Enzymes and Metabolism: Thermodynamics, ATP, and Regulation in Biology

Metabolism

All the chemical processes that occur within living organisms.

Catabolic pathways

Breaking down of complex molecules that release energy.

Anabolic pathways

Building of larger and complex molecules from smaller and simple molecules that consume energy.

Thermodynamics

The study of energy transformations in a collection of matter.

Isolated system

A system unable to exchange energy or matter with its surroundings.

Open system

A system where energy and matter can be transferred between the system and its surroundings.

Kinetic energy

Energy associated with motion.

Thermal energy

The kinetic energy associated with random movement of atoms or molecules.

Chemical energy

Potential energy available for release in a chemical reaction.

Potential energy

Energy that matter possesses because of its location or structure.

1st Law of Thermodynamics

Energy can be transferred or transformed but cannot be created or destroyed.

2nd Law of Thermodynamics

Every energy transfer or transformation increases entropy.

Entropy

A measure of molecular disorder or randomness.

Spontaneous Process

Any process that leads to an increase in entropy that can proceed without requiring an input of energy.

Non-spontaneous process

Any process that leads to a decrease in entropy.

Non spontaneous process

Any process that leads to decrease in entropy is said non spontaneous process. This process will occur only if energy is supplied.

Free-energy change

The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously.

Energy and entropy changes

Biologists follow the energy and entropy changes during chemical reactions to determine whether they require an input of energy or occur spontaneously.

Spontaneous reaction inquiry

Will this particular reaction happen or will we need to pay into it with energy?

Gibbs free energy (G)

The portion of a system's energy that can do work when temperature and pressure are uniform throughout the system, as in a living cell.

Change in free energy (ΔG)

Used to determine whether a process is spontaneous or not.

Spontaneous processes

Processes that decrease the system's free energy and have a negative ΔG.

Nonspontaneous processes

Processes that have a zero or positive ΔG.

ΔG formula

ΔG = Gfinal state - Ginitial state.

Negative ΔG

Indicates that the system loses free energy and becomes more stable.

ΔG and temperature

Change in free energy during a reaction is related to temperature and changes in enthalpy and entropy.

ΔG formula with variables

ΔG = ΔH - TΔS, where ΔH is change in enthalpy, ΔS is change in entropy, and T is temperature in Kelvin.

Kelvin scale

Same as Celsius, but shifted down so that 0°K = -273°C.

Exergonic reaction

A reaction that proceeds with a net release of free energy to the surroundings.

Endergonic reaction

A reaction that absorbs free energy from the surroundings.

ATP (adenosine triphosphate)

Composed of ribose, adenine, and three phosphate groups.

ATP hydrolysis

Energy is released from ATP when the terminal phosphate bond is broken by hydrolysis.

Energy from ATP

Does not come directly from the phosphate bonds, but from the chemical change to a state of lower free energy in the products.

Phosphorylation

Transfer of a phosphate group from ATP to another molecule, typically used to power endergonic reactions.

Phosphorylated intermediate

The recipient molecule that is more reactive and has more free energy than the original molecule.

Regeneration of ATP

ATP is regenerated by addition of a phosphate group to adenosine diphosphate (ADP).

ATP cycle

The shuttling of inorganic phosphate and energy that couples energy-yielding processes to energy-consuming ones.

Enzymes

Speed up metabolic reactions by lowering energy barriers.

Spontaneous reactions

Do not need added energy, but can be very slow.

Example of slow spontaneous reaction

The hydrolysis of sucrose to glucose and fructose can take years at room temperature without appreciable hydrolysis.

Free-energy change (ΔG)

The change in free energy for a process can be used to determine whether it is spontaneous or not.

Zero or positive ΔG

Indicates that a process is non-spontaneous.

ΔG equation

ΔG = Gfinal state - Ginitial state.

Stable system

A system with negative ΔG loses free energy and becomes more stable.

Example of spontaneous reaction

The hydrolysis of sucrose to glucose and fructose is spontaneous but can take years at room temperature.

Catalysts

Chemical agents that speed up a reaction without being consumed in the reaction.

Enzyme

A macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction.

Sucrase

An enzyme that catalyzes the complete hydrolysis of sucrose within SECONDS when added to a sucrose solution at room temperature.

Activation Energy (EA)

The initial energy needed to break the bonds of the reactants.

Transition State

A highly unstable state that a molecule must reach for bonds to break and start a reaction.

Catalysis

The process by which a catalyst selectively speeds up a reaction without itself being consumed.

Substrate Specificity

The complementary fit between the shape of the active site of an enzyme and the shape of the substrate.

Active Site

The region on the enzyme, often a pocket or groove, that binds to the substrate.

ΔG

The change in free energy; enzymes cannot change ΔG.

Denature

The process by which proteins lose their structure and function due to heat or other factors.

Energy Profit

The excess energy released in an exergonic reaction after new bonds are formed.

High Activation Energy

Most reactions that require additional energy (usually heat) to reach the transition state.

Moderate Temperatures

The temperature range at which enzymes lower the activation energy barrier enough for reactions to occur.

Chemical Reaction

A process involving the breaking and forming of bonds between molecules.

Molecule Stability

Molecules become unstable when enough energy is absorbed to break bonds.

Heat in Reactions

Adding heat is impractical in cells as it speeds up all reactions, not just those needed.

Enzyme Function

Enzymes speed up reactions that would eventually occur anyway.

Bonds Breaking

The process that must occur for a chemical reaction to start.

Bonds Forming

The process that occurs after bonds break, leading to the release of energy.

Substrates

Molecules that enzymes act upon, which may be oriented or stretched to facilitate reactions.

Optimal Temperature

The temperature at which an enzyme catalyzes its reaction at the maximum possible rate.

Denaturation

The process by which enzymes lose their functional shape due to extreme temperature or pH.

Optimal Temperature for Human Enzymes

Approximately 37°C.

Optimal Temperature for Thermophilic Bacteria

About 75°C.

Optimal pH

The pH level at which an enzyme is most active.

Optimal pH for Pepsin

2, which is suitable for the human stomach.

Optimal pH for Trypsin

8, which is suitable for the intestine.

Cofactors

Non-protein helpers that assist enzymes, which can be either inorganic or organic.

Inorganic Cofactors

Metal atoms such as zinc, iron, and copper in ionic form.

Coenzymes

Organic cofactors that assist enzymes, often derived from vitamins.

Enzyme Inhibitors

Chemicals that selectively inhibit the action of specific enzymes.

Irreversible Inhibition

When an inhibitor forms covalent bonds with an enzyme, permanently disabling it.

Reversible Inhibition

When inhibitors bind to enzymes through weak interactions, allowing for recovery of enzyme function.

Competitive Inhibitors

Inhibitors that resemble substrates and bind to the enzyme's active site, blocking substrate access.

Noncompetitive Inhibitors

Inhibitors that bind to an enzyme at a site other than the active site, altering enzyme shape and function.

Metabolic Pathway

A series of chemical reactions in a cell, where a specific molecule is altered to produce a final product.

Allosteric Regulation

Regulation of enzyme activity through the binding of a regulatory molecule at a site other than the active site.

Feedback Inhibition

A regulatory mechanism where the end product of a metabolic pathway inhibits an earlier step in the pathway.