Subject Guides

Subject Guide

Biochemistry

October 2024

For the undergraduate level, with basic graduate level exploration.

How to use this guide

  • Draw everything.
  • Do problems, don't just read.
  • Learn the lab bench.
  • Read papers after you do the core - make sure you learn how the field actually works.

Part 0: Basics

Calculus

Topics: derivatives, integrals, multivariable calculus, gradients, exponentials/logs, and basic differential equations.
Primary option: James Stewart, Calculus, or Thomas, Thomas' Calculus.

Statistics and Data Analysis

Topics: distributions, error bars, confidence intervals, regression, nonlinear curve fitting, p-values, multiple testing, and reproducibility.
Primary option: John Taylor, An Introduction to Error Analysis.
Biology/data alternative: Whitlock & Schluter, The Analysis of Biological Data.

Programming

Topics: Python or R, plotting, data cleaning, sequence files, curve fitting, and basic statistics packages.
Primary options: Python with NumPy/pandas/matplotlib, or R with tidyverse.

Physics

Topics: mechanics basics, electrostatics, magnetism, circuits, induction, waves, materials.
Primary option: Halliday, Resnick & Walker, Fundamentals of Physics, or Young & Freedman, University Physics.

Part 1: Chemistry Foundation

General Chemistry

Topics: atomic structure, bonding, equilibrium, acid-base chemistry, thermodynamics, kinetics, and redox.
Primary option: Zumdahl & Zumdahl, Chemistry, or Brown, LeMay, Bursten et al., Chemistry: The Central Science.

Organic Chemistry

Topics: stereochemistry, substitution/elimination, carbonyl chemistry, aromaticity, radicals, pericyclic basics, protecting groups, and biological mechanisms.
Primary option: David Klein, Organic Chemistry.
Deeper: Clayden, Greeves & Warren, Organic Chemistry.

Physical Chemistry

Topics: thermodynamics, chemical potential, statistical mechanics basics, kinetics, quantum chemistry, spectroscopy, and electrochemistry.
Primary option: Atkins & de Paula, Physical Chemistry.
Biochemistry-focused alternative: Tinoco, Sauer, Wang, Puglisi, Harbison & Rovnyak, Physical Chemistry: Principles and Applications in Biological Sciences.

Analytical Chemistry and Instrumentation

Topics: calibration, chromatography, mass spectrometry, UV-vis/fluorescence, NMR basics, electrophoresis, assay design, and uncertainty.
Primary option: Daniel Harris, Quantitative Chemical Analysis.
Reference: Skoog, Holler & Crouch, Principles of Instrumental Analysis.

Part 2: Biology Foundation

Introductory Biology

Why: one full pass over cells, genetics, evolution, physiology, and molecular biology.
Primary option: Campbell Biology.
Alternative resource: MIT OCW 7.01SC Fundamentals of Biology.

Genetics

Topics: Mendelian genetics, chromosomes, linkage, recombination, mutation, gene regulation, population genetics, genetic screens, and modern sequencing-based genetics.
Primary option: Hartwell et al., Genetics: From Genes to Genomes.
Alternative option: Pierce, Genetics: A Conceptual Approach.

Cell Biology

Topics: membranes, organelles, cytoskeleton, trafficking, signaling, cell cycle, apoptosis, extracellular matrix, and cellular organization.
Primary option: Alberts et al., Molecular Biology of the Cell.
Gentler option: Alberts et al., Essential Cell Biology.
Alternative option: Lodish et al., Molecular Cell Biology.

Molecular Biology

Topics: DNA replication, repair, recombination, transcription, RNA processing, translation, regulation, chromatin, and experimental logic.
Primary option: Watson et al., Molecular Biology of the Gene.

Part 3: Core Biochemistry

Biochemistry I: Structure, Enzymes, and Metabolism

Topics: water, pH/buffers, amino acids, protein structure, enzymes, carbohydrates, lipids, membranes, nucleic acids, vitamins/cofactors, glycolysis, TCA cycle, oxidative phosphorylation, lipid metabolism, amino acid metabolism, nitrogen metabolism, and pathway regulation.
Primary option: Berg, Tymoczko, Gatto & Stryer, Biochemistry. You could also do Nelson & Cox, Lehninger Principles of Biochemistry.
Alternative option: Voet, Voet & Pratt, Fundamentals of Biochemistry, or Miesfeld & McEvoy, Biochemistry.

Enzymology and Mechanism

Topics: Michaelis-Menten kinetics, inhibition, allostery, transition states, catalytic strategies, pH rate profiles, isotope effects, enzyme assay design.
Primary option: Cornish-Bowden, Fundamentals of Enzyme Kinetics.

Metabolism and Regulation

Topics: energy charge, redox logic, flux, compartmentalization, hormonal control, fed/fasted state, metabolic disease, cancer metabolism, experimental tracing.
Primary option: Berg / Stryer, or the Lehninger metabolism chapters.

Biophysical Chemistry

Topics: binding equilibria, cooperative binding, protein folding, thermodynamic cycles, macromolecular interactions, membranes, diffusion, electrochemical gradients, kinetic models, spectroscopy.
Primary option: Tinoco et al., Physical Chemistry: Principles and Applications in Biological Sciences.
Alternative choice: Cantor & Schimmel, Biophysical Chemistry.

Structural Biology

Topics: protein domains, ligand binding, crystallography, NMR, cryo EM, AlphaFold / model interpretation, structure validation, and molecular graphics.
Primary option: Rupp, Biomolecular Crystallography.

Part 4: Laboratory and Research Methods

Core Biochemistry Lab

Topics: pipetting, buffers, pH, sterile technique, centrifugation, protein purification, chromatography, SDS-PAGE, Western blotting, ELISA, enzyme assays, spectrophotometry, fluorescence, basic mass spectrometry.
Primary option: Wilson & Walker, Principles and Techniques of Biochemistry and Molecular Biology.

Molecular Biology Lab

Topics: PCR, cloning, restriction enzymes, plasmids, bacterial transformation, gel electrophoresis, qPCR, sequencing, mutagenesis, reporter assays, basic cell culture.
Primary option: Green & Sambrook, Molecular Cloning: A Laboratory Manual.

Experimental Design

Topics: controls, replicates, blinding where relevant, positive & negative controls, dose response curves, calibration, statistical power, figure interpretation.
Primary option: read the methods and figures of strong papers.

Part 5: Advanced Branches

[I did not do the readings in this subsection! The listings within this subsection are from consulting trusted friends and mentors.]

Chemical Biology and Drug Discovery

Topics: probes, inhibitors, bioorthogonal chemistry, chemical genetics, target engagement, medicinal chemistry basics, SAR, ADME, and resistance.
Primary option: Miller & Tanner, Essentials of Chemical Biology.

Molecular Genetics and Genomics

Topics: sequencing, chromatin, enhancers, transcription factor binding, RNA-seq, ChIP-seq, CRISPR screens, single cell genomics, and regulatory networks.
Primary option: Watson et al., Molecular Biology of the Gene.

Cell Signaling and Cancer Biology

Topics: receptors, kinases, phosphatases, second messengers, feedback, cell cycle, apoptosis, oncogenes, tumor suppressors, DNA damage, and targeted therapy.
Primary option: Alberts, Molecular Biology of the Cell.

Immunology and Host–Pathogen Biology

Topics: antibodies, T/B cells, innate immunity, antigen presentation, cytokines, vaccines, viral replication, bacterial pathogenesis, and immune disease.
Primary: Murphy & Weaver, Janeway's Immunobiology.

Systems, Synthetic, and Computational Biology

Topics: gene circuits, feedback, network motifs, stochasticity, modeling, omics integration, synthetic circuits, and protein engineering.
Primary option: Alon, An Introduction to Systems Biology.

Biotechnology and Protein Engineering

Topics: recombinant protein expression, directed evolution, display technologies, antibodies, enzymes, biologics, fermentation, purification, formulation, and quality control.
Primary option: Walsh, Biopharmaceuticals: Biochemistry and Biotechnology.

Suggested Order

  1. General chemistry, calculus
  2. Introductory biology, orgo I
  3. Organic chemistry II, bio lab basics
  4. Physics, statistics / data analysis
  5. Physical chemistry or biophysical chemistry
  6. Core biochemistry - structure, enzymes, metabolism
  7. Molecular biology, genetics
  8. Cell biology, lab methods
  9. One advanced branch: structural biology, chemical biology, genomics, cancer/signaling, immunology/virology, systems/synthetic biology, or biotech