BIOCHEMISTRY (I)

LIFS2210

Amino Acids

1
 Biochemistry I (LIFS2210)

• You are expected to

learn the structure &
function of these
organic compounds:

2
 1. What are amino acids?

• Amino acids are organic acids

containing an amine group.

• Amino acids are the monomeric units

or "building blocks" of proteins.

3
 General Structure of Amino Acids

• Twenty common -amino acids have carboxyl

and amino groups bonded to the -carbon atom
• A hydrogen atom and a side chain (R) are also
attached to the -carbon atom

2 2

4
 2. Stereochemistry

• Stereoisomers - compounds that have the same

molecular formula but differ in the arrangement of
atoms in space
• Enantiomers - nonsuperimposable mirror images
• Chiral carbons - have four different groups
attached

5
Stereoisomers of -amino acids
mirror plane

Mirror-image pairs of amino acids

6
Mirror-image pairs of serine

7
 Stereochemistry of amino acids

• 19 of the 20 common amino acids have a

chiral -carbon atom (Gly does not)
• Threonine and isoleucine have 2 chiral
carbons each (4 possible stereoisomers each)
• Mirror image pairs of amino acids are
designated L (levo) and D (dextro)
• Proteins are assembled from L-amino acids
(a few D-amino acids occur in nature)
8
 3. Structures of the 20 common
amino acids found in proteins

 Abbreviations can be one letter or three letters

9
 Side Chains of the Amino Acids

• Side groups are what distinguish the

amino acids from each other.

• The 20 L--amino acids are frequently

grouped according to the chemical
nature of their side chains.

10
 A. Aliphatic R Groups

• Glycine (Gly, G) - the -carbon is not chiral

since there are two H’s attached (R=H)
• Four amino acids have saturated side chains:
Alanine (Ala, A) Valine (Val, V)
Leucine (Leu, L) Isoleucine (Ile, I)

11
Aliphatic amino acid structures

12
 Aliphatic Amino Acids

• A diverse group - more nonpolar ones, such as VAL, LEU,

ILE prefer interior of protein molecule

• The more hydrophobic amino acids, like Valine, Leucine

and isoleucine, are usually found in the interior of a
protein molecule, where they are shielded from water.

• Glycine has the smallest functional group (hydrogen) of

any of the -amino acids.

13
 B. Cyclic Amino Acid - Proline

• Proline (Pro, P) - has a three carbon

side chain bonded to the -amino
nitrogen
• Proline has a nitrogen in the
aliphatic ring system
• Cyclic Amino Acid - The heterocyclic
pyrrolidine ring restricts the geometry
of polypeptides

14
 C. Aromatic R Groups
• Side chains have aromatic groups
Phenylalanine (Phe, F) - benzene ring
Tyrosine (Tyr, Y) - phenol ring
Tryptophan (Trp, W) - bicyclic indole group
• Tyrosine and Tryptophan have some hydrophobic
character, but it is tempered by the polar groups in their
side chains.
• Phenylalanine, together with the aliphatic amino acids
Valine, Leucine, and Isoleucine, are the most
hydrophobic amino acids.

15
Aromatic amino acid structures

16
 Aromatic Amino Acids: Strong
absorption of light in near UV
• Tyrosine, Phenylalanine and Tryptophan exhibit strong
absorption of light in the near-ultraviolet region of the spectrum.

• This absorption is frequently used for the analytical detection of

proteins.

Absorption spectra of the

aromatic amino acids in the
near-ultraviolet region

17
 D. Sulfur-Containing R Groups

• Methionine (Met, M) - (-CH2CH2SCH3)

• Cysteine (Cys, C) - (-CH2SH)
• Two cysteine side chains can be cross-linked by
forming a disulfide bridge (-CH2-S-S-CH2-)
• Disulfide bridges may stabilize the three-
dimensional structures of proteins

18
Methionine and cysteine

19
Formation of cystine

20
 E. Side Chains with Alcohol Groups

• Serine (Ser, S), Threonine (Thr, T) and Tyrosine (Tyr,

Y) have uncharged polar side chains

21
 Phosphorylation of Ser, Thr & Tyr

• The alcohol chain of Serine, Threonine and Tyrosine is a site of

phosphorylation of many proteins.

22
 F. Basic R Groups

• Histidine (His, H) - imidazole

• Lysine (Lys, K) - alkylamino group
• Arginine (Arg, R) - guanidino group
• Side chains are nitrogenous bases which are
substantially positively charged at pH 7
(except His)

23
Structures of histidine, lysine and arginine

24
 Basic Amino Acids

• The basic amino acids are strongly polar, and as

a consequence, they are usually found on the
exterior surfaces of proteins, where they can be
hydrated by the surrounding aqueous
environment.

• Histidine is the least basic of the three basic

amino acids.

25
G. Acidic R Groups and Amide Derivatives

• Aspartate (Asp, D) and Glutamate (Glu, E)

are dicarboxylic acids, and are negatively
charged at pH 7
• Asparagine (Asn, N) and Glutamine (Gln, Q)
are uncharged but highly polar

26
Structures of aspartate, glutamate,
asparagine and glutamine

27
 Acidic Amino Acids and Their Amides

• Asp and Glu strongly acid.

– Aspartic acid (Aspartate)
– Glutamic acid (Glutamate)

• Asn and Gln polar but not charged.

• Asparagine and Glutamine are classified as

amides because they are an amide derivative of
Aspartic acid and Glutamic acid, respectively.

28
 4. Ionization of Amino Acids

• Ionizable groups in amino acids: (1) -carboxyl,

(2) -amino, (3) some side chains
• Each ionizable group has a specific pKa
AH A- + H+
• For a solution pH below the pKa, the protonated
form predominates (AH)
• For a solution pH above the pKa, the unprotonated
form predominates (A)

29
pKa values of
amino acid
ionizable groups

30
 Titration curve for alanine

• Titration curves
are used to
determine pKa
values
• pK1 = 2.4
• pK2 = 9.9
• pIAla = isoelectric
point

31
 Zwitterionic form of amino acids

• A zwitterion is a molecule with equal

numbers of positive and negative charges -
thus the net charge is zero.
• Under normal cellular conditions amino acids
are zwitterions (dipolar ions):
Amino group = -NH3+
Carboxyl group = -COO-

32
33