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Biol 4890 > Chapter 29 > Flashcards

Chapter 29 Flashcards

1
Q

splicing removes >

A

introns

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2
Q

homology between RNAPs

A

have central metal atom in active sites. important c terminal domain critical for processing RNa

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3
Q

3 steps of RNA transcription

A

initiation, elongation, termination

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4
Q

post-transcriptional processing in RNA

A

base modification (methylation), addition of nucleotides (poly A tails), splicing

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5
Q

RNA polymerases bing to DNA sequences called ?

A

promoters

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6
Q

In the absence of ? (2), RNAP can bind to promoters but cannot continue elongation steps

A

Mg++, NTPs

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7
Q

binding of ? protects DNa from enzyme digestion

A

RNAP

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8
Q

stronger promoters are better matches to ?

A

consensus

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9
Q

optimal promoters have ? bp between consensus sequences

A

17

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10
Q

changes in growth conditions lead to appearance of additional ?

A

sigma factors

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11
Q

housekeeping sigma factor

A

sigma 70

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12
Q

RNAP error

A

1 in 10^4

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13
Q

RNAP elongation reaction

A

PPPXOH + YTP&raquo_space; PPPXPYOH + PPi

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14
Q

RNAP polymerization reaction is identical to DNA polymerase and also requires ? assisted phosphoryl transfer

A

Mg++

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15
Q

RNAP elongates at ? nucleotides/second

A

50

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16
Q

? polymerase needs no primer

A

RNA

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17
Q

RNAP uses free energy of ? to drive conformational change

A

PPi release

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18
Q

Incorporation of a ? changes the active site and pushes newly formed duplex base pair into the ? region. Release of PPi returns the active site to a ? binding region

A

Incorporation of a NMP changes the active site and pushes newly formed duplex base pair into the helix binding region. Release of PPi returns the active site to a NTP binding region

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19
Q

RNA:DNA hybrid is slightly more/less stable than DNA:DNA

A

more

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20
Q

determines when transcription stops

A

the RNA molecule being made

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21
Q

Three methods of Transcription pausing or termination

A

1) form stem loop 2) Recruit accessory proteins (attenuators) 3) additional factors can antagonize attenuation

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22
Q

rho independent termination

A

formation of step loop structure causes pause. if next residues are uridines, thranscription stops and rna is released. free energy of stem loop is greater than RNA:DNA duplex

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23
Q

Rho

A

a hexameric RNA helicase. binds to C rich regions. removes rna from polymerase.

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24
Q

rifampicin

A

inhibitor of many bacterial RNAPs. binds to aromatic AAs at site of formation of RNA:DNA hybrid and prevents initial elongation steps. Mutations in aromatic rings leads to rifampicin resistance.

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25
Q

In procaryotes, ? is directly used for protein synthesis

A

mRNA

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26
Q

rRNA and tRNA undergo these types of processing

A

Cleavage, modification, addition of nucleotides (methylation, flipping)

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27
Q

In E Coli, a primary transcript is cleaved by RNase 3 and RNase P to produce rRNAs and a tRNA that undergo ?. tRNAs have the nucleotide sequence ? added to their 3’ ends if needed

A

base modifications. CCA

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28
Q

eucaryotes have ? RNAPs differentiated by their sensitivity to ?

A
  1. alpha-amanitin
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29
Q

RNAP that is strongly inhibited by alpha-amanitin

A

type 2

30
Q

RNAP that is inhibited by alpha-aminitin at high concentrations

A

type 3

31
Q

A type 4 RNAP found in plants is used to make ?

A

siRNAs and RNA dependent RNA polymerases involved in RNA interference

32
Q

Type 1 RNAPs used to make ?

A

rinosomal RNA

33
Q

Type 2 RNAPs used to make ?

A

mRNA precursors and snRNA

34
Q

different RNAPs transcribe from different ?

A

promoters

35
Q

RNAP ? and ? produces RNAs needed by all cell types and have relatively simple sequences in their promoters

A

1 and 3

36
Q

? promoters are complex

A

RNAP

37
Q

eucaryotic RNAP binding

A

general transcription factors bind to promoter elements and recruit RNAPs

38
Q

? elements of promoters are recognition sites for protein factors

A

cis

39
Q

RNAP 2 is recruited by GTFs ?

A

TFIIA-TFIIH

40
Q

In TATA-box promoters, ?, containing the TATA-binding protein binds first and distorts the DNA helix

A

TFIID

41
Q

TATA box binding protein binds TATA box that contains sequences related to TATAAAA and ?

A

bends the DNA into a horseshoe shape

42
Q

TFIID provides ? to form basal transcription apparatus

A

docking sites for additional GTFs and RNAP2

43
Q

Assembly of transcription initiation complex generates a ? complex that determines the orientation of transcription

A

asymmetric

44
Q

TFIIH functions

A

helicase activity opens DNA helix to start transcription. phosphorylation of C-terminal domain of RNAPII releases RNAP from initiation factors that recruited it and binds RNA processing enzymes

45
Q

basal transcription complex initiates transcription at a low/high frequency

A

low

46
Q

many promoters are activated by ? that may be far from transcription start sites either up or down stream

A

enhancer sequences

47
Q

Cis promoter elements are recognized by ?

A

protein factors

48
Q

complex called ? coordinates positive activators with recruitment of RNAP 2

A

mediator

49
Q

SrB8-II represses

A

RNAP 2

50
Q

RNAP 1 produces ? that undergo base and ribose modification in the nucleolus by ?

A

rRNA. snoRNPs

51
Q

RNAP III transcript processing to tRNA

A

5’ and 3’ cleavage. additon of 3’ CCA sequence. base and ribose modification. spliced by endonuclease and ligase

52
Q

RNAP II transcript processing to mRNA

A

5’-5’ triphosphate cap at 5’ end by GTP marks as pre-mRNA and protects from exonucleases. PolyA polymerase adds a tail to 3’ end. methylation can occur at 2’-OH groups of nucleotides 1 and 2

53
Q

Tissue specific RNA editing. Liver produces mRNA that translates to ? while intestines generate a deaminase for the same mRNA that modifies it to translate to ?

A

ApoB-100. ApoB-48

54
Q

ApoB-100

A

transports lipids to other cells

55
Q

ApoB-48

A

Carries fat in chylomicrons

56
Q

? is most common way eucaryotes generate diversity

A

splicing

57
Q

splicing involves ? reactions

A

transesterification

58
Q

splicing transesterification reactions are similar to tyrosine mediated reactions by ?

A

topo 2

59
Q

Draw splicing reaction

A

do it. 2’ Oh of branch site attacks 3’ OH of phosphodiester bond at 5’ splice site to generate lariat intermediate. Newly generated 3’ OH attacks 3’ OH of phosphodiester bond at 3’ splice site

60
Q

spliceosome

A

snRNPs that contain RNA and a large number of proteins assemble to help guide and catalyze splicing reactions

61
Q

Since transesterification reactions are freely reversible, what is the energy source that drives splicing to proceed

A

ATP powered helicases drive the spliceosome through the conformational changes that involve the release of U1 and U4

62
Q

specificity of splicing due to ?

A

complementary pairing of pre-mRNA and snRNAs

63
Q

phosphorylation of CTD causes

A

release of RNAP from initiation complex and sequentially recruits enzymes of processing

64
Q

15% of all genetic diseases due to ?

A

mutations that affect splicing

65
Q

Cis effects

A

mutations in the pre-mRNA

66
Q

Trans effects

A

mutations in the spliceosome

67
Q

some defects in hemoglobin production are the result of a mutation within an ? that creates a new splice site

A

intron

68
Q

ribozymes

A

catalytic RNAs

69
Q

group 1 introns use ? to attack 5’ splice site

A

guanosine

70
Q

group 2 introns and the spliceosome activate an ? to initiate splicing

A

adenine

Biol 4890 (16 decks)

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