Mechanisms Responsible for Food Intolerances Biochemical and Physiological Reactions.
Bioenergetics and Biochemical Reactions
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Transcript of Bioenergetics and Biochemical Reactions
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Bioenergetics and Biochemical Reactions
Chapter 13
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Life needs energy
• Living organisms are built of complex structures
• Building complex structures (low in entropy) is only possible when energy is spent in the process
• The ultimate source of this energy on Earth is the sunlight
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Metabolism sum of all chemical reactions in the cell
• Series of related reactions: metabolic pathways
• Pathways that are primarily energy-producing
– Catabolism
• Pathways using energy to build complex structures
– Anabolism or Biosynthesis
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Metabolism uses a limited chemical toolset
• All metabolic reactions involve the formation or breaking of a covalent bond
• Five classes of reactions that occur in biochemistry
1. Oxidation-Reduction (REDOX)
2. Carbon-Carbon bond formation/breaking
3. Internal Rearrangements
- Isomerizations and Eliminations
4. Group Transfers
5. Free Radical Reactions
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Living Systems Follow the Laws of Thermodynamics
• Living organisms cannot create energy from nothing
• Living organisms cannot destroy energy
• Living organism may transform energy from one form to another
• In the process of transforming energy, living organisms must increase the entropy of the universe
• Living organisms extract useable energy from their surroundings, and release useless energy (heat)
– cells are open systems
– living systems are never at equilibrium
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DG = DH - TDS
• G: Gibbs Free Energy (J/mol) – negative – exergonic
– positive – endergonic
• H: Enthalpy (J/mol) – reflects the number and kind of bonds in reactants vs. products
– negative: exothermic (releases heat)
– positive: endothermic (takes up heat from surroundings)
• S: Entropy (J/mol*K) – positive: products are more disordered
– negative: products are more ordered
• T: Temperature (K)
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Gibbs Free Energy: DG
• DG for spontaneously reacting systems is always NEGATIVE
• Source of energy for living cells & their reactions
• Measure of how far from equilibrium a system or reaction is:
– amount of work that can be done
– DG at equilibrium is 0
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Living Systems are NOT at Equilibrium
• Tendency of a reaction to move towards equilibrium is a driving force
• DG represents the magnitude of this driving force
• DG is a function of the standard free energy change DG°
DG = DG° + RTln [products]/[reactants]
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Biochemical Standard Free Energy Change
DG'° • Biochemical Standard conditions:
– 298 K (25°C)
– reactants & products initially at 1 M concentrations
– partial pressures of 101.3 kPa (1 atm)
– [H+] = 10-7 (pH = 7.0)
– [H2O] = 55.5 M
• Standard transformed constants: DG'° & K'eq
• DG'° and K'eq are both physical constants
– describe the difference in free energy content between reactants and products under standard conditions
– measure of driving force under physiologically relevant conditions.
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DG'° and K'eq
DG'° = -RT lnK'eq
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DG and DG'° are Different
• DG'° - standard free energy – is a constant physical characteristic of a reaction
• DG – actual free energy – Function of reactant & product concentrations, and temperature that may
not match standard conditions
– DG is changes as the reaction progresses
• negative in spontaneous reactions progressing towards equilibrium
• less negative as reaction proceeds (closer to equilibrium)
• 0 at the point of equilibrium
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DG and DG'° are Related
• Consider a chemical reaction:
aA + bB cC +dD
DG = DG'° + RT ln [C]c [D]d
[A]a [B]b
• Actual prevailing concentrations in the system
• defined as the mass-action ratio, Q
DG = DG'° + RTlnQ
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DG = DG'° + RT ln [C]c [D]d [A]a [B]b
• To find the actual free energy, DG
– enter in actual concentrations of A, B, C, D
– R, T, and DG'° are standard constant values
• When a reaction has reached equilibrium: DG'° = -RTlnK'eq
• Spontaneity depends on DG, not DG'°
– DG is a maximum for energy delivery (always thermal loss)
– does not take into account activation energy
– DG is independent of pathway by which reactions occur
• Living cells utilize catalysts (enzymes) to lower activation energies and speed up reaction rates (will not change DG)
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For coupled reactions (1) and (2)
(1) A B ΔG’1
(2) B C ΔG’2
• Standard free-energies for two coupled reactions
are additive: – A C DG ’1+2 = ΔG’1 + ΔG’2
• Equilibrium constants for two coupled reactions is multiplicative:
– A C K'eq 1+2 = (K'eq1)(K'eq2)
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Review of Organic Chemistry
• Most reactions in biochemistry are heterolytic processes
– bonding electrons move as pairs (no radicals)
• Nucleophiles react with Electrophiles
– nucleophiles – donate electrons
– electrophiles – seek electrons
• Heterolytic bond breakage often gives rise to transferable groups, such as protons
• Oxidation of reduced fuels often occurs via transfer of electrons and protons to a dedicated redox cofactor
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Chemical Reactivity
Most reactions fall within few categories:
• Cleavage and formation of C–C bonds
• Cleavage and formation of polar bonds
• Internal rearrangements
• Eliminations (without cleavage)
• Group transfers (H+, CH3+, PO3
2–)
• Oxidation-Reduction (e– transfers)
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Chemistry at Carbon
• Covalent bonds can be broken in two ways
• Homolytic cleavage is very rare
• Heterolytic cleavage is common, but the products are highly unstable and this dictates the chemistry that occurs
• carbanion
• carbocation
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Homolytic vs. Heterolytic Cleavage
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Common Nucleophiles and Electrophiles in Biochemistry
nucleophiles donate e-
electrophiles seek e-
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Carbonyl Groups are Important in Chemical Transformations in Metabolic Pathways
• Carbonyl oxygen is electron withdrawing: electrophilic carbon
• Facilitate carbanion formation
• Delocalizes carbanion negative charge
• Capacity as electron sinks often augmented by metal ion or acid interactions
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Examples of Nucleophilic Carbon-Carbon Bond Formation Reactions (common carbonyl chemistry)
related biochemical process
glycolysis
citric acid cycle
fatty acid catabolism
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Isomerizations and Eliminations: No Change in Oxidation State
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Addition–Elimination Reactions
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Group Transfer Reactions
• Proton transfer, very common
• Methyl transfer, various biosyntheses
• Acyl transfer, biosynthesis of fatty acids
• Glycosyl transfer, attachment of sugars
• Phosphoryl transfer, to activate metabolites
‒ also important in signal transduction
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Phosphoryl Transfer: Nucleophilic Displacement
Nucleophile forms a partial bond to the phosphorous center
giving a pentacovalent intermediate or a pentacoordinated
transition state
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Phosphoryl Transfer from ATP
ATP is frequently the donor of the phosphate in the biosynthesis of phosphate esters.
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Hydrolysis of ATP is highly favorable under standard conditions
• Better charge separation in products
• Better solvation of products
• More favorable resonance stabilization of products
o DG'° = -30.5 kJ/mol
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Actual DG of ATP hydrolysis differs from DG'
• DGp (phosphorylation potential) depends on:
– The standard free energy
– The actual concentrations of reactants and products
• The free-energy change is more favorable if the reactant’s
concentration exceeds its equilibrium concentration
• True reactant and the product are Mg-ATP and Mg-ADP, respectively
• In vivo, energy released by ATP hydrolysis is greater then the
standard free energy change (more negative: ≈ -(50 to 70) kJ/mol)
]MgATP[
]P[]MgADP[ln'
2
i
DD RTGGp
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Several phosphorylated compounds have large DG' for hydrolysis
• electrostatic repulsion within the reactant molecule is relieved
• The products are stabilized via resonance, or by more favorable solvation
• The product undergoes further tautomerization
(Phosphoenolpyruvate, 1,3-biphophosphoglycerate, phosphocreatine)
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Phosphates: Ranking by the Standard Free Energy of Hydrolysis
Reactions such as PEP + ADP => Pyruvate + ATP are favorable, and can be used to synthesize ATP.
Phosphate can be transferred from compounds with more negative ΔG' to those with less negative ΔG'.
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Hydrolysis of Thioesters
• Hydrolysis of thioesters is strongly favorable
– such as acetyl-CoA
• Acetyl-CoA is an important donor of acyl
groups
– Feeds two-carbon units into metabolic
pathways
– Synthesis of fatty acids
• In acyl transfers, molecules other than water
accept the acyl group
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Coenzyme A • The function of CoA is to accept and carry acetyl groups • CoA is a reactive thiol group attached to a modified ADP
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Molecular Basis for Thioester Reactivity The orbital overlap between the carbonyl group and sulfur is not as good as the resonance overlap between oxygen and the carbonyl group in esters.
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ATP
• The energy in the ATP anhydride bonds is not liberated DIRECTLY via hydrolysis
• There is almost always a covalent intermediate
• The phosphoryl-intermediate is converted into product which has lower free energy than the reactants
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ATP • When ATP donates a group it is typically via an SN2 mechanism
• The nucleophile is part of the protein/compound that will gain the group
• ATP can also donate a pyro-phosphate or an adenylyl-phosphate
• Adenylylations gain more energy via the cleavage of the pyrophosphate side product
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Energy Requirements
• Macromolecular Synthesis
– Construction of proteins and nucleic acids or precursors
• Transport
– Energy is required to transport molecules against concentration gradients
• Motion
– Actin-myosin contractions and cell motility
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Shuffling Phosphates: Enzymes
• Nucleoside diphosphate kinase shuffles diphosphates from one class of nucleotide to another
• Adenylate kinase converts 2ADPs into 1 ATP and 1 AMP
• Creatine kinase phosphorylates ADP into ATP using Creatine-monophosphate as a source of Pi
• Polyphosphate Kinases (PPKs) catalyze phosphoryl transfers between polyphosphate and Nucleotides
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Oxidation-Reduction Reactions Reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation.
oxid
ation
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REDOX (oxidation-reduction reactions)
• Oxidation-reduction reactions are another major source of energy for cells
• Redox is simply electron shuffling
• The forces that accompany the movement of electrons can be optimized to do work
• Oxidation reactions are coupled to reduction reactions
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Conjugate Redox Pairs
Fe2+ + Cu2+ Fe3+ + Cu+ electron shuffling split into half reactions: Fe2+ Fe3+ + e- Cu2+ + e- Cu+
electron donor (reductant) e- + electron acceptor (oxidant) reducing agent (reductant): electron donating molecule oxidizing agent (oxidant): electron-accepting molecule
Fe2+ & Fe3+ make up a conjugate redox pair
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Reversible Oxidation of a Secondary Alcohol to a Ketone
• Many biochemical oxidation-reduction reactions involve transfer of two electrons
• In order to keep charges in balance, proton transfer often accompanies electron transfer
• In many Dehydrogenases, the reaction proceeds by a stepwise transfers of proton (H+) and hydride (:H–)
• catalyze oxidation reactions
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Electron Transfers
• Reducing equivalents refers to the number of electrons transferred in a reaction
• Biological systems use 4 mechanisms to transfer electrons – Directly as electrons (our Fe2+ + Cu2+ example)
– as Hydrogen atoms (one proton + 1 e-)
– as Hydride ion (one proton + 2 e-)
– direct combination with oxygen (oxidation of hydrocarbon to alcohol)
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Reduction Potential (E)
• Reduction Potential is a measure of the affinity of the acceptor for electrons
• E’ is the standard reduction potential in V
• More positive E means more affinity for electrons
DE = DE’ + RT ln [electron acceptor] nF [electron donor] R = gas constant (8.315 J/mol*K) T = temperature (K) F = Faraday constant (96,480 J/V*mol) n = number of electrons transferred per molecule
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Reduction Potential (E)
• Reduction Potential is a measure of the affinity of the acceptor for electrons
• E0 is the standard reduction potential in V
• More positive E means more affinity for electrons
• We calculate the E via the Nernst Equation
DE = DE’ + 0.026V ln [electron acceptor] n [electron donor] R = gas constant (8.315 J/mol*K) T = 298 K F = Faraday constant (96,480 J/V*mol) n = number of electrons transferred per molecule
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Reduction Potential & Free Energy
• Electron acceptor has a higher E' then the donor
∆E' = E'(e- acceptor) – E'(e- donor)
DE'° is positive for energetically favorable reactions
• Reduction potential is related to free energy
DG = -nFDE
DG'° = -nFDE'°
For negative DG need positive DE E(acceptor) > E(donor)
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Below are the E’ for the indicated electron carriers: E’ Cyt c1 (Fe3+) + e- Cyt c1 (Fe2+) 0.22 NAD+ + H+ + 2e- NADH -0.32 ½ O2 + 2H+ + 2e- H2O 0.82 Place the electron carriers in order in which they are most likely to act in carrying electrons.
NAD+
Cyt c1
O2
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Electron Shuttles
• Oxidation of glucose is used to supply energy for ATP synthesis
• Enzymes act on the glucose to shuffle electrons
• Most redox enzymes use cofactors designed to shuttle electrons
– NADH/NADPH – pyridine nucleotide cofactors
– FMN/FAD – flavin nucleotide cofactors
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NAD and NADP are common redox cofactors
• These are commonly called pyridine nucleotides
• They can dissociate from the enzyme after the reaction
• In a typical biological oxidation reaction, hydride from an alcohol is transferred to NAD+ giving NADH
NAD : Nicotinamide adenine dinucleotide NADP: Nicotinamide adenine dinucleotide phosphate
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NAD and NADP are common redox cofactors
• NAD+ : usual coenzyme in oxidations
- mitochondrial matrix
• NADPH: usual coenzyme in reductions
- cytosol
functional and spatial specialization
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Formation of NADH can be monitored
by UV-spectrophotometry • Measure the change of absorbance at 340 nm
• Very useful signal when studying the kinetics of
NAD-dependent dehydrogenases
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Rossmann fold:
• structural motif for binding NAD or NADP in dehydrogenases
• loose association between the dehydrogenase and the coenzyme
• NAD/NADP can readily diffuse from one enzyme to another
• water soluble electron shuttle
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Flavin cofactors allow one- or two- electron transfers
• Can participate in a greater diversity of reactions then NAD(P)-linked dehydrogenases
• Also undergo a shift in absorption spectrum upon oxidation
• Permits the use of molecular oxygen as an ultimate electron acceptor
– flavin-dependent oxidases
• Flavin cofactors (FAD & FMN) are tightly bound to proteins
– do not diffuse from enzyme to enzyme
– temporary electron storage for flavoproteins during catalysis
FAD : flavin adenine dinucleotide FMN: flavin mononucleotide
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FAD/FMN
Pathway involvement:
• oxidative phosphorylation
• photophosphorylation
• photolyase reactions
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Chapter 13: Summary
• The rules of thermodynamics and organic chemistry still apply to living
systems
• Reactions are favorable when the free energy of products is much lower
than the free energy of reactants
– DG depends on Q as well as DG’
– DG dictates whether reactions will occur in the cell
• Unfavorable reactions can be made possible by chemically coupling a highly
favorable reaction to the unfavorable reaction
• Redox reactions commonly involve transfer of electrons from reduced
organic compounds to specialized redox cofactors
– Reduced cofactors can be used in biosynthesis & ATP synthesis