Metabolism and Chemical Reactions

• Ligands match up with their receptors based on shape and charge.
• Ligand binding is reversible.
• A binding site is a region to which ligands bind.
• Binding sites possess four characteristics: specificity, affinity, saturation, and competition.
• Chemical specificity refers to the ability of a binding site to bind specific ligands.
• The shape of the binding site determines chemical specificity.
• If a related ligand binds to a binding site, it may or may not produce the same effect as the intended ligand.
• An enzyme's binding site can recognize a specific ligand or a class of substrates.
• Substrate (ligand) + enzyme results in a substrate enzyme complex, which then becomes Product + enzyme
• Proteins vary in their diversity of ligands, ranging from wider to narrower specificity.
• Affinity is how tightly a ligand binds to a protein.
• High-affinity binding results in tighter bonding.
• Saturation is the degree to which binding sites are occupied by ligands influenced by ligand concentration and the affinity of the binding site.
• Competition occurs when multiple ligands can bind to the same binding site.
• Allosteric modulation involves a modulator molecule binding to a protein.
• Modulators typically bind to a regulatory site but can bind to functional site.
• When a modulator binds to the protein, it alters the protein's shape and activity.
• Modulator molecules can either activate or inhibit the functional site, or alter the affinity for the site for the ligand.
• Modulator molecules can alter protein activity without changing the ligand concentration.
• Covalent modulation involves the covalent bonding of a chemical group to a protein, which alters the protein's activity.
• Covalent modulation can either activate or inactivate the binding site for the ligand.
• Covalent modulation requires ATP and enzymes to change the protein's shape.
• Anabolism is the synthesis of larger molecules from smaller ones, consuming energy.
• Catabolism is the breakdown of larger molecules into smaller ones, producing energy.
• Metabolism encompasses all chemical reactions in the body, including both anabolism and catabolism.
• Energy is the capacity to do work.
• Kinetic energy is the energy of motion.
• Potential energy is stored energy.
• Work is the transfer of energy from one form to another to accomplish a task.
• Energy conversion is inefficient, producing waste product during energy conversion.
• A calorie is the amount of heat required to raise the temperature of 1 gram of water by 1 degree Celsius.
• Four factors determine reaction rates: reactant concentration, activation energy, temperature, and the presence of a catalyst.
• The greater the concentration, the greater rate of a reaction.
• Activation energy is the energy required to initiate a reaction.
• The larger the activation energy, the slower the reaction.
• Increasing temperature enhances the chances of acquiring activation energy from collisions.
• Catalysts increase reaction rates by lowering activation energy, and do not require a change in temperature.
• Catalysts are not altered or consumed in a chemical reaction and they can be used over again.
• Catalysts increase both the forward and reverse reactions.
• Energy-releasing reactions proceed spontaneously in the forward direction; while energy-requiring reactions do not go forward and require energy.
• Chemical equilibrium is the state where the rate of the forward reaction equals the rate of the reverse reaction.
• The Law of Mass Action states the direction of a reversible reaction is dependent on the concentration of reactants and products.
• Enzymes are made of proteins, and typically end in the suffix "-ase."
• Cofactors are inorganic ions or molecules required for enzyme activity.
• Coenzymes are organic molecules that act as cofactors.
• FAD and NAD are both important coenzymes
• A multienzyme reaction involves multiple enzymes catalyzing sequential steps in a pathway.
• The rate-determining factor in a multienzyme reaction is the step that limits the overall rate of the pathway.
• A reversible reaction is one that can proceed in both the forward and reverse directions.
• How easily a reaction is reversed depends on the energy difference between reactants and products.
• ATP functions to store energy in a cell.
• The three main metabolic pathways for breaking down fuel molecules like glucose are glycolysis, the citric acid cycle, and the electron transport chain.
• Cellular Respiration

Step, Location, Inputs, Outputs, Oxygen Required and ATP amounts in Cellular Respiration

• Glycolysis occurs in the cytoplasm.
• It's Inputs are glucose, 2 ATP, 2 NAD+.
• Its outputs are 2 pyruvate, 4 ATP, 2 NADH.
• It does not require O2 (anaerobic), and results in 2 net ATP amounts.
• Preparatory Reaction occurs in the mitochondrial matrix.
• It's input is 2 pyruvate.
• Its output is 2 Acetyl CoA, 2 CO2, 2 NADH.
• It requires O2 (aerobic), and results in 0 net ATP amounts.
• Citric Acid Cycle occurs in the mitochondrial matrix.
• It's inputs are 2 Acetyl CoA, 6 NAD+, 2 FAD, 2 ADP
• Its outputs are 4 CO2, 6 NADH, 2 FADH2, 2 ATP.
• It requires O2 (aerobic), and results in 2 net ATP amounts.
• Electron Transport Chain (ETC) occurs in the inner mitochondrial membrane.
• It's inputs are 10 NADH, 2 FADH2, 6 O2.
• Its outputs are 10 NAD+, 2 FAD, 6 H2O.
• It requires O2 (aerobic), and results in 32 net ATP amounts.

Simplified chart fo the process

• Glycolysis results in 2 ATP, 2 NADH, 0 FADH2, 0 CO2 and 0 H2O.
• Preparatory reaction results in 0 ATP, 2 NADH, 0 FADH2, 2 CO2 and 0 H2O.
• Citric Acid Cycle results in 2 ATP, 6 NADH, 2 FADH2, 4 CO2 and 0 H2O.
• Electron Transport Chain (ETC) results in 32-34 ATP, 0 NADH, 0 FADH2, 0 CO2 and 6 H2O.
• If there is not enough oxygen to allow pyruvate to go into the Krebs cycle, it undergoes fermentation.
• Fermentation yields only 2 ATP per glucose molecule
• Oxygen debt refers to the additional oxygen required to recover from anaerobic metabolism
• Oxidative phosphorylation is the process where ATP is synthesized using the energy released from the electron transport chain and occurs in the inner mitochondrial membrane.
• The final products are ATP and H2O.
• The final electron acceptor in the electron transport chain is oxygen.
• Chemiosmotic coupling is the process where the energy from the electron transport chain is used to create a proton gradient across the inner mitochondrial membrane, which then drives ATP synthesis.
• ATP synthase is the enzyme used during the synthesis of ATP.
• The electron transport chain generates the most ATP in cellular respiration.
• Three other sources of energy besides glucose are fats, proteins, and glycogen.
• Glycogenolysis is the breakdown of glycogen to release glucose.
• Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors.

Explore the effect of temperature on activation energy, Gibbs free energy, and factors influencing reaction rates. Understand the roles of FAD and NAD in metabolism, the Law of Mass Action, and ATP production. Investigate the Citric Acid Cycle, electron transport chain, and glycolysis.