Metabolism and Energy: Foundations of Cellular Processes

Metabolism & Energy

Introduction to Metabolism

• Metabolism is the totality of an organism’s chemical reactions.

• It is an emergent property of life that arises from orderly interactions between molecules.

• Energy is the capacity to cause change.

Organization of the Chemistry of Life into Metabolic Pathways

Metabolic Pathways

• A metabolic pathway begins with a specific molecule and ends with a product.

• Each step is catalyzed by a specific enzyme.

Example: Glycolysis is a metabolic pathway that breaks down glucose into pyruvate, involving multiple enzyme-catalyzed steps.

Types of Metabolic Pathways

• Catabolic pathways release energy by breaking down complex molecules into simpler compounds (e.g., cellular respiration).

• Anabolic pathways consume energy to build complex molecules from simpler ones (e.g., synthesis of proteins from amino acids).

Free Energy and Biological Reactions

Free Energy Change and Spontaneity

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

• Biologists determine spontaneity by analyzing energy and entropy changes in chemical reactions.

Free-Energy Change, $\Delta G$

• A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell.

• The change in free energy ($\Delta G$) during a process is related to the change in enthalpy ($\Delta H$), change in entropy ($\Delta S$), and temperature in Kelvin (T):

$\Delta G = \Delta H - T\Delta S$

• $\Delta G$ is negative for all spontaneous processes; processes with zero or positive $\Delta G$ are never spontaneous.

• Spontaneous processes can be harnessed to perform work.

Exergonic and Endergonic Reactions in Metabolism

• An exergonic reaction proceeds with a net release of free energy and is spontaneous.

• An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous.

Equilibrium and Metabolism

• Reactions in a closed system eventually reach equilibrium and can then do no work.

• Cells are open systems, experiencing a constant flow of materials, and are never at equilibrium.

• A defining feature of life is that metabolism is never at equilibrium.

• A catabolic pathway in a cell releases free energy in a series of reactions.

ATP: The Energy Currency of the Cell

ATP Powers Cellular Work

• ATP (adenosine triphosphate) is the cell’s energy shuttle.

• ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups.

• ATP powers cellular work by coupling exergonic reactions to endergonic reactions.

• Most energy coupling in cells is mediated by ATP.

The Structure and Hydrolysis of ATP

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis.

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

• This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.

How the Hydrolysis of ATP Performs Work

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction.

• Overall, the coupled reactions are exergonic.

The Regeneration of ATP

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

• The energy to phosphorylate ADP comes from catabolic reactions in the cell.

• The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways.

Enzymes & Energy

Enzymes as Catalysts

• A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction.

• An enzyme is a catalytic protein.

The Activation Energy Barrier

• Every chemical reaction between molecules involves bond breaking and bond forming.

• The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy ($E_a$).

• Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings.

How Enzymes Speed Up Reactions

• In catalysis, enzymes or other catalysts speed up specific reactions by lowering the $E_a$ barrier.

• Enzymes do not affect the change in free energy ($\Delta G$); instead, they hasten reactions that would occur eventually.

Substrate Specificity of Enzymes

• The reactant that an enzyme acts on is called the enzyme’s substrate.

• The enzyme binds to its substrate, forming an enzyme-substrate complex.

• While bound, the activity of the enzyme converts substrate to product.

• The reaction catalyzed by each enzyme is very specific.

• The active site is the region on the enzyme where the substrate binds.

• Induced fit is the process that brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction.

• Enzymes are extremely fast acting and emerge from reactions in their original form.

Enzyme Regulation

Effects of Temperature and pH

• Each enzyme has an optimal temperature and pH in which it can function.

• Optimal conditions favor the most active shape for the enzyme molecule.

Cofactors

• Cofactors are nonprotein enzyme helpers.

• Cofactors may be inorganic (such as a metal in ionic form) or organic.

• An organic cofactor is called a coenzyme (e.g., vitamins).

Enzyme Inhibitors

• Competitive inhibitors bind to the active site of an enzyme, competing with the substrate.

• Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective.

• Examples of inhibitors include toxins, poisons, pesticides, and antibiotics.

Regulation of Enzyme Activity

• Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated.

• A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes.

Allosteric Regulation of Enzymes

• Allosteric regulation may either inhibit or stimulate an enzyme’s activity.

• It occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site.

• Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site.

Feedback Inhibition

• In feedback inhibition, the end product of a metabolic pathway shuts down the pathway.

• This prevents a cell from wasting chemical resources by synthesizing more product than is needed.