Microbial Metabolism
Period 1 2022-2023
Bioenergetics
Essential elements:
- Carbon C
- Nitrogen N
- Oxygen O
- Hydrogen H
- Phosphorus P
- Sulfur S
- Selenium Se
- Trace metals (Fe, Co, Mn, Ni, Cu, Zn, Mo, V, W).
Trace metals help enzymes to function.
Macromolecules % Dry weight
Protein Many proteins are enzymes. 55
RNA 20.5
Lipid 9.1
Polysaccharide 5.0
Lipopolysaccharide 3.4
DNA 3.1
Metabolism
Metabolism = Anabolism + Catabolism.
Anabolism: Energy consuming biosynthetic reactions: ‘biosynthesis’. Reactions that are
involved in cell compounds. These reactions use energy. Anabolism uses the energy created
by catabolism.
Catabolism: Energy metabolism. Energy releasing metabolic reactions: ‘energy metabolism’.
Not all cells encode all reactions, but protein synthesis is for example a quite similar process
in most cells. The overall reactions of anabolism are often similar in different organisms.
Catabolism energy sources can be very different.
,Energy carriers are ATP and NADH.
- Can be used as energy source and can be reused.
- Can be used for movement.
- Can be used for active transport.
Different energy sources
Making ATP is the ultimate goal for all microorganisms.
1st Law of thermodynamics
‘Energy can be transformed from one form to another but not been generated or destroyed’.
Energy required for ATP comes from chemical reactions and is measured in kJ.
In any chemical reaction energy is either required or released.
Free energy (G) is energy that is released that is available to do work. Change in free energy
is ΔG0’ (in standard conditions).
,Exergonic = release of energy
- ΔG0’ = -
- Release of energy which can be used to make ATP
Endergonic = use of energy
- ΔG0’ = +
- ATP is required
Endergonic and exergonic reactions often get coupled. The burn of sugar (energy release)
can be coupled to making ATP (costs energy).
- From the burn of sugar your get ΔG0’ = -2863 kJ/mol. To make ATP ΔG 0’ = + 31
kJ/mol is needed. Up to 2863/31 = 92 mol of ATP can be generated from 1 mol of
glucose.
- BUT some energy is lost as heat, so it will be a bit less than 92 mols of ATP.
If ΔG0’ = 0, the reaction is in equilibrium, nothing happens in this case.
The efficiency of chemical reactions is 20-30%, to compare the efficiency of a car is 15%.
How to tell which reaction is growing faster?
This can not be told by just ΔG0’. To be able to tell the reaction rate you need a combination
of:
- Thermodynamics (ΔG0’)
- Kinetics (velocity of catalysis)
Thermodynamics
Is about electron donors and acceptors. These drive the energy metabolism of cells.
H2 is the electron donor and gets oxidized.
O2 is the electron acceptor and gets reduced.
Redox reactions occur in pairs.
ΔE0’ tells you something about the tendency to donate or accept electrons. ΔE0’ is the redox
potential. The biological redox range is between -500 and +1000. If the donors are close to
-500 this means they are very likely to donate electrons. If the acceptors are close to 1000+
they are very likely to accept electrons.
, You can calculate ΔG0’ from ΔE0’.
Notice that -n is negative. The redox potential is in V instead of mV because Faraday’s
constant is also in V.
Redox tower
Contains the standard potentials for redox couples.
E0’:
0
Stands for standard conditions:
- 1 mol/L substrate and 1 mol/L product.
- 1 atm in the case of gasses.
’
Stands for the biological conditions:
- pH = 7.0
- 25 degrees celsius.
Electron donors are highest in the tower. They are on the right side of the / and are reduced.
Electron acceptors are lowest in the tower. They are on the left side of the / and are oxidized.
Oxidized / reduced.
Enzymes
Enzymes only catalyze exergonic reactions (ΔG0’ = negative, energy is released).
There is an activation barrier, this is why for example sugar doesn’t burn spontaneously.
Enzymes lower the activation energy. Activation energy is still needed, but less.
Enzymes are catalysts:
- Not being consumed in the reaction.
- Lowers the activation energy.
- Increase the reaction rate.
- Do not affect energetics or equilibrium of a reaction.
Many biochemical reactions would not happen without enzymes, ever, because the energy
barrier is too high.
Period 1 2022-2023
Bioenergetics
Essential elements:
- Carbon C
- Nitrogen N
- Oxygen O
- Hydrogen H
- Phosphorus P
- Sulfur S
- Selenium Se
- Trace metals (Fe, Co, Mn, Ni, Cu, Zn, Mo, V, W).
Trace metals help enzymes to function.
Macromolecules % Dry weight
Protein Many proteins are enzymes. 55
RNA 20.5
Lipid 9.1
Polysaccharide 5.0
Lipopolysaccharide 3.4
DNA 3.1
Metabolism
Metabolism = Anabolism + Catabolism.
Anabolism: Energy consuming biosynthetic reactions: ‘biosynthesis’. Reactions that are
involved in cell compounds. These reactions use energy. Anabolism uses the energy created
by catabolism.
Catabolism: Energy metabolism. Energy releasing metabolic reactions: ‘energy metabolism’.
Not all cells encode all reactions, but protein synthesis is for example a quite similar process
in most cells. The overall reactions of anabolism are often similar in different organisms.
Catabolism energy sources can be very different.
,Energy carriers are ATP and NADH.
- Can be used as energy source and can be reused.
- Can be used for movement.
- Can be used for active transport.
Different energy sources
Making ATP is the ultimate goal for all microorganisms.
1st Law of thermodynamics
‘Energy can be transformed from one form to another but not been generated or destroyed’.
Energy required for ATP comes from chemical reactions and is measured in kJ.
In any chemical reaction energy is either required or released.
Free energy (G) is energy that is released that is available to do work. Change in free energy
is ΔG0’ (in standard conditions).
,Exergonic = release of energy
- ΔG0’ = -
- Release of energy which can be used to make ATP
Endergonic = use of energy
- ΔG0’ = +
- ATP is required
Endergonic and exergonic reactions often get coupled. The burn of sugar (energy release)
can be coupled to making ATP (costs energy).
- From the burn of sugar your get ΔG0’ = -2863 kJ/mol. To make ATP ΔG 0’ = + 31
kJ/mol is needed. Up to 2863/31 = 92 mol of ATP can be generated from 1 mol of
glucose.
- BUT some energy is lost as heat, so it will be a bit less than 92 mols of ATP.
If ΔG0’ = 0, the reaction is in equilibrium, nothing happens in this case.
The efficiency of chemical reactions is 20-30%, to compare the efficiency of a car is 15%.
How to tell which reaction is growing faster?
This can not be told by just ΔG0’. To be able to tell the reaction rate you need a combination
of:
- Thermodynamics (ΔG0’)
- Kinetics (velocity of catalysis)
Thermodynamics
Is about electron donors and acceptors. These drive the energy metabolism of cells.
H2 is the electron donor and gets oxidized.
O2 is the electron acceptor and gets reduced.
Redox reactions occur in pairs.
ΔE0’ tells you something about the tendency to donate or accept electrons. ΔE0’ is the redox
potential. The biological redox range is between -500 and +1000. If the donors are close to
-500 this means they are very likely to donate electrons. If the acceptors are close to 1000+
they are very likely to accept electrons.
, You can calculate ΔG0’ from ΔE0’.
Notice that -n is negative. The redox potential is in V instead of mV because Faraday’s
constant is also in V.
Redox tower
Contains the standard potentials for redox couples.
E0’:
0
Stands for standard conditions:
- 1 mol/L substrate and 1 mol/L product.
- 1 atm in the case of gasses.
’
Stands for the biological conditions:
- pH = 7.0
- 25 degrees celsius.
Electron donors are highest in the tower. They are on the right side of the / and are reduced.
Electron acceptors are lowest in the tower. They are on the left side of the / and are oxidized.
Oxidized / reduced.
Enzymes
Enzymes only catalyze exergonic reactions (ΔG0’ = negative, energy is released).
There is an activation barrier, this is why for example sugar doesn’t burn spontaneously.
Enzymes lower the activation energy. Activation energy is still needed, but less.
Enzymes are catalysts:
- Not being consumed in the reaction.
- Lowers the activation energy.
- Increase the reaction rate.
- Do not affect energetics or equilibrium of a reaction.
Many biochemical reactions would not happen without enzymes, ever, because the energy
barrier is too high.
