BIO20A: Enzymes and Energy

Unit 3 covers Thermodynamics, Free Energy/ Delta G, ATP, and the roles of enzymes

What are the 4 types of basic energy?

1. Kinetic Energy - Energy of motion

2. Thermal Energy - Kinetic energy of randomly moving molecules, heat is thermal energy being transferred

3. Potential Energy - Energy from location or structure

4. Chemical Energy - potential energy released in a chemical reaction

What are the Laws of Thermodynamics?

1. Energy can be transfered of transformed but never destroyed

2. Every energy transfer increases the entropy (chaos) of the universe. Some energy is always lost as heat.

What is Metabolism and a Metaboic Pathway?

• Metabolism is all of an organism’s chemical reactions

• A metabolic pathway changes a molecule step by step, each step catalyzed by a specific enzyme.

Describe a Catabolic Pathway

The Catabolic Pathway breaks down complex molecules and releases energy

Describe a Anabolic pathway

The Anabolic Pathway builds complex molecules and consumes energy

What is Free energy?

It’s part of a system’s energy that can work at uniform pressure and temperature. If G is high then the system is unstable and will move towards lowering G

When is the system at equilibrium?

When the forward and reverse rate of a reaction is equal and the system is stable

Describe an Exergonic Reaction

• Neg. Delta G

• Releases Energy

• Spontaneous reaction

Describe an Endergonic Reaction

• Pos. Delta G

• Consumes energy

What does Spontaneous mean for a reaction?

It means that the reaction is energetically favorable

Do living Cells reach equilibrium?

Living cells never reaches equilibrium as materials flow in and out constantly

What do Cells do?

Cells do chemical (driving endergonic reactions), transport (pumping across the membrane), and mechanical (cilia and muscle) work

Describe Energy Coupling

Where an Exergonic reaction drives an Endergonic reaction. ATP is involved in most couplings

What is the structure of ATP and what reaction produces ADP?

• ATP is Adenine + Ribose + Three Phosphate groups

• Hydrolysis causes ATP + H₂O → ADP + P_i where Delta G = -7.3 kcal/mol

Describe Phosphorylation

Where ATP transfers a phosphate to another molecule to make it more reactive

Describe the ATP cycle

ATP is regenerated from ADP + P_i using energy from catabolism

How do Enzymes work?

• A Catalyst speeds a reaction without being used up

• An Enzyme is a catalytic macromolecule (usually a protein)

• Activation energy (E_a) is the energy needed to break reactant bonds and reach a unstable transition state

• Enzymes lower E_a but do not change Delta G, speeding up reactions

• A Substrate is the reactant an enzyme acts on that binds to the active site, forming the enzyme-substrate complex

• Specificity comes from the complementary shape of the active site and substrate

• Induced fit is when an enzyme changes shape slightly to grip the substrate. Weak bonds hold on to it

How does the active site lower E_a?

• Orienting substrates

• Stretching Bonds

• Providing a favorable microenvironment

• Amino acids taking part directly in the process

What affects enzyme activity?

• Substrate concentration: if there are more substrates then activity is faster until the enzyme is saturated

• Temperature: Human enzymes work best around 30-40 Celsius while thermophilic bacteria works best around 75 Celsius. Hotter would denture the enzyme

• pH: pepsin (stomach) works best at a pH of 2 while trypsin (intestine) is at pH of 8

• Cofactors: non protein helpers where organic ones are coenzymes (e.g. vitamins)

What is irreversible inhibition?

• Where it binds: Covalent bonds to the enzyme

• Effect: Permanently disables it

• overcome by more substrate: NO

What is compeititve reversible inhibtion?

• Where it binds: Active site by resembling a substrate

• Effect: Blocks substrate entry

• overcome by more substrate: YES

What is noncompetitve reversible inhibition?

• Where it binds: Elsewhere on the enzyme

• Effect: Changes enzyme shape causing the active site to work poorly

• overcome by more substrate: NO

How do cells regulate pathways?

Either by switching genes for enzymes on and off or by regulating existing enzymes

Describe Allosteric Regulation

A molecule binds at one site and changes the proteins function at another site which can inhibit or activate it

Describe Feedback Inhibtion

The pathways end product inhibits an earlier enzyme so the cell doesn’t make more than it needs