Protein synthesis Flashcards
4 characteristics of protein synthesis
- can use 90% of the cell’s energy
- number of proteins copied= number of proteins needed
- proteins are targeted to cellular locations (ex: transcription factors will go in the nucleous because this is the place where they do their role)
- degradation, a method of regulation (so every protein will be degrade depending on its role…)
5 biomolecules required for the protein synthesis process
- more than 70 r-proteins
- environ 20 AA activation enzymes
- environ 20 factors for initiation, elongation and termination ** similar to transcription
- environ 100 additional enzyme for the final processing (after the chain of AA is made, requires other modifications for the function of the protein)
- environ 40 kinds of tRNAs and rRNAs
difference between overlapping and non-overlapping code + the advantages
non-overlapping: Codons (numbered consecutively) do not share nucleotides.
It provides much more flexibility in the triplet sequences of the neighboring codons (because in overlapping sequence, if the codon before has an A, it means that the next codon will have this A in its sequence too whereas in the non-overlapping, codons are completely independent). Therefore, there is more flexibility in the possible amino acid sequences designated by the code
what are the 3 termination codon and the initiation one
termination : UAA, UGA, UAG
initiation: AUG (as well as Met codon)
4 features of the genetic code
- the code is written in the 5-3 prime direction
- the first codon establishe the reading frame
- 61/62 codons code for AA
- third base is less important in binding to tRNA
which AA only have one codon
Met
Trp
What are the slightly different codes by mitochondria
- mitochondria has its on genome so it can code for 13 proteins when the other ones are coded by the nuclear genome
- UGA encodes Trp (instead of STOP)
- AGA/AGG encode for STOP (instead of Arg)
- mitochondria has its on genome so it can code for 13 proteins when the other ones are coded by the nuclear genome
5 steps of protein synthesis in prokaryotes
- activation of amino acids: the tRNA is aminoacetylated
- initiation: mRNA and the aminoacetylated tRNA bind to the small ribosomal subunit. The large subunit then binds as well.
- elongation: successive cycles of aminoacyl-tRNA binding and peptide bond formation occur until ribosome reaches a stop codon
- termination: translation stops when a stop codon is encountered. The mRNA and protein dissociates and the ribosomal subunits are recycled
- protein folding
what is the general cloverleaf secondary structure of tRNAs
- amino acid arm which contains the CCA sequence
- anticodon arm contains the anticodon
- D arm
- T C arm
what are the steps for the aminoacetylation of tRNA (what is the difference for class 1 and class 2)
- carboxyl of amino acid attacks alpha phosphorus of ATP, forming 5prime-aminoacyl adenylate
- the aminoacyl group is transferred to the tRNA (2 methods depending on the class of aminoacyl-tRNA synthetases)
for class 2: it is directly transferred to the 3prime carbon (OH) of the terminal A residue of tRNA (the A in the sequence CCA in the amino acid arm), generating the aminoacyl-tRNA product)
for class 1: aminoacyl group is transferred to the 2prime carbon (OH) of the A of the CCA sequence (terminal A residue of tRNA, releasing AMP) and then, transtesterification moves aminoacyl group to 3prime carbon of the same tRNA residue
what is specific to methionine and what are the two tRNAs used fot it
methionine has only one codon which is AUG and every organism has two tRNAs that for methionine depending on where it is in the sequence
- one is used exclusively when 5prime AUG is the initiation codon for protein synthesis. the tRNA will be tRNA^fMet and the AA that will be incorporated in response to 5prime AUG initiation codon is N-formylmethionine (fMet).
- one is used when the Met residue is in an internal position in a polypeptide. The tRNA that is used is the tRNA^Met
what are the three sites on ribosomes
A: aminoacyl site
P: peptidyl site
E: exit site
4 things for the elongation to occurs (formation of peptide bonds)
- Aminoacyl-tRNAs
- The initiation complex
- set of 3 soluble cytolosic proteins called elongation factord (EF-Tu, EF-Ts, EF-G)
- GTP
what are the three steps for the formation of the peptide bonds
- Binding of an Incoming Aminoacyl-tRNA (bind to the EF-Tu-GTP) and all of this complex will bind to the A site. Then GTP is hydrolyzed and EF-T-u-GDP is released.
- Peptide bond formation: transfer of the fMet from its tRNA to the amino group of the second amino acid in the A site. It will produce a dipeptyl-tRNA in the A site and the now uncharged tRNA^fMet remains in the P site
- Translocation: the ribosome moves one codon toward the 3prime end of the mRNA. This movement shifts than anticodon of the dipeptyl-tRNA (which is still attached to the second codon of the mRNA) from the A site to the P site, and shifts the deacylated tRNA from the P site to the E site. So the third codon of the mRNA is now lies in the A site and the second codon in the P site ** movement of ribosome along the mRNA require EF-G + GTP
what is the elongation factor for the peptide bond formation
elongation factor P (EF-P)
