Organic Molecules Organic Chemistry and Biochemistry Lecture Text Chapter 2 Molecules containing both carbon and hydrogen Carbon 4 valence electrons in outer orbital Needs 8 total for full complement Carbon Can form 4 covalent bonds Can form 1-2 bonds with multiple atoms, including other carbon atoms Form chains of carbons, rings, etc. Reactive Groups Hydrocarbon chains may be linked to more reactive elements E.g., oxygen, nitrogen Molecular Formulas Number of atoms of each element in the molecule E.g. water = H 2 O E.g. methane = CH 4 E.g. glucose = C 6 H 12 O 6 Does not indicate how atoms bond Structural Formulas Indicate bonds among atoms within molecules Single line indicates single covalent bond Double line indicates double covalent bond E.g. Acetone (C 3 H 6 O) 1
Condensed Structural Formulas Not all bonds drawn Central atoms shown with atoms bonded to them E.g. Acetone (C 3 H 6 O) (CH 3 )CO(CH 3 ) or (CH 3 ) 2 CO or O CH 3 CCH 3 Line-Angle Formulas Bonds represented by lines Carbon atoms assumed to be present at the end of any line Oxygen and Nitrogen shown, Hydrogen is not Each carbon is assumed to have enough hydrogens bonded to it by single bonds to give it four bonds total Line-Angle Example Line-Angle Structural Formula Biomolecules Complex organic molecules used in biological systems Polymers Made up of repeated subunits Major Groups 1. Carbohydrates energy sources, cell communication 2. Lipids energy storage, cell membrane structure, cushioning, cell communication 3. Proteins structure, cell function (enzymes), cell communication 4. Nucleic Acids information storage molecules that contain H, O and C relative amounts of each are the same in all simple carbohydrates #C atoms = #O atoms #H atoms = 2x the number of either C or O general formula = (CH 2 O) n e.g. glucose C 6 H 12 O 6 monosaccharide - individual unit basic CH 2 O formula name possesses the suffix ose e.g. glucose, galactose, fructose, ribose Monosaccharides can have the same formula but different arrangements of atoms Isomers molecules of same formula but different structures 2
Disaccharide two monosaccharides linked e.g. sucrose = glucose + fructose e.g. maltose = glucose + glucose Polysaccharide Many monosaccharides linked E.g. glycogen Polymer of glucose Carbohydrate Synthesis Monosaccharides are linked by dehydration employs specific enzymes H is removed from one monosaccharide, an -OH group from the other covalent bond (glycosidic bond) formed between the two water formed as an end-product Carbohydrate Digestion polysaccharides are broken apart via hydrolysis a water molecule is split H + added to one of the free monosaccharides OH group added to the other Lipids (Fats, Oils, Waxes) very general category contain compounds that are not soluble in water (hydrophobic) Major classes Triglycerides Phospholipids Steroids Triglycerides fats and oils formed by dehydration combine glycerol with three molecules of fatty acid 3
Triglycerides different types of fatty acids Saturated all carbons in chain linked by single bonds Unsaturated one or more carbons in chain linked by double bonds Unsaturated fatty acids tend to be more fluid Phospholipids contain a phosphate group (PO 4 ) commonly a combination of a phosphate group to a glycerol molecule attached to two fatty acids e.g. lecithin Phospholipids possess both polar an nonpolar ends (amphipathic) nonpolar ends aggregate form micelles when mixed in water interact with water lowers surface tension of water Steroids Consist of 3 six-carbon rings and a single five-carbon ring interlocked different functional groups attached to basic structure e.g. sex steroids produced by gonads (testosterone, progesterone) e.g. corticosterones produced by adrenal glands e.g. cholesterol precursor for hormones, regulation of cell membrane fluidity Proteins Diverse in structure and function Polymers of amino acids 20 common amino acids each with: an amino group a carboxyl group a functional side-group (differs among a.a. s) Peptide Bonds Amino acids are joined by dehydration NH 3 group of one joined to the COOH group of another to form a peptide bond two joined amino acids = dipeptide many joined amino acids = polypeptide 4
Primary Structure Sequence of amino acids in a polypeptide chain From free amino end (Nterminus) to the free carboxyl end (C-terminus) May be 1000 s of a.a. s long Secondary Structure Formation of helix or sheet shape in a protein chain due to hydrogen bonds forming between the amino group of one peptide bond and the carboxyl group from another peptide bond Tertiary Structure Twisting and folding of a single protein chain due to chemical interactions among the different sidechain groups Quaternary Structure Bonding and interactions of multiple polypeptide chains e.g. insulin = two separate chains e.g. hemoglobin = four separate chains Conjugated Biomolecules Combinations of two or more types of biomolecules Glycoprotein = carbohydrate + protein Lipoprotein = lipid + protein Glycolipid = carbohydrate + lipid 5