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Spring 2015 > Block 4 Biochem part 1 > Flashcards

Block 4 Biochem part 1 Flashcards

1
Q

who discovered that DNA is the source of heritable info?

A

oswald avery

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2
Q

who noticed the relationship btw AT and GC?

A

erwin chargaff

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3
Q

most common conformation of DNA

A

B DNA

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4
Q

dehydrated form of DNA

A

A DNA

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5
Q

form of DNA thought to help relieve stress of the helix around a transcription complex

A

Z DNA

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6
Q

Which enzyme binds the origin of replication in prokaryotes?

A

DnaA

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7
Q

how do bacteria regulate DNA replication?

A

they only make enough DNAA for 1 replication

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8
Q

what unwinds the DNA in prokaryotes?

A

helicase

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9
Q

what breaks the phosphodiester backbones to relieve supercoiling in prokaryotes?

A

Topoisomerase I

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10
Q

what makes clean breaks through both strands of DNA to unknot it?

A

Topoisomerase II

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11
Q

Main enzyme that copies DNA in prokaryotes

A

DNA pol III`

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12
Q

which enzyme in prokaryotes has 3’–>5’ exonuclease activity for proofreading?

A

DNA pol III

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13
Q

what does DNA pol I do?

A

in prokaryotes, it excises the RNA primer and adds DNA

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14
Q

what is the eukaryotic equivalent of DNA pol I?

A

Fen-1 nuclease and RNase H

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15
Q

what does DNA ligase do?

A

in prokaryotes it ensures all phosphodiester bonds are formed

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16
Q

Polymerase alpha-

A

contains primase and initiates DNA synthesis

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17
Q

Polymerase delta-

A

synthesizes lagging strand (okizaki fragments) Has 3’–>5’ exonuclease activity

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18
Q

polymerase epsilon-

A

synthesizes leading strand, has 3’–>5’ exonuclease activity

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19
Q

polymerase beta-

A

repairs DNA. cannot excise ribonucleotides or proofread

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20
Q

polymerase gamma-

A

replicates mitochondrial DNA

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21
Q

the hexameric sequence of telomeres is:

A

AGGGTT

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22
Q

which end of a DNA strand does telomerase elongate?

A

the 3’ end

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23
Q

After telomerase elongates a 3’ end, ____ puts on a new primer at the end of the 3’ telomere, _____ extends fills in the nucleotides, and _____ removes the RNA primer

A
  • primase
  • DNA pol delta
  • FEN1 exonuclease
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24
Q

what nucleosides are often used to inhibit DNA synthesis?

A

AZT and 2’,3’ dideoxyinosine

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25
Q

most common base excision repair-

A

correcting deaminated cytosines

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26
Q

mismatch-directed DNA repair is mediated by ______

A

Mut proteins

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27
Q

Mut proteins work under the assumption that:

A

the template strand contains the correct base

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28
Q

in E. coli, the template strand is identified by:

A

methylation of adenine residues

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29
Q

in eukaryotes, the template strand is identified by:

A

being the “un-nicked strand”

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30
Q

_____ nicks the strand at mismatched nucleotides and _____ removes the them

A
  • endonuclease

- exonuclease

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31
Q

mutations in Mut proteins is associated with __________

A

hereditary nonpolyposis colorectal cancer (Lynch syndrome)

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32
Q

homologous repair of a double stranded DNA break is achieved using _____ for a template and ______ genes for repair.

A
  • sister chromatid

- BRCA 1 and 2

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33
Q

non homologous double stranded DNA breaks are fixed by ______ but are very error prone

A

DNA ligase

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34
Q

thymine dimers caused by UV light are excised in a process known as __________

A

nucleotide excision repair

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35
Q

what do XP proteins do?

A

fix thymine dimers

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36
Q

Cockayne syndrome-

A

CSA and CSB mutations causing neurological symptoms

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37
Q

are skin cancers common in Cockayne syndrome?

A

no

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38
Q

Mutation in ____ gene can manifest as either cockayne or xeroderma pigmentosum, or a blend of both

A

XPD

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39
Q

which genetic disease is closely related to XP, although manifests differently?

A

cockayne syndrome

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40
Q

the 5 classes of histones:

A

H1, H2A, H2B, H3, H4

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41
Q

what does the H1 histone do?

A

binds linker DNA, it is the stabilizer

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42
Q

constitutive vs facultative heterochromatin:

A

constitutive is heterochromatin in all cell types, facultative has cell specific expression (ability to turn genes on or off)

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43
Q

when a gene is switched on the histones are acetylated/unacetylated?

A

acetylated

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44
Q

when a gene is switched on, the cytosines are methylated/unmethylated?

A

unmethylated

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45
Q

polycistronic mRNA-

A

carries info for more than one gene

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46
Q

how is uracil different from thymine-

A

uracil lacks a methyl group at the 5’ position

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47
Q

how is RNA different from DNA-

A

RNA has 2’ OH group while DNA just has 2’ H

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48
Q

do eukaryotes have poly or monocistronic mRNA?

A

mono

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49
Q

both eukaryotes and prokaryotes mRNA have these 2 untranslated regions which are for stability and initiation of protein synthesis

A

5’ and 3’ untranslated regions

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50
Q

Besides the untranslated regions, what structural characteristics do eukaryotic mRNA have? (2)

A

poly A tail and 5’ cap

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51
Q

the most abundant type of RNA in a cell

A

rRNA

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52
Q

rRNA acts like an _____

A

enzyme

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53
Q

rRNA acts like an _____, so it is also known as ______

A

enzyme; ribozyme

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54
Q

what does miRNA do?

A

inhibits protein synthesis

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55
Q

what does miRNA do?

A

inhibits protein synthesis

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56
Q

what is the core enzyme of sigma factor made up of:

A

2 alpha, 2 beta subunits

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57
Q

role of sigma factor in RNA polymerase

A

provides specificity to RNA pol to recognize the promoter sequence

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58
Q

2 characteristic DNA consensus sequences in prokaryotic promoter-

A

-35 sequence and the Pribnow box (-10 seq.)

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59
Q

when does RNA pol open up DNA for transcription?

A

when it binds to the promoter sequence (unwinds about 14 bp)

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60
Q

when does RNA pol open up DNA for transcription?

A

when it binds to the promoter sequence (unwinds about 14 bp)

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61
Q

abortive transcripts-

A

several short pieces of RNA that are generated at the beginning of transcription then discarded

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62
Q

what must happen for the prokaryotic RNA pol to break away from initiation site and transcribe?

A

sigma factor must be released

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63
Q

rho independent termination depends on-

A

the sequence of the nascent RNA species

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64
Q

how does prokaryotic rho independent termination work?

A

RNA sequence is self complementary and capable of base pairing with itself to generate a hairpin structure, followed by a series of U bases.

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65
Q

why does rho independent termination form a poly U tail at the end?

A

U forms the weakest of bonds and facilitates removal of the RNA from the DNA template strand

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66
Q

Prokaryotic Rho dependent termination requires-

A

help of rho protein and ATP

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67
Q

what is Rho?

A

hexameric ATPase with helicase activity.

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68
Q

how does prokaryotic rho dependent termination work?

A

rho binds to the rho recognition site near the 3’ end of nascent RNA strand and moves along the RNA strand until it riaches the polymerase (which is paused at the termination sequence) then rips the RNA strand from the DNA template

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69
Q

Rifampicin MOA-

A

inhibits initiation of transcription by blocking prokaryotic RNA pol from progressing with initiation

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70
Q

why does rifampicin not stop eukaryotic transcription?

A

eukaryotic RNA pol does not have a beta subunit

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71
Q

Dactomycin MOA-

A

inhibits elongation of transcription

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72
Q

RNA pol I-

A

eukaryotic; transcribes rRNA

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73
Q

RNA pol II-

A

eukaryotic; transcribes mRNA

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74
Q

RNA pol III-

A

eukaryotic; transcribes mostly tRNA and snRNA

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75
Q

prokaryotes only have one transcription factor, but eukaryotes have 6-

A

TFIIA,B,D,E,F,H

76
Q

prokaryotes only have one transcription factor, but eukaryotes have 6-

A

TFIIA,B,D,E,F,H

77
Q

Eukaryotic promoters-

A 
CAAT box (80 bases upstream) and TATA box (25 bases upstream)
*sometimes a GC rich region
78
Q

eukaryotic RNA pol does not directly contact ____

A

DNA

79
Q

TFIID-

A

recognizes and binds the TATA box

80
Q

TFIIF-

A

interacts with and recruits RNA pol II to the promoter

81
Q

TFIIH-

A

contains helicase activity to unwind the DNA at the transcription start site

82
Q

3 eukartyotic TF’s needed to recognize promoter and recruit RNA pol II

A

TFIID,F,H

83
Q

Eukaryotic transcription enhancers-

A

-Cis acting elements upstream or downstream of transcription start site (can be up to a few thousand bases away and can occur on either strand of DNA)

84
Q

how do eukaryotic enhancers work?

A

bind specific transcription factors (not the general ones) and loop or bend DNA to interact with transcription initiation complex at the promoter to enhance or further activate transcription

85
Q

a-amanitin MOA-

A

inhibits EUKARYOTIC RNA pol II; causes death

86
Q

a-amanitin MOA-

A

inhibits EUKARYOTIC RNA pol II; causes death

87
Q

Prokaryotic rRNAs

A

23S, 16S, and 5S

88
Q

Eukaryotic rRNAs

A

28S, 18S, 5.8S (made by RNA pol I) and 5S (made by RNA pol III)

89
Q

role of snoRNA-

A

base modification of rRNA

90
Q

eukaryotes synthesize rRNA in the _____

A

nucleolus

91
Q

after 3’ end of tRNA is trimmed off, ____ is added, forming the aminoacylation site for the addition of the amino acid

A

CCA

92
Q

what is the 5’ cap on eukaryotic mRNA?

A

it is a 7-methylguanosine attached backwards (5’–>5’ triphosphate linkage)

93
Q

capping of mRNA occurs in the ____ and methylation occurs in the _____

A
  • nucleus

- cytosol

94
Q

what enzyme adds GMP to the 5’ end of mRNA?

A

guanylyltransferase

95
Q

how is a poly A tail added to mRNA?

A

the enzyme polyadenylate polymerase recognizes the polyadenylation sequence and cleaves the RNA right after this sequence. It then adds lots of A’s

96
Q

what is the polyadenylation sequence?

A

AAUAAA

97
Q

In the splicing process, _____ form small nuclear ribonucleoprotein complexes called ______. The snRNA’s base pair with consensus sequences at the exon/intron boundaries.

A
  • snRNA

- snurps

98
Q

how do snurps remove introns?

A

2’ OH of adenosine residue on the branch site attacks phosphate at the 5’ end of the intron, forming a 2’–>5’ lariat. The newly free 3’ OH of exon 1 attachs the 5’ phosphate at the splice acceptor site, releasing the lariat and joining the 3’ end of exon 1 to the 5’ end of exon 2

99
Q

5’ end of an intron is called

A

the splice donor site

100
Q

3’ end of intron is called

A

splice acceptor site

101
Q

the 3 stop codons

A

UAG, UGA, UAA

102
Q

a disease caused by incorrect splicing

A

beta thalassemia

103
Q

an autoimmune disease against your own snRNPs

A

systemic lupus erythematosus

104
Q

How does Cystic Fibrosis occur (genetically)-

A

loss of a trinucleotide that causes loss of phenylalanine and subsequent protein misfolding

105
Q

aminoacyl tRNA synthetases-

A

specific for the amino acid and all tRNA species for the amino acid

106
Q

aminoacyl tRNA synthetases-

A

specific for the amino acid and all tRNA species for the amino acid. 20 in all

107
Q

aminoacyl-tRNA synthetase catalyzes tRNA charging by:

A

adding AMP to the amino acid, transferring the amino acid to the tRNA and releasing the AMP

108
Q

prokaryotic ribosome __S + __S = ___S

A

50S + 30S = 70S

109
Q

eukaryotic ribosome __S + __S = __S

A

60S + 40S = 80S

110
Q

prokaryotic mRNA has a ______ sequence at the 5’ end to position mRNA for translation initiation

A

Shine-Dalgarno

111
Q

How do eukaryotes find start sequence on mRNA during initiation?

A

bind to 5’ cap and scan for AUG

112
Q

the only aminoacyl tRNA inserted into the P site is-

A

met-tRNA for initiation

113
Q

recognition and recruitment of AUG to the P site is facilitated by which initiation factor?

A

IF-2

114
Q

the energy cost of adding 1 amino acid to a polypeptide chain-

A

2 ATP and 2 GTP

115
Q

which 2 things require GTP hydrolysis during translation?

A

putting a new charged tRNA in the A site and moving the tRNA in the P site to the E site

116
Q

which release factors cause hydrolysis of the polypeptide from the final tRNA?

A

RF-1 and 2

117
Q

which RF causes the ribosome complex to dissociate?

A

RF-3

118
Q

eukaryotic RF that hydrolyzes polypeptide chain from final tRNA-

A

eRF

119
Q

what eukaryotic RF breaks apart the ribosome complex

A

eRF-3

120
Q

polysome-

A

a single piece of mRNA that can be translated by multiple sequential ribosomes simultaneously

121
Q

protein targeting-

A

sequences in protein that control its cellular location

122
Q

is a signal sequence hydrophilic or phobic?

A

hydrophobic

123
Q

O-glycosylation of proteins occurs where and on what amino acids?

A

in the Golgi on serine, threonine, and hydroxylysine

124
Q

N-glycosylation of proteins occurs where and on what amino acids?

A

ER on asparagine residues

125
Q

N-glycosylation of proteins occurs where and on what amino acids?

A

ER on asparagine residues

126
Q

the purpose of farnesylation-

A

anchor proteins to membranes

127
Q

_____ and _____ lead to proteosomic protein destruction

A

PEST sequences and ubiquitination

128
Q

duchenne muscular dystrophy is caused by a ______ mutuation

A

nonsense

129
Q

thalassemia is caused by a _____ mutation

A

nonsense

130
Q

tay sachs, hypertrophic cardiomyopathy and cystic fibrosis are caused by ______ mutations

A

frameshift

131
Q

huntingtons and fragile x are caused by ______ mutations

A

trinucleotide repeat

132
Q

streptomycin MOA-

A

binds 30S to block initiation

133
Q

Tetracycline MOA-

A

binds 30S to block entry of tRNAs to A site, stops elongation

134
Q

Chloramphenicol MOA-

A

inhibits peptidyltransferase

135
Q

Clindamycin/erythromycin MOA-

A

binds to 50S, blocks translocation

136
Q

diptheria toxin MOA-

A

inactivates eIF, blocks translocation in eukaryotes

137
Q

cycloheximide MOA-

A

block E site

138
Q

Puromycin MOA-

A

AA-tRNA analogue, causes termination

139
Q

Puromycin MOA-

A

AA-tRNA analogue, causes termination. (works on pro and eukaryotic)

140
Q

Puromycin MOA-

A

AA-tRNA analogue, causes termination. (works on pro and eukaryotic)

141
Q

Operator-

A

a segment of DNA that represses the expression of genes present in the operon

142
Q

inducers repress ______

A

repressors

143
Q

lacZ-

A

encodes beta-galactosidase

144
Q

lac-Y-

A

encodes lactose permease

145
Q

lac-A-

A

encodes thiogalactosidase transacetylase (rids cell of thiogalactosides)

146
Q

Lac repressor is encoded by-

A

lacI

147
Q

CAP (catabolite activator protein)-

A

activated by camp and enhances recruitment of RNA pol to promoter

148
Q

when lactose is high, it is transported into prokaryotic cells and turned into allolactose. Allolactose then goes on to do what?

A

binds the repressor, preventing it from binding the operator

149
Q

when lactose is high, prokaryotes increase cAMP production, leading to what change in the lac operon?

A

cAMP binds to the activator (CAP)

150
Q

if a prokaryote is exposed to high glucose and lactose, is the lac operon on or off?

A

On, but barely because it is neither being activated or repressed

151
Q

Trp operon codes for-

A

5 genes that are needed to synthesize tryptophan

152
Q

what is the repressor of the Trp operon?

A

the product, tryptohan

153
Q

what is the repressor of the Trp operon?

A

the product, tryptohan

154
Q

Besides repression, how does tryptophan regulate the Trp operon?

A

creates a stem loop structure that blocks RNA pol and terminates transcription early

155
Q

Attenuation-

A

RNA pol is paused during transcription

156
Q

The stringent response-

A

a slow down in translation during a time of amino acid starvation

157
Q

when an uncharged tRNA enters A site, ________ catalyzes the formation of _____.

A
  • stringent factor

- ppGpp

158
Q

elevated levels of ppGpp inhibits the synthesis of

A

rRNA

159
Q

r-protein

A

ribosomal protein

160
Q

when r-protein levels are high, they repress:

A

polycistronic mRNA from their operon.

161
Q

r-proteins inhibit expression of:

A

all r-proteins

162
Q

how does r-protein inhibit an operon?

A

it blocks the shine-dalgarno sequence

163
Q

trans-acting molecules have at least 2 distinct domains:

A

DNA binding domain and transcriptional activation domain

164
Q

transcriptional activation domain-

A

allows the binding of additional proteins (HATs) or to facilitate the recruitment of the transcriptional initiation complex

165
Q

combinatorial control-

A

regulation of a gene depends on the specific combination of proteins present on a promoter at any one given time

166
Q

nuclear hormone receptors also act as _______

A

the transcription factor

167
Q

tissue-specific isoforms of a protein product are achieved through ______

A

alternative splicing

168
Q

combinatorial control-

A

one protein, activator, or regulator is involved with the regulation of the expression of multiple different genes. This is achieved through the ability of the one protein to interact with multiple different factors in different biological contexts (different combos of proteins activate different genes)

169
Q

tissue-specific isoforms of a protein product are achieved through ______

A

alternative splicing

170
Q

RNA editing-

A

fully processed mRNA can undergo additional modifications by altering a single base

171
Q

ApoB-100 can undergo RNA editing to become ___

A

Apo-B48 via deamination of a C residue to a U

172
Q

Trasferrin-

A

plasma protein that transports iron

173
Q

Trasferrin mRA has IRE (stem loop structure) at 3’ end. In low iron conditions, what happens with the expression of transferrin.

A

IRP binds IRE, which stabilizes the mRNA and increases translation

174
Q

RNAi-

A

gene regulation that occurs either through repressed protein translation or increased mRNA degradation

175
Q

RNAi is mediated through

A

miRNA

176
Q

micro RNA (miRNA) folds onto itself to be dsRNA. It is cleaved by ______ to be mature miRNA.

A

dicer

177
Q

a single strand of miRNA (one of the strands from the dsRNA) is incorporated into ____

A

RISC

178
Q

miRNA facilitates the binding of RISC to _____

A

mRNA

179
Q

a strand of miRNA that is very complimentary to the mRNA it binds causes

A

degredation of the mRNA

180
Q

a strand of miRNA that has low complimentarity to the strand of mRNA it binds causes

A

inhibition of translation

181
Q

example of miRNA being used for RNAi therapy:

A

using it to suppress production of VEGF, which causes macular degeneration

182
Q

how do we get such variability in the light chains of Ig’s?

A

one Variable, Diversity, and Joining gene segment all recombine together to make a unique light chain gene. there are tons of different gene segments for each of the 3 categories

183
Q

Transposons are DNA segments moved around by the enzyme _______

A

transposase

184
Q

trasposase is encoded by ______

A

transposon

185
Q

transposons can be moved around but they can also be copied, which requires _____. In this case the transposon is called a _____

A
  • RNA intermediate

- retrotransposon

Spring 2015 (9 decks)

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