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Ch. 3 Notes: Organic Chemistry Aside from water, most biologically important molecules are carbon-based (organic). Organic Chemistry = study of C (and H) compounds. THE CARBON ATOM Valence Electrons: 4 Lewis Dot Structure: . ∙C∙ ∙ It makes large, complex molecules possible, due to its: Small size Ability to form up to 4 covalent bonds (single, double, or triple) o In organic compounds, usually bonded to members of CHNOPS Ability to be arranged in long carbon chains = carbon skeleton o C-C bonds are very stable o These are the framework for organic molecules o These determine the organic molecule’s 3-D shape, which affects its function! Hydrocarbons = molecules made of only C’s and H’s Major components of fossil fuels Are hydrophobic because the C-C and C-H bonds are nonpolar FUNCTIONAL GROUP = a specific combination of bonded atoms that always reacts in the same way, regardless of the C-skeleton it is bonded to Are often the chemically reactive part of the molecule Determine the unique chemical properties of the organic molecules in which they occur Please note that chemists use the letter R to represent the C-skeleton these groups are attached to, which is considered the “remainder” of the molecule. 1. Hydroxyl Group = R-OH Polar this makes the molecule water soluble! Called alcohols 2. Carbonyl Group = R-C=O Polar and water soluble Found in sugars If on the end of the carbon skeleton = aldehyde If in the middle of the C-skeleton = ketone O ║ May also see as: R-C=O 3. Carboxyl Group = R-COOH or Polar and water soluble Can donate the last H as H+ (a proton), so it has acidic properties Things with these attached are often called carboxylic acids 4. Amino Group = R-NH2 May also see as: R-NH3+ Polar and water soluble Acts as a weak base by accepting a proton (H+) Called amines 5. Sulfhydryl Group = R-SH Nonpolar group Helps stabilize structure of proteins Called thiols 6. Phosphate Group Actually the dissociated form of phosphoric acid Looks like: O│ O - P – O║ O Has acid properties Polar and water soluble Important for energy storage 7. Methyl Group = -CH3 Nonpolar Useful in making nonpolar amino acids and in controlling genes ISOMERS = organic molecules with the same molecular formula but with different arrangements of atoms Will also have different properties BIOMOLECULES Polymer = (poly = many; mer = part); large molecules made of many identical or similar subunits connected together Monomer = a single subunit of a polymer Macromolecule = large organic polymer Put together by DEHYDRATION (a.k.a. CONDENSATION) reactions = reaction that link two or more small monomers to form larger polymer by the net removal of a water molecule An –OH is removed from one molecule and a –H is removed from the other H2O Each leave behind an unpaired electron on their monomer which can then be used to create a new covalent bond between them A Dehydration Reaction looks like: Requires energy Requires biological catalysts or enzymes Hydrolysis (hydro- = water; lysis = to split); a reaction that breaks covalent bonds between monomers by the addition of a water molecule (-OH and –H) Ex. Digestive enzymes work this way