Exam 2 Flashcards

1
Q

What are the pyrimidines?

A

Cytosine
Uracil
Thymine

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2
Q

What are the purines?

A

Adenine
Guanine

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3
Q

What is the only nucleotide explicit to DNA?

A

thymine

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4
Q

What is the only nucleotide explicit to RNA?

A

uracil

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5
Q

Are purines or pyrimidines a 6 atom ring?

A

pyrimidines

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6
Q

Are purines or pyrimidines a 9 atom ring with 2 rings?

A

purines

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7
Q

Why are bases insoluble in water?

A

aromaticity

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8
Q

What are nucleosides?

A

nitrogen base + sugar

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9
Q

What bond links bases to sugars in nucleosides?

A

beta–glycosidic bond

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10
Q

What number type are sugars in DNA?

A

pentose

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11
Q

_________ makes nucleosides more water soluble than free bases

A

sugars

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12
Q

What does the hydroxyl group of at the 2-position affect?

A

susceptibility to hydrolysis
secondary structure

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13
Q

Why is DNA more stable?

A

it has an H and not an OH

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14
Q

What do syn and anti nucleosides look like?

A

syn: base on same side as sugar
anti: base on opposite side as sugar

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15
Q

What are the 4 common ribonucleosides?

A
  1. cytidine
  2. uridine
  3. adenosine
  4. guanosine

(–ine)

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16
Q

What is the two and four letter symbol for deoxyadenosine?

A

dA
dAMP

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17
Q

What is the two and four letter symbol for deoxyguanosine?

A

dG
dGMP

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18
Q

What is the two and four letter symbol for deoxythymidine?

A

dT
dTMP

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19
Q

What is the two and four letter symbol for deoxycytidine?

A

dC
dCMP

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20
Q

What is the one and three letter symbol for adenosine?

A

A
AMP

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21
Q

What is the one and three letter symbol for guanosine?

A

G
GMP

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22
Q

What is the one and three letter symbol for uridine?

A

U
UMP

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23
Q

What is the one and three letter symbol for cytidine?

A

C
CMP

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24
Q

Some minor nucleosides have “methyl” in the beginning of their name; these nucleosides are an example of a _____________ marker

A

epigenetic marker

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25
Q

N6-Methyladenosine is a minor DNA nucleoside common in _________ but not found in __________?

A

bacteria
eukaryotes

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26
Q

What 2 ways are minor DNA nucleosides helpful?

A
  1. markers own DNA to protect from degradation and degrade of bacterial DNA
  2. mark genes that need to be activated
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27
Q

The minor RNA nucleoside, ____________, is found in the wobble position

A

inosine

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28
Q

What are 2 minor RNA nucleosides?

A
  1. inosine
  2. pseudouridine
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29
Q

nucleosides are ___________ for nucleic acids

A

substrates

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30
Q

What is known as the energy carrier for nucleosides?

A

5’-triphosphate

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31
Q

Where is energy stored in nucleotides?

A

phosphoric bond

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32
Q

What does GTP drive?

A

protein synthesis

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33
Q

What does CTP drive?

A

lipid synthesis

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34
Q

What does UTP drive?

A

carb metabolism

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35
Q

What do cyclic nucleotides regulate?

A

regulators of cellular metabolism
(found in all cells)

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36
Q

What are polynucleotides?

A

chains of nucleic acids

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37
Q

What bond links nucleic acids?

A

3’-5’ phosphodiester bonds

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38
Q

What is the charge of DNA’s back bone?

A

negative

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39
Q

Is DNA or RNA more stable?

A

DNA

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40
Q

What are the 5 types of RNA?

A

1.ribosomal RNA
2. messenger RNA
3. transfer RNA
4. small nuclear RNA
5. small non-coding RNA

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41
Q

What are the 2 fundamental chemical differences between DNA and RNA?

A
  1. DNA contains 2-deoxyribose instead of ribose
  2. DNA contains thymine instead of uracil
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42
Q

How does nature solve this issue of cytosine spontaneously deaminating into uracil?

A

uses thymine with a 5-methyl group to replace uracil

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43
Q

What is Chargaff’s rule?

A

A=T
G=C

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44
Q

What did Rosalind Franklin do?

A

x-ray fiber diffraction to find the helix

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45
Q

What did Watson and Crick do?

A

base pairing and double helix

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46
Q

How many hydrogen bonds does A:T have?

A

two

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47
Q

How many hydrogen bonds does G:C have?

A

three

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48
Q

What regions of DNA are most stable?

A

G:C rich regions

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49
Q

Describe the major groove of DNA

A

large enough to accommodate an alpha helix from a protein

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50
Q

How is DNA antiparallel?

A

the two stands run in the opposite direction of each other

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51
Q

What is the consequence of DNA being antiparallel?

A

complementary strands

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52
Q

Base pairing is done by ____________ bonds

A

hydrogen

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53
Q

What is the only known left-handed DNA?

A

Z-DNA

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54
Q

What is the most common DNA?

A

B-DNA

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55
Q

What DNA is dehydrated?

A

A-DNA

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56
Q

What DNA is right handed?

A

A-DNA
B-DNA

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57
Q

What are 2 ways to sequence nucleic acids?

A
  1. Chain termination (sanger)
  2. base specific chemical cleavage
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58
Q

How are dideoxynucleotides used in chain termination sequencing?

A

they are randomly added to DNA being synthesized by DNA pol causing chain termination

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59
Q

How does base specific chemical cleavage sequencing work?

A

like sanger but chain is terminated by chemical agents

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60
Q

Can the secondary structure of DNA be denatured then renatured?

A

yes

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61
Q

what is reeannealing?

A

reassociation of the DNA strands into double helix

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62
Q

The rate of re-association is___________ proportional to genome complexity

A

inversely

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63
Q

What is the tertiary structure of DNA?

A

supercoils

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64
Q

What is the job of topoisomerase?

A

relaxing supercoils

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65
Q

o

A

o

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66
Q

What is the difference between toroidal and interwound supercoils?

A

toroidal: spirals out
interwound: spirals in

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67
Q

how do you find linking number?

A

L = twists + writhe

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68
Q

What are twists and writhes?

A

twists: number of helical turns
writhe: number of times helix crosses over on itself

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69
Q

_________ super coils makes it easier for DNA to unwind

A

negative

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70
Q

How is torsional stress on molecules resovled?

A

DNA is unwound

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71
Q

What is a type of topoisomerase?

A

gyrase

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72
Q

what does DNA gyrase do?

A

introduce negative supercoils

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73
Q

What are bacterial DNA gyrase inhibitors known for?

A

antibiotics

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74
Q

Supercoiled DNA in a torodial form wraps around ____________-

A

protein spools

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75
Q

What is an an example of a protein spool?

A

histones

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76
Q

What are the 3 parts of a chromosome?

A
  1. origin of replication
  2. two telomeres
  3. centromere
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77
Q

_________ is the genetic material for cellular organisms

A

DNA

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78
Q

Why is DNA replication semiconcervative?

A

the replication DNA is made of one new strand and one old strand

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79
Q

What did Meselson and Stahl’s experiment prove?

A

DNA replication is semiconservative
N14 and N15 created mixed strands

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80
Q

How is DNA replication bidirectional?

A

two replication forks which move in opposite directions

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81
Q

How id DNA replication semi-discontinous?

A

one strand synthesizes smoothly and one in fragments (lagging)

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82
Q

What does DnaA do in bacterial DNA replication?

A

initiator

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83
Q

What does DnaB do in bacterial DNA replication?

A

unwinds DNA

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84
Q

What does DnaG do in bacterial DNA replication?

A

primase

85
Q

What does DnaC do in bacterial DNA replication?

A

helicase inhibitor

86
Q

Where does DNA polymerase add nucleotides?

A

3’ end

87
Q

What is the purpose of 3’-5’ exonuclease activity in DNA polymerase I?

A

proof reading
removes incorrect nucleotides

88
Q

What is the purpose of 5’-3’ exonuclease activity in DNA polymerase I?

A

removes primer

89
Q

What fixes the nick between Okazaki fragments during DNA replication?

A

DNA ligase

90
Q

DNA polymerase III uses an _________ primer for DNA synthesis

A

RNA primer

91
Q

What is the “real” DNA polymerase for bacteria?

A

DNA polymerase III

92
Q

What is special about the beta subunit of bacterial DNA polymerase III?

A

it forms a ring around DNA

93
Q

supercoiling must be compensated by ___________

A

DNA gyrase

94
Q

why do eukaryotes have multiple origins of replication?

A

there are so many genes

95
Q

The earlier in S phase the DNA is replicated the ________ condensed it is

A

less condensed

96
Q

What was identified as the origin of replication identified in yeast?

A

ARS (autonomously replicated sequence)

97
Q

What is ORC?

A

origin of replication

98
Q

o

A

o

99
Q

What does MCM, Cdt1 and Cdc6 do in DNA replication?

A

loads helicase

100
Q

At ORC what is formed to start DNA replication?

A

Pre-RCs (prereplication complex)

101
Q

______ proteins are replication licensing factors

A

MCM

102
Q

__________ complexes control cell cycle

A

cyclin-Cdk

103
Q

What are the 3 major cyclin types?

A
  1. G1/S-cyclin-Cdks
  2. S-cyclin-CDKs
  3. M-cyclin-CDKs
104
Q

What does G1/S-cyclin-Cdks trigger?

A

trigger progression through the start checkpoint

105
Q

What does S-cyclin-CDKs trigger?

A

trigger DNA replication

106
Q

What does M-cyclin-CDKs trigger?

A

triggers mitosis

107
Q

What does the inactive state of Cdk look like?

A

T loop

108
Q

What does the partially active state of Cdk look like?

A

cyclin is bound

109
Q

What does the active state of Cdk look like?

A

Cdk is phosphorylated

110
Q

Checkpoints of the cell cycle depend on ________ and ________

A

cyclin and Cdk

111
Q

DNA replication occurs _______ per cell cycle

A

once

112
Q

What are the two steps to ensure only one DNA replication per cell cycle?

A
  1. licensing of replication (late M or early G1)
  2. activation of replication (S phase)
113
Q

What did cell-fusion experiments give evidence of?

A

re-replication block

114
Q

_____ phase cytoplasm contains all the factors needed to drive G1 nucleus to DNA synthesis

A

S phase

115
Q

What are the 3 mechanisms that prevent re-replication?

A
  1. inhibition of MCM2-7 loading by geminin
  2. replication-dependent Cdt-1 degradation
  3. Cdk-dependent inhibition pf pre-RC formation
116
Q

What are the two challenges of tightly packed DNA for replication?

A
  1. DNA template needs to be accessed
  2. nucleosomal organization has to be reproduced on daughter strands
117
Q

What does PCNA do in chromatin restoration?

A

sliding clamp that scans for damage

directs DNA methylation

118
Q

What is endoreduplication?

A

DNA replication without cytokinesis

119
Q

___________ is replication of DNA with completion of mitosis but not cytokinesis

A

polyploidy

120
Q

___________ is repeated replication of DNA without forming new nuclei

A

polyteny

121
Q

What enzyme maintains telomere length?

A

telomerase

122
Q

Telomerase uses an internal ______ template

A

RNA

123
Q

telomerase uses _______ transcriptase activity

A

reverse transcriptase

124
Q

What cell type lacks telomerase causing shortening telomeres?

A

somatic

125
Q

What did Howard Temin discover?

A

RNA-directed DNA polymerase (reverse transcriptase)
DNA is an intermediate in RNA tumor virus replication

126
Q

What is RNA-directed DNA polymerase also known as?

A

reverse transciptase

127
Q

What are the three enzymes involved in reverse transcriptase?

A
  1. RNA-directed DNA polymerase
  2. RNase H
  3. DNA-directed DNA polymerase
128
Q

What does DNA-directed DNA polymerase do in reverse transcriptase?

A

makes DNA duplex (seconda DNA strand) after RNase H destroys the viral genome (RNA removed)

129
Q

What does RNase H do in reverse transcriptase?

A

degrades RNA in the DNA:RNA hybrids

130
Q

All RNA tumor viruses contain ____________

A

reverese transcriptase

131
Q

What has reverse trancriptase aided in the treatment of?

A

AIDs

132
Q

What is the process of reverse transcriptase?

A

complementary DNA is synthesized using a strand of RNA

133
Q

An _________ primer is required for reverse transcriptase

A

unusual primer

134
Q

What was the first approved drug/nucleoside to treat aids?

A

AZT

135
Q

What substrate of AZT binds to HIV reverse transcriptase?

A

AZTTP

136
Q

___________ recombination involves similar DNA sequence

A

homologous

137
Q

____________ recombination involves very different nucleotides sequences

A

non-homologous

138
Q

_________________ is the enzymatic insertion of transposon

A

transposition

139
Q

________________ and ______________ play a significant role in evolution

A

non-homolgous recombination
transpositions

140
Q

What did Meselson and Weigle’s experiment show?

A

recombination of chromosomes (using heavy and light phages)

141
Q

What are the 6 steps of Holliday Model Homologous Recombination?

A
  1. SYNAPSIS – two homologous DNA duplexes align
  2. SINGLE STRAND NICK
  3. STRAND INVASION – partial strand unwinding
  4. LIGATION – Holliday junction created
  5. BRANCH MIGRATION – unwinding then rewinding of two duplexes
  6. STRAND EXCHANGE – nick introduced to fix Holliday junction
142
Q

What enzyme initiates the Holliday model and makes a nick and unwinds the DNA?

A

RecBDC

143
Q

What enzyme is responsible for strand invasion in the Holliday model?

A

RecA

144
Q

What enzyme is responsible for branch migration in the Holliday model?

A

RuvA RuvB

145
Q

What enzyme is responsible for strand exchange?

A

RuvC

146
Q

What enzyme has helicase, nuclease, and ATPase activity?

A

RecBCD

147
Q

What is a x (chi) site?

A

recombinational hotspot

148
Q

Why do bunny ears form when RecBCD unwinds DNA?

A

the rate of unwinding is faster than the rate of ssDNA release

149
Q

What enzyme in the Holliday Model aids in homologous pairing?

A

RecA

150
Q

RecA forms a __________ with a groove to accommodate the ssDNA

A

helical filament

151
Q

Once RecA:ssDNA complex is bound what happens?

A

it binds to dsDNA to search for a homologous region

152
Q

What is the loop called made by RecA in strand invasion of Holliday model?

A

D loop

153
Q

What class of enzymes solve the Holliday junction?

A

Ruv

154
Q

What Ruv cleaves the Holliday junction to fix it?

A

RuvC

155
Q

Gene transfer techniques make it possible to introduce genes into animals by _________

A

transfection (transgenic animals)

156
Q

What did Barbara McClintock discover?

A

transposons

157
Q

What are class I transposons called?

A

retrotransposons

158
Q

What is the phrase used to describe class I (retrotransposons) transposons?

A

copy and paste

159
Q

What are class II transposons called?

A

DNA transposons

160
Q

What is the phrase used to describe class II (DNA transposons) transposons?

A

cut and paste

161
Q

How do class I (retrotransposons) work?

A

RNA is reverse transcribed into DNA and DNA is inserted back into genome in a new spot

162
Q

What class of transposons require RNA intermediate?

A

Class I (retrotransposons)

163
Q

What are transposase?

A

target sequence for transposons

164
Q

Can RNA and DNA have mutations?

A

yes

165
Q

Mutations are usually ________ to gene function

A

deleterious

166
Q

Are mutations usually recessive or dominant?

A

recessive

167
Q

Can DNA be replaced?

A

No, so it must be fixed

168
Q

What does the Ames test indicate?

A

the mutagenic potential of a chemical

169
Q

How does the Ames test work?

A

Bacteria with a mutation causing no HIS production so the bacterial will not be able to grow without HIS in environment
The bacteria is introduced to a chemical that mutates the HIS gene and now it can grow even without the presence of HIS

170
Q

What are 3 major DNA repair systems?

A
  1. double stranded breaks
  2. direct reversal
  3. single-stranded damage repair
171
Q

Why is double stranded breaks a dangerous DNA repair system?

A

the broken of strands cannot be recovered

172
Q

How does the DNA repair system, direct reversal work?

A

chemical reactions reverse the damage of DNA

173
Q

What does the DNA repair system, single-stranded damage repair, rely on to guide repair?

A

complementary strand

174
Q

What are 3 examples of single strand damage repair?

A
  1. mismatch repair
  2. base excision reapir
  3. nucleotide excision repair
175
Q

What mechanism does double stranded DNA breaks use to repair?

A

NHEJ

176
Q

In NHEJ for double stranded breaks, what enzyme recruits the two exposed ends?

A

Ku70/80

177
Q

double stranded break repairs cause _________ to form when its HOMOLOGOUS DNA recombination

A

D loops

178
Q

pyrimidine dimers can be repaired by __________

A

photolyase

179
Q

In base excision repair, __________ removes damaged bases creating _________

A

DNA glycosylase
AP sites

180
Q

How do AP endonucleases reverse chemical damage?

A

cleave DNA backbone so that exonuclease can remove several residues and new ones added

181
Q

What repair system repairs large regions not just bases?

A

nucleotide excision repair

182
Q

What does photolyase break to fix chemical mutations?

A

rings

183
Q

Base excision repair uses specific ______________

A

DNA glycosylases

184
Q

What is an AP site?

A

where DNA glycosylase has removed damaged nucleotides

185
Q

Why is uracil glycosylase important?

A

removes U from DNA because C spontaneously deaminates into U

186
Q

What polymerase synthesizes new DNA at AP sites?

A

DNA pol I

187
Q

What enzyme seals AP sites?

A

DNA ligase

188
Q

__________ remove DNA segments for nucleotide excision repair?

A

excinuclease

189
Q

Nucleotide excision repair in bacteria uses _________ exinucleases

A

ABC

190
Q

Do human or bacteria have larger sections removed in nucleotide excision repair?

A

humans

191
Q

Mismatch repair systems _______ DNA duplexes for mismatched bases

A

scans

192
Q

How do repair enzymes know which strand is correct in bacterial methyl-directed mismatch repair?

A

The errors will be in unmethylated sections

193
Q

What proteins are involved in bacteria methyl-directed mismatch repair?

A

Mut

194
Q

Why is Nitrosoguanidine used in labs?

A

mutagen in labs

195
Q

Mutations in the ____________ cause Meier-Gorlin syndrome

A

pre-replication complex

196
Q

Do DNA polymerases require primers?

A

yes

197
Q

What DNA polymerase lengthens Okazaki framgents?

A

DNA polymerase I

198
Q

What DNA polymerase removes primers?

A

DNA polymerase I

199
Q

Which DNA polymerase is very processive?

A

DNA polymerase III

200
Q

Which DNA polymerase is specific for the lagging strand in bacteria?

A

DNA polymerase I

201
Q

DNA polymerase III can work on _______ strands in bacteria

A

both

202
Q

What DNA polymerase fills in Okazaki fragments in eukaryotes?

A

DNA polymerase I

203
Q

In eukaryotes, the epsilon subunit of DNA polymerase I works of the ________ strand

A

leading

204
Q

In eukaryotes, the delta subunit of DNA polymerase I works of the ________ strand

A

lagging

205
Q

What DNA polymerase was the first discovered?

A

I

206
Q

Which DNA polymerase has 5’-3’ and 3’-5’ exonuclease activity?

A

DNA polymerase I

207
Q

Is DNA polymerase III found in eukaryotes?

A

No only in prokaryotes

208
Q

Which DNA polymerase is enormously processive?

A

DNA polymerase III

209
Q

Which DNA polymerase has the beta subunit ring?

A

DNA polymerase III