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L 211 > exam 2 (prokaryote transcription) > Flashcards

exam 2 (prokaryote transcription) Flashcards

1
Q

first step in the flow of genetic information

A

transcription

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2
Q

what is used to transcribe RNA to DNA

A

RNA polymerase

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3
Q

what does RNAP need to conduct RNA synthesis

A

normally need a DNA template strand, but sometimes they use RNA template strands

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4
Q

what occurs for a phosphodiester bond to form

A

3’ OH group of growing RNA chain makes a nucleophile attack on the alpha phosphoryl group

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5
Q

what drives reaction drives the phosphodiester bond to completion

A

hydrolysis of pyrophosphate, releasing a lot of energy

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6
Q

what is reverse transcription

A

strings deoxyribonucleotides together, just like DNA replication

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7
Q

what occurs during therapeutic inhibition of (reverse) transcription

A

retroviruses must convert their RNA genome into DNA for integration in the host cell’s genome

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8
Q

characteristics of nucleoside analog reverse transcriptase inhibitors

A

lack 3’ -OH
no attachment point
nonspecific
can be used by DNAP

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9
Q

how are nucleoside analog reverse transcriptase inhibitors converted into nucleotides

A

addition of phosphate groups

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10
Q

what is the difference between nucleoside/nucleotide analog reverse transcriptase inhibitors

A

NtARTIs (nucleotide) do not require phosphorylation to be in cells

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11
Q

the nascent RNA chain grows only in what direction

A

5’ –> 3’

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12
Q

what is the difference between RNAPs and DNAPs when synthesizing

A

RNAPs doesn’t need a primer to start synthesizing a nucleic acid chain

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13
Q

what direction is upstream? downstream?

A

upstream goes towards 3’ direction

downstream goes towards 5’ direction

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14
Q

the newly transcribed RNA strand is based off of what DNA strand

A

template strand

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15
Q

core bacterial RNAP contains 5 subunits, what are they?

A

a1, a2, b1, b’, w

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16
Q

what is a transcription promoter

A

initiation signal that is required in transcription

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17
Q

is downstream positive or negative? upstream?

A 
downstream = positive 
upstream = negative
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18
Q

what are consensus sequences

A

sequences derived from alignments

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19
Q

pribnow box

A

-10 sequence

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20
Q

what is DNase

A

enzyme that cuts up DNA in nonspecific way and isolates the the protected DNA fragment

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21
Q

mutations in the -35 box result in

A

decreased lac expression

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22
Q

mutations in the -10 box result in

A

increased lac expression

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23
Q

altering the space between boxes results in

A

decreased expression

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24
Q

what are sigma factors

A

expressed by bacteria and RNAP
6th factor in DNAP gives brain
tells what sequences to go to and what to do

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25
Q

Sigma54 RNAP function

A

activator proteins bind enhancer elements and loop to promoters

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26
Q

the complete bacterial RNAP holoenzyme contains 6 subunits, which ones is added on?

A

sigma

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27
Q

what is a holoenzyme

A

complete form of an enzyme complex that contains all subunits for needed activity

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28
Q

how is DNA melted during transcription

A

hydrolyzing with ATP

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29
Q

what occurs when DNA interacts with open complex

A
  • RNAP open complex is made
  • RNAP unwinds DNA adjacent to open complex, scrunching it
  • transcribes 8-10 nucleotides
  • scrunched DNA is rewound
  • abortive transcript is released
  • builds up enough energy to spring away from promoter
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30
Q

why does RNAP pause

A
  • mediated by various sequence elements
  • important for proofreading the chain
  • mismatches promote pausing
  • cuts out extruded DNA
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31
Q

what are the 2 mechanisms for transcription termination

A

intrinsic and Rho-dependent

32
Q

why does intrinsic termination depend on 2 DNA sequences

A

lead to specific structures in growing RNA molecule, that causes RNAP to terminate transcription

33
Q

what allows for the formation of a stem loop in the RNA molecule

A

being G and C rich

34
Q

why is having a stretch of 8-10 nucleotides, rich in U important?

A

release of newly generated RNA chain from RNAP

35
Q

what is negative regulation

A

regular transcription takes place until a repressor protein binds to DNA repressor site

36
Q

what is positive regulation

A

transcription doesn’t take place until activator protein binds to DNA activator site

37
Q

what is an operon

A
  • segment of DNA containing multiple genes regulated by a single promoter
  • generates mRNA with multiple protein-coding sequences
38
Q

are operons more common in eukaryotes or prokaryotes

A

common in prokaryotes.

rare in eukaryotes

39
Q

what is B-galactosidase

A

breaks down lactose into galactose and glucose. produced by the lacZ gene

40
Q

what is lactose permease

A

allows lactose to get into cells. produced by the lacY gene

41
Q

what is B-galactoside transacetylase encoded by

A

lacA gene

42
Q

how do the levels in B-galactosidase, permease, and transacetylase change as lactose is added to a previously lactose-free solution

A

the protein levels/synthesis increases as lactose is added to the solution

43
Q

what does it mean if enzymes are repressible

A

their synthesis is decreased in response to a small molecule

44
Q

what does it mean if enzymes are constitutive

A

they are always expressed and generally perform basic cellular “housekeeping” functions

45
Q

what 2 classes were the mutations discovered by Monod and Jacob

A

lacl and lacOc

46
Q

are lacOc mutations dominant or recessive

A

some were dominant and some were recessive

47
Q

are lacl mutations dominant or recessive

A

recessive

48
Q

what is the lac repressor

A

lacI encodes a factor that represses lac mRNA transcription

49
Q

when can lacOc cause synthesis of lac mRNA`

A

when it is on the same DNA molecule as lacZ+

50
Q

what is the established gene order

A

lacI, lacO, lacZ, lacY, lacA

51
Q

what is referred to as the operator

A

lacO, which was later found to be the binding site for the lac repressor

52
Q

describe the lac operon model

A

transcription occurs as the repressor binds to site and inducer attaches to fot lac mRNA to be transcribed (into the 3 proteins)

53
Q

what segments are the antiterminator

A

2 + 3

54
Q

what segments are the terminator

A

3 + 4

55
Q

what is tryphtophan responsible for in termination

A

it makes sure the ribosome doesn’t get stuck at the adjacent Trp codons, therefore it’s important to have a high concentration

56
Q

when transcribing trp mRNA, RNAP pauses. when and why?

A

it pauses as its reaches segment 2 in the ribosome, to synchronize transcription and translation

57
Q

what allows the 1-2 and 3-4 hairpins to form

A

dissociation of the ribosome

58
Q

the trpL has 4 segments, what distinct structures can be formed

A

terminator 3+4

antiterminator 2+3

59
Q

function of the trpR protein

A

on/off switch for the trp operon at the level of transcription initiation

60
Q

attenuation

A

control mechanism, involves regulation of elongation and termination via RNA and ribosome

61
Q

what is the attenuator

A

sequence of 28 bases in the leader

62
Q

what is designated as the leader of trpL

A

trpE, the first codon

63
Q

the trp mRNA has how many nucleotides and in which direction

A

162 nt upstream

64
Q

function of the trp operon

A

-encodes genes involved in tryptophan synthesis

-

65
Q

structure of trp operon

A

promoter, operator, and 5 structural genes

66
Q

trp operon is regulated at what levels of transcription

A

initiation, elongation, and termination

67
Q

what occurs when cells grow in glucose

A

shut off transcription of lac genes

68
Q

describe catabolite repression

A

cAMP forms a complex with a cAMP receptor protein, that binds to an activator site upstream of the lac promoter

69
Q

what does E. coli use for fuel

A

glucose

70
Q

what is the dimer of dimers, and binds to an operator

A

lac repressor

71
Q

how many lac operators are there?

A

3

72
Q

what structure does each DNA binding domain have?

A

supersecondary structure

73
Q

purpose of the tetramerization helix

A

allows multiple repressor molecules to interact with one another

74
Q

what is a result of low tryptophan

A

ribosome stalls, removes segment 1, allowing 2-3 hairpin to form, rather than 3-4

75
Q

allolactose causes the lac repressor to??

A

to fall off the lac operator

76
Q

tryptophan causes the lac repressor to??

A

to be able to bind to the trp operator

L 211 (12 decks)

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