Exam 1 Flashcards

1
Q

The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:
A) always link A with T and G with C.
B) are susceptible to alkaline hydrolysis.
C) are uncharged at neutral pH.
D) form between the planar rings of adjacent bases.
E) join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next.

A

E) join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next.

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2
Q

B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a rise of ____ Å
per base pair.
A) left; 20; 3.9
B) right; 18; 3.4
C) right; 18; 3.6
D) right; 20; 3.4
E) right; 23; 2.6

A

D) right; 20; 3.4

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3
Q

In the laboratory, several factors are known to cause alteration of the chemical structure of
DNA. The factor(s) likely to be important in a living cell is (are):
A) heat.
B) low pH.
C) oxygen.
D) UV light.
E) both C and D.

A

E) both C and D.

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4
Q

The most precise modern definition of a gene is a segment of genetic material that:
A) codes for one polypeptide.
B) codes for one polypeptide or RNA product.
C) determines one phenotype.
D) determines one trait.
E) codes for one protein.

A

B) codes for one polypeptide or RNA product.

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5
Q

The DNA in a eukaryotic chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
C) a single linear single-stranded molecule.
D) multiple linear double-helical molecules.
E) multiple linear single-stranded molecules.

A

B) a single linear double-helical molecule.

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6
Q
  1. Introns:
    A) are frequently present in prokaryotic genes but are rare in eukaryotic genes.
    B) are spliced out before transcription.
    C) are translated but not transcribed.
    D) can occur many times within a single gene.
    E) encode unusual amino acids in proteins.
A

D) can occur many times within a single gene.

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7
Q

Topoisomerases can:
A) change the linking number (Lk) of a DNA molecule.
B) change the number of base pairs in a DNA molecule.
C) change the number of nucleotides in a DNA molecule.
D) convert D isomers of nucleotides to L isomers.
E) interconvert DNA and RNA.

A

A) change the linking number (Lk) of a DNA molecule.

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8
Q

Which of the following does not contribute to the octameric histone core?
A) H1
B) H2A
C) H2B
D) H3
E) H4

A

A) H1

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9
Q

The fundamental repeating unit of organization in a eukaryotic chromosome is the:
A) centrosome.
B) lysosome.
C) microsome.
D) nucleosome.
E) polysome.

A

D) nucleosome.

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10
Q
  1. When a DNA molecule is described as replicating bidirectionally, that means that it has two:
    A) chains.
    B) independently replicating segment.
    C) origins.
    D) replication forks.
    E) termination points.
A

D) replication forks.

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11
Q
  1. An Okazaki fragment is a:
    A) fragment of DNA resulting from endonuclease action.
    B) fragment of RNA that is a subunit of the 30S ribosome.
    C) piece of DNA that is synthesized in the 3’ -> 5’ direction.
    D) segment of DNA that is an intermediate in the synthesis of the lagging strand.
    E) segment of mRNA synthesized by RNA polymerase.
A

D) segment of DNA that is an intermediate in the synthesis of the lagging strand.

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12
Q

Prokaryotic DNA polymerase III:
A) contains a 5’ -> 3’ proofreading activity to improve the fidelity of replication.
B) does not require a primer molecule to initiate replication.
C) has a b subunit that acts as a circular clamp to improve the processivity of DNA synthesis.
D) synthesizes DNA in the 3’ -> 5’ direction.
E) synthesizes only the leading strand; DNA polymerase I synthesizes the lagging strand.

A

C) has a b subunit that acts as a circular clamp to improve the processivity of DNA synthesis.

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13
Q

At replication forks in E. coli:
A) DNA helicases make endonucleolytic cuts in DNA.
B) DNA primers are degraded by exonucleases.
C) DNA topoisomerases make endonucleolytic cuts in DNA.
D) RNA primers are removed by primase.
E) RNA primers are synthesized by primase.

A

E) RNA primers are synthesized by primase.

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14
Q

In contrast to bacteria, eukaryotic chromosomes need multiple DNA replication origins
because:
A) eukaryotic chromosomes cannot usually replicate bidirectionally.
B) eukaryotic genomes are not usually circular, like the bacterial chromosome is.
C) the processivity of the eukaryotic DNA polymerase is much less than the bacterial enzyme.
D) their replication rate is much slower, and it would take too long with only a single origin per
chromosome.
E) they have a variety of DNA polymerases for different purposes, and need a corresponding
variety of replication origins.

A

D) their replication rate is much slower, and it would take too long with only a single origin per
chromosome.

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15
Q

The function of the eukaryotic DNA replication factor PCNA (proliferating cell nuclear
antigen) is similar to that of the b-subunit of bacterial DNA polymerase III in that it:
A) facilitates replication of telomeres.
B) forms a circular sliding clamp to increase the processivity of replication.
C) has a 3’ -> 5’ proofreading activity.
D) increases the speed but not the processivity of the replication complex.
E) participates in DNA repair.

A

B) forms a circular sliding clamp to increase the processivity of replication.

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16
Q

Which of the following is not usually essential for the catalytic activity of ribozymes?
A) Correct base pairing
B) Correct base sequence
C) Correct interaction with protein
D) Correct secondary structure
E) Correct three-dimensional structure

A

C) Correct interaction with protein

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17
Q

Which of the following is not true about telomerase?
A) Telomerase is a reverse transcriptase.
B) Telomerase utilizes a RNA template.
C) The primer for telomerase is the 3’-end of the DNA chromosomes.
D) Telomerase synthesizes DNA in the 5’ -> 3’ direction.
E) Telomerase consists of both RNA and protein.

A

B) Telomerase utilizes a RNA template.

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18
Q

The ABC excinuclease is essential in:
A) base-excision repair.
B) methyl-directed repair.
C) mismatch repair.
D) nucleotide-excision repair.
E) SOS repair.

A

D) nucleotide-excision repair.

18
Q

Which of these enzymes is not directly involved in methyl-directed mismatch repair in E.
coli?
A) DNA glycosylase
B) DNA helicase II
C) DNA ligase
D) DNA polymerase III
E) Exonuclease I

A

A) DNA glycosylase

19
Q

Which mechanism is primary used to repair a thymidine dimer in Bacterial DNA?
A) Mismatch repair
B) Base-excision repair
C) Nucleotide-excision repair
D) Direct repair
E) More than one is used for this type of lesion

A

D) Direct repair

20
Q

In homologous genetic recombination, RecA protein is involved in:
A) formation of Holliday intermediates and branch migration.
B) introduction of negative supercoils into the recombination products.
C) nicking the two duplex DNA molecules to initiate the reaction.
D) pairing a DNA strand from one duplex DNA molecule with sequences in another duplex,
regardless of complementarity.
E) resolution of the Holliday intermediate.

A

A) formation of Holliday intermediates and branch migration.

21
Q

T or F: In base-excision repair, the first enzyme to act is: Dam methylase.

A

False: DNA glycosylase

22
Q

T or F: In the Watson-Crick model of DNA structure: both strands run in the same direction, 5’ to 3’; they are parallel.

A

F; opposite direction, anti-parallel

23
Q

T or F: A major component of RNA but not of DNA is thymine

A

F; uracil

23
Q

T or F: In contrast to bacteria, eukaryotic chromosomes need multiple DNA replication origins
because: eukaryotic chromosomes cannot usually replicate bidirectional.

A

F; their replication rate is much slower, and it would take too long with only a single origin per
chromosome

24
Q

Type of bond with role:
(a) phosphodiester
(b) N-glycosidic
(c) phosphate ester
(d) hydrogen

1.___ links base to pentose in nucleotide
2. ___ joins adjacent nucleotides in one strand
3.___ joins complementary nucleotides in two strands
4.___ difference between a nucleoside and a nucleotide

A
  1. b
  2. a
  3. d
  4. c
25
Q

What is the approximate length of a DNA molecule (in the B form) containing 10,000 base pairs?

A

3.4 Å * 10,000 = 34,000 Å = 3.4 μm.

26
Q

The Meselson-Stahl experiment showed that the nitrogen used for the synthesis of new dsDNA becomes equally divided between the two daughter genomes. This result suggested a semiconservative replication mechanism. Please describe how this experiment was performed?

A

Cells grown for multiple generations in a medium of heavy nitrogen N15.
When transferred into a medium of light nitrogen N14 had a higher density gradient. The second replication cycle had a hybrid DNA band and a band with only N14.

27
Q

Why is RNA more unstable?

A

Because it has an extra OH that can pair with other things. HAs 3 oxygen instead of 2 (DNA)

28
Q

DNA replication in E. coli begins at a site in the DNA called the (a) ___________. At the
replication fork the (b) ___________ strand is synthesized continuously while the (c) _________
strand is synthesized discontinuously.

A

a: origin
b:leading
c:lagging

29
Q

On the strand synthesized discontinuously, the short
pieces are called (d) ____________ fragments. An RNA primer for each of the fragments is
synthesized by an enzyme called (e) __________,

A

d: Okazaki
e: primase

30
Q

This RNA primer is removed after the
fragment is synthesized by the enzyme (f) ___________, using its (g) _____________ activity.
The nicks left behind in this process are sealed by the enzyme (h) _____________.

A

f: DNA polymerase I
g: 5’->3’exonculase
h: DNA ligase

31
Q

Cytosine deamination

A

Uracil N-glycosylase

32
Q

Base loss

A

AP endonuclease

33
Q

Adine deamination

A

hypoxanthine-N-glycosylase

34
Q

Binds to GATCH sequences

A

mutH protein

35
Q

Binds to mismatch in DNA

A

mutD-mutL complex

36
Q

DNA synthesis in gaps

A

DNA polymerase I

37
Q

Seals nicks

A

DNA ligase

38
Q

O6 methylguanine

A

O6 methyguangine methyltransferase

39
Q

Direct chemical reversal of pyridine dimer formation

A

DNA photolyase

40
Q

Double strand break

A

restriction endonuclease

41
Q

Excision of a lesion containing oligonucleotide

A

ABC excinuclease