Block 4 Biochem part 1 Flashcards
(185 cards)
1
Q
who discovered that DNA is the source of heritable info?
A
oswald avery
2
Q
who noticed the relationship btw AT and GC?
A
erwin chargaff
3
Q
most common conformation of DNA
A
B DNA
4
Q
dehydrated form of DNA
A
A DNA
5
Q
form of DNA thought to help relieve stress of the helix around a transcription complex
A
Z DNA
6
Q
Which enzyme binds the origin of replication in prokaryotes?
A
DnaA
7
Q
how do bacteria regulate DNA replication?
A
they only make enough DNAA for 1 replication
8
Q
what unwinds the DNA in prokaryotes?
A
helicase
9
Q
what breaks the phosphodiester backbones to relieve supercoiling in prokaryotes?
A
Topoisomerase I
10
Q
what makes clean breaks through both strands of DNA to unknot it?
A
Topoisomerase II
11
Q
Main enzyme that copies DNA in prokaryotes
A
DNA pol III`
12
Q
which enzyme in prokaryotes has 3’–>5’ exonuclease activity for proofreading?
A
DNA pol III
13
Q
what does DNA pol I do?
A
in prokaryotes, it excises the RNA primer and adds DNA
14
Q
what is the eukaryotic equivalent of DNA pol I?
A
Fen-1 nuclease and RNase H
15
Q
what does DNA ligase do?
A
in prokaryotes it ensures all phosphodiester bonds are formed
16
Q
Polymerase alpha-
A
contains primase and initiates DNA synthesis
17
Q
Polymerase delta-
A
synthesizes lagging strand (okizaki fragments) Has 3’–>5’ exonuclease activity
18
Q
polymerase epsilon-
A
synthesizes leading strand, has 3’–>5’ exonuclease activity
19
Q
polymerase beta-
A
repairs DNA. cannot excise ribonucleotides or proofread
20
Q
polymerase gamma-
A
replicates mitochondrial DNA
21
Q
the hexameric sequence of telomeres is:
A
AGGGTT
22
Q
which end of a DNA strand does telomerase elongate?
A
the 3’ end
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
24
Q
what nucleosides are often used to inhibit DNA synthesis?
A
AZT and 2’,3’ dideoxyinosine
25
most common base excision repair-
correcting deaminated cytosines
26
mismatch-directed DNA repair is mediated by ______
Mut proteins
27
Mut proteins work under the assumption that:
the template strand contains the correct base
28
in E. coli, the template strand is identified by:
methylation of adenine residues
29
in eukaryotes, the template strand is identified by:
being the "un-nicked strand"
30
_____ nicks the strand at mismatched nucleotides and _____ removes the them
- endonuclease
| - exonuclease
31
mutations in Mut proteins is associated with __________
hereditary nonpolyposis colorectal cancer (Lynch syndrome)
32
homologous repair of a double stranded DNA break is achieved using _____ for a template and ______ genes for repair.
- sister chromatid
| - BRCA 1 and 2
33
non homologous double stranded DNA breaks are fixed by ______ but are very error prone
DNA ligase
34
thymine dimers caused by UV light are excised in a process known as __________
nucleotide excision repair
35
what do XP proteins do?
fix thymine dimers
36
Cockayne syndrome-
CSA and CSB mutations causing neurological symptoms
37
are skin cancers common in Cockayne syndrome?
no
38
Mutation in ____ gene can manifest as either cockayne or xeroderma pigmentosum, or a blend of both
XPD
39
which genetic disease is closely related to XP, although manifests differently?
cockayne syndrome
40
the 5 classes of histones:
H1, H2A, H2B, H3, H4
41
what does the H1 histone do?
binds linker DNA, it is the stabilizer
42
constitutive vs facultative heterochromatin:
constitutive is heterochromatin in all cell types, facultative has cell specific expression (ability to turn genes on or off)
43
when a gene is switched on the histones are acetylated/unacetylated?
acetylated
44
when a gene is switched on, the cytosines are methylated/unmethylated?
unmethylated
45
polycistronic mRNA-
carries info for more than one gene
46
how is uracil different from thymine-
uracil lacks a methyl group at the 5' position
47
how is RNA different from DNA-
RNA has 2' OH group while DNA just has 2' H
48
do eukaryotes have poly or monocistronic mRNA?
mono
49
both eukaryotes and prokaryotes mRNA have these 2 untranslated regions which are for stability and initiation of protein synthesis
5' and 3' untranslated regions
50
Besides the untranslated regions, what structural characteristics do eukaryotic mRNA have? (2)
poly A tail and 5' cap
51
the most abundant type of RNA in a cell
rRNA
52
rRNA acts like an _____
enzyme
53
rRNA acts like an _____, so it is also known as ______
enzyme; ribozyme
54
what does miRNA do?
inhibits protein synthesis
55
what does miRNA do?
inhibits protein synthesis
56
what is the core enzyme of sigma factor made up of:
2 alpha, 2 beta subunits
57
role of sigma factor in RNA polymerase
provides specificity to RNA pol to recognize the promoter sequence
58
2 characteristic DNA consensus sequences in prokaryotic promoter-
-35 sequence and the Pribnow box (-10 seq.)
59
when does RNA pol open up DNA for transcription?
when it binds to the promoter sequence (unwinds about 14 bp)
60
when does RNA pol open up DNA for transcription?
when it binds to the promoter sequence (unwinds about 14 bp)
61
abortive transcripts-
several short pieces of RNA that are generated at the beginning of transcription then discarded
62
what must happen for the prokaryotic RNA pol to break away from initiation site and transcribe?
sigma factor must be released
63
rho independent termination depends on-
the sequence of the nascent RNA species
64
how does prokaryotic rho independent termination work?
RNA sequence is self complementary and capable of base pairing with itself to generate a hairpin structure, followed by a series of U bases.
65
why does rho independent termination form a poly U tail at the end?
U forms the weakest of bonds and facilitates removal of the RNA from the DNA template strand
66
Prokaryotic Rho dependent termination requires-
help of rho protein and ATP
67
what is Rho?
hexameric ATPase with helicase activity.
68
how does prokaryotic rho dependent termination work?
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
69
Rifampicin MOA-
inhibits initiation of transcription by blocking prokaryotic RNA pol from progressing with initiation
70
why does rifampicin not stop eukaryotic transcription?
eukaryotic RNA pol does not have a beta subunit
71
Dactomycin MOA-
inhibits elongation of transcription
72
RNA pol I-
eukaryotic; transcribes rRNA
73
RNA pol II-
eukaryotic; transcribes mRNA
74
RNA pol III-
eukaryotic; transcribes mostly tRNA and snRNA
75
prokaryotes only have one transcription factor, but eukaryotes have 6-
TFIIA,B,D,E,F,H
76
prokaryotes only have one transcription factor, but eukaryotes have 6-
TFIIA,B,D,E,F,H
77
Eukaryotic promoters-
```
CAAT box (80 bases upstream) and TATA box (25 bases upstream)
*sometimes a GC rich region
```
78
eukaryotic RNA pol does not directly contact ____
DNA
79
TFIID-
recognizes and binds the TATA box
80
TFIIF-
interacts with and recruits RNA pol II to the promoter
81
TFIIH-
contains helicase activity to unwind the DNA at the transcription start site
82
3 eukartyotic TF's needed to recognize promoter and recruit RNA pol II
TFIID,F,H
83
Eukaryotic transcription enhancers-
-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
how do eukaryotic enhancers work?
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
a-amanitin MOA-
inhibits EUKARYOTIC RNA pol II; causes death
86
a-amanitin MOA-
inhibits EUKARYOTIC RNA pol II; causes death
87
Prokaryotic rRNAs
23S, 16S, and 5S
88
Eukaryotic rRNAs
28S, 18S, 5.8S (made by RNA pol I) and 5S (made by RNA pol III)
89
role of snoRNA-
base modification of rRNA
90
eukaryotes synthesize rRNA in the _____
nucleolus
91
after 3' end of tRNA is trimmed off, ____ is added, forming the aminoacylation site for the addition of the amino acid
CCA
92
what is the 5' cap on eukaryotic mRNA?
it is a 7-methylguanosine attached backwards (5'-->5' triphosphate linkage)
93
capping of mRNA occurs in the ____ and methylation occurs in the _____
- nucleus
| - cytosol
94
what enzyme adds GMP to the 5' end of mRNA?
guanylyltransferase
95
how is a poly A tail added to mRNA?
the enzyme polyadenylate polymerase recognizes the polyadenylation sequence and cleaves the RNA right after this sequence. It then adds lots of A's
96
what is the polyadenylation sequence?
AAUAAA
97
In the splicing process, _____ form small nuclear ribonucleoprotein complexes called ______. The snRNA's base pair with consensus sequences at the exon/intron boundaries.
- snRNA
| - snurps
98
how do snurps remove introns?
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
5' end of an intron is called
the splice donor site
100
3' end of intron is called
splice acceptor site
101
the 3 stop codons
UAG, UGA, UAA
102
a disease caused by incorrect splicing
beta thalassemia
103
an autoimmune disease against your own snRNPs
systemic lupus erythematosus
104
How does Cystic Fibrosis occur (genetically)-
loss of a trinucleotide that causes loss of phenylalanine and subsequent protein misfolding
105
aminoacyl tRNA synthetases-
specific for the amino acid and all tRNA species for the amino acid
106
aminoacyl tRNA synthetases-
specific for the amino acid and all tRNA species for the amino acid. 20 in all
107
aminoacyl-tRNA synthetase catalyzes tRNA charging by:
adding AMP to the amino acid, transferring the amino acid to the tRNA and releasing the AMP
108
prokaryotic ribosome __S + __S = ___S
50S + 30S = 70S
109
eukaryotic ribosome __S + __S = __S
60S + 40S = 80S
110
prokaryotic mRNA has a ______ sequence at the 5' end to position mRNA for translation initiation
Shine-Dalgarno
111
How do eukaryotes find start sequence on mRNA during initiation?
bind to 5' cap and scan for AUG
112
the only aminoacyl tRNA inserted into the P site is-
met-tRNA for initiation
113
recognition and recruitment of AUG to the P site is facilitated by which initiation factor?
IF-2
114
the energy cost of adding 1 amino acid to a polypeptide chain-
2 ATP and 2 GTP
115
which 2 things require GTP hydrolysis during translation?
putting a new charged tRNA in the A site and moving the tRNA in the P site to the E site
116
which release factors cause hydrolysis of the polypeptide from the final tRNA?
RF-1 and 2
117
which RF causes the ribosome complex to dissociate?
RF-3
118
eukaryotic RF that hydrolyzes polypeptide chain from final tRNA-
eRF
119
what eukaryotic RF breaks apart the ribosome complex
eRF-3
120
polysome-
a single piece of mRNA that can be translated by multiple sequential ribosomes simultaneously
121
protein targeting-
sequences in protein that control its cellular location
122
is a signal sequence hydrophilic or phobic?
hydrophobic
123
O-glycosylation of proteins occurs where and on what amino acids?
in the Golgi on serine, threonine, and hydroxylysine
124
N-glycosylation of proteins occurs where and on what amino acids?
ER on asparagine residues
125
N-glycosylation of proteins occurs where and on what amino acids?
ER on asparagine residues
126
the purpose of farnesylation-
anchor proteins to membranes
127
_____ and _____ lead to proteosomic protein destruction
PEST sequences and ubiquitination
128
duchenne muscular dystrophy is caused by a ______ mutuation
nonsense
129
thalassemia is caused by a _____ mutation
nonsense
130
tay sachs, hypertrophic cardiomyopathy and cystic fibrosis are caused by ______ mutations
frameshift
131
huntingtons and fragile x are caused by ______ mutations
trinucleotide repeat
132
streptomycin MOA-
binds 30S to block initiation
133
Tetracycline MOA-
binds 30S to block entry of tRNAs to A site, stops elongation
134
Chloramphenicol MOA-
inhibits peptidyltransferase
135
Clindamycin/erythromycin MOA-
binds to 50S, blocks translocation
136
diptheria toxin MOA-
inactivates eIF, blocks translocation in eukaryotes
137
cycloheximide MOA-
block E site
138
Puromycin MOA-
AA-tRNA analogue, causes termination
139
Puromycin MOA-
AA-tRNA analogue, causes termination. (works on pro and eukaryotic)
140
Puromycin MOA-
AA-tRNA analogue, causes termination. (works on pro and eukaryotic)
141
Operator-
a segment of DNA that represses the expression of genes present in the operon
142
inducers repress ______
repressors
143
lacZ-
encodes beta-galactosidase
144
lac-Y-
encodes lactose permease
145
lac-A-
encodes thiogalactosidase transacetylase (rids cell of thiogalactosides)
146
Lac repressor is encoded by-
lacI
147
CAP (catabolite activator protein)-
activated by camp and enhances recruitment of RNA pol to promoter
148
when lactose is high, it is transported into prokaryotic cells and turned into allolactose. Allolactose then goes on to do what?
binds the repressor, preventing it from binding the operator
149
when lactose is high, prokaryotes increase cAMP production, leading to what change in the lac operon?
cAMP binds to the activator (CAP)
150
if a prokaryote is exposed to high glucose and lactose, is the lac operon on or off?
On, but barely because it is neither being activated or repressed
151
Trp operon codes for-
5 genes that are needed to synthesize tryptophan
152
what is the repressor of the Trp operon?
the product, tryptohan
153
what is the repressor of the Trp operon?
the product, tryptohan
154
Besides repression, how does tryptophan regulate the Trp operon?
creates a stem loop structure that blocks RNA pol and terminates transcription early
155
Attenuation-
RNA pol is paused during transcription
156
The stringent response-
a slow down in translation during a time of amino acid starvation
157
when an uncharged tRNA enters A site, ________ catalyzes the formation of _____.
- stringent factor
| - ppGpp
158
elevated levels of ppGpp inhibits the synthesis of
rRNA
159
r-protein
ribosomal protein
160
when r-protein levels are high, they repress:
polycistronic mRNA from their operon.
161
r-proteins inhibit expression of:
all r-proteins
162
how does r-protein inhibit an operon?
it blocks the shine-dalgarno sequence
163
trans-acting molecules have at least 2 distinct domains:
DNA binding domain and transcriptional activation domain
164
transcriptional activation domain-
allows the binding of additional proteins (HATs) or to facilitate the recruitment of the transcriptional initiation complex
165
combinatorial control-
regulation of a gene depends on the specific combination of proteins present on a promoter at any one given time
166
nuclear hormone receptors also act as _______
the transcription factor
167
tissue-specific isoforms of a protein product are achieved through ______
alternative splicing
168
combinatorial control-
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
tissue-specific isoforms of a protein product are achieved through ______
alternative splicing
170
RNA editing-
fully processed mRNA can undergo additional modifications by altering a single base
171
ApoB-100 can undergo RNA editing to become ___
Apo-B48 via deamination of a C residue to a U
172
Trasferrin-
plasma protein that transports iron
173
Trasferrin mRA has IRE (stem loop structure) at 3' end. In low iron conditions, what happens with the expression of transferrin.
IRP binds IRE, which stabilizes the mRNA and increases translation
174
RNAi-
gene regulation that occurs either through repressed protein translation or increased mRNA degradation
175
RNAi is mediated through
miRNA
176
micro RNA (miRNA) folds onto itself to be dsRNA. It is cleaved by ______ to be mature miRNA.
dicer
177
a single strand of miRNA (one of the strands from the dsRNA) is incorporated into ____
RISC
178
miRNA facilitates the binding of RISC to _____
mRNA
179
a strand of miRNA that is very complimentary to the mRNA it binds causes
degredation of the mRNA
180
a strand of miRNA that has low complimentarity to the strand of mRNA it binds causes
inhibition of translation
181
example of miRNA being used for RNAi therapy:
using it to suppress production of VEGF, which causes macular degeneration
182
how do we get such variability in the light chains of Ig's?
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
Transposons are DNA segments moved around by the enzyme _______
transposase
184
trasposase is encoded by ______
transposon
185
transposons can be moved around but they can also be copied, which requires _____. In this case the transposon is called a _____
- RNA intermediate
| - retrotransposon
