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Biochemistry – Ch 14 – Metabolism

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Definition of Metaoblism
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It is the overal process through which living systems acquire and utilize free energy to carry out their functions Thye couple exergonic reactions of nutrient breakdown to endergonic processes required to maintain the living state
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Catabolism
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(Degradation): Nutrients and cell constituents browken down to salvage componenets and/or generate energy.
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Anabolism
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(Biosynthesis): Biomolecules are synthesized from simpler components
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Autotrophs
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Self-feeders (synthesize thier own cellular constituents from H₂O, CO₂, NH₃, H₂S
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Photoautotrophs
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Acquire free energy from sunlight
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Chemolithotrophs
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Obtain free energy form oxidation of inorganic compounds such as NH₃, H₂S. Fe²⁺
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Heterotorphs
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Oxidize organic compounds to make ATP
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General on ATP
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ATP is the energy carrier for most biological reactions
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Organisms can be classified by the identitiy of the oxidizing agent. (4)
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1. Obligate Aerobes 2. Anaerobes 3. Faculatative Anaerobes 4. Obligate Anaerobes
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Obligate Aerobes
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Must use O2
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Anaerobes
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Use sulfate or nitrate
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Faculattive Anaerobes
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Can grow in presence or absence of O2 (i.e. E. coli)
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Obligate Anaerobes
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Poisoned by O2
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Metabolic pathyways are..
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Metabolic pathways are series of connected enzymatic reactions that produce specific products. There are over 2000 known metabolic reactions
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Metabolites
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The reactants, intermediates and products of metabolic pathways.
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Metabolic Reaction links
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Box 14-2
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Carbohydrate Metabolism
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This figure shows most of the metabolic pathways that we will discuss in this half of the course, namely, the glycolysis pathway, gluconeogenesis, the citric acid cycle, and the pentose phosphate pathway. If you click on the glycolysis/ gluconeogenesis node, you will get the map on the next slide
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Glycolysis/Gluconeogenesis
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• This figure shows the glycolysis and gluconeogenesis pathways. • It also give the enzyme classification (EC) code that will help you search for structures, sequences, and other information about it
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Metabolic Pathways are comparmentalized.
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Pathways in eukaryotic cells occur in separate organelles or cellular locations. This exerts a greater control over opposing pathways and intermediates can be controlled by transport across the separating membraines
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Oxidative Phosphorylation Occurs where?
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In the mitochondria
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Glycolysis Occurs Where?
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Cytosol
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Fatty acid Biosynthesis Occurs Where?
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Cytosol
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Gluconeogenesis occurs where?
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In the liver to maintain constant level glucose in the circulation
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Triacylglycerols are stored where?
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Adipose Tissues
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Isozymes
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Enzymes that catalyze the same reaction but are encoded by different genes that have different kinetic of regulatory properties
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Examples of Isozymes
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Lactate dehydrogenase (LDH): type M [skeletal muscle and liver] participates in the reduction of pyruvate to lactate (using NADH) while type H [heart muscle] catalyzes the reverse reaction.
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Where is ATP made?
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In the mitochondria
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Where is ATP used?
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In the cytosol
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Where are fatty acids made?
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In the cytosol with the use of acetyl-CoA
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Where is acetyl-CaA made?
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In the mitochondria
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Major functions of the mitochondrion (5)
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1.TCA 2.ETC 3. oxidative phosphoylation 4. FA oxidation 5. amino acid breakdown
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Major functions of the cytosol (4)
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1. Glycolysis 2. Pentose phosphate pathway 3. Fatty acid biosynthesis 4. Many rxns of gluconeogenesis
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Major Functions of Nucleus (2)
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1. DNA replication and transcription 2. RNA processing
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Major Function of the Lysosome (1)
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1. Enzymatic digestion of cell components and ingested matter.
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Major Functions of the Golgi apparatus (2)
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1. Post translational processing of memraine and secretory proteins 2. Formation of plasma membrane and secretory vesicles
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Major Functions of the RER (2)
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1. Synthesis of membrane-bound and secretory proteins
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Major Function of the SER (1)
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Lipid and steroid biosynthesis
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Major Function of the Peroxisome (glyoxysome in plants) (2)
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1. Oxidative reactions catalyzed by aa oxidases and catalase 2. Glyoxylate cycle reaction in plants
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Roles of ATP and NADP+ in Metabolism
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In catabolic pathways, complex metabolites are exergonically broken down into simpler products, creating ATP or NADPH. In anabolic processes, simple molecules are converted inot complex molecules at the expense of degradation of the energy sotrage molecules, ATP and/or NADPH.
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Very few metabolites are used to synthesize a large variety of biomolecules (3)
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• Acetyl-Coenzyme A (acetyl-CoA) • Pyruvate • Citrate cycle intermediates
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Three main pathways for energy production
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• Glycolysis • Citric acid cycle • Oxidative-Phosphorylation
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Overview of Catabolism (4)
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• Complex metabolites are broken down into their monomeric units • Then to the common intermediate, acetyl-CoA • The acetyl group is then oxidized to CO2 via the citric acid cycle while NAD+ and FAD are reduced to NADH and FADH2. • Reoxidation of NADH and FADH2 by O2 during oxidative phosphorylation yields H2O and ATP
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Co2 is…
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The most oxidized state
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Thermodynamic considerations
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A + B ↔ C + D; ΔG = ΔGo’ + RT ln ([C][D]/[A][B]) When close to equilibrium, [C][D]/[A][B]≈Keq and ΔG ≈ 0. • This is true for many metabolic reactions – near-equilibrium reactions • When reactants are in excess, the reaction shifts toward products • When product are in excess, the reaction shifts toward reactants
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However, some reactions are not near equilibrium and are thus irreversible
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– This is true of highly exergonic reactions – These metabolic reactions therefore control the flow of reactants through the pathway/cycle and they make pathways irreversible. 1. Metabolic pathways are irreversible 2. Every metabolic pathway has a first committed step 3. Catabolic and anabolic pathways must differ (so that they can be separately regulated)
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Metabolic Pathways are irreversible
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They have large negative free energy changes to prevent them running at equilibrium. If two metabolites are interconvertible, the two interconversion pathways must be different Independent routes means independent control of rates. The need to control the amounts of either 1 or 2 independent of each other.
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4 Types of control Flux at committed step(s)
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1. Allosteric control 2. Covelent modification 3. Substrate cycles 4. Genetic control
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Allosteric Control
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By sustrates, products or coenzymes of the pathway (i.e. CTP in ATCase)
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Covelent Modification
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(de) phosphorylation by (phosphatases) kinases which are themselves regulated.
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Substrate Cycles
Substrate Cycles
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Fluxes through r and f can be separately regulated. One way exercgonic reaction (intermediates)
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Genetic Control
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up or down regulated production or activation of an enzyme
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Thermodynamics of phosphate compounds
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Adenosine diphosphate, one phosphoester bond and one phosphoanhydride bond Adenosine monophosphate one phosphoester bond. Which bonds are exergonic? High energy bonds. Hydrolysis of ATP
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Phosphoryl-transfer reactions
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Coupling of Reactions
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These highly exergonic reactions are coupled to numerous endergonic biochemical processes so as to drive them to completion.ATP is generated by coupling its formation to more highly exergonic metabolic reactions The bioenergetic utility of phosphoryl-transfers stems from their kinetic stability to hydrolysis combined with their capacity to transmit relatively large amounts of free energy. ΔG of ATP hydrolysis varies with pH, divalent metal ion concentration, and ionic strength
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∆G of ATP hydrolysisi is in the middle of biological phosphate hydrolysis
∆G of ATP hydrolysisi is in the middle of biological phosphate hydrolysis
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∆G of phosphoenolpyruvate
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-61.9 kJmol⁻¹
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∆G of ATP
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-30.5 kJmol⁻¹
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The P~P is a high energy bond
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Because of the concentrations of ATP, ADP, and Pi, the ΔG of a reaction is usually -50 kJ/mol. Usually anything over 25 kJ/mol is called a high energy bond. These bonds are sometimes designated as a ~, or a squiggle: AR-P~P~P (adenyl, ribosyl, phosphoryl).
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Why is the hydrolysis of ATP energetic?
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1. Resonance stabilization of a phosphoanhydride bond is less than that of its hydrolysis products. 2.Electrostatic repulsion between three of four negative charges on the phosphate at neutral pH.ΔG becomes even lower at higher pH values which produces more charge. 3.Solvation energy of a phosphoanhydride bond is less than that of its hydrolysis products.
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Coupled Reactions
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The hydrolysis will be high nerg. The tautomerization will be very exergonic. Add together.
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Resonance structures for phosphate bonds
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In phosphoanhydride, the P=O are each competing for the same anhydride oxygen lone pairs. In the separated phosphates, there is no competition so the resonance is better. Finally, there is electrostatic repulsion between adjacent O- atoms in the phospho- anhydride (see zigzag line). This repulsion leads to destabilization of this form, favoring hydrolysis. They repulse each other (trying to escape each other) now water can stabilize each other.
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Sample ∆G and K calculations
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Other High Energy Compounds
Other High Energy Compounds
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All have properties like ATp
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Compounds liek α-D-glucose-6-phosphat and 1-Glycerol-3-phosphat have…
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…smaller ∆G’s than ATP and have no significant resonance differences or charge repulsions
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∆G of hydrolysis
∆G of hydrolysis
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Thioesters***
Thioesters***
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• Thioesters are found today in Coenzyme A (CoA) which links to various groups, most notably acetyl and is a common product of carbohydrate, fatty acid, and amino acid catabolism • Coenzyme A is sometimes written as CoASH since it has a reactive SH group • ΔG0′ for hydrolysis of the thio- ester bond is -31.5kJ/mol, 1kJ/mol more then ATP hydrolysis!!
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The Role of ATP
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1. Kinases 2. Introconversion of nutcleoside triphosphates ATP, GTP, CTP, UTP 3. Physiological Processes 4. Additional phophoanhydride cleavage in highly endergonic reactions.
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ATP with interconversion of nucleoside triphosphates ATP, GRP, CTP, UTP
ATP with interconversion of nucleoside triphosphates ATP, GRP, CTP, UTP
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ATP as Kinases
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Early stages of nutrient breakdown transfers a phosphate to sugars
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ATP and additional phosphoanhydride cleavage in highly endergonic reactions
ATP and additional phosphoanhydride cleavage in highly endergonic reactions
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Formation of ATP
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1. Substrate level phosphorylation – direct transfer of a phosphate group to ADP from a high energy compound. 2. Oxidative phosphorylation and photophosphorylation- electron transfer generates an ion gradient that is used to generate ATP. 3. Adenylate kinase reaction AMP + ATP ↔ 2ADP ATP turnover per hour for the average person (about 3 moles) ATP + creatine ↔ phosphocreatine + ADP for ATP storage; ATP buffer in muscle and nerve cells.
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Oxidation and Reductions
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Electron transfer reactions are of great biological importance
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Oxidation and reductions: The mitochondrial electron transport chain
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In mitochondrial electron-transport chain, electrons are passed from NADH along a series of acceptors of increasing reduction potential (including FAD) until O2
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Oxidation and reductions: ATP generation
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ATP is generated from ADP and Pi by coupling its synthesis to this free energy cascade.
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Oxidation and reductions: NADH
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NADH thereby functions as an energy-rich electron transfer coenzyme
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Oxidation and reductions: NADH and NAD+
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Oxidation of NADH to NAD+ supplies sufficient free energy to generate 3 ATPs.
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Oxidation and reductions: NAD+
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NAD+ is an electron acceptor of many exergonic metabolite oxidations
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Oxidation
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Loss of electorns
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Reduction
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Gain of Electrons
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Oxidation and reductions
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Many redox reactions involve the breaking of a C-H bond and the loss of two bonding electrons. Electron acceptors will lose electorns until it his state of CO2. NADH will provide extra electrons in mitochondria for ATP
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Reduction of NAD+ to NADH
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NAD+/NADH and FAD/FADH2 are the main electron carriers • A hydride ion (H-) attacks NAD+ resulting in NADH, the reduced form of NAD+ • The final recipient of electrons is O2, however, O2 can only accept electrons one at a time • FAD can provide electrons one at a time
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Reduction of FAD to FADH₂
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Better for providing electrons • FAD accepts two hydrogen atoms (H•), one at a time resulting in FADH• And FADH2 • FAD is the oxidized form and FADH2 is the reduced form H2O at end of ETC
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Experimental approaches to study metabolism (3)
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Metabolic pathways can be understood at several levels 1. Sequence of reactions by which a nutrient is converted to end products. 2. Mechanism by which a intermediate is turned into its successor. 3. Regulation of the flow of metabolites in a pathway.
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Inhibitor and growth studies
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Inhibitors and growth studies are used to see what is blocked. If a reaction pathway is inhibited, products before the block increase and intermediates after the block decrease in concentration
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Genetic defects cause intermediates to accumulate (alcaptunurea)
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Usually degradates into water and CO2. But causes phenylpyruvate to accumulate and hurts brain. So must minimize ingestion of compound to minimize accumulation of intermediates.. The last step of Phyenyalanine→Tyrosine→p-hydroxyphenylpyruvate→Homogentisate to H2O + Co2 doesn’t work
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Phenylalanine
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Tyrosine
Tyrosine
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ATP in PHysiological Processes
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Muscle contraction Transport of ions agains concentration gradiets
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Radioactive tracers
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Can determine precursor in reactions and degradation time of precursor by seeing how long it took for it to get lableld. Example: heme. Label each possible precursor, will be radioactive when the right one is used