Ch. 22: Protein Synthesis, Post Translational Modification, and Transport Flashcards
Codon
A triplet of 3 nucleotides which together form a genetic code for DNA or RNA
tRNA (Transfer RNA)
The adaptor molecule, has the capacity to incorporate different kinds of bases
What kind of complementary pairing does tRNA use?
Codon-anticodon base pairing
Aminoacyl transferase
Enzyme required to catalyze the attachment of an amino acid to tRNA
What does amino transferase do?
Attaches a specific amino acid to the 3’ acceptor stem of the cognate tRNA molecule
AUG (Met)
The start codon
What direction is the code read in with mRNA?
5’ to 3’ direction
What does the D arm of tRNA do?
Makes sure that amino-acylation occurs
Ribothymidine pseudouridine cytosine (T sai C loop)
Locates ribosomal binding site
Acceptor Arm
Recognizes the cognate amino acid and binds to tRNA
Inosine Base Pairing
Inosine in tRNA is formed by deamination of adenosine by the enzyme tRNA-specific adenosine deaminase
What direction is tRNA in?
3’ to 5’ direction (Note: mRNA is antiparallel)
Wobble Hypothesis
Base-pairing rules may be relaxed at the 3rd position of the codon (1st position of anticodon)
Proofreading Functions of tRNA Synthetases (Correct)
When the correct tRNA (tRNAThr) and cognate amino acid (Thr) bind to the active site in step 1, then amino acylation occurs in the active site and this amino-acylated tRNA is not hydrolyzed by the editing site in step 2, thus generation the correct aminoacylated tRNA (the-tRNAThr)
Proofreading Functions of tRNA Synthetases (Incorrect)
When a chemically similar, but incorrect, amino acid (Val) binds loosely to the active site with the same tRNA (tRNAThr) in step 1, then the aminoacylated tRNA is still generated. However, the incorrect amino acid is hydrolyzed at the editing site in step 2
AUG
Start codon for both prokaryotes and eukaryotes
Translation
Protein synthesis, occurs on the ribosome
Where is translation terminated?
Terminated by stop codons on the mRNA transcript; release factor binds to the ribosome in place of a charged tRNA, and the polypeptide chain is released from the ribosome
Ribosomal Complex
Recruitment of a large subunit to a small subunit
Where does the ribosomal complex land?
On one of three sites:
1. E site (Exit site)
2. P site (Peptidyl site)
3. A site (amino acyl site)
Initiation (Prokaryotic)
Uses 30S and 50S subunits to form the 70S ribosome
Three initiation factors involved
Shine-Dalgarno sequence appears 5-13 base pairs upstream of the first AUG codon to orient mRNA within the ribosome
Initiation (Eukaryotic)
Uses 40S and 60S subunits to form the 80S ribosome
Requires specific mRNA sequences at both the 5’ and 3’ ends of the mRNA (5’ cap is a vital feature that protects mRNA during transport)
Multiple elongation factors as well as GTP and ATP
Steps of Initiation (Prokaryotes)
- Met recognizes correct tRNA and binds
Gets methylated (FMet tRNA) - The mRNA and fMet-tRNAMet bind to the complex with the Shine-Dalgarno sequence of mRNA aligning with the complementary sequences in the 16S rRNA in the 30S ribosomal subunit, and IF3 is released
- Hydrolysis of GTP facilitates binding of the 50S ribosomal subunit, with the release of IF1 and IF2 to form the functional 70S ribosomal initiation complex. Conists of fMet-tRNAMet bound in the P site, with the E and A site empty until elongation begins
Steps of Initiation (Eukaryotes)
- 43S pre-initiation complex is formed between the 40S small ribosomal subunit and a complex consisting of the elF2, elF3, elF5, elFA, the amino-acylated met-tRNAimet, and GTP
- mRNA transcript (contains a number of RNA binding proteins associated with the 5’ cap and poly A tail) associates with the 43S pre-initiation complex to form the 48S pre-initiation complex
- 60S large ribosomal subunit associates with the 48S pre-initiation complex, resulting in the exchange of initiation factor proteins and the formation of the fully assembled 80S complex
Which of the following is similar in eukaryotes and prokaryotes: Initiation, elongation, termination
Elongation
Elongation
The 6 step elongation cycle requires the hydrolysis of 2 GTP, one to promote the binding of the AA-tRNA^AA to the A site, and one to facilitate translocation of the ribosome in the 3’ direction
How many GTP does translational elongation require?
2 GTP
What does each of the two GTP molecules do in elongation?
- Promote the binding of the AA-tRNA^AA to the A site
- Facilitate the translocation of the ribosome in the 3’ direction
Peptidyl transferase reaction
Creates a peptide bond that holds the polypeptide together
How does the peptide transferase reaction work?
The amino group of the amino acid attached to the 3’ terminus of the tRNA in the A site attacks the carbonyl carbon of the peptidly-tRNA in the P site, resulting in an extended A-site peptidyl tRNA
Release of the polypeptide
Release factors bind to the termination codon and lead to the release of the polypeptide chain
How many termination codons are there?
3 Stop Codons: UAG, UGA, UAA
What bases can inosine wobble with?
A, C, U
In the wobble phenomenon, the base that wobbles is found in the ___?
tRNA
How many codons are known for each amino acid?
1 to 6 depending on the nature of the amino acid
Are there any exceptions to the universality of the genetic code?
Yes, in mitochondria and 16 other organisms, including some algae and fungi
Which amino acids have unique codons?
- Trp
- Met (AUG)
The genetic code is said to be degenerate. What does this mean?
Many amino acids are coded for by different codons.
