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Metabolism - Respiration

©2000 Timothy Paustian, University of Wisconsin-Madison

Respiration is the oxidation of a source of energy by removal of electrons and donation to an inorganic terminal electron accepter. The path the electrons follow from source to accepter usually involves a membrane bound system that creates a proton gradient. This proton gradient can do work and is used to create ATP.

General Concepts

Respiration is much more efficient than fermentation and respiring organisms, including us, have come to dominate the earth. Fermenting organisms are restricted to niches where oxygen is lacking (or they are at an advantage) and suitable carbon sources exist. Again, the diversity of respiring microbes is vast, but they do have many things in common.

• ATP is generated by ETLP involving a membrane system.

• The energy yield from respiration is much higher than fermentation and the substrate often has all available electrons removed; it is fully oxidized.

• The terminal electron accepter is inorganic. For aerobic respiration this is oxygen, but bacteria are also capable of using nitrate, sulfate, methane and others.

• Substrates for respiration include

  • Organic molecules - Sugars, amino acids, nucleotides, organic acids, fats. Some microbes can even catabolize benzene or toluene. The point is, the list is large.

  • Inorganic - Certain groups of bacteria are capable of using an inorganic compound as their source of electrons. For example iron bacteria will start with Fe⁺² and oxidize it to Fe⁺³. Sulfur oxidizing bacteria will take inorganic sources of sulfur (H₂S) and oxidize them.

• Products of Respiration tend to be highly oxidized.

  • Organic molecules are most often oxidized to CO₂ and H₂O.

  • Inorganics change to CO₂, N₂ and SO₄^-2

Catabolism of Sugar (glucose)

We will again concentrate first on the degradation of glucose because it is a very common and well understood pathway. The initial steps used by aerobic organisms to break down glucose are identical to that used by many fermentative microbes. The Emden-Meyerhoff-Parnas pathway converts glucose to pyruvate with 2 net ATP formed. In contrast to fermentation, the electrons donated to NADH do not end up reducing the substrate, but instead are given to the electron transport chain. The goal in respiration is to extract as many high potential electrons as possible from the substrate and then use that energy to create ATP.

In the first step of this process the pyruvate dehydrogenase complex acts on pyruvate to form CO₂ and acetyl coenzyme A (acetyl-CoA). Electrons extracted from pyruvate during this reaction are used to reduce NAD⁺ to NADH.

Figure 1 - Formation of Acetyl CoA from pyruvate. One carboxyl group hilited in blue leaves as CO₂. The remaining carboxyl group and methyl group of pyruvate, hilited in red, form the acetyl group or acetyl-CoA.

An important coenzyme in this reaction is Coenzyme A. The molecule is synthesized from the vitamin pantothenic acid and is a carrier of carboxyllic acids such as acetate and propionate around the cell. The pyruvate dehydrogenase complex also contains a derivative of thiamin as a coenzyme.

Acetyl-CoA is then fed into the Tricarboxylic Acid Cycle (TCA) cycle where the two carbons on the acetate molecule are converted to CO₂ and water. Almost all microorganisms have at least some of the enzymes of the TCA cycle and many have all of them.

Figure 2 - The TCA cycle. Acetyl CoA condenses with oxaloacetate to form citrate. The acetyl molecule is in the red box and attaches to the blue hilited carbon on oxaloacetate. Energy is extracted in the various reactions of the cycle (hilited in purple).

The TCA cycle can be broken into three phases, a 6 carbon phase (pink), a 5 carbon phase (green) and 4 carbon phase (yellow). In the first step, the two carbons of Acetyl-CoA combine with oxaloacetate to form citrate. The reaction is catalyzed by the enzyme citrate synthase, a key enzyme in many organisms. The subsequent reactions of the cycle concern themselves with the oxidation of citrate, the release of energy and regeneration of oxaloacetate. In this way, oxaloacetate (and the other intermediates of the TCA cycle) are not used up and can flow through many turns of the cycle. One turn of the TCA cycle generates 1 GTP, 3 NADH, and 1 FADH

The TCA cycle is central to the metabolism of many microorganisms (and macroorganisms). Many of the intermediates in the TCA cycle are also starting points for the synthesis of cellular constituents such as amino acids, nucleic acids and cell wall components.

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