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. 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

6. (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

7. 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

8. (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)

9. 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”

10. 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

11. 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

12. 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

13. 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

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

15. carbonyl R

16. + 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

17. Cannot
Dissociate
To ions
carbonyl R

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

19. Examples of weak acids and bases
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. 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+

24. 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

25. 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

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. 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

28. 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

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

30. 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

31. 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

32. 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

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

34. Functional Groups
react with one another
“Condensation
dehydration”

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

36. (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

37. 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

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

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

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