Lecture 4Carbon Chemistry, Functional Groups, Buffers

9/7/05

Today’s Topics

Diversity of Carbon CompoundsTypes of Functional Groups, propertiesProperties of Carboxylic Acids and Organic BasesAffect of pH on Protein StructureBuffersChirality (Handedness)

Carbon ( Carbon ( CC ) )

most important atom in biological moleculesmost important atom in biological molecules

Valence of 4 – diversity & stabilityValence of 4 – diversity & stability

• Covalent bonds – O, N, S, HCovalent bonds – O, N, S, H

• Single, double, triple bondsSingle, double, triple bonds•Conjugated double bonds & aromaticsConjugated double bonds & aromatics

• C-C bonds are Very Stable can make “limitless” chains

• Carbon chains can “branch”

Hydrocarbons

• Hydrocarbons– Are molecules consisting of only carbon and

hydrogen

methanemethane

2 carbons2 carbons ethaneethane

3 carbons3 carbons propanepropane

• C-C bonds are Very Stable can make “limitless” chains

CH3

14 carbonhydrocarbon

H

HH

H

H

H H H

H

H

H

H H H

H H H

H H

H

H

H

H

H

H

H

H

H

H H H H

H H

H H

H H H H

H H

H H

H

H

H

HH

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

C

C

C

C

C

C

CC

C

C

C

H

H

H

H

H

H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane(commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene

H H H HH

Figure 4.5 A-D

• Carbon chains can “branch”

• Carbon chains can “circularize”Forms RINGS

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model Space-Filling

Model

H

H

H

H

H

H

H

H

H

H

H H

HH

C

C C

C C

CH4

C2H6

C2H4

Name and Comments

Figure 4.3 A-C

Different ways to illustrate carbon Different ways to illustrate carbon compoundscompounds

H

HH

H

H

H H H

H

H

H

H H H

H H H

H H

H

H

H

H

H

H

H

H

H

H H H H

H H

H H

H H H H

H H

H H

H

H

H

HH

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

C

C

C

C

C

C

CC

C

C

C

H

H

H

H

H

H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane(commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene

H H H HH

Figure 4.5 A-D

• Carbon chains Form double bonds

•ConjugatedConjugatedDouble BondsDouble Bonds

(Shared)(Shared)

C

C

H

C

H

C

Conjugated Double Bonds

A series of double bonds

Very stable

Sharing electrons Through all 4 carbons

H H

HH

“delocalized electrons”

ConjugateConjugatedd

C

C

C

C

C

C

Aromatic Ring Systems

A series of double bondsin a ring

Conjugated

Special properties

Left theH atomsOut forsimplicity

Aromatic RingAromatic Ring

C

C

C

C

C

C

Aromatic Ring Systems

A series of double bonds

Conjugated

Left theH atomsOut forsimplicity

Extremely stableFlat

Hydrophobic

Tolerates “excitement ” of electrons

Carbon is specialCovalently bondsWith a number of differentelements

C

H

H

H C

H

O H

H

even long chains with a variety of different atoms

H C C C=C C C=O

O

NH

H H

HH H H H

H H

Most Commonly-H-C-O-N-S

FunctionalFunctionalGroupsGroups

ReactiveReactiveEntitiesEntities

Functional Groups of Biological Molecules

Hydrophobic

Straight Chain Hydrocarbons

Branched Chain Hydrocarbons

Hydrocarbons with Double Bonds

Hydrocarbon Rings

Aromatic Rings

HydrophilicPolar 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-HHPhosphate

- C – O-P=O

O-H

O-H

Water-Loving Groups: Water-Loving Groups: HydrophilicHydrophilic

alcoholalcohol

sulfhydrylsulfhydryl SSHHThe -SH is called The -SH is called a a sulfhydryl sulfhydryl groupgroup

“thiol”

carbonylcarbonyl RR

basesbases H HH HR-N-H + HR-N-H + H++ R-N-H R-N-H

HH

acidsacids

amineamine

++

Carboxylic acidCarboxylic acid

Electron (-)Shared

..

Can DissociateCan DissociateTo IonsTo Ions

carbonylcarbonyl RR

CannotCannotDissociateDissociate

To ionsTo ions

Water-Loving Groups: Water-Loving Groups: HydrophilicHydrophilic

alcoholalcohol

sulfhydrylsulfhydryl SSHHThe -SH is called The -SH is called a a sulfhydryl sulfhydryl groupgroup

CannotCannotDissociateDissociate

To ionsTo ions

Examples of weak acids and basesExamples of weak acids and bases

AcidsAcids

BasesBases

Sometimes are ionized, sometimes are notSometimes are ionized, sometimes are not

Acetate Acetate ionion

HydroniumHydroniumionion

++ ++

What determines whether acids &What determines whether acids &bases are ionized? bases are ionized?

pH !pH !

Whether ACIDS and BASES are in the

CHARGED IONIC FORMor the

UNCHARGED MOLECULAR FORM

is dependent on the pH

THE CONCENTRATION OF H+

in the solution

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OH

H

+

H+

H+

H+H+

H+

H+

H+

H+H+

H

H+

H+

H+H+H+

H+

H+

H+

H+H+

H+H

H+H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

LOW pH

(Lots of H(Lots of H++))

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

High pH High pH Excess -Excess -OHOH

-OH-OH

-OH-OH

-OH-OH

-OH-OH

-OH-OH

-OH-OH

-OH-OH

OHOH-OH-OH

-OH-OH -OH-OH

-OH-OH-OH-OH -OH-OH

-OH-OH

-OH-OH

-OH-OH

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

Balance Point pH

pKa

Balance Point pH

pKb

50% molecular

form

50% Ionized

form50%

Ionized form

50% molecular

form

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

pKaMost

organicAcids

3-to-5

pKbMost

organicAcids

8-to-11

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

Dissociate to IONS

pH 7.0pH 7.0

pKaMost

organicAcids

3-to-5

pKbMost

organicAcids

8-to-11

At the At the usualusual physiological physiological pH = 7.0pH = 7.0 most organic most organic acids acids andand basesbases are ionized are ionized

CHARGEDCHARGED

A lot A lot of Hof H++

If If pH dropspH drops, , acidsacids can can LOSE LOSE their ionic their ionic charge and revert to the molecular formcharge and revert to the molecular formbasesbases stay ionized at low pH stay ionized at low pH

LittleLittle HH++ aroundaround

If If pH increasespH increases, , BasesBases can can LOSE LOSE their ionic their ionic charge and revert to the molecular formcharge and revert to the molecular formacidsacids stay ionized at high pH stay ionized at high pH

neutralneutralHH++ = = --OHOH

Nonpolar gutsNonpolar guts

COO- +NH3

Nonpolar gutsNonpolar guts

COOH +NH3

COOH

+NH3Nonpolar gutsNonpolar gutsEXPOSED!EXPOSED!

COOH

+NH3

Nonpolar gutsNonpolar guts

+ NH 3

Non

pola

r gut

s

Non

pola

r gut

sCOOH

+NH3

Nonpolar guts Nonpolar guts

Low pHLow pH

“oily” amines

HIGH pH (few H+ around)

LOW pH (a lot of H+ around)

NH2-nonpolar +NH3-nonpolar

Insoluble in water Soluble in water

• Buffers– Are substances that minimize changes in the

concentrations of hydrogen and hydroxide ions in a solution

ORGANIC ACIDS and ORGANIC BASESAct as good buffers

When pH is near their pKa or pKb

Ionizable Functional Groups

AcidsAcids BasesBases

R-COOH

Carboxylic acid Amine

R-CH2N-H

H

HOH

R-COO- H+R-CH2N-H

H

-OHH

+

Balance Point pH

pKa

Balance Point pH

pKb

50% molecular

form

50% Ionized

form50%

Ionized form

50% molecular

form

PHOSPHATEPHOSPHATE

Ionizable AcidIonizable Acid

““always charged”always charged”--

--

““portable” chargesportable” charges

------

--

pKa1 ~ 1

pKa2 ~ 7.0 Great buffer around pH 7 !

pKa3 ~ 13

R-

Functional GroupsFunctional Groupsreactreact with one another with one another

““CondensationCondensationdehydration”dehydration”

• Isomers– Are molecules with the same

molecular formula but different structures and properties

H H H H H

H

H H H H H

H

H

HH

H

H

H

H

H

H

H

HH

H

H

H

H

CO2H

CH3

NH2

C

CO2H

H

CH3

NH2

X X

X

X

C C C C C

C

C

C C C

C C C C

C

(a) Structural isomers

(b) Geometric isomers

(c) Enantiomers

H

• Three types of isomers are– Structural– Geometric– Enantiomers (chrial, handed)

Carbon with Carbon with 4 different functional groups 4 different functional groups

Chiral or asymmetric carbonChiral or asymmetric carbon = = “handed” carbon“handed” carbon

Many carbon compoundsMany carbon compounds differ by differ by SPATIAL GEOMETRYSPATIAL GEOMETRY

CANNOTCANNOTSuperimposeSuperimpose

RightRighthandedhanded

““D” formD” form

LeftLefthandedhanded

““L” formL” form

Stereoisomers Stereoisomers not the same not the same

Plane Plane of of

symmetrysymmetry

L-Dopa

(effective against Parkinson’s disease)

D-Dopa

(biologically inactive)Figure 4.8

D-glucoseL-glucose

Summary

1. 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. Buffers5. Isomers

- Structural, geometric- Enantiomers (Chirality)