Molecular Biology

How DNA is copied, read and regulated, and how we now edit it

About this course

The central dogma worked through experiment — replication, fidelity and repair, transcription, the genetic code and translation — then gene regulation in bacteria and eukaryotes, and the tools from recombinant DNA to CRISPR.

What you will be able to do

  • Describe the experiments that established DNA as the genetic material and its semiconservative replication
  • Explain how replication fidelity is achieved and how DNA damage is repaired
  • Trace a eukaryotic gene from transcription through processing to a translated protein
  • Model the lac operon as a regulatory switch and compare it with eukaryotic regulation
  • Explain how PCR, recombinant DNA and CRISPR are used to read and edit genes

What this course covers

  • Griffith's Transformation and the Transforming Principle
  • Avery's Purification and Three Lines of Evidence
  • Hershey–Chase Experiment: Proof by Counting Atoms
  • Chargaff's Rules: Fixed and Free Ratios
  • Franklin's Photograph and the Watson–Crick Double Helix
  • Rise per Base Pair and Genome Length
  • Integrative Worked Example: Reading a DNA Sample Backwards
  • Repressor occupancy and the core switch
  • Facilitated diffusion and the repressor search
  • Hill function and switch steepness
  • Why ten repressors, not one
  • Positive feedback, bistability, and cellular memory
  • Generality of the four numbers and the capstone worked example
  • Two-input AND gate and the cost–benefit switch
  • Restriction enzymes: sites, fragments, and selection
  • Origins of molecular biology tools
  • CRISPR guide specificity and off-target neighborhood
  • DNA repair outcomes and knockout arithmetic
  • Why 53% efficiency is a revolution, not a failure
  • Cas9 PAM search time and copy-number dependence
  • First CRISPR medicine: cutting an enhancer for sickle cell
  • RNA polymerase transcription rate and pausing
  • Promoter as a probability score
  • Steady-state mRNA copy number: rate × lifetime
  • Measuring mRNA half-life and the kinetics of response
  • Transcriptional bursting and the Fano factor
  • Integrated one-gene budget: four rates unified
  • The triplet code: word length and surplus
  • Open reading frames and stop-codon statistics
  • Fixed reading frame and frameshift mutations
  • Cracking the code: experimental decipherment
  • Wobble: loose reading of the third codon position
  • Mutation classes: silent, nonsense, and missense rates
  • The shuffle experiment: the code is not arbitrary
  • Balancing selection and the sickle allele
  • Why single-base changes vary in impact
  • Reading-frame rule separating two dystrophinopathies
  • Limits of exon-skipping therapy
  • CAG repeat as a disease clock and expanding walk
  • Two-hit kinetics: hereditary vs. sporadic cancer
  • mRNA vaccine as a message with a chosen lifetime
  • Disease as a number gone wrong; medicine as that number used
  • Chromatin packing levels and ratios
  • Nucleosome as a site dimmer
  • Histone marks and the writer-reader copying loop
  • Bistability and failure rate of chromatin memory
  • DNA looping and enhancer–promoter communication
  • Enhancer logic: combination specificity
  • Enhancer computation: stripe formation from four gradients
  • Semi-conservative replication and Meselson–Stahl experiment
  • Replication fork speed and origin arithmetic
  • Lagging strand synthesis and Okazaki fragments
  • The end-replication problem and telomere counting
  • Integrated S-phase budget: one cell worked example
  • Ribosome translation rate and error rate
  • Division of proofreading labor between two machines
  • Kinetic proofreading: squaring discrimination
  • Energy cost of translation: four ATP per peptide bond
  • Ribosome fleet sizing: output divided by speed
  • Ribosome self-replication and the growth-rate ceiling
  • Polysome traffic model and per-message yield ceiling
  • The Human Genome Budget
  • Conservation as Missing Mutations
  • Functional Fraction vs. Biochemical Activity
  • The C-Value Paradox and Genome Size
  • Complexity Beyond Gene Count
  • Writing and Reading a Genome
  • Handoff: Clock, Energetics, and Three Filters
  • The three-rung fidelity ladder
  • Strand discrimination in mismatch repair
  • The human mutation count reconciled
  • Spontaneous DNA damage as a continuous rate
  • Repair diseases as computable rate multipliers
  • Five DNA repair systems
  • Thymine, uracil, and CpG hypermutability
  • microRNA seed: targets, dimming, and design
  • Target titration and the copy-count threshold
  • Intrinsic vs. extrinsic noise and the two-color decomposition
  • Cell design around a noise floor of one-third
  • Lifetime ratio as a noise filter and its response-time cost
  • Integrated single-gene worked example
  • Post-transcriptional regulation: lecture summary and habits
  • PCR: exponential amplification, efficiency, and plateau
  • PCR contamination risk and sensitivity as dual-edged number
  • Primer specificity: the N/4^K search
  • DNA sequencing: Sanger termination and sequencing by synthesis
  • Coverage as a Poisson distribution
  • Genome assembly and the repeat problem
  • The eukaryotic gene in pieces
  • Context supplements the splice signal
  • Splice-site information content and decoys
  • Alternative splicing and combinatorial isoforms
  • Co-transcriptional splicing and nuclear timeline
  • Nonsense-mediated decay and the faulty-message race
  • The gene budgeted: full nuclear lifecycle

Syllabus

  1. DNA and Its Replication

    1. L1 · The Molecule, Proved
    2. L2 · Copying: Semiconservative, and the Machine
    3. L3 · Getting It Right: Fidelity and Repair
    4. L4 · PCR, and Reading the Molecule

  2. From Gene to Protein

    1. L5 · Transcription
    2. L6 · The Code, Cracked
    3. L7 · Translation, and the Cost of a Protein
    4. L8 · Processing and the Eukaryotic Gene

  3. Gene Regulation

    1. L9 · The Operon: A Switch, Modelled
    2. L10 · Eukaryotic Regulation: Chromatin, Enhancers, Combinations
    3. L11 · RNA in Control: Small RNAs, Riboswitches, and Noise

  4. Engineering, Medicine and Genomes

    1. L12 · Recombinant DNA to CRISPR
    2. L13 · The Molecule in Disease and Medicine
    3. L14 · Genomes, and Where This Leads