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. Metabolic reactions require enzymes
Reactions operate in pathways:
A B C D Where A-D are different molecules
Each step is catalyzed by a different enzyme.
A Catalyst is something that speeds up a chemical reaction and is not consumed in the reaction, but can be re-used.
Enzymes are biological catalysts; 99.99% of them are proteins.
Enzymes are very specific; a different one is required for each type of chemical reaction.
Because the 3-D shape of an enzyme is critical for its function, anything that alters that (heat, high salt, extreme pH) will affect how fast or whether it works.

8. Importance of 3D shape
Every enzyme has an active site, a location where the substrate (the molecule to be acted on) fits into the enzyme.
The enzyme then performs chemistry on the substrate, producing a product(s) which then diffuses away, leaving the enzyme free to act on the next substrate.
Every metabolic reaction we will look at happens in this way.

9. Enzyme function depends on shape
Product
Substrates
Enzyme brings substrates together in active site, increasing the rate at which they react.

10. More about Enzymes Sometimes an enzyme needs help
Protein alone = apoenzyme
Helper molecule: cofactor
Could be inorganic like a metal ion (Fe+2)
Could be organic coenzyme (like CoA, NAD)
Apoenzyme + cofactor = holoenzyme.
Cofactors have an effect on nutrition
Bacteria have certain mineral requirements.
Vitamins are cofactors that are needed in the “diet”.

11. Enzymes can be stopped
Conditions that disrupt the 3D shape (‘denature”)
These conditions thus affect growth of cell also.
Inhibitory molecules affect enzymes
Covalent: bind to enzyme permanently
Competitive inhibitors
Fit in active site but are not changed; prevent normal substrate from binding, prevent reaction.
Non-competitive inhibitors
Bind to other site which changes molecular shape; slows reaction.
Allosteric inhibitor: temporary binding, regulates.

12. Competitive Inhibition
Both the substrate and the inhibitor fit into the active site, but the inhibitor isn’t altered by the enzyme. As long as the inhibitor is in the active site, the substrate cannot enter the active site and react. The more inhibitor molecules that are present, the more often one of them occupies the active site.
ghs.gresham.k12.or.us/.../ competitiveinhib.htm

13. Allosteric sites
In allosteric site, inhibitor is not reacted, but causes a shape change in the protein. The substrate no longer fits in the active site, so it is not chemically changed either.
ghs.gresham.k12.or.us/.../ noncompetitive.htm

14. 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.

15. Structure of ATP

16. 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

17. 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.

18. 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).

19. 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

20. 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 .