DNA Structure and Key Experiments

Discovery of DNA as Genetic Material

Understanding the structure and function of DNA was made possible by a series of landmark experiments and discoveries:

• Griffith: Demonstrated transformation in bacteria, suggesting a "transforming principle" (later identified as DNA).

• Hershey & Chase: Used bacteriophages to confirm that DNA, not protein, is the genetic material.

• Chargaff: Discovered that the amount of adenine (A) equals thymine (T), and guanine (G) equals cytosine (C) in DNA.

• Franklin: Used X-ray diffraction to reveal the helical structure of DNA.

• Watson & Crick: Proposed the double helix model of DNA structure.

• Meselson & Stahl: Demonstrated semiconservative replication of DNA.

DNA Structure

DNA is a double helix composed of two antiparallel strands. The sugar-phosphate backbone is on the outside, and nitrogenous bases are on the inside.

• Antiparallel: One strand runs 5'→3', the other 3'→5'.

• Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U in RNA).

• Purines: Adenine (A), Guanine (G).

• Base Pairing: A=T (2 hydrogen bonds), G≡C (3 hydrogen bonds).

DNA Replication

Mechanism of Replication

DNA replication is semiconservative, meaning each new DNA molecule consists of one old and one new strand. Replication begins at origins, forming bubbles and forks, and proceeds bidirectionally.

• DNA Polymerase: Adds nucleotides only to the 3' OH end; synthesizes DNA 5'→3'; reads template 3'→5'.

• Leading Strand: Synthesized continuously.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments.

• Prokaryotes: Circular DNA, one origin.

• Eukaryotes: Linear chromosomes, many origins.

Key Enzymes in Replication

• Helicase: Unzips the DNA helix.

• Single-Strand Binding Proteins (SSB): Stabilize unwound DNA.

• Topoisomerase: Relieves supercoiling ahead of the fork.

• Primase: Synthesizes RNA primers.

• DNA Polymerase: Builds DNA and proofreads.

• Ligase: Seals Okazaki fragments.

DNA Repair

• Proofreading: DNA polymerase corrects errors during replication.

• Mismatch Repair: Corrects errors missed by proofreading.

• Nucleotide Excision Repair: Removes UV-induced damage.

• Unrepaired Damage: Leads to mutations.

Telomeres

• Function: Protect chromosome ends and prevent gene loss.

• Shortening: Telomeres shorten with each division; telomerase maintains length in germ cells, stem cells, and many cancer cells.

Central Dogma: DNA → RNA → Protein

DNA vs RNA

• DNA: Double-stranded, deoxyribose sugar, bases A, T, C, G.

• RNA: Single-stranded, ribose sugar, bases A, U, C, G.

Transcription

Transcription is the synthesis of RNA from a DNA template.

• Location: Nucleus (eukaryotes), cytoplasm (prokaryotes).

• Enzyme: RNA polymerase (no primer needed).

• Direction: RNA synthesized 5'→3'.

• Initiation: Promoter region signals start.

• Termination: Terminator sequence signals end.

RNA Processing (Eukaryotes)

• 5' Cap: Added to the 5' end for stability and ribosome binding.

• Poly-A Tail: Added to the 3' end for stability.

• Splicing: Introns removed, exons joined by the spliceosome.

• Alternative Splicing: Allows one gene to code for multiple proteins.

Translation and Mutations

Translation

Translation is the synthesis of proteins from mRNA at the ribosome.

• mRNA: Contains codons (three-base sequences).

• tRNA: Matches anticodons to codons and brings amino acids.

• Ribosome Sites: A (Arrival), P (Peptide), E (Exit).

• Start Codon: AUG (Methionine).

• Stop Codons: UAA, UAG, UGA.

• Steps: Initiation, elongation, termination; release factor frees the protein.

Protein Targeting

• Signal Peptide: Directs proteins to the endoplasmic reticulum (ER) via the signal recognition particle (SRP).

• Ribosomes: Free ribosomes synthesize cytosolic proteins; bound ribosomes synthesize secreted, membrane, and lysosomal proteins.

Mutations

• Point Mutation: Single base change.

• Silent Mutation: No amino acid change.

• Missense Mutation: Changes one amino acid.

• Nonsense Mutation: Introduces a stop codon.

• Insertion/Deletion: May cause frameshift, altering the reading frame (often severe).

Gene Regulation

Operons (Prokaryotes)

• lac Operon: Inducible; normally OFF, turned ON by lactose (allolactose); strongest expression when glucose is low.

• trp Operon: Repressible; normally ON, turned OFF by high tryptophan.

Positive Regulation

• Low Glucose: Increases cAMP, activates CAP (CRP), increases transcription.

• High Glucose: Decreases cAMP, reduces transcription.

Epigenetics

• Histone Acetylation: Loosens chromatin, genes ON.

• DNA Methylation: Tightens chromatin, genes OFF.

Regulatory Proteins

• Promoter: RNA polymerase binding site.

• Enhancer: Activator binding site.

• Activator: Increases transcription.

• Repressor: Decreases transcription.

RNA Regulation

• miRNA: Blocks translation or degrades mRNA.

• siRNA: Gene silencing.

• piRNA: Silences transposons.

• lncRNA: X chromosome inactivation.

CRISPR

• Guide RNA: Directs Cas9 to target DNA.

• Cas9: Cuts DNA for gene editing.

High-Yield Exam Facts and Vocabulary

• Replication: DNA → DNA, DNA polymerase, primer required, nucleus.

• Transcription: DNA → RNA, RNA polymerase, no primer, nucleus.

• Translation: RNA → Protein, ribosome.

• Chromosome Packing: DNA → histones → nucleosomes → chromatin → chromosomes.

• Key Terms: Origin, bubble, fork, template strand, daughter strand.

Developmental Biology Concepts

• Differentiation: Cells become specialized.

• Morphogenesis: Development of body shape.

• Cytoplasmic Determinants: Maternal molecules influencing development.

• Induction: Signals from neighboring cells affect development.

• Bicoid: Determines anterior/posterior axis in embryos.

• Pattern Formation: Organization of tissues and organs.

• Positional Information: Cells determine their location in the embryo.

Chromatin and Protein Regulation

• Histone Tails: Chemical modifications regulate gene expression.

• Proteasome: Degrades proteins tagged with ubiquitin.

Key Mnemonics

• Pure As Gold: Purines = A, G.

• CUT the PY: Pyrimidines = C, U, T.

• APE: Ribosome sites: Arrival, Peptide, Exit.

• DNA Pol needs primer; RNA Pol does not.

• DNA synthesis: 5'→3' only; DNA Pol adds to 3' end.

• Replication: Semiconservative, bidirectional, many origins in eukaryotes.

• Introns OUT, Exons stay.

• Alternative splicing: 1 gene → many proteins.

• Histone acetylation = ON; DNA methylation = OFF.

• dNTPs: DNA building blocks and energy source; pyrophosphate released when nucleotide added.

• Chromatin: DNA + histones; nucleosome = DNA wrapped around 8 histones.

Replication, Transcription, and Translation Comparison Table

Key Equations

• Base Pairing:

• Direction of Synthesis:

• Hydrogen Bonds: