Protein synthesis Flashcards
why #proteins produced= # needed?
Process of protein synthesis is very energetically demanding
What is the adaptor hypothesis?
Kreek proposed that in order for mRNA to be translated in AA there need to be an adaptor molecule- each specific for one AA
What does non-overlapping code mean
Thecodeisnon-overlapping. This means that successive triplets are read in order.
_ base is the least important in binding to tRNA
3rd base is the least important in binding to tRNA
__ codon establishes the reading frame
First codon establishes the reading frame
__/__ codons code for amino acids
61/64 codons code for amino acids
What are the 3 terminal codons?
UAA
UGA
UAG
What’s the initiation codon?
AUG, also the Met codon
What are the 2 AA that have only 1 codon
Met an Trp
How’s the code different in mitochondria?
- UGA encodes for Trp instead of STOP
- AGA/AGG encode Stop instead of Arg
What’s the cycle of protein synthesis in prokaryotes
- tRNAs are aminoacetylated to activate amino acids
- Initiation: First codon recognizing tRNA brings in methionine and attaches to ribosomal subunit. Only after attachment of mRNA and tRNA to small ribosomal subunit, the large subunit bind
- Elongation. Next tRNAs with AA are brought in and peptide bond is formed until nonsense codon is reached
- Termination- translation stops when a stop codon is reached. The mRNA and proteins dissociate, are ribosomal units are recycled
- Protein folding. Post translational processing
What’s the general structure of tRNA?
All tRNAs have clover leaf structure
Anti-codon arm is complimentary to codon
Amino acid arm has CCA sequence- it is added at post-transcriptional modification
Where is CCA sequence on amino end of tRNA important?
Important in first step of translation which is aminoacylation of tRNA
At which end is CCA sequence?
At 3’ end
How does aminoacylation of tRNA occurs?
- Carboxyl of amino acid attacks a phosphorus of ATP, forming 5-aminoacyl adenylate. 2 P are thrown away
- Aminoacyl group is transferred to the tRNA. The mechanism of this step is somewhat different for the two classes of aminoacyl-tRNA synthetases. For class I enzymes, the aminoacyl
group is transferred initially to the 2’-hydroxyl group of the 3’-terminal A residue, then to the 3’-hydroxyl group by a transesterification reaction. For class II enzymes, the
aminoacyl group is transferred directly to the 3’-hydroxyl group of the terminal adenylate.
What are the 2 tRNAs for met and where are they found?
In prokaryotes and mitochondria
- tRNA that brings first AA- formylmethionine by tRNAfMet - All the others Met are brought in by tRNAMet
Describe initiation in eukaryotes
- eIF1A and eIF3 bind ot 40S subunit. The factor eIF1 binds to the E site. The charged initiator tRNA (with Met) is bound by the initiation factor eIF2, which also has bound GTP. elF5B binds forming pre-initiation complex
- mRNA is brought in by elF4F. mRNA attachment to preinitiation complex also requires energy
- This complex scans the bound mRNA, starting at the 5’ cap, until an AUG codon is
encountered. Scanning requires an existence of tRNA already at P site - Large 60S ribosomal subunit comes in, accompanied by the release of many of the initiation factors
How’s peptide bond formed?
This occurs by the transfer of the initiating N-formylmethionyl group from its tRNA to the amino group of the second amino acid, now in the A site. The -amino group of the amino acid in the A site acts as a nucleophile, displacing the tRNA in the P site to form the
peptide bond. This reaction produces a dipeptidyl-tRNA in the A site, and the now “uncharged” (deacylated) tRNAfMet remains bound to the P site. T
Peptidyl transferase catalyzes peptide bond formation
The tRNA at A site has more than 1 AAs. It has a growing peptide chain. tRNA at has to be pushed to P site. The one at P has to be pushed to E and thrown out of the system
Elongation factors help in peptide bond formation is called elongation factor P
What does elongation factor P do?
Help in peptide bond formation
How does elongation occur?
Elongation factor TU-GTP that comes in associated with energy providing GTP helps new tRNA to bring new AA to A site- GTP is converted to GDP
Once tRNA is brought to A site, the role of TU is done and it can leave
How does translocation occur?
EF- G-GTP pushes empty tRNA to E site, tRNA containing peptide chain is pushed to P site. Energy is provided by GTP
EF- G-GDP leaves when this is done
A site becomes empty for another tRNA
How does termination occur?
Termination happens when nonsense codon arrives to A site- no tRNA can come there
Release factor comes and binds to A site
It releases the synthesized peptide from tRNA that is present in the P site
What is the role of RRF?
Ribosome recycle factor uses elongation factors and energy to dissociate translational machinery
How can translation machinery be recycled?
After it is degraded IF-3 attached to small ribosomal subunit is left- another cycle of translation can be started again
What are some of the post-translational modification of proteins?
– Enzymatic removal of formyl group from first residue, or removal of Met and sometimes additional residues
– Acetylation of N-terminal residue
What are signal sequences?
Sequences in proteins that are removed
Which proteins are short lived?
v Proteins for rapidly changing needs are short-lived
v Defective proteins are short-lived
What is the purpose of ubiquitin attachment?
Attachment of ubiquitin is common step that triggers degradation
How’s ubiquitin attached?
Ub first attached to E1 to SH group. E1 brings in Ub Ub is then transferred to E2 E3 is needed to transfer Ub from U2 to amino group of lysine Only Lysine can be ubiquitinated Can be just one, can be several Ub
What happens after ubiquitin is attached?
This is how a cell recognizes a protein to be degraded
It is brought to peroxisomes
This decided how long a protein be functional
What are the names of E1, E2 and E3 enzymes?
E1 – activating enzyme
E2 – conjugating enzyme
E3 – ligating enzyme
How and where are amino acids attached to tRNA?
In the cytoplasm
They are covalently bonded at the expense of ATP
Elongation in translation requires ___ factors
Elongation in translation requires elongation factors
Which steps in protein synthesis require energy?
- Bonding of AA to tRNA- ATP
- Initiation- GTP
- Movement of ribosome along the mRNA - GTP
Protein synthesis begins at the __ end and proceeds by the stepwise addition of amino acids to the ___end of the growing polypeptide
Protein synthesis begins at the amino-terminal end and proceeds by the stepwise addition of amino acids to the carboxyl-terminal end of the growing polypeptide
All organisms have __ tRNAs for methionine
All organisms have 2 tRNAs for methionine
How does initiation differ in mitochondria and chloroplasts?
Polypeptides synthesized by mitochondrial and chloroplast
ribosomes begin with N-formylmethionine.
To which site does tRNA carrying the first Met binds?
To P site
Name the release factors
RF-1, RF-2, and RF-3
