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Molecular Biology > Exam 3 > Flashcards

Exam 3 Flashcards

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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
antirepression
activator binds before H1 or moves nucleosome, triggering gene expression (makes DNA more accessible to transcriptional machinery)
19
helix-loop-helix-loop-helix motif
histone fold
20
MSK1
(mitrogen-and-stress-activated kinase) phosphorylates nucleosomes next to a methylated amino acid to enhance transcription
21
HAT
(histone acetyltransferase) transfer acetyl groups (COCH) from Acetyl-CoA to lysine residues on histone tails; loosens chromatin
22
tRNA endonuclease
recognizes precursor tRNA and cuts out intron
23
removes phosphates on 3' end of tRNA (2+ from end) following RNase II cutting; requires ATP
PNPase (polynucleotide phosphorylase)
24
82kD protein with RNA-binding domain (RBD), polymerase module, 2 nuclear localization signals (NLS), & 2 serine/threonine-rich regions
PAP (poly(A) polymerase)
26
binds methylated histones to block gene expression
HP1
26
Slu 7
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)
28
HDAC
(histone deacetylase) remove acetyl groups from histones to repress gene expression
29
group 1 intron that exhibits ribozyme activity driving recognition, splicing, and product formation (lacks lariat structure)
26S RNA
29
directly binds signal sequence to initiate poly(A) formation and cleaves the pre-mRNA
CPSF (cleavage and polyadenylation specificity factor)
29
cuts each nucleotide on the 3' tRNA first
RNase II
30
polyadenylation signal/sequence
occurs ~20 nt upsteam of poly(A) site: AAUAAA
32
HMTase
(histone methyl transferase) add methyl groups to DNA; reduces transcription and condenses chromatin
33
SUV39H
HMTase that specifically methylates lysine #9 and #4 on H3 tails; triggers HP1 binding, additional methylation, and gene silencing
34
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)
Slu 7
35
signal sequence
5'- AG/GUAAGU-intron-YNCUR**_A_**C-YnNAG/G -3' R = AorG; Y = CorT; **_A_**=branchpoint intermediate
36
intron (aka?)
IVS (intervening sequence)
37
helix 1 (splicing)
formed with U2 base-pairing to U6 at nucleotides 23, 26, 27, 28, 56, 57, 58, & 59
38
intron definition
the introns direct the formation of the spliceosome
40
splicing: step 1
branch point adenosine hydroxyl group attacks phosphodiester bond at first exon, forming branched lariot structure (loop)
41
nuclosome-free zones (active genes/some control regions of genes)
hypersensetive to DNase
41
binds GU-rich motif in mRNA and stabalizes CPSF
CstF (cleavage stimulation factor)
43
control elements
segments of noncoding DNA that recruit DABPolFEH
44
phosphorylates nucleosomes next to a methylated amino acid to enhance transcription
MSK1 (mitrogen-and-stress-activated kinase)
45
NCoR
nuclear receptor repressor that forms a tertiary nuclear complexes with HDACs
47
group II self-splicing introns (rRNA & tRNA)
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
CstF
(cleavage stimulation factor) binds GU-rich motif in mRNA and stabalizes CPSF
49
PAB II
(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
cuts precursor tRNAs to generate free 5' and 3' ends
RNase III
52
RNA triphosphatase
starts capping by removing the gamma-phosphate from the growing end of the RNA
53
works with U6 to displace U1
Prp28 (protein)
55
nuclear receptor repressor that forms a tertiary nuclear complexes with HDACs
NCoR
57
starts capping by removing the gamma-phosphate from the growing end of the RNA
RNA triphosphatase
57
RNase T
removes final nucleotide of 3' tRNA to yield mature tRNA
58
genes of proteins controlling alternative splicing through snRNP regulation in *Drosophila*
Tra genes
59
RNA ligase
acts like U5 to ligate 2 exons of tRNA together after they've been phosphorylated by protein kinases & ATP
60
CPSF
(cleavage & polyadenylation specificity factor) directly binds signal sequence to initiate poly(A) formation and cleaves the pre-mRNA
61
methyltransferase
methylates guanine at position 7 (terminal nucleotide) of cap
62
exon definition (recognition)
CTD requires intact exon to assemble the splicesome through recognition of the 2nd exon, facilitating close proximity of exon 1 and 2
64
R-looping
Process where RNA is hybridized to DNA; revealed evidence for introns (A-C loops)
65
attaches GMP to the 5' end of the RNA
Guanylyl transferase
65
occurs ~20 nt upsteam of poly(A) site: AAUAAA
polyadenylation signal/sequence
66
Sm proteins
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
SIN
corepressor that forms a tertiary nuclear complexes with HDACs
69
hypersensetive to DNase
nuclosome-free zones (active genes/some control regions of genes)
70
IVS
(invervening sequence) aka intron
71
acts like U5 to ligate 2 exons of tRNA together after they've been phosphorylated by protein kinases & ATP
RNA ligase
73
participates in enhancing translation
PAB 1 (poly(A) binding protein 1)
74
removes final nucleotide of 3' tRNA to yield mature tRNA
RNase T
75
PAB 1
(poly(A)=binding protein 1) participates in enhancing translation
76
Process where RNA is hybridized to DNA; revealed evidence for introns (A-C loops)
R-looping
77
RAR
Retinoic acid receptor that forms a tertiary nuclear complexes with HDACs
79
HMTase that specifically methylates lysine #9 and #4 on H3 tails; triggers HP1 binding, additional methylation, and gene silencing
SUV39H
80
Tra genes
genes of proteins controlling alternative splicing through snRNP regulation in *Drosophila*
81
removes terminal nucleotide(s) of 3' tRNA following PNPase phosphate removal, but requires ATP
RNase PH
82
RNase PH
removes terminal nucleotide(s) of 3' tRNA following PNPase phosphate removal, but requires ATP
83
PAP
(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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