Organic chemistry: The Chemistry of Carbon Carbon tetravalence tetrahedron shape determines function

Hydrocarbons and Isomers Hydrocarbons –Only carbon & hydrogen (petroleum; lipid ‘tails’) –Covalent bonding; nonpolar –High energy storage Isomers (same molecular formula, but different structure & properties) –structural~differing covalent bonding arrangement –geometric~differing spatial arrangement around a double bond –enantiomers~mirror images pharmacological industry (thalidomide)

Functional Groups, I Attachments that replace one or more of the hydrogen(s) bonded to the carbon skeleton of the hydrocarbon These regions are commonly reactive. Each has a unique property and behave consistently from one organic molecule to another. Hydroxyl Group H bonded to O Very polar (oxygen is much more electronegative than hydrogen); soluble in water The main functional group of ALCOHOLS Carbonyl Group C double bonded to O Also very polar/soluble Main functional group of SUGARS At end : aldehyde Otherwise: ketone

Functional Groups, II Carboxyl Group O double bonded to C to hydroxyl Main functional group of carboxylic acids H in the OH extremely polar dissociates to form H ion Amino Group N to 2 H atoms; amines acts as base (accepts H+) Converts to NH 3 as it accepts protons Isomers! (LinkIsomers! (Link)

Functional Groups, III Sulfhydral Group sulfur bonded to H Attract each other to help stabilize proteins (disulfide bridges) thiols Phosphate Group phosphate ion covalently attached: 1 of its O to the C skeleton Polar/hydrophilic Important in cellular energy & transfer

Polymers Most Macromolecules are POLYMERS: Large molecules consisting of many identical or similar subunits called: Monomers (different kinds of monomers for different kinds of polymers) Condensation reaction (dehydration reaction): One monomer provides a hydroxyl group while the other provides a hydrogen to form a water molecule Hydrolysis: bonds between monomers are broken by adding water (digestion) D:\chapter5\deluxe.html

Carbohydrates (Sugars, etc…) Monomer = “monosaccharide” Used for energy & structure “-ose” ending! -OH attached to all carbons except 1which has a carbonyl (C=O) group Monosaccharides are 3-7 carbons in size: Most common: Triose-3 ; Ribose-5 ; Hexose-6 Form rings in aqueous solutions Monosaccharides link to form….

Disaccharides Disaccharides glycosidic linkage: (covalentbond) between 2 monosaccharides covalent bond by dehydration reaction Sucrose (table sugar) most common disaccharide There are also “Trisaccharides”, and even “Oligosaccharides” Once you get more than a couple dozen in a row, you then call them…..

Polysaccharides: 100s to 1000s of linked Monosaccharides Polysaccharides Storage : Plants: Starch –can be used for energy by animals –Straight chains of glucose Animals: Glycogen –Highly branched chains of glucose Polysaccharides Structural: Cellulose~ what plants are mostly made of… – Earth’s most abundant organic compound! Chitin~ exoskeletons; cell walls of fungi; surgical thread D:\chapter5\deluxe.html

Lipids No long chain polymers; glycerol and fatty acid Fats, phospholipids, steroids Hydrophobic; H bonds in water exclude fats Carboxyl group = fatty acid Non-polar C-H bonds in fatty acid ‘tails’ Ester linkage: 3 fatty acids to 1 glycerol (dehydration formation) Triacyglycerol (triglyceride) Saturated vs. unsaturated fats; single vs. double bonds

Lipids, II

Phospholipids 2 fatty acids instead of 3 (phosphate group) ‘Tails’ hydrophobic; ‘heads’ hydrophilic Micelle (phospholipid droplet in water) Bilayer (double layer); cell membranes Considered “Amphipathic”: One part hydrophobic, one part Hydrophilic Hydrophilic head Hydrophobic Tail

Steroids Lipids with 4 fused carbon rings Ex: cholesterol: cell membranes; precursor for other steroids (sex hormones); atherosclerosis D:\chapter5\deluxe.html

Proteins Importance: instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known Monomer: amino acids (there are 20) ~ carboxyl (-COOH) group, amino group (NH 2 ), H atom, variable group (R)…. Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base hyperlink Three-dimensional shape (conformation) Polypeptides (dehydration reaction): peptide bonds~ covalent bond; carboxyl group to amino group (polar)

Primary Structure Conformation: Linear structure Molecular Biology: each type of protein has a unique primary structure of amino acids Amino acid substitution: hemoglobin; sickle-cell anemia

Secondary Structure Conformation: coils & folds (hydrogen bonds) 2 main types of 2 ndary structures: Alpha Helix: coiling; keratin Pleated Sheet: parallel; silk

Tertiary Structure Conformation: irregular contortions from R group bonding √hydrophobic √disulfide bridges √hydrogen bonds √ionic bonds

Quaternary Structure Conformation: 2 or more polypeptide chains aggregated into macromolecule √collagen (connective tissue) √hemoglobin D:\chapter5\deluxe.html

Nucleic Acids, I Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA  RNA  protein Polymers of nucleotides (polynucleotide): nitrogenous base pentose sugar phosphate group Nitrogenous bases: pyrimidines~cytosine, thymine, uracil purines~adenine, guanine

Nucleic Acids, II Pentoses: √ ribose (RNA) √deoxyribose (DNA) √nucleoside (base + sugar) Polynucleotide: √ phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, III Inheritance based on DNA replication Double helix (Watson & Crick ) H bonds~ between paired bases van der Waals~ between stacked bases A to T; C to G pairing Complementary D:\chapter5\deluxe.html