Molecular Genetics: DNA, RNA, Transcription, Translation, Mutations, and Gene Regulation

DNA Structure

Nucleotides

DNA is composed of repeating units called nucleotides, each consisting of three components:

• Nitrogen bases: Four types should be named

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Cytosine (C), Thymine (T)

• Deoxyribose: A five-carbon sugar

• Phosphoric acid: Forms the backbone of DNA

DNA strands are differentiated by their directionality: 5' to 3' and 3' to 5'.

• Double helix: DNA consists of two antiparallel strands twisted into a helix.

• Antiparallel: The two strands run in opposite directions (5' to 3' and 3' to 5').

• Hydrogen bonds form between complementary nitrogen bases (A-T, G-C).

• Covalent bonds (phosphodiester bonds) connect the sugar and phosphate groups in the backbone.

RNA vs DNA

Key Differences

RNA and DNA are both nucleic acids but differ in several important ways:

• RNA is single-stranded, while DNA is double-stranded.

• RNA contains uracil instead of thymine.

• RNA has ribose sugar; DNA has deoxyribose.

Transcription

Process Overview

Transcription is the synthesis of RNA from a DNA template.

• Initiation:

  • Transcription factors bind to the promoter region (often includes a TATA box).

  • RNA polymerase binds and begins RNA synthesis (only builds in the 5' to 3' direction).

• Elongation: RNA polymerase synthesizes pre-mRNA by adding nucleotides.

• Termination:

  • Occurs at a terminator sequence.

  • RNA polymerase detaches from the DNA.

RNA Processing

Post-Transcriptional Modifications

• Pre-mRNA is processed before becoming mature mRNA.

• Spliceosome (contains snRNPs) removes introns and joins exons.

• Alternative splicing allows for different proteins from the same gene.

• Mature mRNA receives a 5' methyl cap and a 3' poly-A tail for stability and export.

Translation

Protein Synthesis

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

• Mature mRNA is read by the ribosome.

• Ribosome has three sites:

  • A site: Accepts incoming tRNA

  • P site: Holds tRNA with growing polypeptide

  • E site: tRNA exits

• Aminoacyl tRNA synthetase attaches amino acids to tRNA.

• tRNA molecules bring amino acids; can be charged (with amino acid) or uncharged.

• Start codon (AUG) initiates translation.

• Codons: Three-nucleotide sequences on mRNA; wobble allows flexibility in base pairing.

• Anticodon: Sequence on tRNA complementary to mRNA codon.

• Polypeptide: Chain of amino acids formed during translation.

• GTP provides energy for translation steps.

Mutations

Types of Mutations

Mutations are changes in the DNA sequence that can affect protein structure and function.

• Point mutations:

  • Missense: Changes one amino acid; may affect protein function.

  • Nonsense: Changes a codon to a stop codon; results in truncated protein.

  • Silent: No change in amino acid; usually no effect.

• Frameshift mutations:

  • Deletion: Removes nucleotides; shifts reading frame.

  • Insertion: Adds nucleotides; shifts reading frame.

Gene Regulation in Eukaryotes

Mechanisms of Regulation

Gene expression in eukaryotes is controlled at multiple levels.

• Histone acetylation: Loosens DNA-histone interaction, promoting transcription.

• DNA methylation: Silences genes by adding methyl groups to DNA.

• Switches (e.g., Pitx1 in stickleback activity): Regulatory elements that control gene expression.

• Enhancers: DNA sequences that increase transcription by binding activators.

• Activators: Proteins that bind to enhancers and promote transcription.

Gene Regulation in Prokaryotes

Operon Model

Prokaryotic gene regulation often involves operons, which are clusters of genes under control of a single promoter.

• Promoter: DNA sequence where RNA polymerase binds.

• Operator: DNA segment where repressor binds.

• Regulatory gene: Codes for repressor protein.

• Repressor: Protein that inhibits transcription by binding to operator.

• Inducible operon (e.g., Lac operon):

  • Transcription is turned on in presence of inducer (e.g., lactose).

  • Conformational change in repressor prevents binding to operator.

• Repressible operon (e.g., Trp operon):

  • Transcription is turned off when corepressor is present (e.g., tryptophan).

Lac Operon Regulation

• Glucose and lactose levels regulate transcription.

  • When glucose is low and lactose is high, transcription is frequent.

  • cAMP (cyclic AMP) is a signal molecule; high when glucose is low.

  • cAMP binds to CAP (catabolite activator protein), which binds to promoter and increases transcription.

Operon Type	Regulation	Example
Inducible	Transcription ON in presence of inducer	Lac operon
Repressible	Transcription OFF in presence of corepressor	Trp operon

Summary Table: DNA vs RNA

Feature	DNA	RNA
Strands	Double	Single
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C

Key Equations

• Directionality of DNA/RNA synthesis: $5' \rightarrow 3'$

• cAMP formation: $\text{ATP} \xrightarrow{\text{Adenyl cyclase}} \text{cAMP} + 2\,P_i$

Example

Example of a Missense Mutation: Sickle cell anemia is caused by a missense mutation in the beta-globin gene, changing glutamic acid to valine.

Example of Lac Operon Regulation: In E. coli, when lactose is present and glucose is absent, the lac operon is activated, allowing the cell to metabolize lactose.