Metabolism and Metabolic Control Notes

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Introduction

Cells have millions of metabolic reactions going on at any given second. If one looks at metabolic charts showing individual reactions, it resembles a gigantic roadmap. Like a roadmap, there are "interstate highways" that serve as common central thoroughfares through which much of the traffic will pass at any given time. These are the central metabolic pathways. Figure 15.2 (HERE) in your book presents a brief overview of metabolism.

Thermodynamics

Metabolic processes involve chemical reactions and these usually involve changes in energy states. The Gibbs free energy change for a reaction (symbolized by Delta G) provides a way of determining if a reaction goes forward as written (Delta G < 0), backward as written (Delta G >0) or is at equilibrium (Delta G = 0).

Consider the reaction aA + bB <=> cC + dD, where a is the number of moles of component A, b is the number of moles of component B, etc.

For this system,

Delta G = Delta G0' + RT ln {([C]c[D]d)/([A]a[B]b)}, where

Delta G0' is the free energy change of the reaction under STANDARD CONDITIONS (1M products and reactants) and Delta G is the free energy change under any other set of conditions. Note that Delta G0' does not absolutely tell ANYTHING about a reaction, but that a large positive or large negative value will likely have an influence on the sign of Delta G.

Simplifying (and remembering that each product and reactant must be raised to the appropriate power) yields the following general equation for determining Delta G under any set of conditions:

Delta G = Delta G0' + RT ln{[Products]/[Reactants]}

Thus, as the reactants increase, the Products/Reactants ratio DECREASES, making the natural log of it become more NEGATIVE and making Delta G more NEGATIVE. Conversely, as the products increase, the Products/Reactants ratio INCREASES, making the natural log of it become more POSITIVE and making Delta G more POSITIVE.

At equilibrium, the equilibrium constant K for the reaction is given by

K = {([C]c[D]d)/([A]a[B]b)}

Recall that Delta G = 0 at equilibrium, so substituting yields

0 = Delta G0' + RT ln Keq,

- Delta G0' = RT lnKeq

Whenever a system is displaced from equilibrium, it will spontaneously proceed in the direction necessary to reestablish the equilibrium state. Negative Delta G is the driving force for such a reaction.

ATP

Metabolic energy capture occurs largely through the synthesis of ATP (structure HERE), a nucleotide that stores energy in phosphate bonds. Hydrolysis of ATP by water to yield ADP + phosphate yields -30.5 kJ/mol. This energy can be applied to chemical reactions that are energetically unfavorable otherwise to make them be favorable. This is accomplished not by the direct transfer of energy from ATP to another molecule, but instead by coupling (combining) the hydrolysis of ATP to the reaction. Consider a hypothetical reaction

A <=> B (where the <=> symbol indicates a reversible reaction) with a theoretical Delta G0' of +16.7 kJ/mol. If the concentration of A = B, then the reaction will be unfavorable and go BACKWARDS, as the Delta G will be +16.7 kJ/mol. However, if the reaction is coupled to hydrolysis of ATP, as in

A + ATP + H2O <=> B + ADP + Pi + H+, then the Delta G0' for the overall reaction is -13.8 kJ/mol, so that if all products and reactants are at equal concentrations, then the reaction will go FORWARDS. Thus, the energy of ATP, when coupled to a reaction, can make the reaction go forwards, whereas the same reaction would go backwards without it. As a consequence, cells maintain high stocks of ATP to provide energy for needed reactions.

Besides metabolic chemistry, ATP energy can also be converted to mechanical energy (muscular contraction), and movement of molecules across membranes (ion pumping).

ATP Structure and Energy

There are good reasons ATP is used as a cellular energy source. As a triphosphate, ATP contains two phosphoanhydride bonds and these bonds release significant amounts of energy when they are hydrolyzed by water. Cleavage of a single phosphate by water (creating ADP + Pi) yields -30.5 kJ/mol under standard conditions and cleavage of pyrophosphate by water (creating AMP + PPi) yields - 45.6 kJ/mol. Other triphosphates, such as UTP, CTP, TTP, and GTP yield equivalent amounts of energy, indicating that the energy source is the triphosphate, not the base in the nucleotide. Though they are not GENERAL energy sources, it is worth noting that UTP, CTP, and GTP are all used in metabolism as energy sources for specific classes of reactions. Since cells maintain high concentrations of ATP, it can serve as a driving force for coupled reactions, due to the fact that as a reactant, increasing reactant concentrations favor LOWERING of Delta G (see above).

To MAKE ATP, cells must EXPEND metabolic energy and this will be a topic in BB 451. At a simple level, compounds containing phosphate that are at a higher energy state than ATP, such as 1,3 bisphosphoglycerate (1,3BPG), creatine phosphate, and phosphoenolpyruvate (PEP) (HERE), can directly transfer their high energy phosphate to ADP, making ATP in the process. Such a transfer is called substrate-level phosphorylation. Transfer of phosphate from creatine phosphate to ADP is an important way of making ATP in muscles under exertion.

Creatine phosphate + ADP + Pi <=> ATP + Creatine

Under normal conditions (no or light exercise), the reaction goes backwards. Under conditions of prolonged exercise, however, ATP gets used up. When this happens, the reaction moves in the rightward direction, making ATP. Creatine phosphate is normally MADE in the reverse direction when ATP concentration is HIGH. Consequently, creatine phosphate acts like a cellular battery, storing energy needed to make ATP until it is needed.

Oxidation and Cellular Energy

ATP is an excellent source of IMMEDIATE energy, but is not used for long-term storage.

Thermodynamically, biological oxidation of organic substrates is comparable to nonbiological oxidations, such as the burning of wood. The total free energy released is the same, whether the source is a biological substance, such as glucose, or the oxidation of a compound in a wood fire, calorimeter, or cell. Breakdown of biological molecules as a process is called catabolism, whereas the reversal - synthesis of biological molecules is called anabolism. Catabolism releases energy / anabolism requires energy.

Biological oxidations, however, are far more complex processes than combustion. When wood is burned, all of the energy is released as heat; that is, useful work cannot be performed, except through the action of a device such as a steam engine. In biological oxidations, by contrast, oxidation reactions occur without a large increase in temperature and with capture of some of the free energy as chemical energy. The oxidation state of a molecule determines how much energy can be derived from it by oxidation. Note in Figure 15.9 how the molecule with the lowest oxidation state (methane) provides the most energy, while the molecule with the highest oxidation state (carbon dioxide) provides the least energy. Glucose, polysaccharides, amino acids, proteins, and fatty acids are oxidizable cellular compounds that provide the bulk of a cell's metabolic energy.

Metabolic energy capture occurs largely through the synthesis of ATP. Unlike the oxidation of glucose by oxygen (as in a fire), most biological oxidations do not involve direct transfer of electrons from a substrate directly to oxygen. Instead, a series of coupled oxidation-reduction reactions occurs, with the electrons passed to intermediate electron carriers, such as NAD+ before they are finally transferred to oxygen.

Because the potential energy stored in the organic substrate is released in small increments, it is easier to control oxidation and capture some of the energy as it is released-small energy transfers waste less energy than a single large transfer. Oxidation in cells is very regimented. Cellular oxidation largely involves transfer of electrons to or through specialized carriers (called electron carriers - see HERE and HERE). The most abundant of these are NAD+/NADH, NADP+/NADPH and FAD/FADH2. In each case, the carrier with the most 'H's' is the reduced form and the other form is the more oxidized one. Electrons can pass from one carrier to another, but usually they are ultimately transferred to the cell's "terminal electron carrier." For aerobic organisms, like humans, the terminal electron carrier is oxygen.

Substances other than oxygen can serve as terminal electron acceptors. For example, some microogranisms growing anaerobically (in the absence of oxygen) generate energy by transferring electrons to inorganic substances, such as sulfate ion or nitrate ion. Other microorganisms, like the lactic acid bacteria, reduce organic substances, such as pyruvate, to form lactate. Still others, like yeast, transfer electrons to acetaldehyde, making ethanol. Most of these organisms derive their energy from fermentations, which are energy-yielding catabolic pathways that proceed with no net change in the oxidation state of the products as compared with that of the substrates.

Because metabolic energy comes primarily from oxidative reactions, the more highly reduced a substrate, the higher its potential for generating biological energy. Thus, combustion of fat provides more heat energy than combustion of an equivalent mass of carbohydrate.

Other Metabolic Carrier Molecules

Another important carrier in cells is Coenzyme A (usually called 'CoA' - see HERE). This carrier has nothing to do with oxidation/reduction. It serves primarily as a carrier of fatty acids and fatty acid-like compounds and chemically joins to these groups through formation of a thioester. This chemical bond has a high energy of hydrolysis and serves consequently to "activate" a molecule it is carrying, donating energy for its transfer to another group. Importantly, CoA (and other carriers) are chemically stable in the absence of enzymes that catalyze their breakdown. This allows cells to have an energy source that is released almost exclusively by enzymes. Some other metabolic carriers are shown in Table 15.2

Reaction Categories

All of the thousands of metabolic reactions can be grouped into six distinct categories of reaction. They are as follows:

• Oxidation-reduction (HERE) - involves gain/loss of electrons. Usually involves energy.
• Ligation (HERE) - forms bonds using free energy from ATP cleavage.
• Isomerization (HERE) - molecular rearrangement reactions
• Group transfer (HERE) - movement of a group from one molecule to another
• Hydrolytic reactions (HERE) - cleavage of bonds by addition of water
• Lyases (HERE and HERE) - addition of functional groups to double bonds or removal of groups to make double bonds.

Figure 14.7 shows common reactions found in very different cellular pathways employing some of these categories of reaction.

Metabolic Process Regulation

Mechanisms for controlling metabolic pathways are varied in cells. Some include the following:

• Control of enzyme levels - The concentrations of different enzymes vary widely in cellular extracts. Enzyme levels are controlled in large part by controlling the enzyme's rate of synthesis. Enzyme synthesis can often be induced or repressed by the presence or absence of certain metabolites. The rate of enzyme degradation can also be a factor in controlling enzyme levels.
• Control of enzyme activity - The catalytic activity of an enzyme can be controlled in two ways: by reversible interaction with ligands and by covalent modification of the enzyme itself. Low molecular weight ligands can interact with enzymes and exert allosteric effects. Frequently, the first or most important step in a metabolic pathway is under allosteric control in this way, enabling a cell to turn on or turn off an entire pathway easily and efficiently. Covalent modifications include phosphorylations, ADP-ribosylation, and other, more complex alterations. Covalent modification often occurs as a result of action of regulatory cascades. Glycogen metabolism is regulated in this fashion. Enzymes that phosphorylate other enzymes are called protein kinases.
• Accessibility of Substrates - Eukaryotic cells contain many different organelles and enzymes are distributed unevenly throughout them. For example, RNA polymerases are found in the nucleus and the nucleolus, where DNA transcription occurs. Enzymes of the citric acid cycle, on the other hand, are found in the mitochondria. Enzymes of fatty acid synthesis are found in the cytoplasm, but enzymes for fatty acid degradation are found in mitochondria.