AMINO ACID: BUILDING BLOCKS OF PROTEIN
MPS-301 (E) :
STRUCTURES,
PROPERTIES, AND
FUNCTIONS OF
BIOMOLECULES
BY JITESH BARMAN
DEPARTMENT OF PHYSICS, BHU DATE – 30-10-2023
Proteins : Amino Acids
➢ In all biological systems, proteins play a major role from structural role
to defensive role.
➢ Amino acids are the basic building blocks of the proteins.
➢ Amino acids have the zwitterionic form that means it consists of a
basic amino group (NH3+), an acidic carboxylate group (COO-). In-
addition to that a hydrogen atom, and a substituent group (R).
➢ The c-α- carbon is a chiral atom (that means that the carbon atom
contains four different groups)
Proteins : Amino Acids
➢ Two configurations of amino acids: L and D
➢ All life on earth has evolved to use only L-amino acids in proteins
➢ There are only a few exceptions to this rule, such as peptidoglycans
made of D-amino acids which are found in bacterial cell walls
➢ Artificial, synthetic proteins made of D-amino acids are the exact mirror
images of their natural counterparts made of L-amino acids and their
substrate specificity reflects this inverted chirality
Characteristics of Amino Acids
➢ The side chains (R) are very important for amino acids as they decides
the characteristics of the amino acids
➢ There is a library of twenty (20) amino acids
➢ Can be categorized based on the shape, size and the chemical nature
of the side chain
➢ From there chemical nature it can be divided into three categories
having (i) Charged, (ii) Neutral or polar (iii) Non-polar – R-groups
Characteristics of Amino Acids
Characteristics of Amino Acids
Amino acids could be divided
into different categories
depending upon the various R-
groups
•Aromatic (phenylalanine,
tyrosine, tryptophan)
•Aliphatic (leucine,
isoleucine, alanine,
methionine, valine)
•Hydroxyl/Sulfhydryl
(threonine, serine, tyrosine,
cysteine)
•Carboxyamide (glutamine,
asparagine)
•R-Acids (glutamic acid,
aspartic acid)
•R-Amines (lysine, histidine,
arginine)
•Odd (glycine, proline)
Characteristics of Amino Acids
❖ Glycine is the simplest amino acid which is usually grouped with the
hydrophobic amino acids, but due to its unique properties it is often
considered to form a separate group
❖ The polar amino acids can be further classified into charged and
uncharged
❖ Hydrophobic, apolar amino acids can be further classified into aromatic
and aliphatic side chains
Structure of proteins : Peptide bond
➢ Proteins are linear polymers of amino acids, synthesized from a library
of twenty amino acids.
➢ They linked through covalent peptide (C-N) bonds by the hydrolysis
between α-amino and α-carboxyl of successive amino acids.
Characteristic of Peptide bond
➢ Incorporation of an amino acid in protein results in the loss of both the
amino and acidic groups due to peptide bonding; hence it will be called
as “amino acid residue” instead – or, for simplicity, “residue.”
➢ The nature of the peptide bond is of a partial double bond, or
resonance, implying that the bond is not free to rotate and the four
atoms involved in this bond are coplanar
Resonance of molecules
Ramachandran angles
➢ The conformational flexibility of the backbone derives from the
remaining bonds which are able to rotate around their axes: the N–Cα
bond and the Cα–C bond which define, respectively, the torsion angles
phi (φ) and psi (ψ)
Ramachandran plot
➢ There is a limited rotation range for each of these angles in proteins due
to steric clashes. A two-dimensional plot of phi and psi angles, the
Ramachandran plot.
➢ Glycine behaves differently because its side chain consists of a hydrogen
atom, and its allowed range of phi and psi angles is considerably broader
than those of other amino acids
Ramachandran plot
➢ In general, staggered conformations are favored for tetragonal
carbons, and trans are usually favored over cis conformations. The only
way to accurately determine the conformation of one given amino acid
within a protein is experimentally, usually by X-ray crystallography
➢ The Staggered conformation is a molecular conformation in which the
groups/substituents on the adjacent atoms are most evenly spaced out
with each other
In next class
➢ Primary structure of proteins
➢ Secondary structure : alpha – helix and beta- sheet structures
➢ Tertiary structure and quaternary structure
Structure of proteins
➢ Proteins are divided at four levels depending upon the hierarchy of
their organisations
Primary proteins
➢ Proteins are divided at four levels depending upon the hierarchy of
their organisations
Thank you
Namaskaar !!
Recapitulations
➢ Introduction to the course and the syllabus
➢ Why we should do the Biophysics and what are the questions to be
asked and problems to be solved in Biophysics
➢ Scope and the impact of Biophysics in human society
➢ Areas of research where the biophysics is applicable
➢ Molecules of biological interests
➢ Hydrophobic, hydrophilic and amphiphilic molecules
