Chapter 6 Notes (Genetics, Replication, Transcription, Translation, Regulation, Mutations, Recombination)

Genetic Material: Genome and Genes

  • Genetics: study of heredity; genome = sum of genetic material; gene = DNA segment that codes for a protein or RNA molecule.

  • Levels of study: organismal, chromosomal, molecular.

  • Genotype vs Phenotype: genotype = total genes; phenotype = traits expressed; not all genes are expressed at once.

Genome and Chromosome Organization

  • Genome: complete set of genetic material in an organism.

  • Chromosomes: discrete DNA packages.

  • Extra-genomic elements: plasmids (small, circular DNA), organellar DNA (mitochondria/chloroplasts) in eukaryotes with bacterial-like chromosomes.

  • Genomics: study of an organism’s entire genome.

Chromosome Structure: Eukaryotes vs Prokaryotes

  • Eukaryotes: linear chromosomes, nucleus, histones, diploid/haploid, multiple chromosomes.

  • Prokaryotes: usually a single circular chromosome, histone-like proteins (no canonical histones), no nucleus, often plasmids; nucleoid region; genome organized via loop domains, supercoiling, and DNA loops.

Genes and Genotype/Phenotype

  • Gene: DNA segment with information for a cellular function; may be structural (protein-coding), code for RNA machinery, or regulatory.

  • Types of genes: structural, regulatory, RNA-related.

  • The sum of all genes = genotype; phenotype results from expressed genes, environmental interaction, and regulation.

The Nature of the Genetic Material

  • Must self-replicate accurately; duplication/separation into daughter cells.

  • Levels: Genome, Chromosome, Gene.

  • Bacterial chromosomes lack histones.

The DNA Code: Nucleotides and Base Pairing

  • DNA basics: nucleotides consist of sugar (deoxyribose), phosphate, and a nitrogenous base.

  • Bases: Purines = A, G; Pyrimidines = C, T.

  • A pairs with T (2 hydrogen bonds); G pairs with C (3 hydrogen bonds).

  • DNA is double-stranded and antiparallel: one strand 5'→3', the other 3'→5'.

  • Backbone: sugar-phosphate; 5' end carries a phosphate; 3' end has a hydroxyl.

  • Only 4 bases; DNA sequences generate enormous diversity: 4^{n} possibilities for a sequence of length n.

DNA vs RNA

  • RNA uses ribose (has an -OH at C2) and uracil (U) instead of thymine (T).

  • DNA is typically double-stranded; RNA is usually single-stranded and more versatile structurally.

Antiparallel DNA and Base Pairing

  • Antiparallel arrangement: two strands run in opposite directions (5'→3' and 3'→5').

  • Base pairing held together by hydrogen bonds; base pairing enables strand separation during replication and transcription.

  • Hydrogen bonds: A–T (2 bonds); G–C (3 bonds).

DNA Replication: Semiconservative and Bidirectional

  • Semiconservative: each daughter molecule contains one old strand and one new strand. ext{Semiconservative replication: one old + one new strand per daughter}

  • Bidirectional: replication proceeds in two directions from the origin.

  • Key players: helicase (unwinds), primase (RNA primer), DNA polymerase III (extends new strand), DNA polymerase I (replaces primer), ligase (joins fragments), single-strand binding proteins (stabilize ssDNA), topoisomerase (relieves supercoiling).

  • Origin of replication (ori): AT-rich regions ease strand separation; bacteria typically have a single ori; eukaryotes have multiple origins.

  • Leading strand: synthesized continuously 5'→3' toward fork.

  • Lagging strand: synthesized discontinuously as Okazaki fragments (≈100–1000 bases long) 5'→3' away from fork; fragments joined by ligase.

  • RNA primer: laid down by primase to provide 3'OH for DNA polymerase.

  • Overall process: two replication forks form at ori and move bidirectionally; replication is highly accurate due to proofreading.

Enzymes and Steps in Replication (high level)

  • Helicase: unwinds double helix.

  • Single-strand binding proteins (SSB): stabilize exposed single strands.

  • Topoisomerases: relieve supercoiling tension.

  • Primase: lays down RNA primer.

  • DNA polymerase III: adds nucleotides to 3' end of primer; synthesizes new DNA in 5'→3' direction; leading strand continuous; lagging strand discontinuous.

  • DNA polymerase I: replaces RNA primer with DNA.

  • DNA ligase: seals nicks between Okazaki fragments.

  • Replication is semi-conservative and often described as bidirectional with two replisomes.

Replication in Linear Eukaryotic DNA

  • Similar principles but more complex; uses multiple DNA polymerases; linear chromosomes require telomere maintenance; replication occurs in S phase.

Central Dogma and Transcription/Translation

  • Central dogma: DNA → RNA → Protein; most organisms follow this flow.

  • Exceptions: RNA viruses and retroviruses; regulatory RNAs also influence gene expression.

  • RNA types directly involved in translation: mRNA, tRNA, rRNA; other regulatory RNAs (miRNA, siRNA, riboswitches, etc.).

From DNA to mRNA to Protein

  • Transcription: synthesis of mRNA from DNA template by RNA polymerase; promoter recognition; initiation, elongation, termination.

  • In bacteria: polycistronic mRNA (one transcript can encode >1 protein).

  • In eukaryotes: monocistronic mRNA (one gene, one protein); additional RNA processing required (promoter, enhancers, splicing, capping, poly-A tail).

  • mRNA codons read in triplets; codons specify amino acids; start codon: AUG; stop codons: UAA, UAG, UGA; universal code with wobble flexibility at third base.

  • tRNA: adaptor molecule; anticodon pairs with codon; carries specific amino acid.

  • Ribosome: large and small subunits (prokaryotes: 70S; eukaryotes: 80S); A site, P site, E site.

  • Translation initiation: ribosome assembles on mRNA; initiator tRNA (in bacteria) carries formyl-methionine (fMet) and recognizes start codon; elongation adds amino acids via peptide bonds; termination at stop codon releases polypeptide.

  • Post-translational modifications: folding and chemical modifications (methylation, phosphorylation, glycosylation, etc.).

The Genetic Code: Codons and Anticodons

  • Triplet code: 3 nucleotides in mRNA (codon) specify one amino acid.

  • Universality: code is largely universal across bacteria, archaea, eukaryotes, and many viruses.

  • Redundancy: multiple codons can code for the same amino acid (wobble at the 3' base of codon).

  • Start: AUG; formyl-Methionine in bacteria; Stop: UAA, UAG, UGA (nonsense codons).

Regulation of Protein Synthesis: Operons

  • Operon: a cluster of genes regulated as a unit; includes promoter, operator, regulator gene, and structural genes.

  • Inducible operons (e.g., lac): usually off; turned on by an inducer (substrate) that inactivates the repressor; enables transcription of multiple genes from a single polycistronic mRNA.

  • Repressible operons (e.g., trp/arginine pathway): usually on; turned off by a corepressor that activates the repressor.

  • Lac operon components: regulator gene (lacl), promoter (lacP), operator (lacO), structural genes lacZ, lacY, lacA; induction by lactose converting to allolactose; transcription produces a single mRNA encoding multiple enzymes.

  • Triggering conditions: lactose presence relieves repression; arginine presence can repress arginine-synthesis operon.

Mutations and Repair

  • Mutations: changes in the genetic code; can be point mutations (single base change) or frameshift (insertion/deletion).

  • Point mutations types: missense (different amino acid), nonsense (stop codon), silent (no amino acid change).

  • Frameshift: insertion/deletion shifts reading frame, usually nonfunctional protein.

  • Spontaneous vs induced mutations; mutations can be harmful or beneficial and drive evolution.

  • Repair mechanisms: proofreading by DNA polymerases; mismatch repair; base excision repair; nucleotide excision repair; photoreactivation.

  • Mutagen testing: Ames test used to screen for mutagenic chemicals.

DNA Recombination and Horizontal Gene Transfer

  • Recombination: transfer of DNA between organisms; yields recombinant organisms.

  • Plasmids: small, circular DNA elements that replicate independently and can move between cells; often carry useful traits (e.g., antibiotic resistance).

  • Horizontal gene transfer (HGT): transfer of genes between organisms, not via inheritance from parent to offspring.

  • Modes of HGT in bacteria:

    • Conjugation: donor with pilus transfers plasmid to recipient (direct contact).

    • Transformation: uptake of free DNA from environment by competent cells.

    • Transduction: phage-mediated transfer of DNA between bacteria; can be generalized or specialized.

  • Transposable elements (jumping genes): can move within a genome; insertions can disrupt genes or create new traits; include insertion sequences and retrotransposons.

  • Pathogenicity islands: groups of genes that enhance virulence; often acquired via HGT.

Beginning of Protein Synthesis (Overview)

  • Protein synthesis begins with transcription, followed by translation on ribosomes.

  • Translation requires mRNA, tRNA, ribosomes, and amino acids; three stages: initiation, elongation, termination.

  • Coupling in prokaryotes: transcription and translation can occur simultaneously in the cytoplasm.

Quick Reference Formulas and Key Points

  • Base pairing: A-T (2 H-bonds), G-C (3 H-bonds).

  • DNA strands are antiparallel: 5'→3' and 3'→5'.

  • Replication direction: 5'→3' for new strand synthesis.

  • Codons are read in triplets; start codon: AUG; stop codons: UAA, UAG, UGA.

  • Semiconservative replication: each daughter has one old and one new strand.

  • Inducible operon example: Lac operon; activated by lactose via allolactose.

  • Repressible operon example: Trp/Arg operon; turned off by corepressor buildup.

  • Major RNA types: mRNA, tRNA, rRNA (plus regulatory RNAs).

  • Universal genetic code is largely conserved across domains with wobble flexibility at the 3' base of codons.