Week 3 (Translation) Flashcards
Why is the genetic code said to be like a written language?
1 base= 1 letter
1 codon= 1 word
1 gene= 1 sentence
Why is a codon 3 bases long?
1 base= 4 possibilities
2 bases = 16 possibilities
3 bases = 64 possibilities
10 bases= 1,000,000 possibilities
What is the start codon?
AUG
What are stop codons?
UAA
UAG
UGA
What is the consensus sequence of the ribosome binding site?
AGGAGGU
Why start transcription ahead of the genes
To leave space for the ribosome to bind before they get to the start codon
What is the direction used to describe polypeptides?
From the amino terminus, NH2 (corresponds to the start of the gene) to the carboxyl end, COOH (corresponds to the end of the gene)
Explain the 10 stages of translation (E.Coli)
- The small ribosomal subunit binds to the ribosome binding site (consensus sequence: 5’-AGGAGGU-3’)
- The small subunit moves along the mRNA to the start codon (5’-AUG-3’) which encodes methionine
- The first tRNA binds to the P site (tRNAfmet- formyl
methionine that is modified to protect the amino group) requires IF2 (initiation factor 2) - The large subunit binds (requires hydrolysis of GTP to GDP + Pi) forming E, P and A sites within the ribosome
- The second tRNA binds to the A site- requires EFTu (elongation factor)
- A petite bond is formed by peptidyl transferase (part of the ribosome)
- The uncharged tRNA is freed from the ribosome by tRNA deacylase via the E site
- Translocation occurs (requires hydrolysis of GTP to GDP + Pi) require EFG
- Stages 5 to 8 repeat in a continuous cycle until
- A termination codon is encountered (no tRNA exists)
RF1 or RF2 (releasefactor) binds A site and cleaves the polypeptide from the tRNA in the P site. RF3 cooperates
What are the 3 translation signal?
- Start codon
- Ribosome binding site
- Stop codon
What is the C-terminal end of an amino acid also known as?
The carboxyl end
What is the N terminal of amino acids also known as?
The amine terminus
A peptide chain grows by the addition of amino acids. To which end are consecutive amino acids added?
To the C terminal end
Why is the formation of a peptide bond energetically favourable?
Because the growing C terminus has been activated by the covalent attachment of a tRNA molecule
Why do amino acids carry energy for the addition for the next amino acid rather than its own?
Addison disrupts the high energy covalent linkage (amino acid-tRNA) , but immediately replaces it with an identical linkage on the most recently added amino acid (peptide bond)
What is the function of the small subunit of a ribosome?
Provides a framework on which tRNAs are accurately matched to the codons of mRNA
What is the function of the large subunit of the ribosome?
Catalysed the formation of the peptide bonds that link the amino acids together in a polypeptide chain
What happens when the ribosomes are not synthesising proteins?
The two subunits separate
What does the A, P and E sites stand for ?
A: aminoacyl (tRNA)
P: peptidyl (tRNA)
E: Exit
What helps the ribosome maintain the correct reading frame on the mRNA?
The A and P sites are close enough together for their two tRNA molecules to be forced to form base pairs with adjacent codons on the mRNA molecule
How does the entire ribosome positioned to start the next cycle?
- Translocation of the large subunit followed by that of the small subunit causing the entire ribosome to move 3 nucleotides along the mRNA
- This resets the ribosome with a fully empty A site ready for the next aminoacyl- tRNA molecule to bind
What enzyme catalysed the formation of a peptide bond?
Peptidyl transferase
Why do both bacterial and eukaryotic cells have transcription elongation factors?
They make translation especially efficient and accurate by proofreading the codon-anticodon match. In this way am incorrectly paired tRNAs are selectively rejected
They hydrolyse GTP to GDP*
What are the transcription (elongation) factors in bacteria called?
EF-TU and EF-G
What are the transcription (elongation) factors in eukaryotes called?
EF 1 and EF2
What is responsible for the high level of accuracy of the ribosome in translating RNA into protein?
- The small subunit assesses the correctness of the codon-anticodon match by folding around it and probing molecular details. When a correct match is found the rRNA closes tightly around the codon- anticodon pair the EF-TU hydrolysis GTP causing the EF-TU to release its grip on the aminoacyl tRNA and allow it to be used in protein synthesis. Incorrect tRNAs fall of the ribosome before they can be used in protein synthesis
- There is a short time delay as the amino acid carried by tRNA moves into position on the ribosome. the time delay is shorter for correct than incorrect codon-anticodon pairs. Moreover incorrectly matched tRNAs dissociate more rapidly than those correctly bound because their interaction with the codon is weaker
What is a way the cell can correct a misincorporated amino acid?
Successive rounds of amino acid misincorporstion eventuslly lead to premature termination of the protein by release factors. Although this mechanism doesn’t correct the original error, it releases the flawed protein for degradation so no additional peptide synthesis is wasted on it
What is the composition of a ribosome?
Two thirds RNA
One third protein
What are ribozymes?
RNA molecules that posses catalytic activity
How does the small ribosomal su it recognise the 5’ end of an mRNA molecule?
The 5’ end is capped and has previously bound two initiation factors eIF4E and EIF4G
Why do both the 5’ cap and the poly A tail interact with initiation factors e.g. eIF4G?
The translation apparatus ascertains that both ends of the mRNA are intact before protein synthesis
What is leaky scanning?
Ribosomal subunits will sometimes ignore the first AUG codon in the mRNA and skip to the second or third AUG codon instead.
Cells use this phenomenon to produce two or more proteins differing in the N terminals from the Same mRNA molecule. This mechanism allows some genes to produce the same protein so that the proteins can be directed to two different compartments of the cell
What do bacterial cells have instead of 5’ caps to signal the ribosome where to begin searching for the start of translation?
They have a specific ribosome binding site (Shine-Dalgarno sequence)
Define polycistronic?
several different proteins each translated from the same mRNA molecule
How does translation end?
Release factor (proteins) bind to a stop codon positioned in a ribosomes A site. This forces the peptidyl transferase in the ribosome to catalysed the addition of a water ole cube instead of an amino acid to the peptidyl tRNA which frees the carboxy end of the growing polypeptide chain from its attachment to a tRNA molecule
What is a polysome?
Multiple ribosomes translating a single mRNA strand
What is the name of the extra amino acid possess by bacteria, archaea and eukaryotes?
Selenocysteine
What are the functions of molecular chaperones?
Help proteins fold correctly
What are heat shock proteins?
A large class of molecular chaperones that are synthesised in dramatically increased amounts after a brief exposure to an elevated temperature
