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6: Metabolism I - Oxidative/Reductive Processes

  • Page ID
    1644
  • The cost of living is energy and the producers and consumers of energy in the cell are the chemical reactions known collectively as metabolism. Metabolic processes are governed by the same laws of energy as the rest of the universe, so they must be viewed in the light of Gibbs free energy. For the most part, the drivers of changes in Gibbs free energy are changes in concentration of reactants and products but for some reactions, the concentration changes required to run a reaction in the desired direction are not practical. In such cases, cells may use alternative strategies, such as energy coupling reactions (combining an energetically unfavorable reaction with a favorable one, such as the hydrolysis of ATP) to help “drive" the unfavorable reaction. In other cases, cells use alternate pathways around energetically unfavorable reactions.

    Depending on your mathematical perspective, life is the sum of the product of the biochemical reactions that occur in cells. The collection of these reactions is known as metabolism. We break the subject into two broad areas: 1) oxidative/reductive metabolism and 2) pathways that involve little oxidation/reduction. This chapter deals with the former.

    • 6.1: Definitions
      Anabolic processes refer to collections of biochemical reactions that make bigger molecules from smaller ones. Examples include the synthesis of fatty acids from acetyl-CoA, of proteins from amino acids, of complex carbohydrates from simple sugars, and of nucleic acids from nucleotides. Just as any construction project requires energy, so, too, do anabolic processes require input of energy. Anabolic processes tend to be reductive in nature, in contrast to catabolic processes, which are oxidative
    • 6.2: Perspectives
      We can view metabolism at several levels. At the highest level, we have nutrients, such as sugars, fatty acids and amino acids entering cells and carbon dioxide and other waste products (such as urea) exiting. Cells use the incoming materials for energy and substance to synthesize sugars, nucleotides, and other amino acids as building blocks for the carbohydrates, nucleic acids, fatty compounds, and proteins necessary for life.
    • 6.3: Glycolysis
      Glycolysis, which literally means “breakdown of sugar," is a catabolic process in which six-carbon sugars (hexoses) are oxidized and broken down into pyruvate molecules. The corresponding anabolic pathway by which glucose is synthesized is termed gluconeogenesis. Both glycolysis and gluconeogenesis are not major oxidative/reductive processes by themselves, with one step in each one involving loss/gain of electrons, but the product of glycolysis, pyruvate, can be completely oxidized to CO₂.
    • 6.4: Gluconeogenesis
      The anabolic counterpart to glycolysis is gluconeogenesis, which occurs mostly in the cells of the liver and kidney. In seven of the eleven reactions of gluconeogenesis (starting from pyruvate), the same enzymes are used as in glycolysis, but the reaction directions are reversed. Notably, the ΔG values of these reactions in the cell are typically near zero, meaning their direction can be readily controlled by changing substrate and product concentrations.
    • 6.5: Citric Acid Cycle
      The primary catabolic pathway in the body is the citric acid cycle because it is here that oxidation to carbon dioxide occurs for breakdown products of the cell’s major building blocks - sugars, fatty acids, amino acids. The pathway is cyclic and thus, doesn’t really have a starting or ending point. All of the reactions occur in the mitochondrion, though one enzyme is embedded in the organelle’s membrane.
    • 6.6: Glyoxylate Pathway
      The glyoxylate pathway is related to the Citric Acid Cycle (CAC), which overlaps all of the non-decarboxylation reactions of the CAC does not operate in animals, because they lack two enzymes necessary for the pathway – isocitrate lyase and malate synthase. Isocitrate lyase catalyzes the conversion of isocitrate into succinate and glyoxylate. Because of this, all six carbons of the CAC survive and do not end up as carbon dioxide.
    • 6.7: Acetyl-CoA Metabolism
      Acetyl-CoA is one of the most “connected" metabolites in biochemistry, appearing in fatty acid oxidation/reduction, pyruvate oxidation, the citric acid cycle, amino acid anabolism/catabolism, ketone body metabolism, steroid/bile acid synthesis, and (by extension from fatty acid metabolism) prostaglandin synthesis. Most of these pathways will be dealt with separately. Here we will cover the last three.
    • 6.8: Cholesterol Metabolism
      The cholesterol biosynthesis pathway is a long one and it requires significant amounts of reductive and ATP energy, which is why it is included here. Cholesterol has important roles in the body in membranes. It as also a precursor of steroid hormones and bile acids and its immediate metabolic precursor, 7-dehydrocholesterol, is a precursor of Vitamin D. The pathway leading to cholesterol is known as the isoprenoid pathway and branches of it lead to other molecules including other fat-soluble vit
    • 6.9: Ketone Body Synthesis
      In ketone body synthesis, an acetyl-CoA is split off from HMG-CoA, yielding acetoacetate, a four carbon ketone body that is somewhat unstable, chemically. It will decarboxylate spontaneously to some extent to yield acetone. Ketone bodies are made when the blood levels of glucose fall very low. Ketone bodies can be converted to acetyl-CoA, which can be used for ATP synthesis via the citric acid cycle.
    • 6.10: Prostaglandin Synthesis
      The pathway for making prostaglandins is an extension of the fatty acid synthesis pathway. Prostaglandins, molecules associated with localized pain, are synthesized in cells from arachidonic acid (see previous page) which has been cleaved from membrane lipids. The enzyme catalyzing their synthesis is known as prostaglandin synthase, but is more commonly referred to as a cyclooxygenase (or COX) enzyme.
    • 6.11: Fatty Acid Oxidation
      Breakdown of fats yields fatty acids and glycerol. Glycerol can be readily converted to DHAP for oxidation in glycolysis or synthesis into glucose in gluconeogenesis. Fatty acids are broken down in two carbon units of acetyl-CoA. To be oxidized, they must be transported through the cytoplasm attached to coenzyme A and moved into mitochondria. The latter step requires removal of the CoA and attachment of the fatty acid to a molecule of carnitine.
    • 6.12: Fatty Acid Synthesis
      Synthesis of fatty acids occurs in the cytoplasm and endoplasmic reticulum of the cell and is chemically similar to the beta-oxidation process, but with a couple of key differences. The first of these occur in preparing substrates for the reactions that grow the fatty acid. Transport of acetyl-CoA from the mitochondria occurs when it begins to build up. Two molecules can play roles in moving it to the cytoplasm – citrate and acetylcarnitine
    • 6.13: Metabolism of Fat
      Breakdown of fat in adipocytes requires catalytic action of three enzymes, hormone sensitive triacylglycerol lipase (called LIPE) to remove the first fatty acid from the fat, diglyceride lipase to remove the second one, and monoglyceride lipase to remove the third. Only LIPE is regulated and it appears to be the rate limiting reaction. Synthesis of fat starting with glycerol-3-phosphate requires action of acyl transferase enzymes to catalyze addition of fatty acids to the glycerol backbone.
    • 6.14: Connections to Other Pathways
      There are several connections between metabolism of fats and fatty acids to other metabolic pathways. As noted, phosphatidic acid is an intermediate in the synthesis of triacylglycerols, as well as of other lipids, including phosphoglycerides. Diacylglycerol (DAG), which is an intermediate in fat synthesis, also acts as a messenger in some signaling systems.

    Thumbnail: Metabolic Metro Map. Image used with permission (CC BY-SA 4.0; Chakazul).​​​​

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