Biochemistry 3070

Amino Acids
&
Proteins

Biochemistry 3070 – Amino Acids & Proteins 1

 Biochemistry 3070

Learning Objectives:
1. Point out amino acids as building blocks of proteins;

2. Draw the general type of formula of amino acids;

3. Illustrate optical isomerism of amino acids;

4. Classify amino acids based on their R groups and

give interactions associated with R-groups;

5. Explain the acid-base behavior of amino acids and

their importance;

6. Calculate pH of amino acids and indicate the charge

of amino acids and proteins and explain the principle
behind the methods.
Biochemistry 3070 – Amino Acids & Proteins 2
 Biochemistry 3070

Outline:
A. Amino acid structure
B. Acid- base Properties of Amino acids
C. Classification of Amino acids
D. How amino acid are linked together

Biochemistry 3070 – Amino Acids & Proteins 3

 • Proteins are linear copolymers built from
monomeric units called amino acids - C,H,O,N
(S)
• Twenty amino acids are commonly found in
proteins also known as “STANDARD AMINO
ACID”
– Nonpolar
– Polar neutral
– Polar acidic
– Polar basic

Biochemistry 3070 – Amino Acids & Proteins 4

 • These amino acids contain a variety of different
functional groups:
– Alcohols (R-OH)
– Phenols (Ph-OH)
– Carboxylic acids (R-COOH)
– Thiols (R-SH)
– Amines (R-NH2)
– and others…

Biochemistry 3070 – Amino Acids & Proteins 5

 • Protein function depends on both
– amino acid content, and
– amino acid sequence.
• Protein fold into diverse shapes such as
– spherical
– elipsoidal
– long strands, etc.
• All information for 3-D structure is
contained in the linear sequence of amino
acids.

Biochemistry 3070 – Amino Acids & Proteins 6

Biochemistry 3070 – Amino Acids & Proteins 7
 • To understand protein function, we must first
understand the nature of amino acids.
• Amino acids are essentially α-amino acids:
alpha carbon (IUPAC #2 position)

H2N – C – COOH
|
R

• When R is not H, the alpha carbon is

asymmetric, giving rise to isomers.
Biochemistry 3070 – Amino Acids & Proteins 8
 • To understand protein function, we must first
understand the nature of amino acids.
• Amino acids are essentially α-amino acids:
alpha carbon (IUPAC #2 position)

H2N – C – COOH
|
R

• When R is not H, the alpha carbon

is asymmetric, giving rise to isomers.
Biochemistry 3070 – Amino Acids & Proteins 9
 • To understand protein function, we must first understand
the nature of amino acids.
• Amino acids are essentially α-amino acids:
alpha carbon (IUPAC #2 position)

H2N – C – COOH
|
R

• When R is not H, the alpha carbon is asymmetric,

giving rise to isomers.
• R group/ variable group – defines the chemical nature
Biochemistry 3070 – Amino Acids & Proteins 10
 Only L-amino acids are constituents of proteins.

“L” and “D” isomeric nomenclature is similar to the

“R” and “S” utilized in modern organic chemistry.
Biochemistry 3070 – Amino Acids & Proteins 11
 • Amino acids have an acidic group (-
COOH) and a basic group (-NH2) on the
same alpha-carbon atom.
• Amino acid are amphoteric

Biochemistry 3070 – Amino Acids & Proteins 12

 • Carboxylic acids are traditional Bronsted-Lowery acids,
donating a proton in aqueous solution.
• The pKa for carboxylic acids is normally around 2 to 5.
That is, the pH at which these acids are 50% ionized:

R-COOH  R-COO- + H+

pH= [less than 2]  [above 5]

Biochemistry 3070 – Amino Acids & Proteins 13

 • Amino groups function as bases, accepting a proton.
• The pKa for amino groups is usually around 9 – 10.
Again, at the pKa these groups are 50% ionized:

R-NH3+  R-NH2 + H+

pH= [below 8]  [above 9]

Biochemistry 3070 – Amino Acids & Proteins 14

 • Even though both acids and amines are present in the
same molecule, they mostly behave as though they were
separate entities:

Biochemistry 3070 – Amino Acids & Proteins 15

Biochemistry 3070 – Amino Acids & Proteins 16
 • Summary:
At low pH, proton concentration [H+]is high. Therefore,
both amines and carboxylic acids are protonated. (-NH3+
& -COOH)
At high pH, proton concentration is low. Therefore, both
amines and carboxylic acids are deprotonated. (-NH2 & -
COO-)
At neutral pH, amines are protonated(-NH3+) and
carboxylates are deprotonated(-COO-)

Biochemistry 3070 – Amino Acids & Proteins 17

 • Carboxylic acids are traditional Bronsted-Lowery acids,
donating a proton in aqueous solution.
• The pKa for carboxylic acids is normally around 2 to 5.
That is, the pH at which these acids are 50% ionized:

R-COOH  R-COO- + H+

pH= [less than 2]  [above 5]

Biochemistry 3070 – Amino Acids & Proteins 18

 • Amino groups function as bases, accepting a proton.
• The pKa for amino groups is usually around 9 – 10.
Again, at the pKa these groups are 50% ionized:

R-NH3+  R-NH2 + H+

pH= [below 8]  [above 9]

Biochemistry 3070 – Amino Acids & Proteins 19

 • Even though both acids and amines are present in the
same molecule, they mostly behave as though they were
separate entities:

Biochemistry 3070 – Amino Acids & Proteins 20

Biochemistry 3070 – Amino Acids & Proteins 21
 • Summary:
At low pH, proton concentration [H+]is high. Therefore,
both amines and carboxylic acids are protonated. (-NH3+
& -COOH)
At high pH, proton concentration is low. Therefore, both
amines and carboxylic acids are deprotonated. (-NH2 & -
COO-)
At neutral pH, amines are protonated(-NH3+) and
carboxylates are deprotonated(-COO-)

Biochemistry 3070 – Amino Acids & Proteins 22

 • “Zwitter” Ions:
• A molecule having a positive charge on an atom, a
negative charge on a different atom, and no net charge.

Amino acid occur as neutral on

both solid and in neutral solutions.

Biochemistry 3070 – Amino Acids & Proteins 23

 • “Zwitter” Ions:
• Ions bearing two charges were named zwitter ions by
German scientists; the name still applies today,
especially for amino acids at neutral pH:

+H N – CH2 – COO-
3

Biochemistry 3070 – Amino Acids & Proteins 24

 Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1:

pH=7:

pH=12:

Biochemistry 3070 – Amino Acids & Proteins 25

 Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1: +H N
3 – CH2 - COOH

pH=7:

pH=12:

Biochemistry 3070 – Amino Acids & Proteins 26

 Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1: +H N
3 – CH2 - COOH

pH=7: +H N
3 – CH2 – COO-

pH=12:

Biochemistry 3070 – Amino Acids & Proteins 27

 • Amino acid Proline
(The only secondary (2°) amino acid or (“imino” acid.)

Biochemistry 3070 – Amino Acids & Proteins 28

 • Amino acids (Polar - Alcohols)

Biochemistry 3070 – Amino Acids & Proteins 29

 • Amino acids (Sulfur)

cystine

Biochemistry 3070 – Amino Acids & Proteins 30

 • Amino acids (Polar: Acids and related amides)

Biochemistry 3070 – Amino Acids & Proteins 31

 • Amino acids (Polar: Basic)

Biochemistry 3070 – Amino Acids & Proteins 32

 • Histidine (Acid/Base Activity)

Biochemistry 3070 – Amino Acids & Proteins 33

Biochemistry 3070 – Amino Acids & Proteins 34
Biochemistry 3070 – Amino Acids & Proteins 35
 Essential Amino Acids: Codes (three-/one-letter)
Arginine b Arg R

Histidine b His H

Isoleucine Ile I
Leucine Leu L
Lysine Lys K
Methionine Met M
Phenylalanine a Phe F

Threonine Thr T
Tryptophan a Trp W

Valine Val V
a Aromatic b Probably essential

Biochemistry 3070 – Amino Acids & Proteins 36

 The two types of protein-energy
malnutrition

Biochemistry 3070 – Amino Acids & Proteins 37

 The two types of protein-energy
malnutrition

Biochemistry 3070 – Amino Acids & Proteins 38

 The two types of protein-energy
malnutrition

• Kwashiorkor is a Ghanaian
word that means "the disease that
the first child gets when the new
child comes"
• characteristic symptom
• = swollen abdomen
• Energy intake could be adequate,
but protein consumption is too low.

Biochemistry 3070 – Amino Acids & Proteins 39

 The two types of protein-energy
malnutrition

• Marasmus means "to waste

away" or "dying away", and thus
occurs in individuals who have
severely limited energy intakes.

Biochemistry 3070 – Amino Acids & Proteins 40

 The two types of protein-energy
malnutrition

Biochemistry 3070 – Amino Acids & Proteins 41