I. Energy and Work

1. Energy is the capacity to do work
2. Living cells carry out three major types of work
1. Chemical work--synthesis of complex molecules
2. Transport work nutrient uptake, waste elimination, ion balance
3. Mechanical work internal and external movement
3. In ecosystems, photoautotrophs and chemolithoautotrophs trap energy and use some of it to transform carbon dioxide into organic molecules; the organic molecules then serve as sources of carbon and energy for chemoheterotrophs, which in turn oxidize the organic molecule by processes such as aerobic respiration, releasing carbon dioxide
4. The major energy currency in a living cell is adenosine-5'-triphosphate (ATP)

II. The Laws of Thermodynamics

1. The science of thermodynamics analyzes energy changes in a collection of matter called a system; all other matter in the universe is called the surroundings
2. First law energy can be neither created nor destroyed
1. The total energy in the universe remains constant
2. Energy may be redistributed either within a system or between the system and its surroundings
3. Energy is measured in calories where 1 calorie is the amount of heat energy needed to raise 1 gram of water from 14.5° C to 15.5°C
3. Second law physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible

III. Free Energy and Reactions

1. The changes in energy that can occur in chemical reactions is expressed by the equation for free energy change (@ G = @ H – T ?@ S); free energy change (@G) is the amount of energy in a system that is available to do work
2. The change in free energy of a chemical reaction is directly related to the equilibrium constant of the reaction
1. The standard free energy change (@ G⁰´) is the change in free energy under standard conditions of concentration, pH, pressure, and temperature
2. When @ G⁰´is negative, the equilibrium constant is greater than one and the reaction goes to completion as written; the reaction is said to be exergonic
3. When @ G⁰´is positive, the equilibrium constant is less than one and little product will be formed at equilibrium; the reaction is said to be endergonic

IV. The Role of ATP in Metabolism

1. ATP is a high-energy molecule; removal of the terminal phosphate by hydrolysis goes almost to completion with a large negative standard free energy change (i.e., the reaction is strongly exergonic); ATP also has high phosphate group transfer potential
2. These characteristics make ATP well suited for its role as an energy currency; ATP is formed from ADP and P_i by energy-trapping processes; exergonic breakdown of ATP can be coupled with various endergonic reactions to facilitate their completion

V. Oxidation-Reduction Reactions and Electron Carriers

1. The release of energy during metabolic processes normally involves oxidation-reduction reactions
1. Oxidation-reduction (redox) reactions involve the transfer of electrons from a donor (reducing agent or reductant) to an acceptor (oxidizing agent or oxidant)
2. The equilibrium constant for an oxidation-reduction reaction is called the standard reduction potential (E₀) and is a measure of the tendency of the reducing agent to lose electrons; the more negative the reduction potential, the better the reducing agent is as an electron donor
2. When electrons are transferred from an electron donor to an electron acceptor with a more positive reduction potential, free energy is released and can be used to form ATP
3. Electron transport is important in a variety of metabolic processes (e.g., respiration and photosynthesis); cells use a variety of electron carriers organized into a chain to move electrons; electron carriers include NAD⁺, NADP⁺, flavoproteins, coenzymes, and cytochromes; these carriers differ in terms of how they carry electrons, and this impacts how they function in electron transport chains

VI. Enzymes

1. Structure and classification of enzymes
1. Enzymes are protein catalysts with great specificity for the reaction catalyzed and the molecules acted upon
1. A catalyst is a substance that increases the rate of a reaction without being permanently altered
2. The reacting molecules are called substrates and the substances formed are the products
2. An enzyme may be composed only of protein or it may be a holoenzyme, consisting of a protein component (apoenzyme) and a nonprotein component (cofactor)
1. Prosthetic group is a cofactor that is firmly attached to the apoenzyme
2. Coenzyme a cofactor that is loosely attached to the apoenzyme; it may dissociate from the apoenzyme and carry one or more of the products of the reaction to another enzyme
2. The mechanism of enzyme reactions
1. Enzymes increase the rate of a reaction, but do not alter the equilibrium constant (or the standard free energy change) of the reaction
2. Enzymes lower the activation energy required to bring the reacting molecules together correctly to form the transition-state complex; once the transition state has been reached the reaction can proceed rapidly
3. Enzymes bring substrates together at the active site to form an enzyme-substrate complex; this can lower activation energy in several ways:
1. Local concentrations of the substrates are increased at the active (catalytic) site of the enzyme
2. Molecules at the active site are oriented properly for the reaction to take place
3. The effect of environment on enzyme activity
1. The amount of substrate present affects the reaction rate, which increases as the substrate concentration increases until all available enzyme molecules are binding substrate and converting it to products as rapidly as possible
1. No further increase in rate occurs with subsequent increases in substrate concentration, and the reaction is said to be proceeding at maximal velocity (V_max)
2. The Michaelis constant (K_m) of an enzyme is the substrate concentration required for the reaction to reach half maximal velocity and is used as a measure for the apparent affinity of an enzyme for its substrate
2. Enzyme activity is affected by alterations in pH and temperature; each enzyme has specific pH and temperature optima; extremes of pH, temperature, and other factors can cause denaturation (loss of activity due to disruption of enzyme structure)
4. Enzyme inhibition
1. Competitive inhibition occurs when the inhibitor binds at the active site and thereby competes with the substrate (if the inhibitor binds, then the substrate cannot, and no reaction occurs); this type of inhibition can be overcome by adding excess substrate
2. Noncompetitive inhibition occurs when the inhibitor binds to the enzyme at some location other than the active site and changes the enzyme's shape so that it is inactive or less active; this type of inhibition cannot be overcome by the addition of excess substrate

VII. The Nature and Significance of Metabolic Regulation

1. Regulation is essential for microorganisms to conserve energy and material and to maintain metabolic balance despite frequent changes in their environment
2. Metabolic processes can be regulated in three major ways:
1. Metabolic channeling the localization of metabolites and enzymes in different parts of a cell
2. Stimulation or inhibition of critical enzymes in a pathway
3. Increasing or decreasing the number of enzyme molecules present (regulation of gene expression)

VIII. Metabolic Channeling

1. Compartmentation is a common mechanism for metabolic channeling; enzymes and metabolites are distributed in separate cell structures or organelles
2. Channeling can generate marked variations in metabolite concentrations and therefore directly affect enzyme activity

IX. Control of Enzyme Activity

1. Allosteric regulation of enzyme activity by an effector or modulator, which binds reversibly and noncovalently to a regulatory site on the enzyme; the regulatory site is distinct from the catalytic site
2. Covalent modification of enzymes regulation of enzyme activity by the covalent addition or removal of a chemical group (e.g., phosphate, methyl group, adenylic acid)
3. Feedback Inhibition
1. Every pathway has at least one pacemaker enzyme that catalyzes the slowest (rate-limiting) reaction in the pathway; often this is the first reaction in a pathway
2. In feedback inhibition (end product inhibition), the end product of the pathway inhibits the pacemaker enzyme
3. In branched pathways, balance between end products is maintained through the use of regulatory enzymes at branch points; multiply branched pathways often use isoenzymes, each under separate and independent control