Metabolism: the chemical reactions of a cell

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 compunds (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. Chemistry is done by enzymes • 99.99999% of enzymes are protein molecules • More than half of protein molecules function as enzymes • Enzymes are biological catalysts • A catalyst speeds up the rate of a chemical reaction • Reactions would not occur fast enough for life to exist otherwise • A catalyst is not used up in the reaction • Just like a hammer used to pound many nails, though the hammer can wear out eventually. • Enzymes are specific, only catalyze one kind of reaction

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. • (DNA contains the instructions for making enzymes. If there are many reactions that occur, there needs to be many different enzymes, so there has to be a lot of DNA. ) • 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. Enzyme structure • Every enzyme has an active site • The enzyme performs chemistry on the substrate, producing a product(s) • Every metabolic reaction we will look at happens in this way. Active site http://www-biol.paisley.ac.uk/courses/stfunmac/images/Hexokin.gif

6. 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”.

7. Enzymes can be stopped • Conditions that disrupt the 3D shape • Acidic, alkaline, high salt, high temperature, etc. • These conditions thus affect growth of cell also. • Inhibitory molecules affect enzymes • Competitive inhibitors • Fit in active site but are not changed; prevent normal substrate from binding, prevent reaction. • Non-competitive inhibitors • Bind permanently to active site or other site which changes molecular shape; prevents reaction. • Allosteric inhibitor: temporary binding, regulates.

8. 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

9. 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).

10. Redox reactions release energy for use • Depends on concentration, redox potential, etc. • XH2 + Y X + YH2shows oxidation of X, reduction of Y • Note that 2 H atoms are transferred, not just electrons • Familiar redox reaction that releases energy: CH4 + 2O2 CO2 + 2H2O natural gas burning.

11. 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

12. 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.

13. Structure of ATP Four negative chargeson oxygens of phosphate groups http://www.ustboniface.mb.ca/cusb/abernier/Biologie/Module1/Images/atp.jpg

14. Important molecules: the electron carriers • 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. • The most common electron carrier 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). • Other electron carriers: NADP which is used to donate H for biosynthesis; also FAD.