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Y Biochemistry I > stupid biochem factors > Flashcards

stupid biochem factors Flashcards

1
Q

Histone H1

A

the histone outside of the nucleosome, easy to take off, responsible for chromatin tightening

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2
Q

the histone is made of 4 parts

A

H2a, H2b, H3, H4

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3
Q

histone modification occurs on the ___ of the histone

A

N terminus basic tail of the histone

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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

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5
Q

constitutive heterochromatin

A
  • always inactive
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6
Q

faculative heterochromatin

A

sometimes inactive, sometimes active

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7
Q

telomeres

A

on the ends of DNA chromosomes, TG repeats

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8
Q

teleomerase

A

the RNA complex responsible for replicating the telomeres

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9
Q

centromeres

A

the the center, connected to kinetichore for DNA chromosome separation. AT repeats

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10
Q

LINES

A

long interspersed repeat sequences

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11
Q

SINES

A

short interspersed repeat sequences

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12
Q

dnaA proteins

A

bound to the origin in e. coli

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13
Q

SSBs

A

single strand binding proteins stabilize ssDNA (single strand DNA) in E.coli

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14
Q

Replication protein A

A

single strand binding proteins stabilize ssDNA (single strand DNA) in eukaryotes

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15
Q

primase

A

makes RNA primers for replication

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16
Q

helicase

A

unwinds DNA, ATP driven

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17
Q

topoisomerase

A

makes single or double strand cuts in DNA to add or take out supercoils

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18
Q

DNA ligase

A

seals nicks in between okazaki fragments on lagging strand

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19
Q

DNAG

A

primase in prokaryotes

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20
Q

In Prokaryotes, there are 3 DNA polymerases

A

DNA pol I, II, and III

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21
Q

DNA polymerase I function

A

repair, gap filling, recombination

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22
Q

DNA polymerase II function

A

DNA proof reading and repair

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23
Q

DNA polymerase III function

A

DNA synthesis of both leading and lagging strand, can also proof read

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24
Q

in eukaryotes there are 5 DNA polymerase

A

DNA polymerase Alpha, beta, gamma, eplison, delta

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25
Q

DNA polymerase Beta function

A

DNA repair

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26
Q

DNA polymerase gamma function

A

Mitochondrial DNA synthesis

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27
Q

DNA polymerase epsilon function

A

leading strand synthesis

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28
Q

DNA polymerase delta function

A

lagging strand synth

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29
Q

DNA polymerase alpha function

A

primase

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30
Q

beta clamp or sliding clamp

A

on pol III (and maybe Pol epsilon or delta?), helps processivity of the polymerase

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31
Q

polymerase adds nucleotides how?

A

nucleophilic attack of 3’ hydroxyl group, pyrophosphase (ppi) comes off

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32
Q

cyclins are?

A

proteins that inc or decr in concentration at specific times in cell cycle. they activate the cyclin dependant protein kinases (CDKs)

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33
Q

Cyclin dependent protein kinases (CDK) do what?

A

they phosphorylate (kinase!!!) things to help the cell cycle progress

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34
Q

cyclin D activates which CDKs? during what cycle to do what?

A

Cyclin D -> CDK4 and CDK6. moves g1 –> s phase

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35
Q

cyclin E activates which CDKs? during what cycle to do what?

A

Cyclin E bonds to CDK2. moves g1 –> s phase when cyclin E is replaced by cyclin A in the complex

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36
Q

cyclin A activates which CDKs? during what cycle to do what?

A

Cyclin A -> CDK2 in the S phase

Cyclin A -> CDK1 in the G2 phase

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37
Q

cyclin B activates which CDKs? during what cycle to do what?

A

Cyclin B -> CDK1, this is the rate determining step for the G2-> M transition

38
Q

5 DNA repair pathways

A

nucleotide excision, Base excision, mismatch repair, homologous recombination, nonhomologous end joining

39
Q

in mismatch repair: what are the first 3 factors?

A

Mut S, finds mismatch, binds daughter strand
Mut L, binds daughter strand
mut H, binds, nicks DNA, recruits DNA Helicase

40
Q

After the first 3 factors of mismatch repair have bound, what binds next?

A

helicase and exonuclease.

DNA is eaten and then DNA pol 3 can polymerize, followed by ligase

41
Q

base excision repair. what initiates it?

A

DNA glycosylase recognizes and removes the dammaged BASE only. Forms ap site (apurinic/apyramidic)

42
Q

after the base is removed in base excision repair, what happens next?

A

AP endonuclease takes off the backbone portion and then DNA pol 3 can polymerize, followed by ligase

43
Q

in nucleotide excision repair, are there specific factors?

A

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
Q

what are the important steps in double stranded break repair?

A

Sensors - recognize break
transducers - send message
mediators - amplify signal response, gather effectors
effectors - determine the outcome of the Damage, how to fix

45
Q

what are the important sensors in double stranded breaks?

A

PARP and KU70, KU80

46
Q

what are the important transducers in double stranded breaks?

47
Q

what are the important mediators in double stranded breaks?

48
Q

what are the important effectors in double stranded breaks?

A

p53, p19, BAX, p21

49
Q

p21 does what?

A

its a the ultimate cyclin dept kinase inhibitor. inhibits all CDKs, thus halts cell cycle

50
Q

in prokaryotes, the promoter is ?

A

-35 proximal element and -10 tata or prinbrow box

51
Q

in eukaryotes, the promoter consists of two elements? function?

A

core promoters determine where transcription will begin

proximal elements determine how frequently it happens

52
Q

what are the 3 core promoters?

A 
initiation sequence (Inr) around -3 - +5
tata box around -10
downstream promoter (DPE) around +25
53
Q

what are the proximal elements in eukaryotes?

A

GC box with Sp1 bound protein
CAAT box with CTF bound protein
-35 in prokaryotes

54
Q

Sp1

A

protein that binds the GC proximal element

55
Q

CTF

A

protein that binds CAAT box

56
Q

RNA polymerase I encodes

57
Q

RNA polymerase II encodes

A

mRNA, miRNA, SnRNA, lncRNA

58
Q

RNA polymerase III encodes

A

tRNA, 5s rRNA

59
Q

RNA polymerase IV encodes

A

mitochondial RNA

60
Q

in eukaryotes, there are ___ RNA polymerase. In prokaryotes, there is ___.

A

4 in eukaryotes, 1 in prokaryotes (this encodes all RNA in the prokaryotes)

61
Q

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

A

TFIID

TFII A, B, D, E, F H exist

62
Q

TBP

A

tata binding protein is one of the subunits of TFIID

63
Q

TFIIH

A

gives the RNA pol the go! signal

64
Q

what are the 5 snRNAs responsible for splicing?

A

U1, U2,U4,U5,U6

65
Q

which snRNAs bond to the 5’ and 3’ end?

A

U1 to the 5’ and U2 to the 3’

66
Q

which end is first to be cleaved in splicing? what kind of rxns?

A

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
Q

the genetic code is described as degenerate and unambiguous, non overlapping and non punctunated. these mean

A

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
Q

what is the enzyme that activates amino acids? what kind of bond? what are the types and what other function can it do?

A

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
Q

aminoacyl tRNA synthetase uses what energy source?

A

I ATP -> 1 AMP

70
Q

inosine can bond to which nucleotides?

71
Q

hoogsteen base pair

72
Q

the prokaryote ribosome has what parts? what is the total svedberg unit?

A

70s made up of 50s (large) and 30s (small)

*** less important:
their small subunit = 16s rRNA unit
large = 5s and 23s

73
Q

the Eukaryote ribosome has what parts? what is the total svedberg unit?

A

80s made up of 60s (large) and 40s (small)

*** less important:
their small subunit = 18s rRNA unit
large = 5s, 28s, 5.8s

74
Q

what are the initiation sequences of translation?

A

before the AUG codon, there is a shine delgarno sequence in prokaryotes
Kozak sequence in eukaryotes

75
Q

which part of the ribosome is responsible for finding the shine delgardo sequence?

A

the small subunit attaches and scans, the 16s piece bonds to the sequence

76
Q

in prok and euk, what is typically the first amino acid to be added in translation?

A

prok - fmet

euk - met

77
Q

after the initiation sequence is found, what initiation factors bond?

A

IF3 to the small ribosome unit and IF1 to the A site of the ribosome

78
Q

IF2 does what?

A

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
Q

elongation factors in translation:

A

EFTu, EFG, EFTs

80
Q

EFTu does what?

A

EFTu bonds to GTP and the incoming tRNAs and helps them into the A site

81
Q

EFTs does what?

A

reloads EFtu with GTP, serves as an intermediate

82
Q

does the peptide bond formation take energy? what is the rRNA piece that helps form the peptide bond?

A

no, due to atp–> amp in tRNA activation

the 23s rRNA adenine is the active site

83
Q

EFG does what

A

EFG-GTP helps in translocation

84
Q

the release factors of translation do what?

A

RF1 and RF2 are responsible for recognizing the stop codons.

RF3-GTP help release happen, cause hydrolysis of the growing peptide chain.

85
Q

in eukaryotes, Inititation factors are eIF_. what factors bind the 5’ cap to begin initiation?

A

eIF 4A, 4B, 4G,

86
Q

what eukaryotic initiation factor can make translation stop if phosphorylated?

87
Q

what is on a polypeptide that tells the cell where to send the polypeptide?

A

signal peptide or signal patch. can be continuous sequences or not.

88
Q

what atp dependent molecule brings polypeptides to the ER?

A

signal recognition particles (SRP)

89
Q

what is RISC

A

RISC is RNA-induced silencing complex that uses miRNA or siRNA to silence genes via destroying mRNA or binding to the DNA gene

90
Q

actions of p53

A 
activates expression (transcrition/translation) of several genes:
activate DNA repair proteins when DNA has sustained damage, causing repari, arrest, or apoptosis
91
Q

what is satellite dna?

A

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)

Y Biochemistry I (6 decks)

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