Chapter 14 - Exam 2

ATP, ADP, AMP, & Adenosine

be able to identify

Oxidation-Reduction Reactions

• The reduction potential describes the tendency for an oxidized compound to gain electrons (become reduced); the change in reduction potential for a reaction describes the tendency for a given oxidized compound to accept electrons from a given reduced compound. • Free energy and reduction potential are negatively related: the greater the reduction potential, the more negative the free energy and the more favorable the reaction. When ∆E is positive, ∆G is negative ~

H bond

give off -40k j/mol energy when broken

reduction occurs

occurs from the more positive Eo to the more negative Eo

Oxidation-Reduction Reactions

oil rig oxidation is the loss of electrons (gain O) reduction is the gain of electrons (gain H) E and G inversely related

ATP can be Replenished by Transfer of a Phosphoryl Group to ADP from a Compound with a Higher Phosphoryl Group- Transfer Potential ~

phosphocreatine is a lipid bilayer thing

The Nature of "High-Energy" Compounds

• High energy compounds have large negative ∆G values upon hydrolysis (< 25 kJ/mole).

Control of Flux in the Rate-Determining Step Requires Control of the Enzyme Catalyzing that Step.

• The flux varies with the activities of the enzymes that catalyze irreversible reactions. • These flux-controlling enzymes are regulated by: 1) allosteric control & feedback regulation 2) covalent modification of the enzyme 3) substrate cycling in which interconversion of 2 substrates utilize different rate-determining enzymes 4)changes in gene expression which regulate the steady state levels of the enzymes involved.

anabolism

(biosynthesis) is the synthesis of biomolecules from simpler components.

catabolism

(degradation) is the breakdown of nutrients and cell constituents to salvage their components and/or to generate energy.

AcetylCoA: A High-Energy Thioester

- transfers Acetyl group - Coenzyme A functions as a carrier of acetyl & other acyl groups. ~

phosphoanhydride

ATP is considered an "energy rich" compound because it contains two ______________ bonds

Endergonic Reactions are Coupled to Exergonic ATP Hydrolysis to Drive Many Processes

ATP's aggressive spontaneity makes nonspontaneous things happen energy for dna rna stuff

Reduction of NAD+ to NADH

Eo = -0.315

high and low energy phosphates

low energy are not resonance stabilized ~

ATP structure

adenine, ribose, 3 phosphate groups

ATP phosphate hydrolysis

-30.5 kJ/mol energy given off

• The "high energy" character of phosphoanhydride bonds results from:

1) Increased resonance stabilization of the hydrolysis product 2) The destabilizing effect of electrostatic repulsions between the charged phosphates at neutral pH. 3) Increased solvation energy of the hydrolysis product.

Metabolic pathways have 3 key characteristics

1) Whole pathway is irreversible. 2) Rate-determining step: They have an highly exergonic step (∆G << 0)that usually is the 1st committed step. Since it goes to completion, it confers directionality & insures irreversibility. 3) Catabolic & anabolic pathways involving the interconversion of 2 metabolites differ in key exergonic reactions.

Electrochemical cell ~

Iron will be reduced since it has a more positive Eo

Metabolism

set of life-sustaining chemical reactions in cells. It is the process by which cells use free energy to carry out their various functions. - anabolism and catabolism are concerted pathways

Catabolism & Anabolism are Concerted Pathways

• In degradative pathways (catabolism) complex nutrients (proteins, carbohydrates & lipids) are broken down and free energy (∆G) is released in the form of ATP and/or NADPH. • In synthetic pathways (anabolism) small molecules (amino acids, sugars & glycerol) are converted to complex molecules using ATP or NADPH as the free energy source.

Experimental Approaches to the Study of Metabolism

• Metabolic pathways are often studied by tracing metabolites labeled with radionuclides or NMR-active isotopes. • The steps of a pathway can be identified by examining how metabolic inhibitors and genetic defects lead to the accumulation of pathway intermediates. • DNA microarrays and proteomics techniques are used to determine the genetic expression of metabolic enzymes.

Key Concepts: Overview of Metabolism

• Metabolism is the set of life-sustaining chemical reactions in cells. It is the process by which cells use free energy to carry out their various functions. * Catabolism (degradation) is the breakdown of nutrients and cell constituents to salvage their components and/or to generate energy. * Anabolism (biosynthesis) is the synthesis of biomolecules from simpler components. • Mammalian nutrition involves the intake of macronutrients (proteins, carbohydrates & lipids) and micronutrients (vitamins & minerals) • Different organisms use different strategies for capturing free energy from their environment and can be classified by their requirement for oxygen. * Aerobes require O2 for nutrient breakdown. * Anaerobes do not use O2 but use sulfates or nitrates as oxidizing agents.

Metabolic Pathways are Controlled by Thermodynamics

• Most pathways are near equilibrium (∆G = 0), and the law of mass action dictates the rate of flow (flux) of metabolites. • However, in any given pathway there is 1 reaction that is far from equilibrium. This is referred to as the rate-determining step, & it controls the flux in the pathway. (usually first step)

Key Concepts 14.2: "High-Energy" Compounds: ATP is the Primary Energy Currency of Cells!!!

• Organisms capture the free energy released on degradation of nutrients as "high-energy" compounds such as ATP, whose subsequent breakdown is used to power otherwise endergonic reactions. • The "high energy" of ATP is related to the large negative free energy change for hydrolysis of its phosphoanhydride bonds. • ATP hydrolysis can be coupled to an endergonic reaction such that the net reaction is favorable. • Phosphoryl groups are transferred from compounds with high phosphoryl group-transfer potentials to those with low group-transfer potentials. • The thioester bond in acetyl-CoA is a "high-energy" bond.

Experimental Approaches to the Study of Metabolism Summary

• Studies of metabolic pathways determine the order of metabolic transformations, their enzymatic mechanisms, their regulation & their relationships in metabolic processes in other tissues. • Metabolic pathways are studied using isotopic tracers, enzyme inhibitors, natural & engineered mutations, DNA microassays & proteomics techniques. • Systems biology endeavors to quantitatively describe the properties & dynamics of biological networks as a whole through the integration of genomic, transcriptomic, proteomic & metabolomic information.

Oxidation-Reduction Reactions Summary

• The coenzymes NAD+ and FAD are reversibly reduced during the oxidation of metabolites. • The Nernst equation relates the electromotive force of a redox reaction to the standard reduction potentials & concentrations of the electron donors & acceptors. • Electrons flow spontaneously from the reduced member of a redox couple with the more negative reduction potential to the oxidized member of a redox couple with the more positive reduction potential.

"High-Energy" Compounds Summary

• The free energy of the "high-energy" compound ATP is made available through cleavage of 1 or both of its phosphoanhydride bonds. • An exergonic reaction such as ATP or PPi hydrolysis can be coupled to an endergonic reaction to make it more favorable. • Substrate-level phosphorylation is the synthesis of ATP from ADP by phosphoryl group transfer from another compound. • The common product of carbohydrate, lipid & protein catabolism, acetyl-CoA is a "high-energy" thioester.

Overview of Metabolism Summary

• The free energy released from catabolic oxidation reactions is used to drive endergonic anabolic reactions. • Hetertrophic organisms obtain their free energy from compounds synthesized from chemolithotrophic or photoautotrophic organisms. • Food contains proteins, carbohydrates, fats, water, vitamins & minerals. • Metabolic pathways are sequences of enzyme-catalyzed reactions that occur in different cellular locations. • Near-equilibrium reactions are freely reversible, whereas reactions that function far from equilibrium serve as regulatory points & render metabolic pathways irreversible. • Flux through a metabolic pathway is controlled by regulating the activities of enzymes that catalyze its rate-determining steps.

Conformational Changes Drive Adenylate Kinase Reaction ~

• When substrate binds to adenyl kinase, two 30-residue domains close over the substrates which prevent H2O from entering the active site. • The movement of one of the domains in response to 4 charged residues nearby triggers the rearrangement around the substrate-binding site & phosphoryl group-transfer.

Overview of Catabolism

•Carbohydrates, proteins & lipids are first degraded to simple sugars (glucose), amino acids & fatty acids & glycerol-and then to the common intermediates, pyruvate & acetyl CoA. • Enzymes catalyze all of these reactions by oxidation-reduction, group transfer, eliminations, isomerizations & reactions that break carbon-carbon bonds (hydrolases, lyases & ligases)