Microbiology - Chapter 13

Catabolism refers to the breakdown and oxidation of larger molecules, yielding energy needed for anabolism, which is the biosynthesis of macromolecular cell components from smaller molecular units.

Enzymes. Enzymes catalyze the conversion of a substrate to a product. An enzymes active site binds to specific substrates to convert them into products.

Enzymes jump-start reactions by lowering their activation energy, Ea, by placing substrates in optimal arrangements.

It transfers energy between catabolic reactions and biosynthetic reactions (anabolic reactions).

Substrate-level phosphorylation Photophosphorylation Oxidative phosphorylation

Substrate-level phosphorylation is an enzymatically coupled reaction that produces ATP by the transfer of a phosphate group from a reactive intermediate generated during catabolism to ADP. In cells, substrate-level phosphorylation begins with the breakdown of an organic molecules. This process occurs in chemoorganotrophs, although they can use a wide variety of molecules to generate energy. One that is most commonly used is glucose, during the process of glycolysis. Glycolysis is, simply, the catabolism of glucose to pyruvate. These pyruvate molecules proceed through the TCA cycle, which dismantles the carbon intermediates into 6 CO2 molecules, 6 water molecules, and 38 ATP molecules (per 1 glucose molecules)

Photophosphoylation involves the synthesis of ATP from free ADP and Pi using energy and electrons to create a proton gradient across a membrane. The flow of protons back across the membrane releases energy that is harnessed to produce ATP. This method of ATP generation requires light energy, giving it its name.

In chemotrophs, the energy is derived from the oxidation of chemical substrates and is termed oxidative phosphorylation. First, electrons are transferred such an electron carrier molecules, such as NAD. NAD transports electrons to an electron transport system, which transfers electrons in a series of steps that ultimately yields energy to move protons across the membrane. The kinetic energy of the flowing protons back across the membrane through ATP synthase converts it to chemical energy which synthesizes ATP from free ADP and Pi.

Catabolism of glucose begins with glycolysis, producing two ATP molecules and two pyruvate molecules from each molecules of glucose. Each pyruvate proceeds through the TCA cycle, a series of reactions that dismantles the carbon intermediates into 6 CO2 molecules. Substrate-level phosphorylation in the TCA cycle produces two more ATP (one per pyruvate) for a total of four ATP molecules. In total, however, 38 molecules of ATP are produces from the complete catabolism of glucose.

The Embden-Meyerhof-Parnas (EMP) Pathway The Entner-Doudoroff Pathway The Pentose Phosphate Pathway

The EMP pathways is the most common pathway. It is divided into two phases; the 6-carbon and 3-carbon phase. It produces ATP and small precursor molecules used in other biosynthetic reactions, such as NADH. The formula is below. Glucose + 2 ADP + 2 Pi + NAD+ --> 2 pyruvate + 2 ATP + 2 NADH + 2 H+

The Entner-Doudoroff pathway produces 2 pyruvate, 1 ATP molecules, 1 NADH and 1 NADPH.

The Pentose phosphate pathways produces carbon precursors for other pathways, 2 NADPH, and one ATP.

Nicotinamide adenine dinucleotide (NAD+) is a common electron carrier molecules.

Recycling can be performed through either respiration or fermentation.

Fermentation is the transfer of electrons from NADH, or some other reduced electron carrier, to an organic molecule, commonly pyruvate, which is used as an electron acceptor. Various products of glucose fermentation include Ethanol and Lactic Acid.

Respiration is the process by which electrons generated from the oxidation of an energy substrate are transferred through the electron transport system to yield energy. Respiration can be either aerobic (Where oxygen is used as a terminal electron acceptor) or anaerobic (where some other organic or inorganic molecule is used.

Respiration is a three step process that begins with glycolysis to generate pyruvate, which is further oxidized to CO2 in the TCA cycle. Finally, the electrons generated during glycolysis and the TCA cycle are passed to an electron carrier, such as NAD, and down the electron transport system to generate more ATP by oxidative phosphorylation.

Organisms that carry out aerobic respiration use atmospheric oxygen (O2) as the electron acceptor in the final step of respiration, and can only be carried out under aerobic conditions. Organisms that cary out anaerobic respiration use alternative inorganic molecules, such as CO2 or NO3-, or organic molecules, such a fumarate. They also use different cytochromes and quinones than those found in the aerobic transport system.

At the end of glycolysis, most of the chemical energy of glucose is still trapped in pyruvate with only a max two molecules of ATP and two NADH released so far. Fermenting microbes lose out on this potential energy, as pyruvate is used as an electron acceptor, not to be further oxidized. However, many microbes can further oxidize pyruvate to yield a large amount of energy.

Pyruvate + 4 NAD + FAD + ADP + Pi ? 3 CO + 4 NADH + FADH + GTP(ATP)

As the electron transport system moves electrons from one acceptor to the next, protons are pumped out of the membrane. This creates a potential difference across the membrane, which forms the proton motive force. The proton motive force drives a stream of H+ through ATP synthase to produce ATP, but it can also be used to spin flagella and to assist in nutrient transport.

ATP synthase is the enzyme used to produce ATP. As protons move through it, they cause the gamma subunit to rotate, changing active site conformation. This facilitates addition of Pi to ADP to form ATP.

Chemolithotrophs use inorganic molecules as an electron source. They directly couple ATP synthesis by oxidative phosphorylation to oxidation of the inorganic source. They pass electrons down an electron transport system to generate ATP via the proton motive force.

These kinds of microbes may break down polymers of carbohydrates into smaller subunits, which can then be processed to substrates processed by glycolytic pathways. Proteases can also break polypeptides into individual amino acids. If the amino group is detached, an organic acid is left that can be used in the TCA cycle.