Carbon Chemistry, Functional

Groups, & Buffers

Todays Topics
Finish Buffers
Carbon Chains and Functional
Groups
Properties of Acids and Bases
Isomers

Carbon

First
shell

Second
shell

Third
shell

Macromolecules:

Helium
2He

Hydrogen
1H
Lithium
3Li

Beryllium
4Be

Boron
3B

Sodium Magnesium Aluminum

13Al
11Na
12Mg

Carbon
6C

Nitrogen
7N

Silicon
14Si

Phosphorus
15P

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

09/09/11

Carbohydrates

Valence of 4
Diversity and Stability
Name and
Comments

Molecular
Formula

Structural
Formula

Ball-and-Stick
Model

Space-Filling
Model

(a) Methane

CH4

(b) Ethane

Can form chains

or

branched chains

or

C 2H 6

rings

C H

(c) Ethene
(ethylene)

See Figure 4.5

C 2H 4

H
C C

Carbon can form covalent bonds

with many different elements

Hydrocarbons
contain only carbon and hydrogen

H3C

CH2

CH2

CH2

CH2

CH2

CH2

C-C bonds are very stable-can make very long chains

CH2

CH2

CH3

First
shell

Second
shell

Third
shell

Helium
2He

Hydrogen
1H
Lithium
3Li

Beryllium
4Be

Boron
3B

Sodium Magnesium Aluminum

13Al
11Na
12Mg

Carbon
6C

Nitrogen
7N

Silicon
14Si

Phosphorus
15P

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Fig. 4-9

Functional Groups determine the

biological properties

Types of Functional Groups

Hydrophobic

Estradiol!

Hydrophilic
Polar things

Straight-chain
hydrocarbons
Branched-chain
hydrocarbons
Hydrocarbons with
double bonds
Hydrocarbon rings
Aromatic rings

Testosterone!

Alcohols
Sulfhydryls
Carbonyl (aldehydes,
ketones)

Polar Ionizable Things

Carboxylic Acids
Bases (amines)
Phosphate

Many sizes and

shapes, but all are
hydrocarbons

Know the functional groups in Fig. 4.10,

page 64-65

R-OH
R-SH
R-C=O
R-COOH
R-NH2
R-PO4
R-CH3

hydroxyl
sulfhydryl
carbonyl
carboxyl
amino
phosphate
methyl

pKa3 ~ 13

R-COOH

R-CH2N-H
H

Most
organic
Acids

3 to 5

R-COO-

H+

H
+
R-CH2N-H

pKa1 ~ 1

R-

Amine

pKa

hydroxyl
sulfhydryl
carbonyl
carboxyl
amino
phosphate
methyl

Each has a
balance point

Ionizable Functional Groups

Carboxylic acid

R-OH
R-SH
R-C=O
R-COOH
R-NH2
R-PO4
R-CH3

HOH
pKb

Most
organic
Acids

pKa2 ~ 7.0

In a cell its always charged

(PO4-)

Useful buffer around pH 7

8 to 11

-OH

Oily Amines in fish

Isomers are molecules with the same

(a) Structural isomers

Structural

cadaverine

High pH
Little H+
NH2 molecular form
insoluble

Low pH
Lots of H+
NH3+, ionized
soluble

H
CO2H

(c) Enantiomers

CO2H

Enantiomers

Geometric

X
C

(b) Geometric isomers

putrescine

molecular formula but different structures and

H H H H H
properties

C
NH2

NH2

CH3

CH3

Figure 4.7 A-C

Isomers can have very different effects

Macromolecules
Carvone
Caroway
Spearmint

Carbohydrates
Lipids
Proteins
Nucleic Acids

Ibuprofen

Figure 5.2

Figure 5.2

1
Unlinked monomer

Dehydration
Synthesis

make by
taking water
away

Hydrolysis

Longer polymer

3
Unlinked monomer

Dehydration
Synthesis

make by
taking water
away

Longer polymer

Hydrolysis

Split by water

Split by water
1

Monosaccharides vary in Length and

Geometry
Triose sugars
(C3H6O3)

Pentose sugars
(C5H10O5)

H
C

Aldoses

Hexose sugars
(C6H12O6)

OH

OH

OH

OH

HO

OH

OH

OH

OH

Ribose

H
H

OH

OH

HO

OH

HO

OH

OH

Glucose

Galactose

H
H

C OH
C

H
H

C OH
C

C OH

C OH

HO

C OH

C OH

C OH

Dihydroxyacetone

Glyceraldehyde

Ketoses

5 and 6 Carbon Sugars CIRCULARIZE in Water

To FORM RINGS

C H
C OH
C OH
C OH

Ribulose

Figure 5.3

Fructose

Simple sugars can be coupled together by

Dehydration Synthesis
CH2OH

CH2OH
H
Glucose + GlucoseHO
= Maltose

O
H
OH H
H

H
OH

HO

O
H
OH
H

OH

CH2OH
H
OHOH

H
HO

O
H
OH H

CH2OH
H

1 4
1 glycosidic
linkage

H
4

O
H
OH H

10 !m

OH

O
H

OH

Polysaccharides

OH

0.5 !m

OH

H 2O
Glucose

Glucose

CH2OH
H

O
H
OH

HO
Glucose + Fructose

CH2OH
H
OH

HO

HO
CH2OH

OH

OH

Maltose

CH2OH

H
OH

O
H

HO
H

12
1 glycosidic
linkage

Glucose

Fructose

HO
CH2OH

OH H

OH

H 2O

= Sucrose

CH2OH
O
2

Sucrose

E.g. Cellulose

Figure 5.5

! Glucose
monomer!

Fig. 5-8

Fig. 5-7bc

Some Modified Sugars:

Missing one or more components:

Deoxyribose
missing one alcohol

Glycerol -

H H H

3 Carbon Sugar with alcohol in

place of an aldehyde

H-C-C-C-H
- OH
- OH
- OH