Transcript Slide 1

Metabolism = breaking molecules down and building up new ones
Important processes in metabolism
Discuss processes in order in which they (might have) evolved
1. Anaerobic breakdown of organic molecules = fermentation.
Fits with ‘primordial soup’ argument (first organisms heterotrophic).
2. Respiration – electron transport chains (still heterotrophs but much
more efficient).
3. Chemosynthesis (autotrophs – can carry out carbon fixation. No longer
limited by the soup).
4. Photosynthesis (autotrophs – huge amounts of energy for free! Major
increase in biomass).
Glycolysis – breakdown of sugar
Essentials worth remembering
1 glucose (6C)  2 pyruvate (3C)
Generates 2 ATP and 2 NADH
Essentials
In anaerobic bacteria
pyruvate is broken
down to waste
products (e.g. lactate).
NAD+ is regenerated
(a cycle)
also occurs in
muscles
Other examples of fermentation processes:
CO2 CO2 + ethanol;
Pyruvate
Pyruvate  CO2 + acetic acid
These occur in yeast
Glucose is only partly oxidized by these reactions. Relatively inefficient.
In aerobic organisms, pyruvate feeds into the Citric Acid Cycle (Krebs cycle)
Acetyl CoA
Essentials
This produces NADH and
FADH2.
These are electron donors
(reducing agents) for the
electron transport chain.
All the C from the glucose is
now oxidized to CO2.
Many other biosynthetic
pathways branch off from
glycolysis and citric acid cycle.
Important processes in metabolism
Discuss processes in order in which they (might have) evolved
1. Anaerobic breakdown of organic molecules = fermentation.
Fits with ‘primordial soup’ argument (first organisms heterotrophic).
Relatively simple.
2. Respiration – electron transport chains (still heterotrophs but much
more efficient). Really clever, but complicated.
3. Chemosynthesis (autotrophs – can carry out carbon fixation. No longer
limited by the soup).
4. Photosynthesis (autotrophs – huge amounts of energy for free! Major
increase in biomass).
Oxidation-Reduction again Nicotinamide
adenine
dinuclotide
NAD+
FAD
Flavin adenine dinucleotide
oxidizing agent
(electron
acceptor)
FADH2
NADH
reducing agent
FADH2  FAD + 2H+ + 2e-
(electron donor)
NADH  NAD+ + H+ + 2e-
Now we are going to make use of those electron donors we just made two
slides back. Hang onto your hats!
H+
H+
H+
2e-
NADH
H+
ubiquinone
H+
cytochrome c
H2O
H+
2H+ + ½ O2
NAD+
NADH dehydrogenase
cytochrome b-c1
cytochrome oxidase
complex
complex
complex
Essentials
Aerobic respiration (in aerobic bacteria
or in mitochondria in eukaryotes)
High energy electron donor eventually
donates electrons to O2
Electron goes “downhill” in G
Proton gradient is generated.
heme group in
cytochrome c
ATP synthetase complex
proton
channel
Electron transport chain + ATP
synthesis = oxidative phosphorylation
chemiosmotic process
For each molecule of glucose about 30
ATPs generated by ox. phos.
but only 2 from glycolysis.
Much more energy from the same food!
ADP + Pi
ATP
protons moving
downhill provide
energy for uphill
synthesis of ATP
Other respiratory chains
In each case organic molecules are oxidized. The terminal electron acceptor
is reduced. The energy released is used to generate a proton gradient that is
used for ATP synthesis. In aerobic respiration O2 is the electron acceptor. In
anaerobic respiration another molecule is the electron acceptor.
Type of
metabolism
Electron
acceptor
Products
Organisms
Aerobic
respiration
O2
H2O
Many aerobic bacteria and archaea.
Eukaryotes (mitochondria)
Denitrification
NO3-
NO2-.
NO2-,, N2O
or N2
Many bacteria can do this facultatively (eg.
E. coli, B. subtilis).
Paracoccus denitrificans (B)
Sulphate
reduction
SO42-
H2S
Desulfovibrio desulfuricans (B)
Archaeoglobus fulgidus (A#)
Elemental sulphur
metabolism
S
(red. with
H2)
H2S
Delsulfuromonas acetoxidans (B)
Pyrococcus, Desulfurococcus (A)
Sulfolobus, Thermoproteus (A#)
Iron reduction
Fe3+
Fe2+
Thermus (B)
A – Archaea; B – Bacteria; # can also be chemoautotrophic
Evolution of respiratory chains
Early organisms probably used fermentation only (anaerobic).
Fermentation usually leads to excretion of acids (lactic, formic, acetic....).
Proton pump would be favoured to keep the acid out.
H+
ATP synthase works both ways. May have
originated as an ATP driven proton pump.
ATP  ADP + Pi
H+
Electron transport chain enabled H+ to be
pumped without using ATP.
e-
H+
If electron transport chain pumps became
more efficient than necessary, the proton
gradient could be used to drive ATP
synthase to make ATP.
eH+
ADP + Pi  ATP
Important processes in metabolism
Discuss processes in order in which they (might have) evolved
1. Anaerobic breakdown of organic molecules = fermentation.
Fits with ‘primordial soup’ argument (first organisms heterotrophic).
 Relatively simple. Maybe these kind of reactions were catalyzed by
ribozymes in the RNA world. NADH, FADH2, CoA all involve
nucleotides (clue?).
2. Respiration – electron transport chains (still heterotrophs but much
more efficient). Really clever, but complicated. Each complex in the
respiratory chain involves many proteins. No RNAs known to do this.
 probably this comes after RNA world but before LUCA
 Now we can efficiently generate energy from food, but we are
running out of food...
3. Chemosynthesis (autotrophs – can carry out carbon fixation. No longer
limited by the soup).
4. Photosynthesis (autotrophs – huge amounts of energy for free! Major
increase in biomass).
Chemoautotrophy (Chemolithotrophy)
An inorganic reducing agent feeds into an electron transport chain. Generates a
proton gradient (more ATP synthesis) and an organic reducing agent (like NAD(P)H),
which reduces CO2 to organic molecules. Several different carbon fixation cycles are
known – “opposite” of citric acid cycle.
Type of metabolism
Energy producing reaction
Organisms
Hydrogen oxidation
H2 + ½ O2  H2O
Alcaligenes, Hydrogenobacter (B)
Nitrification (from
nitrite or ammonia)
NO2- + ½ O2  NO3NH4+ + 1 ½ O2  NO2- + H2O + 2H+
Nitrobacter(B)
Nitrosomonas (B)
Sulphur oxidation
(from thiosulphate,
sulphur or
hydrogen sulphide)
S2O32- + 2O2 + H2O  2SO42- + 2H+
S + 1 ½ O2 + H2O  SO42- + 2H+
2H2S + O2  2S + 2H2O
Sulfolobus (A)
Thiobacillus (B)
Thiobacillus (B)
Iron oxidation
2Fe2+ + 2H+ + ½ O2  2Fe3+ + H2O
Thiobacillus (B)
Methylotrophy
CH4 or CH3OH or CO  CO2
Methylomonas (B)
Methanogenesis
4H2 + CO2  CH4 + 2H2O
Methanococcus (A)
Elemental sulphur
metabolism
H2 + S  H2S
Thermoproteus (A)
Sulphate reduction
H2 + SO42- (or SO32- or S2O32-)  H2S
Archaeoglobus (A)
Essentials
Many possible energy sources from redox reactions.
Can go “both ways” - 2 examples:
• can oxidize S to SO42- in aerobic conditions or reduce S to H2S in presence of
H2 gas but absence of O2 ---- both have G < 0 in the right conditions.
• methylotrophy (aerobic) v. methanogenesis (anaerobic)
Sometimes the same organism goes both ways:
e.g. Sulfolobus can be an anaerobic heterotroph with sulphur reduction, or an
autotrophic aerobic sulphur oxidizer
clever cloggs!
Redox reactions in previous table have G < 0. They look simple, but remember
they don’t just happen in one step as an inorganic reaction.
These reactions are coupled to electron transport chains and proton gradients....
Important processes in metabolism
Discuss processes in order in which they (might have) evolved
1. Anaerobic breakdown of organic molecules = fermentation.
Fits with ‘primordial soup’ argument (first organisms heterotrophic).
 Relatively simple. Maybe occurred in the RNA world.
2. Respiration – electron transport chains (still heterotrophs but much
more efficient). Really clever, but complicated. Each complex in the
respiratory chain involves many proteins. No RNAs known to do this.
 probably this comes after RNA world but before LUCA
3. Chemosynthesis (autotrophs – can carry out carbon fixation. No longer
limited by the soup).
 Many possible sources of chemical energy.
 Some of these types of metabolism are found in both archaea and
bacteria, i.e. before LUCA.
4. Photosynthesis (autotrophs – huge amounts of energy for free! Major
increase in biomass).
 Only in bacteria, i.e. after LUCA
 requires light-harvesting protein complexes (photosystems)
Complementary processes of photosynthesis and respiration
Carbon fixation into sugars
reduction of CO2
(Some forms of photosynthesis
do not produce oxygen)
Oxidation of sugars
into CO2
(In anaerobic organisms sugars
are oxidized incompletely via
fermentation. O2 not required.)
Two types of chlorophyll absorb visible
light at slightly different wavelengths.
Chlorophyll contained in the
photosystem I and II protein complexes
high energy
electron
enters the
transport
chain
light excites
an electron
delocalized electrons in ring structure
low energy
electron
replaces it
Photosynthesis: a light-driven electron transport chain
Thylakoid membrane of chloroplasts (or outer membrane of photosynthetic bacteria)
light
light
H2O
2H+ + ½ O2
H+
2e-
plastoquinone
plastocyanin
H+
Photosystem II
cytochrome
b6-f complex
Generates proton
gradient that can be
used by ATP synthase
NADPH
ferredoxin
NADP+
Photosystem I
FerredoxinNADP
reductase
NADPH is a reducing
agent that can reduce
CO2 to organic molecules
The “dark reactions” of photosynthesis.
Carbon fixation cycle (Calvin cycle).
CO2 is reduced to sugars.
Requires energy and reducing power.
Types of photosynthesis
5 groups of bacteria perform photosynthesis.
In oxygenic photosynthesis H2O is the electron donor and O2 is produced.
In anoxygenic photosynthesis H2S is the electron donor and O2 is not produced.
Type of
photosynthesis
Photo-system
Organisms
Anoxygenic
PS I
Green sulphur bacteria - Chlorobium
Anoxygenic
PS I
Heliobacteria
Anoxygenic
PS II
Purple sulphur bacteria (Chromatiales – Gamma
proteobacteria)
Purple non-sulphur bacteria (Rhodospirillum – Alpha
proteobacteria). Use H2 not H2S
Anoxygenic
PS II
Green filamentous bacteria - Chloroflexus
Oxygenic
PS I and PS II
Cyanobacteria and Chloroplasts (in Eukaryotes)
Evolution of photosynthesis (see Olsen and Blankenship, 2004)
PS I – Chlorobium and Heliobacteria
divergence in
separate
lineages
fusion
PS I & II
Cyanobacteria
endosymbiosis:
chloroplasts
ancestral PS
PS II – Chloroflexus and Purple bacteria
PSs contain different types of chlorophyll. Genes for pigment synthesis
may not follow same tree as genes for the components of the PSs.
Evidence for horizontal transfer.
Archaea do not have these photosystems. They evolved after the LUCA.
However: Halobacteria (which are salt-loving extremophile archaea) have
an independent light harvesting protein called bacteriorhodpsin in their
purple membrane. Contains retinal chromophore. Different to chlorophyll.
Archaea
Eukaryotes
Bacteria
chloroplasts
Methanogenesis/
Bacteriorhodopsin
only in Archaea
mitochondria
origin of
eukaryotic
nucleus ?
Plausible summary of
“Everything”
Oxygenic Photosynthesis
Anoxygenic Photosynthesis
Genes for sulphate reduction, nitrate reduction, sulphur
oxidation, oxygen respiration all present in A and B
LUCA
Modern organisms:
DNA + RNA + proteins
Chemosynthesis
Electron transport chains
Genetic code:
RNA + proteins
RNA world
Metabolism first ?
Origin of life
Simple heterotrophic
metabolism /
fermentation
Alternative viewpoint # 1 – Early evolution of photosynthesis
Mauzerall argues that only photosynthesis could supply sufficient energy for
life. Light absorbing pigments must have existed very early. These would have
initiated redox reactions. But these would be independent of today’s
membrane bound electron transport chains.
?? But some proteins in the respiratory and photosynthetic chains are related.
Suggests that (current form of) photosythesis was later.
Alternative viewpoint # 2 – Chemoautotrophic origin
Wächtershäuser argues that an autotrophic metabolism based on pyrite was
first. FeS + H2S  FeS2 + H2
?? This may be a plausible energy source but (current forms of) autotrophs
use complex electron transport pathways. If this existed, evidence of it is lost.
?? The first organisms must have been made of something! Presumably
organic molecules .... This brings us back to the primordial soup....
Alternative viewpoint # 3 – Clay mineral origin
Cairns-Smith argues that organic molecules were not important originally.
Clay minerals stored information. Genetic takeover occurred (e.g. to RNA).
Extremophiles
What counts as extreme? Depends on our viewpoint.
What limits organisms?
Challenges in different environments. How to overcome them?
What can they tell us about possibility of life elsewhere?
Congress pool. Yellowstone.
pH3
80oC
Sulfolobus acidocaldarius
Pictures from Rothschild &
Mancinelli (2001)
See also Lunine Chap 10
Chapters by Rothschild and
Stetter in OI book.
Temperature
>80 Hyperthermophiles
60-80 Thermophiles
15-60 Mesophiles
<15 Psychrophiles
Eukaryotes more limited at
high temp than bacteria
and archaea
Low temp organisms from
all domains
Growth rate measurements
distinguish tolerant organisms
from true “philes”
Challenges of high T:
stability of molecular structures, membranes, and molecules themselves
Examples of molecular adaptation to high T:
GC content in rRNA correlated with growth
temp. (Galtier & Lobry, 1997)
In proteins Gunfolding found to
be large in “thermozymes”
Higher helix melting temp
Tunfolding is higher
More hydrogen bonds with
water.
More salt bridges between +
and – charged residues.
More disulphide bonds
between cysteines.
10
60
110
But overall genomic GC content does not
correlate with T. DNA must be stable anyway...
Folded structures more rigid,
fewer cavities.
Psychrophiles – challenges of low temps
Membrane becomes too rigid – need to change lipid structure
Slows down reaction rates
Liquid water usually required for reactions
Ice crystals expand relative to water – can tear cells apart.
Antifreeze proteins found in fish that live at < 0
Small helical proteins can bind to the surface of
small ice crystals and prevent them growing.
Sea-ice diatoms (unicellular
photosynthetic eukaryotes)
Salinity – Halophiles
Salt conc in ocean is 3.5%, but this
is too high for us.
Some organisms are adapted to
concs up to 35% in salt lakes
Water will diffuse out of the cell by osmosis.
Causes dessication.
Many halophiles use ‘Compatible solutes’ - small
organic molecules that do not interfere with
metabolism when accumulated to high conc.
Extreme halophiles use ‘salt-in-cytoplasm’ – K+
are selectively allowed into cell to balance the
osmotic pressure. Enzymes have to adjust to
working in this situation.
Halobacteria in a salt lake
(Archaea with photosynthetic
purple membrane)