Handoff nodes to Layer 3 biochemistry: amino acids, peptide bonds, nucleotides, ATP hydrolysis. Built from L2 functional groups, hydrogen bonding, and thermochemistry; sit at the L2/L3 boundary.
biochemistry-bridge
Amino acid
Generic α-amino acid: H₂N-CHR-COOH, with 20 canonical side chains R used in ribosomally-translated proteins. Zwitterionic at physiological…
Peptide bond
Amide linkage formed by condensation between the α-carboxyl of one amino acid and the α-amine of another, with release of water. Partial…
Nucleotide
Phosphate-sugar-base unit: a nitrogenous base (A/G/C/T/U) β-linked to a pentose (ribose or deoxyribose) carrying 1-3 phosphate groups.…
ATP hydrolysis
Exergonic hydrolysis of ATP's γ-phosphate to yield ADP + Pi with ΔG'° ≈ −30.5 kJ/mol at cellular conditions. Universal energy coupling…
Sugar ring tautomers
Aldoses/ketoses cyclize to furanose (5-ring) or pyranose (6-ring); α/β anomers at anomeric carbon. Mutarotation equilibrium in water.…
Michaelis-Menten kinetics (chemical view)
Enzyme kinetics: v=Vmax[S]/(KM+[S]). KM≈Kd for rapid equilibrium; Lineweaver-Burk linearization. Foundation of chemical biology.
Cofactors (NAD+, FAD, CoA, heme)
Non-protein chemical groups assisting enzyme catalysis. NAD+/NADH hydride transfer; FAD/FADH2 2e⁻/2H+; CoA thiol ester carriers; heme…
Metalloenzymes
~50% of enzymes require metal cofactors: Zn (carbonic anhydrase, matrix metalloproteinase), Fe (cytochromes, ribonucleotide reductase), Cu…
Biological homochirality
Life uses only L-amino acids + D-sugars. Origin hypotheses: parity violation (Vester-Ulbricht), amplification by Soai reaction, meteoritic…
Fluorescent probes (GFP, fluorescein, cyanines)
Bioimaging reporters: GFP chromophore (auto-forms from SYG tripeptide), fluorescein (xanthene), Alexa dyes, cyanine (Cy3/Cy5) for…
Michaelis–Menten & Lineweaver–Burk
v = V_max[S]/(K_M+[S]); L-B plot 1/v vs 1/[S]; inhibitor types (comp/uncomp/noncomp) from K_M, V_max changes.
MWC & KNF allosteric models
MWC: concerted T↔R; KNF: sequential; Hill coefficient n_H quantifies cooperativity; hemoglobin paradigm.
NAD(P)H / FAD(H₂) redox cofactors
2e⁻/H⁻ vs 2e⁻/2H (flavins); E°' ≈ -320 mV (NAD⁺/NADH), -219 mV (FAD/FADH₂); central in metabolism.
Chemiosmotic coupling (Mitchell)
Mitchell's chemiosmotic coupling hypothesis (1961): ATP synthesis is driven by an electrochemical proton gradient across the inner…
Covalent vs acid-base enzyme catalysis
Ser proteases acyl-enzyme; Cys-ases thiol; aspartyl proteases general acid/base; metallo-proteases Zn/Mg Lewis acid.
Shikimate pathway
PEP + E4P → shikimate → chorismate → aromatic amino acids; EPSP synthase target of glyphosate herbicide.
Biological nitrogen fixation
Mo/Fe cofactor in nitrogenase; N₂ + 8H⁺ + 8e⁻ + 16 ATP → 2 NH₃ + H₂; ambient T,P; ~100 Mt N/yr globally.
Photosynthesis light reactions
PSII (Z-scheme) splits H₂O to O₂, H⁺, e⁻; PQ, cyt b6f, PC, PSI, Fd reduce NADP⁺; ATP via CF₀F₁; quantum yield ≈ 0.1.
Glycolysis & Warburg effect
Glucose → 2 pyruvate + 2 ATP + 2 NADH; cancer cells prefer lactate fermentation even under normoxia.
CRISPR-Cas9 chemistry
Chemistry-layer anchor for CRISPR-Cas9 gene editing: the Cas9 RNA-guided endonuclease, PAM recognition, protein-DNA / protein-RNA…