Plant Biochemistry
From photosynthesis to metabolic engineering โ enzyme mechanisms, metabolic pathways, reaction kinetics, and the molecular basis of plant life.
Plant Central Metabolism
Key Equations of Plant Biochemistry
Photosynthesis (overall)
\( 6\text{CO}_2 + 6\text{H}_2\text{O} \xrightarrow{h\nu} \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \)
Michaelis-Menten Kinetics
\( v = \frac{V_{\max}[S]}{K_m + [S]} \)
Nernst Equation (redox)
\( E = E^\circ - \frac{RT}{nF}\ln Q \)
Gibbs Free Energy
\( \Delta G = \Delta G^\circ + RT\ln\frac{[\text{products}]}{[\text{reactants}]} \)
ATP Synthase
\( \text{ADP} + \text{P}_i + nH^+_{\text{out}} \rightarrow \text{ATP} + \text{H}_2\text{O} + nH^+_{\text{in}} \)
RuBisCO (carbon fixation)
\( \text{RuBP} + \text{CO}_2 \xrightarrow{\text{RuBisCO}} 2 \times \text{3-PGA} \)
About This Course
Plants are the foundation of nearly all life on Earth. Through photosynthesis, they convert solar energy into chemical energy, fix atmospheric carbon into organic molecules, and produce the oxygen we breathe. This course explores the molecular machinery that makes this possible โ from the quantum mechanics of light harvesting to the engineering of metabolic pathways for crop improvement.
Every chapter includes detailed reaction mechanisms with MathJax (enzyme kinetics, thermodynamics, redox potentials), SVG pathway diagrams showing metabolic flow, and Python simulations of enzyme kinetics, metabolic flux, and photosynthetic efficiency that run in the browser.
The course connects to our Biochemistry course (general biochemistry) and our Machine Learning course (Ch 21 uses ML for metabolic flux prediction).
Course Structure
Energy & Transport
Water and mineral uptake, photosynthetic light reactions (PSII, PSI, electron transport chain, chemiosmosis), and the Calvin cycle (RuBisCO kinetics, carbon fixation, regeneration phase).
Core Metabolism
Glycolysis (all 10 steps with mechanisms), the TCA cycle (8 reactions with stereochemistry), mitochondrial electron transport and oxidative phosphorylation, and fatty acid biosynthesis.
Nitrogen & Amino Acids
Amino acid biosynthesis pathways (shikimate, aspartate, glutamate families), nucleotide de novo synthesis, and biological nitrogen fixation (nitrogenase mechanism, energetics).
Hormones & Signaling
Plant hormones (auxin, cytokinin, gibberellin, ABA, ethylene, brassinosteroids, jasmonate, salicylate), signal transduction, and the phenylpropanoid pathway (lignin, coumarins).
Specialized Metabolites
Terpenoid biosynthesis (MEP and MVA pathways, terpene synthases), alkaloid biosynthesis (from amino acid precursors), and flavonoid/anthocyanin pigment pathways.
Carbohydrates
Cell wall biosynthesis (cellulose, hemicellulose, pectin), starch and sucrose metabolism (AGPase, SPS, invertase), and photorespiration with C4 and CAM adaptations.
Stress & Systems Biology
Oxidative stress and ROS scavenging (ascorbate-glutathione cycle), drought/salt/cold stress responses, metabolic engineering of plant pathways, and systems-level flux analysis.
Recommended Textbooks
- Plant Biochemistry โ Heldt & Piechulla (5th ed., 2021)
- Biochemistry & Molecular Biology of Plants โ Buchanan, Gruissem & Jones (2nd ed., 2015)
- Plant Physiology and Development โ Taiz, Zeiger, Mรธller & Murphy (7th ed., 2022)
- Lehninger Principles of Biochemistry โ Nelson & Cox (8th ed., 2021)
- Plant Metabolism and Biotechnology โ Ashihara, Crozier & Komamine (2011)