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Biochemistry > New: RNA synthesis, regulation, and processing > Flashcards

New: RNA synthesis, regulation, and processing Flashcards

1
Q

transcription of genes is

A

regulated

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2
Q

expression of housekeeping genes is

A

constitutive

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3
Q

housekeeping genes usually have strong promoter and are efficiently and continuously

A

transcribed

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4
Q

housekeeping genes whose products are required at low levels have

A

weak promoter and are infrequently transcribed

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5
Q

________ ____ are expressed at different levels under different conditions

A

regulated genes

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6
Q

HAT

A

modify histones and open up DNA so other things can bind

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7
Q

gene expression is also regulated by ______ such as estradiol

A

hormones

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8
Q

the estrogen receptor is part of a larger class of regulatory proteins called ______ _____ ______

A

nuclear hormone receptors

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9
Q

nuclear hormone receptors are all activated by binding of small molecules or ligands and bind to specific regions of the DNA called

A

response elements

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10
Q

nuclear hormone receptors have two conserved domains which are

A
  1. the DNA binding domain

2. ligand binding domain

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11
Q

has zinc finger domains that confer specific DNA binding

A

DNA binding domain

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12
Q

ligand binding to the ligand binding domain causes a

A

structural change that enables the receptor to recruit other proteins to regulate transcription

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13
Q

coactivators and corepressors are recruited by

A

nuclear hormone receptors

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14
Q

proteins that bind the receptor after ligand binding are called

A

coactivators

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15
Q

ligand binding leads to structural rearrangements in the receptor that promotes

A

recruitment of additional proteins

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16
Q

_______ proteins bind to nuclear hormone receptors when ligand is absent to assist in repression of transcription

A

corepressor

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17
Q

ligands that activate a nuclear hormone receptor

A

agonists

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18
Q

ligands that inhibit the receptor

A

antagonists

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19
Q

some cancers require the estradiol-receptor complex, and growth of these cancers can be slowed by administering receptor antagonists such as

A

tamoxifen and raloxifene

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20
Q

good and bad effects of tamoxifen

A

good: decrease cancer and cholesterol; increase bone strength
bad: increase blood clots and uterine cancer

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21
Q

histone acetylation results in chromatin

A

remodeling

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22
Q

*how do coactivators stimulate transcription?

A

loosening the interactionbtwn histones and DNA, so the DNA is more accessible to transcription machinery

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23
Q

acetylation reduces the affinity of histones for

A

DNA

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24
Q

histone acetyllysine residues are interaction sites for many proteins which regulate ________, including factors which bind the TATA-box

A

transcription

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25
Q

acetyllysine residues also bind and recruit

A

chromatin remodeling proteins

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26
Q

histone acetylation is carried out by

A

histone acetyltransferases (HATS)

27
Q

lysine residues can be

A

acetylated

28
Q

histone acetylation ________ net positive charge - weakens interactions with other nucleosomes and proteins, loosens higher order structure

A

decreases

29
Q

HATS directed to sites where chromatin must unravel to

A

transcribe a gene

30
Q

histone deacetylases (HDCs)

A

remove acetyl groups - allow for re-compacting of DNA

31
Q

in RNA processing of eukaryotes, large precursor RNA (45S) is processed to

A

18s, 28s, and 5.8s rRNAs…which are components of the ribosome

32
Q

before cleavage, some bases and riboses are modified in a process catalyzed by RNA-protein complexes called

A

small nucleolar ribonucleoproteins (snoRNP)

33
Q

tRNA endonucleases remove nucleotides from the

A

5’ end

34
Q

tRNA nucleotidyl transferase* adds _____ to the ____ end

A

CCA; 3’

35
Q

in prokaryotes the primary mRNA transcript is translated

A

directly

36
Q

in eukaryotes transcription occurs in the

A

nucleus

37
Q

in eukaryotes translation occurs in the

A

cytoplasm

38
Q

splicing

A

in some mRNA pieces are removed from the middle and the ends joined

39
Q

eukaryotic mRNA molecules have modified ends: eukaryotic mRNA precursors undergo modification to

A

increase their stability* and make them better substrates for translation

40
Q

eukaryotic mRNA molecules have modified ends: ends are modified to they are no longer susceptible to

A

exonuclease degradation*

41
Q

eukaryotic mRNA molecules have modified ends: the 5’ ends are modified (capped) before the mRNA precursors are completely

A

synthesized

42
Q

addition of ___ required for splicing and other processing events

A

CAP

43
Q

cap site is where _______ bind

A

ribosomes

44
Q

cap is added by

A

gyanylyl transferase

45
Q

poly A tails at the 3’ ends of ____ precursors

A

mRNA

46
Q

eukaryotic mRNA precursors are also modified at their

A

3’ ends

47
Q

a poly A polymerase adds up to ____ ____ residues to the 3’ end of the mRNA precursor

A

250 adenylate

48
Q

poly a tail is progressively shortened by

A

3’ exonucleases

49
Q

the poly A tail increases the time before nucleases reach

A

the coding region

50
Q

sequences at the ends of introns specify

A

splice sites in mRNA precucrsors

51
Q

most genes in eukaryotes consist of

A

exons and introns

52
Q

introns

A

internal sequences that are removed from the primary RNA transcript.

53
Q

exons

A

sequences that are present in the primary transcript and the mature mRNA

54
Q

splice sites

A

junctions of the introns and exons where mRNA precursor is cut and joined

55
Q

exons are joined by

A

splicing

56
Q

small nuclear RNAs in splicosomes catalyze

A

splicing of mRNA precursors

57
Q

defects in ______ may cause up to 15% of all genetic diseases

A

splicing

58
Q

introns allow formation of alternative forms of a protein called

A

splice variants

59
Q

alternative splicing is a powerful mechanism for expanding

A

protein diversity

60
Q

in alternative splicing, a pre-mRNA can be splices in different patterns, generating proteins with

A

different funcitons

61
Q

transcription and processing of mRNA are

A

coupled

62
Q

transcription and splicing of mRNA are coordinated by the

A

carboxyl-terminal domain (CTD) or RNA pol 2

63
Q

functions of the CTD include:

A
  1. recruit enzymes to synthesize the 5’ cap
  2. recruit components of the splicing complex
  3. recruit an endonuclease that cleaves the pre-mRNA to expose the site for poly A additio

Biochemistry (6 decks)

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