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

CO2

Other examples of fermentation processes:

Pyruvate CO2 + ethanol; 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)

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.

Acetyl CoA

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+

oxidizing agent

(electron acceptor)

NADH

reducing agent

(electron donor)

NADH NAD+ + H+ + 2e-

Flavin adenine dinucleotide

FAD

FADH2

FADH2 FAD + 2H+ + 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+

H+

H+

H+

NADH

NAD+

2e-

NADH dehydrogenase

complex

cytochrome b-c1

complex

cytochrome oxidase

complex

ubiquinone cytochrome c

2H+ + ½ O2

H2O

heme group in cytochrome c

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.

ATP synthetase complex

proton channel

ADP + Pi

ATP

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!

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.

ATP synthase works both ways. May have originated as an ATP driven proton pump.

ATP ADP + Pi

H+

H+

e-Electron transport chain enabled H+ to be pumped without using ATP.

ADP + Pi ATP

H+

H+

e-If electron transport chain pumps became more efficient than necessary, the proton gradient could be used to drive ATP synthase to make 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 NO3

-

NH4+ + 1 ½ O2 NO2

- + H2O + 2H+

Nitrobacter(B)

Nitrosomonas (B)

Sulphur oxidation (from thiosulphate, sulphur or hydrogen sulphide)

S2O32- + 2O2 + H2O 2SO4

2- + 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 SO3

2- 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

Oxidation of sugars into CO2

(In anaerobic organisms sugars are oxidized incompletely via fermentation. O2 not required.)

(Some forms of photosynthesis do not produce oxygen)

delocalized electrons in ring structure

Two types of chlorophyll absorb visible light at slightly different wavelengths.

Chlorophyll contained in the photosystem I and II protein complexes

light excites an electron

low energy electron replaces it

high energy electron enters the transport chain

Photosynthesis: a light-driven electron transport chain

H+

H+

2e-

Photosystem II cytochrome b6-f complex

Photosystem I

2H+ + ½ O2

H2O

Thylakoid membrane of chloroplasts (or outer membrane of photosynthetic bacteria)

plastoquinone plastocyanin ferredoxin

Ferredoxin-NADP reductase

light light

NADP+

NADPH

Generates proton gradient that can be used by ATP synthase

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)

ancestral PS

divergence in separate lineages

fusion

PS I – Chlorobium and Heliobacteria

PS I & II Cyanobacteria

PS II – Chloroflexus and Purple bacteria

endosymbiosis: chloroplasts

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.

Origin of life

Simple heterotrophic metabolism / fermentation

Chemosynthesis

Electron transport chains

LUCAGenes for sulphate reduction, nitrate reduction, sulphur oxidation, oxygen respiration all present in A and B

BacteriaArchaea Eukaryotes

Modern organisms: DNA + RNA + proteins

RNA world

Metabolism first ?

Genetic code: RNA + proteins

origin of eukaryotic nucleus ?

mitochondriaAnoxygenic Photosynthesis

Oxygenic Photosynthesischloroplasts

Methanogenesis/ Bacteriorhodopsin only in Archaea

Plausible summary of “Everything”

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)

Higher helix melting temp

10 60 110

But overall genomic GC content does not correlate with T. DNA must be stable anyway...

In proteins Gunfolding found to be large in “thermozymes”

Tunfolding is higher

More hydrogen bonds with water.

More salt bridges between + and – charged residues.

More disulphide bonds between cysteines.

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

Halobacteria in a salt lake

(Archaea with photosynthetic purple membrane)

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.