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

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)

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

Hydrocarbons Hydrocarbons Are molecules consisting of only carbon and hydrogen

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

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

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

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

A series of double bonds 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”

A series of double bonds 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

A series of double bonds 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

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

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

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

carbonyl R

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

Cannot Dissociate To ions carbonyl R

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

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

What determines whether acids & bases are ionized? pH !

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

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

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

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

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

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

pH 7.0 Ionizable Functional Groups R-CH2N-H HOH R-COOH H H R-COO- H+ 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

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

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

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

ORGANIC ACIDS and ORGANIC BASES When pH is near their pKa or pKb 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

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

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

Functional Groups react with one another “Condensation dehydration”

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

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

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

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

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

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 4. Buffers 5. Isomers Structural, geometric Enantiomers (Chirality)