Genome and Chromosome Structure Quiz

Genome Structure and Function

• Genome: The complete genetic material of an organism, composed of nucleotides.
• Transposable Elements: DNA sequences that can move within a genome ("jumping genes").
• C-Value Paradox: Genome size does not directly correlate with organismal complexity.
• Repetitive Sequences: Occur in various forms:
  • Highly Repetitive: Multiple copies (e.g., satellite DNA).
  • Moderately Repetitive: Functional sequences (e.g., rRNA genes).
  • Tandem Repeats: Short sequences repeated in a row (e.g., Alu elements).

Chromosome Structure and Compaction

• Bacterial Chromosome:
  • Compacted by supercoiling.
  • Negative Supercoiling: DNA unwound (left-handed twist), aiding replication and transcription. Achieved by DNA gyrase.
  • Positive Supercoiling: DNA overwound (right-handed twist) relaxed by topoisomerase I.
  • Looped Domains: Organized by nucleoid-associated proteins (NAPs) into micro and macrodomains.
• Eukaryotic Chromosome:
  • Chromatin: DNA-protein complex.
    • Euchromatin: Less condensed; transcriptionally active.
    • Heterochromatin: Highly condensed; inactive.
      • Constitutive Heterochromatin: Always condensed; found at centromeres.
      • Facultative Heterochromatin: Variable condensation; location can change.

Chromosome Compaction Steps

• DNA Double Helix: Basic structure.
• Nucleosome: DNA wrapped around histone proteins.
• Zigzag/30 nm Fiber: Nucleosomes further compacted.
• Looped Domains: Formed by CTCF and SMC proteins.
• Heterochromatin: Compaction of loops.
• Metaphase Chromosome: Highest compaction during cell division.

DNA Replication Models

• Conservative: Parental DNA stays together; daughter strands are entirely new.
• Semi-Conservative: Each new DNA molecule has one original strand and one new strand (confirmed by Meselson-Stahl experiment).
• Dispersive: Original and new DNA segments are interspersed within both strands.

DNA Replication Process

• Initiation: Begins at oriC in E.coli; DnaA proteins bind to DnaA box sequences. AT-rich regions unwind easily.
• Unwinding: Helicase unwinds DNA; SSBPs stabilize separated strands; Topoisomerase relieves tension.
• Primer Synthesis: Primase synthesizes short RNA primers to start DNA synthesis.
• Elongation: DNA polymerase III extends strands, proofreading; Leading strand synthesized continuously; Lagging strand synthesized discontinuously as Okazaki fragments.
• Primer Removal and Gap Filling: DNA polymerase I removes primers, fills gaps; DNA ligase joins Okazaki fragments.

Challenges in Eukaryotic Replication

• Large DNA Volume: Multiple replication origins manage the task (pulse-chase experiment).
• Chromosome End Problem: Telomerase adds repetitive sequences to telomeres to prevent loss.

Transcription (RNA Synthesis)

• Overview of RNA Types:

  • mRNA: Carries genetic instructions.
  • tRNA: Transfers amino acids.
  • rRNA: Forms ribosomes.
  • snRNA: Involved in splicing.

• Prokaryotic Transcription:

  • Initiation: RNA polymerase holoenzyme binds to promoter region (Pribnow box).
  • Elongation: Core RNA polymerase adds rNMPs.
  • Termination:
    • Rho-Independent: GC hairpin loop and U-rich sequence cause detachment.
    • Rho-Dependent: Rho protein binds, stopping transcription.

• Eukaryotic Transcription:

  • Initiation: Transcription factors like TFIID bind promoter elements (TATA box) recruiting RNA Polymerase II.
  • Elongation: Produces hnRNA (pre-mRNA), including introns.
  • Termination: Polyadenylation signal (AAUAAA) sequence signals end; cleavage occurs downstream.

• RNA Polymerases in Eukaryotes:

  • Polymerase I: rRNA synthesis
  • Polymerase II: mRNA synthesis
  • Polymerase III: tRNA and 5S rRNA synthesis

hnRNA Processing (Eukaryotes)

• Capping: 5' cap added for stability and ribosome recognition.
• Polyadenylation: Poly-A tail added to 3' end for stability.
• Splicing: Introns removed; exons joined by snRNPs (lariat formed).

Gene Function and Hypotheses

• Genes: Segments of DNA encoding instructions for making proteins.
• Theories and Experiments:
  • Garrod: Inborn errors of metabolism link genes to enzymes.
  • Beadle and Tatum: "One gene-one enzyme" hypothesis (refined to "one gene-one polypeptide").

Degenerate Code and Triplet Codons

• Degenerate Code: Most amino acids have more than one codon.
• Triplet Codons: Three nucleotides per codon; 64 combinations, enough for 20 amino acids.

tRNA and the Wobble Hypothesis

• tRNA: Carries amino acids to ribosomes (matching anticodons to mRNA codons).
• Wobble Hypothesis: Flexible base pairing at the third codon position reduces the number of tRNA molecules needed.

Translation

• Initiation: Small ribosomal subunit binds mRNA and initiator tRNA.
  • Prokaryotes: Initiator tRNA carries N-formylmethionine; Shine-Dalgarno sequence.
  • Eukaryotes: Initiator tRNA uses 5' cap and poly-A tail.
• Elongation: Charged tRNA enters A site; peptide bonds form (catalyzed by peptidyl transferase).
• Termination: Release factors recognize stop codons; ribosome complex disassembles.