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
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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
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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 energyrequiring 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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