BIO PROTEIN SYNTHESIS

Codon definition

3 nucleotides on mRNA coding for a specific amino acid or stop signal

Start codon

AUG

Stop codons

UAA, UAG, UGA

Total possible codons

64 (4³)

Why only 64 codons for 20 amino acids

Genetic code is degenerate — multiple codons can code for same amino acid

Degenerate genetic code

More codons than needed; multiple codons code for same amino acid (e.g. Leucine = 6 codons)

Universal genetic code

Same codons = same amino acids across all organisms

Non-overlapping genetic code

Each nucleotide belongs to only one codon, no sharing between codons

4 steps of protein synthesis

Transcription, Amino Acid Activation, Translation, Post-translational modification

Transcription definition

mRNA synthesized from DNA template strand; DNA code passed to mRNA

RNA Polymerase role in transcription

Binds promoter, unwinds DNA bubble, reads template strand, synthesizes mRNA

Promoter

DNA region where RNA Polymerase binds before transcription begins

Template strand

3'→5' strand read by RNA Polymerase; aka antisense/coding strand

noncoding strand

Strand NOT read by RNA Polymerase; aka sense strand; same sequence as mRNA (T→U)

Why RNA Polymerase reads 3'→5'

New mRNA must be synthesized 5'→3'; antiparallel rule forces template to run 3'→5'

What happens to DNA behind RNA Polymerase

Re-anneals/re-winds spontaneously as bubble moves forward

Termination sequence

DNA sequence signaling RNA Polymerase to stop transcription; aka terminator

Pre-mRNA vs mature mRNA

Pre-mRNA needs processing (5' cap, poly-A tail, splicing) before becoming functional mRNA

Topoisomerase role in transcription

Relieves torsional stress ahead of moving RNA Polymerase

tRNA shape

Cloverleaf

tRNA function

Carries specific amino acid to ribosome during translation

Anticodon

3 nucleotide sequence on tRNA that base-pairs with mRNA codon; antiparallel to codon

Aminoacyl-tRNA synthetase

Enzyme that attaches correct amino acid to correct tRNA (activation step)

Why Aminoacyl-tRNA synthetase accuracy matters

Ribosome reads anticodon not amino acid — wrong attachment = wrong amino acid in polypeptide

Charged vs uncharged tRNA

Charged = has amino acid attached; Uncharged = already delivered amino acid, needs recharging

D loop function

Helps tRNA fold into 3D structure; helps Aminoacyl-tRNA synthetase recognize correct tRNA

TΨC loop function

Helps tRNA bind to ribosome and stabilizes tRNA during translation

Variable loop function

Distinguishes one tRNA from another (tRNA identity region)

RBS (ribosome binding site) function

Positions tRNA correctly in ribosome so anticodon can accurately pair with codon

Ribosome structure

Large + small subunit; site of protein synthesis

Small ribosomal subunit function

Binds mRNA; where codon-anticodon decoding happens

Large ribosomal subunit function

Contains A/P/E sites; where peptide bond formation happens

A site

Aminoacyl site — entry point for incoming charged tRNA

P site

Peptidyl site — holds growing polypeptide chain; where peptide bond forms

E site

Exit site — where uncharged tRNA exits ribosome

Translation initiation

Small subunit binds mRNA, scans for AUG, initiator tRNA enters P site, large subunit joins

Translation elongation cycle

Charged tRNA enters A site → peptide bond forms → ribosome translocates → uncharged tRNA exits E site

Translation termination

Stop codon reached → release factor enters A site → polypeptide released → ribosome disassembles

Post-translational modification definition

Processing of polypeptide after translation into functional protein

RER role in PTM

Site of initial folding and glycosylation; ribosomes dock here for secreted/membrane proteins

Golgi apparatus role in PTM

Further modifies, sorts, tags, and packages proteins for final destination

Disulfide (SS) bonds

Covalent bonds between Cysteine residues; stabilizes 3D protein structure