Protein Synthesis Flashcards
What are the key features of the Genetic Code?
1) The genetic code is universal: All organisms use the same genetic code
2) The genetic code is degenerate: Multiple codons encode for the same amino acid. e.g. GGU, GGC, GGA and GGG all encode for glycine. Degeneracy is usually at the third nucleotide or the wobble base.
3) Some codons have multiple functions: AUG for example encodes for Methionine but it is also the START codon. UAA, UAG, and UGA all are STOP codons.
There are 64 total triplets of nucleotides but only 20 amino acids that are coded for so we clearly have more than one triplet coding for a specific amino acid.
Codons for the same amino acid tend to share the same first two nucleotides (but this is not always true). Also, not every amino acid has more than one codon that codes for it.
Identify features of an mRNA that can affect its translation.
An mRNA needs to contain a 5’-cap and a Polyadenylated tail in order to be read as a “good” mRNA. Also, the mRNA must have the correct reading frame. The sequence of nucleotides are read 5’ to 3’ in translation in consecutive sets of 3 nucleotides. Thus, there are hypothetically 3 reading frames that exist and thus the same mRNA could give 3 different polypeptides. In reality, only one of these reading frames contains the actual message and if the wrong reading frame is read, there tends to be a lot of sporadic STOP codons.
Translation START codons
AUG
Codes for Methionine
Translation STOP codons
UAA, UAG and UGA
They do NOT code for amino acids.
Degenerate
Multiple codons code for the same amino acid
4 Major Steps in Translation
1) Charging of the tRNA: Placing of the amino acid
2) Initiation
3) Elongation
4) Termination
Transfer RNA (tRNA)
It is synthesized by RNA Pol III. Also, it is synthesized as a precursor, it will be trimmed, spliced, and modified. There are over 50 different modifications for tRNA and one out of every 10 bases will be modified. This modification is thought to be important for the final folding of the tRNA and to get the anticodon region in the right position to get good base pairing with the codon.
tRNA contains some unusual bases that are created during the modification of it such as pseudouridine and dihydrouridine which are derive amino acids from uracil.
There are 2 areas of interest:
1) anticodon
2) 3’ acceptor stem
Anticodon
it is a region on the tRNA that is 3 nucleotides long and is responsible for base pairing with the codon to ensure correct amino acid addition to the newly synthesized polypeptide chain. The pairing proceeds from the 5’ end of the codon. Once the first two positions are paired, the exact base pairing of the third (wobble position) is less critical. Wobble positions allow some tRNAs to recognize more than one mRNA codon making it possible for less than 64 tRNAs to recognize all 64 codons. The wobble position in terms of the tRNA though is in the FIRST position, but we call it the third position in regards to the mRNA.
READ mRNA 5’ to 3’ NOW!!!
3’ Acceptor Stem
This is where the amino acid is physically attached to. Aminoacyl-tRNA synthetase catalyzes the two step activation reaction of the tRNA.
Aminoacyl-tRNA Synthetase
Catalyzes the two step activation reaction of the tRNA. It catalyzes the addition of the amino acid to the 3’ acceptor site. Eukaryotes have a DIFFERENT aminoacyl-synthetase for EACH amino acid whereas in prokaryotes, each synthetase couples more than one amino acid. The aminoacyl-synthetase is also crucial in regards to proofreading. It is the last check to make sure that the correct amino acid was added to the tRNA.
Explain the differences between prokaryotic and eukaryotic cells with respect to aminoacyl-synthetases.
Eukaryotes have DIFFERENT aminoacyl-synthetases for EACH amino acid.
Prokaryotes have ONE synthetase which couples for more than one amino acid.
Identify important structural features in tRNA molecules, including features that contribute to fidelity in protein synthesis.
Two major structural features are:
1) anticodon
2) 3’ acceptor site
the anticodon ensures correct base pairing with the codon sequence of the mRNA, specifically with the first two nucleotides. It is what reads the codon to see what amino acid is supposed to be added. If the sequences don’t match, they will not bind which gives it fidelity.
The 3’ Acceptor site adds to the fidelity because it binds specifically to the correct amino acid via the assistance of the Aminoacyl-tRNA Synthetase. The specific aminoacyl-tRNA Synthetase has an editing site that ensures the correct amino acid is bound.
Draw an aminoacylated tRNA molecule and diagram the reactions that produced it.
View reaction in handout. IT IS A 2 STEP ACTIVATION OF THE tRNA. Basically, carboxy-end’s OH reacts with ATP, adding AMP to the O, losing 2 inorganic phosphates and the H. Then, the now adenylated amino acid (AMP-Amino acid) reacts with the OH of the 3’ acceptor site, giving off AMP and resulting in the amino acid bound to the tRNA via a high energy ester-linkage, thus activating it. This energy is important because it plays a crucial role in providing the energy to create the polypeptide chain. Overall it is using the energy from ATP hydrolysis to add the amino acid to the tRNA.
Explain the role of editing by some aminoacyl-tRNA Synthetases in determining the fidelity of protein synthesis.
The synthetase is actually sensing that the correct amino acid is bound to the correct tRNA. It plays a crucial editing step to ensure high fidelity because it is one of the only steps to do this. The synthetase is able to do this so well because it is physically interacting with both the amino acid and the tRNA. It is interacting with the various parts of the tRNA and will make sure the 3 anticodons are correct and match this amino acid. However, some anticodons that code for the same amino acid are very different so it also relies on other parts of the tRNA as well.
What are the two “adaptors” that the genetic code is translated by means of?
1) The first adaptor is the aminoacyl-tRNA synthetase, which couples a particular amino acid to its corresponding tRNA
2) The second adaptor is the tRNA molecule itself, whose anticodon forms base pairs with the appropriate codon on the mRNA.
These two occur directly after one another and an error i neither step would cause the wrong amino acid to be incorporated into the protein chain.
“Second Genetic Code”
The recognition of the correct tRNA by the aminoacyl-tRNA Synthetase
Aminoacyl-tRNA Synthetase and tRNA interactions to ensure correct tRNA and amino acid binding
The aminoacyl-tRNA Synthetase recognizes multiple regions on the tRNA to ensure that it is indeed the correct amino acid that is binding. The 2 most important and most commonly used regions are the anticodon loop and the 3’ acceptor stem. These are particularly important in controlling the specificity of the aminoacylation reaction. However, some aminoacyl-tRNA synthetases use other regions on the tRNA to distinguish some tRNAs that are difficult to tell apart. There are many regions on the tRNA that the synthetase recognizes that are crucial for this high fidelity.