Chapter 8

What is Thermodynamics?

• The study of energy transformations in a collection of matter.

• Helps explain how energy is transformed and used in cells

First Law of Thermodynamics

• Energy cannot be created or destroyed.

• Energy can only be:

  • Transformed

  • Transferred

Second Law of Thermodynamics

• The total entropy of an isolated system cannot decrease.

• Energy transformations are not 100% efficient.

• During energy transformations, entropy tends to increase.

• Some energy naturally becomes less available for doing work

Energy

the capacity to cause change or do work

Types of energy

• Kinetic energy → energy of motion.

• Thermal energy → energy associated with heat and particle movement.

• Potential energy → stored energy due to position or structure.

• Chemical energy → potential energy stored in chemical bonds.

Types of Systems

Isolated and open system

Isolated system

Exchanges neither matter nor energy with its surroundings.

Open system

• Exchanges both matter and energy with its surroundings.

• Cells are open systems because materials can flow in and out.

Spontaneous Process

• A process that can occur naturally without continuous outside energy input.

• Important: spontaneous does NOT mean fast.

Gibbs Free Energy (G)

Energy available to do useful work when temperature and pressure are uniform.

ΔG — Change in Free Energy

Describes the change in energy available to do work during a reaction

What ΔG tells you

Negative: Free energy is released/lost, Spontaneous

Positive: Energy is required, non-spontaneous

Zero: No net change in free energy, Equilibrium

Negative ΔG

• Reaction is spontaneous.

• System loses free energy.

• Products have less free energy.

• Products are more stable.

Free Energy & Stability

• High G = less stable

• Low G = more stable

Equilibrium

• Forward and reverse reactions occur at the same rate.

• System is at maximum stability.

• It cannot spontaneously move away from equilibrium.

Closed Systems

• Eventually reach equilibrium.

• Once at equilibrium, the system can no longer do work.

Metabolism

• All the chemical reactions inside cells that use matter and energy.

Metabolism has two major parts

Catabolism and Anabolism

Catabolism

Catabolism

• Breaks molecules down

• Usually releases energy

Examples from the notes:

• Catabolic pathways break down molecules.

• Energy released can be used by the cell.

Anabolism

• Builds molecules up

• Requires energy

Metabolic Pathway

• A series of reactions inside a cell.

• Each reaction is catalyzed by a specific enzyme.

• The product of one reaction can become the reactant for the next reaction.

Catholic Pathways

Break down molecules

Release free energy

Can be thought of like a multistep open hydroelectric system releasing energy

What happens between metabolic pathways between steps

• The product of one reaction becomes the reactant for the next reaction.

• This keeps the pathway moving forward.

Why don't metabolic pathways simply reach equilibrium?

• Living cells are open systems.

• Materials can continuously enter and leave.

• This allows metabolic reactions to continue rather than simply reaching equilibrium.

Exergonic

• Releases free energy.

• Associated with negative ΔG.

• Can occur spontaneously.

Endergonic

• Requires an input of energy.

• Associated with positive ΔG.

• Does not occur spontaneously by itself.

Energy Coupling

• An exergonic process drives an endergonic process.

• Cells use energy released from one process to power another process that requires energy.

Connection

Cells use energy for three major types of work

Chemical work, transport work and mechanical work

Chemical work

Building molecules

Transport Work

Moving substances across membranes

Mechanical work

Movement

Example: Muscle contraction

What is ATP?

ATP= Adenosine Triphosphate

Main mediator of cellular energy coupling

ATP structure

Ribose, adenine, 3 phosphate groups

ATP hydrolysis

ATP to ADP + phosphate

• The terminal phosphate is removed.

• Free energy is released.

Phosphorylation

• Transfer of a phosphate group from ATP to another molecule.

• This can power an endergonic reaction.

• The molecule receiving the phosphate becomes a phosphorylated intermediate.

• It becomes:

  • More reactive

  • Less stable

  • Higher in free energy

ATP hydrolysis can power

• Transport work

• Mechanical work

• Chemical work

The released energy can change the shape of proteins and affect their binding ability.

ATP Regeneration

ADP + phosphate to ATP

• Energy needed to regenerate ATP comes from exergonic catabolic reactions.

Why do cells need enzymes?

• Some spontaneous reactions can happen extremely slowly.

• Enzymes make reactions happen faster.

Example from the notes:

• Sucrose hydrolysis is spontaneous.

• Without an enzyme, it can take a very long time

Catalyst

• A chemical agent that speeds up a reaction.

• Is not consumed by the reaction.

Enzyme

• A biological catalyst.

• Usually a protein.

• Catalyzes a specific reaction.

Activation Energy

• The initial energy required to break bonds in reactants.

• Acts as an energy barrier.

What enzymes do

• Enzymes lower activation energy.

• This allows reactions to occur faster at moderate temperatures.

What enzymes DON'T do

• They do not change ΔG.

• They only make the reaction happen faster.

Substrate

Reactant that an enzyme acts on

Enzyme-Substrate Complex

Enzyme + substrate to enzyme-substrate complex

• The enzyme binds its substrate.

• The enzyme then catalyzes the reaction.

• Substrate is converted into product.

Active Site

• Region of an enzyme where the substrate binds.

• Often a pocket or groove

Induced Fit

• Substrate enters the active site.

• Enzyme changes shape slightly.

• Enzyme tightens around the substrate.

Enzyme Specificity

• Each enzyme catalyzes a specific reaction.

• Enzymes recognize specific substrates.

Example:

• Sucrase hydrolyzes sucrose into:

  • Glucose

  • Fructose

How enzymes catalyze reactions

1. Orienting substrates

• Positions substrates correctly so they can react.

2. Stretching substrates

• Makes bonds easier to break.

3. Providing a microenvironment

• Creates conditions that help the reaction occur.

4. Using amino acids in the active site

• Amino acids can participate directly in catalysis.

Factors that affect enzyme Activity

Enzyme activity is affected by:

• Temperature

• pH

• Specific chemicals

Optimal Conditions

• Each enzyme has an optimal temperature and pH.

• These depend on the environment where the enzyme normally functions.

Cofactors and Coenzymes

Cofactors

• Nonprotein helpers needed by some enzymes.

• Can bind:

  • Permanently

  • Reversibly

Coenzymes

• Organic cofactors

Enzyme Inhibitors

A substance that selectively inhibits a specific enzyme.

Covalent Inhibition

• Inhibitor forms a covalent bond.

• Usually irreversible.

Noncovalent Inhibition

• Inhibitor binds through noncovalent interactions.

• Reversible.

Competitive Inhibition, What happens?

• Inhibitor resembles the substrate.

• Inhibitor binds to the active site.

• It competes with the substrate.

Connection

Substrate and inhibitor
→ compete for the same active site.

Noncompetitive Inhibition What happens?

• Inhibitor binds away from the active site.

• Does not compete directly for the active site.

• Changes enzyme function.

Where do enzymes come from?

• Enzymes are proteins.

• Proteins are encoded by genes.

Mutations

• Mutations can change the amino acid composition of an enzyme.

• If amino acids change, especially at the active site, enzyme activity can change.

Possible results:

• Novel enzyme activity

• Altered substrate specificity

Why regulate enzymes?

• Cells have many metabolic pathways happening at the same time.

• Without regulation, this could cause chemical chaos.

• Regulation helps control metabolism.

Cells can regulate metabolism by

1. Switching genes on/off

• Controls production of enzymes.

2. Regulating existing enzymes

• Changes the activity of enzymes already present.

Allosteric Regulation, What is it

• A regulatory molecule binds to one site on an enzyme.

• This affects the enzyme's function at another site.

The molecule can:

• Inhibit the enzyme

• Stimulate/activate the enzyme

Regulatory Site

• Activating or inhibiting molecules may bind to a regulatory site.

• This site is often where enzyme subunits join.

Cooperatively, What is it?

• Substrate binding to one active site causes a shape change.

• This stabilizes the active form of the enzyme.

• Other active sites become more likely to bind substrate.

Feedback What is it? Why?

The end product of a metabolic pathway shuts down the pathway.

Prevents:

• Overproduction

• Waste of chemical resources

Why localize enzymes

• Helps organize metabolic pathways.

• Keeps different reactions in appropriate locations.

Localizing Enzymes Examples

• Multienzyme complexes organize reactions.

• Some enzymes are fixed in membranes.

• Eukaryotic enzymes can be located in specific organelles.

• Enzymes for the second and third stages of cellular respiration are located in mitochondria.