CH.4: CARBON CHEMISTRY

1. CH.4: CARBON CHEMISTRY • Water required for life as the MEDIUM for all the reactions • Actual chemistry of living organisms is CARBON- BASED. • Organic compounds are those built around long chains or rings of carbons. • Carbon is elementally unique. (almost as unique as the water molecule is …hybridization of s and p orbitals.)

2. Carbon • 6 protons, 6 neutrons (8), 6 electrons. • 2,4 configuration • sp hybridization • 4 unshared electrons • Forms 4 bonds. • Bonds readily to other carbons - creating chains (and rings in aqueous solution) • Also bonds to CHNOPS

3. A little philosophy….. • Historically interested in synthesis of compounds • Mechanism vs. vitalism • Mechanism = all natural phenomenon are governed by laws of chemistry and physics. • Vitalism = belief in a life force outside the jurisdiction of chemistry and physics. • Berzelius (organic cpds), Wohler / Kolbe (make organic cpds), Miller (spontaneous)

4. Bonding • Carbon chemistry is that of COVALENT BONDING. Usually nonpolar. • Single bond • Double bond • C-C, C-N, C-S, C-O….? S-S • Because S is the closest in chemical structure to C its possible their would be unique compounds with sulfur and in areas with lots of sulfur (ocean vents) their would be S-S life forms (instead of C based life forms…… • Hydrogen bonding and sulfur bonds are also important to emerging properties of organic molecules….the folding of proteins, so C-N or C-C makes the structure but the 3D shape depends on S attractions and H bonding in various regions/zones • Hydrocarbons….lots of variety

5. Isomers - see pages 61 and 62 • Vary in architecture, not empirical formula • Structural isomers : butane and isobutane on pg 61. 18 versions of C8H18 • Geometric isomers : same covalent partnerships but different spatial arrangement. (often double bond) • Enantiomers (stereo isomers) : mirror images around a central carbon. • Enantiomers are important pharmaceutically

7. Functional Groups • Common grouping that occur on C chains. • Give distinct properties to molecules. • Difference between estrogen and testosterone is one functional group • (actually just a H) See next slide

8. Functional groups • Hydroxyl –OH, alcohols, solubility • Carbonyl -CO, -COH, double bonds, aldehydes and ketones, • Carboxyl -COOH, carboxylic acids, sour taste, good source of H ions, • Amino -NH2, basic • Sulfhydryl -SH, thiols, stability • Phosphate -PO4, negativity, energy transfer • Methyl – CH3, expression of genes

10. Ch. 5: Structure and Function of Organic Macromolecules • Hierarchy • Structure and function • Emergent properties • Highly organized • Many organic macromolecules are very large and very complex, but are made from smaller, repeating subunits liked in a specific way. ‘letters of alphabet’

11. Polymerization • Monomer = small piece, ‘building block’ • Dimer • Polymer = long chain made from many repeating pieces. Variety and specificity • Polymerization is the process of constructing large molecules from smaller pieces. • Dehydration (condensation) reactions remove waters and create covalent bonds between monomers. • Hydrolysis reactions are used to split polymers into monomers.

12. Organic macromolecules • Carbohydrates • Lipids • Proteins • Nucleic Acids

14. Carbohydrates • C and H, some oxygen • Ratio is CH2O • Sugars , carbohydrates and starches • Monosaccharides (glucose C6H12O6) are for energy in cells • Disaccharides (like sucrose) are for transport in plants after photosynthesis (sap and fruit) • Polysaccharides (starches) are for storage in plants. Also found in animal liver. • Carbs can also be structural - cellulose

15. Lipids • Hydrophobic • Glycerol and 3 fatty acids • Fatty acids are hydrocarbon chains of 12 – 24 carbons. • “saturated fats” have no double bonds and are solid ( animal ) • “unsaturated fats” have double bonds are more fluid. • Fats are for energy storage ( fat, oils, waxes, seeds, nuts ) • They are also for insulation – heat and electrical • Lipids are also used for protection/ cushion • Some lipids ( cholesterol ) are important as components of chemical messengers in the body (hormones) • They are a MAJOR component of the phospholipid bilayer of cell membranes

16. Proteins • Proteios means ‘of first importance’ • 50 % of dry weight (just chemicals; no water, “ashes”) • Variety of structures and shapes • Variety of functions • UNIQUE 3-D SHAPE known as the proteins ‘CONFORMATION’ • Based on amino acid sequence • Peptide bonds are between C and N

17. Functions of proteins FUNCTION definition examples • Structural support silk, collagen, keratin • Storage amino acids albumin, milk, seeds • Transport transport hemoglobin, CM • Hormonal coordinate insulin • Receptor respond neurotransmitters • Contractile movement actin, myosin, flagella • Defensive protection antibodies • Enzymatic chemical reactions digestive enzymes

18. Specific Conformation of Proteins • Primary structure – sequence of amino acids • Linear structure; determined by mRNA code from the DNA; infinite sequences from the 20+ amino acids arranged in rows of 200-300 • Secondary structure – twisting, H bonds • Coils; start of 3D • Globins (glob shaped; hemoglobin, myoglobin) • And sheets (flat, sheet like pieces; actin, collagen) • Tertiary structure – cross link, S bonds • ‘coils coil’ – twisted rope that twists again to make a loop; very 3D; ‘form fits function’ – things like enzymes have very specific shapes and active zones • Quaternary structure – multiple pieces • Some proteins are made and transported in pieces and assembled later from subunits. (enzymes and hemoglobin)

21. Nucleic Acids • Nucleic acids store INFORMATION • Deoxyribonucleic acid (DNA) • Ribonucleic acid (RNA) • Groups of 3 bases = codon = amino acid • 5 nitrogenous bases • Adenine A • Cytosine C • Guanine G • Thymine T • Uracil U

22. ATP ADP + P makes ATP which stores energy; needs ATPase enzymes to direct ATP + H2O yields ADP and P and releases energy

23. Phospholipid Bilayers

24. Review: Table on pg. 90 and Hand out over types of organic macromolecules.