Lecture 3

Amino Acids

Lehninger. Principles of Biochemistry

7th Ed.
Chapter 3 Section 1-2
 Learning Objectives

By the end of the lecture you will be able to:

•  Describe the structures, sizes, polarities and charges of the 20

naturally occurring amino acids

•  Understand how planar peptide bonds link amino acid residues

into polypeptides

•  Explain how amino acids are chiral molecules and distinguish

between L and D enantiomers

•  Be able to give examples of amino acids that are chemically

modified to produce biologically active derivatives
 The structure of amino acids

large organic ‘side

chain’

20 different side chains define 20 possible amino acids

(19 amino acids and 1 imino acid)

 Amino acids are dipolar ions

pK ~2.2

pK ~9.4

At physiological pH: amino group is protonated, carboxylic

acid group is unprotonated

Molecules bearing both charges = zwitterions

Amino acids are linked by peptide bonds
Amino acids can be
polymerized by a
condensation reaction to
form polypeptides

Individual amino acids

incorporated into a
polypeptide are known as
‘residues’

All proteins have a free

amino group (N-terminal)
and a free carboxyate group
pep#de bond (C-terminal)
Proteins are linear polymers of amino acids

Amino Acids
(20)

How many different combinations of a

100 amino acid protein exist?
Nonpolar amino acid side chains have a variety
of shapes and sizes
alanine isoleucine phenylalanine
 Uncharged polar side chains have hydroxyl,
amide and thiol groups
serine glutamine

H-bond
H-bond acceptor
donor
Cysteine is an uncharged amino acid that can
form disulfide bonds
Charged polar side chain are positively or
negatively charged
aspartate lysine
 Charged polar side chain are positively or
negatively charged
aspartate lysine

pK = 10.5

pK = 3.9
Amino acids have standard nomenclatures

Ser Gly Tyr Ala Leu

S G Y A L
Amino acids contain chiral centers

Only L-amino acids are found in nature

 Life is based on chiral molecules

Ordinary chemical synthesis

produces racemic mixtures of
both enantiomers

Biosynthesis produces pure

stereoisomers
Side chains may be modified to create non-
standard amino acids
Irreversible modifica0ons Reversible modifica0ons
Some amino acids are biologically active