Chapter 14: Translation

If an ORF(open reading frame) is changed because of mutation in a codon, how could that change the amino acid? 

• Missense mutation: One codon is changed → different amino acids inserted.

• Nonsense mutation: Codon changed to a stop codon → truncated protein.

• Silent mutation: Codon changes but still codes for the same amino acid (due to code degeneracy).

What are the properties of the genetic code? 

• Triplet: 3 nucleotides = 1 codon → 1 amino acid.

• Non-overlapping: Codons read sequentially.

• Degenerate: Multiple codons can code for the same amino acid.

• Unambiguous: Each codon codes for only 1 amino acid.

• Nearly universal: Same code used by most organisms.

What are codon usage bias and wobble? How are these properties related to code degeneracy?

• Codon usage bias: Some codons are preferred over others for the same amino acid in different organisms.

• Wobble: Flexibility at the third codon position, allowing one tRNA anticodon to recognize multiple codons.

• Relation to degeneracy: Degeneracy of the code is accommodated by wobble pairing, reducing the number of tRNAs needed.

What is meant by polypeptide primary structure? Secondary structure? Tertiary structure? Quaternary structure? 

• Primary: Linear sequence of amino acids.

• Secondary: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds.

• Tertiary: 3D structure of a single polypeptide, stabilized by R-group interactions (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

• Quaternary: Assembly of multiple polypeptides into a functional protein complex.

How do amino acid R groups contribute to protein structure? What happens when one R group is switched out for another R group, as would happen in mutation? 

• Determine chemical properties (polar, nonpolar, acidic, basic).

• Drive folding and interactions in tertiary and quaternary structures.

• Mutation effect:

  • Substituting one R group can alter folding, stability, or activity (e.g., sickle cell mutation Glu → Val).

What is the relationship between a polypeptide and protein? What is a protein subunit? 

• Polypeptide: Linear chain of amino acids.

• Protein: Polypeptide (or multiple polypeptides) folded into a functional 3D structure.

• Protein subunit: Individual polypeptide in a multi-subunit protein

Describe the nomenclature of tRNA and a charged tRNA. 

• Charging: Attaching amino acid to tRNA.

• Enzyme: Aminoacyl tRNA synthetase (one per amino acid, ~20 in humans).

• Importance: Ensures correct codon-amino acid pairing; fidelity of translation depends on it.

How is the anticodon related to the mRNA codon? 

• The anticodon is a sequence of three nucleotides on tRNA that is complementary to the codon on the mRNA. Base-pairing of the anticodon to the codon holds the correct amino acid in position for peptide bond formation

What is meant by charging the tRNA? 

• Charging is the process of chemically linking a tRNA molecule to its corresponding amino acid so it can participate in translation.

What is meant by aminoacylation? 

• Aminoacylation is another term for tRNA charging; it describes the formation of a high-energy ester bond between the tRNA’s 3′ end and its cognate amino acid.

What enzyme performs this reaction? 

• Aminoacyl tRNA synthetase catalyzes the attachment of amino acids to their specific tRNAs

Approximately how many types of these enzymes are present in a cell? 

• About 20 aminoacyl tRNA synthetases exist, one for each amino acid/isoacceptor tRNA class.

Describe the structure of the ribosome. 

• Ribosomes consist of a large and small subunit, each made of rRNA and proteins. In bacteria, the monosome is 70S (50S + 30S); in eukaryotes, the monosome is 80S (60S + 40S). rRNA performs catalytic functions, and proteins help with binding and process fine-tuning.

What are the three tRNA binding sites?

• A site (Aminoacyl site): Holds incoming charged tRNA.

• P site (Peptidyl site): Holds tRNA attached to growing polypeptide.

• E site (Exit site): Holds uncharged tRNA before it leaves the ribosome.

What molecule is the peptidyl transferase and where is it located? 

• rRNA is the catalytic component responsible for peptide bond formation (peptidyl transferase activity), located in the ribosome.

Describe the mechanism of translocation. 

• mRNA runs through the ribosome, allowing successive tRNAs to bring amino acids into position for repeated peptide bond formation.

What is a polysome? 

• A polysome is a structure where multiple ribosomes simultaneously translate a single mRNA.

Why do they result in many polypeptides being produced from one mRNA molecule? 

• Because multiple ribosomes can translate the same mRNA at once, many copies of the polypeptide are synthesized simultaneously.

What are the major differences between prokaryotic and eukaryotic translation?

• Ribosome size: Prokaryotes 70S (50S+30S), Eukaryotes 80S (60S+40S).

• rRNA composition: Bacteria: 23S, 16S, 5S; Eukaryotes: 28S, 18S, 5.8S, 5S.

• Initiation codon: Bacteria use fMet, eukaryotes use Met.

• Initiation mechanism: Bacteria use Shine–Dalgarno sequence; eukaryotes recognize the 5′ cap.

• Process complexity: Eukaryotic translation involves more initiation factors and post-transcriptional regulation; bacterial translation is simpler.

• Ribosome size: Prokaryotes 70S (50S+30S), Eukaryotes 80S (60S+40S).

• rRNA composition: Bacteria: 23S, 16S, 5S; Eukaryotes: 28S, 18S, 5.8S, 5S.

• Initiation codon: Bacteria use fMet, eukaryotes use Met.

• Initiation mechanism: Bacteria use Shine–Dalgarno sequence; eukaryotes recognize the 5′ cap.

• Process complexity: Eukaryotic translation involves more initiation factors and post-transcriptional regulation; bacterial translation is simpler.