Ch 6: Intro to Metabolism

Chapter 6: Intro to Metabolism Metabolism  All of the chemical processes that occur in a living organism. Metabolism  All of the chemical processes that occur in a living organism. Metabolic Pathways Metabolic Pathways Specific, orderly, and stepwise series of chemical reactions Specific, orderly, and stepwise series of chemical reactions Manage the material and E resources of the cell. Manage the material and E resources of the cell.

Metabolic Pathways Catabolic Pathways Catabolic Pathways Breakdown resources to release E. Breakdown resources to release E. Complex Molecule  Simple Molecules Complex Molecule  Simple Molecules Ex: C 6 H 12 O 6 (glucose)  CO 2 + H 2 O + E Ex: C 6 H 12 O 6 (glucose)  CO 2 + H 2 O + E Always release E stored in the bonds of complex molecules. Always release E stored in the bonds of complex molecules. Anabolic Pathways Anabolic Pathways Simple Molecule  Complex Molecules Simple Molecule  Complex Molecules Require the usage of E. Require the usage of E.

Bioenergetics Bioenergetics is the study of how organisms manage their E resources. Bioenergetics is the study of how organisms manage their E resources. Catabolic reactions provide the E needed for anabolic reactions. Catabolic reactions provide the E needed for anabolic reactions.

Energy Capacity to do work. (work = pretty much everything) Capacity to do work. (work = pretty much everything) Various forms (light, chemical, heat, mech.) Various forms (light, chemical, heat, mech.) organisms live because of their ability to transform that E from one form to another. organisms live because of their ability to transform that E from one form to another. Conversions are governed by the laws of thermodynamics. Conversions are governed by the laws of thermodynamics.

Energy Conversions Kinetic Energy  E possessed by matter that is in motion. Kinetic Energy  E possessed by matter that is in motion. Potential Energy  E stored by matter because of location or structure. Potential Energy  E stored by matter because of location or structure. Ex: Water behind a dam, gasoline, glucose Ex: Water behind a dam, gasoline, glucose Light E  Chemical E  Kinetic E Light E  Chemical E  Kinetic E - Conv. 1 (Plants)  Photosynthesis - Conv. 2 (Animals)  Cell. Respiration

Thermodynamics Open System  Matter under study as well as all of its surroundings. (Organisms = Open) Open System  Matter under study as well as all of its surroundings. (Organisms = Open) Closed System  Matter under study is isolated from its surroundings. Closed System  Matter under study is isolated from its surroundings. In open systems, E (and matter) flows freely between the matter (organisms) and its surroundings. In open systems, E (and matter) flows freely between the matter (organisms) and its surroundings. Organisms are open systems, can you list what they absorb from and release to their surroundings? Organisms are open systems, can you list what they absorb from and release to their surroundings?

1st Law of Thermodynamics E cannot be created nor destroyed, only transferred and transformed. E cannot be created nor destroyed, only transferred and transformed. But, if E can’t be destroyed, why don’t organisms act as closed systems and recycle E? But, if E can’t be destroyed, why don’t organisms act as closed systems and recycle E?

2 nd Law of Thermodynamics Entropy  Measure of disorder, randomness. Greater disorder, randomness = higher entropy. Entropy  Measure of disorder, randomness. Greater disorder, randomness = higher entropy. Every E transfer or transformation increases the entropy (disorder) of the universe. (Ex: the universe = your bedroom) Every E transfer or transformation increases the entropy (disorder) of the universe. (Ex: the universe = your bedroom)

2 nd Law of Thermodynamics Every E transfer generates some heat. Every E transfer generates some heat. Heat is E in its most random state (least usable form). Heat is E in its most random state (least usable form). This 2 nd Law is why organisms need to constantly replenish their E and remain open systems. This 2 nd Law is why organisms need to constantly replenish their E and remain open systems.

Thermodynamics Amount of E in the organisms universe is constant, its quality is not. Amount of E in the organisms universe is constant, its quality is not. Organisms take organized forms of matter from their surroundings, and replace them with less ordered forms. Organisms take organized forms of matter from their surroundings, and replace them with less ordered forms. For example, E flows into an ecosystem as light (less random) and leaves as heat (more random) For example, E flows into an ecosystem as light (less random) and leaves as heat (more random)

Spontaneous Reactions Certain processes occur spontaneously, while others are non-spontaneous. Certain processes occur spontaneously, while others are non-spontaneous. A spontaneous change is one that takes place without outside help. (Ex: Water flows downhill) A spontaneous change is one that takes place without outside help. (Ex: Water flows downhill) It can be predicted whether or not a certain change will be spontaneous. It can be predicted whether or not a certain change will be spontaneous.

Free Energy The portion of a system’s E that is available to perform work (at uniform temp.) The portion of a system’s E that is available to perform work (at uniform temp.) Free energy (G) is dependent upon: Free energy (G) is dependent upon: The system’s total energy (H) The system’s total energy (H) The temperature (T) The temperature (T) The change in entropy (ΔS) The change in entropy (ΔS) ΔG = ΔH - TΔS

Free Energy and Spontaneity ΔG determines rxn spontaneity. ΔG determines rxn spontaneity. ( - ) ΔG = spontaneous ( - ) ΔG = spontaneous ( + ) ΔG = non-spontaneous ( + ) ΔG = Equilibrium, ΔG = Equilibrium, ΔG = 0

Exergonic vs Endergonic Rxns Exergonic reactions produce E, while endergonic reactions absorb E. Exergonic reactions produce E, while endergonic reactions absorb E. Exergonic = (-) ΔG values and are spontaneous. Exergonic = (-) ΔG values and are spontaneous. Endergonic = (+) ΔG values and are non- spontaneous. Endergonic = (+) ΔG values and are non- spontaneous.

Metabolic Disequilibrium If the ΔG of the metabolic processes in a living cell = 0, then the cell is dead. If the ΔG of the metabolic processes in a living cell = 0, then the cell is dead. Disequilibrium keeps the cell alive. Disequilibrium keeps the cell alive. Metabolic Pathways Metabolic Pathways Products of one step as reactants in another. Products of one step as reactants in another. Energy coupling Energy coupling Exergonic reactions power endergonic reactions. Exergonic reactions power endergonic reactions.

ATP Couples Exergonic/Endergonic Reactions Cells do three kinds of work: Cells do three kinds of work: Mechanical (muscles, chromosome movement) Mechanical (muscles, chromosome movement) Transport (pumping across membranes) Transport (pumping across membranes) Chemical (anabolic (endergonic) reactions) Chemical (anabolic (endergonic) reactions) ATP is the immediate E source for cellular work. ATP is the immediate E source for cellular work.

Structure of ATP (Adenosine Tri-Phosphate) Adenine + Ribose + 3 Phosphate groups Adenine + Ribose + 3 Phosphate groups

Hydrolysis of ATP Hydrolysis is when water is added to a compound and a bond is broken. Hydrolysis is when water is added to a compound and a bond is broken. When ATP is hydrolyzed, its products are: When ATP is hydrolyzed, its products are: ADP (di-phosphate) + Phosphate + Energy

Hydrolysis of ATP

Phosphorylation (ATP E Transfer) Transfer P = Transfer E Transfer P = Transfer E This phosphorylated intermediate is more reactive than the original molecule and now has been “energized”. This phosphorylated intermediate is more reactive than the original molecule and now has been “energized”.

ENZYMES Proteins Proteins Speed up (catalyze) chemical reactions Speed up (catalyze) chemical reactions Lower the E barrier to a chemical reaction. Lower the E barrier to a chemical reaction. Not consumed in the reactions. Not consumed in the reactions. Every reaction has an initial E barrier (activation E) that must be overcome. Every reaction has an initial E barrier (activation E) that must be overcome. Do not change the ΔG of the reaction. Do not change the ΔG of the reaction.

Catalyzed vs Uncatalyzed Rxns

Enzyme Specificity Substrates are the reactants that enzymes work upon. Substrates are the reactants that enzymes work upon. While the enzyme is bound to its substrate, the substrate is converted into the product. While the enzyme is bound to its substrate, the substrate is converted into the product. The specificity of enzymes is directly related to their shape and the shape of the substrate. The specificity of enzymes is directly related to their shape and the shape of the substrate.

Enzyme-Substrate Complex active site -- region of the enzyme that binds to the substrate. active site -- region of the enzyme that binds to the substrate. The specificity of an enzyme is due to a compatible fit between the active site and the substrate. (Lock and Key) The specificity of an enzyme is due to a compatible fit between the active site and the substrate. (Lock and Key) Induced Fit Induced Fit When the substrate enters the enzymes active site, the enzyme changes shape to fit even better with the substrate. When the substrate enters the enzymes active site, the enzyme changes shape to fit even better with the substrate.

Enzyme-Substrate Complex Weak interactions (H-bonds, ionic bonds) Weak interactions (H-bonds, ionic bonds) This often orients the substrate in such a way as to make it more reactive. This often orients the substrate in such a way as to make it more reactive. Once the reaction is complete, the enzyme and substrate separate. Once the reaction is complete, the enzyme and substrate separate. Often, the active site provides a microenvironment (Ex: low pH) more conducive to specific reaction. Often, the active site provides a microenvironment (Ex: low pH) more conducive to specific reaction.

Factors Affecting Enzymes Enzyme function is highly dependent upon temperature and pH. Enzyme function is highly dependent upon temperature and pH. Each enzyme has an optimal range for each. Each enzyme has an optimal range for each. Optimal orientation within its ranges. Optimal orientation within its ranges.

Factors Affecting Enzymes

Cofactors and Coenzymes Some enzymes require the help of other atoms, ions or molecules to operate. Some enzymes require the help of other atoms, ions or molecules to operate. Cofactors- Nonprotein inorganic helpers (Ex: Zn, Fe, Cu) Cofactors- Nonprotein inorganic helpers (Ex: Zn, Fe, Cu) CoEnzymes – Nonprotein organic helpers (generally vitamins) CoEnzymes – Nonprotein organic helpers (generally vitamins) Generally aid by binding to enzyme and helping it orient itself more efficiently. Generally aid by binding to enzyme and helping it orient itself more efficiently.

Enzyme Inhibition Some chemicals inhibit the action of enzymes. Some chemicals inhibit the action of enzymes. Competitive inhibitors compete with the substrate for the active site. Competitive inhibitors compete with the substrate for the active site. Noncompetitive inhibitors Noncompetitive inhibitors bind elsewhere on the enzyme bind elsewhere on the enzyme changes the orientation to a less effective position. changes the orientation to a less effective position.

Enzyme Inhibition

Metabolic Control Allosteric Control Allosteric Control - A regulatory molecule binds to enzyme and changes its shape - Enzymes have two orientations (active or inactive)

Feedback Inhibition Metabolism’s “thermostatic” control Metabolism’s “thermostatic” control When the end-product of a reaction accumulates in the cell, it can cause the pathway to be inhibited. When the end-product of a reaction accumulates in the cell, it can cause the pathway to be inhibited. The end-product acts as an enyzme inhibitor (generally allosteric inhibition) The end-product acts as an enyzme inhibitor (generally allosteric inhibition) Prevents cell from wasting E Prevents cell from wasting E

Cooperativity Some enzymes have multiple subunits with multiple active sites Some enzymes have multiple subunits with multiple active sites When a substrate binds to one active site, it often causes a domino effect and triggers the enzyme to bind to additional substrate molecules When a substrate binds to one active site, it often causes a domino effect and triggers the enzyme to bind to additional substrate molecules Binding of first substrate causes favorable allosteric change in enzyme configuration Binding of first substrate causes favorable allosteric change in enzyme configuration

Metabolic Organization Remember, metabolism is an ordered, stepwise set of chemical reactions. Remember, metabolism is an ordered, stepwise set of chemical reactions. Therefore, enzymes are found in structures throughout the cell to make their use more efficient. Therefore, enzymes are found in structures throughout the cell to make their use more efficient. For example, enzymes for cellular respiration are found in mitochondria (where they will be needed) For example, enzymes for cellular respiration are found in mitochondria (where they will be needed)