Bmb 462 ***exam 3*** Fall 2006

Front 1

Nucleotides are used in cells to :

A synthesize nucleic acids.

B attach cofactors in enzyme active sites.

C carry cell signals as second messengers.

D provide energy for anabolism.

E all of the above.

Back 1

E
all of the above.

Front 2

Which statement about purine synthesis is FALSE?
2. A Glycine, glutamine, and aspartate all donate nitrogen to the purine ring.
B IMP is an intermediate in the synthesis of both AMP and GMP.
C ATP is required to synthesize the purine ring.
D S-adenosyl methionine (SAM) is used to donate carbon groups that become part of the purine ring.
E AMP synthesis from IMP requires GTP hydrolysis.

Back 2

D
S-adenosyl methionine (SAM) is used to donate carbon groups that become part of the purine ring.

Front 3

Which statements about ribonucleotide reductase are TRUE?

i) High ATP levels inhibit the overall activity of this enzyme.
ii) As dGTP accumulates, ribonucleotide reductase increases dADP production.
iii) This enzyme requires reducing power from NADPH + H+.

A Only i is true.
B All three are true.
C Only i and iii are true.
D Only iii is true.
E Only ii is true.
F Only i and ii are true.
G Only ii and iii are true.

Back 3

G
Only ii and iii are true.

Front 4

During purine salvage, the following three enzymes are required to produce dADP from adenine and 5- phosphoribosyl 1-pyrophosphate (PRPP). Put the enzymes in the order they would be used in this process.

i) Adenylate Kinase
ii) Ribonucleotide Reductase
iii) Adenosine Phosphoribosyltransferase

A First used - ii, iii, i - Last used
B First used - i, ii, iii - Last used
C First used - iii, ii, i - Last used
D First used - i, iii, ii - Last used
E First used - iii, i, ii - Last used
F First used - ii, i, iii - Last used

Back 4

E
First used - iii, i, ii - Last used

Front 5

Which disease/disorder is NOT associated with purine degradation?

A ADA SCIDs (adenosine deaminase severe combined immunode_ciency disease)
B Lesch-Nyhan syndrome
C Alkaptonuria
D Gout

Back 5

C
Alkaptonuria

Front 6

How does methotrexate function as a chemotherapeutic agent?

A It inhibits phosphoribosyltransferases.
B It inhibits amidotransferases.
C It inhibits thymidylate synthase.
D It inhibits dihydrofolate reductase.
E It inhibits adenosine deaminase.

Back 6

D It inhibits dihydrofolate reductase.

Front 7

Two bacteria are isolated from separate locations, one from a hot springs and one from the arctic tundra.
Adenine makes up 20% of bacteria X's genome and 30% of bacteria Y's genome. Which statement below is most likely CORRECT?

A Bacteria Y's genome contains 20% guanine and it is from the hot springs.
B Bacteria X's genome contains 20% guanine and it is from the hot springs.
C Bacteria X's genome contains 30% guanine and it is from the hot springs.
D Bacteria Y's genome contains 30% guanine and it is from the hot springs.
E It is possible to predict the guanine content of both bacterial genomes but there is no scienti_c basis on which to predict their origins.

Back 7

C Bacteria X's genome contains 30% guanine and it is from the hot springs.

Front 8

If 06-methylguanine occurs in DNA and is repaired by 06-methylguainine-DNA methyltransferase, this is an example of:

A methyl-directed mismatch repair.
B recombination repair.
C nucleotide-excision repair.
D direct repair.
E base-excision repair.

Back 8

D direct repair.

Front 9

Which description BEST explains why the Tm of a duplex changes when the salt concentration of the solution
containing the duplex changes?
A This changes interactions between the phosphodiester backbones of the two strands.
B This changes the number of H-bonds between the duplex strands without changing the H-bonding pattern
of individual bases.
C This changes the con_guration of individual bases and adds or removes H-bond donors and acceptors at
certain positions on the bases.
D This changes hydrophobic interactions between the planar faces of the bases in the double helix.

Back 9

A This changes interactions between the phosphodiester backbones of the two strands.

Front 10

Which of the following statements is FALSE?

A The major physiological form of the DNA helix is the B form.

B The A from helix typically consists of either RNA:RNA or RNA:DNA duplex and is more compact (less
helical rise per base pair) than B from helix.

C In genomic DNA, most bases are found in the syn conformation relative to the pentose sugar in the DNA
molecule.

D The two strands of the double helix are antiparallel and complementary.

E The Z form of DNA is a left-handed helix and is more elongated (more helical rise per base pair) than a B
form helix.

Back 10

C In genomic DNA, most bases are found in the syn conformation relative to the pentose sugar in the DNA
molecule.

Front 11

In a closed circular piece of DNA, changes in linking number .

A are caused by histone proteins without the aid of other proteins.
B can occur whenever the double helix is denatured.
C can occur only when at least one phosphodiester bond in the backbone is broken and rejoined.
D require hydrolysis of ATP.
E are caused by structural maintenance of chromosome (SMC) proteins without the aid of other proteins.

Back 11

C can occur only when at least one phosphodiester bond in the backbone is broken and rejoined.

Front 12

Which BEST describes the current model of how underwinding of eukaryotic chromatin occurs?

A The coiling of 146 bp of DNA around each histone core introduces negative supercoils into the chromosome.
B SMC proteins condense the DNA.
C DNA gyrase uses ATP to introduce negative supercoils.
D Topoisomerases relax positive supercoils following nucleosome formation.
E It is impossible to underwind eukaryotic DNA as eukaryotes do not contain DNA gyrase.

Back 12

D Topoisomerases relax positive supercoils following nucleosome formation.

Front 13

Which CORRECTLY compares or contrasts type 1 and type 2 topoisomerases?

i) Both are capable of breaking and reforming a phosphodiester bond.
ii) Both require ATP to function.
iii) E. coli has both type I and type II topoisomerases.

A Only ii and iii are true.
B Only i and ii are true.
C Only i is true.
D Only i and iii are true.
E Only ii is true.
F Only iii is true.
G All three are true.

Back 13

D Only i and iii are true.

Front 14

Put the steps involved in initiation of replication at E. coli 's oriC in the proper order.
i) DnaC loads DnaB onto the DNA.
ii) DnaA and HU melt the duplex at the 13 bp A-T rich repeats.
iii) DnaB begins to unwind the DNA duplex.
iv) DAM fully methylates GATC sites in oriC.

A First - iv, ii, i, iii - Last
B First - ii, i, iii, iv - Last
C First - i, ii, iii, iv - Last
D First - iv, iii, ii, i - Last
E First - iii, ii, i, iv - Last

Back 14

A First - iv, ii, i, iii - Last

Front 15

Which experiment provides the best evidence that DNA replication of the E. coli chromosome is bidirectional?
A The Franklin X-ray di_raction pattern of DNA.
B The Okazaki experiment in which both high molecular weight and low molecular weight DNA fragments
were isolated from replicating bacteria.
C The Meselson-Stahl experiment in which bacteria grown on 15N were switched to 14N and their DNA was
isolated and centrifuged.
D The Cairns experiment in which replicating DNA was pulse-labeled using 3H-labeled thymidine and visualized
using photomicrographs.
E The Hershey-Chase experiment in which bacteria were mixed with phage labeled with 35S or 32P.

Back 15

D The Cairns experiment in which replicating DNA was pulse-labeled using 3H-labeled thymidine and visualized using photomicrographs.

Front 16

Choose the statements that apply to BOTH DNA pol I and the DNA pol III holoenzyme.
i. It adds nucleotides to the free 5' hydroxyl of the primer.
ii. It reads the template strand moving in a 3'!5' direction along the template strand.
iii. It has exonuclease activity that allows removal of mispaired bases as part of its proofreading function.

A Only i
B Only ii
C Only ii and iii
D Only iii
E Only i and iii
F Only i and ii
G All three

Back 16

C
Only ii and iii

Front 17

Which of the following statements regarding telomeres is FALSE?

A Prokaryotes do not require telomeres to maintain their chromosomes.
B Telomeres can fold back on themselves by inserting a 3' ssDNA region into duplex DNA to protect the ends
of the chromosome from degradation.
C Since telomerase is only active in germ line cells and not somatic cells, it is hypothesized that telomere loss
may play a role in aging.
D The problem associated with telomeres in eukaryotic replication is the loss of genetic information from the
chromosomal end when RNA primers are degraded.
E Maintenance of telomeres requires a DNA-dependent DNA polymerase that carriers its own RNA template.

Back 17

E
Maintenance of telomeres requires a DNA-dependent DNA polymerase that carriers its own RNA template.

Front 18

The Beta-sliding clamp from E. coli and PCNA from eukaryotes are analogous proteins. Which statement is
FALSE?

A Both proteins form rings that surround the DNA double helix.
B The Beta-sliding clamp functions as a dimer and PCNA functions as a trimer.
C Both proteins are involved in replication.
D These proteins have nearly identical primary structures.
E Both proteins increase the processivity of DNA polymerases.

Back 18

D These proteins have nearly identical primary structures.

Front 19

Which enzymes are required for nucleotide-excision repair?
i) a helicase
ii) a DNA glycosylase
iii) a DNA Polymerse

A Only i and ii
B Only ii and iii
C Only i
D Only iii
E Only i and iii
F Only ii
G All three

Back 19

E Only i and iii

Front 20

Put the steps involved in base-excision repair in the proper order.
i) Cleavage by AP endonuclease.
ii) Cleavage by a DNA glycosylase.
iii) Phosphodiester bond formation by DNA Ligase.
iv) Nick translation by DNA polymerase I.
29. A First - iv, iii, ii, i - Last
B First - i, ii, iv, iii - Last
C First - ii, i, iv, iii - Last
D First - ii, iii, i, iv - Last
E First - ii, iv, i, iii - Last

Back 20

C
First - ii, i, iv, iii - Last

Front 21

The Ames test is used to:

A measure the mutagenic effects of various chemical compounds.
B examine the potency of antibiotics.
C detect bacterial viruses.
D quantify the damaging effects of UV light in DNA molecules.
E determine the rate of DNA replication.

Back 21

A measure the mutagenic effects of various chemical compounds.

Front 22

What function does RecA serve in E. coli?

A RecA mediates strand invasion during homologous recombination.
B RecA binds to oriC and initiates replication.
C RecA is the exinuclease responsible for initiation of nucleotide-excision repair.
D RecA is responsible for recombination of immunoglobulin genes.
E RecA is the site-speci_c recombinase responsible for _ phage integration.

Back 22

A RecA mediates strand invasion during homologous recombination.

Front 23

pt Which statement about site-speci_c recombination is TRUE?

A The reaction mechanism involves transesteri_cation to tyrosine residues in the recombinase.
B Site-speci_c recombination is used to generate diversity during mitosis.
C Site-speci_c recombinases require ATP hydrolysis to drive phosphodiester bond formation.
D Direct repeats result in inversion of the sequence between them.
E Site-speci_c recombination is frequently used to repair damage at replication forks.

Back 23

A The reaction mechanism involves transesteri_cation to tyrosine residues in the recombinase.

Front 24

Plasmids used to clone DNA:
33. A have a start site for replication.
B have at least one unique restriction site.
C are small and easily separated from the bacterial chromosome.
D have a gene encoding a selectable marker.
E All of the above.

Back 24

E All of the above.

Front 25

The sequence G/GATCC is recognized and cut by the restriction endonuclease BamHI as indicated. Which
of these statements is true?
i) This produces a 5' overhang.
ii) This produces an end that is compatible with the end from BglII digestion of A/GATCT.
iii) This produces a blunt end.

A Only i is true.
B Only iii is true.
C Only ii is true.
D Only i and ii are true.
E Only i and iii are true.

Back 25

D Only i and ii are true.

Front 26

Which enzyme is required to make a cDNA library but not a genomic library?

A reverse transcriptase
B DNA glycosylase
C ABC exinuclease
D DNA ligase
E a restriction endonuclease

Back 26

A reverse transcriptase

Front 27

The PCR reaction mixture does NOT include:

A all four deoxynucleoside triphosphates.
B DNA ligase.
C DNA containing the sequence to be ampli_ed.
D oligonucleotide primer(s).
E heat-stable DNA polymerase.

Back 27

B DNA ligase.

Front 28

This type of RNA is part of the spliceosome required for intron removal.

A miRNA
B tRNA
C rRNA
D mRNA
E snRNA

Back 28

E snRNA

Front 29

About 80% of the RNA in a typical cell is this type of RNA.

A miRNA
B tRNA
C rRNA
D mRNA
E snRNA

Back 29

C rRNA

Front 30

This type of RNA has a cloverleaf secondary structure.

A miRNA
B tRNA
C rRNA
D mRNA
E snRNA

Back 30

B tRNA

Front 31

This type of RNA is able to catalyze the formation of peptide bonds.

A miRNA
B tRNA
C rRNA
D mRNA
E snRNA

Back 31

C rRNA