Chapter 5: Gibbs Free Energy

Chapter 5-Gibbs Free Energy

Problems: 5.1,3,5,11; concept:5.9,19,21,22,23

1.G-energy to drive chemical reactions

-ΔpG- tabulated (in table)

-ΔrxnG- usually calculated

eq.1: ΔrG- ∑v*Δ_fG_products –∑v*Δ_fG_reactants

-if 0, reaction is at equilibrium

-if negative, reactions proceeds towards right (spontaneous)

-if positive, reaction will not proceed (non-spontaneous)

2.Phase Transitions

-Phase 1 --> Phase 2:

eq.2:ΔrxnG= n* ΔfG_{phase 2} – n* ΔfG_phase1 (ΔG is molar)

-if ΔGf phase 2 > phase 1, ΔGrxn is positive (non-spontaneous)

-if ΔGf phase 1 > phase 2, ΔGrxn is negative (spontaneous)

-if ΔGf phase 1 = phase 2, ΔGrxn is 0 (equilbrium)

-stable phase- phase with lowest ΔGf

3.Molar ΔGf vs Pressure- ΔGf,m or ΔGm = Vm*ΔP

-ΔG is directly proportional to changes in pressure

-larger molar volume- ΔG changes more as pressure changes for substances with larger molar volumes

eq.3:Vm=ΔG/ΔP

-solids,liquids: final ΔGm= ΔGm,i + Vm(Pf-Pi), where pressure is in bars

-gases: final ΔGm*(Pf)= ΔGm*(Pi)+RTln(Pf/Pi)

-reactions:  ΔGrxn= ∑V*ΔGm,final (products) – ∑V*ΔGm,final (reactants)

4.Molar ΔGf vs Temperature

-for small changes in T, entropy values are nearly constant

eq.4:ΔGm=-Sm*ΔT

5.Phase boundaries- on phase diagrams, show the pressure and temperature combinations at which 2+ phases are stable

-liquid-vapor boundary-liquid is in contact with and in equilbrium with a gas of that composition; pressure of the vapor is its vapor pressure, which substantially increases with temperature

-solid-vapor boundary-solid in contact with and in equilbrium with vapor; sublimination vapor pressure of the solid can be determined in the same way as the liquid vapor pressure

-slope- slope of boundary determined by thermodynamic properties

 6. Clapeyron equation- finds slope of boundary (ΔP/ΔT), ONLY fo small changes in P and T

-ΔtrsH- change of heat during transition between phases (where temperature and pressure stay constant)

eq.5: ΔP/ΔT=ΔtrsH/T*ΔtrsV

7.Clausius-Clapeyron equation: Δ(lnP)= ΔvapH/RT² *ΔT

-liquid-gas boundaries

eq.6:lnP’=lnP+ΔvapH/R*(1/T-1/T’), where P’ is final P, and T’ is final T

-Table 5.1- log(P in kPa)=A-(B/T), where A and B are constants (see derivation on p.113)

8.Critical point-terminal point on liquid-gas boundary curve

-highest pressure at which liquid can be condensed

-fluid- above critical point, state of matter is called “fluid”, no boundary

-observed between states of matter as seen between liquid and gas

9.Normal boiling point- boiling temperature at 1 atm

-Standard boiling point- boiling temperature at 1 bar

-Normal boiling point- melting temperature at 1 atm

-Standard melting point- melting temperature at 1 bar

10. Phase Rule- for a system at equilbrium, F=C-P+2

-F=degrees of freedom, C=number of component, P=number of phases, 2=T+P

-components- minimum number of species necessary to define all the phases present in a system

-degrees of freedom- number of intensive variables (P,T,mol fraction, etc.) that can be changed without disturbing equilbrium

-triple point- F=0 (C=1, P=3)

-phase boundary- F=1 (C=1, P=2)

General Biochemistry 2: Lecture 10,11 (Photosynthesis, Photosystems, Cyclic)

LECTURE 10,11: PHOTOSYNTHESIS, REACTION CENTERS, PHOTOSYSTEMS

A. Photosynthesis- light driven synthesis of CH2O from CO₂; also produce oxygen by oxidating water; overall: CO₂ + 2 H₂O à CH₂O + O₂ + H₂O

Chloroplasts-site of photosynthesis; 1-1k chloroplast per cell, very in size/shape, usualy 5 um long ellipsoids.

-3 membranes: inner, outer, thylakoid membranes (where light driven reactions take place)

-3 regions: intermembrane space, stroma (dark reactions), thylakoid lumen

-thylakoid membrane- light reactions; invaginations of inner membrane cause these, resemble cristae

-thylakoid vesicle- arranged to have disk-like sacs (grana), stacked in piles, connected to each other by stroma lamellae.

-1 chloroplast=10-100 grana

-stroma-concentrated solution w enzymes, dna, rna, ribosomes

B. Reaction Centers

I. Light reactions (thylakoid membrane)- use light to generate nadph, atp and O₂. Resembles ET and OP in mitochondria.

1. Photosynthetic Reaction Center(RC)-primary photochemical rxns take place in RC.

-chlorophyll- green pigments that capture sunlight, located in and around photosystems embedded in thylakoid membrane of chloroplasts. Structure- porphyrin with magnesium at the center.

-Bacteriopheophytin- a bacteriochlorophyll where Mg²⁺ ion is replaced by 2 H⁺; Reaction center from a purple bacteria (rhodopseudomonas viridis) is a transmembrane protein with several chromophores (BchI a and b, nonheme Fe(II), Bpheo b, ubiquinone, menaquinone)

-antenna chlorophyll- chlorophylls not in RC;  don’t participate directly in photochemical reaction, but capture photons from sunlight.

2.Light Harvesting Complex B (antenna complex)- has several membrane-bound hydrophobic proteins, each with many chlorophylls and other pigments.

-carotenoid- accesory pigments; non-chlorophyll pigments that absorb wavelengths chlorophylls don’t strongly absorb.

-number of LHCs- many more LHCs than PRCs.

-lower energy state- light captured by antenna complex, transferred to series of antenna pigment molecules, eventually trapped by PRC (10E-10 seconds, >90% efficiency); PRC has lower excited energy state than antenna pigments.

-all O₂ cells- have psysI and II; non-O₂ cells only have psys I.

C.Photosystems

1.Photosystem 1-forms nadph

-max efficency at 700nm; absorbs 4 quanta, makes strong reductant, weak oxidant

-4[ P₇₀₀ + q à P₇₀₀* (strong reductant) à P₇₀₀⁺ (weak oxidizer)+ e]

-4[ P₇₀₀⁺ + e(from P₆₈₀*) à P₇₀₀]

-P700*- strong reductant provides 4e to reduce 2 NADP+ to 2 NADPH

-P700+ - weak oxidant recieves 4 e from weak reductant made by psys II to regenerate ground state psys I P₇₀₀

- ferridoxin-nadp+ reductase-forms nadph in stroma

2.Photosystem II-forms O₂ by oxygen-evolving center (OEC)

-max efficiency drops at >680nm; absorbs 4 q, makes weak reductant and strong oxidant

-4 [P₆₈₀ + q à P₆₈₀* (weak reducer) à P₆₈₀⁺ (strong oxidant) + e]

-4 [P₆₈₀⁺ + e (from water) à P₆₈₀]

-P680+ -strong oxidant takes 4 e from 2water to make 4H+ and O2

-P680*- weak reductant provides 4 e to weak oxidant formed by psysI

3.H⁺ gradient- drives atp synthesis by atp synthase; similar to OP

-thylakoid lumen- 4e goes from weak reducer P680* to weak oxidant P700+, coupled to pumping of 8 H⁺ into thylakoud lumen.

-Evolution of one O₂- from 2 waters produces 4H+ in thylakoid lumen.

-redox-active factors- chlorophylls, cytochromes, Q, FeS clusters, plastocyanin help transfer 4e between photosystems.

-plastocyanin- peripheral membrane protein on thylakoid luminal surface, cycles between CuI and CuII, a redox-active factor.

4.cyclic transport- produces atp, but no nadph or O₂

-involves only photosystem I;

-allows cells to adjust ATP:NADPH ratio

-regulation unknown

5.efficiency of non-cyclic ET: 1.25 ATP/quantum (10 atp/8 quanta)

-for every O₂ made or 8 quanta absorbed

-water evolution: 4H+ made in lumen from 2H2Oà4H+ + O₂ 

-4e from PSII to PSI: 8H+ pumped into lumen

-H⁺ gradient: 12 H⁺/3 H⁺ to power synthase= 4 ATP

-PSI’s p700*: makes 2 NADPH, 3 atp/nadph, equals 6 ATP

6.efficency of cyclic ET: 0.67 ATP/quanta

-for every 4 q absorbed by PSI, 8H+ pumped into lumen, (8H+/3H+ to power synthase)/4 quanta

Dark reactions- use nadph and atp to make ch2o from water and CO₂. in eukaryotes, happens in stroma.

General Biochemistry 2: Lecture 9 (ATP Synthesis)

LECTURE 9: ATP SYNTHESIS

Energy coupling- free energy released by electron transport must be saved in a form that atp synthase can use.

chemiosmotic theory (1961, peter mitchell)- ETàcoupled to pumping of H⁺ from mitochondria matrix across inner membrane to outside à create H⁺ electrochemical potential gradient across inner membrane à this gradient is energy source which drives atp synthesis

-inner membrane permeability- requires intact inner membrane, impermeable to ions like H⁺, OH-, K+, Cl- (permeable to CO₂, O₂, H₂O)

-electrochemical gradient- ET = H⁺ transport from matrix to outside, creating big gradient across inner membrane

-Potential = 0.168 V (more negative inside);

-pH of matrix = 0.75 units higher than intermembrane space,

-ΔG(transport H⁺ outside) = 21.5kJ/mol

-2,4dinitrophenol (DNP)- compounds that increase permeability of inner membrane to H⁺ allow ET to proceed, but inhibit ATP synthesis. Thus, oxidation (or ET) and phosphorylation can be uncoupled by uncouplers like 2,4-dintrophenol (DNP)

p/o ratio- ratio of atp synthesized to oxygen reduced

p/2e ratio-ratio of atp synthesized to 2-e reduction of some e⁻ acceptor other than o

-FADH₂/O₂(no agent or amytal)=2, (w CN- or DNP)=0

-FADH₂/Fe(w CN-)-3 (no agent or CN-)=1

-NADH/O₂(w CN-)=0

-NADH/Fe(CN6)-3=2

-pH gradient- atp is made by mitochondria/chloroplast when pH gradient artifically generated without ET.

-bacteriorhodopsin-purple membrane protein from halobacteria; pumps H⁺ when illuminated; synthetic lipid vesicles w BR and beef heart mitochondrial ATPase can make ATP when illuminated.

-asymmetric orientation- NADH-Q reductase, Q-Cyt c reductase, Cyt c, cyt c oxidase, ATP synthase all asymmetrically oritented (used mitoc/submitoc particles w inner membrane inside out)

-Efraim Racker- discovered F0 and F1

1.F1- water soluble, peripheral membrane protein; atp hydrolysis in isolated soluble form

-a3b3yE, active in atp synthesis in synthase assembly

2.F0-water insoluble, transmembrane protein; forms proton channel.

-a1b2c9-12 in e. coli, and some addition subunits in mitochondrial F0

3. Binding Change Mechanism- shape change takes place when T has ATP and L has ADP,Pi

-L,O,T(atp)àL(adp,p),O,T(atp) + energyà L,O(ATP),T(adp,p) + ATP,waterà L,O,T(atp)

-shape change takes place when T site has ATP and L site has ADP,Pi; results in conversion of LàT, TàO, OàL;

-shape change requires energy, transmiited to catalytic α3β3 assembly via ye assembly.

-atp synthesize at new t site, original atp released from new o site

General Biochemistry 2: Lecture 8 (Electron Transport Chain, Complexes, Inhibitors)

LECTURE 8: ELECTRON TRANSPORT CHAIN, COMPLEXES, INHIBITORS

A. NADH oxidation- is highly exergonic- -218 kJ/mol

-NAD⁺ + H⁺ + 2e à NADH (-.315 V)

-oxygen + 2H+ + 2e à water (0.815 V)

Overall: oxygen + NADH + H⁺à water + NAD⁺

ATPàADP: -30.5 kJ/mol

ATPàAMP: -32.2 kJ/mol

2. Efficiency of ATP Synthesis- (3 ATP per NADH) ÷ (total energy per NADH) = 42%

-70% in mitochondria

B. ET Carriers- NADH; FMN; Q; FeS; Cyt a+a3,bl+bh,c,c1; Cua; Cub; O₂

1.Hydrogen carriers- FMN; NAD⁺; Q;

-FMN- add 2H⁺ and 2e, get FMNH2. (1H and 1 e= FMNH*)

-NAD+ - add 2H+ and 2e, get NADH + H⁺.

-Q- add 2H+ and 2e, get QH2.

2. Electron carriers- FeS, cytochromes (ET heme proteins), Cu proteins

-Fe3+ à Fe2+

-Cu2+àCu+

C. Complexes that make up ET chain

1. Complex I- NADH-CoenzQ Oxidoreductase;

-NADH à [[[FMN à2 FeS]]]à Q (passes 2e from NADH to Q)

-inside: 8-9 iron-sulfur clusters and 1 FMN

-4H+ go outside

-possible mechanism: differential H⁺ binding and release caused by protein shape change; H bonded groups in proteins and water are like a proton wire.

AH+BàA+BH. Proton moves from AH to B.

-bacteriorhodopsin-model for proton pump through proton wire

a.Cycle 1- QH₂ + Cyt c1 (Fe3+) à Q*- + Cyt c1(Fe2+) + 2H+ (cystol)

-QH2 from complex 1; pump 2H+ to intermembrane space, then to cytosol;

-donate 1e to ISP, which goes to c1;

-makes 1 Q-*

b.Cycle 2- QH₂ + Q-* + Cytc1(Fe3+) + 2H⁺(mito) à Q + QH₂+Cytc1(Fe2+)

-obtain QH₂ from complex I; pump 2H⁺ to cyto;

-Donate 1e to ISP, goes to c1. Take up 2 H⁺ from mito.

-Generate 1 QH₂, not net gain or loss of QH₂.

Net: QH₂ + 2 Cytc1(Fe3+) + 2H⁺ (mitochondria) à Q + 2 Cytc1(Fe2+) + 4 H⁺ (cystol)

-4 H⁺ pumped out, 2 c1 reduced, use 2 H⁺ from matrix.

2.Complex II- Succinate-CoenzQ Oxidoreductase

-Succinateà[[[FAD (succinate DH, 2H+ released)à3 iron-sulfur clusters à Cyt b560]]]à Q

-I and II not in series

-inside: 3 FeS clusters, succinate dehydrogenase FAD, and cyt b560

-2H+ go outside

3.Complex III- CoenzQ-Cytochrome C Oxidoreductase

-QH2à[[[CytB or FeSàCyt c1]]]à Cyt c

-inside: 2 Cyt b (bL for low and bH for high potential), 1 Cyt c1, and 1 Fe-S cluster.

-4H+ go outside, 2H+ inside

4. Complex IV- Cytochrome c oxidase

-2 Cytc(Fe2+) + 2H⁺ + .5O₂ à[[[CuAàCytaàCyta3-CuB]]]à 2 Cytc(Fe3+) + H₂O

-has cyt a, cyt a3, cua, vub

-high potential- (CuA-Cyta) lower potential than (Cyta3-CuB)

-2H⁺ go to cytosol

- Cyt c- between III and IV. Loosely bound to outer surface of inner membrane. Shuttles e⁻ between Cyt c1 and cyt c oxidase.

D. Donaters/Acceptors

1.Physio e⁻ donating systems:

-β-hydroxybutyrate dehydrogenase- β-HOButyr+NAD⁺àAcetoacetate+NADH

-Succinate DH- Succinate+FADàFumarate+FADH₂

2. Artifical e⁻ donating systems: ascorbateàtetramethyl-p-phenylenediamine (TMPD)àCyt C

3. Physio e⁻ acceptor: O₂ as acceptor of e from Complex IV

4. Artifical e⁻ acceptor: Fe(CN6)3- accepts e from Cyt c_red

E. ΔG=-nFΔE, where F=96494 J/mol*V

1.Site 1(Complex 1)- ΔG=-69.5, ΔE=.36V

-NADH+H⁺+QàNAD⁺+QH₂

-reduce NAD=-.315V; reduce Q=.045V

2.Complex II- no phosphorylation

-FADH₂+QàFAD+QH₂

-ΔE=.085 V, ΔG=-16.4 kJ/mol

3.Site 2 (Complex III)- ΔG=-36.7 kJ/mol, ΔE=0.19V

-QH₂+2Cytc_oxàQ+2Cytc_red
4.Site 3 (Complex IV)- ΔG=-112kJ; ΔE=.58V;

-2CytRED+ 2H⁺+ .5O₂à2CytOX+ H₂O

F.Inhibtors

Rotenone and Amytal- block complex I

Antimycin A- blocks complex III

CN^- -blocks complex IV

G.P/O value- ratio of ATP made over oxygens used

- β-HOButyr/NADH and O₂= 3

- Succinate/FADH₂ and O₂= 2

- β-HOButyr/NADH and Fe(CN6)-3= 2

- Succinate/FADH₂ and Fe(CN6)-3= 1

- ascorbate and O₂= 1

-phosphorylation and oxidation tightly coupled, NADH+P+O₂ wont happen until ADP is added.

-Reconsitution- isolated components and phospholipid vesicles remake active sites.