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Dr. Jagdish Kaur,
P.G.G.C.,Sector 11
Chandigarh
Element components of proteins
major
elements
C, H, O, N, S.
trace elements
P, Fe, Cu, Zn, I, …
The basic building blocks of proteins
Amino Acids
only 20 types of amino acids are used for
protein synthesis in biological systems.
L-α-Amino acid
L-α-Amino acid
COOH
H2N
C
¦Á
¹² ͬ²¿ ·Ö
H
R
²à Á´
A Classification of Amino Acids
 Amino acids are grouped as
(1) non-polar, hydrophobic;
(2) polar, neutral;
(3) acidic;
(4) basic.
Special amino acids
 Gly
 Pro
optically inactive
Having a ring structure and imino group
 Cys
active thiol groups to form disulfide bond
Peptide
A
peptide
is
a
compound of amino
acids linked together
by peptide bonds.
peptide bond
A peptide bond is a covalent bond formed
between the carboxyl group of one AA and the
amino group of its next AA with the
elimination of one H2O molecule.
Biologically active
peptides
Glutathione (GSH)
As a reductant to protect nucleic acids and
proteins
Peptide hormones
Neuropeptides responsible for signal
transduction
Molecular Structures of Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Spatial structure
Primary Structure
The primary structure
 A linear sequence of amino acids joined
together by peptide bonds.
 Peptide bonds and disulfide bonds are
responsible for maintaining the primary
structure.
Secondary Structure
The secondary structure
 A local spatial structure of a certain
peptide segment, the relative positions of
backbone atoms of this peptide segment.

H-bonds are responsible for stabilizing
the secondary structure.
Four common types of secondary structure
α-helix
β-pleated sheet
β-turn
random coil
Key ideas and terms
 protein can bind a ligand in the binding
site
 For an enzyme, the ligand is a substrate
and they bind in what is called the active
site
 ligand has to be the correct shape
 ligand has to have the complementary
charges and hydrophobicity or
hydrophilicity
Lock and Key Hypothesis
 Protein and ligand have
complementary shapes.
 Interactions must also
be complementary
 If enzyme charge is
negative, substrate must
be positive
 If pocket is nonpolar,
ligand must be nonpolar
 Antibodies
Induced Fit
 Induced Fit: when the
protein and ligand
bind, the protein may
change conformation
to allow for tighter
binding
 Frequently, both the
ligand and the
protein change
conformation
Examples: O2 binding proteins:
myoglobin and hemoglobin
 oxygen is not water soluble yet needs to be transported
 diffusion is not effective
 myoglobin is found primarily in muscle tissue
 Hemoglobin is in the blood
 Both proteins contain heme
Protein classification
Constituents
simple protein
conjugated protein = protein +
prosthetic groups
Overall shape
Globular protein
Fibrous protein
long/short < 10
long/short > 10
Definition protein classification
Grouping of similar proteins
based on their structure,
function, or size
Globular vs filamentous vs
helical
Cataytic vs structural
Small vs large vs very large
Protein Subunits & Domains
 A single polypeptide may have regions
along its length that fold up separately domains
 More than one polypeptide coming
together to form a protein - subunit
Protein - shapes
 Globular proteins - polypeptide folds tightly
together on itself - most enzymes
 Fibrous proteins - elongated structure - span
great distances - hair - keratin
 Many subunits attached together
 Actin & collagen
 Strong & rigid (Collagen - ligaments)
 Strong & flexible (elastin - skin)
04_24_complexstructure.jpg
04_26_spherical shell.jpg
04_29_Disulfide bonds.jpg
Proteins Bind
 Biological properties of proteins result from
interactions with other molecules
 Antibodies, enzymes, structure, etc
 Binding is always very specific
 Ligand - anything that is bound by a protein
 Ligand binding is by ionic bonds only
 Many ionic bonds required to stabilize link -
matching configurations needed - specificity
04_30_selective binding.jpg
Proteins - Binding
 A ligand binds to a protein at a binding site
 A protein may have more than one binding
site
 It may bind the same ligand many times or it may
bind different ligands
 Ligands can bind to regulate the activity of the
protein
 Interior amino acids have a say in the
conformation of the molecule too.
Proteins - pair with other molecules
 Some biologically active molecules
are a result of a very cozy
relationship
 Rhodopsin & Opsin
 Retinal (a light sensing pigment)
+ opsin protein
 Haem (Fe containing molecule)
+ globin protein
Structure-Function Relationship
Proteins
 Relationship
of
between
primary
structure and function
Primary structure is the fundamental
to the spatial structures and
biological functions of proteins.
Example
1. Proteins having similar amino
acid sequences demonstrate the
functional similarity.
2. The alternation of key AAs in a
protein will cause the lose of its
biological functions.
Relationship between spatial structure and
function
 A particular spatial structure of a protein is
strongly correlated with its specific biological
functions.
Example
1.The denatured protein
remains
its
primary
structure,
but
no
biological function.
2. Allosteric change of
hemoglobin by O2