AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

CONCEPT 1: Metabolism

Metabolism is the totality of an organism’s chemical reactions: includes all processes that involve breaking down energy sources (i.e. cell respiration, digestion, etc.). Metabolism arises from interactions between molecules and cellular environments and is concerned with managing the material and energy resources of the cell. Metabolic pathways:

• Are intricate and numerous.• Utilize steps to minimize loss of energy (most efficient paths are used).• Are selectively accelerated by presence of enzymes (biological catalysts).

Catabolic – degradative processes, where complex molecules are broken down into simpler compounds and energy is released (i.e. cellular respiration).

Anabolic – consume energy to build complicated molecules from simpler ones (i.e. protein synthesis). These pathways intersect in such a way that the energy released from Catabolic can be used to drive Anabolic - this transfer of energy is called Energy Coupling.

CONCEPT 2: Types of Energy

Potential Energy: stored energy that matter possesses because of its location or structure (i.e. chemical energy in organic molecules, water in reservoir behind dam).Kinetic Energy: energy of motion (i.e. water gushing through dam, light energy, heat energy)Activation Energy: energy required to start a chemical reaction.

Thermodynamics: study of the energy transformations that occur in a collection of matter. Scientists use terms system and surroundings to describe –

• system is the matter under study • surroundings are everything outside of the system• closed vs. open Systems - closed systems are isolated from surroundings, and in open systems,

energy can be transferred between the system and its surroundings

1 st Law of Thermodynamics: energy can be transferred and transformed, but it cannot be created or destroyed.Known as Principle of Conservation of Energy – the energy of universe is constant!

2 nd Law of Thermodynamics: every energy transfer or transformation makes the universe more disordered:Entropy is a measure of disorder or randomness. The more random a collection of matter, the greater its entropy. So, restate as “every energy transfer or transformation increases the entropy of the universe.”

Free Energy is the portion of a system’s energy that can perform work when temperature is uniform throughout the system.

• Systems that are rich in energy are unstable.• Systems that are highly ordered are unstable.• In any spontaneous process, the free energy of a system decreases.

Organisms can live only at the expense of free energy acquired from the surroundings. Called “free” energy because it is available for work…NOT because it can be spent without cost to the universe.

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

Unstable systems (top diagrams) are rich in “free” energy. They have a tendency to change spontaneously to a more stable state (bottom)…and it is possible to harness this “downhill” change to perform work.

A system’s quantity of free energy is symbolized by the letter G. Two components to G are the system’s total energy (H) and its entropy (S).

ΔG = ΔH - T ΔS

G→system’s quantity of free energyH→system’s total energyT→absolute temperature in Kelvin S→system’s total entropy

So, for a process to occur spontaneously, the system must either give up energy (decrease H), give up order (increase S), or both. The change in G must be negative. In other words, nature runs downhill in the sense of a loss of useful energy – the capacity to perform work.

Equilibrium is a state of maximum stability. In chemical reactions, as the reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases. Free energy increases when a reaction is pushed away from equilibrium. A chemical reaction or physical process at equilibrium performs no work.

CONCEPT 3: Endergonic and Exergonic Reactions

Classification of reactions is based on the free-energy changes: Exergonic – energy outward; proceed with a net release of free energy -- usually releases energy in

form of heat; these reactions occur spontaneously:• (Δ G is negative)

Endergonic – energy inward; absorbs free energy from its surroundings, containers for these reactions tend to feel cool:

• (Δ G is positive)

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

Reactions in a closed system eventually reach equilibrium and can do no work. Because systems at equilibrium have a ΔG of zero and can do no work, a cell that has reached metabolic equilibrium is dead. Thus, metabolic disequilibrium is a defining feature of life! A cell can maintain metabolic disequilibrium b/c it is an open system – the constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium – and the cell continues to work throughout its life.

CONCEPT 4: ATP and Energy Coupling

There are 3 kinds of work in a cell:1. mechanical2. transport3. chemical

Energy Coupling: use of an exergonic process to drive and endergonic process. ATP mediates most energy coupling in cells!

Exergonic Reaction: ΔG < 0

Reaction proceeds with a net RELEASE of free energy…these reactions occur spontaneously.

Endergonic Reaction: ΔG > 0

Reaction proceeds with an ABSORPTION of free energy…these reactions are not spontaneous.

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

REMEMBER: hydrolysis is a chemical process that splits molecules by the addition of water.

The hydrolysis (splitting) of an ATP molecule yields inorganic phosphate and ADP. In the cell, most hydroxyl groups of phosphates are ionized (negatively charged).

Phosphorylation: recipient of phosphate group when ATP loses it. This phosphorylated intermediate is more reactive (less stable) than the original molecule. Nearly all cellular work depends on ATP’s energizing of other molecules by transferring phosphate

groups.

ATP is a renewable source that can be regenerated:

ENERGY COUPLING: The use of exergonic processes to drive endergonic processes. Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Energy stored as ATP drives most cellular work. Thus, ATP couples the cell’s energy-yielding processes to the energy-consuming ones.

CONCEPT 5: Enzymes

Review the following biological animation as you study this section of the notes:http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html

Catalysts are chemical agents that change the rate of reaction without being consumed by the reaction. Enzymes are catalytic proteins. Enzymes keep chemical traffic through the pathways of metabolism from getting too congested and bogged down.

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

Energy Profile of an Exergonic Reaction:

Uphill - Reactants A & B must absorb enough energy from the surroundings to surmount the hill of activation energy and reach the unstable transition state.

Downhill – Bonds break, and new bonds form. Energy is released to surroundings during this process (EXERGONIC - ∆G negative) – products have less energy than reactants.

THIS IS WITH NO ENZYME ACTIVITY!!!

Enzymes Lower the Barrier of Activation Energy:

Without affecting the free-energy change (∆G) for the reaction, an enzyme speeds the reaction up by lowering the activation energy required to start the reaction.

Black Curve – shows course of reaction w/out enzyme.

Red Curve – shows course of reaction with enzyme.

THINGS TO KNOW ABOUT ENZYMES:• AN ENZYME SPEEDS A REACTION BY LOWERING THE ACTIVATION ENERGY REQUIRED

TO START THE REACTION.• Cannot change the ΔG for a reaction.• Cannot make an endergonic reaction exergonic.• Can only hasten reactions that would occur normally, regardless!• Enzymes ARE NOT USED UP during the course of the reaction!

The reactant an enzyme acts on is its substrate. Enzymes are substrate specific, and can distinguish its substrate from even closely related isomers!

Each enzyme has an active site – the catalytic center of the enzyme! Rate of conversion of substrate into new products depends on initial concentration of substrate! But there is a limit to total speed of reaction – all enzyme molecules may be working (saturated), so the

only way to increase reaction speed is to ADD MORE ENZYME! So…to speed up reaction…add MORE substrate or add more enzyme!!!

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate (induced fit model). Active site of enzyme can be seen in computer model as groove on surface of protein (blue). On entering the active site, the substrate (red) induces a change in the shape of the protein that causes the active site to embrace the substrate.

In this example, the enzyme sucrase catalyzes the hydrolysis of sucrose to glucose and fructose.

THE PHYSICAL AND CHEMICAL ENVIRONMENT AFFECT THE FUNCTION OF ENZYMES!

Substrate enters active site & binds to protein enzyme – enzyme changes shape to embrace substrate (induced-fit)

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

Review the following biological animation as you study this section of the notes:http://www.sumanasinc.com/webcontent/animations/content/proteinstructur e.html

Temperature – too high, denatures protein pH – too high or too low, denatures protein Cofactors – inorganic nonprotein helper bound to active site; must be present for some enzymes to

function (zinc, iron, copper) Coenzymes – organic nonprotein helper bound to active site; again, must be present (vitamins)

CONCEPT 6: Enzyme Inhibitors

Review the following biological animation as you study this section of the notes:http://bcs.whfreeman.com/thelifewire/content/chp06/0602001. html

Enzyme Inhibitors – stop enzyme from working! There are 2 types of enzyme inhibitors: Competitive blocks active site, mimics substrate Noncompetitive bind to another part of enzyme and change shape of enzyme – so can’t work on

substrate

CONCEPT 7: Control of Metabolism

Mimics the substrate and competes for the active site.

Binds to the enzyme at a location away from the active site, but alters the shape of the enzyme so that the active site is no longer fully functional.

AP Biology Notes Outline Chapter 8: An Introduction to Metabolism

A cell regulates metabolic pathways by controlling when and where enzymes are active. This can be achieved in two ways: (1) switching on or off the genes for production of specific enzymes; (2) regulating enzymes once made

Allosteric Regulation of Enzyme Activity: http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.htmlAllosteric regulation is the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme’s activity.

MOST ALLOSTERICALLY REGULATED ENZYMES ARE CONSTRUCTED FROM 2 OR MORE POLYPEPTIDE CHAINS:

a) The enzyme oscillates between 2 conformational states, one active and the other inactive. Remote (away) from the active sites are the allosteric sites, specific receptors for regulators of the enzyme, which may be an activator or an inhibitor.

b) Here we see the opposing affects of an allosteric activator and an allosteric inhibitor on the conformation of all four subunits of enzyme.

Feedback Inhibition:http://highered.mcgraw-hill.com/olc/dl/120070/bio10.swf

Feedback inhibition involves the switching off of a metabolic pathway by its end product, which acts an inhibitor of an enzyme within the pathway. Many metabolic pathways are switched off by an end product, which acts as an allosteric inhibitor of an enzyme earlier in the pathway.

Cooperativity:Similar to allosteric activation – amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to accept more substrate molecules…

In an enzyme molecule with multiple subunits, the binding of one substrate molecule to the active site of one subunit causes all the subunits to assume their active conformation.