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L 211 > exam 2 (prokaryote transcription) > Flashcards

exam 2 (prokaryote transcription) Flashcards

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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
Sigma54 RNAP function
activator proteins bind enhancer elements and loop to promoters
26
the complete bacterial RNAP holoenzyme contains 6 subunits, which ones is added on?
sigma
27
what is a holoenzyme
complete form of an enzyme complex that contains all subunits for needed activity
28
how is DNA melted during transcription
hydrolyzing with ATP
29
what occurs when DNA interacts with open complex
- 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
30
why does RNAP pause
- mediated by various sequence elements - important for proofreading the chain - mismatches promote pausing - cuts out extruded DNA
31
what are the 2 mechanisms for transcription termination
intrinsic and Rho-dependent
32
why does intrinsic termination depend on 2 DNA sequences
lead to specific structures in growing RNA molecule, that causes RNAP to terminate transcription
33
what allows for the formation of a stem loop in the RNA molecule
being G and C rich
34
why is having a stretch of 8-10 nucleotides, rich in U important?
release of newly generated RNA chain from RNAP
35
what is negative regulation
regular transcription takes place until a repressor protein binds to DNA repressor site
36
what is positive regulation
transcription doesn't take place until activator protein binds to DNA activator site
37
what is an operon
- segment of DNA containing multiple genes regulated by a single promoter - generates mRNA with multiple protein-coding sequences
38
are operons more common in eukaryotes or prokaryotes
common in prokaryotes. | rare in eukaryotes
39
what is B-galactosidase
breaks down lactose into galactose and glucose. produced by the lacZ gene
40
what is lactose permease
allows lactose to get into cells. produced by the lacY gene
41
what is B-galactoside transacetylase encoded by
lacA gene
42
how do the levels in B-galactosidase, permease, and transacetylase change as lactose is added to a previously lactose-free solution
the protein levels/synthesis increases as lactose is added to the solution
43
what does it mean if enzymes are repressible
their synthesis is decreased in response to a small molecule
44
what does it mean if enzymes are constitutive
they are always expressed and generally perform basic cellular "housekeeping" functions
45
what 2 classes were the mutations discovered by Monod and Jacob
lacl and lacOc
46
are lacOc mutations dominant or recessive
some were dominant and some were recessive
47
are lacl mutations dominant or recessive
recessive
48
what is the lac repressor
lacI encodes a factor that represses lac mRNA transcription
49
when can lacOc cause synthesis of lac mRNA`
when it is on the same DNA molecule as lacZ+
50
what is the established gene order
lacI, lacO, lacZ, lacY, lacA
51
what is referred to as the operator
lacO, which was later found to be the binding site for the lac repressor
52
describe the lac operon model
transcription occurs as the repressor binds to site and inducer attaches to fot lac mRNA to be transcribed (into the 3 proteins)
53
what segments are the antiterminator
2 + 3
54
what segments are the terminator
3 + 4
55
what is tryphtophan responsible for in termination
it makes sure the ribosome doesn't get stuck at the adjacent Trp codons, therefore it's important to have a high concentration
56
when transcribing trp mRNA, RNAP pauses. when and why?
it pauses as its reaches segment 2 in the ribosome, to synchronize transcription and translation
57
what allows the 1-2 and 3-4 hairpins to form
dissociation of the ribosome
58
the trpL has 4 segments, what distinct structures can be formed
terminator 3+4 | antiterminator 2+3
59
function of the trpR protein
on/off switch for the trp operon at the level of transcription initiation
60
attenuation
control mechanism, involves regulation of elongation and termination via RNA and ribosome
61
what is the attenuator
sequence of 28 bases in the leader
62
what is designated as the leader of trpL
trpE, the first codon
63
the trp mRNA has how many nucleotides and in which direction
162 nt upstream
64
function of the trp operon
-encodes genes involved in tryptophan synthesis | -
65
structure of trp operon
promoter, operator, and 5 structural genes
66
trp operon is regulated at what levels of transcription
initiation, elongation, and termination
67
what occurs when cells grow in glucose
shut off transcription of lac genes
68
describe catabolite repression
cAMP forms a complex with a cAMP receptor protein, that binds to an activator site upstream of the lac promoter
69
what does E. coli use for fuel
glucose
70
what is the dimer of dimers, and binds to an operator
lac repressor
71
how many lac operators are there?
3
72
what structure does each DNA binding domain have?
supersecondary structure
73
purpose of the tetramerization helix
allows multiple repressor molecules to interact with one another
74
what is a result of low tryptophan
ribosome stalls, removes segment 1, allowing 2-3 hairpin to form, rather than 3-4
75
allolactose causes the lac repressor to??
to fall off the lac operator
76
tryptophan causes the lac repressor to??
to be able to bind to the trp operator

L 211 (12 decks)

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