Amino Acids : an

introduction
Likando Chababa
 Amino Acids

•What are amino acids?

•Structure
•Types
•Peptide bond
•Non-standard amino acids

•Derivatives of amino acids

 What are amino acids?
 Amino acids are composed of C,
carboxylic group, amino group, a side
chain (R)
 Side chain groups (R) are variable
 Building blocks of proteins
 Amino acids are joined together by
peptide bond like a chain in a protein
 Amino acids can act as both acid and
base
Voet Biochemistry 3e Page 65
© 2004 John Wiley & Sons, Inc.

General structural formula for -amino acids

 There are 20 “standard” amino acids
present in proteins
 The amino and carboxylic groups of
aa can ionize
Voet Biochemistry 3e Page 65
© 2004 John Wiley & Sons, Inc.
 Isoelectric Point
 The pH at which the molecule carries
no net charge
 In acidic solution-cationic
 In alkaline solution- anionic
 pK Value
 It is the ability of an acid to donate a
proton (dissociate)
 Also known as pKa or acid
dissociation constant
 The pK values of -carboxylic group
is in the range of 2.2
 The pK values of -amino group is in
the range of 9.4
 pK1- The pH at which
50% of molecules are in
cation form and 50% are
in zwitterion form

pK2- The pH at which

50% of molecules are in
anion form and 50% are in
zwitterion form

Buffering action is
maximum around pK
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e Page 70

values and minimum at pI

Titration curve of glycine

 Zwitterions
 An amino acid contains both:
 Basic amino group and

 Acidic carboxylic group

 Creating a negative and a positive charge

 Amino groups are protonated
 Carboxylic groups are unprotonated
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e Page 65

Zwitterionic form of the -amino acids that occur at physiological pH

values
 An amino acid can therefore act as
both an acid and a base
 At physiological pH, amino acids
contain both positive and negative
charges with a net charge of zero
 Equal number of positive and
negative charges
 Types
 There are 20 “standard” amino acids
found in proteins
 All have C, carboxylic and amino
groups
 All have different side chains (R
groups)
 Three major types of amino acids:
Nonpolar

Uncharged polar

Charged polar
 Nonpolar:
Glycine Alanine
Valine Leucine
Isoleucine Methionine
Proline Phenylalanine
Tryptophan
 Proline
 It is an imino acid
 It has a secondary amino group
Voet Biochemistry 3e Page 66
© 2004 John Wiley & Sons, Inc.

side chains
Amino acids
with nonpolar
 Uncharged polar:
Serine Threonine
Asparagine Glutamine
Tyrosine Cysteine
Voet Biochemistry 3e Page 67
© 2004 John Wiley & Sons, Inc.

with

chains
polar side
uncharged
Amino acids
 Charged polar:
Lysine, Arginine

Aspartic acid, Glutamic acid

Histidine
Voet Biochemistry 3e Page 67
© 2004 John Wiley & Sons, Inc.

Amino acids with charged polar side chains

 Peptide bond
 Amino acids can be polymerized to
form chains
 Polymers are composed of two, three,
few (3-10) or more amino acids
known as dipeptides, tripeptides,
oligopeptides or polypeptides
Voet Biochemistry 3e Page 68
© 2004 John Wiley & Sons, Inc.

Condensation of two -amino acids to form a dipeptide

 Amino acids are joined together in a
chain by peptide bond [CO–NH
linkage]
 Known as peptide bond
 Each amino acid in a chain makes
two peptide bonds
Voet Biochemistry 3e Page 68
© 2004 John Wiley & Sons, Inc.

Condensation of two -amino acids to form a dipeptide

 The amino acids at the two ends of a
chain make only one peptide bond
 The aa with a free amino group is
called amino terminus or N-terminus
 The aa with a free carboxylic group is
called carboxyl terminus or C-
terminus
Voet Biochemistry 3e Page 71
© 2004 John Wiley & Sons, Inc.

The tetrapeptide Ala-Tyr-Asp-Gly

 Optical activity
 All aa are optically active except glycine
 They rotate the plane of polarized light
in a polarimeter
 Optically active molecules are
asymmetric:
 They are not superimposable on their
mirror image
 Asymmetric means C is bonded to four
different groups
Glycine contains two hydrogen
atoms on C
The C of glycine is not asymmetric

Therefore glycine is optically

inactive
Voet Biochemistry 3e Page 72
© 2004 John Wiley & Sons, Inc.

Schematic diagram of a polarimeter

 L-Amino acids rotate polarized light to
the left
 D-Amino acids rotate polarized light to

the right
 Both L and D forms are chemically same
Non-standard
amino acids
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e Page 77

Some uncommon amino acid residues that are components of

certain proteins
 Biologically active
amino acids
 Neurotransmitters
 Hormones
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e Page 77

Some biologically produced derivatives of “standard” amino acids

and amino acids that are not components of proteins
That’s all!
 Homework
 Amino acid aspartate has pKa1=2.0,
pKa2=9.9, and pKa3=3.9. Calculate its
overall charge at pH 3.0.
 Classify the 20 amino acids based on
 Essential, semi essential, and non
essential.
 Glucogenic, Ketogenic, and both
ketogenic and glucogenic.