Protein Synthesis Flashcards
How often are proteins synthesized?
- Only when they are required
- Highly energy demanding (90% of cell’s energy)
- Requirement = production
What is a common method of regulation of protein synthesis?
Degradation
In Eukaryotes, protein synthesis requires how many biomolecules?
> 300
In Eukaryotes, protein synthesis requires 70 ____________
ribosomal proteins (r-proteins)
In Eukaryotes, protein synthesis requires 20 ____________, and 20 ____________
amino acid activation enzymes
factors (enzymes) for initiation, elongation, and termination of translation
In Eukaryotes, protein synthesis requires 100 ____________
additional enzymes for final processing of protein synthesis
In Eukaryotes, protein synthesis requires 40 ____________
kinds of tRNAs and rRNAs
What are tRNAs also called? What is their function?
- Adapters
- Brings amino acids to mRNA
What is the structure of tRNAs?
- One end is charged with an amino acid
- An anticodon (triplet) complements the codons present in mRNA
How many codon combinations are there?
- 3-letter code from 4 nucleotides
- 64 combinations
Do cells use overlapping or non-overlapping code? What does this mean?
- Non-overlapping code
- There is a sequence of nucleotides in an mRNA, and they are read in successive triplets
Of the three nucleotides in the codon, which base is less important in binding to tRNA?
The third base
Which codon establishes the reading frame? What happens to the nucleotides before?
- First codon
- The nucleotides before the start codon are ignored by tRNA
What happens if the reading frame is thrown off by a base or two?
All subsequent codons are out of order
____ out of 64 codons code for specific amino acids. What do the others code for?
- 61
- Non-sense codons (stop codons)
What are the three stop codons?
- UAA
- UGA
- UAG
What makes a termination codon terminate?
Since there are no tRNAs that can recognize these codons to bring in amino acids
What is selenocysteine coded by? What is it?
- 21st amino acid
- Coded by UGA (typically a stop codon)
What is the initiation code? What is it also called? Why?
- AUG
- Met codon since it synthesizes methionine
Can multiple codons code for a single amino acid? Which amino acids only have one codon each?
- Yes
- Methionine and tryptophan
Who founded the RNA tie club?
Watson
What is the adaptor hypothesis?
Because nucleotides and amino acids are different, there must be an adaptor enzyme (tRNA)
What did George Gamow discover?
Triplet codon
What did Har Gobind Khorana discover?
- Methods to synthesize short nucleotides
- Proved that three nucleotides form a triplet codon, and that it is a non-overlapping code
Where is the codon? Where is the anticodon?
- Codon: mRNA
- Anticodon: tRNA
How does the mitochondrial genetic code differ?
o UGA encodes for Tryptophan instead of a STOP
o AGA/AGG encode for STOP instead of Arginine
How is the amino acid activated?
tRNA is aminoacylated
What is initiation of protein synthesis?
- mRNA and the aminoacylated tRNA bind to the small ribosomal subunit
- The large subunit then binds as well
What is elongation of protein synthesis?
- Successive cycles of aminoacyl-tRNA binding and peptide formation occur until the ribosome reaches a stop codon
What is termination of protein synthesis?
- Translation stops when a stop codon is encountered
- The mRNA and the protein dissociate and the ribosomal subunit are recycled
What is the general structure of a tRNA?
Cloverleaf
What does the anticodon arm contain?
Anticodon
What is the Wobble position? Is it important or no?
- First nucleotide from the 5’ end of the anticodon
- Least important
- Corresponds to the third position of the codon
Where is the CCA sequence located? Is it 3’ to 5’ or 5’ to 3’
- Amino acid arm of tRNA
- 5’ to 3’
When is the CCA sequence added?
Once the tRNA is completely expressed - after transcription of tRNA
What is the first step to the aminoacylation of tRNA?
- a-carboxyl of the amino acid attacks a-phosphate of ATP, forming an aminoacyl adenylate
- Remains bound to the active site
What happens after an aminoacyl adenylate is formed?
- Amino acyl group is transferred to tRNA
- Mechanism is different between the two classes
What happens to Class I aminoacyl-tRNA synthetases?
o The amino acyl group is transferred initially to the 2’-hydroxyl group of the 3’-terminal A residue
o Then, to the 3’-hydroxyl group by a transesterification reaction
What happens to Class II aminoacyl-tRNA synthetases?
The aminoacyl group is transferred directly to the 3’-hydroxyl group of the terminal adenylate
Where is the activated amino acid charged? Which position is that?
- “A” of the CCA sequence
- 3’ position
What are the two types of tRNAs for met?
fMet and Met
In the mitochondria, what is the first amino acid in a peptide coded by?
Initiation tRNA inserts N-formylmethionine (fMet) with AUG as first codon
In Eukaryotes, do proteins being with Met or fMet?
Met
What are the three spaces in the 40S subunit?
o A: amino acyl site
o P: peptide site
o E: exit site (site from which the tRNA exit)
What is the 43S preinitiation complex formed of?
- 40S
- tRNA (methionine)
- EIF1 to EIF5
What does EIF4F do?
Brings tRNA to the preinitiation complex
When does scanning stop, and initiation being?
When AUG comes to the P site
At which site does elongation occur?
At the A site
What is the function of EF-Tu-GTP?
Brings in aminoacyl-tRNA to the A site
What is the function of Elongation Factor P (EF-P)?
Forms the bond between the carboxyl end of the first AA, and the amino end of the incoming AA
Where does an empty tRNA move to?
To the E site
What is translocation?
Lengthened amino acid shifts from the A site to the P site
What does EF-G-GTP do?
- Pushes dipeptidyl tRNA to the P site
- A site is empty to receive another AA-containing tRNA for the subsequent codon
What happens when a termination codon arrives at the A site?
- A release factor binds
- Peptidyl-tRNA is hydrolyzed and the synthesized AA chain is dissociated
Provide examples of post-translational modifications of proteins.
o Enzymatic removal of the formyl group from the first residue, or removal of methionine and sometimes additional residues
o Acetylation of N-terminal residue
o Removal of signal sequences or other regions
o Forming disulfide links, creating a 3D structure
o Attaching carbohydrates (glycosylation): occurs on most proteins
Are all proteins degraded?
Yes, it is inevitable
How is the half-life of hemoglobin?
Long-lived since they do not have a nucleus
How is the half-life of proteins for rapidly changing needs?
Short-lived
What is the function of ubiquintin?
Ubiquintin is covalently linked to proteins slated for destruction via an ATP-dependent pathway involving three enzymes: E1, E2, E3
What are the three enzymes for ubiquintin protein destruction?
- E1: activating enzyme
- E2: conjugating enzyme
- E3: ligating enzyme
How is ubiquintin activated?
- E1 has a SH (thiol) group that interacts with the carboxyl group of ubiquintin
- Requires energy (ATP)
What happens after ubiquintin is activated?
- Transferred to E2
- Transferred to the target protein at the LYSINE residue (catalyzed by E3)
Ubiquintin is transferred to the target protein at which residue?
Lysine
