Chapter 3: The Chemistry of Life: Organic Compounds

Carbon Atoms and Organic Molecules

• Each carbon atom forms four covalent bonds with up to four other atoms; these bonds are single, double, or triple bonds.
• Carbon atoms form straight or branched chains, or join into rings.
• Carbon forms covalent bonds with a greater number of
• different elements than does any other type of atom.
• Isomers are compounds with the same molecular formula but different structures.
  • Structural isomers differ in the covalent arrangements of their atoms.
  • Geometric isomers, or cis-trans isomers, differ in the spatial arrangements of their atoms.
  • Enantiomers are isomers that are mirror images of each other.
  • Cells can distinguish between these configurations
• Hydrocarbons, organic compounds consisting of only carbon and hydrogen, are nonpolar and hydrophobic.
  • The methyl group is a hydrocarbon group.
• Polar and ionic functional groups interact with one another
• and are hydrophilic.
  • Partial charges on atoms at opposite ends of a bond are responsible for the polar property of a functional group.
  • Hydroxyl and carbonyl groups are polar
• Carboxyl and phosphate groups are acidic, becoming negatively charged when they release hydrogen ions.
  • The amino group is basic, becoming positively charged when it accepts a hydrogen ion.
• Long chains of monomers (similar organic compounds) linked through condensation reactions are called polymers.
  • Large polymers such as polysaccharides, proteins, and DNA are referred to as macromolecules.
  • They can be broken down by hydrolysis reactions.

Carbohydrates

• Carbohydrates contain carbon, hydrogen, and oxygen in a ratio of approximately one carbon to two hydrogens to one oxygen.
• Monosaccharides are simple sugars such as glucose, fructose and ribose.
  • Two monosaccharides join by a glycosidic linkage to form a disaccharide such as maltose or sucrose.
• Most carbohydrates are polysaccharides, long chains of repeating units of a simple sugar.
• Carbohydrates are typically stored in plants as the polysaccharide starch and in animals as the polysaccharide glycogen.
• The cell walls of plants are composed mainly of the structural polysaccharide cellulose.

Lipids

• Lipids are composed mainly of hydrocarbon-containing regions, with few oxygen-containing (polar or ionic) functional groups.
  • Lipids have a greasy or oily consistency and are relatively insoluble in water.
• Triacylglycerol, the main storage form of fat in organisms, consists of a molecule of glycerol combined with three fatty acids.
  • Monoacylglycerols and diacylglycerols contain one and two fatty acids, respectively.
  • A fatty acid can be either saturated with hydrogen or unsaturated.
• Phospholipids are structural components of cell membranes.
  • A phospholipid consists of a glycerol molecule attached at one end to two fatty acids and at the other end to a phosphate group linked to an organic compound such as choline.
• Steroid molecules contain carbon atoms arranged in four attached rings.
  • Cholesterol, bile salts, and certain hormones are important steroids.

Proteins

• Proteins are complex macromolecules made of simpler sub-units, called amino acids, joined by peptide bonds.
  • Two amino acids combine to form a dipeptide.
  • A longer chain of amino acids is a polypeptide.
  • Proteins are the most versatile class of biological molecules, serving a variety of functions, such as enzymes, structural components, and cell regulators.
• Proteins are composed of various linear sequences of 20 different amino acids.
• All amino acids contain an amino group and a carboxyl group
  • Amino acids vary in their side chains, which dictate their chemical properties: nonpolar, polar, acidic, or basic.
  • Amino acids generally exist as dipolar ions at cell pH and serve as important biological buffers.
• Primary structure is the linear sequence of amino acids in the polypeptide chain.
• Secondary structure is a regular conformation, such as an a-helix or a B-pleated sheet; it is due to hydrogen bonding between elements of the backbones of the amino acids
• Tertiary structure is the overall shape of the polypeptide chains, as dictated by chemical properties and interactions of the side chains of specific amino acids.
  • Hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges contribute to tertiary structure.
• Quaternary structure is determined by the association of two or more polypeptide chains.

Nucleic Acids

• The nucleic acids DNA and RNA, composed of long chains of nucleotide subunits, store and transfer information that specifies the sequence of amino acids in proteins and ultimately the structure and function of the organism.
• Nucleotides are composed of a two-ring purine or one-ring pyrimidine nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups
• ATP (adenosine triphosphate) is a nucleotide of special significance in energy metabolism.
  • NAD* is also involved in energy metabolism through its role as an electron (hydrogen) acceptor in biological oxidation and reduction reactions.

Identifying Biological Molecules

• Carbohydrates (C, H, O): Contain approximately 1 C:2 H:1 O (but make allowance for loss of oxygen when sugar units as nucleic acids and glycoproteins are linked)
  • To recognize it, count the carbons, hydrogens, and oxygen
• Lipids (C, H, O, sometimes N, P)
• 1) Monosaccharides (simple sugars). Mainly five-carbon (pentose) molecules such as ribose or six-carbon (hexose) molecules such as glucose and fructose
  • To recognize it, look for the ring shapes
• 2) Disaccharides. Two sugar units linked by a glycosidic bond, e.g., maltose, sucrose
  • To recognize it, count sugar units
• 3) Polysaccharides. Many sugar units linked by glycosidic bonds, e.g., glycogen, cellulose
  • To recognize it, count sugar units
• Contain much less oxygen relative to carbon and hydrogen than do carbohydrates
• 1) Fats. Combination of glycerol with one to three fatty acids.
  • Monoacylglycerol contains one fatty acid; diacylglycerol contains two fatty acids; triacylglycerol contains three fatty acids If fatty acids contain double carbon-to-carbon linkages (C==C), they are unsaturated; otherwise, they are saturated.
  • To recognize it, look for glycerol at one end of the molecule
• 2) Phospholipids. Composed of glycerol attached to one or two fatty acids and to an organic base containing phosphorus
  • To recognize it, look for glycerol and side chain containing phosphorus and nitrogen
• 3) Steroids. Complex molecules containing carbon atoms arranged in four attached rings (Three rings contain six carbon atoms each, and the fourth ring contains five.)
  • To recognize look for four attached rings
• 4) Carotenoids. Orange and yellow pigments; consist of isoprene units
  • To recognize it, look for isoprene units
• Proteins (C, H, O, N, usually S): One or more polypeptides (chains of amino acids) coiled pr folded in characteristic shapes
  • To recognize it, look for amino acids joined by C—N bonds
• Nucleic Acids (C, H, O, N, P): Backbone composed of alternating pentose and phosphate groups, from which nitrogenous bases project.
  • DNA contains the sugar deoxyribose and the bases guanine, cytosine, adenine, and thymine.
  • RNA contains the sugar ribose and the bases guanine, cytosine, adenine, and uracil.
  • Each molecular subunit, called a nucleotide, consists of a pentose, a phosphate, and a nitrogenous base.
  • To recognize it, look for a pentose–phosphate backbone. DNA forms a double helix.