion chromatography works on the same principle as polyacrylamide gel electrophoresis. c. Two-dimensional gel electrophoresis is conceptually the same as combining gel filtration chromatography and ion exchange chromatography. d. Specific antibodies are required for immunoblotting, antibody affinity chromatography as well as immunoprecipitation.

a. Western blotting is a useful technique to isolate proteins for use in downstream assays.

Which tertiary DNA structure has more nucleotide pairs per turn of DNA? a. Z-DNA b. B-DNA c. right-handed DNA d. A-DNA d. left-handed DNA

a. Z-DNA

Mutation in the sequences encoding the exonuclease domain of DNA polymerase would most likely result in: a. an increase in the number of mutations in the newly-synthesized DNA strand. b. a preponderance of A-DNA (rather than the more common B-DNA). c. hydrogen bonds being formed in the sugar-phosphate backbone. d. DNA polymerase that polymerizes in the 3' to 5' direction. e. incorporation of ribonucleotides.

a. an increase in the number of mutations in the newly-synthesized DNA strand.

The function of DNA ligase is to: a. catalyze the formation of covalent bonds between adjacent nucleotides. b. facilitate base pairing between single stranded molecules of DNA. c. unwind the double-stranded DNA prior to replication. d. keep the single strands of DNA apart during replication. e. catalyze the formation of hydrogen bonds between adjacent nucleotides.

a. catalyze the formation of covalent bonds between adjacent nucleotides.

A key to the discovery of PCR was identifying a DNA polymerase from nature that a. does not denature at the high temperature needed to melt the template DNA. b. can polymerize DNA synthesis using an RNA primer. c. can bind DNA and polymerize at the high temperature needed to melt the template DNA. d. can polymerize DNA at an exceptionally high rate.

a. does not denature at the high temperature needed to melt the template DNA.

In a typical sequencing reaction, the amount of dNTPs is much greater than of the ddNTPs. Predict the results if equal amounts of both types of nucleotides were used in each reaction. After gel electrophoresis and visualization: a. mostly short fragments would be present and only sequences very close to the primer could be read. b. only the purine reactions would show termination and be read from the gel. c. mostly long fragments would be present and no sequence could be read close to the primer. d. no bands would be visible because the high concentration of ddNTPs would inhibit the activity of the polymerase. e. the sequence could be read normally; the dNTP/ddNTP ratio does not affect the products of the reaction.

a. mostly short fragments would be present and only sequences very close to the primer could be read.

If you were to take this simulation to the next biological level and synthesize DNA molecules, the deoxyribonucleotides made would interact with: a. other deoxyribonucleotides—through hydrogen bonding between nitrogenous bases and covalent bonds between sugars and phosphates. b. additional sugars and phosphates to make ATP. c. ribonucleotides—through hydrogen bonding between nitrogenous bases and covalent bonds between sugars and phosphates. d. The deoxyribonulceotides would not be involved in DNA synthesis, so they would not interact with any molecules. e. either deoxyribonucleotides or ribonucleotides—through hydrogen bonding between nitrogenous bases and covalent bonds between sugars and phosphates.

a. other deoxyribonucleotides—through hydrogen bonding between nitrogenous bases and covalent bonds between sugars and phosphates.

Each replication fork requires both leading and lagging strand synthesis because a. the DNA templates are antiparallel and yet the DNA polymerases only work in one direction. b. DNA polymerases can only synthesize DNA 3' to 5'. c. the helicase unwinds one strand faster than the other. d. DNA synthesis must be complementary. e. All of these choices are correct.

a. the DNA templates are antiparallel and yet the DNA polymerases only work in one direction.

In which DNA polymerase reaction is H2O used? a. the exonuclease proofreading activity b. the formation of the phosphodiester bond c. the shifting of the DNA polymerase down the DNA molecule d. the formation of the hydrogen bonds e. the addition of a nucleotide to the polymerase

a. the exonuclease proofreading activity

The resulting DNA and RNA sequences from DNA replication and RNA synthesis, respectively, of the DNA encoding amino acids 380-381 of BRCA2 (5'-AGTGAC-3') is: a. 5'-TCACTG-3' and 5'-AGTGAC-3' b. 5'-GTCACT-3 and 5'-AGUGAC-3' c. 5'-TCACTG-3' and 5'-AGUGAC-3' d. 5'-GTCACT-3 and 5'-AGTGAC-3' e. not determinable from the information provided.

b. 5'-GTCACT-3 and 5'-AGUGAC-3'

If PCR analysis shows a mutation in the BRCA2 gene, that person will develop breast cancer. a. True b. False

b. False

An artificial way of separating the two strands of a DNA molecule is by using heat. High temperatures will denature the DNA double helix by breaking the hydrogen bonds between nucleotides. Which base pair bond, respective to the rest, would need higher temperatures to denature? a. A-T b. G-C c. A-U d. G-A e. A-C

b. G-C

What does the "de-" in deoxyribonucleic acid indicate in relation to ribonucleic acid? a. It indicates the gain of a carbon connecting the pentose to the phosphate group. b. It indicates the loss of an oxygen atom on the pentose ring. c. It indicates the loss of a hydrogen atom on the phosphate group. d. It indicates the loss of a carbon atom connecting the pentose to the phosphate group. e. It indicates the gain of an OH group on the pentose ring.

b. It indicates the loss of an oxygen atom on the pentose ring.

(Problem 3b) Arthur Kornberg and his colleagues incubated an extract of E. coli with a mixture of dATP, dTTP, dGTP, and dCTP. Only the dTTP was labeled with 32P in the α-phosphate group. After incubation, the mixture was treated with trichloroacetic acid to precipitate DNA, but not the dNTPs. The precipitate was collected, and the extent of [32P]dTMP incorporated into DNA was determined. Would radioactivity be found in the precipitate if the 32P labeled the β- or γ-phosphate position? Why? a. Yes. DNA synthesis incorporates the β phosphate of dNTPs, so radioactivity would be found in the precipitate if dNTPs labeled at the β phosphate were used. DNA synthesis does not incorporate the γ of phosphate into DNA, so radioactivity would not be detected if this phosphate was labeled. b. No. DNA synthesis releases the β and γ phosphates of dNTPs as pyrophosphate.

b. No. DNA synthesis releases the β and γ phosphates of dNTPs as pyrophosphate.

PCR is useful in identifying suspects in crime scene investigations because a. PCR can identify potentially harmful mutations in the suspect's DNA. b. PCR produces a large amount of DNA for analysis starting from a very small amount. c. PCR uses two different primers for amplification. d. PCR requires the DNA strands to denature prior to amplification. e. PCR amplifies both DNA strands with high fidelity.

b. PCR produces a large amount of DNA for analysis starting from a very small amount.

R-loops are stable RNA:DNA hybrids that may form during transcription. They also have essential biological roles in initiation of DNA replication in mitochondria and prokaryotes. What characteristic of DNA and RNA molecules allows this type of interaction to occur? a. RNA can form intrastrand hydrogen bonds. b. Ribonucleotides and deoxyribonucleotides can hydrogen bond with each other. c. RNA exists primarily as a single-stranded molecule, while DNA primarily exists as a double-stranded molecule. d. The sugars of RNA and DNA are strikingly similar. e. The overall hydrogen bond between G and C is stronger than the bond between A and T.

b. Ribonucleotides and deoxyribonucleotides can hydrogen bond with each other.

Which of the following techniques separates proteins only on the basis of its molecular size? a. Differential centrifugation b. Size-exclusion chromatography c. Ion-exchange chromatography

b. Size-exclusion chromatography

(Problem 9, part 1) Five DNA polymerases have been identified in the bacterium E. coli. Two of them—DNA polymerases IV and V—lack a 3´5´ exonuclease activity. What is the function of the 3´5´ exonuclease activity present in many DNA polymerases? a. The 3´5´ exonuclease function allows the cell to generate dNMP, which can be converted to dNTP and then used for synthesis of essential DNA when nutrients are low. b. The 3´5´ exonuclease is a proofreading function, eliminating mismatched nucleotides incorrectly inserted into the growing DNA strand. c. The 3´5´ exonuclease removes DNA and RNA primers. d. The 3´5´ exonuclease creates blunt ends so ligase can join DNA fragments.

b. The 3´5´ exonuclease is a proofreading function, eliminating mismatched nucleotides incorrectly inserted into the growing DNA strand.

Why does DNA form a double-helical structure? a. The double helix is the most thermodynamically stable structure. It places the hydrophobic bases in the exterior of the molecule, where they protect the DNA from free radicals, and the charged phosphate groups on the inside, where they enhance base pairing. b. The double helix is the most thermodynamically stable structure. It places the hydrophobic bases in the interior of the molecule, where they interact with one another through base stacking. The charged phosphate groups are located on the outside, where they interact with water and ions. c. The double helix is the most thermodynamically stable structure. It places the hydrophobic bases and the phosphate groups in the interior of the molecule. The deoxyribose residues face the exterior where they interact with water and ions.

b. The double helix is the most thermodynamically stable structure. It places the hydrophobic bases in the interior of the molecule, where they interact with one another through base stacking. The charged phosphate groups are located on the outside, where they interact with water and ions.

What is the resulting bond that is formed from a nucleophilic attack during DNA polymerase reactions, and which molecules are involved? a. a hydrogen bond between the base of the nucleotide on the original strand with the base of the newly added nucleotide b. a phosphodiester bond between the OH group of the pentose ring on the last nucleotide added to the growing strand and the α-phosphate of the newly added nucleotide c. There are no nucleophilic attacks during DNA polymerase reactions. A nucleophilic attack only occurs during the synthesis of an mRNA molecule. d. a covalent bond between the exonuclease enzyme of DNA polymerase and the phosphoidester bond of the α-phosphate of the newly added nucleotide e. a phosphodiester bond between the OH group of the pentose ring on the last nucleotide added to the growing strand and the ɣ-phosphate of the newly added nucleotide

b. a phosphodiester bond between the OH group of the pentose ring on the last nucleotide added to the growing strand and the α-phosphate of the newly added nucleotide

Of all the molecules shown in this simulation, which could potentially become part of an RNA molecule? a. only uridine (the uracil-nucleoside) b. all of the molecules shown, except thymine and deoxyribose c. all of the molecules shown, except thymidine and thymidylate d. only uridylate (the uracil-nucleotide) e. all of the molecules shown, except thymine and ribose

b. all of the molecules shown, except thymine and deoxyribose

The three types of RNA required for the transfer of information from DNA to RNA to protein are: a. miRNA, rRNA, and mRNA. b. tRNA, rRNA, and mRNA. c. siRNA, miRNA, and lnRNA. d. rRNA, lnRNA, and miRNA.

b. tRNA, rRNA, and mRNA.

When a protein binds to DNA *nonspecifically*, with which parts of the DNA does the protein interact? a. the phosphate and deoxyribose groups in the DNA backbone b. the phosphate and deoxyribose groups in the DNA backbone and hydrophobic interactions with the nucleotide bases c. AT-rich sequences within the DNA d. GC-rich sequences within the DNA

b. the phosphate and deoxyribose groups in the DNA backbone and hydrophobic

What is the difference between a nucleotide and a nucleoside? a. the sugar b. the phosphate group c. the base d. all of the above

b. the phosphate group

Which of the following statements about probes used in hybridization methods is TRUE? a. The probe could be a gene from another species. b. They are usually radiolabelled or conjugated with a fluorescent tag so they can be visualized. c. All of these statements about hybridization probes are true. d. They can be synthetic DNA sequences based on known amino acid sequences. e. They can be based on DNA sequence information from a sequence database.

c. All of these statements about hybridization probes are true.

Multiple models were proposed to explain replication. What experimental approach allowed researchers to distinguish between them? a. Cells infected with T4 bacteriophage were grown in the presence of radioactive nucleotides. When DNA was analyzed in alkaline CsCl gradients, the presence of short DNA fragments indicated that discontinuous replication had occurred. b. Bacteria were grown on [3H] thymidine until the entire DNA contained heavy thymidine and then the cells were transferred to normal, light media for one round of replication. The resulting DNA molecules were separated in density gradients and compared to the expected results for each proposed model. c. Bacteria were grown on 15NH4 until the entire DNA contained heavy nitrogen and then the cells were transferred to normal, light media for one round of replication. The resulting DNA molecules were separated in density gradients and compared to the expected results for each proposed model. d. None of these choices is correct. e. Cells were pulsed with high specific activity [3H] thymidine to show the direction of DNA synthesis on the chromosome.

c. Bacteria were grown on 15NH4 until the entire DNA contained heavy nitrogen and then the cells were transferred to normal, light media for one round of replication. The resulting DNA molecules were separated in density gradients and compared to the expected results for each proposed model.

Which one of the following statements about the denaturation of nucleic acids is TRUE? a. Increasing pH allows annealing of RNA strands. b. Since RNA is only partially double-stranded it is unaffected by changes in pH and temperature. c. Reducing the temperature will often allow a denatured DNA to renature. d. Returning the pH to 7 will allow the DNA to denature. e. Increasing the temperature will allow the DNA to renature.

c. Reducing the temperature will often allow a denatured DNA to renature.

In the central dogma developed by Francis Crick and others, three kinds of RNA play important roles: rRNAs, tRNAs, and mRNAs. Which of the following are characteristic features of *tRNAs*? a. Small; fold into a characteristic T shape; can link to multiple amino acids as dictated by modified bases; are functional RNAs (do not encode proteins). b. Small; fold into a characteristic T shape; *have many modified bases*; can link to an amino acid; are functional RNAs (do not encode proteins). c. Small; *fold* into a characteristic *L* shape; have many modified bases; can link to an amino acid; are functional RNAs (do not encode proteins). c. Small; fold into a characteristic L shape; can link to multiple amino acids as dictated by modified bases; are functional RNAs (do not encode proteins).

c. Small; *fold* into a characteristic *L* shape; have many modified bases; can link to an amino acid; are functional RNAs (do not encode proteins).

(Problem 15, part 1) The enzyme telomerase is considered a reverse transcriptase, synthesizing DNA on an RNA template. What is the source of the RNA used in the synthesis of telomeres, and where is it located? a. The RNA template is a small tRNA that binds tightly to the telomerase reverse transcriptase (TERT) to form the active telomerase holoenzyme. b. The RNA template is a small nuclear RNA that binds simultaneously to DNA and telomerase reverse transcriptase (TERT). c. The RNA template is telomerase RNA, which is bound tightly to the telomerase reverse transcriptase (TERT) to form the active telomerase holoenzyme.

c. The RNA template is telomerase RNA, which is bound tightly to the telomerase reverse transcriptase (TERT) to form the active telomerase holoenzyme.

(Problem 2, part 1) A DNA polymerase cannot synthesize a DNA strand de novo from a mixture of deoxynucleotide triphosphates. Explain the role of the primer in the reaction promoted by this enzyme. a. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 3´ end. b. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 5´ end. c. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3´ end. d. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 5´ end.

c. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3´ end.

The backbone of a polypeptide consists of: a. carbon and oxygen. b. carbon and sulfur. c. carbon and nitrogen. d. carbon and hydrogen.

c. carbon and nitrogen.

Immunofluorescence methods can be carried out with antibodies that directly recognize the protein of interest. The indirect method is different because it requires that the antibody to the protein of interest be: a. attached to a fluorochrome. b. detected by a secondary antibody attached to luciferin. c. detected by a second antibody that is attached to a fluorochrome. d. detected by a second antibody that recognizes the fluorochrome. e. detected by a secondary antibody attached to luciferase.

c. detected by a second antibody that is attached to a fluorochrome.

The process that involves an end product acting as an inhibitor of an earlier step in a metabolic pathway is called a. competitive inhibition. b. concerted activation. c. feedback inhibition. d. feedback activation. e. positive feedback.

c. feedback inhibition.

When a protein binds to DNA at a site defined by a particular nucleotide sequence, with which parts of the DNA does the protein primarily interact? a. the phosphate and deoxyribose groups in the DNA backbone b. the phosphate and deoxyribose groups in the DNA backbone and hydrophobic interactions with the nucleotide bases c. nucleotides bases within the major grooves of the DNA d. nucleotides bases within the major and minor grooves of the DNA

c. nucleotides bases within the major grooves of the DNA

What is the purpose of DNA polymerase? a. to create single-stranded DNA molecules that can then bind to ribosomes and be translated into protein b. to create single-stranded RNA molecules that can then bind to ribosomes and be translated into protein c. to replicate each strand of a DNA molecule while proofreading along the way d. to introduce mutations into the DNA and so increase genetic diversity in a population e. to proofread an already replicated double-stranded DNA molecule

c. to replicate each strand of a DNA molecule while proofreading along the way

DNA polymerase moves down a DNA strand in the _________ direction and thus replicates the new strand of DNA in the _____________ direction a. 5' to 3', 3' to 5' b. 3' to 5', 3' to 5' c. DNA polymerase does not interact directly with the DNA strand. d. 3' to 5', 5' to 3' e. 5' to 3', 5' to 3'

d. 3' to 5', 5' to 3'

A part of one strand of a double-helical DNA molecule has the sequence 5´-GATTACAGCCTTAGTTAAATTCTAAGGCTGGTA -3´. What is the sequence of the complementary strand of DNA? a. 5´-ATGGTCGGAATCTTAAATTGATTCCGACATTAG -3´ b. 5´-GATTACAGCCTTAGTTAAATTCTAAGGCTGGTA -3´ c. 5´-CTAATGTCGGAATCAATTTAAGATTCCGACCAT -3´ d. 5´-TACCAGCCTTAGAATTTAACTAAGGCTGTAATC -3´

d. 5´-TACCAGCCTTAGAATTTAACTAAGGCTGTAATC -3´

The melting point is the temperature at which double-stranded: a. nucleic acids degrade into free nucleotides. b. DNA is too single-stranded to ever renature back to double strands. c. DNA begins to melt. d. DNA has become 50% single-stranded. e. DNA is completely melted.

d. DNA has become 50% single-stranded.

In the central dogma developed by Francis Crick and others, three kinds of RNA play important roles: rRNAs, tRNAs, and mRNAs. Which of the following are characteristic features of *mRNAs*? a. Each cell type makes >1,000 different mRNAs; can be very long; form base pairs with *rRNA*; encode the sequences of proteins. b. Each cell type makes >1,000 different mRNAs; are typically very *short*; form base pairs with tRNA; encode the sequences of proteins. c. Each cell type makes >1,000 different mRNAs; can be very long; form base pairs with tRNA; are functional RNAs (do not encode proteins). d. Each cell type makes >1,000 different mRNAs; can be very long; form base pairs with *tRNA*; encode the sequences of proteins.

d. Each cell type makes >1,000 different mRNAs; can be very long; form base pairs with tRNA; encode the sequences of proteins.

Which is the correct type and location of bonds formed when a new nucleotide is added to the growing DNA strand? a. Hydrogen bonds form between adjacent bases on the same strand; a phosphodiester bond forms between pentoses. b. Covalent bonds form between the base pairs and the pentose of one nucleotide and the phosphate of the other. c. Phosphodiester bonds form between complementary base pairs; a hydrogen bond forms between the pentose of one nucleotide and the phosphate of the other. d. Hydrogen bonds form between complementary base pairs of the two strands; a phosphodiester bond forms between pentoses. e. There are no bonds formed between the actual DNA strands. Rather, van der Waals interactions hold the DNA molecule together.

d. Hydrogen bonds form between complementary base pairs of the two strands; a phosphodiester bond forms between pentoses.

Which of the following statements about a catalyst is correct? a. It can change the equilibrium constant of a chemical reaction. b. It speeds up the rate of the forward but not the reverse reaction. c. It is used up in the course of a reaction. d. It lowers the activation energy for a reaction.

d. It lowers the activation energy for a reaction.

What would be the result if either RNA or DNA is placed in a high pH (basic / alkali) environment? a. covalent bonds in both DNA and RNA will be broken b. covalent bonds in neither DNA or RNA will be broken c. covalent bonds in DNA only would be broken d. covalent bonds in RNA only would be broken

d. covalent bonds in RNA only would be broken

Scientists traditionally illustrate a DNA sequence, like the BRCA2 gene shown in the simulation, as a single strand, with the assumption that it is written: a. from right to left, from 5' to 3' direction, and showing the template strand, corresponding to what is read by RNA polymerase to produce RNA. b. from left to right, from the 5' to 3' direction, and showing the template strand, corresponding to what is read by RNA polymerase to produce RNA. c. from left to right, from the 3' to 5' direction, and showing the template strand, corresponding to what is read by RNA polymerase to produce RNA. d. from left to right, from the 5' to 3' direction, and showing the complement to the template strand. e. from left to right, from the 3' to 5' direction, and showing the coding strand, corresponding to that strand read by DNA polymerase to produce RNA.

d. from left to right, from the 5' to 3' direction, and showing the complement to the template strand.

Energy for DNA polymerization during replication is derived from: a. ATP provided by the exonuclease domain of the DNA polymerase. b. hydrolysis of water by the exonuclease domain of the DNA polymerase. c. ATP provided by the energy-storage domain of the DNA polymerase. d. hydrolysis of the high-energy phosphate bond between the α-phosphate and β-phosphate of the nucleotide newly incorporated into the growing DNA strand. e. hydrolysis of the high-energy phosphate bond between the β-phosphate and ɣ-phosphate of the nucleotide newly incorporated into the growing DNA strand.

d. hydrolysis of the high-energy phosphate bond between the α-phosphate and β-phosphate of the nucleotide newly incorporated into the growing DNA strand.

DNA ligases repair nicks in DNA where: a. one end is a 5' phosphate and the other a 3' phosphate. b. one end is a 5' hydroxyl and the other is a 5' phosphate. c. one end is a 5' hydroxyl and the other a 3' hydroxyl. d. one end is a 5' phosphate and the other a 3' hydroxyl.

d. one end is a 5' phosphate and the other a 3' hydroxyl.

Which of the following amino acids would most likely NOT be found in an α helix? a. methionine b. lysine c. phenylalanine d. proline e. glutamine

d. proline

Adenine can base pair with either uracil or thymine because a. adenine occurs in both RNA and DNA. b. uracil and thymine are both pyrimidines. c. phosphate binds equally effectively to ribose and deoxyribose. d. uracil and thymine have similar structures that can hydrogen-bond in the same way with adenine. e. adenine does not bind with uracil or thymine and instead binds with cytosine.

d. uracil and thymine have similar structures that can hydrogen-bond in the same way with adenine.

The DNA double helix is composed of two single-stranded DNA molecules. Which of the below statements is accurate when considering how the two single-stranded DNA molecules interact with each other (interstrand) and how the nucleotides interact within the same strand (intrastrand)? a.Antiparallel DNA strands interact only during replication. b. At both the interstrand and intrastrand level, nucleotides interact via covalent bonds. c. At the intrastrand level, nucleotides interact via hydrogen bonds; while at the interstrand level, nucleotides interact via covalent bonds. d. At the intrastrand level, nucleotides interact via hydrogen bonds; while at the interstrand level, nucleotides interact via phospodiester bonds. e. At the intrastrand level, nucleotides interact via phosphodiester bonds; while at the interstrand level, nucleotides interact via hydrogen bonds.

e. At the intrastrand level, nucleotides interact via phosphodiester bonds; while at the interstrand level, nucleotides interact via hydrogen bonds.

Why is there a problem replicating the ends of linear DNA? a. Primase cannot copy telomere DNA. b. Leading strand synthesis primed at the replication origin of a linear DNA can't remove and replace the primer. c. Since replication only initiates at the ends of linear DNA, the priming of each leading strand leaves a primer at the end that cannot be removed. d. Okazaki fragments are generated along both strands but DNA ligase is inhibited by the Tus-Ter complexes at the ends of the DNA. e. Lagging strand synthesis primed at the ends of a linear DNA can't be removed and replaced because there is no 3'-OH available.

e. Lagging strand synthesis primed at the ends of a linear DNA can't be removed and replaced because there is no 3'-OH available.

Why is a high temperature needed during the denaturing step in PCR? a. To denature the DNA polymerase so it can bind to the template strands b. To break the covalent bonds of the template DNA backbone and separate the strands, giving access to the strands for primers to bind c. To break the hydrogen bonds between the base pairs of the template DNA strands, giving access to the strands for the DNA polymerase to bind d. To help the primers anneal to the DNA template strands e. To break the hydrogen bonds between the base pairs of the template DNA strands, giving access to the strands for primers to bind

e. To break the hydrogen bonds between the base pairs of the template DNA strands, giving access to the strands for primers to bind

Which of the following techniques can be used to determine the size of a target protein? a. Isoelectric-focusing gel b. Immunoprecipitation c. Affinity chromatography d. Immunofluorescence e. Western Blot

e. Western Blot

Each nucleotide contains one each of these components: a. a base and a phosphate. b. a nitrogenous base and a pentose. c. a sugar, a phosphate, and a pentose. d. a base, a nitrogenous base, and a phosphate. e. a nitrogenous base, a phosphate, and a pentose.

e. a nitrogenous base, a phosphate, and a pentose.

Observing replication of circular plasmid DNAs by electron microscopy showed that: a. the plasmid DNA must become linear before replication can initiate at each end of the linear plasmid. b. replication occurred only at one replication fork of the bubble created. c. template strands completely unwind before replication starts. d. replication initiates at multiple origins, creating multiple replication bubbles in the plasmid. e. replication initiates from a single origin, creating a single replication bubble in the plasmid.

e. replication initiates from a single origin, creating a single replication bubble in the plasmid.