biochemistry

name	biochemistry
description	Chemical processes in living organisms
license	MIT
compatibility	opencode
metadata	{"audience":"biochemists, molecular biologists, researchers","category":"biology"}

What I do

• Analyze chemical reactions and processes in living systems
• Study enzyme kinetics and catalytic mechanisms
• Investigate metabolic pathways and regulation
• Characterize biomolecules (proteins, nucleic acids, lipids, carbohydrates)
• Research protein structure-function relationships
• Apply biochemical techniques to solve biological problems

When to use me

• When studying enzyme mechanisms and inhibition
• When analyzing metabolic pathways and disorders
• When characterizing biomolecules and their interactions
• When investigating cellular biochemistry and signaling
• When developing biochemical assays and diagnostics

Key Concepts

Major Metabolic Pathways

Glycolysis: Glucose → Pyruvate + ATP Citric Acid Cycle: Acetyl-CoA oxidation + electron carriers Oxidative Phosphorylation: ATP synthesis via electron transport Gluconeogenesis: Glucose synthesis from non-carbohydrates Beta-Oxidation: Fatty acid catabolism Photosynthesis: Light reactions + Calvin cycle

Enzyme Kinetics

# Example: Michaelis-Menten kinetics
import numpy as np

def michaelis_menten(S, Vmax, Km):
    """
    Calculate reaction velocity.
    S: Substrate concentration
    Vmax: Maximum velocity
    Km: Michaelis constant
    """
    return (Vmax * S) / (Km + S)

def lineweaver_burk(S, v, Vmax, Km):
    """Linearize Michaelis-Menten for parameter estimation."""
    return 1/v, 1/S, 1/Vmax, -1/Km

Key Techniques

• Spectroscopy: UV-Vis, fluorescence, circular dichroism
• Chromatography: HPLC, FPLC, affinity chromatography
• Electrophoresis: SDS-PAGE, native PAGE, 2D gel
• Mass spectrometry: MALDI-TOF, LC-MS
• Calorimetry: ITC, DSC
• Microscopy: Confocal, cryo-EM