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Exam 2 Flashcards

memorize

1
Q

CTD has

A

repeated pattern of 7 amino acids

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2
Q

phosphorylation of CTD causes…

A

transcription signals to be sent

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3
Q

RNA cap

A

has capping enzymes
protects 5’ end
necessary for translation

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4
Q

splicing

A

removal of introns and joining of exons

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5
Q

spliceosome

A

splices; made up of SNRPs

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6
Q

SNRPs

A

small nuclear RNA and ribonucleoproteins

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7
Q

polyadenylation signal (PAS)

A

stops RNA elongation at 3’ end, abt 20 bases down

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8
Q

polyadenylation signal sequences

A

AAUAAA or AUUAAA

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9
Q

poly-A tail

A

added at the end of transcription
made up of 150-200 adenine bases

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10
Q

CPSF - cleavage polyadenylation specificity factor # of subunits

A

6; endonuclease activity in 1

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11
Q

where does CPSF bind

A

polaydenylation sequence

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12
Q

where is the cut site

A

10-30 bps after PAS

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13
Q

where do cleavage factors (C1 and C2) bind

A

cut site

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14
Q

CPSF recruits..

A

polyA polymerase (PAP)

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15
Q

polyA polymerase

A

adds polyA binding proteins (PABP)

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16
Q

cleavage stimulation factor (CStF)

A

cleaves the mRNA and falls off

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17
Q

polyA binding protein purpose

A

prevents degradation of polyA tail

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18
Q

downstream sequence element (DSE)

A

site where CStF binds

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19
Q

allosteric termination model

A

similar to intrinsic method of termination in prokaryotes
built-in signal causes destabilization

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20
Q

torpedo termination model

A

similar to rho dependent method of eukaryotes - outside protein Xrn2 helps with termination process

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21
Q

Xrn2

A

protein that assists with torpedo termination model of eukaryotic transcription

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22
Q

_____ rule in introns

A

GU-AG; introns almost always start with GU and end with AG

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23
Q

bases between last AG and A at branch point

A

15-45

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24
Q

how does splicing start

A

spliceosome recognizes intron sequences

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25
Q

first step of splicing

A

SNPs U1 and U2 bind to the 5’ splice site and internal A (branch point), respectively

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26
Q

second step of splicing

A

U4, U5, U6 complex joins spliceosome and forms a bend

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27
Q

third step of splicing

A

U1, U4, and U6 fall off

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28
Q

first splicing reaction

A

one end of the intron separates and attaches to the internal A

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29
Q

second splicing reaction

A

the other end of the intron is cleaved from the exon; the two exons join
forms lariat

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30
Q

transesterification is directed by

A

CTD

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31
Q

translation

A

mRNA codons -> amino acid sequences

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32
Q

translation and transcription in prokaryotes

A

coupled

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33
Q

ingredients in an amino acid

A

carboxyl group, amino group, R group (central carbon atom)

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34
Q

total # codons

A

64

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35
Q

degenerate

A

multiple codons code for the same amino acid

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36
Q

stop codons

A

UAA, UAG, UGA

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37
Q

start codon

A

AUG (methionine)

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38
Q

tRNA loop contains _____ of mRNA codon

A

anticodon

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39
Q

tRNA D-loop

A

stability of molecule; involves displacement of the 2 strands, held apart for brief sections by a 3rd strand

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40
Q

T-loop

A

interacts w/ ribosomes

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41
Q

variable loop

A

interacts w/ aminoacyl tRNA synthetase

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42
Q

aminoacyl tRNA synthetase

A

enzyme that charges tRNA by adding an amino acid

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43
Q

of different synthetases and # of different forms of charged tRNA

A

20

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44
Q

tRNAs can be _____ by adding another amino acid

A

recycled

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45
Q

large ribosome subunit in prokaryotes

A

50S
23S rRNA
5S rRNA
31 proteins

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46
Q

small ribosomal subunit in prokaryotes

A

30S
16S rRNA
21 proteins

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47
Q

large subunit in eukaryotes

A

60s
28S rRNA
5.8S rRNA
5S rRNA (highly preserved)
49 proteins

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48
Q

40S subunit in eukaryotes

A

18S rRNA
33 proteins

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49
Q

ribosome in eukaryotes

A

50% RNA, 50% proteins

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50
Q

decoding center

A

location in the ribosome where incoming tRNA is matched w/ mRNA codon, in the A site

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51
Q

peptidyl-transferase center

A

region on larger ribosomal subunit involved in catalyzing peptide bond formation (between new AAs) and peptide release

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52
Q

E site

A

exit site; releases now-uncharged tRNA

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53
Q

P site

A

peptidyl site; tRNA binds to the growing chain of AAs

54
Q

A site

A

binds an incoming charged tRNA whose anticodon matches the codon in the A site of the small subunit

55
Q

charged tRNA

A

bonded to an aminoacyl

56
Q

tRNAMeti

A

initiator tRNA that inserts methionine to establish correct reading frame

57
Q

N-formylmethionine (fMet)

A

formyl group added to methionine while the amino acid is attached to initiator, to help w/ translation

58
Q

Shine-Dalgarno Sequence

A

ribosome binding site on mRNA strand
AGGAGGU

59
Q

where is the SDS

A

in the 5’ UTR, preceding the initiation codons

60
Q

how does the ribosome bind to the SDS

A

the 3’ end of the 16S rRNA in the small subunit binds to the SDS

61
Q

IF1

A

initiation factor - blocks ribosome A site

62
Q

IF3

A

initiation factor - blocks ribosome E site and keeps large subunit from attaching prematurely

63
Q

IF2

A

initiation factor - escorts fMet-tRNA to the small ribosomal subunit at the P site, using ATP

64
Q

IF2-GTP

A

allows release of the initiation factors

65
Q

when IFs are released…

A

large subunit joins complex, ribosome becomes functional

66
Q

EF-Tu

A

elongation factor
brings charged tRNAs to A site to be joined to polypeptide chain in P site

67
Q

EF-G

A

elongation factor
binds in A site to promote translocation of tRNAs from the P and A sites to the E and P sites as ribosome moves along the strand

68
Q

termination begins when…

A

tRNA is unable to recognize stop codons - they have no anticodons

69
Q

tripeptides

A

sequences in release factor proteins to recognize stop codons

70
Q

RF1 recognizes ____

A

UAA and UAG

71
Q

RF2 recognizes ____

A

UAA and UGA

72
Q

how do RFs stop translation

A

water molecule positions itself on peptidyl transferase site -> peptide chain falls off

73
Q

RF3

A

has GTPase activity, causes RF1 +2 to fall off

74
Q

RF3 also falls off because of…

A

change in structure due to hydrolysis of GTP

75
Q

RRF (ribosomal recycling factor), EF-G, IF3

A

dismantles the translation mechanism

76
Q

IF3 ______ to 30S subunit

A

remains attached

77
Q

eIF1a

A

blocks A site

78
Q

eIF1 and eIF3

A

prevent premature association of small and large subunits

79
Q

eIF2 and eIF5

A

bring in initiator tRNA

80
Q

eIF5b

A

promotes interaction between small and large subunits

81
Q

eIF4F has _ subunits

82
Q

eIF4A

A

ATPase activity, helicase activity

83
Q

eIF4G

A

interacts w/ polyA binding proteins

84
Q

eIF4E

A

binds to cap

85
Q

Kozak’s sequence

A

RCCAUGG
-3 +1 +4

86
Q

ternary complex

A

small ribosomal subunit, eIF3, eIF2, MetTRNAi

87
Q

micF

A

regulates ompF expression by inhibiting translation

88
Q

ompF

A

synthesized in large amounts during normal growth
under stress conditions such as antibiotic use, its expression is decreased so less antibiotics can enter the cell

89
Q

2 types of post-translational regulation

A

inactive protein (covalent modification) or negative feedback inhibition

90
Q

attenuation

A

premature end of transcription; proteins start gene expression and then stop

91
Q

repressors

A

bind to operators to inhibit transcription

92
Q

corepressors

A

effector molecules that bind to repressors and allow them to bind to DNA

93
Q

activators

A

bind to activator binding sites to stimulate transcription

94
Q

inhibitors

A

effector molecules that bind to the activator so it cannot bind to DNA

95
Q

genes were transcription is on but can be turned off

A

repressible

96
Q

most anabolic rxns are ….

A

repressible

97
Q

inducers

A

bind to repressors to keep them away from the operator (ex. allolactose)
bind to activators to allow them to bind to the DNA

98
Q

genes in catabolic rxns

A

inducible; off but can be turned on

99
Q

tryptophan codon

100
Q

enzyme adaptation

A

enzyme appears in the cell only after it has been exposed to the enzyme’s substrate

101
Q

who found out abt this in lactose in e. coli?

A

Francois Jacob and Jacques Monod

102
Q

polycistronic

A

mRNA contains the coding sequences for 2+ structural genes

103
Q

lac Z

A

encodes B-galactosidase

104
Q

B-galactosidase is necessary for

A

cleavage of lactose and analogs into simpler sugars
converts lactose to allolactose

105
Q

lac Y encodes

A

lactose permease

106
Q

lactose permease

A

membrane protein for lactose transport

107
Q

lac A

A

encodes galactoside transacetylase

108
Q

galactoside transacetylase

A

covalently modifies lactose to prevent toxic amnts of lactose analog buildup

109
Q

lac I gene is expressed…

A

constitutively at low levels

110
Q

diauxic growth

A

use of two sugars sequentially by a bacteria

111
Q

cAMP

A

effector molecule in catabolite repression

112
Q

cAMP-CAP complex and glucose have a ___ relationship

113
Q

cAMP-CAP complex binds to

114
Q

CAP protein ___ transcription

115
Q

adenylyl cyclase

A

enzyme that produces cAMP; inhibited by lots of glucose

116
Q

lactose and glucose both present

A

transcription is low

117
Q

lactose but no glucose

A

transcription is high

118
Q

no glucose no lactose

A

no transcription

119
Q

no lactose

A

no transcription

120
Q

genes in trp operon

A

E, C, D, B, A

121
Q

trp R gene

A

encodes trp repressor protien

122
Q

trp L gene

A

encodes 14-AA leader peptide necessary in attenuation

123
Q

tryptophan is the ___ of the trp operon

A

co-repressor

124
Q

low tryptophan

A

repressor not functional; transcription “on”

125
Q

high tryptophan

A

repressor bound to operator; transcription “off”

126
Q

transcription with lots of tryptophan

A

ribosome moves past region 1, blocks region 2, terminator forms in regions 3+4, ribosome and AA strand fall off

127
Q

transcription with no tryptophan

A

ribosome pauses at the 2 tryptophan genes in the leading strand
pause allows antiterminator sequence to form in the 2-3 region
ribosome takes charged tRNAs and continues
RNAP transcription proceeds

128
Q

different cell tissue types are differentiated by

A

gene expression

129
Q

gene expression allows cells to

A

respond to environmental signals, ex, enzyme adaptation

130
Q

germ layers become differentiated in the

131
Q

total potential

A

when the cells of a zygote can be differentiated into any cell type

Genetics (8 decks)

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