1
Q
What are the three defining components of a nucleotide?
A
A nitrogenous base, a pentose, and one or more phosphates.
2
Q
What is a molecule called if it lacks a phosphate group but contains a base and a pentose?
A
A nucleoside.
3
Q
What are the two parent compounds of nitrogenous bases?
A
Pyrimidine and purine.
4
Q
Which pyrimidine base is uniquely found in DNA?
A
Thymine.
5
Q
Which pyrimidine base is uniquely found in RNA?
A
Uracil.
6
Q
What type of bond connects a nucleotide’s base to its pentose?
A
An N-beta-glycosyl bond.
7
Q
What are the two major purine bases in both DNA and RNA?
A
Adenine and guanine.
8
Q
What pentose sugar uniquely defines a nucleic acid as DNA?
A
2’-deoxy-D-ribose.
9
Q
What pentose sugar uniquely defines a nucleic acid as RNA?
A
D-ribose.
10
Q
In what ring conformation do pentoses exist within nucleotides?
A
The beta-furanose form.
11
Q
What type of linkage covalently joins successive nucleotides?
A
Phosphodiester linkages.
12
Q
What is the standard directional polarity of a nucleic acid strand?
A
5’ to 3’.
13
Q
How does RNA react under alkaline conditions compared to DNA?
A
It is rapidly hydrolyzed.
14
Q
What functional group makes RNA susceptible to alkaline hydrolysis?
A
The 2’-hydroxyl groups.
15
Q
What term describes a short nucleic acid of 50 or fewer nucleotides?
A
An oligonucleotide.
16
Q
What term describes a longer nucleic acid polymer?
A
A polynucleotide.
17
Q
At what wavelength do all nucleotide bases strongly absorb ultraviolet light?
A
Near 260 nm.
18
Q
What interactions minimize the contact of bases with water to stabilize the double helix?
A
Hydrophobic stacking interactions.
19
Q
According to Watson and Crick, which base strictly pairs with Adenine?
A
Thymine (or Uracil).
20
Q
According to Watson and Crick, which base strictly pairs with Guanine?
A
Cytosine.
21
Q
How many hydrogen bonds stabilize a G-C base pair?
A
Three.
22
Q
How many hydrogen bonds stabilize an A-T base pair?
A
Two.
23
Q
What is the relative orientation of the two strands in a DNA double helix?
A
Antiparallel.
24
Q
How many base pairs are present per helical turn in aqueous B-form DNA?
A
10.5 bp.
25
What forces primarily stabilize the DNA double helix?
Metal cations and base-stacking interactions.
26
Why are DNA duplexes with high G-C content thermodynamically more stable?
G-C base-stacking interactions are stronger than A-T interactions.
27
What is the most stable, standard reference structure for random-sequence DNA?
B-form DNA (B-DNA).
28
How does A-form DNA structurally differ from B-form DNA?
It has a wider helix and 11 base pairs per helical turn.
29
What physical change unwinds the double helix when DNA is exposed to heat or extreme pH?
Denaturation (melting).
30
What is the process of separated DNA strands spontaneously rewinding called?
Annealing (renaturation).
31
What is the decrease in UV absorption caused by base stacking called?
The hypochromic effect.
32
What is the increase in UV absorption that occurs upon DNA denaturation called?
The hyperchromic effect.
33
What term defines the temperature at which half of a DNA sample is present as single strands?
The melting point (Tm).
34
How does base composition affect a DNA molecule's melting point?
A higher G-C content results in a higher Tm.
35
Which type of nucleic acid duplex is generally more stable to heat denaturation?
RNA duplexes.
36
What is an alteration in DNA structure that permanently changes the genetic information called?
A mutation.
37
What spontaneous reaction causes the loss of exocyclic amino groups from nucleotide bases?
Deamination.
38
What is the product of spontaneous cytosine deamination?
Uracil.
39
What DNA lesion is created by the hydrolysis of the N-beta-glycosyl bond?
An AP (abasic) site.
40
Which type of base is lost at a higher rate via hydrolysis?
Purines.
41
What is the biochemical definition of a gene?
All the DNA encoding the primary sequence of a final polypeptide or RNA product.
42
What is the function of regulatory DNA sequences?
They provide signals for processes like replication and transcription.
43
How many consecutive nucleotides code for a single amino acid?
Three.
44
What is the topological shape of the E. coli chromosome?
A single, circular DNA molecule.
45
What is the diploid chromosome number in a normal human somatic cell?
46
46
What are small, circular, extrachromosomal DNA elements in bacteria called?
Plasmids.
47
What are the noncoding DNA segments that interrupt eukaryotic genes called?
Introns.
48
What are the coding DNA segments within eukaryotic genes called?
Exons.
49
Approximately what percentage of the human genome encodes proteins (exon DNA)?
About 1.5%.
50
What is highly repetitive, simple-sequence DNA also known as?
Satellite DNA.
51
Which chromosomal DNA sequence serves as an attachment point for the mitotic spindle?
The centromere.
52
Which sequences at the ends of eukaryotic chromosomes help stabilize them?
Telomeres.
53
Which enzyme is responsible for adding repeated telomeric sequences?
Telomerase.
54
What term describes the further coiling of the DNA double helix axis upon itself?
Supercoiling.
55
What is the topological state of DNA when there is no net bending of its axis?
The relaxed state.
56
In what topological state do all cells maintain their DNA to aid in compaction?
An underwound state.
57
What does underwinding induce in the DNA molecule?
Structural strain and supercoiling.
58
What topological property of circular DNA remains unchanged under continuous deformations?
The linking number.
59
What class of enzymes can actively alter the linking number of DNA?
Topoisomerases.
60
Which two eukaryotic organelles contain their own DNA?
Mitochondria and chloroplasts.
61
What is the evolutionary origin of mitochondrial and chloroplast DNA?
Ancient bacteria.
62
What proteins package and order eukaryotic DNA into structural units called nucleosomes?
Histones.
63
What molecules neutralize the negative charges of the DNA backbone to allow compaction?
Cations (like Mg2+) and polyamines.
64
What is a viral particle genome typically composed of?
A single RNA or DNA molecule surrounded by a protein coat.
65
Can viral DNA genomes exist as circles?
Yes, many are circular for at least part of their life cycle.
66
What enzyme encoded by plasmids confers resistance to penicillin?
Beta-lactamase.
67
What is the approximate total length of DNA in a single human diploid cell?
2 meters.
68
How does the movement of a polymerase replication fork affect the DNA ahead of it?
It overwinds the DNA.
69
How does DNA underwinding affect strand separation?
It makes strand separation easier.
70
What happens if an isolated, underwound circular DNA molecule suffers a single-strand break?
Free rotation causes it to spontaneously revert to the relaxed state.
71
What are circular DNA molecules that differ only in their linking number called?
Topoisomers.
72
How is the linking number of a DNA molecule changed?
By breaking and rejoining the DNA backbone.
73
What are transposable elements (transposons)?
Molecular parasites that make up nearly half of human DNA.
74
How many introns does the avian ovalbumin gene have?
Seven.
75
Are introns common in bacterial genomes?
No, few bacterial genes contain introns.
76
What central biological paradigm describes the passage of information guiding cell function?
Information passes from DNA to RNA to protein.
77
What is the mechanism of DNA replication called where each new molecule has one old and one new strand?
Semiconservative replication.
78
What is the unique starting point for replication on a chromosome called?
An origin.
79
What are the dynamic points where parent DNA is unwound and replicated called?
Replication forks.
80
Does DNA replication typically proceed in one or both directions from the origin?
It usually proceeds bidirectionally.
81
In what specific direction is a new DNA strand always synthesized?
The 5' to 3' direction.
82
What functional group acts as the nucleophile during DNA polymerization?
The free 3'-hydroxyl group on the growing strand.
83
What is the DNA strand that is synthesized continuously called?
The leading strand.
84
What is the DNA strand that is synthesized discontinuously called?
The lagging strand.
85
What are the short pieces of newly synthesized DNA on the lagging strand called?
Okazaki fragments.
86
How long are typical bacterial Okazaki fragments?
1,000 to 2,000 nucleotides.
87
What class of nucleases degrades nucleic acids from the ends of the molecule?
Exonucleases.
88
What class of nucleases cleaves at specific internal sites?
Endonucleases.
89
What enzymes catalyze the synthesis of DNA?
DNA polymerases.
90
What molecule is released as a byproduct of a phosphoryl group transfer in DNA synthesis?
Inorganic pyrophosphate.
91
How many Mg2+ ions are prominently involved at the DNA polymerase active site?
Two.
92
What two components are strictly required by all DNA polymerases to initiate synthesis?
A template and a primer.
93
What is a primer in the context of DNA replication?
A pre-existing strand segment complementary to the template with a free 3'-OH group.
94
What term defines the average number of nucleotides a polymerase adds before dissociating?
Processivity.
95
In which direction does the proofreading exonuclease activity of a polymerase operate?
3' to 5' direction.
96
By what factor does proofreading improve the accuracy of the polymerization reaction?
100 to 1,000-fold.
97
Which specific enzyme is the principal replication polymerase in E. coli?
DNA polymerase III.
98
What is the primary role of DNA polymerase I in E. coli?
Cleanup functions during replication, recombination, and repair.
99
What unique enzymatic activity allows DNA polymerase I to remove RNA primers?
A 5' to 3' exonuclease activity.
100
What process replaces a segment of DNA or RNA by simultaneously degrading it and synthesizing a new strand?
Nick translation.
101
How many different kinds of subunits make up the E. coli DNA polymerase III holoenzyme?
Nine.
102
What subassembly dramatically increases the processivity of DNA polymerase III?
The beta sliding clamp.
103
What is the entire multi-enzyme complex that promotes rapid DNA synthesis called?
The replisome.
104
Which enzymes physically separate the two DNA strands at the replication fork?
Helicases.
105
What is the energy source required by helicases to unwind DNA?
ATP.
106
What proteins bind and stabilize the separated single strands of DNA?
Single-stranded DNA-binding proteins (SSB).
107
Which enzymes synthesize the short RNA segments used as primers?
Primases.
108
Which enzymes seal the broken phosphodiester bonds (nicks) in the DNA backbone?
DNA ligases.
109
What are the three distinct stages of DNA replication?
Initiation, elongation, and termination.
110
What is the name of the E. coli replication origin?
oriC.
111
How many base pairs long is the oriC sequence in E. coli?
245 bp.
112
What is the key initiator protein that binds to oriC?
DnaA protein.
113
What is the specific A-T rich region in the origin where strand separation occurs?
The DNA unwinding element (DUE).
114
Why is the DUE region rich in A-T base pairs?
Because A-T pairs have only two hydrogen bonds, making them easier to separate.
115
Which protein loads the replicative helicase onto the separated DNA strands?
DnaC protein.
116
How many DnaB helicase hexamers are loaded at the origin?
Two (one for each strand).
117
Which specific topoisomerase relieves topological stress ahead of the E. coli replication fork?
DNA gyrase (topoisomerase II).
118
Which enzyme regulates replication timing by methylating oriC?
Dam methylase.
119
What specific sequence and nucleotide does Dam methylase target?
It methylates the N6 position of adenine in the sequence (5') GATC.
120
In what physical conformation is the lagging strand template arranged to coordinate synthesis with the leading strand?
It is looped.
121
What is the function of the clamp-loading complex in DNA polymerase III?
It links core polymerases and loads beta subunits onto the lagging strand.
122
Which two enzymes can remove RNA primers during bacterial replication?
DNA polymerase I and RNase H1.
123
What molecular switch regulates the activity of the DnaA protein?
ATP hydrolysis.
124
Which nucleotide-bound state of DnaA is active for initiation?
The ATP-bound form.
125
What defines a permanent change in the cellular DNA sequence?
A mutation.
126
What is the inherent error rate of DNA polymerases before proofreading occurs?
One incorrect nucleotide per 10^4 to 10^5 correct ones.
127
What is the proteolytic fragment of DNA Pol I called that retains proofreading but lacks 5'-3' exonuclease activity?
The Klenow fragment.
128
Which phase of DNA replication is the only one known to be stringently regulated?
Initiation.
129
Which E. coli gene encodes the polymerization subunit of DNA polymerase III?
polC (or dnaE).
130
Which subunits make up the core of DNA polymerase III?
The alpha, epsilon, and theta subunits.
131
Which specific subunit of DNA Pol III houses the primary polymerization activity?
The alpha subunit.
132
Which specific subunit of DNA Pol III houses the proofreading exonuclease activity?
The epsilon subunit.
133
What is the specific name of the replicative helicase protein in E. coli?
DnaB protein.
134
What is the specific name of the primase enzyme in E. coli?
DnaG protein.
135
How many base pairs long is the entire E. coli chromosome?
4,641,652 bp.
136
What is the form of bacteriophage lambda DNA when replicating inside a host cell?
A circular double helix (replicative form).
137
What type of DNA molecules exist in chloroplasts?
Circular duplexes (cpDNA).
138
What bioengineered tool uses yeast replication mechanics to carry large DNA fragments?
Yeast artificial chromosomes (YACs).
139
What three components are required to construct a stable artificial linear chromosome?
A centromere, telomeres, and replication origins.
140
Aside from hydrogen bonds, what critical factor allows DNA polymerase to discriminate between correct and incorrect incoming nucleotides?
The common geometry of standard base pairs fitting the active site.
141
What transient chemical phenomenon can lead a polymerase to insert a mismatched base?
Bases entering unusual tautomeric forms.
142
What part of human anatomy does the DNA polymerase active site physically resemble?
The palm of a hand.
143
Energetically, what is the cost of removing a mispaired nucleotide via proofreading?
The expenditure of three high-energy bonds.
144
What is the approximate polymerization rate of DNA polymerase I in vitro?
10-20 nucleotides per second.
145
Which E. coli DNA polymerases are primarily dedicated to DNA repair rather than standard replication?
DNA polymerases II, IV, and V.
146
Which subunit physically links the core polymerases within the DNA polymerase III holoenzyme?
The tau subunit.
147
How many core polymerases can be linked within a single clamp-loading complex?
Up to three.
148
Which AAA+ ATPase acts as the specific loading complex for the DnaB helicase?
DnaC protein.
149
Which DNA-binding proteins facilitate DNA bending and origin opening alongside DnaA?
HU, IHF, and FIS proteins.
150
After replication, what unique state distinguishes the newly synthesized strand from the template strand for repair enzymes?
It is transiently unmethylated (hemimethylated).
BIOMG 3300
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