Bio-Inorganic

Chemistry
 Md. Mohinuddin
Lecturer
University of Barishal
 Properties of Biological molecules
1. Protein and Their constituents
2. Nucleic Acids and their constituents
3. Other metal binding biomolecule
The chemical constituents of living cells can be broadly categorized into
two main classes:
1. Inorganic Molecules:
Water: Making up around 70-80% of a cell's weight, water is essential for
various cellular processes like transport, regulation, and metabolic
reactions.
Inorganic ions: These include cations (positively charged) like sodium
(Na⁺), potassium (K⁺), calcium (Ca²⁺), and magnesium (Mg² ⁺), and anions
(negatively charged) like chloride (Cl⁻), phosphate (PO ₄³ ⁻), and
bicarbonate (HCO₃⁻). They play crucial roles in maintaining cell structure,
electrical potential, and various physiological functions.
 Organic Molecules:
Carbohydrates: These provide energy for cells and come in various forms,
including simple sugars like glucose and fructose, and complex
carbohydrates like starches and cellulose.
Proteins: These are the most abundant organic molecules in cells and are
responsible for diverse functions like catalysis (enzymes), structure (e.g.,
collagen in bones), and transport (e.g., hemoglobin in blood).
Lipids: These are a diverse group of molecules, including fats, oils, and
phospholipids. They serve as energy storage, provide insulation, and form
cell membranes.
Nucleic acids: These store and transmit genetic information, including DNA
(deoxyribonucleic acid) and RNA (ribonucleic acid).
 Additionally, living cells may contain other organic molecules in smaller
amounts, such as:

Vitamins: Essential for various metabolic processes.

Hormones: Chemical messengers that regulate various physiological
functions.
Enzymes: Proteins that act as biological catalysts to accelerate chemical
reactions within the cell.
Waste products: Molecules like carbon dioxide and urea that are removed
from the cell.
CONTENTS
 Protein
 Amino Acids
 Naturally occurring Amino Acids
 Classification of protein
 Function of protein
 Structure of Protein
 Protein as a ligand
 Protein:

Proteins are very large molecules composed of basic units called

amino acids. Proteins contain carbon, hydrogen, oxygen, nitrogen,
and Sulphur.

Protein molecules are large, complex molecules formed by one or

more twisted and folded strands of amino acids. Proteins are highly
complex molecules that are actively involved in the most basic and
important aspects of life. These include metabolism, movement,
defense, cellular communication, and molecular recognition.
 Function of Proteins
Proteins perform a vast array of functions within organisms,
including…
Catalyzing metabolic reactions (Enzyme): Most enzymes are made
predominantly of proteins, either a single protein chain or many such chains in a
multi-subunit complex. Enzymes often also incorporate non-protein components,
such as metal ions or specialized organic molecules known as cofactor (e.g.
adenosine triphosphate). Many cofactors are vitamins, and their role as vitamins is
directly linked to their use in the catalysis of biological process within metabolism.
Catalysis of biochemical reactions in the cell is vital since many but not all
metabolically essential reactions have very low rates when uncatalyzed.
 Function of Proteins

DNA replication: DNA replication is the biological process of

producing two identical replicas of DNA from one original DNA
molecule. DNA replication occurs in all living organisms acting as the
most essential part of biological inheritance. This is essential for cell
division during growth and repair of damaged tissues, while it also
ensures that each of the new cells receives its own copy of the DNA. The
cell possesses the distinctive property of division, which makes
replication of DNA essential.
 Function of Proteins

Cell signaling: Cell signaling or cell communication is the ability of a cell

to receive, process, and transmit signals with its environment and with itself.
Cell signaling is a fundamental property of all cellular life.
Receptors play a key role in cell signaling as they are able to detect
chemical signals or physical stimuli. Receptors are generally proteins
located on the cell surface or within the interior of the cell such as the
cytoplasm, organelles, and nucleus. Cell surface receptors usually bind with
extracellular signals
Receptors : Receptors are chemical structures, composed of protein, that
receive and transduce signals that may be integrated into biological systems.
 Function of Proteins

 providing structure to cells and organisms

 They constitute about 50% of cellular dry weight.
 transporting molecules from one location to another.
Proteins may be purified from other cellular components using a variety of
techniques such as ultracentrifugation, precipitation, electrophoresis, and
chromatography; the advent of genetic engineering has made possible a
number of methods to facilitate purification. Methods commonly used to
study protein structure and function include immunohistochemistry, site-
directed mutagenesis, X-ray crystallography, nuclear magnetic resonance
and mass spectrometry.
Amino Acids
Structure of Amino Acids ( Protein forming)
Properties of Amino Acids
Physical properties of amino acids
 Amino acids are colorless, crystalline substance.
 Most amino acids are tasteless but some are sweet. (E.g. Glycine, Alanine) and
some are bitter (Eg. Arginine)
 Amino acids have high melting point (200-300)℃ due to ionic property.
Solubility:
 Solubility of amino acids depends upon polarity, iso-electric point, nature of
solvent (pH) and temperature.
 Amino acids are soluble in water and ethanol (i.e. polar solvent) and insoluble in
non-polar solvent like benzene, ether etc.
 Amino acids are insoluble at iso-electric point.
 Solubility depends upon pH of solvent and temperature.
 Eg. Tyrosine is soluble in hot water.
Properties of Amino Acids

Amphoteric property:
Amino acids can act as acid and base due to their dipolar i.e. zwitter
ion nature.
Properties of Amino Acids

Chemical properties of amino acids:

Why chemical properties of amino acid is importance?
Chemical reactions of amino acids are important:
 For identification and analysis of amino acids in protein.
 For identification of amino acid sequences in protein.
 For identification of specific amino acid residue of native protein that
are required for biological functioning e.g. hemoglobin (Histidine has
role in it).
 For chemical modification of amino acids residue in protein molecules
to produce change in biological activity.
 For chemical synthesis of the polypeptides (for medical purpose).
Properties of Amino Acids

Types of chemical reactions given by amino acids:

1.Reaction due to -COOH group.

2. Reaction due to –NH2 group
3. Reaction due to both
4. Reaction due to –R group
Properties of Amino Acids

Reaction due to -COOH group.

I. Formation of Esters
II. Reduced by LiBH4 to form alcohol
III. Decarboxylation of amino acids to form amine
IV. Formation of Amide
Properties of Amino Acids

2. Reaction due to –NH2 group

i. Methylation of amino acids
ii. Reaction with Nitrous Acids
iii. Reaction with formaldehyde
 Properties of Amino Acids
Methylation of amino acids: Methylation of amino acids is a crucial
process in biology that involves adding a methyl group (CH₃) to
specific amino acid side chains within proteins. This chemical
modification, catalyzed by enzymes called methyltransferases, plays a
significant role in regulating various cellular functions, including:
1. Protein activity: Methylation can alter the protein's structure and
folding, thereby affecting its interaction with other molecules and
its overall function.
2. Protein-protein interactions: Methylation can regulate how
proteins interact with each other, impacting various cellular
processes.
 Properties of Amino Acids
3. Gene expression: Methylation plays a role in regulating gene
expression by modifying histone proteins, which package DNA within
the nucleus.
Properties of Amino Acids

When amino acids react with nitrous acid (HNO₂) under acidic
conditions, they undergo a deamination reaction. This means they
lose their amino group (NH₂) and an equivalent of water (H ₂O),
resulting in the formation of a hydroxy acid with the same carbon
skeleton and retention of configuration at the chiral center (if
present) as the original amino acid.

R-CH(NH₂)COOH + HNO₂ → R-CH(OH)COOH + N₂↑ + H₂O

Properties of Amino Acids

Reaction with formaldehyde: Amino acids can react with

formaldehyde (HCHO) in various ways, depending on several
factors including:
 Reaction conditions: Temperature, pH, and the presence of
catalysts can significantly influence the specific products
formed.
 Side chain properties of the amino acid: The chemical nature of
the side chain (R group) plays a crucial role in determining the
reaction pathway and product formation.
 Properties of Amino Acids

1. N-methylation: Formaldehyde can react with the amino group

(NH₂) of the amino acid, forming a methylated amino acid. This
reaction is most prevalent for primary amino groups (those with only
one carbon atom attached to the nitrogen) like in glycine and
alanine.

2. Schiff base formation: Under specific conditions, formaldehyde

can condense with the amino group of the amino acid, forming a
Schiff base. This is a transient, unstable intermediate product that
can further react to form other products depending on the
surrounding environment.
 Properties of Amino Acids
 Cyclization: In the case of cysteine (Cys), which has a thiol group
(-SH) in its side chain, formaldehyde can react to form a
thiazolidine ring structure. This reaction is specific to cysteine due
to the unique reactivity of the thiol group.
 Cross-linking: Under specific conditions, formaldehyde can react
with the amino groups of different amino acids, forming covalent
bonds and leading to the cross-linking of these molecules. This can
impact protein structure and function.
 Disproportionation: Formaldehyde can undergo disproportionation
in the presence of certain amino acids, leading to the formation of
products like methanol and formic acid.
Properties of Amino Acids

3. Reaction due to both functional group

i. Peptide formation
ii. Ninhydrin test
Classification of Proteins
 Classification of Proteins

1. Classification of protein on the basis of Structure and

composition:

 This Classification of protein is based on shape or structure and

composition.
 They are classified into three types; fibrous, globular and
derived protein.
Classification of Proteins

1. Fibrous protein:
 They are elongated or fiber like protein.
 Axial ratio (length: breadth ratio) is more than 10
 They are static in nature with simple structure.
 They have less biological functions
 They are mostly present in animals
Examples;
Fibrous proteins are further classified as a simple and
conjugated
 Classification of Proteins

2. Globular protein:
 They are spherical or globular in shape.
 Axial ratio is always less than 10
 They are dynamic in nature (can flow or move) with higher degree of
complexity in structure.
 They have variety of biological functions
Examples; enzymes, hormones etc.
Globular protein is further classified on the basis of composition or
solubility.
 Classification of Proteins

i. Simple or homo globular protein:

They are composed of amino acids only.
Some examples are; Protamine, histone, Albumin, Globulin etc.

ii. Complex or conjugate or hetero globular protein:

These proteins in which protein are always linked by non-protein moiety
to become functional. So, they are composed of both protein and non-
protein components. The non-protein component is known as prosthetic
group.
On the basis of prosthetic group, they are classified as follows;
 Classification of Proteins

A.Metalloprotein:
 They have metal prosthetic group.
 Some metals such as Hg, Ag, CU, Zn, Fe etc, strongly binds with proteins such
as collagen, albumin, casein by –SH group of side chain of amino acids. Eg.
Ceruloplasmin; contains copper as prosthetic group
 Some other metals such as Calcium weakly binds with protein. Eg.
Calsequestrin, calmodulin
 Some metals such as Na, K etc. do not binds with protein but associate with
nucleic acids protein.
 Classification of Proteins

B. Chromoprotein:
 They have colored prosthetic group.
Some examples are;
Hemoprotein: Hemoglobin, myoglobin, chlorophyll, cytochrome,
peroxidase, haemocyanin
Flavoprotein: Riboflavin (Vit B2) give yellow/orange color to FAD
requiring enzymes.
 Classification of Proteins

C. Glycoprotein/Mucoprotein:
They have carbohydrate as prosthetic group
Eg. Antibody, complement proteins, Heparin, Hyaluronic acid

D. Phosphoprotein:
They have phosphate group as prosthetic group.
Eg. Caesein (milk protein binds with calcium ion to form calcium salt of
caseinate)
Ovovitellin; present in egg yolk
Calcineurin
Classification of Proteins

E. Lipoprotein:
They have lipid as prosthetic group.
Eg. Lipovitelline, chylomicrons
F. Nucleoprotein
Conjugated protein consisting of a protein linked to a nucleic acid, either DNA
(deoxyribonucleic acid) or RNA (ribonucleic acid). The protein combined with
DNA is commonly either histone or protamine; the resulting nucleoproteins are
found in chromosomes.
 Classification of Proteins

3. Derived protein:
 These protein are the derivatives of either simple or complex protein
resulting from the action of heat, enzymes and chemicals.
 Some artificially produced protein are included in this group.
 They are classified as primary derived protein and secondary derived
protein.
i. Primary derived protein:
The derived protein in which the size of protein molecules are not altered
materially but only the arrangement is changed.
Some examples are;
 Classification of Proteins

2. Secondary derived protein:

 The derived protein in which size of original protein are altered.
 Hydrolysis has occurred due to which size of protein molecule
are smaller than original one.
Examples;
a) Proteoses:
They are produced by the action of dilute acid or digestive
enzymes when the hydrolysis proceeds beyond the level of
metaprotein.
They are soluble in water
They are not coagulated by heat. • Eg. Albumose, Globulose etc.
Classification of Proteins

2. Classification of protein on the basis of biological

functions:
1. Catalytic protein:
They catalyze biochemical reaction in cells. Eg. Enzymes
and co-enzymes.
Classification of Proteins

2. Structural protein;
They make various structural component of living beings.
Eg. Collagen make bone, Elastin make ligamnets and keratin make
hair and nails

3. Nutrient protein:
They have nutritional value and provide nutrition when consumed.
Eg. Casein in milk
Classification of Proteins

4. Regulatory protein:
They regulate metabolic and cellular activities in cell and
tissue.
Eg. Hormones
5. Defense protein:
They provide defensive mechanism against pathogens.
Eg. Antibodies, complement proteins
Classification of Proteins

6. Transport protein:
They transport nutrients and other molecules from one
organ to other.
Eg. Haemoglobin
7. Storage protein:
They stores various molecules and ions in cells.
Eg. Ferritin store Iron
Classification of Proteins

8. Contractile or mobile protein:

They help in movement and locomotion of various body
parts.
Eg. Actin, myosin, tubulin etc
9. Toxic protein:
They are toxic and can damage tissues.
Eg. Snake venom, bacterial exotoxins etc.
Structure of Protein

 Depends upon the spatial arrangement of polypeptide

Chain
 Three Arrangement are possible
 Four structure are possible
Those are
1. Primary
2. Secondary
3. Tertiary
4. Quaternary
Structure of Protein

Primary Structure of Protein:

 The Primary structure of proteins is the exact ordering of amino acids forming
their chains.
 The exact sequence of the proteins is very important as it determines the final
fold and therefore the function of the protein.
 The number of polypeptide chains together form proteins. These chains have
amino acids arranged in a particular sequence which is characteristic of the
specific protein.
 Any change in the sequence changes the entire protein.
Structure of Protein
Structure of Protein

Secondary Structure of Protein

 Secondary structure of protein refers to local folded structures that form within
a polypeptide due to interactions between atoms of the backbone.
 The proteins do not exist in just simple chains of polypeptides.
 These polypeptide chains usually fold due to the interaction between the amine
and carboxyl group of the peptide link.
 The structure refers to the shape in which a long polypeptide chain can exist.
They are found to exist in two different types of structures α – helix and β –
pleated sheet structures.
Structure of Protein

Secondary Structure of Protein

 This structure arises due to the regular folding of the backbone of
the polypeptide chain due to hydrogen bonding between -CO
group and -NH groups of the peptide bond.
 However, segments of the protein chain may acquire their own
local fold, which is much simpler and usually takes the shape of a
spiral an extended shape or a loop. These local folds are termed
secondary elements and form the proteins secondary structure.
Structure of Protein

a) α – Helix:
α – Helix is one of the most common ways in which a polypeptide chain forms all
possible hydrogen bonds by twisting into a right-handed screw with the -NH
group of each amino acid residue hydrogen-bonded to the -CO of the adjacent
turn of the helix. The polypeptide chains twisted into a right-handed screw.

(b) β – pleated sheet:

In this arrangement, the polypeptide chains are stretched out beside one another
and then bonded by intermolecular H-bonds. In this structure, all peptide chains
are stretched out to nearly maximum extension and then laid side by side which is
held together by intermolecular hydrogen bonds. The structure resembles the
pleated folds of drapery and therefore is known as β – pleated sheet
Structure of Protein
 Structure of Protein

Tertiary Structure of Protein

 This structure arises from further folding of the secondary structure of the
protein.
 H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces
stabilize this structure.
 The tertiary structure of proteins represents overall folding of the polypeptide
chains, further folding of the secondary structure.
 It gives rise to two major molecular shapes called fibrous and globular.
 The main forces which stabilize the secondary and tertiary structures of
proteins are hydrogen bonds, disulphide linkages, van der Waals and
electrostatic forces of attraction.
Structure of Protein
Structure of Protein

Quaternary Structure of Protein

 The spatial arrangement of various tertiary structures gives rise
to the quaternary structure. Some of the proteins are composed
of two or more polypeptide chains referred to as sub-units. The
spatial arrangement of these subunits with respect to each other
is known as quaternary structure.
Structure of Protein
Structure of Protein
Structure as a Ligands

The available metal binding sites of Proteins are

1. N-terminal NH2
2.C-terminal COO-
3.Functional side chain of amino acid residue.
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