Protein:

MONOMER
AMINO ACID

PROTEINS

Objectives
acid definition, general structure,
enantiomer

Amino

Zwitterion form
Name, 1-letter and 3-letter abbreviation for
20 amino acids
Classification

What is protein?
Proteins are polymers of amino acids.
Primary
Structure

Secondary
Structure

Tertiary
Structure

Quaternary
Structure

What is amino acid?

Amino acid: a compound that
contains both an amino group and a
carboxyl group attach to -carbon
-carbon also bound to side
chain group, R
R gives identity to amino acid
Amino acid = - amino acid,
is the building block for protein
= standard amino acid

Terminology
- carbon = the carbon that
attach next to the carboxyl group
- amino group = amino group
that attach to -carbon
Other type of amino group
eg. in Lysine, has
-amino group
- amino acid, is the building
block for protein = standard
amino acid

Lysine

Amino acid
1. All 20 are -amino acids
2. For 19 of the 20, the -amino group is
primary; for proline, it is secondary amino
acid

-Amino acid has an amino group attached to the

carbon (-carbon) adjacent to the carboxyl group

Enantiomer
The amino acids can exist in two enantiomeric forms
(nonsuperimposable mirror image) forms exceptional for
glycine
Two steroisomers of amino acids are designated L- or D-.
L amino
acid:
abundant in
nature, found
in proteins,
amino group
on the left

O
C
+

H3N

carbon

C
R1

Mirror plane

O
C
C
R1

NH3

Generic amino acid at physiological

pH amino acids exist as dipolar
ionic species (have positive and
negative charge on the same
molecule) - zwitterion form
Amino acid is an amphoteric
molecule act either as an
acid or a base
GENERAL
STRUCTURE?

HYDROPHILIC?

Amino acid
Only the L - form of amino acids is commonly
found in proteins. Vs monosaccharide : D - form
Depending on the nature of the R group,
amino acids are classified into four groups.
1. nonpolar
2. polar neutral/uncharged side
chain
3. acidic
Polar, charged
4. basic

Classification of amino acid

Nonpolar (9 amino acids)
Polar
neutral/uncharged (6 amino acids)
charged
basic (3 amino acids)
acidic (2 amino acids)
Depending on the nature of the R group, amino acids
are classified into four groups

Classification of amino acids

Simplest amino acid due to the R group = H
No stereoisomer because the is achiral

Nonpolar

* Second stereocenter
Sulfur atom

Aliphatic cyclic structure N is bonded to C2 atoms

Amino group of become secondary amine often called an imino acid

Amino acids with nonpolar side chains - hydrophobic

Polar uncharged

* Second stereocenter

Amide bond highly

polar

Phenol
Thiol / sulfhydryl group polar
under oxidizing condition, with other thiol groups to form disulfide
bridges (-S-S-) important in 3o structure

Polar charged

Basic
Aspartate

Glutamate

Acidic

Essential Amino acid

An essential amino acid or
indispensable amino acid
is an amino acid that
cannot be synthesized de
novo by the organism
(usually referring to
humans), and therefore
must be supplied in the
diet.
vs non-essential amino
acid

Protein:
MONOMER
AMINO ACID
12 Feb 2009

Protein
Structure
4 level

Amino acid (-amino acid)

is an amphoteric molecule
Physiological
pH

- carboxyl group
carboxylate ion
- amino group
protonated
amino acid

Amino acids
as dipolar ions

Classification of amino acid

Nonpolar
Polar

(9 amino acids) Gly (G), Ala (A), Val(V), Leu(L), Ile(I), Met(M), Pro(P), Phe(F), Trp(W)

neutral/uncharged(6 amino acids) Ser(S), Thr(T), Asn(N), Gln(Q), Tyr(Y), Cys(C)

charged

basic
acidic

(3 amino acids) Lys(K), Arg(R), His(H)

(2 amino acids) Glu(E), Asp(D)

Depending on the nature of the R group, amino acids are

classified into four groups at physiological pH (7.4)

Nonpolar hydrophobic
Polar hydrophilic

Objectives
Definitions peptide, polypeptide, pI
Zwitterion, anionic, cationic form
Peptide bond - features

Ionization of Amino Acids

Remember, amino acids without charged groups on side chain
exist in neutral solution as zwitterions with no net charge
In acidic solution as
base (protonation)

In basic solution as
acid (deprotonation)

Ionization of amino acids

At physiological pH, the carboxyl group of the
amino acid is negatively charged and the amino
group is positively charged.
Amino acids without charged side chains
(Group 1 and 2) are zwitterions and have no net
charge. (H3+N-HCR-COO- ).

A titration curve shows how the amine and

carboxyl groups react with hydrogen ion.

Titration of amino acid

At low pH a nonacidic/nonbasic amino acid is protonated and has the structure
H3N+HCRCOOH (amino acid in cationic form)
Increase of pH, dissociation of proton (H+) from COOH group form
H3N+HCRCOO- (amino acid in zwitterionic form)
At pK1, amount of cationic form = amount of zwitterionic form

Beyond pK1, additional base ions will results in all amino acids in cationic forms
deprotonated to zwitterionic forms all amino acids have no net charge
pI = isoelectric point = pH at which the amino acid has no net
charge/all amino acids are in zwitterionic form
Increase of pH beyond pI, will cause the dissociation of H+ / deprotonation
from H3N+ resulting in formation of H2NHCRCOO- (anionic form)

Increase of pH, more dissociation of proton (H+) from H3N+group, more amino
acids in anionic form

At pK2, amount of zwitterionic form = amount of anionic form

Titration of Alanine
When an amino acid is titrated, the titration curve represents the reaction of
each functional group with the hydroxide ion

Anionic form
pI = isoelectric point =
pH at which the amino
acid has no net
charge/ all amino acids
are in zwitterionic form
Cationic form

All amino acids

are in the
zwitterion form
at isoelectric
point (pI)

Titration of amino acid

pK1 and pK2 are proton dissociation constant from
carboxyl group and amino group
From titration of amino acid, the pI can be calculated

The charge behavior of acidic and basic amino acids

is more complex. Group Polar/charged amino acid

Terminology
peptide: the name given to a short polymer of amino
acids joined by peptide bonds; they are classified by
the number of amino acids in the chain
dipeptide: a molecule containing two amino acids
joined by a peptide bond
tripeptide: a molecule containing three amino acids
joined by peptide bonds
polypeptide: a macromolecule containing many amino
acids joined by peptide bonds
protein: a biological macromolecule of molecular
weight 5000 g/mol or greater, consisting of one or
more polypeptide chains
Primary structure = one polypeptide

Peptide bond: Feature

1

Free
rotation
COO-

NH3+

Peptide bond in trans configuration, acts as a rigid

and planar unit. Has limited rotation around the peptide
bond (C-N).

END OF CHAPTER