6.) Mechanisms of Protein Translation Flashcards
Define codon.
A sequence of three nucleotides that compose one unit of a genetic code.
Define genetic code.
This is the collection of triplet nucleotide molecules on DNA and RNA that synthesize a nucleotide.
Define reading frame.
This refers to the potential ways that a nucleotide sequence can be read. There are three ways a nucleotide sequence can be read, but in reality, only one is the correct “reading frame.” (check out slide 4)
Define wobble base.
The wobble base is the base in position 3 on the codon (read 5’ to 3’). This base can pair with multiple bases on the anti codon. Note that the wobble position on the tRNA is position 1, and sometimes this may also be referred to as the wobble position.
Define anticodon.
This is the sequence of three nucleotides that are present on a tRNA molecule that will bind complementary to the mRNA.
Define polyribosome.
This is a “structure” with one mRNA molecule with multiple ribosomes attached to it translating the mRNA into a protein.
What is the difference between a cytosolic ribosome and a ER bound ribosome?
- Cytosolic ribosomes* will typically code for proteins that will either remain in the cytoplasm or transfer to other organelles like the nucleus.
- ER bound ribosomes* will code for proteins that are typically intended to be part of the cellular membrane or to be excreted into the extracellular environment.
How are tRNA molecules important for protein synthesis?
The two structures on the tRNA that illustrate this is the anti-codon and the amino-acyl linkage.
The tRNA is responsible for matching the correct amino acid to the genetic code. It will dissociate from the ribosome-mRNA complex once its amino acid has been added to the peptide chain.
Describe the structural and functional components of the ribosome.
1.) 1 mRNA binding site (small subunit)
2.) 3 tRNA binding sites (large subunit):
A site: aminoacyl-tRNA site
P site: Peptidyl-tRNA site
E site: Exit site
Describe the initiation of protein synthesis in eukaryotes.
Small ribosomal subunit binds with the initiator tRNA that contains methionine (this WILL be incorporated into the peptide) at the P site. This is mediated by eukaroytic initiation factor 2 (eIF2). This complex is intended to recognize the 5’ cap of a mRNA molecules. This attracts more initiation factors to build the initiation complex. With the help of an ATP powered helicase, the initiation complex will run up the mRNA until it runs into the start codon (AUG) which binds to the anticodon of the methionine tRNA. The complex will pause and eIF2 will hydrolyze GTP. Then it will recruit the large ribosomal subunit. Elongation then proceeds.
What protein searches for the first start codon for the initiation complex?
ATP powered helicase
True or False: The initiator complex will always begin protein synthesis after matching with the first AUG sequence it encounters.
False: As Sherman says, it needs to be in the correct context. Researchers have found certain sequences that provide this context (eg shine-dalgarno sequence).
What would happen if there was a mutation in eIF2?
GTP could not be hydrolyzed, protein synthesis would halt.
Describe the general process of elongation.
tRNA leaves from the E site, the P site catalyzes the formation of a peptide bond between the A-site tRNA and the P-site tRNA via peptidyl transferase activity. At this point, there are two tRNA’s present in the large subunit/on the mRNA: one in the P site, one in the A site. The large subunit “ratchets” and shifts the tRNA’s to the E site and P site, while the small subunit remains. The large subunit shortly shifts back to line up with the small subunit, a new tRNA enters the A site, and the E site tRNA leaves and the process starts over again.
What is the name of the enzymatic activity of the ribosome?
Peptidyl transferase
True or false: The ribosome provides protein-mediated catalysis of the elongation of a peptide.
False: Its catalytic activity is RNA mediated.
Describe the general process of termination.
Ribosome will reach the stop codon on the mRNA, and will recruit the release factor to the A site. This signals hydrolysis of the C terminal end from the tRNA in the A site. The large subunit “ratchets” over where the release factor is now in the A site and the tRNA is in the E site. This triggers dissociation of the ribosome from the mRNA.
In what direction is the protein snythesized during translation?
N terminus to C terminus
The rate of translation of a protein can be regulated by…
altering the frequency of initiation.
What protein(s) during elongation help(s) to mediate the fidelity of protein translation? How do they function?
Elongation factors.
EF1 and EF2 for eukaryotes. EF-Tu for prokaryotes. These factors have GTP attached.
They are attached to the tRNA’s and will chaperone the tRNA to the ribosome. If the tRNA does not contain the correct anti-codon, the tRNA will dissociate from the ribosome. If it is the correct tRNA, then EF1 will trigger hydrolysis of the GTP to keep the tRNA bound to the complex. Once the amino acid is bound to the peptide, EF2 will associate with the complex and will provide the energy for the “ratcheting” of the large subunit. Hydrolysis of the GTP will realign the large subunit with the small subunit.
How are amino acids activated for protein synthesis? Describe process.
They are attached to a tRNA molecule via the aminoacyl-tRNA synthetase.
Two active sites on aminoacyl-tRNA synthetase, one for the amino acid, one for the tRNA. With the help of ATP, the amino acid is adenylated, then a high energy bond between the carboxy terminus of the amino acid and the 3’ hydroxyl of the tRNA forms.
How is the fidelity of protein synthesis maintained at the level of the tRNA?
each tRNA has an anticodon that is specific to that amino acid. The aminoacyl-tRNA synthetase enzymes will only attach the proper amino acid to the proper tRNA.
