Gen 3 exam

Translation Overview

  • Main Components of Translation:

    1. Ribosomes

    2. tRNA

    3. Processed mRNA

  • Ribosomes:

    • Functional structure of ribosomes is conserved across all organisms.

  • tRNA (Transfer RNA):

    • Nucleotide-based structures with 3’ and 5’ ends.

    • Cloverleaf structure.

    • Role: brings amino acids to be translated, this process is called "charging."

    • Anticodon matches with the corresponding mRNA sequence.

Steps of Translation

1. Initiation

  • The start codon, AUG, is always the beginning of the coding sequence.

  • Shine-Dalgarno sequence typically aids in ribosomal binding at the start of mRNA (GGAGG).

  • AUG must initiate because fMet (formyl methionine) has to be present.

  • Ribosome's binding sites include A site (aminoacyl), P site (peptidyl), and E site (exit).

  • AUG primarily occupies the P site.

2. Elongation

  • Elongation Factor Tu:

    • Responsible for bringing charged tRNA into the A site.

    • After matching, it departs, allowing peptide bonds to form between amino acids at the P site and the A site.

  • The ribosome shifts down the mRNA by three nucleotides, advancing all tRNA positions accordingly.

  • Peptide bond formation occurs when the tRNA is located in the A site.

3. Termination

  • Termination involves the release factors (RF1 and RF2) that signal end of translation.

  • Upon reaching the stop codon, the release factor binds, leading to the disassembly of the ribosome, resetting everything for a new translation cycle.

Polyribosomes (Polysomes)

  • Commonly found in bacteria as simultaneous transcription and translation occur here.

  • In eukaryotes, these processes cannot happen simultaneously at the same level due to compartmentalization.

Wobble Hypothesis

  • Refers to flexibility in codon-anticodon pairing allowing the third position (wobble position) to vary without affecting the overall coding efficiency.

Eukaryotic Translation Dynamics

  • Translation occurs separately from transcription — slower process compared to prokaryotes.

  • Eukaryotic ribosomes are larger and rely on a Kozak sequence (e.g., A/G NNAUGG) for recognition and initiation instead of a Shine-Dalgarno sequence.

  • Circular translation structure due to interactions between the 5' cap and poly A tail.

  • Reading Frame: Every AUG establishes a new reading sequence; multiple reading frames can arise from alternate DNA structures.

DNA Mutations

Classification of Point Mutations

  • Missense Mutation:

    • Switches one amino acid for another.

  • Nonsense Mutation:

    • Codon change results in a premature stop codon, terminating protein synthesis early.

  • Silent Mutation:

    • Change in nucleotide that does not affect the amino acid sequence.

Indel/Frameshift Mutations

  • Result from insertions or deletions of nucleotides that shift the reading frame, affecting downstream protein synthesis.

Effects of DNA Mutations

  • Replication Errors:

    • Include misincorporation of nucleotides and slippage during DNA replication.

  • Tautomeric Shifts:

    • Bases can exist in tautomeric forms leading to incorrect pairings.

  • Depurination and Deamination:

    • Loss of purines or deamination of cytosine can lead to point mutations.

  • Oxidative Damage:

    • Involves damage from reactive oxygen species leading to mutations.

Mutagens and Their Effects

  • Base Analogs:

    • Compounds resembling nitrogenous bases leading to tautomeric shifts.

  • Alkylating, Intercalating, and Adduct-forming Agents:

    • Chemicals that cause mutations by altering the DNA structure.

  • UV Radiation:

    • Can cause thymine dimers which interfere with DNA replication.

  • Ionizing Radiation:

    • Such as X-rays that cause breaks in DNA.

DNA Repair Mechanisms

  • DNA Polymerase:

    • Has proofreading abilities to remove and replace incorrect nucleotides.

  • Mismatch Repair:

    • Exonuclease and endonuclease activities correct mismatched bases.

  • Base and Nucleotide Excision Repair:

    • Removal of damaged bases or nucleotides to preserve DNA integrity.

  • Post-replication Repair and SOS Mechanisms:

    • Homologous recombination and the SOS response act as last resort repair methods in high mutation contexts.

Eukaryotic Gene Organization

  • Levels of Organization:

    • Transcriptional, RNA Processing, and Transport.

  • Transcription Regulation:

    • Involves tightly wrapped DNA around histones limited gene expression.

  • Cis and Trans Acting Regulation:

    • Cis-regulatory regions are on the same chromosome, while trans-regulatory are separated by distance.

Enhancers and Silencers

  • Enhancers:

    • Regulatory elements that can be far away from the gene they regulate.

  • Silencers:

    • Elements that can turn off gene expression.

mRNA Processing and Degradation

  • 5' Cap and 3' Poly A Tail:

    • Required for mRNA stability, transport, and translation initiation.

  • mRNA Degradation Mechanism:

    • Involves short RNA segments (e.g., microRNA) that regulate mRNA stability.