Discussion 2

Question 1

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.

Answer 1

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

Question 2

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.

Answer 2

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

Question 3

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.

Answer 3

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

Question 4

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.

Answer 4

It cuts DNA.

Question 5

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.

Answer 5

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

Question 6

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

Answer 6

all of the above

Question 7

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

proteins

cholesterol

Cl− counterions

fatty acids

Mg2+ counterions

Answer 7

Mg2+ counterions

Question 8

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

stable

high energy

biocompatible

large

low energy

Answer 8

high energy

Question 9

Which of the following nucleotides contain energy rich bonds?

ATP

TTP

GTP

CTP

all of the above

Answer 9

all of the above

Question 10

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

ADP

GDP

AMP

CDP

all of the above

Answer 10

AMP

Question 11

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.

Answer 11

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

Question 12

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

Answer 12

N-9, C-1’.

Question 13

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

alcohol; 2

alcohol; 3

amine; 2

amine; 3

none of the above

Answer 13

alcohol; 2

Question 14

What type of bond is made between nucleotides?

ester

phosphoester

phosphodiester

glycosidic

none of the above

Answer 14

phosphodiester

Question 15

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

Answer 15

C-G; T-A

Question 16

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

Answer 16

2; 3

Question 17

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

Answer 17

all of the above

Question 18

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

Answer 18

complementary

Question 19

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

ribonucleic acid

deoxyribonucleic acid

proteins

enzymes

deoxynucleotides

Answer 19

deoxyribonucleic acid

Question 20

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

Answer 20

2; many

Question 21

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

Answer 21

lagging strand

Question 22

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

Answer 22

a negative copy of the template

Question 23

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

Answer 23

bidirectional; replication origin

Question 24

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

dATP

dCTP

ddTTP

dGTP

none of the above

Answer 24

ddTTP

Question 25

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

Answer 25

electrophoresis; fluorescence spectroscopy

Question 26

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

Answer 26

polymerase chain reaction

Question 27

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

Answer 27

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

Question 28

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

Answer 28

strand separation, primer annealing, primer extension

Question 29

What term describes the production of multiple identical organisms from a single ancestor? transcription cloning sequencing phenotyping ligation

Answer 29

cloning

Question 30

Double-stranded DNA molecules can be cleaved at specific recognition sites by _____. RNA polymerase DNA ligase DNA polymerase reverse transcriptase Type II restriction endonucleases

Answer 30

Type II restriction endonucleases

Question 31

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

Answer 31

a thymine at position 16

Question 32

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

Answer 32

an antibiotic resistance gene

Question 33

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.

Answer 33

N/A 3 1 N/A 2

Question 34

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.

Answer 34

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