Biochemistry

A comprehensive course on biochemistry โ€” from amino acid chemistry and enzyme kinetics through glycolysis, the citric acid cycle, and oxidative phosphorylation to DNA replication, transcription, and gene regulation โ€” with full derivations, MathJax equations, and interactive tools.

Course Overview

Biochemistry is the study of the chemical processes that underpin life. This course develops a rigorous understanding of protein structure and enzyme catalysis, the metabolic pathways that harvest and store energy, and the molecular machinery of DNA replication, transcription, and translation. Following the tradition of Lehninger, Stryer, Voet, and Berg, every key equation is derived from first principles with full mechanistic detail.

What You Will Learn

  • โ— Amino acid structure, peptide bond formation, and protein folding thermodynamics
  • โ— Enzyme catalysis: Michaelis-Menten kinetics, inhibition, and allosteric regulation
  • โ— Glycolysis, the citric acid cycle, and oxidative phosphorylation โ€” ATP yield calculations
  • โ— Fatty acid oxidation, amino acid catabolism, and metabolic integration
  • โ— DNA replication fidelity, transcription regulation, and the genetic code
  • โ— Ribosomal translation, post-translational modifications, and gene expression control

Key Reactions & Equations

Peptide Bond: $\text{AA}_1\text{-COOH} + \text{H}_2\text{N-AA}_2 \rightarrow \text{AA}_1\text{-CO-NH-AA}_2 + \text{H}_2\text{O}$

Michaelis-Menten: $v = \frac{V_{\max}[\text{S}]}{K_M + [\text{S}]}$

ATP Hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i \quad \Delta G^\circ = -30.5\;\text{kJ/mol}$

Central Dogma: $\text{DNA} \xrightarrow{\text{replication}} \text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

๐Ÿงฌ

Part I: Proteins & Enzymes

Amino acid chemistry, enzyme catalysis and mechanisms, protein higher-order structure, folding thermodynamics and dynamics.

4 chapters โ†’
๐Ÿ”ฅ

Part II: Core Metabolism

Glycolysis, the citric acid cycle, oxidative phosphorylation and chemiosmotic coupling, gluconeogenesis and reciprocal regulation.

4 chapters โ†’
๐Ÿงซ

Part III: Metabolic Pathways

Fatty acid ฮฒ-oxidation and synthesis, amino acid catabolism, nucleotide biosynthesis, and metabolic integration across tissues.

4 chapters โ†’
๐Ÿงช

Part IV: Molecular Biology

DNA replication and repair, RNA transcription, ribosomal translation, and gene regulation โ€” operons, enhancers, and epigenetics.

4 chapters โ†’

Prerequisites & References

Prerequisites

  • โ€ข General chemistry (bonding, equilibrium, acid-base)
  • โ€ข Organic chemistry fundamentals (functional groups, stereochemistry)
  • โ€ข Introductory biology (cell structure, macromolecules)
  • โ€ข Basic thermodynamics and kinetics

Recommended Texts

  • โ€ข Nelson & Cox, Lehninger's Principles of Biochemistry
  • โ€ข Berg, Tymoczko & Stryer, Biochemistry
  • โ€ข Voet & Voet, Biochemistry
  • โ€ข Berg, Tymoczko, Gatto & Stryer, Biochemistry: A Short Course