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BIOC 302 Part 2 > Genetic Code and Translation > Flashcards

Genetic Code and Translation Flashcards

1
Q

tRNA function

A
  • serves as adaptor that carries amino acid to correct code on mRNA
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2
Q

how are proteins synthesized

A
  • proteins are synthesized on ribosomes using mRNA as a template
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3
Q

how many letters in RNA language

A
  • 4 letters
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4
Q

how many letters in protein language

A
  • 20 letters
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5
Q

tRNA components (2)

A
  • anticodon loop

- amino acid attachment site

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6
Q

anticodon loop (2)

A
  • recognizes codon on mRNA

- 4^3 = 64 different codons

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7
Q

amino acid attachment site (2)

A
  • at the 3’ end of tRNA

- amino acid is attached to 3’ OH of adenosine via carboxylic acid group

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8
Q

characteristics of the genetic code (10)

A
  • non-overlapping
  • continuous
  • start and stop signals
  • unambiguous code
  • degenerate code
  • 61 codons for amino acids + 3 stop codons
  • universal code
  • stops codons don’t have corresponding tRNAs, release factors instead
  • ~40 tRNAs
  • AUG is always start codon
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9
Q

non-overlapping

A
  • no overlap between triplets
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10
Q

continuous

A
  • no breaks or pauses
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11
Q

unambiguous code

A
  • 1 codon = 1 amino acid
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12
Q

degenerate code

A
  • 64 codons for 20 amino acids; many AA are coded by several codons
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13
Q

wobble rules (3)

A
  1. 1st and 2nd base in codon form strong Watson-Crick pairing with 3rd and 2nd base in anticodon
  2. 3rd base in codon forms Wobble pair with 1st base in anticodon
  3. 3rd base is G-C; U-A normally, but in Wobble A/G-U; C/U-G;A/U/C-I
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14
Q

what does AUG encode

A
  • methionine
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15
Q

how is translation started in prokaryotes (2)

A
  • RNA has Shine-Dalgano Sequence (SD) upstream of AUG start codon
  • forms H-bonds with 16S rRNA to help position mRNA on a ribosome
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16
Q

how is translation started in eukaryotes (2)

A
  • mRNA has 5’ cap

- ribosome recognizes 5’ cap and scans mRNA until it encounters the start codon

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17
Q

tRNA structure

A
  • has complexed L-shaped 3D structure with anticodon loop and AA-attachment site on opposite ends
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18
Q

what are the modified bases present in tRNA (3)

A
  • pseudouridine
  • dihydrouridine
  • 5-methylcytidine
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19
Q

aminoacyl-tRNA synthetases (ARS)

- activities (2)

A
  • functions to connect AA to correct tRNA

- have proof-reading activity: if incorrect amino acid is attached, bond will be hydrolyzed

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20
Q

what is the co-factor required for aminoacyl-tRNA synthetases

A
  • Mg2+
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21
Q

how much ATP is needed for aminoacyl-tRNA synthetases

A
  • 2 ATP equivalents x (# of AA) = # of ATP equivalents
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22
Q

class I aminoacyl-tRNA synthetase

A
  • transfer AA to 2’-OH and then transfer AA to 3’-OH
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23
Q

class II aminoacyl-tRNA synthetase

A
  • transfer AA to 3’-OH
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24
Q

do ribosomes have proof-reading activity?

A
  • no, ribosomes cannot check if correct AA is attached to tRNA
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25
Q

ribosome (4)

  • # of subunits
  • size
  • composition and functions
  • what occurs when ribosomes assemble
A
  • 2 subunits: large and small
  • size: 70S
  • 2/3 of ribosome is rRNA; rRNA has structural and catalytic functions of rRNA
  • when ribosome is assembled, 3 sites are formed
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26
Q

large subunit size

A
  • 50S
27
Q

small subunit size

A
  • 30S
28
Q

which sites are formed when ribosomes are formed (3)

A
  • A-site
  • P-site
  • E-site
29
Q

A-site

A
  • where aminoacyl-tRNA binds
30
Q

P-site

A
  • where peptidyl-tRNA binds
31
Q

E-site

A
  • where empty tRNA binds
32
Q

what step of protein synthesis is the rate limiting step

A

initiation of protein synthesis

33
Q

initiation factors (2)

A
  • set of proteins required for initiation

- IF1, IF2, IF3

34
Q

function of IF3 and IF1

A
  • bind to 30S subunit to prevent binding of 50S subunit
35
Q

tRNA^fMet (2)

A
  • special tRNA for first AUG codon

- fMet is the specificity of the tRNA

36
Q

IR2 function

A
  • complex with GTP: delivers fMET-tRNA^fMet to mRNA-30S to P-site
  • hydrolyzes GTP -> GDP
37
Q

how is proper alignment achieved by IF2

A
  • Shine-Dalgano sequence interaction with 16S rRNA
38
Q

what does hydrolyzation of GTP -> GDP signal

A
  • signals IL1 and IL3 to leave 30S so that 50S can bind
40
Q

elongation factors (2)

A
  • set of proteins required for elongation

- EF-Tu, EF-Ts, EF-G

40
Q

release factor function (2)

  • function
  • result
A
  • PTC end will coordinate water molecule to hydrolyze ester linkage between tRNA and peptidyl
  • peptide chain will be released
41
Q

product of protein synthesis initiation

  • product
  • composition of product
A
  • 70S initiation complex formed

- composed of 30S + 50S + mRNA + fMet-tRNA^fMet

41
Q

how many ATP equivalents are used in initiation?

A
  • only one initiation event: 1 AA x 1 GTP = 1 ATP equivalent
43
Q

where does IF2 deliver the fMet-tRNA^fMet to?

A
  • P-site
44
Q

EF-Tu function

A
  • complexed with GTP: delivers animoacyl-tRNA corresponding to next codon to A site
  • if anticodon and codon match, tRNA stays in A site and GTP is hydrolyzed to GDP
45
Q

what happens after EF-Tu completes its function

A
  • Ef-Tu + GDP leaves ribosome
46
Q

Tu-Ts cycle (2)

A
  • Ef-Ts can exchange GDP for GTP making Ef-Tu active again

- GDP is NOT converted to GTP; GDP is removed and a fresh GTP is added

47
Q

peptidyl transferase center (PTC)

A
  • resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release
48
Q

how do peptide bonds form between amino acids

A
  • N amino acid of tRNA in A-site attacks carbonyl group attached to RNA in P-site to form a tetrahedryl intermediate
  • occurs in peptidyl transferase centre
49
Q

product of peptide bond formation

A

tRNA with peptidyl chain in the A-site

50
Q

translocation

A
  • EF-G bound to GTP binds to A-site and pushes peptidyl-tRNA to the P-site of 30S
  • EF-G hydrolyzes GTP -> GDP
51
Q

product of elongation (3)

A
  • empty tRNA is pushed to E-site and leaves the ribosome
  • A-site is empty and ready to accept next EF-Tu
  • aminoacyl-tRNA and P-site has peptidyl-tRNA
52
Q

where are ATP equivalents used in elongation (2)

A
  • 1 GTP from EF-Tu

- 1 GTP from EF-G

53
Q

how many ATP equivalents are used for elongation?

A
  • 2 ATP equivalents x (# of AA - 1) = # of ATP equivalents
54
Q

which tRNA makes stop codons

A
  • no tRNA makes stop codons; stop codons are recognized by release factors instead
55
Q

release factors (RF) (2)

  • general role
  • structure
A
  • special proteins that recognize stop codons

- one end interacts with the stop codon, while the other end interacts with the peptidyl transferase centre

56
Q

how are RFs removed from ribosome (2)

  • process
  • result
A
  • EF-G + GTP + ribosome recycling factor hydrolyze GTP -> GDP
  • complex falls apart and IF3 binds to 30S
57
Q

how many ATP equivalents are used in termination?

A
  • only one termination event: 1AA x 1 GTP = 1 ATP equivalent
58
Q

eukaryotic ribosome (2)

  • # of units
  • size
A
  • 2 subunits: small subunit + large subunit

- size: 80S

59
Q

eukaryotic small subunit (2)

  • size
  • function in initiation
A
  • size: 40S

- 40S binds to cap and scans mRNA to find AUG start codon

60
Q

eukaryotic large subunit

- size

A
  • size: 60S
61
Q

how is initiation in eukaryotes different from prokaryotes (2)

A
  • eukaryotic initiation factor: eIF

- eIF4 complex recognizes both cap and polyA tail to initiate translation

62
Q

how is elongation in eukaryotes different from prokaryotes

A
  • eukaryotic elongation factors: eEF
63
Q

how is termination in eukaryotes different from prokaryotes

A
  • eukaryotic termination factors: eRF
64
Q

compare the first AA in eukaryotic vs prokaryotic protein synthesis (2)

A
  • eukaryotes: AA is Met vs prokaryotes: AA is fMet

- both bacteria and eukaryotes usually remove fMet/Met after translation

BIOC 302 Part 2 (7 decks)

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