1. Metabolism: the chemical reactions of a cell
All organisms need two things with which to grow:
Raw materials (especially carbon atoms)
Energy.
Types of metabolic reactions:
Anabolism: biosynthesis; reactions that create large/complex molecules from smaller, simpler ones. Use raw materials and energy.
Catabolism: degradation; reactions that break down large/complex molecules, used to generate energy for use and to produce smaller, building block molecules.

2. Energy: where from? What for?
Chemotrophs vs. phototrophs
Chemotrophs get energy from molecules
Chemolithotrophs get energy from oxidation of inorganic substances.
Chemoorganotrophs get energy from oxidation of organic compounds (like we do).
Phototrophs get energy from sunlight
Energy is needed to power the cell
Biosynthesis to respond to environment, to grow
Active transport, motility, etc.

3. Bacteria obtain energy through oxidation/reduction reactions
Oxidation: molecule gives up electrons
Reduction: molecule accepts electrons
Oxidation/reduction (redox) reactions always occur in pairs; if electrons are removed, they must go somewhere!
Biological redox reactions usually involve PAIRS of electrons.
Biological redox reactions often involve entire hydrogen atoms, not just the electrons (so called dehydrogenation reactions).

4. Redox reactions release energy for use
Depends on concentration, redox potential, etc.
XH2 + Y X + YH2 shows oxidation of X, reduction of Y
Note that 2 H atoms are transferred, not just electrons
Familiar redox reaction that releases energy:
CH4 + 2O CO2 + 2H2O natural gas burning.
Biological reactions release energy gradually, trap it as ATP

5. Is it good to eat? Reduced molecules have lots of energy.
Have lots of H, few O
Oxidized molecules have little energy;
lots of O or few H.
Carbon dioxide
glucose

6. Redox Calculations
One can assign an oxidation number to the carbon atoms in a molecule to determine how much energy an organic molecule has.
Oxidation numbers: H = +1 O = -2
For an uncharged organic molecule, all the redox numbers must add up to 0
in methane (CH4): oxidation number C is -4.
For CO2, 2 x -2 = -4; no net charge, then C must be = +4
In going from CO2 to CH4 although a carbon has gained electrons, the oxidation number for the carbon is lower, thus “reduced”.

7. Introduction to important molecules in metabolism
Biological reactions release energy from redox reactions gradually, trap it as ATP
ATP is the energy molecule that cells use to power most of their activities. “energy currency”
ATP is a molecule under stress:
too many negative charges in one place. Release of 1 phosphate: ATP → ADP + Pi relieves that stress, releases energy which can be used for:
cellular activities such as transport, motility, biosynthesis, etc.

8. Structure of ATP

9. The ATP cycle ATP is hydrolyzed to ADP to release energy.
Energy is used to reattach the phosphate to ADP to regenerate ATP.
Other molecules used for energy
include GTP and PEP.
metabolism/energy/fg1.html

10. Important molecules: the electron carriers -1
The energy released in redox reactions is often thought of as the energy in the bonds between the H and the C; when a molecule is reduced by transfer of the H, the energy is conserved in that reduced molecule.

11. Important molecules: the electron carriers -2
The most common electron carrier in biological redox reactions is NAD:
NAD + XH2 X + NADH + H+
where NAD carries 2 e-, 1 H+
Reduced NAD (NADH) is like poker chips, energy that can’t be spent, but can be “cashed in” later to make ATP (which can be “spent”, i.e. used as an energy source for cell activities).

12. Structure of NAD

13. Other electron carriers
NADP
Reduced during some reactions such as those in the Pentose Phosphate pathway, Photosynthesis
NADPH used to donate H for biosynthesis reactions such as the Calvin Cycle, amino acid biosynthesis.
FAD
Reduced to FADH2
Used in the Krebs Cycle, other reactions

14. Oxidations for energy Go = - R T ln K
If this reaction is reversible, and every oxidation is coupled to a reduction, how can the oxidation of XH2 yield energy?
Go = - R T ln K
Describes the tendency of a reaction to occur spontaneously, to release energy. Two major factors are the tendencies of X and Y to give up or accept electrons and their concentrations.
In this example, we expect that YH2 will subsequently be oxidized, driving the reaction to the right and that XH2 has a greater tendency to give up electrons than YH2 .