Biochemistry Biology Expert

---
name: biochemistry-biology-expert
version: 1.0.0
description: Expert-level biochemistry from a biology perspective covering metabolic pathways, enzyme kinetics, bioenergetics, signal transduction, and the biochemical basis of cellular processes.
author: luo-kai
tags: [biochemistry, metabolism, enzymes, ATP, signal transduction, pathways]
---

# Biochemistry Biology Expert

## Before Starting
1. Which metabolic pathway or process?
2. Normal biochemistry or disease state?
3. Biochemistry context — cell biology or clinical?

## Core Expertise Areas

### Metabolic Pathways
Glycolysis: glucose to pyruvate, 10 steps, net 2 ATP, 2 NADH.
TCA cycle: acetyl-CoA to CO2, 3 NADH + 1 FADH2 + 1 GTP per turn.
Oxidative phosphorylation: ETC + ATP synthase, 32-34 ATP per glucose.
Fatty acid oxidation: beta-oxidation, 2C units as acetyl-CoA per cycle.
Gluconeogenesis: non-carbohydrate precursors to glucose, liver and kidney.
Pentose phosphate pathway: NADPH production and ribose-5-phosphate.

### Enzyme Kinetics
Michaelis-Menten: v = Vmax[S]/(Km + [S]).
Km: substrate concentration at half-maximal velocity.
kcat: turnover number — reactions per enzyme per second.
Inhibition: competitive (raises Km), uncompetitive (lowers both), noncompetitive (lowers Vmax).
Allosteric regulation: effectors change enzyme activity without competing with substrate.

### Bioenergetics
Free energy: delta_G = delta_G0 + RTlnQ.
ATP hydrolysis: delta_G = -30.5 kJ/mol (standard), much more negative in cell.
Chemiosmosis: proton gradient across inner mitochondrial membrane drives ATP synthase.
Uncoupling: protonophores (DNP) dissipate gradient as heat without ATP synthesis.

### Signal Transduction
GPCR signaling: ligand -> Gs -> adenylyl cyclase -> cAMP -> PKA -> phosphorylation.
RTK signaling: ligand -> dimerization -> autophosphorylation -> RAS -> MAPK cascade.
PI3K-AKT: RTK -> PI3K -> PIP3 -> AKT -> mTOR — growth and survival.
Second messengers: cAMP, cGMP, IP3, DAG, Ca2+.

## Key Patterns



## Best Practices
- Track cofactor oxidation states through pathways
- Consider subcellular compartmentalization of metabolic reactions
- Account for allosteric regulation at key regulatory enzymes
- Remember that in vivo delta_G differs greatly from standard conditions
- Integrate with hormonal regulation of metabolism

## Common Pitfalls
| Pitfall | Fix |
|---|---|
| Confusing delta_G0 with delta_G | Cellular conditions make delta_G very different from standard |
| Forgetting NADH/FADH2 in ATP count | These carry most of the energy from TCA |
| Ignoring allosteric regulation | Key enzymes are highly regulated, not just kinetically limited |
| Confusing competitive inhibition types | Draw double-reciprocal plots to distinguish |

## Related Skills
- cell-biology-expert
- molecular-biology-expert
- physiology-expert
- biochemistry-expert