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BM330 microbiology > block b lec 1 > Flashcards

block b lec 1 Flashcards

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Biology 101 flashcards
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
Q

what does region 1 interact with (RNA pol holoenzyme)

A

via an alpha helix in the protein

26
Q

what does region 2 interact via (RNA pol holoenzyme)

A

interacts with DNA via a helix turn helix motif, forming H bonds with DNA bases

27
Q

what are the 3 major phases of transcription

A

initiation
elongation
termination

28
Q

how is the holoenzyme formed

A

sigma factor transiently interacts with RNAP core to form holoenzyme

29
Q

what does RNAP holoenzyme do during transcription initiation

A

RNAP holo binds the promoter (closed complex) and opens DNA duplex (open system)

30
Q

when is the sigma factor usually released

A

before transcription elongation
core RNAP continues

31
Q

what does RNAP do in elongation

A

moves along the DNA while maintaining the transcription bubble until the end of the RNA synthesis (transcription termination)

32
Q

what are transcriptional ‘pause’ sites potential for

A

potential for regulation

33
Q

transcription cofactors associate with RNAP and affects what

A

rate of elongation/affect transcription termination
eg NusA, NusG, DksA

34
Q

what are the specific sequnces at the end of genes where mRNA synthesis terminates at called

A

terminators

35
Q

what factors allow RNAP to read through terminators

A

anti termination factors

36
Q

what are the 2 types of transcription termination called

A

intrinsic terminators
rho dependent terminators

37
Q

what is the intrinsic terminator structure

A

palindrome followed by poly-U tract
stem loop causes pause- leads to dissociation of RNAP

38
Q

what do rho dependent terminators req

A

a protein, Rho (p) factor

39
Q

role of Rho dependent terminators

A

binds specific seq in the mRNA moves down the transcript until it contacts the elongating RNAP

40
Q

4 examples of regulation

A

protein stability
translation initiation
mRNA stability
transcription initiation (transcription factors or sigma factors)

41
Q

what is a regulon

A

the set of all genes regulated by a particular factor (sigma factor or TF)

42
Q

what is global regulation

A

genes in a regulon distributed throughout the genome

43
Q

what is E.coli maltose regulon

A

a number of operons involved in transport and utilization of maltose
each operon has a binding site

44
Q

what is local regulation

A

bacteria often need to regulate just a few specific genes

45
Q

4 types of regulation

A

global or local regulation
positive or negative regulation

46
Q

what is the difference between positive and negative regulation

A

positive is turning the gene on
negative is turning the gene off

47
Q

what do sigma factors give RNAP

A

its specificity

48
Q

2 major groups of sigma factors

A

sigma 70
sigma 54

49
Q

sigma 70 group 4 sigmas function

A

extracytoplasmic function (ECF) sigma factors

50
Q

what do TFs bind

A

bind specific DNA sequences, usually close to the promoter and modulate transcriptionn, usually responding to specific signals

51
Q

what is TF activity regulated by

A

small mols called effectors
corepressors or inducers

52
Q

what do TFs regulate

A

gene expression

53
Q

what do dimers bind

A

inverted repeats

54
Q

3 different protein motifs used to bind DNA

A

helix turn helix
zinc finger
leucine zipper

55
Q

what is the general principle of making gene deletions

A

remove/replace most/all of the coding sequence of a gene

56
Q

what does caveat mean

A

cannot delete essential genes

57
Q

general principle of reporter gene fusions

A

expression of a protein with an easy to assat activity is used as a proxy for the expression of a gene of interest

58
Q

role of beta-galactosidase in LacZ reporter fusions

A

cleaves chromogenic substrates (protein expressed and active- colour-)

59
Q

experiments to identify structure

A

NMR
crystalography

60
Q

how does ChIP work

A

freezes protein and DNA together, pull out protein, sequence DNA to figure out where in the genome protein binds (uses formaldehyde)

BM330 microbiology (5 decks)

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