Molecular Biology

Molecular Biology for the MCAT

Part 1 of 7 — DNA Replication

DNA Replication is Semiconservative

Each new double helix has one old strand and one new strand (proven by the Meselson-Stahl experiment using $^{15}$N heavy isotope labeling). After one round, all molecules were intermediate density. After two rounds, half intermediate and half light.

Replication Overview

• Bidirectional: Proceeds in both directions from each origin of replication
• Origins: Bacteria have one origin; eukaryotes have many (to speed up replication of much larger genomes)
• Direction: DNA polymerases can ONLY synthesize $5' \to 3'$ (add nucleotides to the free $3'$-OH)
• Antiparallel template: The template strand is read $3' \to 5'$

Key Enzymes — Complete Table

Leading vs. Lagging Strand

• Leading strand: Template runs $3' \to 5'$ → continuous synthesis toward the fork
• Lagging strand: Template runs $5' \to 3'$ → discontinuous synthesis AWAY from the fork → Okazaki fragments (~1000-2000 nt in bacteria, ~100-200 in eukaryotes)

Telomeres and Telomerase

• Telomeres: Protective caps at chromosome ends (TTAGGG repeats in humans)
• End replication problem: When the last RNA primer on the lagging strand is removed, DNA Pol cannot fill the gap (no upstream $3'$-OH) → telomere shortens each division
• Telomerase: Reverse transcriptase that uses an internal RNA template to extend telomeres
• Active in: stem cells, germ cells, cancer cells
• Inactive in: most somatic cells → cellular aging (Hayflick limit)

DNA Replication 🎯

Eukaryotic vs. Prokaryotic Replication — Comparison

Drugs Targeting DNA Replication (MCAT Favorites!)

Advanced Concepts 🎯

Key Takeaways — Part 1

• Semiconservative replication proven by Meselson-Stahl (heavy isotope experiment)
• DNA Pol III: $5' \to 3'$ synthesis, $3' \to 5'$ proofreading — needs a primer (3'-OH)

Molecular Biology for the MCAT

Part 2 of 7 — Transcription

The Central Dogma

$\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}$

Molecular Biology for the MCAT

Part 3 of 7 — Translation (Protein Synthesis)

The Genetic Code — Properties

• 64 codons = 4 bases in groups of 3 ($4^3 = 64$)
• 61 sense codons (amino acids) + 3 stop codons (UAA, UAG, UGA)
• Start codon: AUG = methionine (also signals ribosome binding in eukaryotes; fMet in prokaryotes)
• Degenerate (redundant): Multiple codons per amino acid (especially at 3rd "wobble" position)
• NOT ambiguous: Each codon specifies exactly ONE amino acid
• Universal (nearly): Same code in almost all organisms (minor exceptions in mitochondria)

Wobble Position — Why Degeneracy Matters

The 3rd base of a codon has "relaxed" base-pairing rules:

• One tRNA can recognize multiple codons that differ only at position 3
• This is why most synonymous mutations (silent) occur at position 3
• Wobble pairing: G-U is allowed at position 3 (not normally allowed elsewhere)

Ribosome Structure and Sites

Molecular Biology for the MCAT

Part 4 of 7 — Gene Regulation

Why Gene Regulation Matters

Every cell has the same DNA, but a neuron looks and acts nothing like a liver cell. Differential gene expression — not different genes — explains cell specialization. The MCAT tests regulation at every level.

Prokaryotic Gene Regulation: The Operon Model

Lac Operon (inducible — normally OFF):

• Structural genes: lacZ (beta-galactosidase), lacY (permease), lacA (transacetylase)
• Without lactose: Repressor (lacI product) binds operator → blocks RNA Pol → genes OFF
• With lactose: Allolactose (isomer of lactose) binds repressor → conformational change → repressor falls off → genes ON
• Dual control: Low glucose → high cAMP → cAMP-CAP binds promoter → enhanced transcription
• Maximum expression: lactose present (repressor off) + glucose absent (cAMP-CAP active)

Trp Operon (repressible — normally ON):

• Without tryptophan: Repressor inactive → genes ON (cell makes tryptophan)
• With tryptophan: Trp acts as corepressor → binds repressor → activates it → repressor binds operator → genes OFF
• Also regulated by attenuation: Secondary structures in mRNA leader sequence cause premature termination when trp is abundant

Eukaryotic Gene Regulation — Five Levels

Molecular Biology for the MCAT

Part 5 of 7 — Mutations & DNA Repair

Types of Point Mutations

Conservative vs. non-conservative missense: Replacing an amino acid with a chemically similar one (conservative, e.g., Leu → Ile) is less damaging than replacing with a dissimilar one (non-conservative, e.g., Glu → Val in sickle cell disease).

Frameshift Mutations

• Insertion or deletion of nucleotides NOT in multiples of 3 → shifts entire reading frame
• Every downstream codon is altered → usually nonfunctional protein
• Almost always more damaging than point mutations
• Insertions/deletions in multiples of 3 → add/remove amino acids WITHOUT shifting the frame

Transitions vs. Transversions

Molecular Biology for the MCAT

Part 6 of 7 — Biotechnology Techniques

PCR (Polymerase Chain Reaction)

Amplifies a specific DNA sequence exponentially from a tiny sample.

• After $n$ cycles: $2^n$ copies from one template molecule

Molecular Biology for the MCAT

Part 7 of 7 — Viruses & Recombinant DNA

Virus Structure & Classification

Viral Life Cycles

Lytic cycle: Virus replicates → lyses host cell → releases new virions Lysogenic cycle: Viral DNA integrates into host genome (prophage) → replicates with host → can switch to lytic

Retroviruses (HIV)

$\text{ssRNA} \xrightarrow{\text{Reverse transcriptase}} \text{dsDNA} \xrightarrow{\text{Integrase}} \text{Provirus (in host DNA)}$