Lecture 2: Amino acids and

Proteins
 Amino acids
• Building blocks of proteins
• Can join with other amino acids to build a
peptide
• Peptides with more than 50 amino acids are
called polypeptides
• All amino acids contain nitrogen,oxygen,
carbon and hydrogen
Amino acids
 AMINO ACIDS
• Can release H+ from either its carboxylic or
amino end in water
• Can be zwitterionic in nature
• All amino acids are chiral molecules except for
glycine
• Enantiomers are formed (nonsuperimposable
images relative to the chrial center)
 AMINO ACIDS
• Optically active – the ability to rotate the
plane of polarization of plane-polarized light
• Clockwise rotation of incident light is
dextrorotatory while the counter clockwise
rotation is levorotatory
 zwitterion
• The amino end is protonated and the
carboxylic end is deprotonated to form the
zwitterion, the dipolar form of an amino acid
AMINO ACIDS
AMINO ACIDS
AMINO ACIDS
 PEPTIDE BOND
• Bond which connects 2 amino acid residues
• Possesses double bond character
• Connects the carboxyl group of one amino
acid to the amino end of the other amino acid
• Formed via a condensation reaction
(formation of a new bond upon the removal of
water)
PEPTIDE BOND
PEPTIDE BOND
PEPTIDE BOND
PEPTIDE BOND
 PEPTIDE CLASSIFICATION
• 2 A.A residues = dipeptide
• 3 A.A residues = tripeptide
• 12-20 A.A residues = oligopeptide
• Numerous A.A residues = polypeptide
 Nomenclature of peptides
• All A.As except the last will be considered a
substituent therefore using the suffix –yl
connected to the last AA in which the original
AA name is used.
• Ex: alanyltyrosylaspartylglycine (AYDG)
• Ex2: phenylalanylglycine
 Exercise #1
Draw the structure of the following peptides
1. GAVAP
2. CHEMISTRY
3. GGAALLPTW
4. ALA
 Proteins and polypeptides
• Proteins are composed of numerous
polypeptide chains
• Size, configuration may depend on the
protein’s function as well as location
proteins
 AMINO ACID DERIVATIVES
• The 20 essential amino acids are not the only
AA which play a big role in many metabollic
pathways
• The Aas may undergo slight modifications via
different reactions to produce amino acid
derivatives
R GROUP MODIFICATION OF AMINO
ACIDS
R GROUP MODIFICATION OF AMINO
ACIDS
 SPECTROSCOPIC PROPERTIES OF
AMINO ACIDS
• None of the AAs absorb light in the visible
region in the electromagnetic region.
• Some absorb in the ultraviolet region and all
absorb in the infrared region
SEPARATION AND ANALYSIS OF AMINO
ACIDS
• May be done through chromatographic
techniques like ion exchange chromatography,
HPLC etc
SEPARATION AND ANALYSIS OF AMINO
ACIDS
 PROTEINS
• May be present in different configurations and
structures (depends on the extent of
complexity)
• Ex: cytochrome c (carries electrons) has only
104 AA residues compared to the 2000+ AA
residues of myosin (makes muscles contract).
 PROTEINS
3 major general classifications:
-globular
-fibrous
-membrane
PROTEIN STRUCTURE
PROTEIN STRUCTURE
 PRIMARY STRUCTURE
• Amino acid sequence (peptide chains)

• Ex: AAAAAA, ALALALALA, GALA, CHEMISTRY

PRIMARY STRUCTURE
 SECONDARY STRUCTURE
• Formed through intramolecular bonding such
as hydrogen bonding.
• 3D form is achieved due to such reasonb,
example of which is the helix
SECONDARY STRUCTURE
SECONDARY STRUCTURE
 TERTIARY STRUCTURE
• When the polypeptide chains of protein
molecules bend and fold in order to assume a
more compact 3-dimensional structure, the
tertiary structure is achieved.
• Usually present in globular form. (minimizes
interaction with the external environment)
TERTIARY STRUCTURE
TERTIARY STRUCTURE
PROTEINS
PROTEIN FUNCTIONS
PROTEIN FUNCTIONS