Metabolism: notes to accompany class coverage.
This is phrased in terms of the human body, but a similar line of explanation applies in all species, since all cells and organisms perform metabolism in similar ways, for similar reasons, using the same types of molecules. Obviously there are some important differences among organisms. Green plants perform photosynthesis but animals don't, for instance. But at the level of individual cells, where nearly all metabolism occurs, there are fundamental similarities among all cells: from unicellular bacteria and protozoans to the cells of trees and mammals.
• Connect metabolism to previous coverage of the families of biologically important organic molecules (BIOM). The foods we consume are composed of these molecules (plus vitamins, minerals).
"Minerals" is a dietary term for essential elements other than CHNOPS; that's Fe, Ca, K, Cu, Zn, Mg, Mn, etc. Nearly all are metals, and exist as ions in solution in cells.
"Vitamins" are organic molecules that the human body must have but cannot manufacture for itself from other organic molecules; so the diet must provide them. Vitamins belong to various families of BIOM. For example, vitamin D is a steroid and vitamin C is a carbohydrate. Why do cells need vitamins? See below.
•These BIOM provide (i) building blocks and (ii) chemical energy; cells need both.
(i) Amino acids are needed for cells to make their proteins (enzymes, carrier proteins, e.g.). Monosaccharides are needed for cells to make oligo- and polysaccharides. Fatty acids are needed for cells to make phospholipids for membrane structure. ...and so on...
(ii) Cells need energy for many purposes. Construction of large complex molecules and cellular structures [see (i) above, e.g.] requires energy. Active transport across all membranes requires energy. Muscle cells require energy to drive their molecular contraction machinery.
•Digestion, after chewing/swallowing, prepares BIOM for absorption, from the interior of the small intestine into the bloodstream. Macromolecules must be degraded to their simpler components (monomers) prior to absorption. The bloodstream transports the molecules to all cells in the body, where they are absorbed. Connect this absorption (from intestine to blood and from blood into cells) to permeability processes already covered.
•The energy involved in metabolism is chemical energy. We all know that "foods" contain energy that the body can use. That energy (measured as calories) is in the BIOM in those foods. Specifically the energy is in the covalent bonds (the shared pairs of electrons) of the molecules. When an energy-rich sugar molecule or fat molecule is degraded in a cell, the chemical energy of the broken bonds may be (i) used to create new bonds in making other molecules that the cell needs, (ii) used to enable active transport across a membrane, (iii) used for movement or contraction, (iv) stored as ATP for later use. Also, since energy conversions such as these just named are never perfectly efficient, some energy will be lost as heat (the 2nd law of thermodynamics tells us that) when the covalent bonds in BIOM are broken. That heat contributes to maintenance of body temperature.
•Metabolism (adjective: metabolic) refers to all chemical reaction within a cell. As the preceding comments say, some chemical reactions are synthetic; i.e. molecules are made/constructed. These are anabolic (noun; anabolism). Other reactions are degradative; i.e. molecules are broken apart. These are catabolic (noun: catabolism). Broadly speaking, catabolic reactions in cells provide the chemical energy needed to support anabolic reactions.
•A familiar example of energy conversion: If you ignite the edge of a piece of paper, it continues to burn on its own. That paper is made of BIOM, mostly cellulose. The energy released as the covalent bonds of the molecules are broken causes rupture of the bonds in adjacent molecules, until there are no more energy-rich bonds to break. That's when the fire goes out. Watching the fire, you should realize that the chemical energy of the covalent bonds of those molecules is being converted into (i) heat and (ii) light, both of which are also forms of energy. The ash that remains is a waste product. This release of energy from the molecules is random, uncontrolled.
•Unlike the example just described, the catabolic release of BIOM's chemical energy within cells occurs in a controlled, stepwise fashion, and that is made possible by enzymes. Each type of enzyme has its own unique 3-D structure (shape), and the shape of every enzyme's active site is such that only the substrate(s) of that enzyme will fit properly into its active site. Once within the active site, the reaction occurs, and the product(s) diffuses out of the active site. Since the enzyme (catalyst) is not consumed in the reaction, it can catalyze the same reaction again, repeatedly.
•Enzyme-catalyzed reactions are organized into metabolic pathways in cells; different pathways occur in different cell compartments. Glycolysis, for example, occurs only in the cytosol of a eukaryotic cell; the Krebs cycle occurs only in the mitosol of mitochondria. Each cellular compartment is functionally specialized. In this generalized view of a pathway each step is catalyzed by a different enzyme (E). The pathway begins with A; the end product is K. The molecules between (B, C, etc.) are called intermediates. Some pathways have very few steps; others have many. Each step (reaction) is catalyzed by a different, specific enzyme.
•Vitamins have various functions in the body but primarily they are used by cells to make coenzymes. Many enzymes cannot function without the proper coenzyme. Cells use the vitamin, niacin, to make the coenzyme, nicotinamide adenine dinucleotide (NAD), and they use riboflavin to make flavin adenine dinucleotide (FAD). The coenzymes participate in many enzyme-catalyzed reactions by accepting or donating electrons from/to the substrate of the reaction. When glucose is completely degraded (oxidized) to CO2 and water by cellular respiration [see graphic below: Schematic of Cellular Respiration] in a cell, some of the energy of the electrons in glucose's bonds is transferred to NAD+ (the oxidized, low energy form of the coenzyme). That converts the NAD+ to NADH (the reduced, high energy form of the coenzyme. [Similarly, the oxidized, low energy FAD molecule is converted to the reduced, high energy FADH molecule.] Every cell has only a limited amount of NAD+ and FAD (the oxidized forms); so these molecules must be reused if glucose degradation is to continue. The process of electron transport in mitochondria removes electrons from NADH and FADH (oxidizes them) and passes those energetic electrons to O2 to make water. That electron transfer provides energy to make ATP, which is the all-purpose energy currency of cells, usable for nearly all of the cell's energy needs. This synthesis of ATP (which is connected to the degradation of glucose via the reduction and oxidation of the coenzymes) is called oxidative phosphorylation; it also occurs in the mitochondria.
•Cellular respiration, mentioned in the previous paragraph is made up of glycolysis, the Krebs cycle, electron transport, and oxidative phosphorylation. [see graphic below: Schematic of Cellular Respiration] Note the compartment location of each part. The following "equation" oversimplifies the process, but does emphasize some important features of glucose breakdown (degradation, oxidation, catabolism) in cells.
For example, all 6 C atoms of glucose become CO2. That's a waste product and must be eliminated; this is why you need to exhale. Further, molecular oxygen (O2) is required; providing this oxygen for cellular respiration is the reason you need to inhale. Note that the O2 is used at the very end of the process of cellular respiration, where the reduced coenzymes must be reoxidized. Note also that the water is produced at the end, where oxygen is consumed. A cell (or human body) deprived of O2 dies as follows: (i) Without O2 the reduced coenzymes (the NADH & FADH that are produced in glucose breakdown) cannot be reoxidized. (ii) Without the oxidized coenzyme form (NAD+ & FAD) several reactions in cellular respiration stop. (iii) Since all the reactions in cellular respiration are connected, any one that stops will stop the whole process. (iv) Since the primary purpose of cellular respiration is to make ATP for the cell (from the energy stored in glucose), the cell now cannot make enough ATP to sustain its many energy-requiring activities; and without that maintenance the cell disintegrates.
•Metabolic pathways are connected to each other like roads in a network. The end product of one pathway may be the starting point for another pathway, e.g. All three of the major types of "food" molecules (carbohydrates, proteins, fats) are degraded to make ATP by connections to cellular respiration. [see graphic below: Integration of Catabolic Pathways]
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