stupid biochem factors Flashcards
(91 cards)
1
Q
Histone H1
A
the histone outside of the nucleosome, easy to take off, responsible for chromatin tightening
2
Q
the histone is made of 4 parts
A
H2a, H2b, H3, H4
3
Q
histone modification occurs on the ___ of the histone
A
N terminus basic tail of the histone
4
Q
6 histone tail modifications
A
acetylation -activates genes, makes DNA more relaxed
methylation - deactivates, more condensed DNA
phosphorylation- on H1, condenses DNA
ADP-Ribosylation - DNA repair marker
monoubiquilyation - activation/silencing
sumoylation - transcription repression
5
Q
constitutive heterochromatin
A
- always inactive
6
Q
faculative heterochromatin
A
sometimes inactive, sometimes active
7
Q
telomeres
A
on the ends of DNA chromosomes, TG repeats
8
Q
teleomerase
A
the RNA complex responsible for replicating the telomeres
9
Q
centromeres
A
the the center, connected to kinetichore for DNA chromosome separation. AT repeats
10
Q
LINES
A
long interspersed repeat sequences
11
Q
SINES
A
short interspersed repeat sequences
12
Q
dnaA proteins
A
bound to the origin in e. coli
13
Q
SSBs
A
single strand binding proteins stabilize ssDNA (single strand DNA) in E.coli
14
Q
Replication protein A
A
single strand binding proteins stabilize ssDNA (single strand DNA) in eukaryotes
15
Q
primase
A
makes RNA primers for replication
16
Q
helicase
A
unwinds DNA, ATP driven
17
Q
topoisomerase
A
makes single or double strand cuts in DNA to add or take out supercoils
18
Q
DNA ligase
A
seals nicks in between okazaki fragments on lagging strand
19
Q
DNAG
A
primase in prokaryotes
20
Q
In Prokaryotes, there are 3 DNA polymerases
A
DNA pol I, II, and III
21
Q
DNA polymerase I function
A
repair, gap filling, recombination
22
Q
DNA polymerase II function
A
DNA proof reading and repair
23
Q
DNA polymerase III function
A
DNA synthesis of both leading and lagging strand, can also proof read
24
Q
in eukaryotes there are 5 DNA polymerase
A
DNA polymerase Alpha, beta, gamma, eplison, delta
25
DNA polymerase Beta function
DNA repair
26
DNA polymerase gamma function
Mitochondrial DNA synthesis
27
DNA polymerase epsilon function
leading strand synthesis
28
DNA polymerase delta function
lagging strand synth
29
DNA polymerase alpha function
primase
30
beta clamp or sliding clamp
on pol III (and maybe Pol epsilon or delta?), helps processivity of the polymerase
31
polymerase adds nucleotides how?
nucleophilic attack of 3' hydroxyl group, pyrophosphase (ppi) comes off
32
cyclins are?
proteins that inc or decr in concentration at specific times in cell cycle. they activate the cyclin dependant protein kinases (CDKs)
33
Cyclin dependent protein kinases (CDK) do what?
they phosphorylate (kinase!!!) things to help the cell cycle progress
34
cyclin D activates which CDKs? during what cycle to do what?
Cyclin D -> CDK4 and CDK6. moves g1 --> s phase
35
cyclin E activates which CDKs? during what cycle to do what?
Cyclin E bonds to CDK2. moves g1 --> s phase when cyclin E is replaced by cyclin A in the complex
36
cyclin A activates which CDKs? during what cycle to do what?
Cyclin A -> CDK2 in the S phase
| Cyclin A -> CDK1 in the G2 phase
37
cyclin B activates which CDKs? during what cycle to do what?
Cyclin B -> CDK1, this is the rate determining step for the G2-> M transition
38
5 DNA repair pathways
nucleotide excision, Base excision, mismatch repair, homologous recombination, nonhomologous end joining
39
in mismatch repair: what are the first 3 factors?
Mut S, finds mismatch, binds daughter strand
Mut L, binds daughter strand
mut H, binds, nicks DNA, recruits DNA Helicase
40
After the first 3 factors of mismatch repair have bound, what binds next?
helicase and exonuclease.
| DNA is eaten and then DNA pol 3 can polymerize, followed by ligase
41
base excision repair. what initiates it?
DNA glycosylase recognizes and removes the dammaged BASE only. Forms ap site (apurinic/apyramidic)
42
after the base is removed in base excision repair, what happens next?
AP endonuclease takes off the backbone portion and then DNA pol 3 can polymerize, followed by ligase
43
in nucleotide excision repair, are there specific factors?
no, there are too many, just know damage is recognized, excision nuclease is used to take out a ton of the DNA strand nucleotides (methylation point to methylation point), DNA pol 3 and ligase follow
44
what are the important steps in double stranded break repair?
Sensors - recognize break
transducers - send message
mediators - amplify signal response, gather effectors
effectors - determine the outcome of the Damage, how to fix
45
what are the important sensors in double stranded breaks?
PARP and KU70, KU80
46
what are the important transducers in double stranded breaks?
ATM, ATR
47
what are the important mediators in double stranded breaks?
Brca1
48
what are the important effectors in double stranded breaks?
p53, p19, BAX, p21
49
p21 does what?
its a the ultimate cyclin dept kinase inhibitor. inhibits all CDKs, thus halts cell cycle
50
in prokaryotes, the promoter is ?
-35 proximal element and -10 tata or prinbrow box
51
in eukaryotes, the promoter consists of two elements? function?
core promoters determine where transcription will begin
| proximal elements determine how frequently it happens
52
what are the 3 core promoters?
```
initiation sequence (Inr) around -3 - +5
tata box around -10
downstream promoter (DPE) around +25
```
53
what are the proximal elements in eukaryotes?
GC box with Sp1 bound protein
CAAT box with CTF bound protein
-35 in prokaryotes
54
Sp1
protein that binds the GC proximal element
55
CTF
protein that binds CAAT box
56
RNA polymerase I encodes
rRNA
57
RNA polymerase II encodes
mRNA, miRNA, SnRNA, lncRNA
58
RNA polymerase III encodes
tRNA, 5s rRNA
59
RNA polymerase IV encodes
mitochondial RNA
60
in eukaryotes, there are ___ RNA polymerase. In prokaryotes, there is ___.
4 in eukaryotes, 1 in prokaryotes (this encodes all RNA in the prokaryotes)
61
in eukaryotic RNA polymerase, sigma is replaced by Transcription factors (also known as basal transcriptional factors). what transcription factor is responsible to locate the TATA box
TFIID
| TFII A, B, D, E, F H exist
62
TBP
tata binding protein is one of the subunits of TFIID
63
TFIIH
gives the RNA pol the go! signal
64
what are the 5 snRNAs responsible for splicing?
U1, U2,U4,U5,U6
65
which snRNAs bond to the 5' and 3' end?
U1 to the 5' and U2 to the 3'
66
which end is first to be cleaved in splicing? what kind of rxns?
the 5' end is first cleaved and attached to the adenine branch point. then the 3 ' is cleaved so that the exons can be connected. 2 transesterfications
67
the genetic code is described as degenerate and unambiguous, non overlapping and non punctunated. these mean
degenerate - several codons = an amino acid
unambiguous - one codon always = one specific amino acid
non overlapping/punctuated - no pauses, skipping or shared nucleotides, just a constant 3 3 3 code
68
what is the enzyme that activates amino acids? what kind of bond? what are the types and what other function can it do?
aminoacyl tRNA synthetase, ester bond on the 2' or 3' end of the tRNA (depending on the type 1 (2') or type 2 (3')).
these enzymes can also conduct proof reading
69
aminoacyl tRNA synthetase uses what energy source?
I ATP -> 1 AMP
70
inosine can bond to which nucleotides?
a, u, c
71
hoogsteen base pair
wobble
72
the prokaryote ribosome has what parts? what is the total svedberg unit?
70s made up of 50s (large) and 30s (small)
*** less important:
their small subunit = 16s rRNA unit
large = 5s and 23s
73
the Eukaryote ribosome has what parts? what is the total svedberg unit?
80s made up of 60s (large) and 40s (small)
*** less important:
their small subunit = 18s rRNA unit
large = 5s, 28s, 5.8s
74
what are the initiation sequences of translation?
before the AUG codon, there is a shine delgarno sequence in prokaryotes
Kozak sequence in eukaryotes
75
which part of the ribosome is responsible for finding the shine delgardo sequence?
the small subunit attaches and scans, the 16s piece bonds to the sequence
76
in prok and euk, what is typically the first amino acid to be added in translation?
prok - fmet
| euk - met
77
after the initiation sequence is found, what initiation factors bond?
IF3 to the small ribosome unit and IF1 to the A site of the ribosome
78
IF2 does what?
IF2 is bonded to GTP and fmet-tRNA, allows the tRNA to bond to the P site, begins translation. the 50s subunit lands on top and all the initiation factors leave
79
elongation factors in translation:
EFTu, EFG, EFTs
80
EFTu does what?
EFTu bonds to GTP and the incoming tRNAs and helps them into the A site
81
EFTs does what?
reloads EFtu with GTP, serves as an intermediate
82
does the peptide bond formation take energy? what is the rRNA piece that helps form the peptide bond?
no, due to atp--> amp in tRNA activation
| the 23s rRNA adenine is the active site
83
EFG does what
EFG-GTP helps in translocation
84
the release factors of translation do what?
RF1 and RF2 are responsible for recognizing the stop codons.
| RF3-GTP help release happen, cause hydrolysis of the growing peptide chain.
85
in eukaryotes, Inititation factors are eIF_. what factors bind the 5' cap to begin initiation?
eIF 4A, 4B, 4G,
86
what eukaryotic initiation factor can make translation stop if phosphorylated?
eIF2
87
what is on a polypeptide that tells the cell where to send the polypeptide?
signal peptide or signal patch. can be continuous sequences or not.
88
what atp dependent molecule brings polypeptides to the ER?
signal recognition particles (SRP)
89
what is RISC
RISC is RNA-induced silencing complex that uses miRNA or siRNA to silence genes via destroying mRNA or binding to the DNA gene
90
actions of p53
```
activates expression (transcrition/translation) of several genes:
activate DNA repair proteins when DNA has sustained damage, causing repari, arrest, or apoptosis
```
91
what is satellite dna?
Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA.
centromeres
ncDNA
SINES
LINES
Telomeres (tandem 5-6bp repeats made by telomerase)
