Biology Chapter 5: Gene Expression

Study Notes

Open reading frames (ORFs) are nucleotide sequences without stop codons, allowing ribosomes to synthesize proteins.
ORFs range from the start codon (AUG) to the nearest stop codon, facilitating the translation process.

Messenger RNA (mRNA)
- Encodes specific protein sequences and varies in length based on the protein size.
- Read in triplets called codons; there are 64 codons, with 61 coding for amino acids and 3 serving as stop signals.
Transfer RNA (tRNA)
- Transfers one amino acid at a time during polypeptide chain elongation.
- Has a cloverleaf structure with an anticodon that pairs with mRNA codons and an amino acid binding site at the 3’ end.
- Becomes 'charged' when an amino acid is linked to it, enabling participation in translation.
Ribosomal RNA (rRNA)
- Composes about 60% of ribosomes, which are essential for protein synthesis.
- Facilitates the coupling of mRNA with tRNA and consists of small and large subunits.

Initiation
- Initiation occurs differently in prokaryotes and eukaryotes.
  - In prokaryotes, recognizes start site via the Shine-Dalgarno box and AUG codon, using a special initiator tRNA carrying fMet.
  - In eukaryotes, the small ribosomal subunit binds to the mRNA's 5’ cap, scans for the first AUG, and assembles with initiation factors before protein synthesis begins.
Elongation
- Involves two elongation factors (EF-Tu/EF1 and EF-G/EF2) that hydrolyze GTP to GDP, aiding the precise addition of amino acids to the growing polypeptide chain.
- EF-Tu ensures the accuracy of tRNA selection and its association with the mRNA codon.
Termination
- Signaled by stop codons (UAA, UAG, UGA) triggering release factors which cause the addition of a water molecule instead of an amino acid.
- This reaction releases the completed polypeptide and disassembles the ribosome, allowing for new translation rounds.

Polycistronic mRNA
- Encodes multiple proteins, common in prokaryotes and chloroplasts.
Monocistronic mRNA
- Encodes a single protein; characteristic of eukaryotic mRNAs.

Eukaryotic cells can reduce protein synthesis in response to stress (e.g., nutrient deprivation, infection) through phosphorylation of the translation initiation factor eIF2.
eIF2, when phosphorylated, tightly binds to its exchange factor eIF2B, disrupting protein synthesis by preventing the reuse of eIF2.

Post-Translational Modification
- Involves chemical changes to proteins that can affect their activity and function.
Protein Degradation
- Proteins tagged with ubiquitin are directed for degradation by the proteasome, marking the end of their functional lifespan.