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YEAR 2 S1 MOLECULAR > Mayerhoff > Flashcards

Mayerhoff Flashcards

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1
Q

RNA polymerase II does what

A

mRNA transcription

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2
Q

how does euk RNA Pol II work

A
  • DNA strand is separated (slightly bent to enable separation)
  • RNA synth in active centre
  • RNA transcript comes out of enzyme
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3
Q

what is the role of the clamp domain in RNA Pol II

A
  • when RNA Pol II engages with DNA, the clamp domain sits MORE TIGHTLY on the enzyme thus BINDING IT
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4
Q

what is the role of the clamp domain in RNA Pol II

A
  • when RNA Pol II engages with DNA, the clamp domain sits MORE TIGHTLY on the enzyme thus BINDING IT
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5
Q

what is the CARBOXY-TERMINAL DOMAIN (CTD) in RNA Pol ll

what is its role

A
  • a seq of SEVEN aa that is repeated 25 TIMES in yeast and 52 TIMES in vertebrates
  • PHOSPHORYLATION SITE (fo those aa) important for REGULATION of enzyme
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6
Q

to transcribe a gene, RNA Poll II has to do what

A 
INITIATION 
1) recognise a start point in dsDNA: PROMOTOR 
2) BIND promotor
3) SEPARATE DNA strands 
4) INITIATE transcription at start site 
ELONGATION 
1) elongate until stop signal
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7
Q

what is a promotor

A

a DNA seq that determines the site of transcription INITIATION for a RNA Pol

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8
Q

what are the 3 main types of promotors in euk

A

1) TATA box
2) Initiator
3) CpG islands

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9
Q

describe TATA boxes

A
  • strong
  • sharp
  • 10-15%
  • inducible genes, prevalent in highly transcribed genes
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10
Q

describe Initiator complexes

A
  • variable
  • sharp
  • 15-30%
  • inducible genes, usually lacking TATA box
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11
Q

describe CpG islands

A
  • weak
  • broad
  • 60-70%
  • genes transcribed at a low rate (eg housekeeping genes)
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12
Q

the TSS (transcription start site) is what

A

+1

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13
Q

where is the TATA box

A

~30 bases BEFORE the TSS

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14
Q

give examples of genes that TATA boxes could act as a promotor for
mutations in the TATA box cause what

A
  • highly transcribed genes O
  • eg viral genes, cell cycle components, tissue specific genes
  • mutations within the seq ABOLISHES function
  • downstream/upstream movement of the TATA box causes shift the TSS
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15
Q

Initiator is what in comparison with the TATA box

A

an ALTERNATIVE

MUTUALLY EXCLUSIVE

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16
Q

where is the Initiator promotor found

A
  • -2 to +4 (O encompasses TSS)
  • if Initiator is moved up or downstream, the TSS moves too
  • Initiator is less well defined
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17
Q

describe the precision of CpG islands

how common are they
whatare they rich in

A
  • less precise TSS
  • 70% of genes
  • housekeeping genes
  • GC rich (O less bendy)
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18
Q

what is req for transcription initiation (“Construction” of the polymerase complex on the promoter)

A
  • RNA Pol

- General Transcription Factors (GTFs)

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19
Q

what is the function of GTFs

A
  • position RNA Pol II on the promotor
  • help separate DNA strands for transcription
  • form the PREINITIATION COMPLEX: GTFs & RNA Pol II
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20
Q

what is the role of TFIID

A
  • a GTF, it is the FIRST protein to bind DNA in formation of pre-initiation comple
  • 14 different subunits (O big)
  • cont TBP (TATA Box Binding Protein)
  • TBP= interacts with minor groove of DNA, causing BEND of DNA
    it is the first protein to bind DNA in formation of pre-initiation comple
  • TAFs (TBP Associaed Factors): recruit to TATA-less promotors (the promotors that don’t use TATA box), contacts to Initiator and DPE
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21
Q

size

what is the role of TFIIA

A
  • 2 subunits
  • binds DNA UPSTREAM of TATA box AFTER TFIID has bound
  • binds to TBP
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22
Q

size

what is the role of TFIIB

A
  • monomer
  • binds DNA on EITHER side of the TATA box AFTER TFIIA
  • binds to TBP
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23
Q

TFIID, TBP, TFIIA ANDTFIIB form what together

A

upstream promotor complex

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24
Q

after the upstream promotor complex is formed, what happens

what is formed

A

RNA Pol II joins

  • it forms a Pol II/ TFIIF complex
  • this complex then binds to the UPSTREAM promotor complex
  • positions Pol II over the TSS
  • forms the CLOSED PREINIIATION COMPLEX (PIC)
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25
after the CLOSED PREINITIATION COMPLEX is formed, what happens next
- TFIIE (heterodimer) binds to Closed Preinitiation complex | - creates docking site for TFIIH
26
TFIIF is what size
heterodimer
27
after TFIIE has bound, what happens
TFIIH binds - 10 subunits - cont HELICASE (unwinds DNA) - cont KINASE (phosphorylate RNA Pol II...?)
28
why is it called a closed preinitiation complex
because DNA is still mostly in a DOUBLE HELIX
29
at every promotor how many peptides are present
33 peptides | combined mass of 1.5MDa
30
what is the order of TFII binding
D A B F E H
31
how do we transition from transition to transcription
by going from CLOSED PREINITIATION COMPLEX to OPEN PREINITIATION COMPLEX (PIC)
32
what happens to form the Open Preinitiation complex
- TFIIH HELICASE subunit unwinds DNA (req ATP) | - this pushes back on the promotor bound GTFs, forming transcription bubble
33
how is the INITIALLY TRANSCRIBING COMPLEX formed
- TFIIB releases RNA exit channel - TFIIH KINASE activity phosphorylates CARBOXY-TERMINAL DOMAIN (CDT) of Pol II - recuits capping factors - TBP/TFIID are left at promotor - other GTFs dissociate
34
the DNA template is read from which direction
3'->5'
35
for PAUSING of transcription which factors are req
1) NELF (negative elongation factor) | 2) DSIF (DRB Sensitivity Inducing Factor)
36
which factor makes transcription continue
P-TEFb= cyclin-CDK - phosphorylates NELF and DSIF - phosphorylates Poll II CTD - causes Pol II to switch to ELONGATION mode, enzymes become processive, splicing factors also recruited
37
give an example of a viral example of the use of RNA Pol II | what is the significance for treatment
HIV uses RNA Pol ll - maximises elongation efficiency - TAR hairpin formed (RNA base pairs with itself) - binds Tat protein - recruits P-TEFb (positive factor to help overcome neg factors) - switches to elongation DRUGGABLE TARGET?
38
what are proximal promotor elements
- seq close to TSS, position may affect activity - short ~6-10bp - often direction INDEPENDENT - often TISSUE SPECIFIC
39
what are distal "enhancer" elements
- far from promotor(up to 50,000bp up/downstream or intronic) - typically ~50-200bp, but composed of several functional elements - direction independent - usuallu tissue specific
40
whta is a transcription factor
transcription factor: protein (other than RNA Pol) that initiates or regulates transcription in eukaryotic cells
41
specific transcription factors are what
- Transcription Activators or Transcription Repressors - Stimulate or inhibit transcription of particular genes by binding to their regulatory sequences - Many: ~1,400 in human genome - Modular domain structure
42
GTFs are for what
combining with RNA Pol ll to make the preinitiation complex
43
what is the structure of a specific transcription factor how are domains linked
2 main domains - DNA binding domain: recognises specific seq - an ACTIVATION or REPRESSION domain: alters transcription rates linked by: flexible, disorded protein domain
44
describe DNA binding domains in specific transcription factors give an example of a DNA binding domain, where is it found
- often DIMERS: homo/hetero - NON-COVALENT INTERACTIONS are SEQ SPECIFIC: H bonds, ionic interactions - a helix inserts into MAJOR GROOVE of DNA eg helix-turn-helix in Bacteriophage 434 repressor
45
describe Zinc-finger proteins | what are they
- a DNA BINDING DOMAIN - short seq folds around co-ordinated Zn2+ - cysteine and histidine side chains
46
what are the 2 types of Zinc-finger proteins
C2H2 zinc finger - most common on humans - monomer C4 - in ~50 transcription factors - steroid receptor superfamily or nuclear rceptors - homo/heterodimer
47
whata re Leucine-zipper proteins | describe them
DNA BINDING DOMAIN - extended alpha helices - basic residues interact with DNA backbone in major groove - coiled coil dimerization (stabilises by HYDROPHOBIC interactions between monomers) - can form heterodimers - dimers 'grip' DNA
48
what are basic helix-loop-helix (bHLH) proteins | describe them
DNA BINDING DOMAIN - bind at N-termini - non-helical loops from leucine zipper-like coiled coil dimerization domains - can form heterodimers
49
describe DNA binding activation domains
- structurally diverse - often rich in one type of aa - may have intrinsically disordered conformation, but become more ordered with a co-activator
50
what do many transcription factors bind as? | why are transcription factor interactions important
DIMERS | - transcription factor interaction increasse gene control options
51
what effect does co-operation of monomeric transcription factors have
- inc affinity | - stabilises binding to composite site
52
what is the enhancosome
Multiple transcription factors co-operate at distant regulatory sites
53
what regulates regulators
- the transcription of TRANSCRIPTION FACTORS themselves is regulated - LIGAND BINDING: interaction w/ ligands eg drugs
54
explain the role of nuclear receptors and ligand binding in
- interact with steroid hormones - have a DNA binding domain and activation domain and ligand binding domain which make TF - bind w/ LIPID SOL HORMONES - family of ~50 transcrtiption factors - bind as HOMO or HETEROdimers C4 zinc finger proteins
55
what does ligand binding do to nuclear receptors
changes subcellular localisation | because TFs can only bind DNA if they are in the NUCLEUS
56
how is subcellular localisation of TFs changed
in cytosol (O cannot bind DNA) - before hormone binds to TF, the TF interacts with CHAPERONES, which prevent TF from moving to nucleus - hormone diffuses into cell, and binds to LIGAND BINDING DOMAIN of TF - causes CHANGE IN SHAPE, conformational change of LF domain - O free from chaperones - O can move to nucleus - DNA binding domain can now bind - Activation domain can activate gene
57
what are the 3 basic mechanisms that underoin transcriptional activation
1) Modulation of chromatin structure - impacts the ability of general transcription factors to bind 2) Recruitment of RNA polymerase - Via mediator complex or recruitment of general transcription factors (TFIID) 3) Stimulation of elongation - Via recruitment of P-TEFb or other elongation factors
58
how is chromatin structure modulated
more tightly packed means less access for TF and RNA Pol II
59
heterochromatin describe
- inactive genes - more condensed - dark staining - histone deacylation - centromeres, telomeres
60
histones being more acetylated means what
- LESS densely packed | - O more accessible
61
histone acetlyl transferases make DNA more/less accessible
MORE
62
which TF is used to repress transcription
``` HISTONE DEACETYLASE CO-REPRESSOR (HDAC) - recruited to promotor via binding to transcription REPRESSOR DOMAIN - causes HYPOACETYATION - inc DNA-HISTONE interaction - inc packaging to 30nm fibre thus preventing GTFs binding ```
63
which TF is used to activate transcription
``` HISTONE ACETYL TRANSFERASE (HAT) - co-activator receruited to promotor via binding to TRANSCRIPTION FACTOR ACTIVATOR DOMAIN - causes HYPERACETYLATION - dec DNA-HISTONE interaction - dec packaging to 30nm fibre thus allowing GTFs to bind ```
64
if DNA is too tightly packed for even TFs to reach, how is it accessed
PIONEER TFs - bind one side of DNA helix even if DNA is wrapped around histone octamer - recruit histone acetlyl transferase - recruits more TFs once DNA= partially accessible
65
how is RNA Pol ll recruited
- via activation domains that recruit TFII - use MEDIATOR (connects RNA Poll ll and TFs) - mediator of transcription - molecular BRIDGE to RNA POL II - multiple subunits : some essential to all genes, some specific to 3-10% of genes
66
how is the mediator recruited
- activation domain interacts with MEDIATOR - mediator can simulatneously contact multiple activators (cooperativity) - DNA looping: enhancers
67
incorrect transcription or transcription of mRNA that should not have been transcribed can cause what
- multiple toes (dominant HOXD13 mutation) | - multiple wings on fly

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