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Molecular Biology > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

SWI/SNF

A

remodel nucleosomes and core histones within chromatin, making DNA more accessible for transcription

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2
Q

Receptor that forms a tertiary nuclear complex with HDACs

A

RAR (retinoic acid receptor)

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2
Q

add methyl groups to DNA; reduces transcription and condenses chromatin

A

HMTase (histone methyl transferase)

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3
Q

RNase II

A

cuts each nucleotide on the 3’ tRNA first

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4
Q

histone fold

A

helix-loop-helix-loop-helix motif

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4
Q

transfer acetyl groups (COCH) from Acetyl-CoA to lysine residues on histone tails; loosens chromatin

A

HAT (histone acetyltransferase)

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4
Q

remove acetyl groups from histones to repress gene expression

A

HDAC (histone deacetylase)

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4
Q

RNase P

A

cuts tRNA 5’ end in one step to yield mature 5’ tRNA product following RNase III cut

-composed mostly of RNA with small proteins; requires Mg2+

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5
Q

facilitates poly(A) elongation through PAP stabilization in the second phase of polyadenylation (~250 As)

-49kD protein, enhanced by but not requiring CPSF

A

PAB II (poly(A)-binding protein II)

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6
Q

helix 2 (splicing)

A

formed from the 5’ end of U2 interacting with the 3’ end of U6 to help orient the snRNPs during splicing

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7
Q

remodel nucleosomes and core histones within chromatin, making DNA more accessible for transcription

A

SWI/SNF

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8
Q

cuts tRNA 5’ end in one step to yield mature 5’ tRNA product following RNase III cut

-composed mostly of RNA with small proteins; requires Mg2+

A

RNase P

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10
Q

segments of noncoding DNA that recruit DABPolFEH

A

control elements

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10
Q

Guanylyl transferase

A

attaches GMP to the 5’ end of the RNA

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11
Q

26S RNA

A

group 1 intron that exhibits ribozyme activity driving recognition, splicing, and product formation (lacks lariat structure)

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11
Q

PNPase

A

(polynucleotide phosphorylase)

removes phosphates on 3’ end of tRNA (2+ from end) following RNase II cutting; requires ATP

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12
Q

Prp28 (protein)

A

works with U6 to displace U1

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13
Q

methylates guanine at position 7 (terminal nucleotide) of cap

A

methyltransferase

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13
Q

RNase III

A

cuts precursor tRNAs to generate free 5’ and 3’ ends

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14
Q

HP1

A

binds methylated histones to block gene expression

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15
Q

splicing: step 2

A

guanosine hydroxyl group attacks (2nd) intron-exon phosphodiester bond, linking exons and resutling in intron release

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16
Q

recognizes precursor tRNA and cuts out intron

A

tRNA endonuclease

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17
Q

activator binds before H1 or moves nucleosome, triggering gene expression (makes DNA more accessible to transcriptional machinery)

A

antirepression

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17
Q

corepressor that forms a tertiary nuclear complexes with HDACs

A

SIN

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18
Q

antirepression

A

activator binds before H1 or moves nucleosome, triggering gene expression (makes DNA more accessible to transcriptional machinery)

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19
Q

helix-loop-helix-loop-helix motif

A

histone fold

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20
Q

MSK1

A

(mitrogen-and-stress-activated kinase)

phosphorylates nucleosomes next to a methylated amino acid to enhance transcription

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21
Q

HAT

A

(histone acetyltransferase)

transfer acetyl groups (COCH) from Acetyl-CoA to lysine residues on histone tails; loosens chromatin

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22
Q

tRNA endonuclease

A

recognizes precursor tRNA and cuts out intron

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23
Q

removes phosphates on 3’ end of tRNA (2+ from end) following RNase II cutting; requires ATP

A

PNPase (polynucleotide phosphorylase)

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24
Q

82kD protein with RNA-binding domain (RBD), polymerase module, 2 nuclear localization signals (NLS), & 2 serine/threonine-rich regions

A

PAP (poly(A) polymerase)

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26
Q

binds methylated histones to block gene expression

A

HP1

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26
Q

Slu 7

A

required for 2nd step of splicing (completing formation of mature mRNA)

-reads the AG phosphodiester bond of the intron and first nucleotide of exon 2 (3’ splice site)

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28
Q

HDAC

A

(histone deacetylase)

remove acetyl groups from histones to repress gene expression

29
Q

group 1 intron that exhibits ribozyme activity driving recognition, splicing, and product formation (lacks lariat structure)

29
Q

directly binds signal sequence to initiate poly(A) formation and cleaves the pre-mRNA

A

CPSF (cleavage and polyadenylation specificity factor)

29
Q

cuts each nucleotide on the 3’ tRNA first

30
Q

polyadenylation signal/sequence

A

occurs ~20 nt upsteam of poly(A) site:

AAUAAA

32
Q

HMTase

A

(histone methyl transferase)

add methyl groups to DNA; reduces transcription and condenses chromatin

33
Q

SUV39H

A

HMTase that specifically methylates lysine #9 and #4 on H3 tails; triggers HP1 binding, additional methylation, and gene silencing

34
Q

required for 2nd step of splicing (completing formation of mature mRNA)

-reads the AG phosphodiester bond of the intron and first nucleotide of exon 2 (3’ splice site)

35
Q

signal sequence

A

5’- AG/GUAAGU-intron-YNCURAC-YnNAG/G -3’

R = AorG; Y = CorT; A=branchpoint intermediate

36
Q

intron (aka?)

A

IVS (intervening sequence)

37
Q

helix 1 (splicing)

A

formed with U2 base-pairing to U6 at nucleotides 23, 26, 27, 28, 56, 57, 58, & 59

38
Q

intron definition

A

the introns direct the formation of the spliceosome

40
Q

splicing: step 1

A

branch point adenosine hydroxyl group attacks phosphodiester bond at first exon, forming branched lariot structure (loop)

41
Q

nuclosome-free zones (active genes/some control regions of genes)

A

hypersensetive to DNase

41
Q

binds GU-rich motif in mRNA and stabalizes CPSF

A

CstF (cleavage stimulation factor)

43
Q

control elements

A

segments of noncoding DNA that recruit DABPolFEH

44
Q

phosphorylates nucleosomes next to a methylated amino acid to enhance transcription

A

MSK1 (mitrogen-and-stress-activated kinase)

45
Q

NCoR

A

nuclear receptor repressor that forms a tertiary nuclear complexes with HDACs

47
Q

group II self-splicing introns (rRNA & tRNA)

A

base-pairing around branch point adenosine, causing bulging by domain VI (U2)

  • Domain ID and V = U5 and U6
  • ribozymes (catalytic RNAs) catalyze splicing
47
Q

CstF

A

(cleavage stimulation factor)

binds GU-rich motif in mRNA and stabalizes CPSF

49
Q

PAB II

A

(poly(A)-binding protein II)

facilitates poly(A) elongation through PAP stabilization in the second phase of polyadenylation (~250 As)

-49kD protein, enhanced by but not requiring CPSF

50
Q

cuts precursor tRNAs to generate free 5’ and 3’ ends

52
Q

RNA triphosphatase

A

starts capping by removing the gamma-phosphate from the growing end of the RNA

53
Q

works with U6 to displace U1

A

Prp28 (protein)

55
Q

nuclear receptor repressor that forms a tertiary nuclear complexes with HDACs

57
Q

starts capping by removing the gamma-phosphate from the growing end of the RNA

A

RNA triphosphatase

57
Q

RNase T

A

removes final nucleotide of 3’ tRNA to yield mature tRNA

58
Q

genes of proteins controlling alternative splicing through snRNP regulation in Drosophila

59
Q

RNA ligase

A

acts like U5 to ligate 2 exons of tRNA together after they’ve been phosphorylated by protein kinases & ATP

60
Q

CPSF

A

(cleavage & polyadenylation specificity factor)

directly binds signal sequence to initiate poly(A) formation and cleaves the pre-mRNA

61
Q

methyltransferase

A

methylates guanine at position 7 (terminal nucleotide) of cap

62
Q

exon definition (recognition)

A

CTD requires intact exon to assemble the splicesome through recognition of the 2nd exon, facilitating close proximity of exon 1 and 2

64
Q

R-looping

A

Process where RNA is hybridized to DNA; revealed evidence for introns (A-C loops)

65
Q

attaches GMP to the 5’ end of the RNA

A

Guanylyl transferase

65
Q

occurs ~20 nt upsteam of poly(A) site:

AAUAAA

A

polyadenylation signal/sequence

66
Q

Sm proteins

A

contained in snRNPs, bind to specific Sm site (sequence) on snRNAs through doughnut-shaped ring lined with basic amino acids allowing for RNA binding

68
Q

SIN

A

corepressor that forms a tertiary nuclear complexes with HDACs

69
Q

hypersensetive to DNase

A

nuclosome-free zones (active genes/some control regions of genes)

70
Q

IVS

A

(invervening sequence) aka intron

71
Q

acts like U5 to ligate 2 exons of tRNA together after they’ve been phosphorylated by protein kinases & ATP

A

RNA ligase

73
Q

participates in enhancing translation

A

PAB 1 (poly(A) binding protein 1)

74
Q

removes final nucleotide of 3’ tRNA to yield mature tRNA

75
Q

PAB 1

A

(poly(A)=binding protein 1)

participates in enhancing translation

76
Q

Process where RNA is hybridized to DNA; revealed evidence for introns (A-C loops)

77
Q

RAR

A

Retinoic acid receptor that forms a tertiary nuclear complexes with HDACs

79
Q

HMTase that specifically methylates lysine #9 and #4 on H3 tails; triggers HP1 binding, additional methylation, and gene silencing

80
Q

Tra genes

A

genes of proteins controlling alternative splicing through snRNP regulation in Drosophila

81
Q

removes terminal nucleotide(s) of 3’ tRNA following PNPase phosphate removal, but requires ATP

82
Q

RNase PH

A

removes terminal nucleotide(s) of 3’ tRNA following PNPase phosphate removal, but requires ATP

83
Q

PAP

A

(poly(A) polymerase)

82kD protein with RNA-binding domain (RBD), polymerase module, 2 nuclear localization signals (NLS), & 2 serine/threonine-rich regions

Molecular Biology (13 decks)

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