Translation

1. Carring the amino acid at its acceptor arm
2. decoding the  codon
3. Help the peptide bond formation

Arm - 5' CCA 3' holds amino acid
D-loop contains two dihydrouridine
T-Loop - contains pseudouridine
Variable loop -  varies 4-13nt
Anticodonloop - bases of anticodon flip out and often contain inosine (for wobble pairing)

Frame shifts often have many stop codons that prevent copying of frame shifts

64 tubes containing one codon. With other translational material and one of 20 amino acids. Pass each reaction on a NC filter. Only ribosome-mRNA-tRNA amino acid complex can bind to NC filter.
If the radioactive maino acid is recognized by and attached to the correct tRNA, it was radioacitvely labeled.
20 sets of 64 reactions required to break genetic code.

Stop: UAA UGA UAG
Initiation: AUG

Genetic codes are redundant.
Arginine, Leucine, Serine are all degenerated the most
Methioinine and Tryptophan are not degenerated
(Methionine is the first one)

One anticodon of tRNA can recognize and base pair with more than one degenerate codons encoding the same amino acid
Mismatching U with A or G
or G with U or C
Or Inosine, can base pair with A, C and U

Aminoacyl-tRNA synthetases (ARS) attaches amino acid to tRNA. Cells have 20 ARS recognizes tRNA by its acceptor arm.
ARS proofreads and remove mistakenly incorporated residues
Using ATP, ARS covalently attaches amino acid  to the 5' phosphate group of AMP
ARS transfers amino acid from AMP to 3' -OH group of tRNA

Starts after the Shine Dalgarno Sequence (SDS) 5bp upstream from translation initiation AUG. Base pairs with 16S-rRNA. Can also use S1 to determine initiation
Can have multiple SDS, all work independently
Initiation factors (1) prevent two free ribosome subunits from binding to each other and (2) help assemble 30S initiation complex.
Always starts with formylated methionine

First Kozak sequence always used, AUG part of Kozack. First met is often acetylated. Initiation factors preventing bonding of subunits and also help initiate translation.

Eukaryotic initiation factor 4
eIF4E - binds to cap
eIF4G - adaptor protein can bind to many other proteins, and binds to polyA tail, creating circular mRNA
eIF4A - RNA helicase activity
eIF4H - stimulates eIF4A helicase cativity

5' UTR plays an important role. Secondary structure at 5' UTR may bind to a regulator protein. also regulated by initiation factors
When insulin is present, it activates a kinase called mTOR. mTOR phosphorylates PHAS-1 which does not bind to eIF4E. Free eIF4E binds to cap of mRNA and activates initiation

CPE of cyclin B binds to CPEB. CPEB brings in Maskin and masking binds to eIF4E, replacing eIF4G and turning off trnaslation.
When the oocyte is activated, a kinase called Eg2 phosphorylates CPEB which brings in CPSF (Poly adenylation specificity factor) and changes conformation of Maskin, releasing eIF4E. eIF4E binds to eIF4g to turn on translation.

APE, in that order
The first amino acid arrives in P site, The first amino acid to attach to that enters A Site.
Peptide formation catalyzed by peptidyl transferase. Believed that 23S or 28S rRNA has catalytic properties.
New aminoacyl enters A site. Peptide bond is formed between A site and P site. The P site is now empty, and ribosome moves toward the 3' end of mRNA, and each tRNA moves over one.

When the stop codon hits, no tRNA enters the A site, so RF/eRF1 have a structure similar to tRNA, so they can fit into the empty A site. RF1/eRF1 promotes cleavage of the last peptidyl tRNA on the P site, and all the components fall apart and recycle