Definition: This is the sum of all the chemical processes taking place within the cell.

Microbes are built up of a whole bunch of things. The nutrients enter the cell and then they are changed into cellular components (see Figure 11:1). Building something is called anabolism (or, alternatively, biosynthesis). Biosynthesis is an energy requiring process. Therefore, to provide energy the cell breaks some component down - this process is called catabolism.

All catabolic reactions involve electron transfer at some point which allows energy to be captured in high energy bonds in ATP.

ATP is the currency of energy

Very important concept: electron transfer involves oxidation and reduction:

oxidation: loss of an electron or gain of oxygen
reduction: gain of an electron or loss of oxygen

When a substance loses an electron (i.e. is oxidised) energy is given out. However, to harness this energy another substance must be there to accept the electron (this receptor molecule is now reduced). These coupled reactions are called redox reactions.

Enzymes

Metabolic pathways generally can be written:

A ----> B ----> C -----> D ------> E

Generally, in biology, each reaction (i.e. A -----> B) is catalysed by an enzyme.

Enzymes are special proteins that serve as catalysts for biochemical reactions.

What is a catalyst? A catalyst is a substance (need not necessarily be a protein) that lowers the activation energy of a reaction (see Figure 11:2), and, most importantly, remains unchanged during the process.

In biological reactions, enzymes provide a surface for a chemical reaction to take place. Each enzyme has a special area within its tertiary structure called the active site. The active site (see Figure 11:3) is where the substrate binds (i.e. the substance that once reacted with the enzyme turns into the product). Enzymes have a high degree of specificity for their substrates.

Competition
Enzymes can be inhibited by various things - called competition. Conceptually, the most simple is competitive inhibition (see Figure 11:4). Here the competing substance mimics the actual substrate, either by being similar in shape, or providing a similar type of chemical reaction at the active site. Consequently, the real substrate for the reaction is prevented from accessing the active site. This is reversible and increasing the concentration of substrate with respect to inhibitor releaves the inhibition. The sulfa drugs are competitive inhibitors of folic acid biosynthesis.

A different type of inhibition is called noncompetitive inhibition. Here substances bind the enzyme at a different place than the active site. This distorts the tertiary structure of the protein. Most noncompetitive inhibitors bind irreversibly.

Cofactors (see Figure 11:5)
Many enzymes can only catalyse a reaction if cofactors are also present. A cofactor is a non-protein organic molecule that is loosely bound to the enzyme. Many cofactors are synthesised from vitamins. Cofactors often improve the fit of the enzyme with its substrate. Examples are NAD+ (nicotinamide adenine dinucleotide; reduced form NADH) and FAD+ (flavin adenine dinucleotide; reduced form FADH2). Cofactors need not necessaryily be complex molecules (Fe2+), however they must be able to undergo oxidation and reduction by either accepting an electron or a hydrogen atom. These are extremely important molecules when it comes to electron transport and energy production.

Focal metabolites
The biosynthetic origins of most building blocks for proteins, DNA, RNA and lipids can be traced to relatively few precursor molecules called focal metabolites (see Figure 11:6). These are:

glucose-6-phosphate
phosphoenolpyruvate (PEP)
oxaloacetate
alpha-ketoglutarate

Bascically, microbial metabolism can be divided up into 4 strategies, either:
i) interconversion of focal metabolites (e.g. glucose-6-phosphate to PEP)
ii) assimilation pathways that lead to the formation of focal metabolites (e.g. phosphorylation of glucose to glucose-6-phosphate)
iii) conversion of focal metabolites to end products (e.g. conversion to nucleic acids; amino acids etc)
iv) conversion of focal metabolites for energy (making ATP)

ATP (adenosine triphosphate) (see Figure 11:7)
Currency of energy. Contains two highly reactive anhydride linkages between the two terminal phosphate groups. These two groups are readily transfered to other molecules and their energy quotient goes with them. Consequently, the newly phosphorylated compound contains more energy than before and can be transformed from an unreactive substance to a reactive one. There are various high energy biological compounds (e.g. GTP, CTP, acyl coenzyme A). However, ATP is by far the most prevalent.

So where do the focal metabolites come from? Essentially they can all arise through the metabolism of sugar molecules via the Embden-Meyerhof pathway and the TCA cycle. If microorganisms are unable to use the above two routes (either theyÕre mutants or just dont have the necessary enzymes available) then they have devised many circuitous routes to arrive at each of above focal metabolites. We shall consider only two pathways in detail. However, remember there are hundreds of variations on this theme that depends on the organism in question.

ANAEROBIC METABOLISM
Embden-Meyerhof pathway (glycolysis)

Simplest way for a bacterium to make energy from 6-carbon sugar molecule. However, the energy yield is low (net two ATPs) when compared to aerobic metabolism.

Essentials of the Embden-Meyeroff pathway (see Figure 11:8):
i) glucose is converted to fructose-diphosphate (two ATPs are used up in this conversion). Once phosphorylated the energy level of glucose is increased with the addtional bonus being that it now cannot leave the cell.
ii) the phosphorylated six membered ring structure (i.e. the fructose-1,6-diphosphate molecule) is broken into two three-carbon structures each carrying a phosphate group
iii) the three carbon phosphate compounds are now converted to PEP (this generates one reduced NAD+ molecule (NADH) as well as generating one ATP through substrate level phosphorylation)
iv) PEP is converted to pyruvate with another ATP being made.

Therefore, the total yield of ATP per glucose molecule via glycolysis is 2 (remember that glucose is converted into two three-membered carbon phosphate structures, therefore the ATP yield from the latter reactions is 2X). Important: if the organism is able to respire aerobically,then the two electrons donated to NAD+ can enter the electron transport chain and generate even more ATP.

Besides the Embden-Meyerhoff pathway, bacteria have other pathways to metabolise glucose anaerobically. Two important pathways are:
i) pentose phosphate shunt - not only breaks down glucose (i.e. hexose) but also 5-membered sugars (pentoses; e.g. ribose)
ii)ÊEntner-Douderoff pathway - specialised pathway that replaces glycolysis and the pentose phosphate shunt Generally glucose is the initial substrate. However, other sugars can be used and if the necessary enzymes are present they convert these sugars into glucose, or, alternatively, convert them into some other component in the pathway. Basically, all pathways have just different enzymes and do just a little bit different chemistry. What they do in common though is provide the focal metabolites.

Fermentation
These are just important spin offs from anaerobic metabolism. Fermentation is essentially glycolysis to pyruvate, with pyruvate being further metabolised to different products. The overall need here for the cell is to recycle NAD because this compound is limiting. There are many different fermentation pathways, we shall consider two:
homolactic-acid fermentation Here pyruvate is converted to lactic acid by the enzyme lactate dehydrogenase. This produces no gas. This step is performed by several types of bacteria; lactobacilli, streptococci. Also occurs in your muscles (gives you cramp). This pathway in lactobacilli is used in making cheese.
alcoholic fermentation
Here pyruvate is converted to CO2 and acetaldehyde; the latter is unstable and is quickly converted to ethanol. This pathway is rare in bacteria but fortunately occurs frequently with yeast.

AEROBIC METABOLISM
Although anaerobic and aerobic organisms both use the glycolytic pathway to obtain small amounts of energy, aerobic organisms use it only as a prelude for a far more productive pathway where glycolysis is hooked up to the TCA cycle. This process is called aerobic respiration (also called the Krebs cycle or oxidative phosphorylation).

Essentially the TCA cycle (see Figure 11:9) is a pathway that converts two-carbon units (acetyl groups) to CO2 and H2O and energy. Before pyruvate can enter the cycle it is converted to acetyl-CoA and CO2. This is a complex reaction that yields one molecule of NADH. The acetyl-CoA then reacts with oxaloacetic acid and enters the pathway. Through one go around the pathway, the acetyl group which enters ends up as CO2 with the formation of one molecule of ATP by substrate level phosphorylation, three molecules of NADH and one molecule of FADH2. Note that as each glucose molecule produces two molecules of acetyl-CoA then the overall energy yield is double these amounts.

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