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BIOL 200 > Final > Flashcards

Final Flashcards

1
Q

SIR 2,3,4

A

silent information regulator
recruited by RAP1/SIR1
binds to hypoacetylated histone tails
SIR2 is a histone deacetelyase

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2
Q

Leucine Zipper, Leu interval

A

every 7th residue

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3
Q

HLH protein

A

Helix Loop Helix protein

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4
Q

TSIX

A

anti-sense version of XIST

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5
Q

General Transcription Factors for Class 2

A 
TFIIA
TFIIB
TFIID
TFIIE
TFIIF
TFIIH
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6
Q

U2 snRNP

A

binds to intron branching point

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7
Q

SIR1

A

silent information regulator

cooperates with RAP1

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8
Q

hnRNP

A

heterogenous nuclear ribonuclear proteins

associate with RNA to protect or mediate reactions

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9
Q

RAP1

A

binds to DNA silencer sequences & telomeres

compacts chromatin

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10
Q

Gcn5

A

Histone acetyl transferase

Forms co-activator with Gcn4

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11
Q

class-1 transcription products

A

pre-rRNA
28S rRNA
18S rRNA
5.8S rRNA

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12
Q

VP16 Domain

A

efficient viral activation domain, recruits host activator proteins

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13
Q

Gcn4

A

Binds to UAS in yeast

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14
Q

Sin3

A

HDAC scaffold protein
Binds Rpd3 among others
mSin3 in humans

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15
Q

TF Activation domain

A

Protein domain that stimulates transcription

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16
Q

PNK

A

Polynucleotide Kinase - Transfers gamma phosphate from ATP to 5’ end of nucleic acids

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17
Q

SWI/SNF

A

chromatin remodeling proteins in yeast

uses ATP to move nucleosomes

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18
Q

Mediator complex

A

Responsible for:
looping DNA by binding to enhancers,
and recruiting general TFs

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19
Q

TAF

A

TBP Associating Factors

Subunits of TFIID

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20
Q

RFLP

A

Restriction Fragment Length Polymorphism

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21
Q

CTD

A

Carboxy-Terminal Domain
Present on large RNA Pol 2 subunit
Heptapeptide repeat

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22
Q

TFIIH Subunits

A

XPB (3’ to 5’ helicase)
XPD (5’ to 3’ helicase)
CDK7 + Cyclin H
TTDA (related to TrichoThioDystrophy)

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23
Q

CTD S5 phosphorylation attractees

A 
capping enzyme
hnRNPs
splicing factors
polyadenylation factors
export factors
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24
Q

C2H2 Zinc Finger

A

2 Cys 2 His
monomers
3+ finger units

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25
Hometic Transformation
When homeotic protein is mutated, causing body plan change
26
Recognition Helix
Alpha-helical domain of protein which binds to major groove of DNA
27
Common DNA Methylations
H3 K4 -> activates histone H3 K9 -> deactivates histone (K = lysine)
28
CAP site
Promoter sequence upstream of lac operon | cAMP + CAP protein binds to it
29
Intron sequence rules
5' | GU A(branching point) (Py rich) AG | 3'
30
Yeast mating type central loci
MAT, becomes MAT alpha or MATa
31
alpha-amanitin
- blocks RNA Pol II - impedes RNA Pol III (no effect on RNA Pol 1)
32
HMT
histone methyl transferase | usually associated with repression
33
Homeodomain
DNA Binding domain associated with homeotic TFs
34
TFIIH functions
``` DNA Helicase CTD Kinase (S5) ```
35
snRNP
small nuclear ribonuclear proteins | U1 U2 U4 U5 U6
36
Yeast mating type locis
HML alpha and HMRa, on Chromosome 3
37
Yeast mating types
alpha and "a"
38
HDAC
histone deacetylase complex
39
Location of TATA Box
Near [-37,-32] to [-31, -26] | Further upstream of yeast (-90)
40
EtBr
Ethidium Bromide - Common nucleic acid stain
41
PAX6
Developmental gene. In charge of eyes. | Some regulation sequence regions are highly conserved.
42
CTD repeat
YSPTSPS
43
Types of histone modifications
``` acetylation methylation phosphorylation ubiquination (could be others..) ```
44
EMSA
Electrophoretic Mobility Shift Assays
45
Spliesome Cycle Steps
``` U1 + U2 U1 + (U4, U5, U6) + U2 [shuffling] U5 + U6 + U2 [transesterifications] spliced exon + lariat intron [debranching enzyme] spliced exon + linear intron RNA ```
46
DNA Acetylation
neutralizes positive charge on histones | makes DNA easier to access
47
HAT
histone acetyl transferase
48
GAL4
Binds to UAS in yeast when in low-glucose environment | C6 Zinc Finger
49
U1 snRNP
binds to 5' splice site
50
TF Binding domain
Protein domain that binds to DNA
51
5' cap molecule
7' methylguanylate
52
ChiP
Chromatin immunoprecipitation
53
hnRNP domains
RRM, KH domain, RGG repeats
54
Lariat structure
Processed intron, RNA loop with 5'-2' link to adenosine
55
C4 Zinc Finger
4 Cys per unit homo-heterodimers 2 finger units ex: nuclear receptors
56
Class-2 Transcription Initiation
``` TFIID Binds to TATA Box TFIIB -> TFIID TFIIA stabilizes structure RNA Pol II + TFFIIF -> TFIIB TFIIE creates docking site TFIIH + TFIIH kinase -> TFIIE ``` (D, B, A, F, E, H)
57
Initiator
cis-acting promoter sequence sitting on start site -2 to +4 weak consensus sequence (C|A usually)
58
UAS
Upstream activating sequence (yeast promoter)
59
TBP
TATA Box Binding Protein | Subunit of TFIID
60
CTD phosphorylation proteins
TFIIH -> S5 | p-TEF6 + CDK9, Cyclin-T -> S2
61
Transcriptome
Snapshot of all transcripts in a cell at one point in time
62
Ume6
Binds to URS in yeast | Recruits Sin3
63
Activator domain
Domain on activator TFs which recruit HATs
64
XIST
non-coding RNA that coats X chromosome to inactivate it | cis-acting
65
class-2 transcription products
mRNA snRNA (except U6) siRNA miRNA
66
C6
6 Cys per unit | ex: GAL4
67
Repressor domain
Domain on repressor TFs which recruit HDACs | Forms co-repressor complex
68
class-3 transcription products
``` tRNA snRNA U6 5S rRNA 7S rRNA (other small stable RNAs) ```
69
Splicesome
Mediates splicing reaction
70
Homebox genes
Code for homeotic proteins
71
Rpd3
HDAC catalytic protein histone deacetylase binds to Sin3

BIOL 200 (3 decks)

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