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BIOL 3421 - molecular biochem > translation > Flashcards

translation Flashcards

1
Q

are amino acids coded by codons or anticodons

A

codons

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2
Q

what are codons

A

3-nucleotide codes for amino acids

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3
Q

is the codon on the mRNA or the tRNA

A

mRNA

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4
Q

is the anticodon on the mRNA or the tRNA

A

tRNA

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5
Q

function of tRNA?

A

required to convert from nucleotide to amino acid

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6
Q

where does translation occur in the cell

A

cytosol

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7
Q

where in the cytosol does translation occur

A

on ribosomes

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8
Q

which main enzyme was important for researchers to be able to determine the nucleotide code

A

polynucleotide phosphorylase

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9
Q

describe the actions of polynucleotide phosphorylase

A

in the presence of NDPs it will create a polynucleotide without a template

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10
Q

describe how UUU was the first codon to be assigned (ie how they figured out UUU=Phe)

A

they incubated polyU mRNA with E coli extracts and one radioactive amino acid (repeated for all 20 amino acids). Only one would produce a radioactive protein, and this would be the one that codes for UUU

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11
Q

describe how researchers determined the code for codons with two different nucleotides (As and Cs)

A

used 5 parts ADP and 1 part CDP + polynucleotide phosphorylase. They determined the likelihood of each possible codon based on the amounts that were added. Based upon the protein product, they determined which aa’s were produced in which amounts

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12
Q

the first base of a codon pairs with the ___ base of the anticodon

A

third

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13
Q

T or F: codon and anticodon are antiparallel

A

true

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14
Q

some tRNAs have which weird nucleotide

A

inosinate (I)

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15
Q

which position of the anticodon is inosinate found in

A

the third position of the anticodon

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16
Q

which nucleotides of the codon can inosinate base pair with

A

A U and C

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17
Q

T or F: base pairs of codon-anticodon that contain inosinate are stronger than watson-crick pairings

A

false; they’re weaker

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18
Q

when more than one codon specifies an amino acid, which nucleotide is often the different one

A

the third nucleotide of the codon

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19
Q

what is the wobble hypothesis

A

first two bases of the mRNA codon are under strong watson-crick pairings with the anticodon and confer most of the coding specificity. The third base only pairs loosely, allowing the rapid dissociation of the tRNA during synthesis. Reduces the need for accuracy and increases speed. These rules allow for only 32 tRNA molecules to translate all 61 codons

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20
Q

how many tRNA molecules are needed to translate all 61 codons

A

32

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21
Q

describe how the wobble hypothesis helps maintain genetic integrity

A

if there is a random mismatch, there is a 1/3 chance it will be in the wobble position, and therefore may still code for the same amino acid (= silent mutation)

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22
Q

what is the most common type of mutation

A

transition mutation

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23
Q

what is a transition mutation

A

a purine is replaced with another purine, or a pyrimidine with another pyrimidine

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24
Q

describe why transition mutations aren’t THAT bad

A

mismatches in codon positions 1 or 2 tend to change the amino acid, but introduce a similar type of amino acid (ie the product is still hydrophobic, so the damage isn’t that bad)

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25
Q

T or F: some mRNAs are edited before translation

A

true

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26
Q

in which RNAs does RNA editing often occur

A

in RNAs made from genes in the mitochondria and chlorplast

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27
Q

describe what happens when RNA editing involves addition or deletion of bases

A

shifts the reading frame

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28
Q

shifting the reading frame requires which molecule

A

guide RNA (gRNA)

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29
Q

describe the actions of gRNA

A

it will pair to the mRNA at the editing site and direct several proteins (endo/exonucleases, ligases, etc) to it. These proteins will introduce extra bases

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30
Q

which weird type of pairing can occur during frame-shift mutations

A

G-U

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31
Q

in deamination RNA editing, describe what happens to C and A bases

A

C becomes U
A becomes I

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32
Q

what are Alu elements

A

repetitive sequences that often exist in introns + the untranslated regions at the end of transcript

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33
Q

in which part of the genome do deaminations occur

A

Alu elements

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34
Q

describe how RNA editing leads to different apoB proteins in different tissues

A

apoB-100 in synthesized in the liver for LDLs and apoB-48 is synthesized in the intestine for chylomicrons. Both are encoded for by the same mRNA which will produce the liver version without editing. However, a cytidine deaminase found only in the intestine can bind to the mRNA at CAA –> UAA. UAA is a stop codon. The shorter apoB-48 is thus translated in the intestine only

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35
Q

bacteria ribosomes are __% rRNA and __% protein

A

65 and 35

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36
Q

how many nm long are ribosomes

A

18

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37
Q

T or F: in bacterial ribosomes, there are no proteins near the active site

A

true

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38
Q

how many rRNAs are in the 30S subunit

A

1

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39
Q

how many rRNAs are in the 50S subunit

A

2

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40
Q

describe the structure of the ribosome in regards to rRNA and protein

A

rRNA have extensive intrachain base pairing and form the structural core of the complex. The proteins have domains on the ribosome surface, but also extensions that protrude into the rRNA core for structural stability

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41
Q

how many rRNAs are in the 40S subunit

A

1

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42
Q

how many rRNAs are in the 60S subunit

A

3

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43
Q

how many amino acids long is tRNA

A

73-93

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44
Q

which nucleotide is at the 5’ end of tRNA

A

G

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45
Q

which 3 nucleotides are at the 3’ end of tRNA

A

CCA

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46
Q

how many unpaired bases are on the anticodon arm of tRNA

A

7

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47
Q

what is a polysome

A

a big string of ribosomes all in a row, translating the mRNA as it has just been synthesized

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48
Q

which enzymes place the appropriate amino acid on the amino arm of the tRNA

A

aminoacyl-tRNA synthetases

49
Q

describe the linkage that binds the aminoacyl group to a tRNA

A

the aminoacyl group is esterified to the 3’ OH on the terminal A residue of the tRNA

50
Q

what stage must occur before translation initiation

A

activation of amino acids

51
Q

how many aminoacyl-tRNA synthetases are there

A

20; 1 per amino acid

52
Q

what does it mean for an amino acid to be activated

A

amino acid + tRNA + ATP –> aminoacyl-tRNA

53
Q

how many ATP are required to make one aminoacyl-tRNA

A

2 ATP

54
Q

describe the 2 step formation of aminoacyl-tRNAs

A

formation of an intermediate occurs first: aminoacyl adenylate (aa + AMP). The enzyme then binds to this intermediate. aminoacyl group is transferred from the enzyme to the corresponding tRNA

55
Q

why is it helpful to have 2 steps to produce aminoacyl-tRNA

A

each step is a chance to notice any errors before we continue

56
Q

T or F: ribosomes can proofread their transcript

A

false; they cannot proofread

57
Q

what are the implications of ribosomes being unable to proofread

A

if the wrong aa gets added to the tRNA by the synthetase, there’s no way to catch the mistake later

58
Q

which aa does the start codon AUG code for

A

methionine

59
Q

describe how the initiation methionine is different from internal methionines

A

it’s attached to a formyl group = fMet

60
Q

T or F: fMet is found in both prokaryotes and eukaryotes

A

false; it’s only in prokaryotes

61
Q

T or F: fMet and Met have different tRNAs

A

true

62
Q

pro initiation: name the consensus sequence important for initiation

A

Shine-Dalgarno sequence

63
Q

describe the structure, location, and binding partner of the shine-dalgarno sequence

A
  • 4-9 purines
  • found 10 nucleotides upstream of AUG
  • binds to pyrimidine rich 16S rRNA in the 30S subunit
64
Q

pro initiation: benefit of the SD sequence?

A

positions AUG over the P site of the ribosome. It does this by pairing to the 16S rRNA in the 30S subunit

65
Q

name the 3 ribosome sites

A

aminoacyl site, peptidyl site, exit site

66
Q

list what each ribosome site can bind

A

A and P bind aminoacyl-tRNAs, E can only bind uncharged tRNAs

67
Q

describe which subunits of the ribosome form the A P and E sites

A

A and P are formed by both large and small, but E is mainly on the large

68
Q

pro initiation: role of IF1

A

blocks tRNA-fMet from entering the A site

69
Q

pro initiation: role of IF3

A

prevents premature binding of 50S subunit

70
Q

pro initiation: what occurs after IF1 and IF3 do their jobs

A

SD sequence of the mRNA transcript aligns and binds to the 16S rRNA of the small subunit. this positions the AUG over the P site

71
Q

pro initiation: what occurs once AUG is over the P site

A

GTP-bound IF2 binds to the small sub and recruits tRNAfMet to the P site

72
Q

pro initiation: when tRNAfMet is brought to the P site, is it charged or uncharged

A

charged

73
Q

pro initiation: which IF blocks tRNAfMet from entering the A site

A

IF1

74
Q

pro initiation: which IF prevents premature binding of the large subunit

A

IF3

75
Q

pro initiation: when IF2 brings tRNAfMet to the P site, is it GTP bound or GDP bound

A

GTP bound

76
Q

pro initiation: once tRNAfMet is at the P site, what happens

A

large subunit associates and GTP is cleaved (GTP was bound to IF2), then all IFs dissociate

77
Q

pro initiation: what is the final product called

A

intiation complex

78
Q

pro initiation: describe the initiation complex

A

AUG over the P site, tRNAfMet over the P site, both subunits intact, no IFs

79
Q

eu initiation: which IF is equivalent to IF1

A

eIF1A

80
Q

eu initiation: which IF is equivalent to IF2

A

eIF2 and eIF5B

81
Q

eu initiation: which IF is equivalent to IF3

A

eIF3

82
Q

eu initiation: role of eIF2

A

initial escort of tRNAfMet to the P site

83
Q

eu initiation: role of eIF5B

A

GTP hydrolysis

84
Q

eu initiation: describe the orientation of the 5’ and 3’ ends of the transcript (ie how is this different from pro initiation)

A

the two ends are linked

85
Q

eu initiation: what links the 5’ and 3’ end

A

eIF4F complex

86
Q

eu initiation: other than the eIF4F complex, which molecule is required for transcript circularization

A

polyA binding protein must bind to the polyA tail

87
Q

eu initiation: when does mRNA bind to the small subunit (ie what mediates this process)

A

mRNA is able to bind to the small subunit due to eIF4F complex

88
Q

eu initiation: how is the first AUG found

A

ribosome scans along the transcript for it

89
Q

eu initiation: what happens once the first AUG is found

A

large subunit associates

90
Q

eu initiation: what happens once the large subunit associates

A

eIF5B enters, hydrolyses its GTP, and most factors leave

91
Q

elongation: which three EFs are needed

A

EF-Tu, EF-Ts, EF-G

92
Q

what are the three substeps of elongation

A

binding of incoming aminoacyl-tRNA in the A site, peptide bond formation, translocation

93
Q

elongation: describe the steps of binding of incoming aminoacyl-tRNA in the A site

A

aminoacyl-tRNA binds to GTP-bound EF-Tu, and all of these enter the A site. GTP is cleaved, Tu leaves (eventually regenerated by EF-Ts)

94
Q

elongation: describe peptide bond formation

A

a peptide bond is formed between the first and second amino acids (in A and P sites). fMet in the P site is treansferred to the amino group of the aa in the A site. This = tRNA in the A site with dipeptide and an uncharged tRNA in the P site

95
Q

elongation: what catalyzes peptide bond formation

A

23S rRNA within the ribosome

96
Q

why is the ribosome considered a ribozyme

A

the 23S rRNA catalyzes peptide bond formation in translation elongation

97
Q

elongation: chemically, describe peptide bond formation

A

amine group in the A site amino acid acts as a nucleophile. It attacks the carbonyl of fMet to form the peptide bond

98
Q

elongation: what can occur after peptide bond formation

A

ribosome can move one codon towards the 3’ end of the mRNA (translocation)

99
Q

elongation: describe how translocation occurs

A

GTP-bound EF-G mimics the structure of EF-Tu complexed with tRNA. It enters the A site and causes a conformational change in the whole ribosome = translocates it downstream

100
Q

termination: list the stop codons

A

UAG, UAA, UGA

101
Q

termination: what happens when a stop codon reaches the A site

A

release factors help cleave the peptide-tRNA bond, release the peptide, and dissociate from the ribosome

102
Q

termination: what are the two types of release factors

A

RF1 and RF2

103
Q

termination: which stop codons does RF1 recognize

A

UAG, UAA

104
Q

termination: which stop codons does RF2 recognize

A

UGA, UAA

105
Q

termination: where do RFs transfer the peptide to

A

a water molecule

106
Q

termination: what happens after the peptide is transferred to water

A

RF binds to the A site and mimics a tRNA. the ester linkage between polypeptide and tRNA in the P site is hydrolyzed

107
Q

termination: what happens once the ester linkage of the polypeptide and tRNA in the P site is hydrolyzed

A

RF leaves and is replaced by GTP-bound EF-G and ribosome release factor (RRF). GTP hydrolysis releases the large subunit

108
Q

termination: what happens once the large subunit is released

A

IF-3 replaces EF-G-GDP, which helps release the tRNA and mRNA and prepares the 30S subunit for the next cycle

109
Q

describe 2 points in time where protein folding may occur

A
  1. some fold as soon as the peptide begins exiting the ribosome
  2. some require chaperones to fold properly
110
Q

list 4 additional post-translational modifications a protein might need

A

removal of fMet, loss of signal sequences, attachment of carbohydrate side chains, attachment of isoprenyl groups

111
Q

list 3 antibiotics that disrupt translation in bacteria

A

tetracycline, streptomycin, puromycin

112
Q

what does tetracycline do

A

blocks A site

113
Q

what does streptomycin do

A

inhibits initiation

114
Q

what does puromycin do

A

forms peptide bond and terminates growing polypeptide

115
Q

list 2 toxins that inhibit translation in mammals

A

diptheria and ricin

116
Q

what does diptheria do

A

inactivates EFs

117
Q

what does ricin do

A

inactivates 60S subunit

118
Q

add: energy cost section

A

BIOL 3421 - molecular biochem (20 decks)

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