7.1 Organic Molecules
- The most abundant elements in cells are hydrogen, carbon, oxygen, nitrogen, phosphorus, and sulfur.
- Life is carbon based. Each carbon atom can bind to another one producing a carbon skeleton that can be straight, branched, or ring shaped.
- The same numbers and types of atoms may bond together in different ways to yield different molecules called isomers. Isomers may differ in the bonding sequence of their atoms (structural isomers) or in the spatial arrangement of atoms whose bonding sequences are the same (stereoisomers), and their physical and chemical properties may vary slightly or drastically.
- Functional groups confer specific chemical properties to molecules bearing them. Common functional groups in biomolecules are hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.
- Macromolecules are polymers assembled from individual units, the monomers, which bind together like building blocks. Many biologically significant macromolecules are formed by dehydration synthesis, a process in which monomers bind together by combining their functional groups and generating water molecules as byproducts.
- Carbohydrates, the most abundant biomolecules on earth, are widely used by organisms for structural and energy-storage purposes.
- Carbohydrates include individual sugar molecules (monosaccharides) as well as two or more molecules chemically linked by glycosidic bonds. Monosaccharides are classified based on the number of carbons the molecule as trioses (3 C), tetroses (4 C), pentoses (5 C), and hexoses (6 C). They are the building blocks for the synthesis of polymers or complex carbohydrates.
- Disaccharides such as sucrose, lactose, and maltose are molecules composed of two monosaccharides linked together by a glycosidic bond.
- Polysaccharides, or glycans, are polymers composed of hundreds of monosaccharide monomers linked together by glycosidic bonds. The energy-storage polymers starch and glycogen are examples of polysaccharides and are all composed of branched chains of glucose molecules.
- The polysaccharide cellulose is a common structural component of the cell walls of organisms. Other structural polysaccharides, such as N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM), incorporate modified glucose molecules and are used in the construction of peptidoglycan or chitin.
- Lipids are composed mainly of carbon and hydrogen, but they can also contain oxygen, nitrogen, sulfur, and phosphorous. They provide nutrients for organisms, store carbon and energy, play structural roles in membranes, and function as hormones, pharmaceuticals, fragrances, and pigments.
- Fatty acids are long-chain hydrocarbons with a carboxylic acid functional group. Their relatively long nonpolar hydrocarbon chains make them hydrophobic. Fatty acids with no double bonds are saturated; those with double bonds are unsaturated.
- Fatty acids chemically bond to glycerol to form structurally essential lipids such as triglycerides and phospholipids. Triglycerides comprise three fatty acids bonded to glycerol, yielding a hydrophobic molecule. Phospholipids contain both hydrophobic hydrocarbon chains and polar head groups, making them amphipathic and capable of forming uniquely functional large scale structures.
- Biological membranes are large-scale structures based on phospholipid bilayers that provide hydrophilic exterior and interior surfaces suitable for aqueous environments, separated by an intervening hydrophobic layer. These bilayers are the structural basis for cell membranes in most organisms, as well as subcellular components such as vesicles.
- Isoprenoids are lipids derived from isoprene molecules that have many physiological roles and a variety of commercial applications.
- A wax is a long-chain isoprenoid that is typically water resistant; an example of a wax-containing substance is sebum, produced by sebaceous glands in the skin. Steroids are lipids with complex, ringed structures that function as structural components of cell membranes and as hormones. Sterols are a subclass of steroids containing a hydroxyl group at a specific location on one of the molecule’s rings; one example is cholesterol.
- Bacteria produce hopanoids, structurally similar to cholesterol, to strengthen bacterial membranes. Fungi and protozoa produce a strengthening agent called ergosterol.
- Amino acids are small molecules essential to all life. Each has an α carbon to which a hydrogen atom, carboxyl group, and amine group are bonded. The fourth bonded group, represented by R, varies in chemical composition, size, polarity, and charge among different amino acids, providing variation in properties.
- Peptides are polymers formed by the linkage of amino acids via dehydration synthesis. The bonds between the linked amino acids are called peptide bonds. The number of amino acids linked together may vary from a few to many.
- Proteins are polymers formed by the linkage of a very large number of amino acids. They perform many important functions in a cell, serving as nutrients and enzymes; storage molecules for carbon, nitrogen, and energy; and structural components.
- The structure of a protein is a critical determinant of its function and is described by a graduated classification: primary, secondary, tertiary, and quaternary. The native structure of a protein may be disrupted by denaturation, resulting in loss of its higher-order structure and its biological function.
- Some proteins are formed by several separate protein subunits, the interaction of these subunits composing the quaternary structure of the protein complex.
- Conjugated proteins have a nonpolypeptide portion that can be a carbohydrate (forming a glycoprotein) or a lipid fraction (forming a lipoprotein). These proteins are important components of membranes.
7.5 Using Biochemistry to Identify Microorganisms
- Accurate identification of bacteria is essential in a clinical laboratory for diagnostic and management of epidemics, pandemics, and food poisoning caused by bacterial outbreaks.
- The phenotypic identification of microorganisms involves using observable traits, including profiles of structural components such as lipids, biosynthetic products such as sugars or amino acids, or storage compounds such as poly-β-hydroxybutyrate.
- An unknown microbe may be identified from the unique mass spectrum produced when it is analyzed by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF).
- Microbes can be identified by determining their lipid compositions, using fatty acid methyl esters (FAME) or phospholipid-derived fatty acids (PLFA) analysis.
- Proteomic analysis, the study of all accumulated proteins of an organism; can also be used for bacterial identification.
- Glycoproteins in the plasma membrane or cell wall structures can bind to lectins or antibodies and can be used for identification.