10/1
Enzymes
• help chemical reactions get done faster; at a temp that’s lower. Chemical reactions
require a flame, typically/higher pressure.
• Enzyme substrate reaction like a key and lock; relationship is very specific;
demonstrates that structure determines function. Active site, key spot (substrate
bonding)
• Enzymes lower energy by positioning reactants together
• High specification
• Induce fit phenomenon – interaction also involves conformational changes
• Proteins that are affected by environment; work in narrow range of temp and pH
• Biocatalyst
• Takes less energy to cause reaction
Enzyme Requirements
- Prosthetic groups: small molecules permanently attached to the enzyme
- Cofactor: usually inorganic ion that temporarily binds to enzyme
- Coenzyme: organic molecule that participates in reaction but is left unchanged
afterward
Enzyme Reactions
- Affinity: degree of attraction between an enzyme and its substrate
- Saturation: plateau where nearly all active sites are occupied by substrate
- Michaelis constant Km : substrate concentration where velocity is half max value,
constant in enzyme-substrate reaction
Proteins are made from polypeptides; polypeptides are made of amino acids (glycine
smallest, different types of amino acids)
Reaction spontaneous: does not require outside energy, increases entropy; free energy is
always negative
Energy: ability to promote change, and do work
- Kinetic vs Potential energy
Thermodynamics
First law:
, • law of conservation of energy
• energy cannot be created or destroyed, but can be transformed from one tup to
another
Second law:
• Transfer of energy from one form to another increases the entropy of a system
• As entropy increases, creates more disorder (less energy available to promote
change)
Gibbs free energy:
• change in free energy determines direction of chemical reactions: Total energy =
usable energy + unusable energy
• H = G + TS:
- H = enthapy
- G = free energy
- S = entropy
- T = constant, absolute temp in Kelvin (K)
Hydrolysis of ATP:
• adenosine triphosphate
• comes from RNA
• OH sugar is only present in RNA
• 3 phosphates + water
• Use this to drive reactions
• Energy currency of cells
Spontaneous Reaction:
• Fast/slow
• Gives free energy/doesn’t need excess energy
• Triangle G is negative, free energy change
Activation energy
• Minimum energy that’s required for a reaction to happen
• Can now achieve transition state where bonds are stretched
• Common ways to overcome activation energy: large amounts of heat, using
enzymes to lower activation energy
ATP
, • Typical cell uses millions of ATP/second to drive endergonic processes
• 10k cycles/day
• 20% of all proteins bind ATP
• particular amino acid sequences in proteins function as ATP-binding sites, make
ATP, substrate level phosphorylation, chemiosmosis
Proteins that use ATP energy: metabolic enzymes, transporters, motor proteins,
chaperones, DNA-modifying enzymes, aminoacyl-tRNA synthetases (important), protein
kinases
Inhibition:
- Competitive Molecule binds to active site, inhibits ability of substrate to bind
- noncompetitive - Lows Vmax without affecting Km, inhibitor binds to allosteric site,
not active site
- Irreversible - Usually bind covalently to an enzyme to inhibit its function, not a
common way for cells to control enzyme function
Types of energy
- Light
- Heat
- Mechanical
- Chemical
- Potential
- Electrical/ion gradient
Terms
Chemical potential energy: energy in molecular bonds
Feedback inhibition: process where the product blocks the initial process
Energy: ability to promote change or do work; kinetic vs potential energy; all reactions have
a threshold of energy, transition state
Entropy: randomness
Enzymes: protein catalysts in living cells
Ribozymes: RNA molecules with catalytic properties
Catalyst: an agent that speeds up the rate of a chemical reaction without being consumed
during the reaction.
Enzymes
• help chemical reactions get done faster; at a temp that’s lower. Chemical reactions
require a flame, typically/higher pressure.
• Enzyme substrate reaction like a key and lock; relationship is very specific;
demonstrates that structure determines function. Active site, key spot (substrate
bonding)
• Enzymes lower energy by positioning reactants together
• High specification
• Induce fit phenomenon – interaction also involves conformational changes
• Proteins that are affected by environment; work in narrow range of temp and pH
• Biocatalyst
• Takes less energy to cause reaction
Enzyme Requirements
- Prosthetic groups: small molecules permanently attached to the enzyme
- Cofactor: usually inorganic ion that temporarily binds to enzyme
- Coenzyme: organic molecule that participates in reaction but is left unchanged
afterward
Enzyme Reactions
- Affinity: degree of attraction between an enzyme and its substrate
- Saturation: plateau where nearly all active sites are occupied by substrate
- Michaelis constant Km : substrate concentration where velocity is half max value,
constant in enzyme-substrate reaction
Proteins are made from polypeptides; polypeptides are made of amino acids (glycine
smallest, different types of amino acids)
Reaction spontaneous: does not require outside energy, increases entropy; free energy is
always negative
Energy: ability to promote change, and do work
- Kinetic vs Potential energy
Thermodynamics
First law:
, • law of conservation of energy
• energy cannot be created or destroyed, but can be transformed from one tup to
another
Second law:
• Transfer of energy from one form to another increases the entropy of a system
• As entropy increases, creates more disorder (less energy available to promote
change)
Gibbs free energy:
• change in free energy determines direction of chemical reactions: Total energy =
usable energy + unusable energy
• H = G + TS:
- H = enthapy
- G = free energy
- S = entropy
- T = constant, absolute temp in Kelvin (K)
Hydrolysis of ATP:
• adenosine triphosphate
• comes from RNA
• OH sugar is only present in RNA
• 3 phosphates + water
• Use this to drive reactions
• Energy currency of cells
Spontaneous Reaction:
• Fast/slow
• Gives free energy/doesn’t need excess energy
• Triangle G is negative, free energy change
Activation energy
• Minimum energy that’s required for a reaction to happen
• Can now achieve transition state where bonds are stretched
• Common ways to overcome activation energy: large amounts of heat, using
enzymes to lower activation energy
ATP
, • Typical cell uses millions of ATP/second to drive endergonic processes
• 10k cycles/day
• 20% of all proteins bind ATP
• particular amino acid sequences in proteins function as ATP-binding sites, make
ATP, substrate level phosphorylation, chemiosmosis
Proteins that use ATP energy: metabolic enzymes, transporters, motor proteins,
chaperones, DNA-modifying enzymes, aminoacyl-tRNA synthetases (important), protein
kinases
Inhibition:
- Competitive Molecule binds to active site, inhibits ability of substrate to bind
- noncompetitive - Lows Vmax without affecting Km, inhibitor binds to allosteric site,
not active site
- Irreversible - Usually bind covalently to an enzyme to inhibit its function, not a
common way for cells to control enzyme function
Types of energy
- Light
- Heat
- Mechanical
- Chemical
- Potential
- Electrical/ion gradient
Terms
Chemical potential energy: energy in molecular bonds
Feedback inhibition: process where the product blocks the initial process
Energy: ability to promote change or do work; kinetic vs potential energy; all reactions have
a threshold of energy, transition state
Entropy: randomness
Enzymes: protein catalysts in living cells
Ribozymes: RNA molecules with catalytic properties
Catalyst: an agent that speeds up the rate of a chemical reaction without being consumed
during the reaction.
