I. INTRODUCTION TO METABOLISM AND CATABOLISM
A. Metabolism is the sum total of all chemical reactions in a cell
1. Divided into catabolism and anabolism a) Anabolism and catabolism are linked through energy currencies
(1) For example, ATP, NADH, and proton motive forces are produced by catabolism and are then used for anabolism
2. Catabolism a) Energy yielding process in which larger compounds are broken down into smaller compounds b) Characteristics
(1) Dissimilative, exergonic, and oxidative
3. Anabolism a) Energy requiring process which build larger molecules (cell constituents) from smaller molecules (biosynthetic pathways) b) Characteristics c) Assimilative, endergonic, and reductive
4. The ultimate source of energy for most organisms is the sun a) Photoautotrophs trap light energy, and store that energy in the form of high energy electrons in organic molecules b) Heterotrophs remove these electrons and give them to more electronegative molecules, releasing the stored energy
B. CATABOLISM
1. The energy released during catabolism must be stored so that it is available for anabolism (energy currency) a) High energy bonds, such as ATP b) Reducing equivalents, such as NAD(P)H & FADH
2 c) Proton gradient (formed by electron transport)
2. Aquiring nutrients a) Polymers broken down into monomers
(1) Proteins  amino acids
(2) polysaccharides  monosaccharides
(3) Lipids  glycerol and fatty acids
(4) Nucleic acids  nucleotides b) Monomers are transported into the cell
(1) diffusion (passive and facilitated)

(2) active transport
(3) group translocation
C. AEROBIC RESPIRATION
1. Breakdown of carbohydrates in animals can be divided into three pathways a) Glycolysis
(1) Removes some electrons / hydrogens from carbohydrates
(a) These electrons / hydrogens are given to NAD to from NADH
(b) The electrons will be given to the electron transport chain where they will eventually reduce oxygen to water
(2) Occurs in the cytoplasm b) Kreb's tricarboxylic acid cycle
(1) Continues to remove all hydrogens from the carbohydrate
(a) CO
2
is the byproduct of the completely oxidized carbohydrate
(b) The electrons / hydrogens are given to NAD or FAD to form NADH and FADH2
(c) These electrons will be given to the electron transport chain and eventually reduce oxygen to water
(2) Occurs in the mitochondria c) Electron transport
(1) NADH and FADH
2
donate electrons / hydrogens removed from the carbohydrate during glycolysis and the TCA cycle to the electron transport chain
(a) They electrons pass through a variety of electron acceptors, such as cytochromes, and eventually to oxygen, the terminal electron acceptor
(2) Occurs in the membranes of the mitochondria
2. Overall reaction a) 1 glucose + 6 O
2
+ 36 ADP + 36 phosphates

6 CO
2
+ 36 ATP + 6 H
2
O
3. Fermentation a) If oxygen is not available, all NAD will be reduced to NADH and ATP synthesis via glycolysis will stop
(1) If there is no ATP being produced, the cell will die b) To survive short times of oxygen deprivation, a cell may oxidize NADH back to
NAD without using oxygen
(1) This will enable to the cell to continue making ATP via glycolysis
(2) If the oxidant is an organic molecule, the oxidation of NADH is referred to as fermentation
II. GLYCOLYSIS
A. Overall reaction
1. Glucose + 2 NAD + 2 ADP = 2 P i

2 pyruvate + 2 NADH + 2 ATP
2. Cell occurs in the cells cytoplasm
B. Steps
1. Glucose is transported into the cell and phosphorylated

a) This step uses one ATP molecule b) This gives rise to glucose-6-phosphate
(1) The phosphorylated glucose cannot leave the cell
2. The glucose-6-phosphate is rearranged into fructose-6-phosphate
3. Fructose-6-phosphate is phosphorylated to fructose-1,6-diphsophate a) This step uses another ATP molecule
4. Fructose-1,6-diphosphate is split into dihydroxyacetone and 3-phosphoglycerate a) The dihydroxyacetone phosphate is converted into another molecule of glyceraldehyde-3-phosphate, thus the net of this reaction is one fructose-1,6diphosphate produces two molecules of glyceraldehyde-3-phosphate b) Since the fructose was split, every reaction below should be doubled
5. Glyceraldehyde-3-phosphate is converted into 1,3-diphosphoglycerate a) Inorganic phosphate was added to the molecule (no ATP used) b) The substrate was oxidized, with hydrogen being added to NAD to form NADH
6. 1,3-diphosphoglycerate forms an ATP molecule by substrate level phosphorylation and is converted into 3-phosphoglycerate a) Net of two ATP molecules, one from each reaction
7. 3-phosphoglycerate is rearranged into 2-phosphoglycerate
8. 2-phosphoglycerate is converted into phosphoenolpyruvate
9. Phosphoenolpyruvate produces ATP by substrate level phosphorylation as it is converted into pyruvate a) A net of 2 ATP, one from each reaction
III. KREB'S TRICARBOXYLIC ACID CYCLE
A. The intermediate reaction
1. The conversion of pyruvate to acetyl CoA and carbon dioxide
2. NADH is formed
B. The cycle
1. The TCA cycle occurs in the mitochondrial matrix
2. Acetyl CoA is attached to oxaloacetate a) Oxaloacetate is regenerated during the cycle
3. The hydrogen are removed from the substrate during the cycle a) They are given to NAD and FAD to form NAD
H
and FADH
2 b) The oxidized carbon is liberated as CO
2
4. During the cycle, one GTP molecule is formed per pyruvate oxidized a) The energy in GTP is equivalent to that of ATP
C. Two turns of the cycle produces (know what happens to each of these)

1. 6 CO
2
2. 2 oxaloacetate
3. 2 GTP
4. 10 pairs of reducing equivalents a) 2 FADH
2 b) 8 NADH
IV. ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION
A. During glycolysis and the TCA cycle, 10 NADHs and 2 FADHs are formed
1. The electron transport chain starts with donation of hydrogens from a molecule with a negative redox potential (such as NADH or FADH2) a) This recycles the NAD and FAD for use in glycolysis and the Kreb's cycle again b) The electron transport chain is located in the inner membrane of the mitochondria
2. The electrons then are transferred through a series of electron transport proteins, each having a higher redox potential then the last a) At the end of the electron transport chain, the electrons are given to a terminal electron acceptor, such as oxygen, which has the highest redox potential
(1) This is why we need to breath oxygen
(2) The oxygen is reduced to water during this reaction
3. The electron-transport chain can be thought of as a series of alternating electron and hydrogen acceptors a) As the electrons are pulled through the chain, their energy is used to form a proton gradient
(1) This gradient is a form of stored energy called the proton motive force
(2) The is often referred to as an electrochemical gradient, as protons have positive charges
(electro) and are chemicals b) The proton gradient is a form of stored energy
(1) Both due to diffusion and electrical attraction, the protons would like to reenter the mitochondrial matrix
(2) Protons are too hydrophilic to pass through the lipid membrane, but can reenter at specific sites to do work
4. A plasma membrane bound ATPase (or ATP synthase) uses the proton motive force to generate ATP a) This could be analogous to how a turbine forms electrical energy from a dam
V. FERMENTATION
A. Definition
1. An organic substrate acts as an electron donor and a product of that substrate acts as an electron acceptor
B. Purpose

1. Recycles NAD so that pathways can continue to operate and produce ATP by substrate-level phosphorylation
C. Characteristics
1. No external electron acceptor required
2. NADH is recycled
3. Less ATP is formed than if respiring
D. Humans use the homolactic acid fermentation pathway
1. Glucose is broken down into 2 pyruvate molecules via glycolysis a) This produces a net of 2 ATP and 2 NADH
2. Each NADH reduces a pyruvate molecule a) This recycles NADH back to NAD b) When reduced, the pyruvate becomes lactic acid
E. Some yeast use the ethanolic fermentation pathway
1. Glucose is broken down into 2 pyruvate molecules via glycolysis a) This produces a net of 2 ATP and 2 NADH
2. Carbon dioxide is removed from the pyruvate giving rise to acetaldehyde
3. Each NADH reduces an acetaldehyde molecule a) This recycles NADH back to NAD b) When reduced, the acetaldehyde becomes ethanol
VI. BREAKDOWN OF MOLECULES OTHER THAN GLUCOSE
A. Sugars other than glucose may be converted to a form that fits into the glycolytic pathway
B. Lipids are broken down into fatty acids and glycerol
1. Glycerol can be converted to glyceraldehyde-3-phosphate and enter glycolysis
2. Fatty acids are broken down into acetaldehyde by the

-oxidation pathway a) Acetaldhyde can be converted to acetyl CoA and enter the TCA cycle
C. Amino acids are deaminated to form organic acids
1. The amine group may be used or excreted as waste
2. The organic acid may enter the TCA cycle