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Biochemistry > Discussion 2 > Flashcards

Discussion 2 Flashcards

1
Q

Phosphodiester bonds link DNA monomers to form a polymer by which mechanism?

a. The OH group on C-2 in the ribose carbohydrate forms a covalent bond to elongate the DNA polymer.

b. The OH group on C-3 in the ribose carbohydrate forms a covalent bond to elongate the DNA chain.

c. The OH group on the C-2 in the 2-deoxyribose monosaccharide forms a covalent to elongate the DNA polymer.

d. The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain.

A

d. The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain.

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2
Q

Read the following three statements carefully and determine which are true and which are false.

i) Nucleic acids are synthesized in the 3’ - 5’ direction.
ii) The sugar-phosphate groups which form the “backbone” of the DNA double-helix are located on the outside of the helix because they are polar.
iii) RNA polymerase “reads” a template strand by running along it in a 5’ - 3’ direction.

i) is false, and ii) & iii) are true.

All three statements are false.

All three statements are true.

i) & ii) are true, and iii) is false.

i) & iii) are false, and ii) is true.

A

i) & iii) are false, and ii) is true.

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3
Q

Which of the following does NOT apply to the reaction catalyzed by a DNA polymerase?

It is a phosphoryl group transfer reaction.

It involves a nucleophilic attack by an –OH group.

It is a biosynthetic (anabolic) reaction and so has a positive free energy change (∆G).

It is facilitated by the hydrolysis of a pyrophosphate group.

It requires an abundant supply of deoxynucleoside triphosphates.

A

It is a biosynthetic (anabolic) reaction and so has a positive free energy change (∆G).

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4
Q

What is the function of a restriction enzyme?

It seals breaks in the sugar-phosphate backbone.

It cuts DNA.

It adds a nucleotide base to the template strand of DNA.

It unwinds DNA.

A

It cuts DNA.

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5
Q

Why does the polymerase chain reaction require a heat-stable DNA polymerase?

High temperatures are necessary to cause strand separation after each cycle of synthesis.
High temperatures are necessary for annealing the primers.
High temperatures are necessary for initiating DNA synthesis.
High temperatures are necessary for high-fidelity in DNA synthesis.

A

High temperatures are necessary to cause strand separation after each cycle of synthesis.

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6
Q

Nucleotides play a central role in living organisms because ______.

they mediate transport of energy within the cell

they are involved in oxidation-reduction reactions

they are involved in intracellular signaling

they function as building blocks for nucleic acids

all of the above

A

all of the above

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7
Q

Inside our cells, free nucleotides are almost always associated with ______.

proteins

cholesterol

Cl− counterions

fatty acids

Mg2+ counterions

A

Mg2+ counterions

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8
Q

Nucleoside triphosphates are useful for energy transfer because the phosphoanhydride bonds are relatively ______.

stable

high energy

biocompatible

large

low energy

A

high energy

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9
Q

Which of the following nucleotides contain energy rich bonds?

ATP

TTP

GTP

CTP

all of the above

A

all of the above

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10
Q

Which of the following molecules does not contain an energy-rich phosphoanhydride bond?

ADP

GDP

AMP

CDP

all of the above

A

AMP

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11
Q

Describe the structure of a DNA molecule by listing six characteristics.

  1. DNA forms a double ______________ .
  2. The two strands run___________.
  3. The sugar is ______________ .
  4. The sugar-phosphate groups are ____________ .
  5. The bases are in _____________.
  6. The bases are planar, and their plane is orientated ___________ to the axis of the helix.
  7. There are __________bases. List them in alphabetical order, separated by comma and without spaces: .
  8. The strands are held together by H-bonding between complementary bases. Enter your answer in form A-B,C-D without spaces:

9.The helix has a minor and a major_________on its surface.

A
  1. Helix
  2. 5’ to 3’
  3. Deoxyribose sugar.
  4. on the outside of the helix
  5. the center of the helix
  6. Perpendicular
  7. 4, A,C,G,T.
  8. A-T, G-C
    9.Groove
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12
Q

The link between a purine and ribose is made from the ____________ of the purine ring to the ____________ of the ribose.

A

N-9, C-1’.

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13
Q

In DNA, the ribose derivative lacks an _____ on C-_____.

alcohol; 2

alcohol; 3

amine; 2

amine; 3

none of the above

A

alcohol; 2

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14
Q

What type of bond is made between nucleotides?

ester

phosphoester

phosphodiester

glycosidic

none of the above

A

phosphodiester

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15
Q

The most common base pairs in DNA are _____ and _____.

A-T; A-G

G-C; C-A

T-A; A-U

C-G; T-A

G-U; A-T

A

C-G; T-A

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16
Q

An A-T base pair consists of _____ H-bond(s); a C-G base pair consists of _____ H-bond(s).

1; 2

2; 1

2; 2

3; 2

2; 3

A

2; 3

17
Q

Which of the following correctly describes the B-DNA double helix?

antiparallel strands

right-handed helix

base pairs are located in the center of the helix

one helical rotation has a rise of 3.4 nm

all of the above

A

all of the above

18
Q

The replication of DNA is made possible by the presence of _____ strands in the double helix of DNA.

antiparallel

hydrogen-bonded

complementary

genomic

none of the above

A

complementary

19
Q

In living organisms, genetic information is most often stored in the form of ______.

ribonucleic acid

deoxyribonucleic acid

proteins

enzymes

deoxynucleotides

A

deoxyribonucleic acid

20
Q

An E. coli has _____ replication fork(s) on its single chromosome; humans have _____ replication fork(s) on each chromosome.

1; 1

1; 2

2; 2

2; many

many; many

A

2; many

21
Q

Which strand of DNA is replicated exclusively in a discontinuous fashion?

forward strand

reverse strand

leading strand

lagging strand

the strand that is read in a 5’ to 3’ direction

A

lagging strand

22
Q

Which of the following best describes a new strand of DNA relative to the template strand used to synthesize it?

an exact duplicate of the template

a negative copy of the template

a palindromic copy of the template

an exact copy of the template but with the 3ꞌ and 5ꞌ ends reversed

none of the above

A

a negative copy of the template

23
Q

In most organisms, replication proceeds in a _____ manner from the _____.

bidirectional; replication origin

bidirectional; theta site

bidirectional; lagging strand

unidirectional; chromosome ends

none of the above

A

bidirectional; replication origin

24
Q

Incorporation of which of the following would result in chain termination during sequencing of DNA?

dATP

dCTP

ddTTP

dGTP

none of the above

A

ddTTP

25
Q

The results of DNA sequencing are obtained by first separating different-sized pieces of DNA using _____ followed by detection of the particular dideoxynucleotide using _____.

HPLC; NMR

HPLC; absorbance spectroscopy

electrophoresis; fluorescence spectroscopy

electrophoresis; X-ray crystallography

none of the above

A

electrophoresis; fluorescence spectroscopy

26
Q

The most commonly used technique for making large numbers of copies of DNA is _____.

polymerase chain reaction

dideoxy sequencing

restriction digestion

genetic engineering

site-directed mutagenesis

A

polymerase chain reaction

27
Q

What reagents are required to perform PCR?

DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase

DNA fragment, primers flanking the region of interest, dNTPs, ddNTPs, DNA polymerase

DNA fragment, one primer, dNTPs, DNA polymerase, DNA ligase

DNA fragment, one primer, dNTPs, DNA polymerase, DNA endonuclease

DNA fragment, primers flanking the region of interest, dNTPs, DNA endonuclease

A

DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase

28
Q

Which of the following represents the correct order of steps in a PCR reaction beginning with double-stranded DNA?

primer annealing, strand separation, primer extension

strand separation, primer extension, primer annealing

strand separation, primer annealing, primer extension

primer extension, primer annealing, strand separation

primer annealing, primer extension, strand separation

A

strand separation, primer annealing, primer extension

29
Q

What term describes the production of multiple identical organisms from a single ancestor?

transcription

cloning

sequencing

phenotyping

ligation

A

cloning

30
Q

Double-stranded DNA molecules can be cleaved at specific recognition sites by _____.

RNA polymerase

DNA ligase

DNA polymerase

reverse transcriptase

Type II restriction endonucleases

A

Type II restriction endonucleases

31
Q

DNA sequencing by the chain-termination method uses DNA polymerase I to make a complementary copy of the target or template DNA molecule. A reaction with a 20 bp template and dideoxyadenosine nucleotides as terminators results in the production of a 5 bp fragment. Based on this result, we can conclude that the template contains _____.

a cytosine at position 5

a thymine at position 5

a cytosine at position 16

a thymine at position 16

a uracil at position 5

A

a thymine at position 16

32
Q

In molecular cloning, transformed organisms must be identified. One common method for accomplishing this involves the inclusion of ______ in the plasmid.

a restriction site

a nuclease gene

a deletion

an origin of replication

an antibiotic resistance gene

A

an antibiotic resistance gene

33
Q

During DNA replication, which of the following events would occur and in what order (n/a = not applicable)?

Ligation of the replicated strands on the leading strand.

Ligation of the replicated strands on the lagging strand.

Formation of a replication bubble.

Replication of the leading strand in 5’ to 3’ direction and lagging strand in the 3’ to 5’ direction.

Replication of the leading and lagging strand in 5’ to 3’ direction.

A

N/A
3
1
N/A
2

34
Q

A PCR experiment was performed on a highly conserved gene from two species, one prokaryotic and one eukaryotic. Which of the following statements best describes the expected results?

The sequences of the PCR products would be identical.

The sequences of the PCR products would be mostly identical except for any random mutations.

The sequences of the PCR products would be completely different since prokaryotes and eukaryotes have differing enzymes.

The sequences of the PCR products would be different since eukaryotes have introns and exons.

The sequences of the PCR products would be different since prokaryotes have introns and exons.

A

The sequences of the PCR products would be different since eukaryotes have introns and exons.

Biochemistry (32 decks)

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