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MCBM EXAM 5 DANIELLE > Translation > Flashcards

Translation Flashcards

1
Q

What are mRNA sequences read by?

A

ribosomes

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2
Q

What is a codon?

A

unpunctuated base triplets (that encode a specific amino acid)

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3
Q

How many codons are there?

A

64

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4
Q

What is degeneracy?

A

some amino acids have more than one codon

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5
Q

What is the special function of AUG?

A

only codon for methionine and is used as the initiation codon (tells ribosome which reading frame to use)

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6
Q

How many codons encode proteins?

A

61

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7
Q

What do the other 3 codons do?

A

stop codons (they do not encode amino acids)

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8
Q

How many standard amino acids are there?

A

20 (obviously they have more than one codon)

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9
Q

Do codons overlap in the RNA?

A

no they do not overlap and there are no spaces

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10
Q

What are the 3 stop codons and what do they do?

A

UAA: You are angry
UGA: You go away
UAG: You are gone
instruct the ribosome to stop translation

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11
Q

What is the first codon to initiate protein synthesis?

A

AUG

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12
Q

What are the codons that we need to know? (8)

A 
AUG
UUU,
CCC,
GGG
AAA
UGA
UAG
UAA
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13
Q

What is the open reading frame or ORF?

A

the in-frame sequence between the initiation codon and the termination codon

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14
Q

The 5’ end of the mRNA corresponds with which part of the protein?

A

the N-terminal

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15
Q

The 3’ end of the mRNA corresponds with which part of the protein?

A

C-terminal

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16
Q

What is the name for the 5’end?

A

amino terminus

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17
Q

What is the name for the 3’ end?

A

carboxy terminus

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18
Q

What did Dintzis do in 1961?

A

(this is how they found out which direction the protein was being made) used radioisotopes to follow globin synthesis in reticulocytes (immature erythrocytes)

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19
Q

Can RNA interact directly with amino acids to specify their order?

A

no

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20
Q

What serves as the adapter molecule specific for each amino acid that binds to specific condons on RNA templates?

A

tRNAs

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21
Q

How are amino acids linked to tRNA molecules prior to their incorporation into the protein?

A

enzymatically

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22
Q

Which step has the most proofreading properties?

A

replication

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23
Q

What organelle has its own set of tRNAs?

A

mitochondria

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24
Q

All cells have at least how many tRNAs?

A

32tRNAs

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25
Q

What size are tRNA molecules?

A

about 73-93 base RNA molecules

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26
Q

Do tRNAs only recognize one codon?

A

no some tRNAs can recognize more than one codon (this is called the wobble rule)

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27
Q

What is the actual form of tRNA?

A

folds into a 3D formed L-shaped structure

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28
Q

What region is always constant on tRNA?

A

ACC region

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29
Q

What does the D arm of tRNA contain?

A

dihydrouridine

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30
Q

What does the TpseudoC arm of tRNA contain?

A

the sequence ribothymidine; pseudouridine; cytosine

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31
Q

What does the anticodon arm of tRNA contain?

A

the anticodon

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32
Q

What does the amino acid arm of tRNA contain?

A

contains CCA and binds the amino acid

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33
Q

What is typically at the 5’ end of most tRNAs?

A

G

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34
Q

How many bases are chemically modified, often by methylation of normal base in tRNA?

A

8 or more

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35
Q

How many base sequences does the anticodon have?

A

the tRNA anticodon has a 3 base sequence in the anticodon loop on the anticodon arm

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36
Q

What does the anticodon of tRNA base pair with?

A

codon in the mRNA

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37
Q

In what orientation does the tRNA and the mRNA base pair?

A

antiparallel to each other

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38
Q

What is the first base of the codon paired with?

A

the third base of the anticodon and vise versa

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39
Q

What is the wobble position?

A

the first base of the anticodon

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40
Q

What is the first step in the wobble hypothesis?

A

first two bases of a codon always form strong standard base pairs with the corresponding bases of tRNA and confer most of the specificity

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41
Q

What is the second step in the wobble hypothesis?

A

the first base of some anticodons (pairs with third base of codon) determines the number of codons read by a given tRNA

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42
Q

What is the third step in the wobble hypothesis?

A

when an amino acid is specified by several different codons, those codons that differ in either of the first two base require different tRNAs

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43
Q

What is the fourth step in the wobble hypothesis?

A

A minimum of 32 different tRNAs are required to translate all 61 codons

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44
Q

What is the first starting codon?

A

Met

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45
Q

Some tRNAs contain the nucleotide inositate which base does it contain and where is it found?

A

contains the base hypoxanthine at the first anticodon position

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46
Q

What nucleotide can hypoxanthine base pair with?

A

base pair (weakly) with U, C, and A

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47
Q

What are ribosomes?

A

complex protein synthesizing machines

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48
Q

Ribosomes are comprised of how many subunits in eukaryotes and prokaryotes?

A

two subunits a large and a small

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49
Q

What is each ribosomal subunit comprised of?

A

one or more rRNA molecules and many different proteins

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50
Q

What is the largest ribosome found in eukaryotes?

A

23nm in diameter

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51
Q

What are the 3 sites that both subunits form on the ribosome?

A

peptidyl P site
Aminoacyl A site
Exit E site

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52
Q

What chromosomes are constantly transcribing new genes?

A

13,14,21,22

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53
Q

Where does protein synthesis occur?

A

in the cytoplasm

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54
Q

What is the S value for the large prokaryote ribosomal subunit?

A

50S

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55
Q

What is the S value for the small prokaryote ribosomal subunit?

A

30S

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56
Q

What is the S value for the ribosome in prokaryotes?

A

70S

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57
Q

What is an S value?

A

sedimentation value (similar to density)

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58
Q

What are the 5 major stages of protein synthesis?

A 
activation of amino acids
initiation
elongation
termination and ribosome recycling
folding and posttranslational processing
59
Q

How do we activate amino acids?

A

stage 1: charging the tRNA with its proper amino acid

60
Q

What type of bonds attach amino acids?

A

ester bonds (carboxylic acid to sugar OH) to the 3’ OH of the corresponding tRNA process (called charging the tRNA

61
Q

What is the reaction of charging the tRNA?

A

an aminoacylation of the 3’ OH of the tRNA

62
Q

What is an amino acyl-tRNA synthetases catalyze reaction?

A

specific for amino acid and one or more corresponding tRNAs

AA+tRNA+ATP —> AA-tRNA +AMP+PPi

63
Q

How many classes of enzymes are in all organisms?

A

2

64
Q

What is charging tRNA?

A

when an amino acid is put on the tRNA

65
Q

How many high energy bonds are needed to charge the tRNA?

A

2 AMP and PPi (therefore irreversible)

66
Q

What is the enzyme-bound intermediate in tRNA charging?

A

aminoacyl adenylate (aminoacyl-AMP) is formed by reaction of ATP and amino acid (carboxyl group anhydride-linked to phosphate; PPi displaced) one high energy bond used

67
Q

What is the second step in tRNA charging?

A

aminoacyl group transferred to corresponding specific tRNA

68
Q

What are the 4 ways that aminoacyl-tRNA synthetases recognize correct tRNAs?

A

recognize the anticodon
recognize 10 or more bases in tRNA
recognize one specific base pair
structure features seem to be important

69
Q

What happens once the tRNA is charged by a synthetase?

A

the aminoacyl tRNA forms a complex with a molecule called EF-Tu that also binds one GTP molecule - now it can bind to the ribosome A site (but first we have to build the initiation complex)

70
Q

What is used in initiation?

A

a specific methionine tRNA

71
Q

What are the 2 tRNAs for methionine?

A

one tRNA is used exclusively for initiation and the other for methionines with polypeptide chain

72
Q

What is regular tRNA in bacteria designated to?

A

tRNA Met

73
Q

What is initiation tRNA in bacteria designated to?

A

tRNA fMet

74
Q

What is the starting amino acid in bacteria for initiation?

A

N-formylmethionine

75
Q

What does tRNA fMet do?

A

it is charged with methionine then a specific enzyme adds formyl group to methionine donated by N10 formltetrahydrofolate

76
Q

How many components are needed for initiation in bacteria?

A

7

77
Q

What are the 7 components needed for initiation in bacteria?

A 
30S ribosomal subunit (contains 16S rRNA)
mRNA
initiation fMet-tRNA fMet
3 initiation factors (IF1-IF3_
GTP
50S ribosomal subunit
Mg2+
78
Q

How many steps does it take to assemble and form the initiation complex?

A

3 steps

79
Q

What is the 1st step in assembling the initiation complex in bacteria?

A

correctly binding the positions of the initiation codon on the 30S subunit

80
Q

If the codon is bound in a region of 30S what site is the subunit a part of?

A

subunit is part of the P site

81
Q

How does the initiation codon distinguish where to go?

A

by the proximity to Shine-Dalgarno sequence

82
Q

Where will the P site of the ribosomal complex be placed?

A

right over the AUG of our start site

83
Q

What is the 2nd step in assembling the initiation complex in bacteria?

A

30S subunit, mRNA, IF-1, IF-3 complex is joined by IF-2 (itself bound to GTP) and fMEt-tRNA fMet

84
Q

Where is the anticodon of the initiator tRNA and the initiation codon paired?

A

at the P site

85
Q

Where does fMet-tRNA fMet bind?

A

to the P site

86
Q

Where do all other tRNAs bind?

A

the A site (except for fMet tRNA

87
Q

What is the 3rd step in assembling the initiation complex in bacteria?

A

large complex binds 50S ribosomal subunit, simultaneously GTP bound by IF-2 is hydrolyzed to GDP, GDP is released by IF-2 and IF-1-IF-3 leave the complex

88
Q

Now the complete ribosome has charged initiator tRNA in complete P site and what is found at the A site?

A

nothing it is empty

89
Q

How many initiation factors eIFS are involved in protein synthesis of eukaryotes?

A

at least 9

90
Q

What steps take place in initiation in eukaryotes?

A

an initiation factor binds to 5’ cap and a complex is formed with 40S subunit, mRNA scans for the first AUG codon (which is typically the start of the reading frame) a complete 80S ribosome is assembled using the other eIFs and initiating Met-tRNA Met

91
Q

What is a Kozak sequence?

A

5’-CCACCAUGG-3’ found at many initiation sites

92
Q

How does elongation occur?

A

stepwise addition of amino acids to polypeptide chain by formation of peptide bonds

93
Q

What is elongation accompanied by?

A

the movement of ribosome along mRNA from 5’ to 3’ end reading codons in stepwise manner

94
Q

How many ribosomes are found bound to each mRNA molecule in prokaryotes and eukaryotes?

A

10-100

95
Q

Can polypeptide chains be synthesized simultaneously?

A

yes it is a very efficient use of mRNA - polypeptide chains can be synthesized simultaneously using just one molecules worth of genetic information

96
Q

What is required for elongation in bacteria?

A 
initiation complex (for first peptide bond)
next aminoacyl-tRNA specified by next codon
elongation factors EF-Tu, Ef-Ts, EF-G
97
Q

How many steps are involved in prokaryotic elongation? Are these steps repeated?

A

3 steps and the process

yes, repeated for each amino acid residue adding to the growing chain

98
Q

What happens in the 1st step in elongation of prokaryotes?

A

bind the next aminoacyl-tRNA (as the aminoacyl-tRNA EF-Tu GTP complex) specified by the codon adjacent to the AUG is bound to the A site of the 70 S initiation complex, GTP is hydrolyzed and EF-TuGDP is relased by the ribosome, EF-TuGTP is regenerated and binds to EF-Ts and releases GDP, EF-Tu binds GTP, and releases EF-Ts

99
Q

What is the 2nds step in elongation of prokaryotes?

A

a peptide bond is formed between the 2 amino acids

100
Q

What is the enzyme catalyzing the second step of elongation in prokaryotes?

A

peptidyl transferase

101
Q

What type of enzyme is peptidyl transferase?

A

a ribozyme (instead of a ribosomal protein it is the large subunit 23S rRNA that catalyzed the reaction)

102
Q

What type of energy is provided in the 2nds step of elongation in prokaryotes?

A

energy is provided by the high energy ester bond between amino acid and tRNA

103
Q

he peptide bond will form between initiation fMet and the second amino acid at which site?

A

the A site

104
Q

What is base paired to the second codon in the A site of the 30 subnunit it step 2 of elongation in prokaryotes?

A

a dipeptidyl tRNA

105
Q

Where does the “spent” initiation tRNA base pair to the aUG on the 30S subunit?

A

in the P site

106
Q

Step 2 of elongation a peptide bond changes formation what does this result in?

A

a change in the interaction of tRNAs with the 50S but not the 30S subunit

107
Q

Where does the deacylated initiation tRNA move to?

A

moves into the E (exit) site on the 50S subunit, stays in P on 30S subunit

108
Q

Where does the new dipeptidyl tRNA move to?

A

moves to the P site on the 50S subunit but stays in the A site on the 30S subunit

109
Q

What happens to the position of the anticodon in the 30S ribosome site?

A

it is unchanged

110
Q

What is the 3rd step in elongation in prokaryotes?

A

translocation: ribosome moves along mRNA precisely one codon towards the 3’ end, movement is mediated by elongation factor G (EF-G) and GTP

111
Q

What is the EF-G GTP bound by?

A

ribosome

112
Q

What happens when GTP is hydrolyzed?

A

EF-G and GDP are released (energy moves the ribosome)

113
Q

How many tRNAs can be bound at any given time?

A

2

114
Q

What does the movement of the ribosome cause to occur?

A

shifts the dipeptidyl tRNA from the A site on the 30S subunit to the P site (now all in the P site)

115
Q

What does the spent tRNA cause to occur?

A

shifts from the P site on the 30S to the E site (all in E) and the A site is empty and ready for next aa-tRNA

116
Q

When the next aa-tRNA begins the next round of elongation what happens to the A and E sites?

A

filling of the A site induces release of spent tRNA from the E site

117
Q

Can the A and E sites be occupied simultaneously?

A

no

118
Q

How many steps and how many elongation factors are required for elongation in eukaryotes?

A

3 elongation factors and 3 steps

119
Q

Why use two steps to move tRNAs in elongation?

A

anchors one end of tRNA while the other moves during peptide bond formation and translocation, also prevents premature release of peptidyl-tRNA (tremendous waste of energy) and enhances processivity

120
Q

What is the proofreading on the ribosome limited to?

A

codon-anticodon interactions (identity of amino acid not checked)

121
Q

When does the proofreading occur?

A

while EF-Tu GTP and EF-Tu GDP bound (milliseconds) codon anticodon base pairing is checked

122
Q

What happens if the incorrect tRNA codon pairs?

A

they would dissociate during this time

123
Q

What is a way that speed and fidelity are optimized?

A

slower speed = higher fidelity and vice versa

124
Q

What happens during termination?

A

elongation continues until ribosome encounters in frame stop codon in A site

125
Q

One of three termination factors bind to termination codon what are they?

A

RF1 for UAG, UAA
RF2 for UGA, UAA
RF3 - not known

126
Q

In termination why is peptidyl transferase induced?

A

to transfer peptide chain to water resulting in the release of peptide chain from the ribosome (uncharged tRNA in P site reelased and 30S and 50S subunit dissociate)

127
Q

How many termination factors do eukaryotes have?

A

just one

128
Q

What 2 things are tightly coupled in bacteria?

A

transcription and translation

129
Q

Why is protein synthesis energy expensive?

A

charging tRNA takes 2 high energy bonds
first elongation step GTP–> GDP
translocaitons tep: GTP–> GDP
therefore at least 4 high energy bonds are expended per peptide bod=122kj/mol foron e 21kj/mol peptide bond

130
Q

Energy is used for specificity. What is specificity?

A

used to maintain proper alignment of a codon, tRNA and growing end of the polypeptide chain

131
Q

What is the overall error rate for protein synthesis?

A

1:10,000 amino acids (Much higher than DNA replication)

132
Q

How correct are the chains typically?

A

about 90% correct

133
Q

How correct are the chains that smaller proteins?

A

about 99%

134
Q

Why is the accuracy not higher?

A

because it would greatly slow protein synthesis down and would only gain modest accuracy

135
Q

What 2 things can inhibit translation in prokaryotes and eukaryotes?

A

antibiotics and toxins

136
Q

Does a prokaryotic inhibitor harm eukaryotes?

A

there are sufficient differences between the organisms so a prokaryotic inhibitor is relatively harmless to eukaryotes

137
Q

What are the 7 inhibitors of translation?

A 
tetracyclines
chloramphenicol
streptomycin
aminoglycosides
cycloheximide
diphtheria toxin
ricin
138
Q

What does tetracycline do?

A

binds to prokaryotes A site; blocks aa-tRNA binding and is useful in treating periodontal disease (stains teeth)

139
Q

What does chloramphenicol do?

A

blocks peptidyl transfer in prokaryotes and mitochondria, not eukaryote 80S ribosomes
useful to treat rickettsial infections (rocky mountain spotted fever, typhus) very toxic ex: blood disorders such as aplastic anemia

140
Q

What does streptomycin do?

A

binds S12 of 30S ribosome
low concentrations cause misreading of code
high concentrations inhibit initiation

141
Q

What does aminoglycosides do?

A

block 50S ribosome binding to initiation complex

142
Q

What does cycloheximide do?

A

blocks eukaryotes 80S peptidyl transferase not prokaryotes or mitochondria

143
Q

What does diphtheria toxin do?

A

catalyzes ADP ribosylation of eEF2 inactivating it

144
Q

What does ricin do?

A

extremely toxic protein from castor bean - inactivates eukaryotes 60S subunit by depurinating A residue of 28S rrNA

MCBM EXAM 5 DANIELLE (6 decks)

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