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Metabolism
Bert Engelen
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Biochemical pathways
http://www.expasy.org/cgi-bin/show_thumbnails.pl
[email protected]
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Metabolism
• Greek bolein = throw (compare ball, ballistics)
• Pathways, reaction chains (!?)
• Primary metabolism involved in growth and energy
metabolism
• Anabolism, assimilation, biosynthesis
• Catabolism, dissimilation, degradation, mineralisation
coupled to energy conservation
• Secondary metabolism produces various compounds
without coupling to growth
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Metabolism – overview
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Brock/Madigan 10th ed.
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Transport
systems
Cytoplasmic
membrane
Catabolism
Anabolism
Metabolism of an
organoheterotrophic
aerobe
=> Substrate used as
building block and as fuel
=> Oxidation to CO2 without
O2 being involved
Respiratory
chain
=> Transport systems
essential for energy
conservation
=> Anabolism divergent,
catabolism convergent
O2 involved in
the last step, only
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Growth with Glucose
Assimilation: C6H12O6 → 6 <CH2O>
<CH2O> ≈ Biomass (C106H263O110N16P1S1)
Redfield 1963
Experience: YATP ≈ 10.5 g dry mass/mol ATP
Dissimilation: C6H12O6 + 6 O2 → 6 CO2 + 6 H2O
ΔG°' = -2872 kJ/mol
2872 : 75 (ΔGbiol of ATP) → thermodyn. expectation
≈ 38 ATP per Glucose
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Variations of the life mode
=> CO2 as carbon source
???
=> Inorganic electron
donor
???
=> Alternative electron
acceptors
???
=> No electron acceptor
???
=> No electron donor?
???
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Some life modes
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Metabolism overview
• Polymerisation/hydrolysis
• Glycolysis
• ATP requirement for
biosynthesis
• Regulation
• Nitrogen requirement
• Acetyl-coenzyme A
• Citric acid cycle
• Reducing equivalents
• Chemiosmotic
energy conservation
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Steps of glucose dissimilation
- Transport (eventually combined with Phosphorylation)
- Glycolysis (e.g., fructose1,6-bisphosphate pathway)
o Activation by phosphate residues
o Cleavage in C3 compounds, partial oxidation, 2 ATP (net)
- Pyruvate decarboxylation
o Oxidation to acetyl-Coenzyme A + CO2
- Citric acid cycle (TCA)
o Complete oxidation (2 ATP) and turning platform for
assimilation
- Respiratory chain
o Transfer of reducing equivalents to oxygen
(no ATP, generation of a proton gradient)
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Glycolysis
Mount two
P-'handles'
cleavage
oxidation and
another 'handle',
-> 2 ATP =
'handles' gained
back
2 ATP won
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Phosphorylated metabolites formed during glycolysis
Phosphorylation
P
C1
Transformation
Phosphorylation
P
C2
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C3-compounds formed during glycolysis
Phosphorylation
Cleavage
P
De-phosphorylation
Transformation
XP
Dehydration
De-phosphorylation
Transformation
XP
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Energetics and
regulation of
glycolysis by
allosteric
mechanisms
• Irreversible step
underly multiple
regulation
AMP
ADP
ΔG < 0,
irreversible
• ATP and G-6-P may be
substrate or product and
inhibitor
• ADP und AMP as
corresponding effectors
ΔG ≈0, reversible
Simplified, incomplete picture,
depends on organism, may be
regulated by hormones (e.g. Insulin).
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Substrate level phosphorylation
Reaction catalysed
by Hexokinase:
Glucose + ATP → G-6-P + ADP
ΔG°' - 15.1 kJ/mol, irreversible
• Glucose activated by means of ATP
• Back reaction via loop: Glucose-6-Phosphatase
Glucose-6-P + H2O → Glucose + Pi
• Regulation required to avoid a 'futile cycle', which does
nothing but dephosphorylating ATP
Energetically comparable with
hexokinase: Reaction of
Phosphofructokinase:
F-6-P + ATP → F-1,6-BP + ADP
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Substrate level phosphorylation
Reaction of
phosphoglycerate kinase
1,3-PGA + ADP → 3-PGA + ATP
ΔG °' close to zero, reversible
• Where does the second, energy-rich phosphate group come from?
GAP + NAD + Pi → 1,3-PGA + NADH2
• Redox reaction: Aldehyde oxidised to acid, NADH2
formed, free energy difference used for phosphate binding
= 'Energy conserved', energy conversion
• Reaction complicated, but reversible
Reaction of pyruvate kinase: PEP + ADP → Pyruvat + ATP
ΔG °' < 0, irreversible
• Yields net ATP, while the upper reaction regenerates ATP needed for
activation ('PEP has Pep!')
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The citric acid cycle or
tricarboxylic acid (TCA) cycle
• Turning platform of
metabolism, connecting
anabolism and catabolism
• Catabolically, acetate is
completely oxidized to CO2,
8 [H] (3 NADH2,1 FADH2) +
1 ATP (substrate level
phosphorylation)
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Metabolites of the citric acid cycle
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Pyruvate oxidation and
tricarboxylic acid cycle
o Succinate formation is
coupled to GTP conservation,
which can transfer its
phosphate group to ADP
o If the TCA cycle is used for
biosynthetic reactions,
anaplerotic sequences
become necessary to
regenerate oxalacetate
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Stoichiometric balances
Glycolysis
Glucose + 2 ADP + 2 Pi → 2 Pyr + 4 [H] + 2 ATP
Pyr-DC
2 Pyr + 2CoA → 2 Acetyl-CoA + 2 CO2 + 4 [H]
TCC
2 Ac-CoA + 2 ADP + 2 Pi → 4 CO2 + 16 [H] + 2 CoA + 2 ATP
Sum
Glucose + 6 H2O + 4 ADP + 4 Pi → 6 CO2 + 24 [H] + 4 ATP
(Complete Oxidation without O2, only 4 ATP conserved
20 [H] as NADH2, 4 as FADH2)
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How to name electrons
• e- ?
← There are no free electrons (electron beam) in a cell!
•H?
← Hydrogen atoms ??
• H+ ?
← Proton without any elctrons??
• H2 ?
•
H+
+
← Molecular hydrogen gas??
e- ?
• [H] ?
← This is often meant, see, however, first line!
← That's it - reducing equivalents!
• [H] describes reducing equivalents or electrons without regarding the
transferring coenzymes (but indicating that there are some). Energetical
calculations require a known coenzyme.
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Coenzymes
and
prosthetic groups
apoenzyme + coenzyme → (functional) holoenzyme
• The coenzyme will be changed after the reaction, leave the
apoenzyme and react with another one ...
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NAD and FAD
• Are the most important coenzymes for electron tranfer
• NADP typical for anabolic, NAD for catabolic reactions
• FMN oft tightly bound as prosthetic group of redox enzymes
• Redox potential of NAD/NADH2: -320 mV
• Redox potential of FAD/FADH2: ≈ -200 mV
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Nicotinamide adenine dinucleotide
Flavin adenine dinucleotide
Wikipedia
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Acetyl Coenzyme A
Acetyl-CoA can easily be transformed to
acetyl phosphate and used to regenerate ATP
Acetyl-CoA + Pi
→ Acetyl-P + HS-CoA
Phosphotransacetylase
Acetyl-P + ADP
→ ATP + acetate
Acetate kinase
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Prosthetic groups
Iron-sulfur centres
and porphyrins are
important prosthetic
groups.
Porphyrin groups are
also present in some
coenzymes.
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