Genetic Code and Translation Flashcards
tRNA function
- serves as adaptor that carries amino acid to correct code on mRNA
how are proteins synthesized
- proteins are synthesized on ribosomes using mRNA as a template
how many letters in RNA language
- 4 letters
how many letters in protein language
- 20 letters
tRNA components (2)
- anticodon loop
- amino acid attachment site
anticodon loop (2)
- recognizes codon on mRNA
- 4^3 = 64 different codons
amino acid attachment site (2)
- at the 3’ end of tRNA
- amino acid is attached to 3’ OH of adenosine via carboxylic acid group
characteristics of the genetic code (10)
- 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
non-overlapping
- no overlap between triplets
continuous
- no breaks or pauses
unambiguous code
- 1 codon = 1 amino acid
degenerate code
- 64 codons for 20 amino acids; many AA are coded by several codons
wobble rules (3)
- 1st and 2nd base in codon form strong Watson-Crick pairing with 3rd and 2nd base in anticodon
- 3rd base in codon forms Wobble pair with 1st base in anticodon
- 3rd base is G-C; U-A normally, but in Wobble A/G-U; C/U-G;A/U/C-I
what does AUG encode
- methionine
how is translation started in prokaryotes (2)
- RNA has Shine-Dalgano Sequence (SD) upstream of AUG start codon
- forms H-bonds with 16S rRNA to help position mRNA on a ribosome
how is translation started in eukaryotes (2)
- mRNA has 5’ cap
- ribosome recognizes 5’ cap and scans mRNA until it encounters the start codon
tRNA structure
- has complexed L-shaped 3D structure with anticodon loop and AA-attachment site on opposite ends
what are the modified bases present in tRNA (3)
- pseudouridine
- dihydrouridine
- 5-methylcytidine
aminoacyl-tRNA synthetases (ARS)
- activities (2)
- functions to connect AA to correct tRNA
- have proof-reading activity: if incorrect amino acid is attached, bond will be hydrolyzed
what is the co-factor required for aminoacyl-tRNA synthetases
- Mg2+
how much ATP is needed for aminoacyl-tRNA synthetases
- 2 ATP equivalents x (# of AA) = # of ATP equivalents
class I aminoacyl-tRNA synthetase
- transfer AA to 2’-OH and then transfer AA to 3’-OH
class II aminoacyl-tRNA synthetase
- transfer AA to 3’-OH
do ribosomes have proof-reading activity?
- no, ribosomes cannot check if correct AA is attached to tRNA
ribosome (4)
- # of subunits
- size
- composition and functions
- what occurs when ribosomes assemble
- 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
large subunit size
- 50S
small subunit size
- 30S
which sites are formed when ribosomes are formed (3)
- A-site
- P-site
- E-site
A-site
- where aminoacyl-tRNA binds
P-site
- where peptidyl-tRNA binds
E-site
- where empty tRNA binds
what step of protein synthesis is the rate limiting step
initiation of protein synthesis
initiation factors (2)
- set of proteins required for initiation
- IF1, IF2, IF3
function of IF3 and IF1
- bind to 30S subunit to prevent binding of 50S subunit
tRNA^fMet (2)
- special tRNA for first AUG codon
- fMet is the specificity of the tRNA
IR2 function
- complex with GTP: delivers fMET-tRNA^fMet to mRNA-30S to P-site
- hydrolyzes GTP -> GDP
how is proper alignment achieved by IF2
- Shine-Dalgano sequence interaction with 16S rRNA
what does hydrolyzation of GTP -> GDP signal
- signals IL1 and IL3 to leave 30S so that 50S can bind
elongation factors (2)
- set of proteins required for elongation
- EF-Tu, EF-Ts, EF-G
release factor function (2)
- function
- result
- PTC end will coordinate water molecule to hydrolyze ester linkage between tRNA and peptidyl
- peptide chain will be released
product of protein synthesis initiation
- product
- composition of product
- 70S initiation complex formed
- composed of 30S + 50S + mRNA + fMet-tRNA^fMet
how many ATP equivalents are used in initiation?
- only one initiation event: 1 AA x 1 GTP = 1 ATP equivalent
where does IF2 deliver the fMet-tRNA^fMet to?
- P-site
EF-Tu function
- 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
what happens after EF-Tu completes its function
- Ef-Tu + GDP leaves ribosome
Tu-Ts cycle (2)
- 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
peptidyl transferase center (PTC)
- resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release
how do peptide bonds form between amino acids
- 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
product of peptide bond formation
tRNA with peptidyl chain in the A-site
translocation
- EF-G bound to GTP binds to A-site and pushes peptidyl-tRNA to the P-site of 30S
- EF-G hydrolyzes GTP -> GDP
product of elongation (3)
- 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
where are ATP equivalents used in elongation (2)
- 1 GTP from EF-Tu
- 1 GTP from EF-G
how many ATP equivalents are used for elongation?
- 2 ATP equivalents x (# of AA - 1) = # of ATP equivalents
which tRNA makes stop codons
- no tRNA makes stop codons; stop codons are recognized by release factors instead
release factors (RF) (2)
- general role
- structure
- special proteins that recognize stop codons
- one end interacts with the stop codon, while the other end interacts with the peptidyl transferase centre
how are RFs removed from ribosome (2)
- process
- result
- EF-G + GTP + ribosome recycling factor hydrolyze GTP -> GDP
- complex falls apart and IF3 binds to 30S
how many ATP equivalents are used in termination?
- only one termination event: 1AA x 1 GTP = 1 ATP equivalent
eukaryotic ribosome (2)
- # of units
- size
- 2 subunits: small subunit + large subunit
- size: 80S
eukaryotic small subunit (2)
- size
- function in initiation
- size: 40S
- 40S binds to cap and scans mRNA to find AUG start codon
eukaryotic large subunit
- size
- size: 60S
how is initiation in eukaryotes different from prokaryotes (2)
- eukaryotic initiation factor: eIF
- eIF4 complex recognizes both cap and polyA tail to initiate translation
how is elongation in eukaryotes different from prokaryotes
- eukaryotic elongation factors: eEF
how is termination in eukaryotes different from prokaryotes
- eukaryotic termination factors: eRF
compare the first AA in eukaryotic vs prokaryotic protein synthesis (2)
- eukaryotes: AA is Met vs prokaryotes: AA is fMet
- both bacteria and eukaryotes usually remove fMet/Met after translation
