AMINO ACIDS AND
PROTEINS
UNIT 3
BT 1501
CREATED BY: SONAL THAKUR
CONTENTS
Peptide bond and its characteristics
Peptides and their ionization behaviour
Structure of proteins: Primary structure
PEPTIDES ARE CHAINS OF AMINO ACIDS
Serylglycyltyrosylalanylleucine
When an amino acid sequence of a peptide, polypeptide, or protein is displayed, the amino terminal end is
placed on the left, the carboxyl-terminal end on the right. The sequence is read left to right, beginning with the
amino-terminal end
PEPTIDES AND THEIR IONIZATION BEHAVIOUR
ACID BASE BEHAVIOUR OF AMINO ACIDS
• α-carboxyl group
• α-amino group
• Nature and number of ionizable R
groups
PEPTIDES AND PROTEINS
▸ Three amino acids can be joined by two peptide bonds to form a tripeptide; similarly,
four amino acids can be linked to form a tetrapeptide, five to form a pentapeptide, and
so forth.
▸ When a few amino acids are joined in this fashion, the structure is called an oligopeptide.
▸ When many amino acids are joined, the product is called a polypeptide.
▸ Proteins may have thousands of amino acid residues.
▸ Although the terms “protein” and “polypeptide” are sometimes used interchangeably,
molecules referred to as polypeptides generally have molecular weights below 10,000,
and those called proteins have higher molecular weights.
HOW LONG ARE THE POLYPEPTIDE CHAINS IN PROTEINS?
▸ Lengths vary considerably.
▸ Human cytochrome c has 104 amino acid residues linked in a single chain; bovine
chymotrypsinogen has 245 residues.
▸ At the extreme is titin, a constituent of vertebrate muscle, which has nearly 27,000
amino acid residues and a molecular weight of about 3,000,000.
▸ The vast majority of naturally occurring proteins are much smaller than this, containing
fewer than 2,000 amino acid residues.
PEPTIDES AND PROTEINS
▸ Some proteins consist of a single polypeptide chain, but others, called multisubunit proteins, have two or
more polypeptides associated noncovalently
▸ The individual polypeptide chains in a multisubunitprotein may be identical or different.
▸ If at least two are identical the protein is said to be oligomeric, and the identical units (consisting of one
or more polypeptide chains) are referred to as protomers.
▸ Hemoglobin, for example, has four polypeptide subunits: two identical α chains and two identical β
chains, all four held together by noncovalent interactions
▸ A few proteins contain two or more polypeptide chains linked covalently.
▸ For example, the two polypeptide chains of insulin are linked by disulfide bonds. In such cases, the
individual polypeptides are not considered subunits but are commonly referred to simply as chains.
Mean molecular weight of an
PRIMARY STRUCTURE amino acid residue is about 110
gm mol -1
• Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as proteins.
• The molecular weights of most proteins are between 5500 and 220,000 gm mol-I .
• The mass of a protein can be expressed in units of daltons; one dalton is equal to one atomic mass unit.
• A protein with a molecular weight of 50,000 gm mol –I has a mass of 50,000 daltons, or 50 kd (kilodaltons).
• In some proteins, the linear polypeptide chain is cross-linked.
PRIMARY STRUCTURE • Each protein has a unique, precisely
defined amino acid sequence.
• The amino acid sequence of a protein
is referred to as its primary structure.
To elucidate
mechanism
of action
Three Knowledge
dimensional Molecular
DNA RNA PROTEIN structures
of protein
sequence
pathology
of proteins
Molecular
Paleontology
THE PEPTIDE BOND IS RIGID AND PLANAR
The α-carbons of adjacent amino acid residues are separated by three covalent bonds, arranged
as Cα—C—N—Cα.
X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tripeptides
showed that the peptide C—N bond is somewhat shorter than the C—N bond in a simple amine
and that the atoms associated with the peptide bond are coplanar.
This indicated a resonance or partial sharing of two pairs of electrons between the carbonyl
oxygen and the amide nitrogen.
The oxygen has a partial negative charge and the hydrogen bonded to the nitrogen has a net
partial positive charge, setting up a small electric dipole
THE PEPTIDE BOND IS RIGID AND PLANAR
The six atoms of From these The backbone of
the peptide group findings Pauling a polypeptide
lie in a single and Corey chain can thus be The rigid peptide
plane, with the concluded that Rotation is pictured as a bonds limit the
oxygen atom of the peptide C—N permitted about series of rigid range of
the carbonyl bonds, because of the N—Cα and planes, with conformations
group trans to the their partial the Cα—C bonds. consecutive possible for a
hydrogen atom of double- bond planes sharing a polypeptide chain.
the amide character, cannot common point of
nitrogen. rotate freely. rotation at C.
PEPTIDE BOND IS RIGID AND PLANAR
• Peptide conformation is defined by dihedral angles (also known as torsion angles) called ϕ(phi) and ψ
(psi), reflecting rotation about each of the three repeating bonds in the peptide backbone.
• A dihedral angle is the angle at the intersection of two planes.
• ϕ involves the C—N—Cα—C bonds (with the rotation occurring about the N—C α bond), and ψ involves
the N—C α—C—N bonds.
• Both phi and psi are defined as 180 when the polypeptide is fully extended and all peptide groups are
in the same plane
• The peptide bond is normally (99.6% of the time) in the trans configuration
RAMACHANDRAN PLOT
