PROTEINS AND AMINO ACIDS

Amino Acids
Amino acids
• Are the building blocks of proteins.
• Contain a carboxylic acid group and an amino
group on the alpha () carbon.
• Are ionized in solution.
• Each contain a different side group (R).

R R
│ + │
H2N—C —COOH H3N—C —COO−
│ │
H H
ionized form 2
Proteins are
macromolecules or COOH COOH
high polymers made NH2 C H H C NH2
up of amino acids
joined together by R R
peptidebonds. The
type formula of an
L-amino acid D-amino acid
amino acid as shown
emphasizes the
By convention if the amino group is on
basic functional the right, they are called D- amino acid
group. and L- amino acids if the NH2 is on the
left.
 Functions of Proteins
• Proteins perform many different functions in
TABLE 19.1
the body.

4
 Examples of Amino Acids
H
+ │
H3N—C—COO−
│
H glycine

CH3
+ │
H3N—C—COO−
│
H alanine

5
 Nomenclature of amino acids

• 1. usual practice is to use common names

• trivial names usually reflect the source or
• Property of the amino acid

Aspargine – first isolated from asparagus juice

Glycine – glykis- means sweet

Designations of amino acids - standard three letter abbreviations

Glycine - gly

Alanine – ala

Valine - val
• By convention if the amino group is on the
right, they are called D- amino acid and L-
amino acids if the NH2 is on the left.
• The following table gives the names and
structures of 26 amino acids that have been
found in proteins. Those with asterisk are
essential amino acids which must be fed to
young animals and man if proper growth is to
take place.
 Types of Amino Acids
Amino acids are classified Nonpolar Polar
as
• Nonpolar (hydrophobic)
with hydrocarbon side
chains.
• Polar (hydrophilic) with Acidic Basic
polar or ionic side
chains.
• Acidic (hydrophilic) with
acidic side chains.
• Basic (hydrophilic) with
–NH2 side chains. Copyright © 2007 by Pearson Education, Inc.
Publishing as Benjamin Cummings
9
 Nonpolar Amino Acids
A nonpolar amino acid has
• An R group that is H, an alkyl group, or
aromatic.

Copyright © 2007 by Pearson Education, Inc. 10

Publishing as Benjamin Cummings
 Polar Amino Acids
A polar amino acid has
• An R group that is an alcohol, thiol, or amide.

Copyright © 2007 by Pearson Education, Inc.

Publishing as Benjamin Cummings 11
 Acidic and Basic Amino Acids
An amino acid is
• Acidic with a carboxyl R group (COO−).
• Basic with an amino R group (NH3+). Basic Amino Acids

Copyright © 2007 by Pearson Education, Inc.

Publishing as Benjamin Cummings
12
 Learning Check
Identify each as (P) polar or (NP) nonpolar.
+
A. H3N–CH2–COO− (Glycine)

CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine)

13
 Solution
Identify each as (P) polar or (NP) nonpolar.
+
A. H3N–CH2–COO− (Glycine) (NP) nonpolar

CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine) (P) polar

14
 Properties of amino acids
1. Optical activity – except for glycine most amino
acids have 4 different groups attached to the
alpha carbon. Thus having asymmetric C they
have the ability to rotate PPL to the left or to the
right.
2. Amphoteric Property
In solution amino acids may exist as dipolar ionic
structures called zwitterion . The ability of
amino acids to act as an acid or a base is called
amphoteric property.
 Fischer Projections of Amino Acids
Amino acids
• Are chiral except for glycine.
• Have Fischer projections that are stereoisomers.
• That are L are used in proteins.

COOH COOH COOH COOH

H2N H H NH2 H2N H H NH2
CH3 CH3 CH2SH CH2SH

L-alanine D-alanine L-cysteine D-cysteine

16
The pH at which there is an equal number of positively
charged NH3+ and negatively charged COO- is called
isoelectric point (PI)
R
NH 2 C C OOH
H

internal acid base reaction

R
+ -
H3N C C OO
H

zwitterion

pH < 7 ( acidic) H+
pH > 7 ( basic) OH-
R
+
R H3N C C OOH
- H
NH 2 C C OO
H cationic
anionic
Zwitterions and Isoelectric Points
A zwitterion
• Has charged —NH3+ and COO- groups.
• Forms when both the —NH2 and the —COOH
groups in an amino acid ionize in water.
• Has equal + and − charges at the isoelectric
point (pI).

O O
║ + ║
NH2—CH2—C—OH H3N—CH2—C—O–
Glycine Zwitterion of glycine

18
 Amino Acids as Acids
In solutions more basic than the pI,
• The —NH3+ in the amino acid donates a
proton.

+ OH–
H3N—CH2—COO– H2N—CH2—COO–
Zwitterion Negative ion
at pI pH > pI
Charge: 0 Charge: 1−

19
 Amino Acids as Bases
In solutions more acidic than the pI,
• The COO− in the amino acid accepts a proton.

+ H+ +
H3N—CH2—COO– H3N—CH2—COOH
Zwitterion Positive ion
at pI pH< pI
Charge: 0 Charge: 1+

20
 Learning Check
CH3 CH3
+ | |
H3N—CH—COOH H2N—CH—COO–
(1) (2)
Which structure represents:
A. Alanine at a pH above its pI?
B. Alanine at a pH below its pI?

21
 Solution
CH3 CH3
+ | |
H3N—CH—COOH H2N—CH—COO–
(1) (2)
Which structure represents:
A. Alanine at a pH above its pI? (2)
B. Alanine at a pH below its pI? (1)

22
 Reactions of Amino Acid

For analytical purposes H For formation of peptide bonds

NH2 C C OOH Proteins are produced

For IMFA
: organizations of proteins
 NH2 group : are important for analytical purposes

1) reactions with HNO2

H H
NH2 C C OOH HNO2 HO C C OOH H2O N2
R R

1o amino Van S lyke: estimates the # of 1o alpha amino

groups in amino acids, peptides
2) Ninhydrin : produces a purple complex dye with 1o amines that have alpha H
attached to the C arbon holding the -NH 2 group . ( H-C - NH2)

C =O H
C OH
+ NH2 C C OOH purple dye
C OH
R
O

3. Sanger’s reagent : 1o amino group of amino acid react with 2,4 dinitrofluoro benzene
(DNFB) Sanger’s reagent to yield a yellow product.
2) Reactions of R group : f

Involves interactions and cross links between different parts of

the peptide chain such as

Hydrophobic and hydrophilic interactions.

Salt bridges.
Hydrogen bonds.
Disulfide bonds.

H H
H H
NH2 C COOH NH2 C COOH
NH2 C COOH NH2 C COOH
CH2 S H HS CH2
CH2 S S CH2
 H H
H H
NH2 C C OOH NH2 C C OOH
NH2 C C OOH NH2 C C OOH
C H2 S H HS C H2
C H2 S S C H2

The presence of disulfide bonds has a direct effect on the shape of the molecule which
In turn determines whether the molecule will function biologically

For example, ribonuclease has 4 disulfide bonds . If any one is broken , the
shape of the
Molecule is changed and the catalytic function is lost

The disulfide bonds can easily be broken with a reducing agent to bring back the
S_H groups.
Agents of denaturation
1. heat

2. urea Being amide like disrupts H

bond
3. mecapthoethanol Disrupts disulfides bonds

4. UV

5. Polar organic solvent 70 % alcohol

6. Strong acids and bases

7. detergents

8. Heavy metals

9. Violent agitation

10. Alkaloidal reagents Tannic acid, picric acid