Lecture 4 Carbon Chemistry, Functional Groups, Buffers 9/7/05

1. Lecture 4 Carbon Chemistry, Functional Groups, Buffers 9/7/05

2. Today’s Topics Diversity of Carbon Compounds Types of Functional Groups, properties Properties of Carboxylic Acids and Organic Bases Affect of pH on Protein Structure Buffers Chirality (Handedness)

3. Carbon ( C ) most important atom in biological molecules Valence of 4 – diversity & stability • C-C bonds are Very Stable • can make “limitless” chains • Carbon chains can “branch” • Single, double, triple bonds • Conjugated double bonds & aromatics • Covalent bonds – O, N, S, H

4. Hydrocarbons • Hydrocarbons • Are molecules consisting of only carbon and hydrogen

5. CH3 2 carbons ethane 3 carbons propane 14 carbon hydrocarbon methane • C-C bonds are Very Stable • can make “limitless” chains

6. H H C C C C H C H H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length Ethane Propane H H H H H H H H H H H H C C C C C C C C (b) Branching H H H H Butane 2-methylpropane (commonly called isobutane) H H H H H (c) Double bonds C H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Figure 4.5 A-D Cyclohexane Benzene • Carbon chains • can “branch” • Carbon chains • can “circularize” • Forms RINGS

7. Name and Comments Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model H (a) Methane CH4 C H H H H H (b) Ethane C C2H6 H C H H H H H (c) Ethene (ethylene) C C C2H4 H H Figure 4.3 A-C Different ways to illustrate carbon compounds

8. H H C C C C H C H H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length Ethane Propane H H H H H H H H H H H H C C C C C C C C (b) Branching H H H H Butane 2-methylpropane (commonly called isobutane) H H H H H (c) Double bonds C H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Figure 4.5 A-D Cyclohexane Benzene • Carbon chains • Form double bonds • Conjugated • Double Bonds • (Shared)

9. Conjugated Double Bonds H H A series of double bonds C C Conjugated C C H H H H Very stable Sharing electrons Through all 4 carbons “delocalized electrons”

10. Aromatic Ring Systems Left the H atoms Out for simplicity A series of double bonds in a ring Conjugated Special properties C C C C C C Aromatic Ring

11. Aromatic Ring Systems Left the H atoms Out for simplicity A series of double bonds Conjugated C C C C C C Extremely stable Flat Hydrophobic Tolerates “excitement ” of electrons

12. H H C C O H H H H even long chains with a variety of different atoms H O H H H H C= C C C=O C C H N H H H H H Carbon is special Covalently bonds With a number of different elements • Most Commonly • H • C • O • N • S Functional Groups Reactive Entities

13. Hydrophilic Polar Things: Hydrophobic Alcohols R-OH Sulfhydryls R-SH Aldehydes/Carbonyls R -C=O Straight Chain Hydrocarbons Branched Chain Hydrocarbons H Polar Ionizable Things: Carboxylic Acids R - C=O Bases (Amines) Hydrocarbons with Double Bonds O-H Hydrocarbon Rings R -N-H Phosphate O-H H - C – O-P=O Aromatic Rings O-H Functional Groups of Biological Molecules

14. alcohol The -SH is called a sulfhydryl group sulfhydryl SH Water-Loving Groups: Hydrophilic “thiol”

15. carbonyl R

16. acids H H R-N-H + H+ R-N-H H bases Can Dissociate To Ions Electron (-) Shared Carboxylic acid + .. amine

17. carbonyl Cannot Dissociate To ions R

18. alcohol The -SH is called a sulfhydryl group sulfhydryl SH Water-Loving Groups: Hydrophilic Cannot Dissociate To ions

19. Examples of weak acids and bases Acids Acetate ion Hydronium ion Bases + + Sometimes are ionized, sometimes are not

20. What determines whether acids & bases are ionized? pH !

21. Whether ACIDS and BASES are in the CHARGED IONIC FORM or the UNCHARGED MOLECULAR FORM is dependent on the pH THE CONCENTRATION OF H+ in the solution

22. Ionizable Functional Groups Acids Bases Carboxylic acid Amine R-CH2N-H HOH R-COOH H H R-COO-H+ R-CH2N-H + -OH H

23. LOW pH Ionizable Functional Groups (Lots of H+) Acids Bases H+ H H+ H+ Carboxylic acid Amine H+ H+ H+ H+ R-CH2N-H HOH R-COOH H+ H+ H+ H+ H H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H H+ R-COO-H+ H R-CH2N-H + -OH H+ H+ H+ H+ H+ H+ H H+ H+ H+ H+

24. Ionizable Functional Groups High pH Excess -OH Acids Bases -OH -OH Carboxylic acid Amine -OH R-CH2N-H HOH R-COOH -OH -OH -OH H -OH -OH -OH -OH H -OH -OH R-COO-H+ OH R-CH2N-H + -OH -OH -OH -OH H -OH

25. Ionizable Functional Groups Acids Bases 50% molecular form 50% molecular form Carboxylic acid Amine R-CH2N-H HOH R-COOH H Balance Point pH pKa Balance Point pH pKb H R-COO-H+ R-CH2N-H + -OH 50% Ionized form 50% Ionized form H

26. Ionizable Functional Groups Acids Bases Carboxylic acid Amine R-CH2N-H HOH R-COOH pKa Most organic Acids 3-to-5 pKb Most organic Acids 8-to-11 H H R-COO-H+ R-CH2N-H + -OH H

27. Ionizable Functional Groups pH 7.0 Acids Bases Carboxylic acid Amine pKa Most organic Acids 3-to-5 R-CH2N-H HOH R-COOH pKb Most organic Acids 8-to-11 H H R-COO-H+ R-CH2N-H + -OH H Dissociate to IONS

28. H+ = -OH If pH drops, acids can LOSE their ionic charge and revert to the molecular form bases stay ionized at low pH A lot of H+ If pH increases, Bases can LOSE their ionic charge and revert to the molecular form acids stay ionized at high pH Little H+ around neutral At the usual physiological pH = 7.0 most organic acids andbases are ionized CHARGED

29. Low pH COOH +NH3 Nonpolar guts +NH3 +NH3 COOH +NH3 Nonpolar guts EXPOSED! Nonpolar guts COOH +NH3 COOH Nonpolar guts Nonpolar guts COO- +NH3 Nonpolar guts

30. “oily” amines HIGH pH (few H+ around) LOW pH (a lot of H+ around) NH2-nonpolar +NH3-nonpolar Soluble in water Insoluble in water

31. Buffers • Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution ORGANIC ACIDS and ORGANIC BASES Act as good buffers When pH is near their pKa or pKb

32. Ionizable Functional Groups Acids Bases 50% molecular form 50% molecular form Carboxylic acid Amine R-CH2N-H HOH R-COOH H Balance Point pH pKa Balance Point pH pKb H R-COO-H+ R-CH2N-H + -OH 50% Ionized form 50% Ionized form H

33. Ionizable Acid “always charged” - - - - “portable” charges PHOSPHATE pKa3 ~ 13 pKa1 ~ 1 - R- - pKa2 ~ 7.0 Great buffer around pH 7 !

34. “Condensation dehydration” Functional Groups reactwith one another

35. Isomers • Are molecules with the same molecular formula but different structures and properties

36. H H H C H H C H H H H H H H (a) Structural isomers H C C C C C H H C H C C H H H H H H H H H X X X C C C C (b) Geometric isomers X H H H CO2H CO2H C C (c) Enantiomers H H NH2 NH2 CH3 CH3 Figure 4.7 A-C • Three types of isomers are • Structural • Geometric • Enantiomers (chrial, handed)

37. Many carbon compounds differ by SPATIAL GEOMETRY CANNOT Superimpose Carbon with 4 different functional groups Chiral or asymmetric carbon = “handed” carbon

38. Plane of symmetry Left handed “L” form Right handed “D” form Stereoisomers not the same

39. L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) D-glucose L-glucose Figure 4.8

40. Summary • Diversity of Carbon compounds • - length of chains • Branching • Double bonds • Conjugation of double bonds (aromatics) • Functional Groups • 2. Functional Groups • alcohols • sulfhydryls • carbonyls • Carboxylic acids • Amines • Phosphate • 3. Ionization, effect of pH • Carboxylic acids • Amines • Phosphate • 4. Buffers • 5. Isomers • Structural, geometric • Enantiomers (Chirality)