Eukaryotic translation Flashcards
What are polysomes?
Ribosomes that work together as a collective
What are ribosomes made up of?
2 subunits
bacteria: 30s & 50s = 70s
eukaryotes: 40s & 60s =80s
In eukaryotes what is the small subunit made up of?
1 rRNA molecule and many proteins
S = svedberg units
Heavier molecules/ribosomes sink more quickly and travel further so get a higher rating
In centrifugation how do different bands form
Sucrose solution - based on how quickly the macromolecules move which depends on how big/heavy they are and due to their shape
What is the active site of a ribosome?
Catalytic site (where the peptide bond in the new protein is formed) made up of rRNA
What is a ribozyme?
ribosomes that are an RNA enzyme
Transfer RNA
Bring amino acids to the ribosome to be added to the new protein
There is a tRNA for each codon as they must recognise the correct amino acid and codon
Describe E.coli 16s Ribosomal RNA
Small subunit of the ribosome. Single RNA molecule made up of a 5’ domain, central domain, 3’ major domain and 3’ minor domain
Anticodons
3 bases complementary to the codon of the mRNA
Aminoacyl tRNA synthetase
Joins a specific amino acid to the tRNA
Specific amino acyl tNRAs are assembled for each different amino acid
It is accurate and corrects its own mistakes
Describe the structure of tRNA
acceptor arm T psi C arm Variable loop Anticodon arm D arm
T psi C arm
Thymine pseudo uridine cytosine arm
The variable loop is…
varied in length and may not be a complete loop
What is the acceptor arm of the tRNA?
The point at which the amino acid will attach. The specificity is achieved through modification to bases
What is the step by step process to form an aminoacyl- tRNA?
Amino acid + ATP => Amino acid-AMP + pyrophosphate
Amino acid-AMP + tRNA => aminoacyl-tRNA + AMP
What is the name of the process of sticking an amino acid on a tRNA?
amino-acyl tRNA charging
What does every tRNA have?
its own synthetase to load the correct amino acid
What are the 3 steps for translation?
Initiation
Elongation
Termination
What is the initiator tRNA?
A special tRNA for the first amino acid (methionine)
Eukaryotes use: met-tRNAi^met
Bacteria use: met-tRNA^fmet
What is used to locate where the small subunit of the ribosome needs to bind?
Shine-Dalgarno sequence
3-10 subunits upstream of the first translated codon
What are the steps to initiation?
mRNA with start/initiation codon
(+small subunit. IF-3)
small subinit and IF-3 locate the AUG & sit there enveloping the AUG initiation codon. IF-3 keeps the large subunit out the way.
(+Initiator tRNA, IF-2, GTP)
IF-2 ensures that the ribosome is lined up with the mRNA and the mRNA is lined up with the initiator tRNA.
(+IF-1)
large subunit binds, all initiation factors released. Assembly complete.
Small and large subunits form on active site
How is initiation in eukaryotes different?
Small SUBUNIT, IFs, Met-tRNAi^met,
Locates the start codon through the kozak sequence
more IFs
Poly(A)tail assists small subunit binding
What do tRNAs need to attach to?
binding sites on ribosomes
E
P
A
E: exit site, tRNA ejected after delivery amino acid
P: peptidyl-tRNA site, second binding site for tRNA in the ribosome
A: aminoacyl-tRNA site, entry
Where does the initiator tRNA go?
Straight into the P site
What is elongation?
Adding to the chain beyond the first initial amino acid
What are the steps to elongation?
The first tRNA is attached to the AUG initiation codon carrying formyl methionine (P site). The A site is empty
aminoacyl-tRNAs are trying to fit onto the next codon. tRNA binds bringing elongation factor (EF) 1A bound to GTP. EF-1A-GTP. tRNA in A site.
GTP must be hydrolysed to provide energy to form the peptide bond between adjacent amin oacids. EF-1A-GTP
Function of EF-1B
re-generates EF-1A after EF-1A has yielded the energy in its attached GTP
Explain how translocation occurs in elongation
Two amino acids are still attached to their transfer tRNAs and attached to eachother by a peptide bond.
EF-2-GTP provides energy to move the second amino acidand tRNA to the next position.
The first amino acid is in the exit position and the enrgy from the hydrolysis of the GTP is used to dissolve the bond between the amino acid and tRNA. De-acylated tRNA is released with EF2 & GDP.
Where does synthesis of the peptide bond occur?
In the P-site. Peptidyl transferase activity that comes from the tRNA catalyses joiningof the carboxyl group of one amino acid with the amino group of another amino acid in the A site.
What are the steps in phase 3- termination
The stop codon enters the A site and does not signal for an aminoacyl-tRNA.
(+RF-1, RF-3 OR RF-2 & RF-3)
RF-1 & RF-2 minic tRNA molecules and they can bind to the A site. Once bound the last amino acid in the chain tries to make a peptide bond with the releasing factor but is unable to. Chain released from tRNA. RF-3 gets rid of RF-1/RF-2. Complete polypeptides. RF leaves.
The 2 ribodomse subunits dissociate. Ribosome recycling factor RRF separates the ribosome subunits and separates it from the mRNA
Why is RF-1 & RF-3 used OR RF-2 & RF-3?
RF-1 recognises UAG & UAA
RF-2 recognises UGA & UAA
Quality control mechanisms
Errors in mRNA could lead to faulty proteins. mRNA surveillance helps stop cells making useless or toxic versions of a protein.
The 2 mechanisms used are:
Non-sense mediated decay (NMD)- elimination of mRNA with premature stop codons (Eukaryotes)
tmRNA (prokaryotes)
tmRNA
Ribosome stalls when the end of an mRNA lacking a termination codon is reached.
tmRNA, which is charged with Ala, binds to the A site of the ribosome. Alanine is added to the polypeptide chain.
The ribosome reads the mRNA and adds amino acids continuing translation.
The amino acids encoded by the tmRNA are added to the polypeptide chain. A stop codon is then reached.
How does tmRNA work?
It allows 10 amino acids in a polypeptide chain to be added and labelled as defective. These amino acids are a tag. This produces a labelled aberrant protein that the cell can recognise and target for degradation.
The system may also detect the aberrant mRNA and destroy this.
