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BIOL 3020 > Powerpoints & Study Guides > Flashcards

Powerpoints & Study Guides Flashcards

1
Q

DNA replication requires what enzymes?

A

helicase, primase, DNA polymerase, DNA ligase, topoisomerase

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2
Q

Small genomes have

A

a single replication origin

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3
Q

DNA is synthesized in what direction?

A

5’ to 3’

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4
Q

What is a dNTP?

A

a building block and energy source for a polymerase catalyzed reaction

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5
Q

DNA primase is

A

an RNA polymerase

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6
Q

What does primase do?

A

Initiates DNA replication by laying down an RNA primer

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7
Q

What does helicase do?

A

unwinds parental DNA

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8
Q

What does topoisomerase do?

A

takes the supercoils out of the parental DNA molecule

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9
Q

Before the fork, which enzyme is first?

A

topoisomerase

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10
Q

E. coli DNA polymerase III is

A

the main DNA synthesis enzyme

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11
Q

E. coli DNA polymerase III makes

A

the leading strand and Okazaki fragments

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12
Q

E. coli DNA polymerase has ___ activity

A

3’ to 5’

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13
Q

What is the point of 3’ to 5’ exonuclease activity?

A

corrects 99% of errors of polymerase

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14
Q

E. coli DNA polymerase I is the

A

DNA repair polymerase

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15
Q

E. coli DNA polymerase I has both

A

5’ to 3’ and 3’ to 5’ exonuclease activity

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16
Q

What is the point of 5’ to 3’ exonuclease activity?

A

removes RNA primers

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17
Q

What does DNA ligase do?

A

seals gap in sugar-phosphate backbone left behind by DNA polymerase I

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18
Q

DNA polymerase binds as a

A

dimer

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19
Q

From the origin, replication proceeds bidirectionally, yielding

A

two replication forks

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20
Q

Bacterial chromosomes have how many replication origins?

A

1

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21
Q

What’s the special DNA sequence found at the origin of replication?

A

A-T rich region

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22
Q

There are more/fewer DNA polymerases in eukaryotes than in prokaryotes

A

More

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23
Q

The DNA pol a/primase complex synthesizes

A

a short RNA/DNA hybrid

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24
Q

Telomerase is

A

a DNA polymerase

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25
Q

What does telomerase do?

A

carries an internal RNA template that directs the synthesis of nucleotide repeats

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26
Q

DNA in eukaryotic chromosomes is

A

wrapped around histones (H2A, H2B, H3 and H4)

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27
Q

Germ-line mutations affect

A

the entire organism

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28
Q

Can germ-line mutations be passed on?

A

Yes

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29
Q

Somatic mutations affect

A

a patch - the earlier the mutation, the larger the patch

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30
Q

Can somatic mutations be passed on?

A

No

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31
Q

Aneuploidy is when there are

A

too few or too many chromosomes

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32
Q

A point mutation is

A

a change in a single base pair

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33
Q

What is a transition?

A

It’s a type of point mutation where a pryimidine (C or T) changes to another pyrimidine or a purine (A or G) to another purine

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34
Q

What is a transversion?

A

A type of point mutation where a pyrimidine changes to a purine or vice versa

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35
Q

Are transitions or transversions more common?

A

Transitions

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36
Q

Mutations distort the

A

double helix

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37
Q

What can happen if there’s a mutation on the promoter?

A

The rate of transcription may be increased or decreased

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38
Q

What can happen if there’s a mutation on the regulatory element/operator site?

A

The gene may not be able to be properly regulated

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39
Q

What can happen if there’s a mutation on 5’ UTR/3’ UTR

A

May alter the ability of mRNA to be translated and it’s stability

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40
Q

What can happen if there’s a mutation on the splice recognition sequence?

A

May alter the ability of pre-mRNA to be properly spliced

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41
Q

What are the two most frequent spontaneous reactions that cause serious DNA damage?

A

depurination and deamination

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42
Q

What is depurination?

A

the process by which purine bases are lost because their N-glycosyl linkages to deoxyribose are spontaneously hydrolyzed

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43
Q

Where does deamination occur?

A

All bases except thymine

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44
Q

What is the most common type of deamination?

A

cytosine to uracil

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45
Q

What is deamination?

A

The loss of an amine group - is replaced with a doubly bonded oxygen

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46
Q

What is a tautomeric shift?

A

A nucleotide changes from a keto to an enol form

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47
Q

Which form is more common? Keto or enol?

A

Keto

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48
Q

What is the result of a tautomeric shift?

A

Fucked up base pairing; tautomeric shifts during DNA replication can cause mutations

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49
Q

What does TNRE stand for?

A

trinucleotide repeat expansion

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50
Q

What happens in people with TNRE disorders?

A

The length of a TNR increases above the critical size

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51
Q

What is a potential cause of TNRE?

A

DNA polymerase slipping on the template

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52
Q

What is one example of a human genetic disease caused by TNRE?

A

Huntington’s disease

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53
Q

What effect does UV light have on DNA?

A

promotes pyrimidine dimer formation (thymine dimers)

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54
Q

What effect do E-rays have on DNA?

A

can cause base deletions, single-stranded nicks in DNA, crosslinking, and chromosomal breaks

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55
Q

What are DNA adducts?

A

chemical groups that are added onto DNA as a consequence of high exposure to a mutagenic chemical

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56
Q

What are the two ways to repair double-stranded breaks?

A

Homologous recombination and non-homologous end-joining

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57
Q

What are the four ways to repair point alterations?

A

direct repair, base excision repair, nucleotide excision repair, and mismatch repair

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58
Q

What enzymes are involved in base excision repair?

A

N-glycosylase, AP endonuclease, DNA poymerase, DNA ligase

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59
Q

What complex tracks along DNA, searching for damage?

A

UvrA/UvrB complex

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60
Q

When UvrA/UvrB complex detects damage, what happens to the complex?

A

UvrA is released and UvrC binds

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61
Q

What does UvrC do with damaged DNA?

A

makes cuts on both sides of the damage

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62
Q

What does UvrD do?

A

removes the damaged DNA that UvrC just cut out

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63
Q

What enzyme fills in the gap left by UvrD?

A

DNA polymerase - DNA ligase seals the gap

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64
Q

What complex deals with mismatch repair?

A

MutS/MutL

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65
Q

Which protein finds a mismatch?

A

MutS

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66
Q

What does MutH do?

A

Binds to hemimethylated sequence and makes a cut in the nonmethylated strand. The complex binds to MutH also

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67
Q

What does MutU do?

A

Separates the DNA strands at the cleavage site

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68
Q

How does mismatch repair end?

A

DNA polymerase fills the gap left behind and DNA ligase seals it

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69
Q

What kind of mutation results in Xoderma pigmentosum?

A

Nucleotide excision repair

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70
Q

What are restriction enzymes?

A

endonucleases

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71
Q

Which class of restriction enzyme have a palindromic recognition sequence?

A

Class II

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72
Q

Restriction enzymes leave

A

blunt or sticky ends

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73
Q

Type I restriction enzymes are not used much as they are

A

complex, multi-subunit, combination restriction-and-modification enzymes, randomly cut DNA far from the recognition site

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74
Q

Type II restriction enzymes are commonly used to

A

cut DNA at defined positions close to the recognition site

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75
Q

Type III restriction enzymes are sometimes used to

A

cut outside of the recognition sequence and require two in opposite orientations within the same DNA molecule

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76
Q

Type IV restriction enzymes can recognize

A

modified (usually methylated) DNA

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77
Q

What does EcoRI do?

A

creates 4 nucleotide sticky ends with 5’ end overhangs of AATT

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78
Q

What color is a colony if it contains the insert from a recircularized vector?

A

white

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79
Q

What is Sanger DNA sequencing?

A

dideoxy method!!!

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80
Q

How does Sanger/dideoxy chain termination work?

A

the chain stops growing at a specific nucleotide that is missing a 3’ OH group

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81
Q

Tagged bases randomly terminate

A

chains at specific nucleotides, denoted by a specific label (color)

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82
Q

What 4 things are needed for PCR?

A

Template DNA, Oligonucleotide primers, deoxynucleoside triphosphates (dNTPs), and Taq polymerase

83
Q

What are oligonucleotide primers?

A

Complementary to sequences at the ends of the DNA fragment to be amplified

84
Q

What are the super vague steps of PCR?

A

Denaturation (double stranded DNA + heat = single strands), primer annealing (lower temperature), extension

85
Q

How many copies of DNA can be made with PCR?

A

a shit ton. like a billion

86
Q

What is gene editing?

A

The process by which a specific, predetermined modification is made to DNA in living cells

87
Q

Gene editing using what type of double stranded break repair?

A

Homologous recombination

88
Q

What are the three classes of programmable nucleases to make breaks?

A

Zinc finger nucleases, TALENs, and CRISPR

89
Q

What’s the point of targeted mutagenesis through non-homologous end-joining?

A

Introduces an insertion or deletion mutation at the break site - can cause a frameshift

90
Q

How long should a PCR primer be?

A

18-22 nucleotides

91
Q

In nucleic acids, what are connected by covalent glycosidic bonds?

A

Sugars are connected to bases by glycosidic bonds

92
Q

How is the sugar in RNA different than the sugar in DNA?

A

The sugar in DNA is missing the 2’ OH group

93
Q

How are the two strands of a DNA molecule held together?

A

hydrogen bonds between the bases

94
Q

What are the purines?

A

Adenine and guanine

95
Q

What are the pyrimidines?

A

cytosine, thymine, and uracil

96
Q

Why do DNA binding proteins usually recognize the bases through the major groove?

A

All four bases can be distinguished in the major groove

97
Q

The backbone of a DNA molecule is composed of alternating

A

sugar and phosphate groups

98
Q

Which nucleic acid contains many modified bases?

A

tRNA

99
Q

Why do the ends of all your chromosomes have the same sequence?

A

They’re synthesized by telomerase

100
Q

What type of enzyme is DNA primase?

A

RNA polymerase

101
Q

Which DNA polymerase does most of the DNA synthesis?

A

DNA polymerase III

102
Q

What is trisomy?

A

An organism has three copies of a specific chromosome

103
Q

What is triploidy?

A

An organism has three complete sets of chromosomes

104
Q

What are three things that are the same between transcription and DNA replicatin?

A

RNA and DNA are synthesized in the 5’ to 3’ direction, both require the DNA to be unwound, and both only begin at specific sites on the DNA

105
Q

For transcription, which strand is the template strand?

A

The strand that is transcribed

106
Q

The sense strand has the same sequence as the

A

transcript, except there is a U where there was a T before

107
Q

Is a primer needed for transcription?

A

No, RNA polymerase doesn’t need it

108
Q

Does transcription require helicase or topoisomerase?

A

No because only a small part of the DNA needs to be unwound at a time

109
Q

Different genes are transcribed at the same/different rate

A

different

110
Q

What are regulatory sequences (DNA)

A

site where regulatory proteins bind, influences the rate of transcription

111
Q

What is the promoter?

A

a site on the DNA for RNA polymerase to bind, which signals the beginning on transcription

112
Q

What is the ribosome-binding site on mRNA?

A

the site where the ribosome binds; translation begins near this site

113
Q

What is the start codon?

A

specifies the first amino acid in a polypeptide sequence

114
Q

What does it mean to be polycistronic?

A

When an mRNA encodes 2+ polypeptides

115
Q

E. coli promoter region includes

A

-35 sequence to +1 transcriptional start site

116
Q

What does the sigma factor do?

A

Recognizes a promoter as it slides along the DNA with RNA polymerase

117
Q

The Rho protein is

A

a helicase

118
Q

What is a constituitive gene?

A

The gene is expressed at a pretty constant level all the time

119
Q

Transcriptional regulation is the most common way to

A

regulate gene expression

120
Q

Repressors bind to ___ and ___ transcription

A

DNA, inhibit

121
Q

Repressors are an example of ___ control

A

negative

122
Q

Activators bind to ___ and ___ transcription

A

DNA, increase

123
Q

Activators are an example of ___ control

A

Positive

124
Q

Small effector molecules bind to

A

regulatory proteins (repressors and activators)

125
Q

What are three types of small effector molecules?

A

Inducers, co-repressors, and inhibitors

126
Q

Corepressors activate

A

repressors - make them repress MORE

127
Q

Inhibitors inhibit

A

activators - makes an activator not work, so no transcript is made

128
Q

What’s an operon?

A

A regulatory unit consisting of a few structural genes under the control of one promoter

129
Q

What are the conditions for efficient utilization of lactose?

A

Lactose is present and glucose is absent

130
Q

What are the three structural genes of the lac operon?

A

lacZ, lac Y, and lacA

131
Q

What does lacZ encode?

A

B-galactosidase

132
Q

What does lacY encode?

A

lactose permease

133
Q

What does lacA encode?

A

transacetylase

134
Q

Four DNA elements of the lac operon

A

Promoter, operator, CAP site, and terminator

135
Q

What does B-galactosidase do?

A

cleaves lactose and lactose analogues, converts lactose to allolactose

136
Q

What does lactose permease do?

A

it’s a membrane protein required for transport of lactose and analogues into the cell

137
Q

What is the lacI gene?

A

it encodes the lac repressor and has it’s own promoter (i promoter)

138
Q

The lac operon is ___ and ___ regulated

A

negatively, positively

139
Q

The lac operon is inducible by

A

lactose, CAP-cAMP

140
Q

What happens to cAMP levels when glucose is around?

A

They decrease

141
Q

Lactose is present, glucose is not

A

cAMP is high
Repressor is off
Activator is on
Yes transcription

142
Q

No Lactose, no glucose

A

cAMP is high
Repressor is on
Activator is on
No transcription

143
Q

Lactose is present, glucose is present

A

cAMP is low
Repressor is off
Activator is off
No transcription

144
Q

Glucose is present, no lactose

A

cAMP is low
Repressor is on
Activator is off
No transcription

145
Q

The lac operon is only expressed when

A

the repressor is off and the activator is on

146
Q

A loop in the DNA brings what sites closer together?

A

Operator sites

147
Q

Five structural genes of the trp operon

A

trpE, trpD, trpC, trpB, and trpA

148
Q

Regulatory genes of the trp operon

A

trpR (repressor) and trpL (encodes the leader peptide)

149
Q

High typtophan levels cause

A

attenuation

150
Q

The promoter for eukaryotic transcription is

A

the TATA box and variable sets of additional DNA elements

151
Q

What proteins are required for initiation in eukaryotic transcription?

A

basal transcription factors (lots)

152
Q

RNA processing that occurs in prokaryotic transcription

A

none

153
Q

RNA processing that occurs in eukaryotic transcription

A

capping, polyadenylation, and splicing

154
Q

RNA polymerase I transcribes

A

45S pre-rRNA in the nucleolus

155
Q

RNA polymerase II transcribes

A

mRNA, snRNA, miRNA in the nucleus

156
Q

RNA polymerase III transcribes

A

tRNA, 5S rRNA in the nucleus

157
Q

Prokaryotic Pribnow box

A

-10 TATAAT

158
Q

TFIID is a complex of

A

proteins, includes TATA binding proteins (TBP) and TAFs

159
Q

TFIID binds to

A

TATA box

160
Q

What binds after TFIID binds to TATA box (second step)?

A

TFIIB binds

161
Q

What does TFIIB do?

A

Acts as a bridge to bind RNA polymerase II and TFIIF

162
Q

What forms the preinitiation/closed complex?

A

TFIIE and TFIIH binding to RNA polymerase II

163
Q

TFIIH forms

A

an open complex, phosphorylates CTD domain

164
Q

True or false: enhancers are close to the basal promoter

A

false

165
Q

Activators bind to

A

enhacers

166
Q

TATA binding protein binds to the TATA box and causes these two changes in DNA structure

A

two bends and a region of unwinding between them

167
Q

Two main jobs of TFIIH

A

unwinds DNA helix, Cdk7 phosphorylates the carboxy terminal domain of RNA polymerase II

168
Q

Where can enhancers not be located?

A

In the promoter proximal region

169
Q

Transcription activation domains work by recruiting

A

RNA polymerase II to basal promoter through interactions with general transcription factors

170
Q

Co-activators are

A

non-DNA binding proteins that serve as bridges between activators and the basal transcriptional machinery

171
Q

What does the Id protein do?

A

produced during early stages of development, prevents MyoD from promoting muscle differentiation too soon

172
Q

Without Id, what happens to MyoD?

A

Forms heterodimers with bHLH factors, allowing the heterodimer to bind to enhancer in the promoters of muscle-specific genes

173
Q

Changes in chromatin structure affect

A

transcription

174
Q

4 types of changes that occur in chromatin structure

A

DNA methylation, nucleosome spacing changes, nucleosome replacement, and histone modification

175
Q

Methylation can inhibit

A

the binding of activators - methyl group blocks the binding of an activator to an enhancer

176
Q

Where does methylation occur?

A

CpG island

177
Q

Nucleosome spacing changes affect

A

the relative spacing and/or positions and/or number of nucleosomes

178
Q

How does histone acetylation affect the strength of DNA binding?

A

Weakens it - DNA is less tightly bound to acetylated histones

179
Q

The affects of methylation of histones on transcription depend on

A

which histone is methylated and where

180
Q

Are histone modifications reversible?

A

Yes

181
Q

What’s the role of the mediator?

A

Brings activator proteins that bind to more distant regulatory sequences of the DNA in contact with the initiation complex - binding of the mediator triggers phosphorylation of the CTD

182
Q

What are the four DNA-binding domains?

A

Helix-turn-helix, helix-loop helix, zinc finger, and leucine zipper

183
Q

In eukaryotes, what event triggers the conversion of the “closed complex” to an “open complex” and the start of transcription?

A

Phosphorylation of the CTD of RNA polymerase II

184
Q

What type of histone modification can inhibit transcription?

A

Methylation and deacetylation

185
Q

Name one example of a protein that binds DNA and bends it

A

restriction enzymes, TBP

186
Q

In prokaryotic RNA, a hairpin structure followed by a strong of Us causes what?

A

termination of transcription

187
Q

What protein is involved in termination in prokaryotes?

A

Rho

188
Q

Which DNA strand is transcribed?

A

Template strand

189
Q

What enzyme modifies histones?

A

Histone acetylase

190
Q

If the template strand is 5’ GCCGCC 3’ what is the mRNA?

A

5’ GGCGGC 3’

191
Q

What is the DNA region that contains binding sites for specific transcription factors?

A

promoter proximal region

192
Q

3 different splicing mechanisms

A

Group I intron splicing, Group II intron splicing, spliceosome

193
Q

Ribosomal RNAs are cleaved out of

A

precursor RNA

194
Q

1st step of mRNA processing

A

5’ cap

195
Q

What is added to the 5’ end of pre-mRNA?

A

non-templated G residue

196
Q

1st step of the formation of the 5’ cap

A

a phosphatase removes a phosphate from 5’ end

197
Q

2nd step of the formation of the 5’ cap

A

guanylyl transferase adds GMP as a 5’-5’ triphosphate linkage

198
Q

3rd step of the formation of the 5’ cap

A

G is modified by methyl transferases - adds methyl groups

199
Q

2nd step in mRNA processing

A

3’ polyadenylation

200
Q

What are the two polyadenylation factors?

A

CPSF and CStF

201
Q

What does the 5’ cap do?

A

protects the 5’ end from 5’ to 3’ nucleases

202
Q

What does the poly A tail do?

A

protects the 3’ end from 3’ to 5’ nucleases

203
Q

3rd step in mRNA processing

A

splicing

204
Q

What occurs in splicing?

A

precursor RNA is made into a mature RNA and the intron is released

BIOL 3020 (2 decks)

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