1. Bacteria need to maintain themselves, and they try to reproduce.
To build more copies of themselves, they require 2 THINGS:
A source of raw materials, and a source of energy. Without both of these, life cannot exist.

2. Metabolism
The chemical reactions used by living cells to obtain energy from their environment and to use that energy to make cell material are called metabolism.
Metabolic reactions are classified as either
Catabolism: reactions that break molecules down into simpler forms to get smaller molecules or TO RELEASE THE ENERGY IN THOSE MOLECULES.
Anabolism: reactions that USE energy to put molecules together to make bigger molecules. (building up)
E.g. reactions that assemble amino acids into proteins

3. Availability of energy is related to control
Bacteria require raw materials and energy to grow
If either one is missing, bacteria cannot reproduce!
If both are readily available, bacteria will likely multiply quickly.
Many bacteria can survive a while without growing, and can be transported from place to place.
Bacteria in a nutrient rich environment can grow rapidly
Infected person
Hamburger left out at room temperature

4. 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.

5. 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.

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

7. 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”.

8. 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).

9. 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

10. 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

11. 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.

12. Structure of ATP

13. The ATP cycle ATP is hydrolyzed to ADP to release energy.
Energy is used to reattach the phosphate to ADP to regenerate ATP.
metabolism/energy/fg1.html

14. 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, energy has been saved in that reduced molecule.
Certain molecules have the job of getting reduced and carrying electrons to save that energy: NAD

15. 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).

16. An overview of bacterial catabolism
Model compound: glucose, C6H12O6
Aerobic metabolism
With oxygen gas (O2)
Fermentation and anaerobic respiration – later
Four major pathways
Glycolysis, Krebs cycle, electron transport, and chemiosmosis
The Goal: gradually release the energy in the glucose molecule and use it to make ATP.
The carbons of glucose will be oxidized to CO2.

17. Glycolysis: glucose is broken
Glucose is activated
Glucose Glu-6-P
2 ATPs are “invested”
Glu (6 C’s) broken into two 3-C pieces
2 oxidations steps
NAD NADH
4 ATPs are produced, net gain: 2 ATPs
2 molecules of pyruvic acid are produced.

18. 3 ways bacteria use glucose
EMP = Embden- Meyerhof-Parnas pathway Traditional glycolysis, yields 2 ATP plus 2 pyruvic acids.
Pentose Phosphate Complicated pathway, produces 5 carbon sugars and NADPH for use in biosynthesis.
Entner-Doudoroff Yields only 1 ATP per glucose, but only used by aerobes such as Pseudomonas which make many ATP through aerobic respiration.

19. Krebs Cycle detailed

20. What happens: carbons of glucose oxidized completely to CO2
Preliminary step: pyruvic acid oxidized to acetyl-CoA.
Things to note: several redox steps make NADH, FADH2
One ATP made
OAA remade, allowing cycle to go around again.

21. Electron transport Metabolism to this point, per molecule of glucose:
2 NADH made during glycolysis, 8 more through the end of Krebs Cycle (plus 2 FADH2)
What next?
If reduced NAD molecules are “poker chips”, they contain energy which needs to be “cashed in” to make ATP.
In order for glycolysis and Krebs Cycle to continue, NAD that gets reduced to NADH must get re-oxidized to NAD.
What is the greediest electron hog we know? Molecular oxygen.
In Electron transport, electrons are passed to oxygen so that these metabolic processes can continue with more glucose.
Electron carriers in membrane are reversibly reduced, then re-oxidized as they pass electrons (or Hs) to the next carrier.

22. About Hydrogens A hydrogen atom is one proton and one electron.
In biological redox reactions, electrons are often accompanied by protons (e.g. dehydrogenations)
In understanding metabolism, we are not only concerned with electrons but also protons.
Also called hydrogen ions or H+
H+ (hydrogen ions) and electrons are opposites!! Don’t get them confused!

23. Electron transport
Electrons are passed carrier to carrier, releasing energy.
All occurs at the cell membrane
NADH is oxidized to NAD
H’s are passed to next electron carrier; NAD goes, picks up more H.
Process can’t continue without an electron acceptor at the end. In aerobic metabolism, the acceptor is molecular oxygen.

24. Chemiosmosis: electron transport used to make ATP
Energy released during
electron transport used
to “pump” protons
(against the gradient) to the outside of the membrane.
The membrane acts as an insulator;
protons can only pass through via
the ATPase enzyme; the energy
released is used to power synthesis
of ATP from ADP and Pi.
Creates a proton current (pmf) much like the current of electrons that runs a battery.

25. Proton motive force
Electrochemical gradient establishes a voltage across the membrane. Flow of protons (instead of electrons) does work (the synthesis of ATP).

26. Overview of aerobic metabolism
Energy is in the C-H bonds of glucose.
Oxidation of glucose (stripping of H from C atoms) produces CO2 and reduced NAD (NADH)
Energy now in the form of NADH (“poker chips”)
Electrons (H atoms) given up by NADH at the membrane, energy released slowly during e- transport and used to establish a proton (H+) gradient across the membrane
Energy now in the form of a proton gradient which can do work.
Electrons combine with oxygen to produce water, take e- away.
Proton gradient used to make ATP
Energy now in the form of ATP. Task is completed!

27. Central Metabolism: Funneling all nutrients into central pathways
Many other molecules besides glucose can serve as a source of carbon.

28. Central Metabolism: A source of building blocks for biosynthesis
BUT, these molecules can’t be broken down to CO2 for energy AND used for biosynthesis