Carbon Chemistry, Functional Groups, Buffers

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

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Todays 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)
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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

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Hydrocarbons

• Hydrocarbons
• Are molecules consisting of only carbon and
  hydrogen

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methane

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

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• Carbon chains
• can branch

• Carbon chains
• can circularize
• Forms RINGS

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Different ways to illustrate carbon compounds
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• Carbon chains
• Form double bonds

• Conjugated
• Double Bonds
• (Shared)

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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
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Aromatic Ring Systems
Left the H atoms Out for simplicity
A series of double bonds in a ring Conjugated Sp
ecial properties
C
C
C
C
C
C
Aromatic Ring
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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
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Carbon is special Covalently bonds With a number
of different elements

• Most Commonly
• H
• C
• O
• N
• S

Functional Groups
Reactive Entities
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Functional Groups of Biological Molecules
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Water-Loving Groups
Hydrophilic
thiol
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R
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Can Dissociate To Ions
Electron (-) Shared
Carboxylic acid

..
amine
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Cannot Dissociate To ions
R
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Water-Loving Groups
Hydrophilic
Cannot Dissociate To ions
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Examples of weak acids and bases
Acids
Acetate ion
Hydronium ion
Bases


Sometimes are ionized, sometimes are not
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What determines whether acids bases are
ionized?
pH !
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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
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Ionizable Functional Groups
Acids
Bases
Carboxylic acid Amine
R-CH2N-H
HOH
R-COOH
H
H
R-COO- H
R-CH2N-H
-OH

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

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

50 Ionized form
50 Ionized form
H
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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
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Ionizable Functional Groups
pH 7.0
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
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H -OH
neutral
At the usual physiological pH 7.0 most
organic acids and bases are ionized CHARGED
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Low pH
COO-
NH3
Nonpolar guts
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oily amines
HIGH pH (few H around)
LOW pH (a lot of H around)
NH2-nonpolar
NH3-nonpolar
Soluble in water
Insoluble in water
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• 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
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Ionizable Functional Groups
Acids
Bases
50 molecular form
50 molecular form
Carboxylic acid Amine
R-CH2N-H
HOH
R-COOH
H
Balance Point pH pKa
Balance Point pH pKb
H
R-COO- H
R-CH2N-H
-OH

50 Ionized form
50 Ionized form
H
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PHOSPHATE
pKa3 13
pKa1 1
-
R-
-
pKa2 7.0
Great buffer around pH 7 !
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Functional Groups react with one another
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• Isomers
• Are molecules with the same molecular formula but
  different structures and properties

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

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Many carbon compounds differ by SPATIAL GEOMETRY
CANNOT Superimpose
Carbon with 4 different functional groups
Chiral or asymmetric carbon handed carbon
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Plane of symmetry
Left handed L form
Right handed D form
Stereoisomers not the same
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• 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
• Carboxylic acids
• Amines
• Phosphate