Topic 4 Biology

Big Picture

Translation is the process where the nucleotide sequence of mRNA is converted into an amino acid sequence to make a protein.

This happens at the ribosome and uses tRNAs to match codons with amino acids.

Central idea:
DNA → mRNA → Protein

Key RNA Players in Translation

• mRNA (messenger RNA)

  • Carries the genetic code copied from DNA

  • Read by the ribosome 5′ → 3′

  • Read in groups of three nucleotides called codons

  • Each codon specifies:

    • An amino acid OR

    • A stop signal

• tRNA (transfer RNA)

  • Function: Acts as the “translator” between nucleotide language and amino acid language

  • Structure

    • Single-stranded RNA that folds into a 3D shape

    • Folding happens through intramolecular base pairing

    • Forms stem-loop structures

    • Two critical regions:

      1. Anticodon loop

         • Contains the anticodon (3 nucleotides)

         • Base pairs with an mRNA codon

      2. 3′ end

         • Amino acid is covalently attached here

• Anticodon–Codon Relationship

  • Codon is on mRNA (written 5′ → 3′)

  • Anticodon is on tRNA (written 3′ → 5′)

    • Example:

      • mRNA codon: 5′ UUU 3′ → Phenylalanine

      • tRNA anticodon: 3′ AAA 5′

      • That tRNA carries phenylalanine

• rRNA (ribosomal RNA)

  • Structural and catalytic component of the ribosome

  • One rRNA in the large subunit catalyzes peptide bond formation

  • Makes the ribosome a ribozyme

Charging tRNAs: Aminoacyl-tRNA Synthetases

• Enzymes that attach the correct amino acid to the correct tRNA

• Extremely specific:

  • Recognize the anticodon

  • Recognize the amino acid

• Amino acid is covalently attached to the 3′ end of tRNA

• A tRNA with an amino acid attached is called “charged”

• The amino acid attached is the cognate amino acid

The Ribosome

• The machinery that builds proteins

• Made of rRNA + proteins

• Has two subunits:

  • Small subunit

  • Large subunit

• Subunits:

  • Come together during translation

  • Separate when translation is finished

tRNA Binding Sites

Located on the large subunit:

• A site (Aminoacyl site) – incoming tRNA

• P site (Peptidyl site) – holds growing peptide

• E site (Exit site) – tRNA leaves

Genetic Code Basics

Codons

• 3 nucleotides long

• 64 total possible codons (4 × 4 × 4)

• 61 code for amino acids

• 3 are stop codons

Start Codon

• AUG

• Codes for methionine

• Sets the reading frame

• ALWAYS part of the protein-coding region

Stop Codons

• UAA, UAG, UGA

• Do not code for amino acids

• Recognized by release factors, not tRNAs

Protein Coding Region

• Starts at the start codon

• Ends at the stop codon

• Includes:

  • Start codon

  • All codons in between

  • Stop codon (even though it doesn’t code for an amino acid)

Steps of Translation (Prokaryotes Example)

Initiation

1. Small ribosomal subunit binds mRNA

2. mRNA contains a ribosome binding site (Shine-Dalgarno sequence)

   • rRNA base-pairs with this sequence

   • Positions the start codon correctly

3. Initiator tRNA binds the start codon:

   • Carries formyl-methionine (fMet)

   • Sits in the P site

4. Large subunit joins → complete ribosome

📌 Eukaryotes difference:
Ribosome binds the 5′ cap and scans for AUG instead.

2. Elongation

1. Correct charged tRNA enters the A site

2. Peptide bond forms

   • Between amino acid in P site and amino acid in A site

   • Catalyzed by rRNA

3. Bond between amino acid and tRNA in P site breaks

4. Ribosome translocates one codon (5′ → 3′)

   • A → P

   • P → E

   • E tRNA exits

5. Process repeats until stop codon appears

3. Termination

1. Stop codon enters A site

2. Release factor binds stop codon

3. Peptide is released from tRNA

4. Ribosome subunits, tRNAs, and mRNA dissociate

5. Protein folds into its functional shape

Point Mutations (in Protein-Coding Regions)

Definition

A mutation affecting one nucleotide:

• Substitution

  • One nucleotide is replaced by another

  • Example: A → G

  • Does not change the length of the sequence

  • Can cause:

    • Silent mutation (same amino acid)

    • Missense mutation (different amino acid)

    • Nonsense mutation (early stop codon)

• Insertion

  • One (or more) nucleotide(s) is added into the DNA sequence

  • Example: adding an extra A

  • Changes the length of the sequence

  • If not in multiples of 3, it causes a frameshift mutation

  • Frameshifts change every codon downstream of the mutation

• Deletion

  • One (or more) nucleotide(s) is removed from the DNA sequence

  • Example: removing a T

  • Changes the length of the sequence

  • If not in multiples of 3, it causes a frameshift mutation

  • Like insertions, this often has major effects on protein function

• Key Reminder (VERY IMPORTANT)

  • Insertions or deletions in multiples of 3 → no frameshift

  • Insertions or deletions not in multiples of 3 → frameshift

  • The start codon sets the reading frame

Reading Frame

• Set by the start codon

• Codons are read only within the protein-coding region

• Every downstream codon depends on that initial frame

• Frameshifts completely alter translation

Final Recap

• mRNA = instructions

• tRNA = adaptor that brings amino acids

• rRNA = catalyst

• Translation reads mRNA 5′ → 3′

• Codons determine amino acids

• Mutations can range from harmless to severe

• The start codon determines everything downstream