Discussion 2 Flashcards
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.
d. The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain.
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.
i) & iii) are false, and ii) is true.
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.
It is a biosynthetic (anabolic) reaction and so has a positive free energy change (∆G).
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.
It cuts DNA.
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.
High temperatures are necessary to cause strand separation after each cycle of synthesis.
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
all of the above
Inside our cells, free nucleotides are almost always associated with ______.
proteins
cholesterol
Cl− counterions
fatty acids
Mg2+ counterions
Mg2+ counterions
Nucleoside triphosphates are useful for energy transfer because the phosphoanhydride bonds are relatively ______.
stable
high energy
biocompatible
large
low energy
high energy
Which of the following nucleotides contain energy rich bonds?
ATP
TTP
GTP
CTP
all of the above
all of the above
Which of the following molecules does not contain an energy-rich phosphoanhydride bond?
ADP
GDP
AMP
CDP
all of the above
AMP
Describe the structure of a DNA molecule by listing six characteristics.
- DNA forms a double ______________ .
- The two strands run___________.
- The sugar is ______________ .
- The sugar-phosphate groups are ____________ .
- The bases are in _____________.
- The bases are planar, and their plane is orientated ___________ to the axis of the helix.
- There are __________bases. List them in alphabetical order, separated by comma and without spaces: .
- 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.
- Helix
- 5’ to 3’
- Deoxyribose sugar.
- on the outside of the helix
- the center of the helix
- Perpendicular
- 4, A,C,G,T.
- A-T, G-C
9.Groove
The link between a purine and ribose is made from the ____________ of the purine ring to the ____________ of the ribose.
N-9, C-1’.
In DNA, the ribose derivative lacks an _____ on C-_____.
alcohol; 2
alcohol; 3
amine; 2
amine; 3
none of the above
alcohol; 2
What type of bond is made between nucleotides?
ester
phosphoester
phosphodiester
glycosidic
none of the above
phosphodiester
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
C-G; T-A
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
2; 3
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
all of the above
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
complementary
In living organisms, genetic information is most often stored in the form of ______.
ribonucleic acid
deoxyribonucleic acid
proteins
enzymes
deoxynucleotides
deoxyribonucleic acid
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
2; many
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
lagging strand
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 negative copy of the template
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
bidirectional; replication origin
Incorporation of which of the following would result in chain termination during sequencing of DNA?
dATP
dCTP
ddTTP
dGTP
none of the above
ddTTP
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
electrophoresis; fluorescence spectroscopy
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
polymerase chain reaction
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
DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase
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
strand separation, primer annealing, primer extension
What term describes the production of multiple identical organisms from a single ancestor?
transcription
cloning
sequencing
phenotyping
ligation
cloning
Double-stranded DNA molecules can be cleaved at specific recognition sites by _____.
RNA polymerase
DNA ligase
DNA polymerase
reverse transcriptase
Type II restriction endonucleases
Type II restriction endonucleases
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 thymine at position 16
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
an antibiotic resistance gene
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.
N/A
3
1
N/A
2
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.
The sequences of the PCR products would be different since eukaryotes have introns and exons.
