block b lec 1 Flashcards

(60 cards)

1
Q

what is the least stable mRNA

A

bacterial mRNAs

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2
Q

what is being translated as mRNA is being synthesised

A

bacterial genes

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3
Q

what is to be said about transcription and translation

A

coupled
occurs at same time in same compartment

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4
Q

what do bacterial mRNAs lack

A

methyl-g caps
poly-a tails

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5
Q

what is the shine dalgarno seq

A

ribosome binding site
upstream of start codon

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6
Q

where is the promoter usually found

A

-10 and -35 elements

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7
Q

where are more highly expressed genes found

A

near oriC

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8
Q

what are operons

A

cluster of protein coding open reading frames transcribed as a single mRNA

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9
Q

where are operons expressed from

A

a single promoter

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10
Q

what are the individual coding regions in operons called

A

intercistronic regions

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11
Q

what are genes in a given operon are often related to

A

function

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12
Q

what does control of an operon do

A

control expression of entire function

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13
Q

what are coding sequences/OFRs transcribed as

A

polycistronic mRNA

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14
Q

what is transcription catalysed by

A

RNA polymerase

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15
Q

what does bacterial RNA polymerase do

A

unwind DNA to form a transcription bubble

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16
Q

what does the transcription bubble contain

A

ss non template DNA and the 8-9bp template DNA/RNA hybrid

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17
Q

what does RNAP do during RNA synthesis

A

moves along DNA while maintaining transcription bubble until end of RNA synthesis

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18
Q

structure fo RNAP core enzyme

A

5 subunits
a2bb’w

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19
Q

RNAP holoenzyme structure

A

a2bb’w(sigma)
core and sigma factor that recognises promoter seq

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20
Q

what forms the main catalytic centre in RNAP

A

B and B’

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21
Q

a2 role in RNAP

A

primary role is in RNAP assembly

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22
Q

role of w

A

non essential

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23
Q

what does RNA pol holoenzyme do

A

helps catalyse the opening of the DNA strands near the transcription start point
transcription initiation

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24
Q

what determines promoter specificity in RNA pol holoenzyme

A

alpha (sigma factor)

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25
what does region 1 interact with (RNA pol holoenzyme)
via an alpha helix in the protein
26
what does region 2 interact via (RNA pol holoenzyme)
interacts with DNA via a helix turn helix motif, forming H bonds with DNA bases
27
what are the 3 major phases of transcription
initiation elongation termination
28
how is the holoenzyme formed
sigma factor transiently interacts with RNAP core to form holoenzyme
29
what does RNAP holoenzyme do during transcription initiation
RNAP holo binds the promoter (closed complex) and opens DNA duplex (open system)
30
when is the sigma factor usually released
before transcription elongation core RNAP continues
31
what does RNAP do in elongation
moves along the DNA while maintaining the transcription bubble until the end of the RNA synthesis (transcription termination)
32
what are transcriptional 'pause' sites potential for
potential for regulation
33
transcription cofactors associate with RNAP and affects what
rate of elongation/affect transcription termination eg NusA, NusG, DksA
34
what are the specific sequnces at the end of genes where mRNA synthesis terminates at called
terminators
35
what factors allow RNAP to read through terminators
anti termination factors
36
what are the 2 types of transcription termination called
intrinsic terminators rho dependent terminators
37
what is the intrinsic terminator structure
palindrome followed by poly-U tract stem loop causes pause- leads to dissociation of RNAP
38
what do rho dependent terminators req
a protein, Rho (p) factor
39
role of Rho dependent terminators
binds specific seq in the mRNA moves down the transcript until it contacts the elongating RNAP
40
4 examples of regulation
protein stability translation initiation mRNA stability transcription initiation (transcription factors or sigma factors)
41
what is a regulon
the set of all genes regulated by a particular factor (sigma factor or TF)
42
what is global regulation
genes in a regulon distributed throughout the genome
43
what is E.coli maltose regulon
a number of operons involved in transport and utilization of maltose each operon has a binding site
44
what is local regulation
bacteria often need to regulate just a few specific genes
45
4 types of regulation
global or local regulation positive or negative regulation
46
what is the difference between positive and negative regulation
positive is turning the gene on negative is turning the gene off
47
what do sigma factors give RNAP
its specificity
48
2 major groups of sigma factors
sigma 70 sigma 54
49
sigma 70 group 4 sigmas function
extracytoplasmic function (ECF) sigma factors
50
what do TFs bind
bind specific DNA sequences, usually close to the promoter and modulate transcriptionn, usually responding to specific signals
51
what is TF activity regulated by
small mols called effectors corepressors or inducers
52
what do TFs regulate
gene expression
53
what do dimers bind
inverted repeats
54
3 different protein motifs used to bind DNA
helix turn helix zinc finger leucine zipper
55
what is the general principle of making gene deletions
remove/replace most/all of the coding sequence of a gene
56
what does caveat mean
cannot delete essential genes
57
general principle of reporter gene fusions
expression of a protein with an easy to assat activity is used as a proxy for the expression of a gene of interest
58
role of beta-galactosidase in LacZ reporter fusions
cleaves chromogenic substrates (protein expressed and active- colour-)
59
experiments to identify structure
NMR crystalography
60
how does ChIP work
freezes protein and DNA together, pull out protein, sequence DNA to figure out where in the genome protein binds (uses formaldehyde)