Protein Synthesis Chap 39,40 Flashcards
(55 cards)
What is tRNA?
tRNA molecules are all different, but similar.
All are a single RNA strand that folds into defined tertiary structure.
tRNA contain 4 base-paired regions and three loops well define loops.
What does the 3’-terminus have?
A 5’-CCA-3’ sequence.
What codes for the amino acid in the protein?
Each triplet of bases on the mRNA strand codes for an amino acid.
Why is protein synthesis called translation?
because the four letter alphabet of nucleic acids is translated into the entirely different 20-letter alphabet of proteins.
What is the genetic code and what does it do?
It is the relation between the sequence of bases in DNA, or in its RNA transcripts, and the sequence of amino acids in proteins.
What are the characteristics of the genetic code?
1.Three nucleotides encode an amino acid- an amino acid is encoded by a group of three bases, a codon
2. The codon is nonoverlapping
3. The code has no punctuation.
4. The code has directionality- Code is read from the 5’ end on the mRNA to 3’ end.
5. The genetic code is degenerate, there is more than one codon that codes for an amino acid.
Why do we need the genetic code to be degenerate?
Because if not, there would be 20 codons that designated amino acids and 44 would lead to chain termination. This also increases the probability of mutating to chain termination, leading to inactive proteins.
Is the genetic code universal?
No, it is nearly but not absolutely universal. The genetic code of mitochondria can differ from that of the rest of the cell because mitochondrial DNA encodes a distinct set of transfer RNAs.
WHat is a transfer RNA and what does it do?
tRNA serves as the adapter molecule between the codon and its specified amino acid. It binds to a specific codon and brings it with an amino acid for incorporation into the polypeptide chain.
All tRNA molecules must be able to interact in nearly the same way with the ribosomes, mRNAs, and protein factors that participate in translation.
What features must a tRNA have?
- Must be a single strain containing between 73 and 93 ribonucleotides
- The 3D molecule is L shaped
- Contain many unusual bases. Some are methylated or dimethylated derivatives if A, U, G, and C.
- All tRNA molecules can be arranged in a cloverleaf pattern.
- The 5’ end of a tRNA is phosphorylated
- The activated amino acid is attached to a hydroxyl group of the adenosine residue at the end of the 3’ end of the acceptor stem.
- The anticodon is present in a loop near the center if the sequence.
What does the methylation of a base do?
Methylation prevents the formation of certain base pairs, rendering some of the bases accessible for interactions with other components of the translation machinery, Methylation also imparts a hydrophobic chatacter to some region sof tRNAs, which may be important for their interaction with proteins required for protein synthesis.
Why do tRNAs arrange in cloverleaf patterns
Half of the nucleotides in tRNA base pair to form double helixes. There are five groups of bases that do not do this, the 3’ CCA terminal region, which apart of the acceptor stem, the TyC loop: the extra arm which contains a variable number of residues, the DHU loop, which contains several UH2 residues, and the anticodon loop.
This structural diversity allows all tRNAs to be unique but structurally similar overall.
Why can some tRNA molecules recognize more than one codon?
Because the steric criteria might be less stringent for pairing of the third base than for the other two. Meaning there is some steric freedom, wobble, in the pairing of the third base of the codon.
What generalizations can be made concerning the codon-anticodon interaction?
- Codons that differ in either of their first two bases must be recognized by different tRNAs.
- Part of the degeneracy of the genetic code arises from imprecision in the pairing of the third base of the codon with the first base of the anticodon, Inosine, I, maximizes the number of codons that can be read by a particular tRNA.
What must first happen before the codon and anticodon meet?
The amino acids that are required for protein synthesis must be attached to specific tRNA molecules.
Why is the linkage of the amino acids to the tRNAs so crucial?
The attachment of a given amino acid to a particulat tRNA establishes the genetic code. The amino acid will then be incorporated into a growing polypeptide chain at a position dictated by the anticodon of the tRNA. The formation of a peptide bond between free amino acids is not thermodynamically favorable so the amino acid must be activated in order for protein synthesis to proceed.
The amino acid links to the 3’ hydroxyl group.
What activates the amino acids?
The activation is catalyzed by specific aminoacyl-tRNA synthetases.
What are the steps of the activation of amino acids?
- The formation of aminoacyl adenylate from an amino acid and ATP
- The transfer of the aminoacyl group of aminoacyl adenylate (aminoacyl-AMP) to a particular tRNA molecule to form amoniacyl-tRNA.
The reaction is driven by the hydrolysis of pyrophosphate and the sum of the reactions is highly exergonic.
The activation and transfer steps are catalyzed by the same aminoacyl-tRNA synthetase.
What is consumed in the synthesis of each aminoacyl-tRNA?
the equivalent of two ATP molecules
How do synthetases choose their tRNA partners?
In a sense, aminoacyl-tRNA synthetases “know” the genetic code and their precise recognition of tRNAs is as important for high-fidelity protein synthesis as is the accurate selection of amino acids. Some synthetases recognize their tRNAs partners primarily on the basis of their anticodons, although they may also recognize other aspects of tRNA structure.
What do ribosomes do?
They coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins that results in protein synthesis.
What are the components of a ribosome?
A large subunit (50S) and a small subunit (30S). These can be further dissociated into their constituent proteins and RNAs.
What are the three RNAs present in ribosomes and why are they present?
5S, 16S, and 23S and they are crucial for ribosomal architecture and function. These ribosomal RNAs (rRNAs) are folded into complex structures with many short duplex regions.
What are the key catalytic sites in the ribosome composed of?
Almost entirely of RNA. This concludes that the ribosome initially consisted only of RNA and that the proteins were added later to fine tune its functional properties.
