Ch2/Ap2: Bioenergetics Section Introduction to bioenergetics. The thermodynamics of biological energy production. Kinetic aspects of bioenergetic processes. The molecular and cellular organization of bioenergetic systems. Photosynthesis Respiration and ATP synthesis Haber-Bosch process and biological nitrogen fixation

Dr. Cara TracewellEmail: cara@caltech.edu

General references

Text: “Chemistry of the Environment”, esp. chaps 4, 15

photosynthesis and the web http://www.life.uiuc.edu/govindjee/photoweb/

DOE genomes to life program http://www.DOEgenomesToLife.org/

D.G. Nicholls and S.J. Ferguson Bioenergetics3Academic Press, (2002)

What is bioenergetics?

Bioenergetics is a way of understanding personality in terms of the body and its energetic processes. Bioenergetic Analysis is a form of therapy that combines work with the body and the mind to help people resolve their emotional problems and realize more of their potential for pleasure and joy in living.

http://www.bioenergetic-therapy.com/

energy changes in biological processes, specifically

“the mechanism by which energy made available by the oxidation of substrates, or the absorption of light, …(is) coupled to ‘uphill’ reactions such as the synthesis of ATP from ADP and Pi, or the accumulation of ions across the membrane”

Bioenergetics 3, DG Nicholls and SJ Ferguson, Academic Press (2002)

why study bioenergetics?

biologically & technologically important process

catalyzed key scientific discoveries

implications for energy science/challenges

Hans Fischer

AV Hill

OttoMeyerhof Nobel Prizes relevant to bioenergetics

Rod MacKinnon

Peter Agre

Paul Boyer

John Walker

Robert Huber

Hans Deisenhofer

Hartmut Michel

chlorophyll and other pigmentsRichard Willstätter, Chemistry 1915Hans Fischer, Chemistry 1930R.B. Woodward, Chemistry1965

AV Hill, Otto Meyerhof, Physiology or Medicine 1922muscle metabolism

Otto Warburg, Physiology or Medicine 1931respiration

Hans Krebs, Fritz Lipmann, Physiology or Medicine 1953citric acid cycle (Krebs cycle)

Hugo Theorell, Physiology or Medicine 1955oxidation enzymes

Melvin Calvin, Chemistry 1961CO2 assimilation in photosynthesis (Calvin cycle)

Peter Mitchell, Chemistry 1978chemiosmotic theory

Hans Deisenhofer, Robert Huber, Hartmut Michel, Chemistry 1988,x-ray structure of bacterial photosynthetic reaction center

Rudy Marcus, Chemistry, 1992theory of electron transfer

Paul Boyer, John Walker, Chemistry 1997mechanism of ATP synthesis

Rod MacKinnon, Peter Agre, Chemistry 2003channel structure and mechanism

Hans Krebs

Fritz Lipmann

Otto Warburg

Richard Willstätter

R. B. Woodward

RudyMarcus

Peter Mitchell

MelvinCalvin

Images: www.NNDB.com“Nobel Faces” by Peter Badge

Hugo Theorell

Magnitude of biological energy metabolism

The basal metabolic rate of humans is ~ 220 mm3 O2/gm tissue/hr O2 + 4H+ + 4 e- 2H2O For a 70 kg person, this corresponds to a rate of electrons through the respiratory pathway of

7.6 x 10-4 moles e-/sec

In terms of current flow, this is equivalent to 74 A (with 1 Amp = 1 C/sec and 96,500 C/mole/e-).

Power = current x voltage drop = 74 A x 1.1V = 84 watts. (during strenuous exercise, wattage may be as high as 800 watts!) daily energy consumption = 0.084 x 24 = ~ 2 kW hrs ~ 1700 Cal (kg) total annual energy consumption (at rest) = 730 kW hrs

comparison to annual per capita electricity use

Physics Today, April 2002, pg. 39

human basal energy production

organismsurvivalgrowthreproduction

ENERGY IN

light

chemical

heat

work

waste products

ENERGY OUT

Bioenergetic Balance

photosynthesis

respiration

glucose (C6H12O6) + 6O2 6CO2 + 6H2O

∆G˚ = -2870 kJ/mole

nH2O + nCO2 + h (CH2O)n + nO2

acceptor

donorh A- use electrons to reduce CO2

D+ replace electrons

(oxidize H2O to O2 in plants)

(sub)cellular organization

Buchanan, Gruissem, JonesBiochemistry and Molecular Biology of Plants

Rb. sphaeroides photosynthetic reaction center (RC)three subunits: L, M and H

A

BC

DDE

A’

B’

C’

D’

E’

PDB IDs 2PRC; 1AIJ

view down membrane normalview in plane of membrane

G. Feher

15

Rb. sphaeroides photosynthetic reaction center (RC)three subunits: L, M and H

A

BC

DDE

A’

B’

C’

D’

E’

PDB IDs 2PRC; 1AIJ

view down membrane normalview in plane of membrane

G. Feher

15

organization of cofactors in the RC

Bchl2

BchlBchl

BphBph

Bchl2

QBQA

B branchA branch

carotenoid

Bchl -bacteriochlorophyllBph - bacteriopheophytinQ - quinone

Feher et al. Nature 339, 111 (1989)

h

ET theoryR. Marcus

16

organization of photosynthetic membranesincident solar radiation ~1 photon/RC/sec the cycling time for the RC is ~ 10-3 sec;light harvesting/antennae complexes to funnel light to the RCrepresent most of the “2480” chlorophylls / photosynthetic unit

http://www.ks.uiuc.edu/Research/psu/PSU_ring.jpg

17

organization of photosynthetic membranesincident solar radiation ~1 photon/RC/sec the cycling time for the RC is ~ 10-3 sec;light harvesting/antennae complexes to funnel light to the RCrepresent most of the “2480” chlorophylls / photosynthetic unit

Roszak et al. Science 302, 1969 (2003)

LH1 - RC

http://www.ks.uiuc.edu/Research/psu/PSU_ring.jpg

17

http://www.bio.ic.ac.uk/research/barber/photosystemII.html

organization of photosynthetic electron transfer assembly

Stowell et al. Science 276, 812 (1997)

O

O

R1

R2 R3

oxidized quinone(Q10)

O•

O-

R1

R2 R3

OH

OH

R1

R2 R3

+e- +e- + 2H+

semiquinone(can be protonated)

hydroquinone

Quinones: the final acceptor in bacterial RCslipid soluble carriers of electrons and protons

18

nicotinamide adenine dinucleotide (NAD)

(derived from niacin)

brings in reducing equivalents

from substrate oxidation

soluble electron transfer carriers

cytochrome c

N+

R

CONH2

N

R

CONH2

HHH

+H+ + 2e-

(+H-)

NAD(P)+ NAD(P)H

ATP + H2O ADP + Pi ∆G˚’ = -30 kJ/mole

N

N N

N

NH2

O

H OH

H H

H H

O P O

O-

O

P O

O-

O

P O-

O-

O

ATP - adenosine triphosphate - phosphoanhydride

central energy currency of cells (Lipmann)

energy released during respiration/ photosynthesis is captured by ATP synthesis through the process of “oxidative phosphorylation”

How does oxidative phosphorylation occur?

direct chemical coupling??

CH2OPO32-

HCOHHC

CH2OPO32-

CHOHO COPO3

2-

CH2OPO32-

CHOHCO2

-

+ NAD+ + HPO42- NADH +

ADP

ATP

high energyintermediate made by coupling substrate oxidation to phosphorylation(this step is inhibited by arsenate

that looks like a phosphateanalog)

O

substrate level phosphorylation in glycolysis

glyceraldehyde-3-phosphatePi

1,3-diphosphoglycerate

3 phosphoglycerate

In spite of exhaustive searches, no high energy phosphorylated intermediates such as 1,3 diphosphoglycerate were ever found...

Important clue: Oxidative phosphorylation can only take place in intact membranes—damaged mitochondria cannot make ATP. This was “curious”, since membrane integrity shouldn’t influence stability of an intermediate.

This situation led to proposal (“the chemiosmotictheory”) by Peter Mitchell in 1961 that energy released during respiration or photosynthesis is not stored in high energy chemical intermediate,but rather in a proton gradient

Peter Mitchell

Nichols and Ferguson, Bioenergetics 3

chemiosmotic principles

Paul Boyer and John Walker

ATP synthesis - molecular motor

Paul Boyer

John Walker

QuickTime™ and a Animation decompressor are needed to see this picture.

http://www.res.titech.ac.jp/~seibutu/projects/fig/f1rot_2.mov

movie of single F1 ATP synthase with fluorescent actin label

biosynthetic processes:

use ATP and reductive power generated during respiration and photosynthesis to build molecules of the cell, ie, biomass

Alberts et al.

Essential Cell Biology

Biological Nitrogen Cycle

Thermodynamic foundations of bioenergetics

energy inputs:

photons

reduced chemicals

photon energy:

E = h = hc/ for a single photon

= Nhc/ for a mole of photons (1 einstein)

= 1.20 x 105/ kJ mol-1 = ( in nm)

= 1.24 x 103/ eV

for = 780 nm, E = 154 kJ mol-1 = 1.6 eV

Buchanan, Gruissem, Jones

Biochemistry and Molecular Biology of Plants

1.6 eV3.1 eV

Gibbs Free Energy, G

∆G = ∆H - T∆S

∆G, ∆H and ∆S are the changes in Gibbs free energy, enthalpy and entropy, respectively

∆G describes the maximum amount of non-expansion work that is available in a process at constant T, P

for a spontaneously occurring process at constant T, P

∆G < 0

and at equilibrium, ∆G = 0

for a reacting system system with

1A + 2B +… iP + i+1Q+…

∆G = ∆G˚ + RTln

at equilibrium, ∆G =0, so that

∆G˚ = -RT ln Keq

civi (products)

i

c jv j (reactants)

j

Keq ci

vi (products)i

c jv j (reactants)

j

vi stoichiometric coefficientsci equilib.concentrations

standard state convention in biochemical systems (∆G˚’);

1M except for water (unity) and (H+)=10-7 M

G for ATP hydrolysis under physiological conditions

While G’ for ATP hydrolysis at pH 7 is -30 kJ/mol, under physiological conditions, the actual G is more negative, due to the non-equilibrium concentrations of reactants (high) and products (low):

For the reaction

ATP + H2O ADP + Pi

G = G + RT ln [(ADP)(Pi)/(ATP)]With ATP = 0.01 M (10 mM)

ADP = 0.0001 M (0.1 mM)Pi = 0.01 M (10 mM)

G = -30 + 2.5 ln (10-6/10-2) = -30 - 23 = -53 kJ/mole