Product stabilizations in hydrolysis Relief of electrostatic repulsion by charge separation Ionization Isomerization Resonance
Jan 04, 2016
Product stabilizations in hydrolysis
Relief of electrostatic repulsion by
charge separation
Ionization
Isomerization
Resonance
ATP Provides Energy by Group Transfers, not by Simple Hydrolysis
Energy from group transfer Two step reaction
Phosphoryl group transfer Phosphoryl group displacement
Energy directly from ATP hydrolysis Hydrolysis of bound ATP (GTP)
protein conformational change mechanical motion, activity
transition (active inactive) Muscle contraction, movement of
enzymes along DNA, movement of ribosome along mRNA, helicase, GTP-binding proteins
Phosphate Compounds
Phosphate compounds in living organisms High-energy compounds : G’o : <-25 kJ/mol
ATP: G’o = -30.5 kJ/mol
Low-energy compounds : G’o : >-25 kJ/mol Glucose-6-phosphate: G’o = -13.8 kJ/mol
Flow of phosphoryl group From a compound with high phosphoryl group transfer
potential to low potential
(1) PEP + H2O pyruvate + Pi ; G’o = -61.9 kJ/mol(2) ADP + Pi ATP + H2O ; G’o = +30.5 kJ/molSum: PEP + ADP pyruvate + ATP ; G’o = -31.4 kJ/mol
Nucleophilic Displacement Reactions of ATP
Reactions of ATP SN2 nucleophilic displacements
Nucleophiles; O of alcohol or carboxylate/ N of creatine, Arg, His
Nucleophilic attacks of the three phosphates
- phosphoanhydride bond has a higher energy (~46 kJ/mol) than - (~31 kJ/mol)
PPi 2 Pi by inorganic phosphatase G’o = -19 kJ/mol
further energy “push” for the adenylylation reaction
Nucleophilic Displacement Reactions of ATP
Energy-coupling mechanism via adenylylation reaction
Bioluminescence of Firefly
Conversion of chemical energy to light energy using ATP
Assembly of Informational Macromolecules Requires Energy
DNA or RNA synthesis
NTP release of PPi and hydrolysis to 2 Pi
Protein synthesis
Activation of amino acid by adenylylation
ATP Energizes Active Transport and Muscle Contraction
ATP for molecular transport 2/3 of the energy at rest is used
for Na+/K+ pump in human kidney and brain
Contraction of skeletal muscle ATP hydrolysis in myosin head Movement along the actin
filament
Transphosphorylation Between Nucleotides
NTPs and dNTPs Energetically equivalent to ATP Generation from ATP
Nucleoside diphosphate kinase ATP + NDP (or dNDP) ADP + NTP (or dNTP)
G’o ≈ 0 Driven by high [ATP]/[ADP] Ping-pong mechanism
Transphosphorylation Between Nucleotides
Adenylate kinase 2ADP ATP + AMP, G’o ≈ 0 Under high ATP demanding conditions
Creatin kinase ADP + PCr ATP + Cr, G’o = -12.5kJ/mol PCr : Phosphoryl reservoir for high ATP demanding conditions
in muscle, brain, and kidney Inorganic Polyphosphate (PolyP) as a Phosphate Group
Donor PolyP
Polymer of phosphate Phosphagen: reservoir of phosphoryl groups
In prokaryotes PolyP kinase-1 : synthesis of polyP
ATP + polyPn ADP + polyPn+1
PolyP kinase-2 : synthesis of GTP or ATP GDP + polyPn+1 GTP + polyPn
13.3 Biological Oxidation-Reduction Reactions
Electron flow can do biological work
Electromotive force (emf) Force proportional to the difference in electron affinity between two
species “Do work”
Glucose (e- source) sequential enzymatic oxidation e- release
Flow e- via e- carriers O2
e.g. generation of proton motive force in mitochondria to
generate ATP emf; provide energy for biological works
Oxidation States of C in the Biosphere
Oxidation state of C Number of electrons owned by C depends on electronegativity of bonding atoms O> N> S> C> H In biological system; biological oxidation = dehydrogenation
Biological Oxidation Often Involve Dehydrogenation
4 ways for electron transfer Direct electron transfer via redox pairs
Fe2+ + Cu2+ Fe3+ + Cu+
Transfer of hydrogen atomsAH2 A + 2e- + 2H+
AH2 + B A + BH2
Transfer of hydride ion (:H-) Direct combination with O2
R-CH3 + 1/2O2 R-CH2-OH Reducing equivalent
A single e- equivalent participating in an oxidation-reduction reaction Biological oxidation
Transfer of two reducing equivalents
Reduction Potential measures for e- affinity
Standard reduction potential, Eo
A measure of affinity of electron Measurement of Eo
Standard reference half reaction (hydrogen electrode)
H+ + e- 1/2H2 , Eo = 0 V
Connection of the hydrogen electrode to another half cell (1M of oxidant and reductant, 101.3 kPa)
The half cell with the stronger tendency to acquire electrons : positive Eo
Reduction potential E E = E o + RT/nF ln [e- acceptor]/[e- donor]
n: the number of e- transferred/molecule F; Faraday constant
E = E o + 0.026V/n ln [e- acceptor]/[e- donor] at 298K
Standard reduction potential at pH 7.0, E’o
Standard Reduction Potentials
Free Energy Change For Oxidation Reduction Reaction
Oxidation-reduction reaction The direction of e- flow
; to the half-cell with more positive E G = -nFE or G’o = -nFE’o
Calculation of G Standard conditions, pH 7, 1M of each components
(1) Acetaldehyde + 2H+ + 2e- ethanol, E’o = -0.197 V (2) NAD+ + 2H+ + 2e- NADH + H+, E’o = -0.320 V (1) - (2) = Acetaldehyde + NADH + H+ ethanol + NAD+ E’o = E’o of e- acceptor - E’o of e- donor = -0.197 V - (-0.320 V) = 0.123 V G’o = -2 (96.5 kJ/V mol)(0.123V) = -23.7 kJ/mol
1 M acetaldehyde and NADH, 0.1M ethanol and NAD+
Eacetaldehyde = E’o + RT/nF ln [acetaldehyde]/[ethanol] = -0.197 V + 0.026 V/2 ln 1/0.1 = -0.167 V ENADH = E’o + RT/nF ln [NAD+]/[NADH] = -0.320 V + 0.026 V/2 ln 1/0.1 = -0.350 V E = -0.167 V - (-0.350 V) = 0.183 V G = -2 (96.5 kJ/V mol)(0.183V) = -35.3 kJ/mol
e- carriers
Complete oxidation of glucose C6H12O6 + 6O2 6 CO2 + 6 H2O G’o = -2,840 kJ/mol e- removed in oxidation steps are transferred to e- carriers
Electron carriers NAD+, NADP+ : soluble carrier FMN, FAD : prosthetic group of flavoproteins Quinones (ubiquinone, plastoquinone) : membrane Iron-sulfur proteins, cytochromes : cytosol or membrane
NADH and NADPH
NAD(P) Nicotinamide adenine dinucleotide (phosphate) Accept hydride (:H-) released from oxidation (dehydrogenation) of
substrate : either A side or B side, not both sides NAD(P)+ + 2H+ + 2e- NADH + H+ NAD(P)+ : + indicates oxidized form, not the net charge of NAD(P) which
is -
Benzenoid ring Quinonoid ring
Metabolic Roles of NADH and NADPH
Metabolic Roles of NADH and NADPH NADH
Functions in oxidations in catabolic reactions (NAD+ > NADH) NADPH
Functions in reductions in anabolic reactions (NADPH > NADP+ ) Oxidoreductases or dehydrogenases
Specific preference to NAD or NADP Spatial segregation
Oxidation of fuels in mitochondria Biosynthesis in cytosol
AH2 + NAD+ A + NADH + H+
Alcohol dehydrogenase CH3CH2OH + NAD+ CH3CHO + NADH + H+
A + NADPH + H+ AH2 + NADP+
Rossmann fold NAD or NADP binding domain Relatively loose binding diffusion to other enzyme
Dietary Deficiency of Niacin: Pellagra
Niacin (nicotinic acid)
Source of the pyridine-like ring of NAD and NADP
Low amount of synthesis from Trp in human
Pellagra (rough skin) Disease from niacin deficiency Can be cured by niacin or nicotinamide, not by nicotine
Flavin Nucleotide
Flavin nucleotides FMN : flavin mononucleotide FAD: falvin adenine dinucleotide Derived from riboflavin One or two electron transfer
Flavoproteins Enzymes catalyzing oxidation-reduction reactions using FMN or
FAD as coenzyme Tight-bound flavin nucleotides
Different E’o from that of free flavin nucleotide FAD in succinate dehydrogenase : E’o = 0 V Free FAD : E’o = -0.219 V
Some contains additional tightly bound inorganic ions (Fe or Mo) c.f. Cryptochromes
Flavoproteins mediating the blue light effect in plant and controlling circadian rhythms in mammals
Flavin Nucleotide
360nm absorption
450nm absorption
370 and 440 nm absorption
Enzymes with Electron Carriers