UNIT-1
• Amino acids and Proteins: Structure and function,
Structure and properties of Amino acids, types of
proteins and their classification, forces stabilizing
protein structure and shape. Different level of
structural organization of proteins, protein
purification, denaturation and renaturation of
proteins. Fibrous and globular proteins.
Proteins
Amino acids are building blocks of proteins
All proteins consist of same 20 amino acids
The aa differ wrt their side chains only
Different combination of aa give rise to different proteins
Amino acids are joined covalently by peptide bonds
1. Amino acids-the building block of protein
Common features of Amino
acids
1. The following groups are attached to (alpha
carbon):
a carboxyl group -COOH
an amine group -NH2
an atom of hydrogen -H
a variable radical -R, the side chain
2.Amino acids differ only in the side chains
The simplest amino acid is the Glycine having H as side chain
3. Except glycine, the α carbon atom in all amino acids is bonded to four
different groups and therefore is a chiral centre
4. They have sterioisomers due the presence of chiral centre
Example: Alanine has two sterioisomers called
enantiomers (non superimposable mirror images)
How many Amino acids ?
Twenty kinds of side chains (R group) are found in amino acids that vary in
in size
shape
Charge
Hydrogen bonding capacity
hydrophobic character
chemical reactivity
So there are 20 common amino acids
They may be grouped into five main classes based on the
properties of their R groups
Amino acids with Nonpolar, aliphatic R groups
Amino acids with Aromatic R groups
Amino acids with Polar, uncharged R groups
Amino acids with Positively charged R groups
Amino acids with Negatively charged R groups
Amino acids with Nonpolar, aliphatic R groups (at pH 7)
Proline is the only amino acids with
amine group directly attached to the R
group
Amino acids with Aromatic
R groups (strong absorbance
at 280nm) (at pH 7)
One of the two
sulphur containing
proteinogenic amino
acids
Absorption of ultraviolet light by aromatic amino
acids. (at pH 6.0)
absorbance of tryptophan is more
than four times that of
tyrosine at a wavelength of 280 nm.
• Note that the maximum light
absorption for both tryptophan and
tyrosine occurs near 280 nm.
•Light absorption by phenylalanine
generally contributes little to the
spectroscopic properties of proteins
Amino acids with Positively charged R groups (at pH 7)
Charged at neutral pH
One of the two
sulphur containing
proteinogenic amino
acids
Amino acids with Polar, uncharged
R groups (Side chain contain
functional group that can form H-
bonds with water) (at pH 7)
Amino acids with Negatively charged R groups (at pH 7)
methylene bridge (-CH2-)
Homocysteine -A non protein amino acids, i.e., not a component of proteins
Homocysteine is a homologue of the amino acid cysteine, differing by an
additional methylene bridge (-CH2-)
Its concentration in blood is linked with hypertension in human
Peptides-The Polymers of Amino acids
Amino acids are joined to each other by peptide bonds
The polymer formed by
two amino acids----Dipeptide
Three amino acids ------Tripeptide
Four amino acids or more --------Tetrapeptide
Many amino acids------Polypeptide
How Peptide bonds formed: Condensation reaction of amino acids
Two amino acid molecules are covalently joined through a peptide bond
The peptide bond is formed by removal of the elements of water (dehydration) from the
α-carboxyl group of one amino acid and the α-amino group of another
Protein Structure/ Levels of protein
organization
Enzyme
What makes a protein Hormone Structure
Antibody
The protein structure can be described at four levels of complexity.
These are
Primary Structure
amino acid sequence; uses covalent peptide bonds
Secondary Structure
Secondary structure refers stable arrangements of amino acid
residues giving rise to structural patterns like alpha helix or beta
sheet
• Tertiary Structure
Three-dimensional folding of a single polypeptide
chain; uses disulfide bonds, hydrogen bonds, ionic
bonds, vander Walls interactions, and hydrophobic
interactions
• Quaternary Structure
When a protein has two or more polypeptide
subunits, their arrangement in space is referred to
as quaternary structure.
Protein Structure/ Levels of protein organization
Primary Assembly
STRUCTURE
Folding
PROCESS
Secondary
Packing
Tertiary
Interaction
Quaternary
Why to study primary structure ?
A] Amino Acid Sequences Provide Important Biochemical
Information such as
•three-dimensional structure and thus its function
•cellular location and
•Evolution
These information are obtained by searching for similarities
between a protein of interest and previously studied proteins
Individual proteins are assigned to families based on the degree
of similarity in amino acid sequence.
Members of a family are usually identical across 25% or more of
their sequences, and proteins in these families generally share at
least some common structural and functional characteristics.
Some families are defined, however, by identities involving only a
few amino acid residues that are critical to a certain function.
Amino acid sequences serve as signals that determine the
cellular location, chemical modification of a protein.
Special signal sequences, usually at the amino terminus, are
used to target certain proteins for export from the cell
Other proteins are targeted for distribution to the nucleus,
the cell surface, the cytosol, or other cellular locations.
B] Study of Primary structure of protein may be used for evolutionary study
If two organisms are very closely related, the sequences of their genes and
proteins should be similar
The sequences increasingly diverge as the evolutionary distance between two
organisms increases.
The amino acid residues essential for the activity of a protein are conserved
over evolutionary time.
The residues that are less important to function may vary over time—that is,
one amino acid may substitute for another—and these variable residues can
provide the information to trace evolution.
Example:
• EF-1α (elongation factor 1) is involved in the synthesis of
proteins in all eukaryotes.
• A similar protein, EF-Tu, with the same function, is found in
bacteria.
• Similarities in sequence and function indicate that EF-1α and
EF-Tu are members of a family of proteins that share a
common ancestor.
• These members of protein families are called homologous
proteins, or homologs.
• If two proteins in a family (that is, two homologs) are present
in the same species, they are referred to as paralogs.
• Homologs from different species are called orthologs.
Protein Secondary Structure
• Secondary structure refers stable arrangements of amino acid residues
giving rise to structural patterns like alpha helix or beta sheet
α-Helix
β sheet
β turn 1930
α-Helix:
It is a helical arrangement of a single polypeptide
chain, like a coiled spring.
In this conformation, the carbonyl and N-H
groups are oriented parallel to the axis.
Each carbonyl is linked by a hydrogen bond to
the N-H of a residue located 4 residues further on
in the squence and this intrachain hydrogen bond
stabilizes the α-Helix structure
All C=O and N-H groups are involved in hydrogen
bonds, making a fairly rigid cylinder
The alpha helix has precise dimensions: 3.6
residues per turn, 0.54 nm per turn.
The right-handed helices are energetically
more favorable because there is less steric
clash between the side chains and the
backbone.
Essentially all α-helices found in proteins
are right-handed.
Different Dimensions of the α-Helix
Five different kinds of constraints affect the stability of an
α-helix:
• The electrostatic repulsion (or attraction) between
successive amino acid residues with charged R groups
• The bulkiness of adjacent R groups
• The interactions between R groups spaced three (or four)
residues apart
• The occurrence of Pro and Gly residues
• β-Sheet (2nd structure elucidated by Pauling and Corey)
The polypeptide chain folds back on itself so that polypeptide strands lie side by
side, and are held together by hydrogen bonds, forming a sheet like structure
The polypeptide N-H and C=O groups form hydrogen bonds to stabilize the
structure
Generally the primary structure folds back on itself in either a parallel or
antiparallel arrangement, producing a parallel or antiparallel β sheet.
In this arrangement, side chains project alternately upward and downward from
the sheet
•The distance between adjacent amino acids along a β strand is approximately
3.5 Aoin contrast to a distance of 1.5 Ao along an α-helix.
Beta-sheet
Antiparallel
The –NH- group and the –CO- group of
each amino acid are respectively bonded
to –CO- group and –NH- group of a
partner on the adjacent chain.
Beta-sheet
Parallel
For each amino acid, the –NH- group is bonded to the –
CO- group of one amino acid on the adjacent strand,
whereas –CO- group is hydrogen bonded to –NH- group
on the amino acid two residues farther along the chain.
Many strands, typically four or five but as many as 10 or more, can
come together in β sheets. Such β sheets can be purely parallel, purely
antiparallel, or mixed.
Two types of β sheet structures. (A) An antiparallel β sheet (B) A
parallel β sheet
a β Turn
Polypeptide chains can turn direction by making reverse turns and loops
which give protein a compact and globular shape
Structure of a β Turn. The
CO group of residue i of the
polypeptide chain is
hydrogen bonded to the NH
group of residue i + 3 to
stabilize the turn.
Loops
Loops on a Protein Surface. A part
of an antibody molecule has surface
loops (shown in red) that mediate
interactions with other molecules.
Turns and loops invariably lie on the surfaces of
proteins and thus often participate in interaction
between protein and other molecules.
Tertiary Structure
This level of structure describes how regions of secondary structure fold together – that
is, the 3D arrangement of a polypeptide chain, including a helices, β sheets, and any other
loops and folds.
Tertiary structure results from interactions between side chains, or between side chains
and the polypeptide backbone, which are often distant in sequence.
Informations needed to fold the protein to a
particular 3D structure lies within the
sequence of the protein.
The tertiary structures are stabilized by
following type of covalent and non covalent
interactions
I. Hydrophobic interactions
II. Electrostatic interactions
III. Hydrogen bonds
IV. Covalent bonds
Quaternary Structure
• Proteins are made up of multiple polypeptide chains (subunits)
• These subunits may be the same (as in a homodimer) or different (as in a
heterodimer).
• The quaternary structure refers to how these protein subunits interact
with each other and arrange themselves to form a larger aggregate protein
complex.
• The final shape of the protein complex is stabilized by various
interactions, including hydrogen-bonding and disulfide bridges.
Protein types and classification
