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20: Molecules in Living Systems

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    It was thought that organic compounds could only be manufactured in living organisms, and chemistry was divided into the subfields of inorganic and organic on this basis. This subdivision persists today, but the definition of organic has changed in response to the discovery of numerous ways to make organic compounds from inorganic starting materials. Biochemistry is the study of chemical elements found in living systems, and how these elements combine to form molecules and collections of molecules which carry out the biological functions and behaviors that we associate with life.

    • 20.1: Prelude to Biochemistry
    • 20.2: The Elements of Life
    • 20.3: The Building Blocks of Biochemistry
      Fortunately nearly all the substances found in living cells are polymeric—they are built up by different combinations of a limited number of relatively small molecules. For example, the basic structures of all proteins in all organisms consist of covalently linked chains containing 100 or more amino acid residues. Only 20 different amino acids are commonly incorporated in proteins, but the number of ways of arranging 100 of these in a chain taking any of the amino acids at random for each place
    • 20.4: Fats and Lipids
      Nonpolar lipids have molecular structures which contain no electrically charged sites, few polar groups, and large amounts of carbon and hydrogen. They are similar to hydrocarbons in being almost completely insoluble in water, and so they are said to be hydrophobic (from the Greek, meaning water-hater). On the other hand, polar lipids consist of molecules which have polar groups (such as —OH) or electrically charged sites at one end, and hydrocarbon chains at the other.
    • 20.5: Nonpolar Lipids
      A great many nonpolar lipids can be made by combining different long- chain acids with glycerol. Because these acids were originally derived from fats, they are collectively referred to as fatty acids.  This most-common form of animal fat serves as a storehouse for energy and as insulation against heat loss. On a molecular level it is constructed from three molecules of stearic acid and one of glycerol.
    • 20.6: Polar Lipids
      As was true of most nonpolar lipids, the structures of polar lipids are based on condensation of fatty acids with glycerol. The main difference is that only two of the three OH groups on glycerol are involved.
    • 20.7: Carbohydrates
      Carbohydrates are sugars and sugar derivatives whose formulas can be written in the general form: Cx(H2O)y. (The subscripts x and y are whole numbers.) Some typical carbohydrates are sucrose (ordinary cane sugar), C12H22O11; glucose (dextrose), C6H12O6; fructose (fruit sugar), C6H12O6; and ribose, C5H10O5.Since the atom ratio H/O is 2/1 in each formula, these compounds were originally thought to be hydrates of carbon, hence their general name.
    • 20.8: Simple Sugars
    • 20.9: Disaccharides
      Disaccharides are made up by condensing two sugar units.
    • 20.10: Polysaccharides
      As the name suggests, polysaccharides are substances built up by the condensation of a very large number of monosaccharide units. Cellulose, for example, is a polymer of β-glucose, containing upwards of 3000 glucose units in a chain. Starch is largely a polymer of α-glucose.
    • 20.11: Proteins
    • 20.12: Polypeptide Chains
      The backbone of any protein molecule is a polypeptide chain obtained by the condensation of a large number of amino acids with the elimination of water. You will recall that the amino acids are bifunctional organic nitrogen compounds containing an acid group, —COOH, and an amine group, —NH2. The amine group is attached to the carbon atom adjacent to the —COOH (the α carbon atom).
    • 20.13: The Amino Acids
      Altogether there are 20 amino acids which commonly occur in all organisms. Under most circumstances amino acids exist as zwitterions.
    • 20.14: Primary Protein Structure
    • 20.15: Secondary Protein Structure
    • 20.16: Higher-Order Structure
    • 20.17: Nucleic Acids
    • 20.18: Nucleic Acid Structure
      Nucleic acids were first isolated from cell nuclei (hence the name) in 1870. Since then they have been found in other portions of cells as well, especially the ribosomes, which are the sites of protein synthesis. Most nucleic acids are extremely long-chain polymers.
    • 20.19: Information Storage
      ow can DNA and RNA molecules act as blueprints for the manufacture of proteins? Each amino acid in a protein is determined by a specific codon of three nitrogenous bases in the DNA or RNA chain. The details of this genetic code are discussed.
    • 20.20: The Double Helix
      There is more to the structure of DNA than just the primary sequence of nitrogenous bases. Secondary structure also plays a crucial biochemical role. Each DNA molecule consists of two nucleotide chains wrapped around each other in a double helix and held together by hydrogen bonds. This hydrogen bonding involves only the nitrogenous bases. Each of the purine bases can hydrogen bond with one and only one of the pyrimidine bases.
    • 20.21: DNA Replication
      DNA is the genetically active component of the chromosomes of a cell and contains all the information necessary to control synthesis of the proteins, enzymes, and other molecules which are needed as that cell grows, carries on metabolism, and eventually reproduces. Thus when a cell divides, its DNA must pass on genetic information to both daughter cells. It must somehow be able to divide into duplicate copies. This process is called replication.
    • 20.22: Transcription and Translation

    This page titled 20: Molecules in Living Systems is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Ed Vitz, John W. Moore, Justin Shorb, Xavier Prat-Resina, Tim Wendorff, & Adam Hahn.

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