Download IMPReS energy conversion 4 web 5-6

Energy-converting
membranes
IMPReS Lecture 5 June 2015
Werner Kühlbrandt
Energy conversion in biology
H+
+
H
energy from
sunlight
H+
H+
H+
H+
H+
+
H+
H+ H H+ H+
+
H+
H+ H+
H
H+
H+ H+ H+ H+
photosynthesis
electron transfer
pumps protons
transmembrane
electrochemical
gradient
H+
H
+
H+
H+
H+
H+
energy
from food
respiration
electron transfer
pumps protons
Alberts et al, Molecular Biology of the Cell, 6th edition
Common principles
H+
+
H
electron
donor
electron
carrier
H+
H+
H+
+
H+
H+ H H+ H+
+
H+
H+ H+
H
H+ +
+
H
H+ H+ H
H+
H+
transmembrane
electrochemical
gradient
e–
proton pump
H+
H+
H
H+
+
H
+
ATP
synthase
ADP
ATP
Alberts et al, Molecular Biology of the Cell, 6th edition
Membrane organelles
plasma membrane
mitochondrion
cytoplasm
nucleus
chloroplast
ribosomes
DNA
vacuole
endoplasmic reticulum
Energy-converting organelles
evolved from endosymbiontic bacteria
bacterium
cytoplasm
inner membrane
outer membrane
mitochondrion
chloroplast
matrix
cristae
stroma
inner membrane
outer membrane
thylakoid
membrane
Alberts et al, Molecular Biology of the Cell, 6th edition
Part 1:
Mitochondria
The mitochondrion
100 nm
= 0.0001 mm
Alberts et al, Molecular Biology of the Cell
The mitochondrion
innerinner
membrane
mitochondrial membrane
outer
membrane
outer mitochondrial
membrane
ATP synthase
cristae
H+
ATP
OUT
H+
H+
H
ADP
O2
IN
O2
ATP
+
ADP
e–
H2O
NADH
NAD+
citric
acid
cycle
CO2
OUT
CO2
acetyl CoA
pyruvate
fatty acids
pyruvate
fatty acids
FOOD MOLECULES FROM CYTOSOL
Alberts et al, Molecular Biology of the Cell, 6th edition
Mitochondria in cells
with high energy demand
mitochondria
flagellar axoneme
myofibril of contractile apparatus
(A) CARDIAC MUSCLE
(B) SPERM TAIL
Alberts et al, Molecular Biology of the Cell, 6th edition
Mitochondria move along microtubules
Mitochondria
Microtubules
Alberts et al, Molecular Biology of the Cell
3D volume of a mouse heart mitochondrion
outer
membrane
intermembrane
space
inner boundary
membrane
matrix
cristae
cristae junctions
Alberts et al, Molecular Biology of the Cell, 6th edition (2014)
The mitochondrial respiratory chain
ADP + Pi
NADH
ATP
NAD+
H+
succinate
O2
H+ H+ H+ H+
H+
2H2O
H+
matrix
UQ
UQ
cristae space
+
H+ H+ H H+
H+
H+
H+
cytochrome c
H+
H+
H+
H+
H+
Complex I
Complex III
Complex II
NADH
dehydrogenase
cytochrome c
reductase
succinate
dehydrogenase
Davies & Daum, 2013
H+
H+
Complex IV
cytochrome c
oxidase
H+
H+
+
H+ H
H+
H+
Complex V
ATP synthase
The three proton pumps of the respiratory chain
Alberts et al, Molecular Biology of the Cell, 6th edition
Reversible and irreversible processes
(A)
COMBUSTION
(B)
½O2
H2
BIOLOGICAL OXIDATION
H2
½O2
separate into H+
and electrons
2H+
+
_
2e
EXPLOSIVE
RELEASE OF
HEAT
ENERGY
H2O
much of the
energy is
harnessed and
converted to
a stored form
_
½O2
2e
2H+
H2O
Alberts et al, Molecular Biology of the Cell, 6th edition
Redox potentials in the respiratory chain
H+
_400
_300
ubiquinone
25
_200
H+
20
15
10
_100
Q
NADH
dehydrogenase
complex
cytochrome c
0
100
H+
200
cytochrome b-c1
complex
c
300
400
500
5
600
cytochrome
oxidase
complex
700
800
0
2H+ + ½O2
redox potential (mV)
free energy per electron (kcal/mole)
NADH
NAD+
H2O
direction of electron flow
Alberts et al, Molecular Biology of the Cell, 6th edition
Heme group covalently attached to protein
H3C
COOH
COOH
CH2
CH2
CH2
CH2
CH3
+
N
N
Fe
H3C
H
C
S
N+
N
CH3
CH3
HC
S
CH3
protein
Alberts et al, Molecular Biology of the Cell, 6th edition
Iron-sulfur (Fe-S) cluster
Cys
S
Fe
S
S
Fe
Fe
Fe
S
S
S
S
S
Cys
Cys
Cys
MBoC6 m14.23/14.14
Alberts et al, Molecular Biology of the Cell, 6th edition
Ubiquinol redox reactions
O
e– + H+
CH3
O
O CH3
O
H3C
H O
O
e– + H+
CH3
O CH3
O
H3C
O
CH3
H O
O CH3
OH
H3C
hydrophobic
hydrocarbon tail
oxidized
ubiquinone
ubisemiquinone
(free radical)
reduced
ubiquinone
Alberts et al, Molecular Biology of the Cell, 6th edition
Complex I - NADH dehydrogenase
NAD++
NAD
NADH
NADH
FMN
FMN
2e–-
matrix arm
2e
proton antiporter
modules
MATRIX
Q
Q
matrix
membrane arm
CRISTAE
(B)
H+
H+
H+
H+
H
H++
H
H++
crista
lumen
adapted from Alberts et al, Molecular Biology of the Cell, 6th edition
Complex III - cytochrome c reductase
electrons out to
cytochrome c
cyt c1
e–
heme c
CRISTAE
SPACE
Fe2S2
heme bL
MATRIX
e–
electrons in from
ubiquinone (QH2)
heme bH
(A)
cyt b
(B)
Alberts et al, Molecular Biology of the Cell, 6th edition
The Q cycle
Alberts et al, Molecular Biology of the Cell, 6th edition
Complex IV - cytochrome c oxidase
electrons in from
cytochrome c
subunit II
e–
Cu
CRISTAE SPACE
heme a
Cu
heme a3
MATRIX
subunit I
(A)
(B)
Alberts et al, Molecular Biology of the Cell, 6th edition
Electron transfer in cytochrome oxidase
e–
4 electrons entering,
one at a time,
from cytochrome c
4 H+ (4 pumped protons)
Cu atom
electrons donated,
one at a time, from
cytochrome c
protein
side chains
e–
CRISTAE SPACE
heme a3
heme a
e–
MATRIX
4 H+
Fe atom
Cu atom
O2
+
4H
inputs
2H2O
outputs
4 electrons
collected and
O2 bound here
active site
Alberts et al, Molecular Biology of the Cell, 6th edition
A proton channel
(A)
H
H+
O H
H
H
O
O
H
H
H
H
O
O
O
O
O
H
H
H
H
H
H
H
H
O H
H+
H
(B)
H+
H
O
O
O
–
H
H
O
HO
O
H
O
O
OH
H
H
O
H
O–
O
H
H+
Alberts et al, Molecular Biology of the Cell, 6th edition
Respiratory chain supercomplex
Alberts et al, Molecular Biology of the Cell, 6th edition
Complex V - ATP synthase
(A)
(B)
H+
H+
H+
H+
CRISTAE
SPACE
Fo rotor
H
+
H+
H+
+
H
H+
H+
a
MATRIX
H+
central
stalk
H+
H+
rotor
Pi + ADP
peripheral
stalk
ATP
F1 head
Alberts et al, Molecular Biology of the Cell, 6th edition
stator
ATP synthase rotor rings
(A)
Thomas Meier,
Denys Pogoryelov,
MPI of Biophysics,
Frankfurt
(B)
Alberts et al, Molecular Biology of the Cell, 6th edition
ATP synthase rotor rings
Laura Preiss, PhD thesis, 2013
Bicycle gears
Re-bicycle repair shop, Frankfurt
Cryo-EM of ATP synthase dimers
class averages
re-projections
Allegretti et al, Nature 2015
3D map of ATP synthase dimer
Allegretti et al, Nature 2015
Fit of atomic X-ray structures
10 nm
Allegretti et al, Nature 2015
Map of rotor and a-subunit
Allegretti et al, Nature 2015
c-ring / subunit a interface
Conserved
Arg
Allegretti et al, Nature 2015
Proton channel on matrix side
Allegretti et al, Nature 2015
Sequence comparison of subunit a
aR239
aQ295
The ATP synthases of bacteria, mitochondria and
chloroplasts work in the same way
Allegretti et al, Nature 2015
Proton gradient drives rotor
hydrophilic cavity
on lumenal side
Arg a239
hydrophilic cavity
on matrix side
Allegretti et al, Nature 2015
The c-ring Rotor drives ATP synthesis
Alberts et al, Molecular Biology of the Cell, 5th edition (2008)
Dimer rows are ubiquitous
50nm
rat liver
bovine heart
Y. lipolytica
P. anserina
S. cerevisiae
potato
green alga
(101)
(49)
(131)
(23)
(121)
(71)
(56)
mammals
yeasts and fungi
Karen Davies
plants
Model of cristae organization
protons
ATP synthase dimers
respiratory chain proton pumps
cristae junction complex (hypothetical)
Mitochondrial ADP/ATP carrier
Alberts et al, Molecular Biology of the Cell, 6th edition
Mitochondrial protein import
nucleus
RNA
cytoplasmic
ribosome
~1500 different
nuclear-encoded
mitochondrial proteins
TOM
mitochondrial DNA
TIM
RNA
10–15 mitochondriallyencoded proteins
mitochondrial
ribosome
Alberts et al, Molecular Biology of the Cell, 6th edition
Mitochondrially encoded membrane proteins
rpl31
rpl27
rpoA
rpl20
rpl34
cox11
rpoB
rpl19
rpoC
rpoD
rpl18
rpl32
rps1
yejR
rrn5
tatC
atp3
yejU
sdh3
yejW
vejV
atp9
rps3
cox3
rps19
rns
rps14
rnl
cox1
cob
nad5
nad4L
atp6
atp4
rpl11
nad8
sdh4
atp1
rpl1
tufA
rps10
sdh2
rpl10
secY
nad2
nad1
atp8
nad3
cox2
nad4
nad6
rps13
rpl14
rps8
nad11
rps7
rpl16
rps4
Reclinomonas
Marchantia
nad9
rps11
rps12
rpl6
nad7
rpl2
rpl5
rps2
Acanthamoeba
Plasmodium
Schizosaccharomyces
Alberts et al, Molecular Biology of the Cell, 6th edition
Human
Mitochondrial fission and fusion
FISSION
FUSION
(B)
(A)
5 µm
(C)
MBoC6 m14.55/14.58
Alberts et al, Molecular
Biology of the Cell, 6th edition
Mitochondrial fission
dynamin-1
GTP
targeting
assembly-driven constriction
Pi
hydrolysis-driven constriction
fission
Alberts et al, Molecular Biology of the Cell, 6th edition
Mitochondrial fusion
GTP
(low)
GTP
(high)
outer
membrane
fusion
inner
membrane
fusion
Alberts et al, Molecular Biology of the Cell, 6th edition
Part 2:
Chloroplasts
Energy-converting organelles
evolved from endosymbiontic bacteria
bacterium
cytoplasm
inner membrane
outer membrane
mitochondrion
chloroplast
matrix
cristae
stroma
inner membrane
outer membrane
thylakoid
membrane
Alberts et al, Molecular Biology of the Cell, 6th edition
The chloroplast
outer envelope
O2
H2O
OUT
inner envelope
O2
H+
e–
NADP+
NADPH
sugars
amino acids
fatty acids
OUT
sugars
amino acids
fatty acids
ATP
ADP
carbon
fixation
cycle
IN
CO2
Alberts et al, Molecular Biology of the Cell, 6th edition
Chloroplasts in a leaf cell
Alberts et al, Molecular Biology of the Cell, 6th edition
Chloroplast grana
GRANA
CHLOROPLAST
grana thylakoid
LEAF
stroma
upper epidermis
2 µm
lower epidermis
stroma
thylakoid
outer
membrane
(A)
(B)
inner membrane
intermembrane space
1 µm
(C)
Alberts et al, Molecular Biology of the Cell, 6th edition
Energy-converting complexes
of the chloroplast thylakoid membrane
Alberts et al, Molecular Biology of the Cell, 6th edition
Chlorophylls attach non-covalently
CH2
CH
H
C
H3C
H
H3C
CH3
C
C
C
C
C
N
N
C
C
N
N
C
C
Mg
C
C
H
C
CH2
C
H C
C
CH2
C
C
C
CH
C
O
O
O
C
CH2 CH3
C
H
C
CH3
O
O
CH3
CH2
CH
C
CH3
CH2
CH2
CH2
HC
CH3
hydrophobic
tail region
CH2
CH2
CH2
HC
CH3
CH2
CH2
CH2
CH
CH3
CH3
Alberts et al, Molecular Biology of the Cell, 6th edition
Chlorophyll absorption spectrum
Alberts et al, Essential Cell Biology, 3rd edition
A photosystem
electron
donor
light
e–
QH2
Q
Q
antenna complexes
Q
reaction
center
Alberts et al, Molecular Biology of the Cell, 6th edition
Light-harvesting complex of photosystem II
THYLAKOID
SPACE
STROMA
Chl a
Chl b
carotenoids
Standfuß, Kühlbrandt et al, EMBO J 2005
Alberts et al, Molecular Biology of the Cell, 6th edition
Charge separation in a reaction centre
sunlight
H2O
special pair
e–
H+, O2
e–
Q
Q–
reaction center
chargeseparated H+
state
QH•
Solar energy is converted into a trans-membrane proton gradient
Alberts et al, Molecular Biology of the Cell, 6th edition
The Z scheme
sunlight
sunlight
H2O
energy
transfer
thylakoid
space
e–
e–
energy
transfer
stroma
NADPH
light
harvesting
complex
photosystem II
photosystem I
light
harvesting
complex
Alberts et al, Molecular Biology of the Cell, 6th edition
Two light reactions
photosystem I
light energy harnessed to produce
ATP and NADPH
–1200
–1000
ferredoxinNADP reductase
–800
photosystem II
ferredoxin
–600
an electrochemical
gradient is formed
that generates ATP
redox potential (mV)
–400
–200
Q
H+
0
200
400
light
produces
charge
separation
NADPH
+ H+
pC
+
plastocyanin
4H+
800
1200
NADP+
cytochrome
b6-f complex
plastoquinone
600
1000
light
produces
charge
separation
O2
Mn
2H2O
+
water-splitting enzyme
direction of electron flow
Alberts et al, Molecular Biology of the Cell, 6th edition
Photosystem II reaction centre
4 H+
O2
e–
Mn cluster
2 H2O
P680
THYLAKOID
SPACE
e–
STROMA
(A)
b559
(B)
MBoC6 n14.325/14.45
QB
Alberts et al, Molecular Biology of the Cell, 6th edition
QA
Photosystem I reaction centre
plastocycanin
e–
P700
THYLAKOID
SPACE
A0
A0
PQ
PQ
FX
STROMA
FA
(A)
ferrodoxin
(B)
Alberts et al, Molecular Biology of the Cell, 6th edition
FB
Cyclic electron flow around PS I
light
light
2 H2O
O2 + 4H
+
2H+
P680
PS-II
Q
pC
QH2
QH2
Q
Q
2H+ 2H+
Fd
pC
P700
PS-I
Fd
FNR
Alberts et al, Molecular Biology of the Cell, 6th edition
NADPH
Cryo section of grana stack
ATP synthase
Daum et al, Plant Cell 2010
ATP-Synthase in chloroplast thylakoids
Bertram Daum
chloroplast ATP synthase
Chloroplast ATP synthase
Böttcher et al. 2005
tomographic
volume
sub-tomogram
average
~ 85% monomeric
single-particle map
(Böttcher et al, 2005)
~ 15% in contact with neighbour
Daum
et al,
CellCell
2010
Daum
et Plant
al, Plant
2010
Comparison of mitochondria
and chloroplasts
Chloroplasts are large
Alberts et al, Molecular Biology of the Cell, 6th edition
ATP synthase in mitochondria and chloroplasts
MITOCHONDRION
matrix
pH 8
H+
H+
H+
intermembrane space
pH 7.4
ADP
+ Pi
ATP
cristae
thylakoid membrane
CHLOROPLAST
stroma
pH 8
thylakoid space
pH 5.5
ADP + Pi
ATP
intermembrane space
pH 7.4
H+ +
H
H+
H+ H+
+
+
H+ H H H+
MBoC6
n14.328/14.49
Alberts et al, Molecular
Biology
of the Cell, 6th edition
Respiration and photosynthesis
(A) MITOCHONDRION
(B) CHLOROPLAST
H+ gradient
H+ gradient
NADH
H+
pump
e–
light
e–
H+
pump
e–
H+
pump
photosystem
I
photosystem
II
fats and
carbohydrate
molecules
NADPH
light
H+
pump
citric
acid
cycle
O2
CO2
H2O
products
carbonfixation
cycle
H2O
O2
carbohydrate
molecules
products
Alberts et al, Molecular Biology of the Cell, 6th edition
CO2
Electron transfer reactions
NAD+ reverse
electron
flow
Q
NADH
dehydrogenase
NADH
H+
light
produces
charge
separation
b-c
complex
cyt
c2
+
PURPLE NONSULFUR BACTERIA
NADP+
H+
Q
light
produces
charge
separation
b-f
complex
light
produces
charge
separation
H2O
pC
NADPH
+
+
PLANT CHLOROPLASTS AND CYANOBACTERIA
NADH
NAD+
NADH
dehydrogenase
H+
Q
b-c1
complex
cyt c
MITOCHONDRIA
cytochrome
oxidase
O2
H2O
Alberts et al, Molecular Biology of the Cell, 6th edition
Chloroplast ATP synthase
ATP synthase
monomers
thylakoid membrane
inner membrane
outer membrane
stroma ~ pH 8
thylakoid lumen
~ pH 5 - 7
H+ H+
H+ H+
Model of cristae organization
protons
ATP synthase dimers
respiratory chain proton pumps
cristae junction complex (hypothetical)
Evolution of reaction centres
cytochrome
EXTRACELLULAR
SPACE
Q
CYTOSOL
LH1
Q
M
L
LH1
(A) PURPLE BACTERIA
2H2O
THYLAKOID
LUMEN
LHCII
STROMA
O2+4H+
Mn
Q
Q
D2
D1
LHCII
core antenna protein
(B) PHOTOSYSTEM II
pC
THYLAKOID
LUMEN
STROMA
Q
Psa B
Q
Psa A
(C) PHOTOSYSTEM I
From: Rhee, Morris, Barber, Kühlbrandt, Nature 1998
Alberts et al, Molecular Biology of the Cell, 6th edition
Evolution of photosynthetic bacteria
CHLOROPLASTS
MITOCHONDRIA
EUKARYOTES
PROKARYOTES
cyanobacteria
gliding bacteria
loss of photosynthesis
loss of photosynthesis
REDUCING
ATMOSPHERE
green filamentous
bacteria
purple nonsulfur
bacteria
blue-green
bacteria
OXIDIZING
ATMOSPHERE
rhizobacteria
E. coli
O2 respiration
O2 respiration
O2 respiration
purple sulfur
bacteria
H2O photosynthesis
carbon-fixation cycle
green sulfur
bacteria
H2S photosynthesis
ancestral
fermenting bacteria
Alberts et al, Molecular Biology of the Cell, 6th edition
All the oxygen in the Earth’s atmosphere
is a side-product of photosynthesis
Alberts et al, Molecular Biology of the Cell, 6th edition (2014)
Iron ore deposits show that
oxygen evolution started 3.5 bn years ago
(billion years)
Hohmann-Marriott et al, Annu. Rev. Plant Physiol. 2011
Stromatolites are large colonies of oxygen-evolving
cyanobacteria
Stromatolites
in Shark Bay,
Western Australia
3.5 bn yr old fossil
stromatolite,
Pilbara, WA
Wikipedia
Invention of the wheel ~3 billion years ago