Chapter 5 Metabolism PDF

Chapter 5 metabolism Metabolism: sum of chemical processes in living system Catabolism: metabolism involved in energy generation anabolism: metabolism involved in biosynthesis What do cells need to grow ○ 1) Minor and major elements (ex carbon, nitrogen, sulfur etc) and water...

Chapter 5 metabolism Metabolism: sum of chemical processes in living system Catabolism: metabolism involved in energy generation anabolism: metabolism involved in biosynthesis What do cells need to grow ○ 1) Minor and major elements (ex carbon, nitrogen, sulfur etc) and water ○ 2) Energy (always from redox rxns) ○ 3) Reducing equivalents: [H+]= H+ + e- Carriers NAD+/NADH, NADP+/NADPH Approx half of E colis games are required for metabolism Both energy (high energy phosphate bonds) and reducing equivalents are required for biosynthesis Classification system for microbes based on energy and carbon source Energy Carbon troph Chemo Organ (organic) Hetero (organic troph (chemical) Litho (inorganic) C) photo Auto (inorganic troph ex CO2) Life is redox Delta G: free energy of rxn ○ Delta G 0 endergonic ○ ΔG𐩑’ Where 𐩑 means standard conditions (conc=1 M, atm=1, temp=25 C) Where ‘ means pH=7 Redox rxn ○ Oxidation: removal of e- from substrate (e donor) Bred → Box + e- ○ Reduction: addition of e- to substrate (e acceptor) Aox + e- → Ared ○ Aox + Bred → Ared + Box  Redox rxn rules (order of importance) ○ Balance C → CO2, balance other elements (respiration) ○ Use H2O to balance O ○ Use H+ to balance H ○ Use e- to balance charges (charges need to cancel out in overall rxn) Oxidation states of H2 and O2 =0 Ex H2 +½ O2 → H2O ○ Oxidation state 0 0 → 2(+1)-2 ○ Oxidation rxn: H2 → 2H+ +2 e- ○ Reduction rxn: ½ O2 + 2e- + 2H+ → H2O ○ Overall rxn: H2 + ½ O2 → H2O Ex Iron (II) oxidation to Iron (III) with molecular oxygen. what are reductive and oxidative halves of rxn? what is electron donor? Acceptor? what is balanced equation? ○ Electron donor: Fe2+ ○ Electron acceptor: O2 ○ Oxidation rxn: (Fe2+ → Fe3+ + e-)*2 ○ 2Fe2+ → 2Fe3+ + 2e- ○ Reduction rxn: ½ O2 + 2H+ + 2e- → H2O ○ Overall rxn: 2Fe2+ + ½ O2 + 2H+ → H2O + 2Fe3+ Ex an organism grows on glucose (C6H12O6) and molecular oxygen. what is the e- acceptor and e donor? what are the half and full reaction? (*goes to CO2) ○ Electron acceptor: oxygen ○ Electron donor: glucose ○ Oxidation: C6H12O6 + 6H2O → 6CO2 + 24H+ + 24e- ○ Reduction rxn: (½ O2 + 2H+ + 2e- → H2O)*12 ○ 6O2 + 24H+ + 24e- → 12H2O ○ Overall rxn: C6H12O6 + 6O2 → 6H2O + 6CO2 Common electron acceptors for redox rxns ○ O2/H2O ○ NO3-/N2 ○ NO2-/N2 ○ SO4^2-/H2S ○ Fe3+/Fe2+ ○ Mn4+/Mn2+  Reduction potential: tendency of compound to become oxidized or reduced ○ Measured in volts (V) ○ E𐩑’ is potential (‘ prime means pH=7, knot means standardized) ○ The more positive the E𐩑’, the better the compound is at accepting electrons Proton motive force/electron transport ○ ○ The greater the difference in redox potential between acceptor and donor, the greater the energy released ○ Not all e- are equal in redox potential ex glucose more negative than iron, smaller potentials have shorter chains  ○ ΔE’= E𐩑’ acceptor - E𐩑’ donor ○ ΔG𐩑’= -nFΔE𐩑’ n= # of electrons transferred F= Faraday Constant = 96.48 KJ/V Ex H2 oxidation with oxygen electron acceptor ○ For 2H+/H2, n=2 ○ F= 96 kJ/V ○ ΔE = E𐩑’ accepting couple - E𐩑’ donating couple ○ H2 + ½ O2 → H2O ○ For electron as electron acceptor ΔE= 0.82 - (-0.42)= 1.24 V ○ ΔG= -2(96)(1.24) = -239 kJ/mol H2 Energy is released, organism can live ○ For mole of O2, x2 on everything because rxn has ½ O2 mol ○ -478 kJ/mol O2 Chapter 6 Energy usable to drive endergonic rxns ○ 1) high energy phosphoryl bonds (ATP, GTP, etc) ○ 2) transmembrane ion gradients (H+, Na+) 2 ways for ATP generation ○ 1) substrate level phosphorylation (SLP) PO4^3- transfer from substrate to ADP → ATP ○ 2) transmembrane ion gradient E- move down electrochemical gradient to more positive acceptor and pump H+/Na+ gradient then used to make ATP Fermentation ○ ATP formation by SLP ○ Fermentation substrate is both oxidized and reduced and serves as carbon source (no net change in oxidation state) ○ Reducing agents (NADH) cant be oxidized by oxygen so it builds up and goes back to pyruvate to form back to NAD+ and makes lactate ○ Challenge of fermentation is getting rid of [H] ○ fermentation end products can vary (doesn't always start with glucose)  ○ Substrate level phosphorylation ○ 1) organic substrate becomes phosphorylated with PO4^3- in rxn that requires no energy Sred —(PO4^3-)→ SredPO4 ○ 2) phosphorylated substrate is oxidized then that energy used to make high energy bond ○ 3) ~PO4 transferred to ATP → ATP ○ All steps can occur in 1 rxn Ex What is the oxidation state of carbon in glucose (C6H12O6) and lactic acid (C3H6O3)? What are the half reactions (pyruvic acid = C3H4O3) ? ○ Glucose to pyruvic acid is oxidation state=0 ○ Pyruvic acid to lactic acid reduction state=0 ○ C6H12O6 → 2C3H4O3 + 4H+ + 4e- ○ (C3H4O3 + 2H+ + 2e- → C3H6O3)*2 ○ 2C3H4O3 + 4H+ + 4e- → 2C3H6O3 ○ Overall rxn: C6H12O6 → 2C3H6O3 ATP synthesis by ATPase ○ F0= hydrophobic membrane traversing subunit  ○ F1= hydrophilic, on interior surface of membrane, uses ion flow to catalyze ADP + Pi → ATP ○ 3-4 H+ transferred per 1 ATP ○ Reversible Transmembrane ion gradient and ATPase ○ In environment where H+ gradient not feasible (high pH) then microbes use Na+ gradient ○ Importance of ion gradient ATP generation Flagella rotation Ion couple transport Maintain turgor pressure Maintain pH NAD+ → NADH via reverse e- flow ○ Generating ion gradients 1) Respiration on cytoplasmic membrane (takes place in cell membrane) Transfer e- from donor to acceptor via e- carriers down an electrochemical gradient 2) photosynthesis Generating ion gradient via respiration ○ 1) energy change of e- transfer → pumped H+ ○ 2) carriers of e- can be e- only carrier or [H] reducing eq carriers Alternating between e- only and [H] carriers ○ H+ outside forms gradient to be used by ATPase or other ○ O2 as e- acceptor Provides greatest amount of energy  Cost is toxic byproducts of O2 Respiration byproducts are H2O2 and O2 ROS oxidation species To protect against ROS Superoxide dismutase, SOD ○ 2O2- + 2H+ → O2 + H2O2 Catalase ○ 2H2O2 → 2H2O + O2 Without SOD, high Mn (abiotic) Mn2+ + 2H+ + O2 → Mn3+ + H2O2 ○ Other e- acceptors can be used besides molecular oxygen ○ Reversible electron flow To produce NADH use by many chemolithoautotrophs (especially autotrophs need lots of NADH to fix CO2) Has to occur with microbes that dont have enough potential Microbial fuel cells ○ Electrode/anode can be electron acceptor and skip steps of chain Quiz ○ Hydrogen peroxide is electron acceptor ○ Electron donor redox potential more negative than electron acceptor redox potential ○ In anaerobic respiration, electron acceptor is nitrate ○ Oxidation state of C in cholesterol is -44/27 ○ Energy for SLP comes from oxidation ○ ATP reversible, hydrolyzes ATP → ADP Generating ion gradient via photosynthesis ○ In only 6 bacteria lineages Cyanobacteria ○ Light changes redox potential of e- on chlorophyll (to more negative) and e- then flows down electrochemical gradient ○ E- is in chlorophyll a or bacteriochlorophyll a ○ Chlorophyll part of reaction center (has proteins and pigments, e- changes in here) ○ Antenna pigments harvest light energy to funnel to reaction center ○ RC and antenna have 50-300 molecules in membrane Types of photosynthesis ○ 1) cyclic: e- flow from activated chlorophyll and back  Lots of ATP, no reducing eq [H] ○ 2) noncyclic Anoxygenic photosynthesis: e- are derived from H2S, Fe2+, or organic acids Oxygenic photosynthesis: e- derived from H2O (electron donor) Only cyanobacteria Requires 2 photosystems since its harder to raise e- potential) no external e- acceptor Generating ion gradient via enzyme pumps ○ Not part of electron transport system, but pump H+, Na+ ○ Ex bacteriorhodopsin Generating ion gradient via scalar rxns ○ Rxns that create ion gradient without transporting ions ○ Ex oxalate decarboxylase Oxalate + H+ → formate + CO2 ○ Consumes protons inside Requires Requires Requires Net redox light external e- external e- rxn acceptor donor respiration no yes yes yes photosynthe yes no Yes yes sis (noncyclic) Enzyme yes no no no pump Scalar rxn no no no no