Library Core Topics
Foundational Science Series

Core Topics: Molecular Biology & Genetics

High-yield reference for DNA replication, transcription, translation, gene regulation, mutations, and epigenetics — mapped to USMLE Step 1/2 CK foundational science objectives.

How to Use This Resource

Each topic section includes: Core Concepts (foundational knowledge), Key Enzymes/Components (mechanistic details), and High-Yield Facts (exam-focused pearls). Use for active recall, spaced repetition, and integration with clinical cases.

DNA Structure & Replication

Semiconservative replication, bidirectional forks, and repair mechanisms

DNA Structure
  • Double helix: Antiparallel strands (5'→3' / 3'→5')
  • Base pairing: A-T (2 H-bonds), G-C (3 H-bonds)
  • Major/minor grooves: Protein binding sites
  • Chromatin: Nucleosomes (DNA + histones H2A/B, H3, H4)
  • Heterochromatin: Condensed, transcriptionally silent
  • Euchromatin: Open, transcriptionally active
Replication Machinery
DNA Pol III (prok) / δ,ε (euk)
Main synthesis; 3'→5' proofreading
DNA Pol I (prok)
Removes RNA primers; fills gaps
Helicase
Unwinds DNA at replication fork
Primase
Synthesizes RNA primers
Ligase
Joins Okazaki fragments
Topoisomerase
Relieves supercoiling ahead of fork
DNA Repair
  • Mismatch repair: Post-replication errors (MSH2/6)
  • Base excision repair: Damaged bases (glycosylases)
  • Nucleotide excision repair: Bulky lesions (e.g., thymine dimers); defective in xeroderma pigmentosum
  • Double-strand break repair: Homologous recombination (BRCA1/2) or non-homologous end joining
  • Telomeres: TTAGGG repeats; maintained by telomerase (active in stem cells, cancer)
High-Yield: DNA Replication
Directionality
Replication fork moves 5'→3' on template; new strand synthesized 5'→3'
Leading vs Lagging
Leading: continuous; Lagging: Okazaki fragments (100-200 nt in eukaryotes)
Proofreading
DNA polymerase has 3'→5' exonuclease activity; RNA polymerase does NOT
Eukaryotic vs Prokaryotic
Eukaryotes: multiple origins, slower; Prokaryotes: single origin, faster

Transcription

RNA synthesis, processing, and regulation in prokaryotes vs eukaryotes

RNA Polymerases
  • RNA Pol I: rRNA (28S, 18S, 5.8S)
  • RNA Pol II: mRNA, snRNA, miRNA ← Most tested!
  • RNA Pol III: tRNA, 5S rRNA
  • Promoters: TATA box (~-25), CAAT box (~-75)
  • Enhancers: Distal regulatory elements; bind activators
Regulation & Processing
  • Transcription factors: TFIID (binds TATA), activators/repressors
  • 5' capping: 7-methylguanosine; protects mRNA, aids export/translation
  • 3' polyadenylation: AAUAAA signal; poly-A tail stabilizes mRNA
  • Splicing: Introns removed by spliceosome (snRNPs: U1, U2, U4/U6, U5)
  • Alternative splicing: One gene → multiple proteins (e.g., troponin, Ig)
Prokaryote vs Eukaryote
FeatureProkaryoteEukaryote
CompartmentalizationCoupled transcription/translationNuclear separation
mRNA processingNone (polycistronic)Capping, splicing, poly-A
Ribosome bindingShine-Dalgarno sequence5' cap scanning (Kozak)
RNA Pol inhibitorsRifampinα-Amanitin (Pol II)
High-Yield: Transcription
Key Mnemonic
RNA Pol II = mRNA (II has 2 letters like "mRNA")
Splice Site Mutations
Cause aberrant splicing → disease (e.g., β-thalassemia)
No Proofreading
RNA polymerase lacks 3'→5' exonuclease → higher error rate
α-Amanitin
Death cap mushroom toxin; inhibits RNA Pol II → liver failure

Translation

Genetic code, ribosome function, and protein maturation

Genetic Code
  • Triplet codons: 64 total; 61 sense, 3 stop
  • Start: AUG → Methionine (euk) / N-formyl-Met (prok)
  • Stop: UAA, UAG, UGA ("U Are Away", "U Are Gone", "U Go Away")
  • Degenerate: Multiple codons → same amino acid
  • Wobble: 3rd base flexibility; one tRNA recognizes multiple codons
tRNA & Ribosome
  • tRNA structure: Cloverleaf; anticodon loop, amino acid acceptor stem
  • Aminoacyl-tRNA synthetases: Attach correct AA to tRNA (ATP-dependent); high fidelity
  • Ribosome: Prok: 70S (50S+30S); Euk: 80S (60S+40S)
  • Sites: A (aminoacyl), P (peptidyl), E (exit)
Translation Stages
  • Initiation: Small subunit + initiator tRNA + mRNA → large subunit joins
  • Elongation: Codon recognition → peptide bond → translocation (EF-Tu/GTP, EF-G/GTP)
  • Termination: Release factors bind stop codon → polypeptide release
  • Post-translational mods: Phosphorylation, glycosylation, ubiquitination, cleavage
  • Protein folding: Chaperones (HSPs) prevent aggregation; misfolding → disease
High-Yield: Translation
Start Codon
AUG = Methionine (euk); N-formylmethionine (prok)
Ribosome Binding
Prok: Shine-Dalgarno; Euk: Kozak sequence (GCCACC)
Antibiotic Targets
Aminoglycosides (30S) cause misreading; Chloramphenicol (50S) blocks peptidyl transferase
Toxins
Diphtheria toxin inactivates EF-2 → blocks translocation

Gene Regulation

Transcriptional control in prokaryotes and eukaryotes

Prokaryotic Regulation
  • Lac operon: Inducible; lactose inactivates repressor → transcription ON
  • Trp operon: Repressible; tryptophan activates repressor → transcription OFF
  • Negative regulation: Repressor blocks RNA Pol
  • Positive regulation: Activator (CAP-cAMP) enhances RNA Pol binding
  • Attenuation: Premature termination based on Trp levels (trp operon)
Eukaryotic Regulation
  • Transcription factors: Activators recruit co-activators (HATs); repressors recruit HDACs
  • Chromatin remodeling: SWI/SNF complex repositions nucleosomes
  • DNA methylation: CpG islands → gene silencing (imprinting, X-inactivation)
  • Enhancers/silencers: Distal elements loop to interact with promoter
  • Hormonal regulation: Steroid receptors → direct DNA binding; peptide hormones → kinase cascades → TF activation
Regulatory RNAs
  • miRNA: Binds 3' UTR → mRNA degradation or translational repression
  • siRNA: Exogenous dsRNA → RISC-mediated cleavage (RNAi)
  • lncRNA: Scaffolds chromatin modifiers; Xist mediates X-inactivation
  • Therapeutic potential: RNAi drugs (patisiran), antisense oligonucleotides

Mutations

Types, mechanisms, and clinical correlations

Mutation Types
Silent
Codon change → same AA (degeneracy)
Missense
Codon change → different AA (e.g., sickle cell)
Nonsense
Codon → premature STOP; truncated protein
Frameshift
Insertion/deletion ≠3 nt; alters all downstream codons
Splice Site
Disrupts intron removal → aberrant mRNA
Trinucleotide Repeat
Expansion → anticipation (Huntington, Fragile X)
Chromosomal Abnormalities
  • Deletion: Loss of segment (Cri-du-chat: 5p-)
  • Duplication: Extra copy (Charcot-Marie-Tooth: PMP22 dup)
  • Inversion: Reversed segment; may disrupt genes at breakpoints
  • Translocation: Exchange between non-homologous chromosomes
  •   • Reciprocal: CML t(9;22) → BCR-ABL fusion
  •   • Robertsonian: Acrocentric fusion (Down syndrome)
  • Mutagens: Chemical (alkylating agents), radiation (UV→thymine dimers), biological (retroviruses)
Transition vs Transversion
TypeDefinitionExample
TransitionPurine→Purine or Pyrimidine→PyrimidineA↔G or C↔T
TransversionPurine↔PyrimidineA→C, G→T, etc.

Note: Transitions are ~2x more common due to tautomeric shifts and deamination.

High-Yield: Mutations
Sickle Cell
Point mutation: GAG→GTG; Glu→Val at β⁶; hydrophobic interaction → polymerization
Nonsense Mutations
Create premature STOP codons → truncated, nonfunctional protein
Frameshift Severity
Most severe: alters entire downstream sequence; often premature STOP
Anticipation
Worsening disease in successive generations due to trinucleotide repeat expansion (e.g., Huntington)

Epigenetics

Heritable changes in gene expression without DNA sequence alteration

DNA Methylation
  • Mechanism: Methyl group added to cytosine in CpG islands (promoters)
  • Effect: Gene silencing — recruits methyl-binding proteins → HDACs → condensed chromatin
  • Clinical: Hypermethylation of tumor suppressors in cancer; hypomethylation → genomic instability
  • Drugs: Azacitidine, decitabine (DNMT inhibitors) for MDS/AML
Histone Modifications
Acetylation (HATs)
Neutralizes + charge on lysine → relaxed chromatin → gene activation
Deacetylation (HDACs)
Restores + charge → condensed chromatin → gene silencing
Methylation (HMTs)
Context-dependent: H3K4me = activation; H3K9me/H3K27me = repression
Genomic Imprinting
  • Definition: Parent-of-origin-specific gene expression via epigenetic marks
  • 15q11-13 region: Critical for Prader-Willi/Angelman syndromes
  • Prader-Willi: Loss of paternal 15q11-13 → hypotonia, hyperphagia, obesity
  • Angelman: Loss of maternal 15q11-13 → severe ID, ataxia, inappropriate laughter
  • Mechanisms: Deletion, uniparental disomy (UPD), imprinting center defect
High-Yield: Epigenetics
Methylation Rule
Methylation = Silencing; Acetylation = Activation
Imprinting Mnemonic
Prader-Willi = Paternal; Angelman = Maternal (same deletion, different parent)
X-Inactivation
Lyonization: Random X silenced in females; Barr body = inactive X; Xist lncRNA mediates
Epigenetic Inheritance
Marks can be mitotically (and sometimes meiotically) heritable without DNA change
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Evidence & Further Reading