Driving Natural Systems: Chemical Energy Production and Use

Driving natural systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Driving natural systems: Chemical Mitochondria and bioenergetic energy production and use control Modelling systems of chemical reactions Driving natural Metabolism systems: Chemical energy production and use I Metabolism: the sum of the physical and chemical processes Chemical energy in an organism by which its and metabolism material substance is produced, maintained, and destroyed ATP usage and production [anabolism], and by which energy is made available Mitochondria and bioenergetic [catabolism] control

I Metabolism allows organisms to Modelling systems control biomass and energy of chemical reactions I A set of chemical transformations, often enzyme-catalysed I A complicated network: simpliﬁed through tools like ﬂux balance analysis I Metabolism provides the energy for inference and control I Metabolism is itself controlled and regulated: metabolic control analysis, active regulation Driving natural Free energy systems: Chemical energy production I Energy that can be harnessed to perform work and use I At constant temperature and pressure (which we shall assume), the appropriate expression is the Gibbs free energy G(p, T ) Chemical energy and metabolism G(p, T ) = U + pV − TS ATP usage and production

I Internal energy U, pressure p, volume V , temperature T , entropy S Mitochondria and bioenergetic I Change in free energy, where αj , Xj are a feature and associated control potential that inﬂuence our system (e.g. N, µ: copy number and Modelling systems chemical potential of chemical species): of chemical reactions X X dG = Vdp − SdT + µi dNi − Xj dαj i j

I We’ll consider chemical reactions, which take place at ﬁxed p and T

I Particle numbers Ni may be changed by reactions, and we also have to include the pair {∆Ψ, q} for charge across a membrane potential I Our Gibbs free energy change

X dG = µi dNi − F∆Ψdq i Driving natural Energy from chemical reactions systems: Chemical energy production I Reversible chemical reaction with Si substrates, Pi products, and and use stoichiometry given by ai , bi :

a1S1 + a2S2 + ... b1P1 + b2P2 + ... Chemical energy and metabolism I Change in free energy ATP usage and X production dG = µi dNi − F∆Ψdq i Mitochondria and bioenergetic I Chemical potential µ is a measure of the ‘concentration gradient’ in a control system Modelling systems 0 of chemical µi ∼ µi + RT ln ci reactions I For above reaction: µ dN = (µ0 + RT ln[S ]) × (−a ) Si Si Si i i µ dN = (µ0 + RT ln[P ]) × b Pi Pi Pi i i

X 0 X bj X aj µi dNi = C(a, b, µ ) + RT ln[Pj ] − RT ln[Sj ] i j j

I Broadly, if Z is total charge carried through a potential ∆Ψ (∆Ψmito ' −160 mV): ! Q [P ]bi ∆G = ∆G0 + RT ln i i − ZF∆Ψ Q ai i [Si ] Driving natural Activation energies systems: Chemical energy production and use

Q bi ∆ = ∆ 0 + i [Pi ] − ∆Ψ Chemical energy I G G RT ln Q ai ZF i [Si ] and metabolism I Reactions with a negative ∆G net release energy and are sometimes ATP usage and described as ‘happening spontaneously’ production I There is still an activation energy / geometric contraints to overcome Mitochondria and bioenergetic (though this is sometimes possible to do thermally) control

I ∆G doesn’t tell us how fast a reaction will progress Modelling systems of chemical reactions Driving natural Rates of chemical reactions systems: Chemical energy production I Chemical reaction and use

a1S1 + a2S2 + ... b1P1 + b2P2 + ... Chemical energy and metabolism I Law of mass action: reaction rate ν ∝ collision probability ∝ reactant ATP usage and concentration [Xi ] production Y Y ν = ν − ν = k [S ]ai − k [P ]bj Mitochondria and + − + i − j bioenergetic i j control

Modelling systems I Equilibrium constant is calculated when ν+ = ν− of chemical reactions Q eq bj k+ [Pj ] keq = = eq k Q ai − [Si ]

I At equilibrium, in absence of charge coupling: ! Q [P ]bi 0 = ∆G = ∆G0 + RT ln i i Q ai i [Si ]

I So 0 ∆G = −RT ln keq 0 I Negative ∆G → k+ > k− → forward reaction Driving natural ATP (adenosine triphosphate) as a cellular fuel source systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

I ATP is used to provide energy for most energy-demanding cellular Mitochondria and processes bioenergetic control I Neurotransmitter synthesis: provides the energy for inference Modelling systems I Gene expression and regulation: provides the energy for control of chemical reactions I Muscle contraction: motion I Active transport across membranes I How do organisms synthesise and obtain energy from ATP? Driving natural ATP (adenosine triphosphate) as a cellular fuel source systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Mitochondria and bioenergetic control I Two phosphate bonds which may be hydrolysed, releasing energy (ATP ↔ ADP ↔ AMP) Modelling systems of chemical I Cells maintain ATP/ADP ratio out of equilibrium reactions 0 −1 I ATP + H2O → ADP + Pi ; ∆G = −30.5 kJ mol I Under physiological conditions and typical cellular ATP/ADP ratio, ∆G ' −(40 − 60) kJ mol−1 I ‘Energy charge’ sometimes used for energetic status

1 [ATP] + 2 [ADP] [ATP] + [ADP] + [AMP]

I The human body contains 0.2 mol ATP. We require the hydrolysis of 100-150 mol ATP per day (50-75 kg). Each ATP molecule is recycled 500-750 times per day. Driving natural ATP production systems: Chemical energy production and use

0 −1 I ATP + H2O → ADP + Pi ; ∆G = −30.5 kJ mol Chemical energy I Under physiological conditions and typical cellular ATP/ADP ratio, and metabolism ∆G ' −(40 − 60) kJ mol−1 ATP usage and I But this is net energy release – ATP rarely breaks down on its own (it production would be a poor energy currency if it did) Mitochondria and I Proteins that harness ATP are usually ATPases – i.e. enzymes that bioenergetic control catalyse the hydrolysis of ATP (hence overcoming the activation energy) Modelling systems of chemical reactions Driving natural Some other players in bioenergetics systems: Chemical energy production and use

Chemical energy I NADH: an electron donor used to transfer high-energy e− and metabolism + 1 + 0 −1 (NADH + H + 2 O2 NAD + H2O : ∆G = −220 kJ mol – one ATP usage and NADH used to synthesis several ATP) production Mitochondria and I Means of producing ATP (and NADH): bioenergetic I Glycolysis: energy production without oxygen (glucose → 2 control + pyruvate + 2 ATP + NADH + H ) Modelling systems I Krebs cycle / citric acid cycle / TCA cycle: a circular set of of chemical reactions that takes in ‘fuel’ once per cycle and feeds oxidative reactions respiration (we’ll look at this in the practical) − I Oxidative phosphorylation: energetic e power proton pumps, setting up a harnessable electrochemical gradient I Fermentation (glucose → lactic acid) I Photosynthesis (photons, proton pumps) I Replenishment with nucleoside diphosphate kinases (GTP → GDP) Driving natural Oxidative phosphorylation systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Mitochondria and bioenergetic control

Modelling systems of chemical reactions Driving natural Oxidative phosphorylation systems: Chemical energy production and use

Chemical energy and metabolism (Biochemical detail is not examinable) I ATP usage and I Krebs cycle produces NADH and succinate production I A series of complexes pump protons through the inner mitochondrial Mitochondria and bioenergetic membrane control + + I Complex I: NADH + H → NAD , pumps 4 protons, reduces coenzyme Modelling systems Q of chemical reactions I Complex II: succinate → fumarate, reduces coenzyme Q I Complex III: Oxidises coenzyme Q, reduces cytochrome C, pumps 4 protons I Complex IV: Reduces cytochrome C, pumps 2 protons I Electrochemical potential (charge separation + chemical gradient) set up across membrane Driving natural Oxidative phosphorylation systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Complex V: energetic protons ﬂow back Mitochondria and I bioenergetic into matrix control

I F1 subunit in membrane; Fo subunit in Modelling systems the matrix of chemical reactions I (Amazing structure best understood by viewing animation) I Structure and function: John E. Walker, 1997 Nobel Prize in Chemistry Driving natural Oxidative phosphorylation systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Mitochondria and bioenergetic control

Modelling systems of chemical reactions Driving natural Energy and life systems: Chemical energy production and use I Nick Lane: energy per gene expressed is key factor in evolution of complex life Chemical energy I Local mitochondrial genomes: local control of mitochondria and metabolism

I Alternative 1: non-local genome, power sources not individually ATP usage and addressable production I Alternative 2: many full genomes localised to power generation: huge Mitochondria and amount of nucleic acid bioenergetic control I Mitochondria: small, individually addressable genomes localised to Modelling systems power generation of chemical reactions

I ‘... being large and having masses of DNA is not enough to attain complexity: cells need to control energy coupling across a wide area of membranes using small, high copy, bioenergetically specialized genomes like mtDNA’ I Express 2 × 105 more genes with no energy penalty Driving natural Mitochondrial bioenergetic control systems: Chemical energy production I How can mitochondria be individually addressed by control? and use I ‘Quality control’: individual mitochondrial performance is sensed (membrane potential ∆Ψ and others)? Chemical energy and metabolism I Good mitochondria are allowed to fuse into a network and remain safe from degradation ATP usage and production Bad mitochondria remain fragmented and, if they don’t recover, are I Mitochondria and targeted for authophagy and recycling bioenergetic control I An exercise: how does this map to the types of control we have considered? Modelling systems of chemical reactions Driving natural Control on mitochondrial respiration systems: Chemical energy production and use

Chemical energy and metabolism

I Cells with ‘good’ and ‘bad’ mitochondria show little difference in ATP usage and respiration rate production I There are pronounced physiological differences but compensatory Mitochondria and bioenergetic mechanisms exist to control respiration (this is modern and debated control research) Modelling systems I Bad mitochondria produce more ROS (damaging ‘exhaust’) production of chemical than good mitochondria reactions I Cells producing more ROS have more mtDNA I → Cells with bad mitochondria produce more mitochondria to retain overall respiratory capacity I An exercise: how does this map to the types of control we have considered? Driving natural Modelling systems of chemical reactions systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and I We will look at several ways of modelling the chemical processes that production drive natural systems Mitochondria and I Now: ODE modelling – physical models for the species concentrations bioenergetic and physical properties of bioenergetic systems (particularly oxidative control phosphorylation and the mitochondrion) Modelling systems of chemical I Next: FBA (ﬂux balance analysis) – coarse-grained representation of reactions large networks of metabolic components with constraints and optimisations I Then: MCA (metabolic control analysis) – analysis of how ﬂuxes and concentrations in metabolic networks respond to perturbations in network properties Driving natural A simple example of ODE modelling systems: Chemical energy production and use

Chemical energy I Adenylate kinases swap high-energy phosphates between adenosine and metabolism frames in the inter-membrance space of the mitochondrion ATP usage and production 2ADP ATP + AMP Mitochondria and bioenergetic control I Rate of this reaction Modelling systems of chemical Y mi Y mj ν = ν+ − ν− = k+ [Si ] − k− [Pj ] reactions 2 = k+[ADP] − k−[AMP][ATP] 2 ≡ XAK KAK [ADP] − [AMP][ATP]

I XAK is the activity; KAK the reaction parameter d[ATP] I For example, dt = ν/V Driving natural An electrochemical example systems: Chemical energy production and use I Complex I uses energy from NADH electrons to pump protons out of the mitochondrial matrix Chemical energy + + + and metabolism H + NADH + Q NAD + QH2 + 4∆H ATP usage and production I 4∆H+ represents four protons pumped across the membrane Mitochondria and I These protons need to work against an electrochemical gradient: bioenergetic + [H ]out control ∆GH = RT ln + − F∆Ψ [H ]in Modelling systems I Reaction rate ∝ collision probability of chemical I We also have dependence on ‘proton ﬂux probability’ represented by the reactions Boltzmann factor e−∆GH /RT /Z I (Model) combination:

reaction rate ν ∝ (collision probability) × (proton ﬂux probability) ∝ (concentrations) × (Boltzmann factor)

0 + 0 + 4∆GH /RT ν = k+[H ][NADH][Q] − k−[NAD ][QH2]e 0 0 + + 4∆GH /RT ≡ XCI KCI [H ][NADH][Q] − [NAD ][QH2]e Driving natural Systems of chemical ODEs systems: Chemical energy production and use

Chemical energy and metabolism

ATP usage and production

Mitochondria and bioenergetic control

Modelling systems of chemical reactions Driving natural Systems of chemical ODEs elucidate biochemical control systems: Chemical energy production and use

I Simulation of physiological ODE model allows us to determine that Chemical energy phosphate control acts on Complex III ﬂux: and metabolism ATP usage and production

Mitochondria and bioenergetic control

Modelling systems of chemical reactions

I Can’t match data without ∝ (1 + [Pi ]/k1)/(1 + [Pi ]/k2) term I We will explore other features of this model in the practical.