Exam 2 Flashcards
memorize (131 cards)
1
Q
CTD has
A
repeated pattern of 7 amino acids
2
Q
phosphorylation of CTD causes…
A
transcription signals to be sent
3
Q
RNA cap
A
has capping enzymes
protects 5’ end
necessary for translation
4
Q
splicing
A
removal of introns and joining of exons
5
Q
spliceosome
A
splices; made up of SNRPs
6
Q
SNRPs
A
small nuclear RNA and ribonucleoproteins
7
Q
polyadenylation signal (PAS)
A
stops RNA elongation at 3’ end, abt 20 bases down
8
Q
polyadenylation signal sequences
A
AAUAAA or AUUAAA
9
Q
poly-A tail
A
added at the end of transcription
made up of 150-200 adenine bases
10
Q
CPSF - cleavage polyadenylation specificity factor # of subunits
A
6; endonuclease activity in 1
11
Q
where does CPSF bind
A
polaydenylation sequence
12
Q
where is the cut site
A
10-30 bps after PAS
13
Q
where do cleavage factors (C1 and C2) bind
A
cut site
14
Q
CPSF recruits..
A
polyA polymerase (PAP)
15
Q
polyA polymerase
A
adds polyA binding proteins (PABP)
16
Q
cleavage stimulation factor (CStF)
A
cleaves the mRNA and falls off
17
Q
polyA binding protein purpose
A
prevents degradation of polyA tail
18
Q
downstream sequence element (DSE)
A
site where CStF binds
19
Q
allosteric termination model
A
similar to intrinsic method of termination in prokaryotes
built-in signal causes destabilization
20
Q
torpedo termination model
A
similar to rho dependent method of eukaryotes - outside protein Xrn2 helps with termination process
21
Q
Xrn2
A
protein that assists with torpedo termination model of eukaryotic transcription
22
Q
_____ rule in introns
A
GU-AG; introns almost always start with GU and end with AG
23
Q
bases between last AG and A at branch point
A
15-45
24
Q
how does splicing start
A
spliceosome recognizes intron sequences
25
first step of splicing
SNPs U1 and U2 bind to the 5' splice site and internal A (branch point), respectively
26
second step of splicing
U4, U5, U6 complex joins spliceosome and forms a bend
27
third step of splicing
U1, U4, and U6 fall off
28
first splicing reaction
one end of the intron separates and attaches to the internal A
29
second splicing reaction
the other end of the intron is cleaved from the exon; the two exons join
forms lariat
30
transesterification is directed by
CTD
31
translation
mRNA codons -> amino acid sequences
32
translation and transcription in prokaryotes
coupled
33
ingredients in an amino acid
carboxyl group, amino group, R group (central carbon atom)
34
total # codons
64
35
degenerate
multiple codons code for the same amino acid
36
stop codons
UAA, UAG, UGA
37
start codon
AUG (methionine)
38
tRNA loop contains _____ of mRNA codon
anticodon
39
tRNA D-loop
stability of molecule; involves displacement of the 2 strands, held apart for brief sections by a 3rd strand
40
T-loop
interacts w/ ribosomes
41
variable loop
interacts w/ aminoacyl tRNA synthetase
42
aminoacyl tRNA synthetase
enzyme that charges tRNA by adding an amino acid
43
of different synthetases and # of different forms of charged tRNA
20
44
tRNAs can be _____ by adding another amino acid
recycled
45
large ribosome subunit in prokaryotes
50S
23S rRNA
5S rRNA
31 proteins
46
small ribosomal subunit in prokaryotes
30S
16S rRNA
21 proteins
47
large subunit in eukaryotes
60s
28S rRNA
5.8S rRNA
5S rRNA (highly preserved)
49 proteins
48
40S subunit in eukaryotes
18S rRNA
33 proteins
49
ribosome in eukaryotes
50% RNA, 50% proteins
50
decoding center
location in the ribosome where incoming tRNA is matched w/ mRNA codon, in the A site
51
peptidyl-transferase center
region on larger ribosomal subunit involved in catalyzing peptide bond formation (between new AAs) and peptide release
52
E site
exit site; releases now-uncharged tRNA
53
P site
peptidyl site; tRNA binds to the growing chain of AAs
54
A site
binds an incoming charged tRNA whose anticodon matches the codon in the A site of the small subunit
55
charged tRNA
bonded to an aminoacyl
56
tRNAMeti
initiator tRNA that inserts methionine to establish correct reading frame
57
N-formylmethionine (fMet)
formyl group added to methionine while the amino acid is attached to initiator, to help w/ translation
58
Shine-Dalgarno Sequence
ribosome binding site on mRNA strand
AGGAGGU
59
where is the SDS
in the 5' UTR, preceding the initiation codons
60
how does the ribosome bind to the SDS
the 3' end of the 16S rRNA in the small subunit binds to the SDS
61
IF1
initiation factor - blocks ribosome A site
62
IF3
initiation factor - blocks ribosome E site and keeps large subunit from attaching prematurely
63
IF2
initiation factor - escorts fMet-tRNA to the small ribosomal subunit at the P site, using ATP
64
IF2-GTP
allows release of the initiation factors
65
when IFs are released...
large subunit joins complex, ribosome becomes functional
66
EF-Tu
elongation factor
brings charged tRNAs to A site to be joined to polypeptide chain in P site
67
EF-G
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
termination begins when...
tRNA is unable to recognize stop codons - they have no anticodons
69
tripeptides
sequences in release factor proteins to recognize stop codons
70
RF1 recognizes ____
UAA and UAG
71
RF2 recognizes ____
UAA and UGA
72
how do RFs stop translation
water molecule positions itself on peptidyl transferase site -> peptide chain falls off
73
RF3
has GTPase activity, causes RF1 +2 to fall off
74
RF3 also falls off because of...
change in structure due to hydrolysis of GTP
75
RRF (ribosomal recycling factor), EF-G, IF3
dismantles the translation mechanism
76
IF3 ______ to 30S subunit
remains attached
77
eIF1a
blocks A site
78
eIF1 and eIF3
prevent premature association of small and large subunits
79
eIF2 and eIF5
bring in initiator tRNA
80
eIF5b
promotes interaction between small and large subunits
81
eIF4F has _ subunits
3
82
eIF4A
ATPase activity, helicase activity
83
eIF4G
interacts w/ polyA binding proteins
84
eIF4E
binds to cap
85
Kozak's sequence
RCCAUGG
-3 +1 +4
86
ternary complex
small ribosomal subunit, eIF3, eIF2, MetTRNAi
87
micF
regulates ompF expression by inhibiting translation
88
ompF
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
2 types of post-translational regulation
inactive protein (covalent modification) or negative feedback inhibition
90
attenuation
premature end of transcription; proteins start gene expression and then stop
91
repressors
bind to operators to inhibit transcription
92
corepressors
effector molecules that bind to repressors and allow them to bind to DNA
93
activators
bind to activator binding sites to stimulate transcription
94
inhibitors
effector molecules that bind to the activator so it cannot bind to DNA
95
genes were transcription is on but can be turned off
repressible
96
most anabolic rxns are ....
repressible
97
inducers
bind to repressors to keep them away from the operator (ex. allolactose)
bind to activators to allow them to bind to the DNA
98
genes in catabolic rxns
inducible; off but can be turned on
99
tryptophan codon
UGG
100
enzyme adaptation
enzyme appears in the cell only after it has been exposed to the enzyme's substrate
101
who found out abt this in lactose in e. coli?
Francois Jacob and Jacques Monod
102
polycistronic
mRNA contains the coding sequences for 2+ structural genes
103
lac Z
encodes B-galactosidase
104
B-galactosidase is necessary for
cleavage of lactose and analogs into simpler sugars
converts lactose to allolactose
105
lac Y encodes
lactose permease
106
lactose permease
membrane protein for lactose transport
107
lac A
encodes galactoside transacetylase
108
galactoside transacetylase
covalently modifies lactose to prevent toxic amnts of lactose analog buildup
109
lac I gene is expressed...
constitutively at low levels
110
diauxic growth
use of two sugars sequentially by a bacteria
111
cAMP
effector molecule in catabolite repression
112
cAMP-CAP complex and glucose have a ___ relationship
inverse
113
cAMP-CAP complex binds to
CAP site
114
CAP protein ___ transcription
increases
115
adenylyl cyclase
enzyme that produces cAMP; inhibited by lots of glucose
116
lactose and glucose both present
transcription is low
117
lactose but no glucose
transcription is high
118
no glucose no lactose
no transcription
119
no lactose
no transcription
120
genes in trp operon
E, C, D, B, A
121
trp R gene
encodes trp repressor protien
122
trp L gene
encodes 14-AA leader peptide necessary in attenuation
123
tryptophan is the ___ of the trp operon
co-repressor
124
low tryptophan
repressor not functional; transcription "on"
125
high tryptophan
repressor bound to operator; transcription "off"
126
transcription with lots of tryptophan
ribosome moves past region 1, blocks region 2, terminator forms in regions 3+4, ribosome and AA strand fall off
127
transcription with no tryptophan
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
different cell tissue types are differentiated by
gene expression
129
gene expression allows cells to
respond to environmental signals, ex, enzyme adaptation
130
germ layers become differentiated in the
gastrula
131
total potential
when the cells of a zygote can be differentiated into any cell type
