---
module: 087-02
language: en
chapter: 87
title: "Biomolecules, Protein Structure, Enzymes, Cofactors, and Biochemical Regulation"
module_title: "Protein structure, folding, enzyme catalysis, kinetics, and inhibition"
source_sha256: 09756a8440b1c3c34618eb64e0631d9a8e275091bf2e51039a120a64e1d7850f
---
# Protein structure, folding, enzymes, and kinetics

## Levels of protein structure
### Primary: sequence plus covalent linkages
#### One substitution can change charge or stability
#### Loss, toxic gain, or no effect
### Processing removes signals, splits precursors
### Secondary: backbone hydrogen bonds
#### Alpha helices and beta sheets
#### Proline disrupts helices, glycine flexible
### Tertiary: hydrophobic interior, polar surface
### Quaternary: subunits enable cooperativity

## Dynamics and allostery
### Proteins fluctuate among conformations
### Induced fit and conformational selection
### Allostery couples distant sites

## Folding and misfolding
### Folding often begins during translation
### Chaperones prevent aggregation
#### Do not encode final structure
### Disulfides, glycosylation, assembly, cofactors
### Quality control retains, refolds, degrades, signals
### Denaturation spares peptide bonds
#### Exposed hydrophobic surfaces aggregate
### Amyloid: cross-beta fibrils disrupt tissue

## Catalysis and energetics
### Transition state stabilised over ground state
### Acid-base, covalent, metal, proximity, strain
### Rates change both ways, equilibrium unchanged
### High barrier makes favourable reactions slow
### Coupling and product removal keep direction
### Active sites distinguish stereoisomers
### Isoenzymes: same reaction, different tissues

## Michaelis-Menten kinetics
### Complex forms, then proceeds to product
### Maximum velocity tracks total active enzyme
### Km: substrate giving half maximum velocity
#### Approximates, but is not, affinity
### Low substrate: first order
### High substrate: zero order in substrate
### Turnover number over Km measures efficiency
### Assumes initial rate and steady state
### Nonlinear fitting over reciprocal plots

## Inhibition and flux
### Competitive: apparent Km up, Vmax unchanged
### Uncompetitive: both lowered
### Pure noncompetitive: Vmax lowered only
### Mixed inhibition is more common
### Irreversible inhibition depends on time
### Mechanism-based inhibitors inactivate enzyme
### Product inhibition and near-equilibrium enzymes
### Sequential versus ping-pong mechanisms

## Cooperativity and conditions
### Interacting subunits give sigmoidal curves
### Hill coefficient is not site number
### pH profile reflects many ionisable groups
### Heat accelerates, then destabilises
### Metal ions and organic coenzymes
#### Apoenzyme inactive, holoenzyme active
#### Prosthetic groups versus cosubstrates

## Zymogens, assays, and methods
### Zymogens: safe storage, amplifying cascades
#### Premature activation injures tissue
#### Activation effectively irreversible
### Assays infer amount from catalytic activity
#### Leakage, synthesis, obstruction, clearance
### Each structural method has limits
### Find the step controlling flux in cells