BIOL 102 Notes
Week 3 - Metabolism
Lecture 7: Introduction to Metabolism
Metabolism: the totality of an organism’s chemical reactions. Arranged as intersecting
metabolic pathways classified as catabolic (breakdown) and anabolic (build-up).
Forms of Energy
Kinetic: energy associated with the relative motion of objects.
Thermal: kinetic energy associated with the random movement of atoms or molecules. The
transfer or thermal energy is heat.
Potential: the energy stored in an object due to its relative position.
Chemical: the potential energy available for release in a chemical reaction.
Gibbs Free Energy (G)
➔ The portion of a system’s energy that can perform work.
➔ Change in free energy calculated as: ΔG = ΔH - TΔS
➔ Change in free energy can also be represented as: ΔG = Gfinal - Ginitial
Activation Energy
➔ The energy required to start a chemical reaction, determines the rate of reaction.
➔ Transition state: molecules in an unstable condition, resulting from having absorbed
enough energy for the bonds to break.
Enzymes
➔ Lower activation energy by:
- Correctly orienting substrates
- Distorting the substrate bonds
- Provide an appropriate microenvironment
- Directly participate in the reaction
➔ Enzyme activity is influenced by temperature and pH
➔ Enzymes may require non-protein cofactors such as coenzymes
Enzyme Inhibitors
➔ Competitive inhibitors: block active site.
➔ Noncompetitive inhibitors: interacts with the enzyme away from the active site.
Allosteric Regulation of Enzymes
● Metabolism in cells must be regulated.
, ● Allosteric regulation: the binding of a regulatory molecule to a protein at one site that
affects function at a different site, can activate or inhibit an enzyme.
● Feedback regulation: a form of allosteric regulation where the regulatory molecule is an
end product of the same metabolic pathway.
Lecture 8: Cellular Respiration and Fermentation Part 1
Cellular Respiration
➔ The catabolic pathways that breakdown organic compounds into waste products and
energy.
➔ Aerobic respiration consumes oxygen as a reactant.
➔ Anaerobic respiration replaces oxygen with other inorganic molecules.
REDOX Reactions
➔ Oxidation is the loss of electrons
➔ Reduction is the gain of electrons
➔ Electron donor is the reducing agent
➔ Electron acceptor is the oxidizing agent
➔ Compounds with C-H bonds (non-polar) are oxidized to products with C-O bonds
(polar).
➔ Organic molecules with many C-H bonds are good sources of energy.
NAD+ and NADH
➔ Dehydrogenases: enzymes that transfer 2 electrons and a proton from an organic
compound to NAD+ producing NADH
Glycolysis
➔ Breakdown of glucose into 2 molecules of pyruvate
➔ Substrate-level phosphorylation: formation of ATP from ADP and a phosphorylated
intermediate.
Glucose + 2 NAD+ + 2 ADP + 2 phosphate → 2 ATP + 2 NADH + 2 H+ + 2 H2O + 2
pyruvate
Lecture 9: Cellular Respiration and Fermentation Part 2
Pyruvate Oxidation
➔ Occurs in the mitochondria (in eukaryotes) or the cytosol (prokaryotes) and connects
glycolysis to the citric acid cycle.
➔ Involves 3 reactions catalyzed by a multi-enzyme complex.
Per 1 pyruvate: pyruvate + NAD+ + CoA → NADH + H + + CO2 + acetyl-CoA
, Per glucose: 2 pyruvate + 2 NAD+ + 2 CoA → 2 NADH + 2 H + + 2 CO2 + 2 acetyl-CoA
Citric Acid Cycle
➔ Considered a cycle as it starts and ends with oxaloacetate.
Per acetyl-CoA: acetyl-CoA + 3 NAD + + FAD + ADP + phosphate + H2O → ATP + FADH 2 +
3 NADH + H+ + 2 CO2 + CoA
Per glucose: 2 acetyl-CoA + 6 NAD + + 2 FAD + 2 ADP + 2 phosphate + 2 H2O → 2 ATP + 2
FADH2 + 6 NADH + 2 H+ + 4 CO2 + 2 CoA
Oxidative Phosphorylation
➔ The synthesis of ATP through the energy released by the transfer of electrons from
NADH to FADH2 to O2
Electron Transport Chain
➔ Transfer of electrons to O2 through a series of redox reactions involving multiprotein
complexes tightly bound to non-protein prosthetic groups.
➔ Some redox reactions are coupled to the export of protons, establishing a proton-motive
force.
Chemiosmosis
➔ An energy-coupling mechanism that uses energy store in the form of an H+ gradient
across a membrane (the proton-motive force) to drive cellular work.
➔ Chemiosmosis provides the energy for ATP production by the enzyme ATP synthase.
How much ATP is made?
➔ A maximum of 30 or 32 ATP, depending on which NADH shunt is used.
➔ Proton-motive force may power other processes, decreasing the amount of ATP.
➔ Efficiency of cellular transport is ~34%.
Regulation of Cellular Respiration
➔ Like all metabolism, cellular respiration must be regulated.
➔ A key step of regulation is the enzyme phosphofructokinase of glycolysis, allosterically
regulated by ATP, AMP, and citrate.
Anaerobic Respiration
➔ Like aerobic respiration, except O2 is replaced by other molecules such as sulphate,
methane, or nitrate.
➔ Less efficient than aerobic respiration as these molecules are weaker oxidizing agents
than O2.
Fermentation
➔ Skips the ETC, relying solely on substrate-level phosphorylation.
Week 3 - Metabolism
Lecture 7: Introduction to Metabolism
Metabolism: the totality of an organism’s chemical reactions. Arranged as intersecting
metabolic pathways classified as catabolic (breakdown) and anabolic (build-up).
Forms of Energy
Kinetic: energy associated with the relative motion of objects.
Thermal: kinetic energy associated with the random movement of atoms or molecules. The
transfer or thermal energy is heat.
Potential: the energy stored in an object due to its relative position.
Chemical: the potential energy available for release in a chemical reaction.
Gibbs Free Energy (G)
➔ The portion of a system’s energy that can perform work.
➔ Change in free energy calculated as: ΔG = ΔH - TΔS
➔ Change in free energy can also be represented as: ΔG = Gfinal - Ginitial
Activation Energy
➔ The energy required to start a chemical reaction, determines the rate of reaction.
➔ Transition state: molecules in an unstable condition, resulting from having absorbed
enough energy for the bonds to break.
Enzymes
➔ Lower activation energy by:
- Correctly orienting substrates
- Distorting the substrate bonds
- Provide an appropriate microenvironment
- Directly participate in the reaction
➔ Enzyme activity is influenced by temperature and pH
➔ Enzymes may require non-protein cofactors such as coenzymes
Enzyme Inhibitors
➔ Competitive inhibitors: block active site.
➔ Noncompetitive inhibitors: interacts with the enzyme away from the active site.
Allosteric Regulation of Enzymes
● Metabolism in cells must be regulated.
, ● Allosteric regulation: the binding of a regulatory molecule to a protein at one site that
affects function at a different site, can activate or inhibit an enzyme.
● Feedback regulation: a form of allosteric regulation where the regulatory molecule is an
end product of the same metabolic pathway.
Lecture 8: Cellular Respiration and Fermentation Part 1
Cellular Respiration
➔ The catabolic pathways that breakdown organic compounds into waste products and
energy.
➔ Aerobic respiration consumes oxygen as a reactant.
➔ Anaerobic respiration replaces oxygen with other inorganic molecules.
REDOX Reactions
➔ Oxidation is the loss of electrons
➔ Reduction is the gain of electrons
➔ Electron donor is the reducing agent
➔ Electron acceptor is the oxidizing agent
➔ Compounds with C-H bonds (non-polar) are oxidized to products with C-O bonds
(polar).
➔ Organic molecules with many C-H bonds are good sources of energy.
NAD+ and NADH
➔ Dehydrogenases: enzymes that transfer 2 electrons and a proton from an organic
compound to NAD+ producing NADH
Glycolysis
➔ Breakdown of glucose into 2 molecules of pyruvate
➔ Substrate-level phosphorylation: formation of ATP from ADP and a phosphorylated
intermediate.
Glucose + 2 NAD+ + 2 ADP + 2 phosphate → 2 ATP + 2 NADH + 2 H+ + 2 H2O + 2
pyruvate
Lecture 9: Cellular Respiration and Fermentation Part 2
Pyruvate Oxidation
➔ Occurs in the mitochondria (in eukaryotes) or the cytosol (prokaryotes) and connects
glycolysis to the citric acid cycle.
➔ Involves 3 reactions catalyzed by a multi-enzyme complex.
Per 1 pyruvate: pyruvate + NAD+ + CoA → NADH + H + + CO2 + acetyl-CoA
, Per glucose: 2 pyruvate + 2 NAD+ + 2 CoA → 2 NADH + 2 H + + 2 CO2 + 2 acetyl-CoA
Citric Acid Cycle
➔ Considered a cycle as it starts and ends with oxaloacetate.
Per acetyl-CoA: acetyl-CoA + 3 NAD + + FAD + ADP + phosphate + H2O → ATP + FADH 2 +
3 NADH + H+ + 2 CO2 + CoA
Per glucose: 2 acetyl-CoA + 6 NAD + + 2 FAD + 2 ADP + 2 phosphate + 2 H2O → 2 ATP + 2
FADH2 + 6 NADH + 2 H+ + 4 CO2 + 2 CoA
Oxidative Phosphorylation
➔ The synthesis of ATP through the energy released by the transfer of electrons from
NADH to FADH2 to O2
Electron Transport Chain
➔ Transfer of electrons to O2 through a series of redox reactions involving multiprotein
complexes tightly bound to non-protein prosthetic groups.
➔ Some redox reactions are coupled to the export of protons, establishing a proton-motive
force.
Chemiosmosis
➔ An energy-coupling mechanism that uses energy store in the form of an H+ gradient
across a membrane (the proton-motive force) to drive cellular work.
➔ Chemiosmosis provides the energy for ATP production by the enzyme ATP synthase.
How much ATP is made?
➔ A maximum of 30 or 32 ATP, depending on which NADH shunt is used.
➔ Proton-motive force may power other processes, decreasing the amount of ATP.
➔ Efficiency of cellular transport is ~34%.
Regulation of Cellular Respiration
➔ Like all metabolism, cellular respiration must be regulated.
➔ A key step of regulation is the enzyme phosphofructokinase of glycolysis, allosterically
regulated by ATP, AMP, and citrate.
Anaerobic Respiration
➔ Like aerobic respiration, except O2 is replaced by other molecules such as sulphate,
methane, or nitrate.
➔ Less efficient than aerobic respiration as these molecules are weaker oxidizing agents
than O2.
Fermentation
➔ Skips the ETC, relying solely on substrate-level phosphorylation.
