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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 ) - PowerPoint PPT Presentation
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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)
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