Translation I Flashcards
How many high-energy bonds to make one peptide bond?
Four!
Where does translation occur?
In the cytoplasm, on the ribosome.
Key players in translation
mRNA tRNA Aminoacyl tRNA syntheses The ribosome Initiation factors Elongation factors and their partners Termination/recycling factors
mRNA
Has nucleotide sequence for the proton.
3 nucloeotide codons
4^3 = 64 possible codons
AUG is the start codon
tRNA
Adapters that “read” the message and deliver the right AA
tRNAs base pair directly to the codons in the mRNA through the tRNA’s anticodon loop
So EACH codon recognized by a SPECIFIC tRNA (some recognize more than one due to wobble-pairing)
Amount of each type of tRNA varies, usually matching codon frequency
Other end has an ACCEPTOR stem, this is where the AA attaches that matches the anticodon loop
Fx of tRNA is dictated by its 3D folded structure
Aminoacyl tRNA synthetases
Protein enzymes that put right AA on right tRNA
use a recognition site to get it right
Each AA/tRNA has its own syntheses (valine onto valtRNA via valyl-tRNA synthetase).
Ribosome
Platform that brings it all together. Has a catalytic center. Made of many RNA and proteins. (mostly RNA), has 2 subunits... 30S and 50S in bacteria, 40S and 60S in eukaryotes). mRNA and tRNA pass b/w the 2 subunits. A, P, and E sites
Small subunit: has DECODING groove through which mRNA passes and tRNAs read the message
Large subunit: catalytic center (peptidyl transferase center, PTC) which is all made of RNA
thus ribosome is a ribozyme (uses RNA to perform catalysis)
Initiation factors
Eukaryotes have dozens, bacteria have 3
Bring ribosome to the message, and help get the machinery assembled
Elongation factors and their partners
Proteins that deliver tRNAs and move the ribosome down the message
Termination/recycling factors
Proteins that end the process at a stop codon, and dissociate the subunits so you can use them again
Kozak sequence
AUG’s can have different efficiencies of recognition
4 steps of translation
- ) Initiation
- ) Elongation
- ) Termination
- ) Ribosome recycling
Initiation
Step w/ most control/regulation
Get machinery in right place, setting reading frame
goal: assemble a ribosome with the AUG and initiator methionine tRNA in the P site, ready to get next aa-tRNA into A site
In euks: eIF4E binds 7-methyl guanosine cap on 5’ end, other eIF bind, ribo small subunit scans until it finds AUG, then large subunit joins. Factors release. Initiation.
Bacteria vs. eukaryotes
Bacteria: ribosome binds right at start codon due to Shine-dalgarno sequence and 3 initiation factors work to assemble the full ribosome
Eukaryotes: you need initiation factor (eIF) 4E to bind the 7-methyl guanosine cap (CAP DEPENDENT) on the 5’ end of the mRNA
This leads to many other eIF binding, and eventually binding to the small ribosomal subunit (which is itself bound to sever factors eIF3 etc.).
Ribosome SCANS down the message to find AUG. Then LARGE SUBUNIT JOINS the small. Factors released. you are initiated.
Cap-independent process
Driven by specific RNA sequences and structures called internal ribosome entry sites.
many viruses use IRESs to initiate translation. Viruses shut down host translation to avoid being fought off. Its uncapped mRNA escapes from setting off alarms.
Produces protease to cleave off eIF4E and shut down cap-dependent translation.
Virus can’t translate on it’s own. so it takes advantage of cap-independ pathways.
Some eukaryotic mRNAs also use IRESs.
Elongation
A cycle in which each step gives one more AA added to chain.
1.) aatRNA enteres the A site (delivered by EF1A), its anticodon loop base pairs with correct codon in the mRNA “reading the message”
AUG is only one that starts in P site
2.) Peptide bon forms when protein chain moves from P site tRNA to A site tRNA
3.) Action of another elongation factor catalyzes translocation (message and tRNA move one codon over)
NOW empty tRNA from P site is in the E site and it leaves. And the nascent peptide chain is attached to the tRNA in the P SITE.
So A site is open again. Cycle repeats.
Remember: each peptide bond requires 4 high energy bonds.
Explain the 4 high energy bonds needed for a peptide bond
To charge tRNA: 2 ATP –> AMP
To deliver aaRNA to A site 1 GTP –> GDP
Translocation: 1 GTP–> GDP
Termination
Reading a stop codon, ending elongation, and dissociating subunits.
Happens when stop codon detected by a recycling factor in the A site.
Recycling factor
proteins that fit in same space as tRNA, but when they do trigger termination of peptide chain and a series of events that lead to release of peptide and dissociation of the subunits.
Protein goes off to fold, get modified etc.
Recycling
Getting rib subunits ready to be used again in initiation
Sense vs missense vs nonsense mutation
Sense: removed stop codon
Nonsense: premature stop codon
Missense: different AA
