lec 2: translation Flashcards
1
Q
creation of protein molecules using mRNA as the template
A
translation
2
Q
to translate the nucleotide sequence of mRNA into the amino acid sequence of protein
A
translation
3
Q
how long does translation take place in cells?
A
20 secs to few minutes
4
Q
give the requirements for protein synthesis (translation)
A
mRNA, tRNA, rRNA
20 amino acids
enzymes and protein factors
ATP and Mg^2+
5
Q
is the template for the protein synthesis
A
mRNA
6
Q
it is polycistronic
A
prokaryotic mRNA
7
Q
a single mRNA molecule may code for more than one peptides
A
polycistron
8
Q
it is monocistronic
A
eukaryotic mRNA
9
Q
each mRNA codes for only one peptide
A
monocistron
10
Q
what do you call the UTR at 5’?
A
leader sequence
11
Q
what do you call the UTR at 3’?
A
trailer sequence
12
Q
these regions are still transcribed into pre-mRNA
A
UTR or untranslated regions
13
Q
true or false: prokaryotes undergo post-transcriptional modification
A
FALSE
only eukaryotes undergo post-transcriptional modification, specifically the hnRNA
14
Q
is a sequence of three adjacent nucleotides on mRNA that corresponds with a specific amino acid
A
genetic codon
15
Q
true or false: one genetic codon codes for one amino acid
A
true
16
Q
give the stop codons
A
UAA, UAG, UGA
17
Q
codon for start signal
also codes for methionine
A
AUG
18
Q
how many codons in total?
A
64 codons
3 stop
61 code
19
Q
a portion of a DNA sequence that does not include a stop codon
A
open reading frame (ORF)
20
Q
give the properties of genetic code
A
degeneracy
commaless
universal
21
Q
genetic codons should be read continuously without spacing or overlapping
A
commaless
22
Q
refers to the insertion or deletion of nucleotide bases in numbers that are not multiples of three
A
frameshift mutation
23
Q
more than one codon can specify the same amino acid
A
degeneracy
24
Q
these degenerated codons differ on the third nucleotide
A
degeneracy
25
non-Watson-Crick base pairing is permissible between the ____ nucleotide of the codon on mRNA and the ____ nucleotide of the anti-codon on tRNA
wobble
third
first
26
genetic codons for amino acids is the same in humans, animals, plants and bacteria
universal
27
but in universality of genetic code, there is an exception, what is it?
in albicans
28
compare and contrast
cytoplasm
AUA -
AUG -
UAA, UAG, UGA -
mitochondria
AUA -
UGA -
AGA, AGG -
cytoplasm
AUA - isoleucine
AUG - methionine
UAA, UAG, UGA - termination
mitochondria
AUA - methionine
UGA - Trp (tryptophan)
AGA, AGG - termination
29
give the tRNA structures
attached amino acid
acceptor stem
anticodon loop
anticodon
30
since tRNA cant pick up the AA, what tRNA does pick it up?
aminoacyl-tRNA
31
this tRNA has the proofreading ability
aminoacyl-tRNA synthetase
32
prokaryotic Met-tRNA^met can be what to?
can be formylated to fMet-tRNA_i^met
33
what is the enzyme used for formylating Met-tRNA^met?
formyl transferase
34
initiation tRNA for prokaryotes: this can only be recognized by initiation codon
fMet-tRNAimet
35
initiation tRNA for prokaryotes: this is used for elongation
Met-tRNA_e^met
36
initiation tRNA for eukaryotes: is used for initiation
Met-tRNA_i^met
37
initiation tRNA for eukaryotes: this is used for elongation
Met-tRNA_e^met
38
is the place where protein synthesis takes place
ribosome
39
composed of a large subunit and a small subunit, each of which is made of ribosomal RNAs and ribosomal proteins
ribosome
40
give the subunits for prokaryotes
large subunit - 50S
small subunit - 30S
41
give the subunits for eukaryotes
large subunit - 60S
small subunit - 40S
42
what is the subunit of prokaryotic ribosome?
70S
43
what is the subunit of eukaryotic ribosome?
80S
44
give the three sites on ribosomes
aminoacyl site (A site)
peptidyl site (P site)
exit site (E site)
45
acceps an aminoacyl-tRNA
A site
46
holds the growing amino acid chain
P site
47
releases the deacylated tRNA
E site
48
give the location of each site
A site - large and small subunits
P site - large and small subunits
E site - large subunit
49
what is the direction of the protein synthesized?
from N-terminal to C-terminal
50
what is the direction of template mRNA?
5' to 3' end
51
give the steps in translation
initiation
elongation
termination
52
give the four steps in prokaryotic initiation
1) separation between 50S and 30S subunits
2) positioning mRNA on the 30S subunit
3) registering fMet-trna_i^met on the P site
4) associatin the 50S subunit
53
give the three initiaion factors in prokaryotes
IF-1
IF-2
IF-3
54
the ribosomal binding site in bacteria
helps start protein synthesis in bacteria and archaea
shine-dalgarno sequence
55
give the sequence of shine-dalgarno
AGGAGGU
56
shine-dalgarno sequence is usually _____ of the start codon AUG
8 bases upstream
57
__ and ___ bind to the 30S subunit, making separation between 50S and 30S subunit
IF-1
IF-3
58
IF-1 binds to what site?
A site
59
IF-3 binds to where?
30S subunit
60
the complex of the ____-bound ____ and the fMet-tRNA enters the ___ site
GTP
IF-2
P site
61
the ____ subunit combines with this complex
50S
62
in the last step of initiation in prokaryotes, GTP is hydrolyzed to ___ and _____
also, what structures do depart from the complex?
GDP and Pi
all three IFs
63
how many GTP is consumed in one initiation course?
only one GTP
64
give the three steps of elongation in prokaryotes
1) positioning an aminoacyl-tRNA in A site (entrance)
2) forming a peptide bond (peptide bond formation)
3) translocating the ribosome to the next codon (translocation)
65
give the elongation factors in bacteria
EF-Tu
EF-G
66
delivers aa-tRNAs to the A-site of the ribosomes
EF-Tu (elongation factor thermos unstable)
67
peptide bond formation occurs at _____ catalyzes by _____
A site
peptidyl transferase
68
EF-G is a ____ enzyme
translocase
69
GTP bound EF-G provides the energy to move the ribosome one codon toward the _____ on mRNA
3’ end
70
after the translocation, the uncharged tRNA is released from the _____
E site
71
true or false: stop codons are not recognized by the tRNA, but instead signal to the ribosome to stop translation
true
72
release factor binds to which site?
A site
73
give the release factors of prokaryotes:
RF-1
RF-2
RD-3
74
recognizes UAA and UAG
RF-1
75
recognizes UGA and UAA
RF-2
76
hydrolyses and causes the release of ribosomal subunits (30S and 50s subunit)
RF-3
77
give the releasing factor of eukaryotes
eRF
78
give the four steps of initiation in eukaryotes
1) separation between 60S and 40S subunits
2) binding Met-tRNA_i^met on the 40S subunit
3) positioning mRNA on the 40S subunit
4) associationg the 60S subunit
79
facilitates binding of initiating Met-tRNAMet to 40S ribosomal subunit
eIF2
80
first factors to bind 40S subunit
eIF2B
eIF3
81
facilitate subsequent steps
eIF2B
eIF3
82
RNA helicase activity removes secondary structure in the mRNA to permit binding to 40S subunit
eIF4A
83
eIF that binds to mRNA
eIF4B
84
facilitates scanning of mRNA to locate the first AUG
eIF4B
85
binds to the 5’ cap of mRNA
eIF4E
86
binds to eIF4E and to poly(A) binding protein (PAB)
eIF4G
87
promotes dissociation of several other IFs from 40S subunit as a prelude to association of 60S subunit to form 80S initiation complex
eIF5
88
facilitates dissociation of inactive 80S ribosome into 40S and 60S subunits
eIF6
89
give the eIF4F complex
eIF4A
eIF4E
eIF4G
90
consensus recognition sequence
signals the start of protein translation in eukaryotes
kozak sequence
91
give the sequence of kozak
ACCAUGG
92
this often contains the start codon
located in the 5' UTR of mRNA
kozak sequence
93
give the elongation factors in eukaryotes
eEF-1A
eEF-1B
eEF-2
94
this eukaryotic release factor recognizes all three termination codons (UAA, UAG and UGA)
eRF-1
95
eukaryotic release factor terminates translation
eRF-3
96
aggregates of numerous ribosomes that are in the process of actively translating mRNA into protein
polysomes
97
the macromolecules assisting the formation of protein SECONDARY STRUCTURE include
molecular chaperon
protein disulfide isomerase (PDI)
peptide prolyl cis-trans isomerase (PPI)
98
a group of conserved proteins that can recognize the non-native conformation of peptides and promote the correct folding of individual domains and whole peptides
chaperons
99
give examples of chaperons
heat-shock protein (HSP)
chaperonin
100
examples of HSP
HSP70
HSP40
GreE family
101
examples of chaperonin
GroEL family
GroES family
102
give mechanisms of chaperons
1) protects unfolded segments of peptide first
2) releases the unfolded segments and promotes the correct folding
3) provides a micro-environment
103
chaperons provide this to promote the correct native conformation of those peptides that cannot have proper spontaneous folding
micro-environment
104
give the modifications of primary protein structure:
1) removal of the first N-terminal methionine residue
2) covalent modification of some amino acids
3) activation of peptides through hydrolysis
105
give the modifications of spatial protein structure:
1) assemble of subunits
2) attachment of prosthetic groups
3) connection of hydrophobic aliphatic chains
106
the correctly folded proteins need to be transported to special cellular compartments
protein targeting
107
proteins need signal sequence to be transported
protein targeting
108
give the interferences of translation
antibiotics
toxins
interferons
109
blocks binding of aminoacyl-tRNA to the A site of the ribosome
tetracycline
110
prevents the transition from translation initiation to chain elongation
causes miscoding
streptomycin
111
blocks the peptidyl transferase reaction on ribosomes in prokaryotes
chloramphenicol
112
binds in the exit tunnel of the ribosome
inhibits elongation of the peptide chain
erythromycin
113
blocks initiation of RNA chains by binding to RNA polymerase
prevents RNA synthesis
rifamycin
114
causes the premature release of nascent polypeptide chains by its addition to the growing chain end
puromycin
115
binds to DNA and blocks the movement of RNA polymerase
prevents RNA synthesis
actinomycin D
116
blocks the A site of the 60S ribosome subunit after translation initiation, but before elongation
harringtonine
117
blocks the peptidyl transferase reaction on ribosomes in eukaryotes
anisomycin
118
blocks mRNA synthesis by binding preferentially to RNA polymerase II
a-amanitin
119
the ribosomes of eukaryotic mitochondria (and chloroplasts) often resemble those of bacteria in their sensitivity to ______
inhibitors
120
some antibiotics can have a _____ effect on human mitochondria
deleterious
121
it has a similar structure to Tyr- tRNA
puromycin
122
it works for both prokaryotes and eukaryotes
puromycin
123
among the most toxic substance known
ricin
124
the size of few grains of table salt can kill an adult human
ricin
125
eliminates a single adenine base from the large ribosomal subunit in all species
ricin
126
ricin is found from what?
castor bean oil (Ricinus communis)
