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BIOL2010 - Flow of Genetic Information > Transcription > Flashcards

Transcription Flashcards

1
Q

how can RNA fold into structures?

A

base pairing and covalent bonds

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2
Q

what functions do RNA molecules have?

A

structural and catalytic

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3
Q

types of RNAs?

A

ribosomal
transfer
messenger
non coding

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4
Q

most common form of protein production control?

A

regulation of transcription as also controls the amount

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5
Q

forms of protein production control?

A 
transcription
RNA processing
RNA transport and localisation 
translation 
mRNA degradation
protein activity
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6
Q

define a gene?

A

entire nucleotide sequence required to direct protein synthesis

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7
Q

components of a gene?

A

5’ promoter region
coding region
3’ control region

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8
Q

why is RNA polymerase proofreading less important?

A

will be replaced very soon, so none occurs

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9
Q

how big is the transcription bubble?

A

12-14 bp

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10
Q

reaction rate of RNA polymerase?

A

40 b s-1

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11
Q

where does RNA strand get released?

A

out of the exit tunnel

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12
Q

how does RNA polymerase bind?

A

has a positively charged cleft, which has a loose association with the negatively charged DNA.

moves until it recognises a promoter sequence and then binds tightly

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13
Q

steps of transcription?

A

template recognition & initiation
elongation
termination

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14
Q

describe initiation?

A

polymerase located promoter and unwinds the DNA

upon binding - closed complex

when strands are melted apart - open complex

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15
Q

how long does the RNA polymerase remain bound to the promoter for?

A

until the chain is 8 bases long

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16
Q

describe elongation?

A

RNA is in the exit hole

once >10 bases, polymerase tightens its grip and transcribes the rest of the gene

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17
Q

describe termination?

A

enzyme dissociates from the template when it reaches a termination sequence and releases a complete RNA chain

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18
Q

where does transcription differ in prokaryotes and eukaryotes?

A

initiation
both have RNA polymerase enzyme, slightly different structures
eukaroytes need a much more regulated process for their complexity

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19
Q

what are constituitive genes?

A

switched on all the time

“housekeeping”

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20
Q

what are regulated genes?

A

controlled - might be due to change in food source that switches on genes to encode enzymes which are needed to metabolise that sugar

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21
Q

define operon?

A

genes encoding for proteins in the same pathway that are located adjacent to one another and controlled as a single unit that is transcribed into a polycistronic RNA - no introns

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22
Q

lac operon?

A

switches on genes that encode enzymes which are needed to metabolise lactose

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23
Q

what is the site of transcription initiation in DNA/

A

promoter

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24
Q

why are promoters recognised by polymerase?

A

consensus sequence

25
Q

structure of bacterial RNA polymerase?

A

2 alpha subunits for enzyme assembly

beta and beta prime form catalytic centre

sigma binds to promoter

26
Q

what is the core enzyme?

A

alpha and beta units

general affinity for DNA du to being positively charged (Zn and Mg)

27
Q

what happens when sigma unit binds?

A

ensures RNA polymerase only binds at promoter sequences

ups the binding strength by 1000

only enough for 1/3 of polymerases

28
Q

different sigma factors?

A

sigma 70, 32 and 54

29
Q

sigma 32?

A

induced by high temperatures and the accumulation of unfolded proteins

recognises different -35 and -10 sequences

30
Q

sigma 70?

A

general use

31
Q

when does RNA polymerase have 4 subunits?

A

during elongation - releases the sigma subunit by changing its shape after 8-10 bases are released

due to the polymerase being attached to the dna by the rna:dna hybrid

32
Q

negative regulation?

A

transcriptional repressors.

stop RNA polymerase binding. bind to operator/repressor sites

33
Q

positive regulation?

A

transcriptional activators.

activator binds to a specific site and helps RNA polymerase to bind

34
Q

lac repressor?

A

CAP activating protein

35
Q

intrinsic terminators?

A

run of ATs in the template strand and a 2 fold symmetric sequence to form a stem loop structure in the RNA.

stalls RNA polymerase

when it pauses, RNA-DNA hybrid unravels due to the weakly bonded AU terminal region

36
Q

what affects efficiency of termination?

A

sequence of the hairpin and the length of the U rich region

37
Q

rho dependent termination?

A

Rho is a prokaryotic transcription protein.

each subunit has:

  • RNA binding domain
  • ATP hydrolysis domain

moves along the RNA just behind. when it stalls at the hairpin loop, breaks the RNA-DNA bps due to helicase activity

38
Q

how is transcriptional control exerted?

A

binding of RNA polymerase - promoters and transcription factors

long range control - locus regions

chromatin remodelling - histones and histone deacetylases

DNA methylation - CpG islands and imprinting

39
Q

which polymerase transcribes all genes that encode proteins and some microRNAs?

A

RNA polymerase III

40
Q

How many subunits does RNA polymerase have?

A

12 not the 5 that bacteria have

cannot initiate transcription as no sigma factor, requires transcription factors instead

41
Q

general transcription factors?

A

common to all promoters

help RNA polymerase II bind

42
Q

transcriptional activators?

A

help attract RNA polymerase II to the promoter

regulate rate and tissue specificity of gene expression

43
Q

where on the DNA do proteins bind?

A

in the major groove of the double helix

44
Q

TFII?

A

General transcription factors for RNA Pol II

Position RNA Pol and separate DNA

Release RNA Pol from promoter

45
Q

Which part of TFIID recognises the DNA sequence?

A

TBP recognises TATA box

46
Q

What must be positioned in order for RNA Pol II to bind and transcribe mRNA?

A

TFIID, TFIIB and TFIIA

47
Q

What can bind to make the PIC?

A

Pre initiation complex

TFIIF/E/H have ATPase activity and helicase activity so provide energy for movement of the complex and elongation of the transcription bubble

48
Q

Subunits of TFIIH?

A

9 subunits

ATPase, helicase and protein kinase

49
Q

Action of TFIIH?

A

Phosphorylates the C terminal domain of RNA Pol II, next to the exit channel for RNA so allows the loading of other proteins onto the RNA to protect it and prepare for future processes

Helicase action - Changes the conformation of Pol II, tightens grip, removing the interactions between TFIIs and DNA. General transcription factors dissociate and acquires new proteins, incl elongation factors

50
Q

Upstream Sequence Elements?

A

Transcription can be enhanced by the binding of transcription factors to these sites. Can be tissue specific activation.

51
Q

GH deficiency?

A

Due to a mutation in Pit-1 (USE)

52
Q

An USE motif that is bound by general transcription factors?

A

Sp1 binds to GGGGGG

Found in all cell types

53
Q

An USE motif that confers tissue specific expression?

A

MyoD binds to CANNTG
N = any base
MyoD is a muscle specific transcription factor

54
Q

An USE motif in response to particular stimuli?

A

Oestrogen receptor binds to AGGTCANNNTGACCT

55
Q

Enhancer region?

A

Sequences of DNA to which a large number of transcription factors bind and fold round to bind to the pre-initiation complex

may provide an entry point for RNA polymerase or bind other proteins that assist RNA

56
Q

Where can enhancers be?

A

upstream, downstream or in intron

57
Q

what don’t work when far away from TATA box?

A

upstream sequence elements

58
Q

Transcription Factor structure?

A

one region of amino acids for DNA binding

activation domains

inhibitory domains

59
Q

post transcriptional processing?

A 
5' cap 
3' processing and polyadenylation 
splicing 
editing 
transport to cytoplasm for translation

BIOL2010 - Flow of Genetic Information (4 decks)

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