Molecular Basis of Inheritance
⚑ Panic box
Base pairing — $A=T$ (2 H-bonds); $G\equiv C$ (3); strands are complementary and antiparallel.
Replication — semiconservative: each daughter DNA has one old and one new strand; synthesis runs $5'\to3'$.
Gene expression — DNA $\to$ RNA $\to$ protein; in some viruses, RNA $\to$ DNA.
Code — triplet, degenerate, nearly universal; AUG starts and codes Met; UAA/UAG/UGA stop.
1. DNA: structure and packaging
Nucleotide — nitrogenous base + pentose sugar + phosphate · nucleoside — base + sugar
Bases — purines: A, G · pyrimidines: C, T, U · DNA has T; RNA has U and a 2′-OH group
Chain links — base–sugar: N-glycosidic · phosphate–sugar: phosphoester · nucleotides: 3′–5′ phosphodiester
Polarity — 5′ end has free phosphate · 3′ end has free OH · sugar–phosphate backbone; bases project inward
| DNA feature | Key point | Recall check |
|---|---|---|
| Strands | Two, right-handed helix; antiparallel | One runs $5'\to3'$, other $3'\to5'$ |
| Pairing | $A=T$; $G\equiv C$ | Purine pairs with pyrimidine |
| Chargaff rule | $A=T$, $G=C$; total purines = pyrimidines | In double-stranded DNA |
| Dimensions | 0.34 nm per bp; 3.4 nm per turn | About 10 bp per turn |
| Stability | H-bonds + stacked base pairs | Complementary strands can re-form |
Packaging — prokaryotic DNA: protein-held loops in nucleoid · eukaryotic DNA: wraps around histone octamers → nucleosomes (~200 bp each) → chromatin fibre → condensed chromosome
Histones — positively charged, lysine- and arginine-rich proteins · Euchromatin — loosely packed, active · Heterochromatin — tightly packed, usually inactive
2. Genetic material: evidence and properties
| Evidence | Experimental pattern | Conclusion |
|---|---|---|
| Griffith (1928) | Heat-killed virulent S + live non-virulent R → mice die; live S recovered | R cells transformed; factor not identified |
| Avery, MacLeod, McCarty | Protease/RNase do not stop transformation; DNase does | DNA is transforming principle |
| Hershey–Chase (1952) | $^{32}P$ labels phage DNA; $^{35}S$ labels protein; only DNA label enters bacteria | DNA, not protein, is inherited by infected bacteria |
Hershey–Chase logic — infect E. coli with labelled phages → blend off coats → centrifuge → radioactivity with bacterial pellet only for DNA-labelled phages
Genetic material must — replicate · remain sufficiently stable · allow mutation · express inherited traits
DNA vs RNA — DNA is less reactive and more stable (deoxyribose; T instead of U) → better information storage · RNA is reactive, less stable, and can act as messenger, adapter, structure or catalyst
RNA world — RNA likely preceded DNA: it could store information and catalyse reactions; more stable DNA later became the main information store
3. Replication
Semiconservative replication — each parental strand templates a complementary new strand; each daughter double helix contains one parental + one newly made strand
Meselson–Stahl — grow E. coli in $^{15}N$ → transfer to $^{14}N$ → separate DNA by CsCl density gradient: generation 1, all hybrid; generation 2, half hybrid and half light. This supports semiconservative copying.
| Replication feature | What to recall | Condition / consequence |
|---|---|---|
| DNA polymerase | DNA-dependent; adds deoxynucleotides | Synthesises only $5'\to3'$ |
| Substrates | Deoxyribonucleoside triphosphates | Building blocks and energy source |
| Replication fork | Local opening of long DNA helix | Whole molecule does not unwind at once |
| Leading strand | Continuous synthesis | Template runs $3'\to5'$ |
| Lagging strand | Discontinuous fragments; DNA ligase joins them | Template runs $5'\to3'$ |
| Origin | Specific DNA site where copying begins | Polymerase cannot initiate randomly |
Timing — eukaryotic DNA replication occurs in S phase · replication errors can cause mutations
4. Transcription and RNA processing
Transcription — copying one DNA segment, using one strand, into RNA · RNA is made $5'\to3'$; A pairs with U
| Transcription unit | Position / role |
|---|---|
| Promoter | Upstream; RNA polymerase binding; sets strand choice and direction |
| Structural gene | DNA region transcribed into RNA |
| Terminator | Downstream; signals transcription end |
Template strand — read $3'\to5'$; RNA is complementary · Coding strand — $5'\to3'$; same sequence as RNA except DNA has T where RNA has U
Transcription in bacteria — RNA polymerase binds promoter (initiation) → extends RNA (elongation) → reaches terminator and releases RNA (termination) · $\sigma$ helps initiation; $\rho$ helps termination
| Eukaryotic polymerase | Main transcripts |
|---|---|
| RNA polymerase I | 28S, 18S, 5.8S rRNA |
| RNA polymerase II | hnRNA, the mRNA precursor |
| RNA polymerase III | tRNA, 5S rRNA, snRNA |
hnRNA processing — splice out introns and join exons · add 5′ methyl-guanosine cap · add 3′ poly-A tail (about 200–300 A residues) → mature mRNA leaves nucleus
RNA roles — mRNA carries codons · tRNA brings amino acids and reads codons · rRNA forms ribosome structure and catalyses peptide-bond formation
Gene terms — Cistron: DNA segment coding for a polypeptide · Exons: retained in mature RNA · Introns: removed during processing · bacterial genes often polycistronic; eukaryotic structural genes usually monocistronic and split
5. Genetic code and translation
Genetic code — triplet (3 bases/codon) · 64 codons total: 61 amino-acid codons + 3 stops · degenerate (several codons may specify one amino acid) · contiguous, no punctuation · nearly universal
Start / stop — AUG: methionine and initiation · UAA, UAG, UGA: termination; no tRNA reads stop codons
Mutation pattern — single-base substitution can change an amino acid (β-globin Glu → Val in sickle-cell anaemia) · insertion/deletion of 1 or 2 bases shifts reading frame · insertion/deletion of 3 or a multiple changes whole codons but preserves downstream frame
| Translation component | Role | Distinguish it by |
|---|---|---|
| mRNA | Codon template | Codons are read in triplets |
| tRNA | Adapter; carries amino acid | Anticodon pairs with codon; amino-acid acceptor end |
| Ribosome | Binds mRNA; positions tRNAs | rRNA catalyses peptide-bond formation; bacterial 23S rRNA is a ribozyme |
| Release factor | Ends translation | Recognises stop codon; releases polypeptide |
Translation sequence — charge each tRNA with its amino acid using ATP → small ribosomal subunit binds mRNA at AUG with initiator tRNA → matching charged tRNAs enter as ribosome advances codon by codon → peptide bonds form → release factor recognises stop codon and frees polypeptide
Translational unit — mRNA sequence from start to stop codon · UTRs — untranslated regions before AUG and after stop; support efficient translation
6. Regulation: lac operon
Gene expression can be regulated — transcription · RNA processing · mRNA transport · translation (eukaryotes)
Operon — coordinated bacterial gene unit: shared promoter and regulatory control for related structural genes · transcription initiation is the main prokaryotic control point
| Lactose condition | Repressor / operator | Outcome |
|---|---|---|
| No lactose | Active repressor binds operator | Transcription blocked |
| Lactose or allolactose present | Inducer binds and inactivates repressor | RNA polymerase can transcribe operon |
| Lactose used up | Repressor becomes active again | Operon switches off |
lac operon parts — i: makes repressor · z: β-galactosidase, splits lactose · y: permease, increases β-galactoside entry · a: transacetylase
Inducer — lactose/allolactose, not glucose or galactose · repressor control is negative regulation; low baseline expression allows lactose entry
7. Human Genome Project
HGP — international genome-sequencing project launched in 1990; completed in 2003 · enabled by DNA sequencing, cloning and bioinformatics
Goals — identify human genes · sequence ~3 billion base pairs · store and analyse data · develop tools and transfer technology · address ethical, legal and social issues (ELSI)
Two approaches — EST: identify genes expressed as RNA · sequence annotation: sequence the whole genome, then assign functions to regions
Workflow — isolate DNA → make random fragments → clone/amplify in host using BAC or YAC vectors → sequence fragments → align overlaps computationally → annotate and assign to chromosomes
| Genome finding (chapter figures) | Recall value |
|---|---|
| Genome size | 3164.7 million bp |
| Protein-coding portion | Less than 2% |
| Human similarity | 99.9% of bases shared among people |
| Repeated DNA | Large fraction; often non-coding, useful for studying genome structure and variation |
| Gene count | About 30,000 in the chapter’s account; over half had unknown function |
| SNPs | About 1.4 million identified variable single-base sites |
SNP — single-nucleotide polymorphism · Bioinformatics — computational storage, retrieval and analysis of biological data
8. DNA fingerprinting
DNA polymorphism — inherited sequence variation in a population; conventionally, a variant at a locus occurs above 1% frequency
Basis — highly variable repetitive DNA (satellite DNA, including minisatellite VNTRs) differs in repeat number → DNA fragments differ in length → individual banding patterns
VNTR — tandem repeats with copy number varying among chromosomes; chapter range: 0.1–20 kb · pattern generally differs between people, except identical twins
Method — isolate DNA → cut with restriction enzymes → separate fragments by electrophoresis → blot onto nylon/nitrocellulose → hybridise labelled VNTR probe → detect bands by autoradiography
Uses — forensic identification · paternity disputes · population and genetic diversity studies · DNA from different tissues of one individual shares the same polymorphism pattern
9. Traps
DNA polymerase works in either direction→ DNA synthesis is only $5'\to3'$.Both DNA strands are transcribed→ one strand per transcription unit; two RNAs could be complementary and encode different products.Every codon has a matching tRNA→ stop codons have no tRNA; release factors terminate translation.All mutations shift the reading frame→ only insertions/deletions not in multiples of three shift it.Lactose permanently keeps lac operon on→ lactose depletion restores active repressor and shuts transcription down.