Chapter 4: Cellular Metabolism

4.1: Energy and the Laws of Thermodynamics

• Cellular metabolism: Refers to the collective chemical processes that occur within living cells to accomplish these activities.
• Potential energy: It is stored energy.
  • Energy that is not doing work but has the capacity to do so.
• Kinetic energy: Energy of motion.
  • Energy which can do work.
• First law of thermodynamics: States that energy cannot be created or destroyed.
  • It can change from one form to another, but the total amount of energy remains the same.
• Second law of thermodynamics: States that a closed system moves toward increasing disorder, or entropy, as energy is dissipated from the system.
• Free energy: The energy in a system available for doing work.
• Exergonic: Reactions in cells release free energy.
• Endergonic: Reactions in cells that require the addition of free energy.

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4.2: The Role of Enzymes

• For any reaction to occur, even exergonic ones that tend to proceed spontaneously, chemical bonds first must be destabilized.
• Activation energy: This must be supplied before the bond is stressed enough to break.
• If exergonic, reaction products will develop and free energy will be lost only then.
• Raising the temperature increases molecule collisions and breaks chemical bonds, providing activation energy to chemical reactants.
  • Activating a reaction requires heat.
  • Metabolic processes must occur at biologically acceptable temperatures, which are too low for life.
• Catalysts: Chemical substances that accelerate reaction rates without affecting the products of the reaction and without being altered or destroyed by the reaction.
• Enzymes: They reduce the amount of activation energy required for a reaction.
  • They steer the reaction through one or more intermediate steps, each of which requires much less activation energy than that required for a single-step reaction.
• Cofactors: Small nonprotein groups which perform their enzymatic functions.
  • These can be metallic ions.
  • Carbonic anhydrase contains zinc.
  • Cytochromes contain iron.
  • Troponin requires calcium to perform its function.
• Coenzymes: Contain groups derived from vitamins, most of which must be supplied in the diet.
  • B-complex vitamins
  • Nicotinamide adenine dinucleotide (NAD) contains the vitamin **nicotinic acid (**niacin).
  • Coenzyme A contains the vitamin pantothenic acid.
  • Flavin adenine dinucleotide (FAD) contains riboflavin (vitamin B2).
• Ribosomal RNA: A major component of ribosomes, provides the activation energy that enables amino acids to assemble into polypeptide chains during the process of translation.
• Substrate: The molecule whose reaction it catalyzes.
• Enzyme-substrate complex (ES complex): Formed during the binding of enzyme to substrate, in which the substrate is secured by covalent bonds to one or more points in the active site of the enzyme.
• Hydrolysis: Breaking with water.
• Hydrolysis reaction: A molecule is cleaved by the addition of water at the cleavage site.
  • A hydrogen atom is attached to one subunit and a hydroxyl (—OH) unit is attached to another.
  • This breaks the covalent bond between subunits.
• Condensation: Subunits of molecules are linked together by removal of water.
  • This is where macromolecules are built.

4.3: Enzyme Regulation

• Although some enzymes appear to function automatically, the activity of others is rigidly controlled.
• If an enzyme acts reversibly, either synthesis or degradation may result.
• Mechanisms exist for critically regulating enzymes in both quantity and activity.
• Mechanisms that alter activity of enzymes can quickly and finely adjust metabolic pathways to changing conditions in a cell.
• Feedback inhibition: The final end product of a particular metabolic pathway inhibits the first enzyme in the pathway.

4.4: Cellular Respiration

• Oxidation-reduction “redox” reaction: Involves a transfer of electrons from an electron donor (the reducing agent) to an electron acceptor (the oxidizing agent).
  • As soon as the electron donor loses its electrons, it becomes oxidized.
  • As soon as the electron acceptor accepts electrons, it becomes reduced.
• In an oxidation-reduction reaction the electron donor and electron acceptor form a redox pair:

• When electrons are accepted by the oxidizing agent, energy is liberated because the electrons move to a more stable position.
• The nature of this final electron acceptor is the key that determines the overall efficiency of cellular metabolism.
• Heterotrophs: Organisms that cannot synthesize their own food but must obtain nutrients from the environment, including animals, fungi, and many single-celled organisms.
  • Aerobes: Those that use molecular oxygen as the final electron acceptor.
  • Anaerobes: Those that employ another molecule as the final electron acceptor.
• Cellular respiration: The oxidation of fuel molecules to produce energy with molecular oxygen as the final electron acceptor.
  • Oxidation of fuel molecules: describes the removal of electrons from fuel molecules and not the direct combination of molecular oxygen with fuel molecules.
  • Aerobic cellular respiration: Uses oxygen as the final electron acceptor and releases carbon dioxide and water from the complete oxidation of fuels.
• Hans Krebs: A British biochemist who described three stages in the complete oxidation of fuel molecules to carbon dioxide and water.
  • Stage I: Food passing through the intestinal tract is digested into small molecules that can be absorbed into the circulation.
  • Stage II: Also called glycolysis, most of the glucose is converted into two 3-carbon units (pyruvic acid) in the cell cytoplasm.
  • The pyruvic acid molecules then enter mitochondria, where in another reaction they join with a coenzyme to form acetyl coenzyme A.
  • Stage III: The final oxidation of fuel molecules occurs, with a large yield of ATP. This stage occurs entirely in mitochondria.
  • Acetyl-CoA is channeled into the Krebs cycle, where the acetyl group is completely oxidized to carbon dioxide.
• Krebs cycle: Also known as citric acid cycle and tricarboxylic acid cycle.
  • A cyclic sequence where oxidation of the 2-carbon acetyl group of acetyl-CoA occurs within the mitochondrial matrix.

4.5: Metabolism of Lipids

• The central purpose of carbohydrate and fat metabolism is to provide energy, much of which is needed to construct and maintain cellular structure and metabolic processes.
• Triglycerides (neutral fats): Are especially rich depots of metabolic energy because the fatty acids of which they are composed are highly reduced and free of water.
• Fatty acids: Are degraded by sequential removal of 2-carbon units, which enter the Krebs cycle through acetyl-CoA.

4.6: Metabolism of Proteins

• When animals eat proteins, most are digested in the digestive tract, releasing their constituent amino acids, which are then absorbed.
• Tissue proteins also are hydrolyzed during normal growth, repair, and tissue restructuring; their amino acids join those derived from protein found in food to enter the amino acid pool.
  • A portion of the amino acid pool is used to rebuild tissue proteins, but most animals ingest a surplus of protein.
• Before an amino acid molecule may enter the fuel depot, nitrogen must be removed by deamination or by transamination.
  • Deamination: the amino group splits to form ammonia and a keto acid
  • Transamination: the amino group is transferred to a keto acid to yield a new amino acid.
• Thus amino acid degradation yields two main products, carbon skeletons and ammonia, which are handled in different ways.
  • Once nitrogen atoms are removed, the carbon skeletons of amino acids can be completely oxidized, usually by way of pyruvic acid or acetic acid.
  • Another product of amino acid degradation is ammonia.
  • It is highly toxic because it inhibits respiration by reacting with α-ketoglutaric acid to form glutamic acid, and effectively removes α-ketoglutarate from the Krebs cycle
• Terrestrial animals cannot get rid of ammonia so conveniently and must detoxify it by converting it to a relatively nontoxic compound; urea and uric acid.
  • Among vertebrates, amphibians and especially mammals produce mainly urea.
  • Reptiles and birds, as well as many terrestrial invertebrates, produce mainly uric acid.

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