Ch/APh2 Bioenergetics Section Lecture of May 19, The thermodynamics of biological energy production.

Transcription

1 Ch/APh2 Bioenergetics Section Lecture of May 19, 2009 Introduction to bioenergetics. The thermodynamics of biological energy production. Kinetic aspects of bioenergetic processes. Energy transfer Electron transfer The molecular and cellular organization of bioenergetic systems. Membrane transport Ion Channels, transporters Photosynthesis Respiration and ATP synthesis Haber-Bosch process and biological nitrogen fixation

2 Kinetics of Bioenergetics light energy transfer electron transfer diffusion distance, time and driving force dependences Dutton et al. Adv. Prot. Chem. 63 (2003)

3 Photon absorption and de-excitation fluorescence time scale ~ ns radiationless transfer time scale ~ ns phosphorescence time scale ~sec

4 absorption and fluorescence of bacteriochlorophyll Q x Q y

5 light (resonance) energy transfer Donor absorbs at higher energy (shorter ) than Acceptor. rate of transfer ~ (R 0 /R) 6 R 0 depends on spectral overlap and quantum yields; typically ~ Å basis of spectroscopic ruler

6 Fluorescence resonance energy transfer (FRET) acceptor donor R 0 ~ 34Å measure fluorescence yield of the donor in the absence and presence of the acceptor: efficiency = R o6 /(R o6 + R 6 )

7 energy transfer in bacterial RC/LHC complexes Sundstrom et al. JPC B103, 2327 (1999) (RC absorbs ~ 870 nm)

8 photosynthetic systems have a common core structure bacterial plants: PSI and PSII Dutton et al. Adv. Prot. Chem. 63, 71 (2003)

9 bacterial photosynthetic reaction center (RC) three subunits: L, M and H view in plane of membrane view down membrane normal E D C B A A D B C E PDB IDs 2PRC; 1AIJ

10 organization of cofactors in the RC Bchl 2 carotenoid Chl Bchl 2 Bchl Bph Bph Q A A branch Q B B branch

11 photosynthesis - the reaction center h Bchl 2 membrane Bchl Bph Q A Fe Q B Bchl -chlorophyll Bph - bacteriopheophytin Q - quinone

12 Bchl 5 Å Bph 10 Å 5 Å Q B (Bchl) 2 QuickTime and a QuickDraw decompressor are needed to see this picture. 13 Å Fe Q A 5 Å Bchl 10 Å 5 Å Bph why is the back reaction (to (Bchl) 2+ ) so unfavorable? why is the B branch so much slower than the A branch?

13 Incident solar radiation ~1 photon/rc/sec Cycling time for the RC is ~ 10-3 sec; Use light harvesting/antennae complexes to transfer light energy to RC

14 Mechanism of light energy transfer is not quantitatively understood: After absorption of a photon, the excited state likely becomes delocalized around the electronically coupled chromophores. h

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16 Electron Transfer Kinetics: classical Marcus theory (Marcus and Sutin, BBA 811, 265 (1985)) activation energy for exchange reaction (ET rate) k ET = A e -( G*/RT)

17 calculation of activation energy - classical model = energy to distort reactant into product geometry G* = (1+ G / ) 2 /4 k ET = Ae -( G*/RT) max. rate when G = - Gray & Winkler Ann. Rev. Biochem. 65, 537 (1996)

18 the inverted region

19 distance dependence of electron transfer kinetics k ET = A(r) e -( G*)/RT

20 distance dependence of electron transfer A(r) ~ e - r s -1 = 1.1 Å -1 Tunneling timetable for ET in Rumodified proteins (open symbols), water (light blue, = Å1), and vacuum (dark blue, = Å1) (adapted from ref. 36). Most coupling-limited electron tunneling times in proteins [cyt c (); azurin (); cyt b562 (); myoglobin (); and high-potential iron-sulfur protein ()] fall in the 1.0- to 1.2-Å1 wedge (pale blue solid lines; pale blue dashed line is the average of 1.1 Å1). Colored circles (*Zncyt c Fe(III)-cyt c, green and Fe(II)-cyt c Zn-cyt c+, red) are interprotein time constants. Tezcan et al. PNAS 98, 5002 (2001)

21 k ET = e - r e -( G*)/RT s -1 hopping vs jumping Page et al. Nature 402, 47 (1999) Using ~ 1.1 Å -1, k et for electron transfer over 10 Å, 15 Å, 20 Å, 25 Å, and 30 Å, are calculated to be approximately 8.8 x 10 9, 3.6x10 7, 1.5x10 5, 6.0x10 2, 2.5 sec -1, respectively. From these values, the time required for electron transfer over 30 Å by either hopping in three 10 Å steps, or by tunneling directly, are calculated to be: 1 t 1 / 2, hopping ~ ln 2 (3 1) sec t 1/ 2, tunneling ~ 1 ln 2 (1 1) sec

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23 Kinetic aspects of getting a molecule or ion across a membrane Thermodynamic driving forces: concentration gradients membrane potential (charged species) Pore geometry (radius, length, electrostatics)

24 kinetics are governed by fundamental empirical laws that relate fluxes (flows) to driving forces Ohm s law relates forces (V) and flows (I) of electrical current I = (1/R) V Fick s laws of diffusion relate forces and flows of particles J L In general, the flux is proportional to the driving force J = L F

25 J = particles/unit area/unit time = molecules cm -2 sec -1 = concentration x velocity = c v total current = J x Area and J = L F L F = c v F = (c/l) v f v f = frictional coefficient ie at steady state, F ~ velocity, not acceleration!

26 Basic equations of microscopic diffusion: Fick s First Law The basic diffusion equation may be derived from random walk considerations N(x) area = A N(x+ ) Consider how many particles will move across from point x to point x+ per unit area per unit time - ie, what is the net flux J in the x direction? For a random walk, where N(x) is the number of particles at x, during the next step (1/2)N(x) (1/2)N(x+ ) (1/2)[N(x)-N(x+ )] will move from x to x+ will move from x+ to x will be the net movement from x to x+ = -(1/2)[N(x+ )-N(x)]

27 cellular and molecular architecture of bioenergetic systems (sub)cellular organization Buchanan, Gruissem, Jones Biochemistry and Molecular Biology of Plants

28 organization of phospholipid membranes

29 S.J. Singer s fluid mosaic model Science 175, 720 (1972) phospholipids assemble into a bilayer through the hydrophobic effect ; the apolar interior of the membrane is largely impermeable to water, ions and other polar molecules. Membrane proteins are required for transport of these species into and out of cells

30 Chandler, Nature 417, 491 (2002)

31 Mitochondria: respiratory organelle, generates ~body weight of ATP daily Contains an outer membrane and a highly convoluted inner membrane with respiratory complexes Total surface area of inner membranes in humans is estimated to be 14,000 m 2. (Rich, Nature 421, 583 (2003)

32 E. coli has two cell membranes

33 membrane spanning polypeptide conformations

34 Looking at Macromolecular Structures Viewer SwissPDB Rasmol imol PyMOL etc. Coordinates PDB - the Protein Data Bank - operated by the Research Collaboratory for Structural Bioinformatics

35 Rich, Nature 421, 583 (2003) Abeles, Nature 420, 27 (2002)

36 If N(x) N(x ), then there will be a net flux through an area element perpendicular to x between x and x+ that is given by Fick s first law. J D dc dc ; if dx dx C b constant, J = constant C a a b there is a next flux from right to left, simply because there are more particles on the right than on the left. This flux depends only on the gradient, and not the value of c. This drive towards equalizing the concentrations (chemical potential) will tend to flatten all concentration gradients, and is principally entropic in origin. Just as Newton s laws give forces are derivatives of energy, the force from a concentration gradient can be expressed as a derivative of the chemical potential.

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38 Looking at Macromolecular Structures Viewer SwissPDB PyMOL etc. Coordinates PDB - the Protein Data Bank - operated by the Research Collaboratory for Structural Bioinformatics

39 membrane spanning polypeptide conformations

40 Membrane proteins are the basic circuit elements of bioenergetic processes matter, energy, information outside channels transporters electron transfer complexes inside

41 µ

42 KcsA potassium channel Doyle et al. Science 280, 69 (1998) PDB ID: 1BL8 tetramer

43 potassium permeation pathway K + ion coordination. Zhou et al. Nature 414, 43 (2000). PDB ID 1K4C

44 mechanism of K + permeation: conduction state diagram Morais-Cabral et al. Nature 414, 317 (2001)

45 MthK channel Ca +2 mediated gating through a K + channel Jiang et al. Nature 417, 505 (2002) PDB ID 1LNQ

46 Voltage gating in Kv potassium channels opening and closing the channel in response to changes in membrane potential: the charged S4 helix closed open voltage sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore Jiang et al. Nature 423, 33; 42 (2003)

47 mechanosensitive channel of small conductance MscS N-terminal membrane spanning domain TM1 TM2 TM3 middle C-terminal domain L105 L109 C-terminal cytoplasmic domain 3.9 Å resolution Bass et al. Science 298, 1582 (2002)

48 MscS gating mechanism mechanosensitivity - open state has larger cross-sectional area voltage sensitivity - open state has (+) charges moving away from cytoplasm R46 R88 R74 TM1 and TM2 likely serve as coupled tension and voltage sensors TM3 forms the pore

49 conformational variability in TM region of MscS coloring by B factor (low to high)

50 How are concentration gradients generated in the first place? Na +,K + ATPase Alberts et al. Essential Cell Biology

51 Two gate mechanism of pumps

52 ABC transporters and the ATP-binding cassette: importers and exporters of a diverse set of substrates contain two copies each of conserved ABC domains membrane spanning domains (diverse)

53 The Escherichia coli B 12 uptake system Btu

54 Experimental electron density 3.5 Å resolution contour level=1

55 periplasm BtuC BtuCD architecture BtuC BtuD BtuD cytoplasm 3.2 Å resolution Locher et al. Science 296, 1091 (2002)

56 BtuCD structural organization membrane spanning BtuC translocation subunits pathway gate mechanistic issues exit pathway consequences of ATP binding and hydrolysis? coupling of ABC and TM domains? role of binding protein BtuF?

57 ATP-binding cassettes (BtuD subunits) ABC signature motif Walker-B P-loops (Walker-A)

58 Proposed B 12 transport mechanism BtuF-B 12 BtuCD alternating access or airlock model

59 Channels and Transporters - summary channels and transporters have common architectural features, namely: translocation pathway closed with either one gate (channels) or two (transporters) specificity elements (eg selectivity filter/binding proteins) gating sensors