Chemistry of Biomolecules
Basic Concepts
Chemical Bonds and Chemical Rections
• Covalent bonds are attractive forces present
between atoms in molecules/compounds and
are formed by sharing electrons between
atoms.
• Covalent bonds generally do not break at
room temperature.
• Chemical reactions involve either forming or
breaking or both of covalent bonds.
Consider the following reactions
involving atoms A and B
• Formation of covalent bond
A + B → A-B
• Breaking of covalent bond
A-B → A + B
• Both formation and breaking
A + A-B → A-A +
Elemental Composition
of the Human Body
• Only about 30 of more than 100 naturally
occurring chemical elements are constituent
of biomolecules in the living organisms.
• The elements needed for life are relatively
common in the earth's crust.
The six most abundant elements in
living organisms,
• in terms of percentage of the total mass and
also total number of atoms, are
hydrogen, oxygen, carbon, nitrogen, calcium
(Ca) and phosphorus (P),
which together make up over 99% of the mass
of most cells,
(with most of the H and O occurring as H2O).
Other elements/minerals
• that are significant constituents of biological
molecules are
• sulphur (S), magnesium (Mg), sodium (Na),
potassium (K) and chlorine (Cl) –
• major elements
(or macro elements/minerals).
In addition, living things use traces of
certain other elements/minerals.
• In humans they are
• iron (Fe), manganese (Mn), copper (Cu), zinc
(Zn), iodine (I), fluorine (F), selenium (Se),
cobalt (Co) and molybdenum (Mo) –
• trace elements (micro or minor
elements/minerals).
Element
Percent
by
Percent by
Number
Mass
of
Atoms
25.6
Potassium
0.2
0.03
18
10
3
9.5
63
1.3
Sulfur
Chlorine
Sodium
0.2
0.2
0.1
0.04
0.04
0.03
1.5
0.24
Magnesium 0.05
Phosphorus 1.2
0.24
Iron
Element
Percent
Mass
Oxygen
65
Carbon
Hydrogen
Nitrogen
Calcium
Percent
by
by
Number
of
Atoms
0.05
Cobalt,
Copper,
< 0.05 each
Zinc, Iodine
Selenium,
Fluorine
< 0.01 each
0.01
Besides these elements that are
necessary for life, our bodies contain
trace quantities of most other
elements,
• including some that are harmful,
such as
mercury, cadmium, and lead.
Carbon Atom
• Organic compounds are the most important
molecular constituents of living systems and
are composed of carbon atoms.
• Carbon is tetravalent and
in organic compounds is
covalently joined with other carbon atoms and
with hydrogen, oxygen, nitrogen or sulfur.
The special bonding properties of carbon permit
the formation of a
great variety of molecules.
O, N, S, P and Cl
• are electronegative atoms (atoms having high
affinity for electrons) on the one hand, and
• Na, K, Ca, Mg, Fe, Cu and Mn
are electropositive atoms (atoms which readily
give up electrons).
This property has much influence on
many physical and chemical properties of
biomolecules.
Biomolecules
Biomolecules are those molecules which
are
present in living organisms
having one or more functions or
metabolically derived
from these molecules.
Biomolecules
• Thus protein is a biomolecule because
it is present in the body and
has functions.
Urea is also present in the body and does not
have any functions.
However, since it is derived from protein,
it is also considered to be a
biomolecule.
Biomolecules
• Nitrogen gas (N2) is present in the blood.
However, neither does it have any function nor
is it metabolically produced in the body.
So clearly, N2 is not a biomolecule.
• There are also many other chemicals
present in the body as contaminants such as
mercury, lead, etc. and
they are not biomolecules either.
Biomolecules
•
•
•
•
•
•
Human body is composed of about
60% water,
15% proteins,
15% lipids,
2% carbohydrates and
8% minerals.
Basic Organic Chemistry for
Biochemistry
• Organic compounds = compounds composed of
carbon and hydrogen or its derivatives
•
• Organic compounds are divided into two classes:
aromatic compounds, which contain benzene or
similar rings of atoms, and aliphatic compounds
which do not contain those rings.
•
• Aliphatic compounds can be cyclic, like
cyclohexane, or acyclic, like hexane. They also can
be saturated, like hexane, or unsaturated, like
hexene.
Functional Groups in Organic
Compounds
• Hydroxyl/alcohol:
R–OH
• Aldehyde:
R-C-H
O
• Keto:
R1-C-R2
O
• Carboxyl:
R-C-OH (R-COOH )
O
Functional Groups in Organic
Compounds
• Amino:
R-NH2
• Imino
R1-NH-R2
Water
• All molecules and ions, in biological systems, are
dissolved or suspended in aqueous medium.
Virtually all biochemical reactions metabolism),
therefore, take place in the aqueous medium.
• Water is the medium, in which the first cells
arose, and it is the solvent the properties of
water that have shaped the course of evolution.
Without liquid water, terrestrial life could not
exist.
• All living organisms on Earth depend on water
and its unique chemical and physical properties.
Water
• Everything is soluble in water to some degree and the
structure and
interaction of biomolecules are profoundly influenced by
the aqueous solution in which biomolecules reside.
The week interaction within and between biomolecules
strongly is affected by the solvent properties of water.
• Unique properties of water are –
high latent heat,
its liquid state at wide range of temperature (0 to 100◦C),
ionization and its ability to form
hydrogen bond and ionic bond
with other water molecules and
also many other molecules.
Non-covalent Bonds
Non-covalent bonds are also attractive forces
between atoms, ions or molecules and
are also called weak bonds or weak interactions
because
they are 10 to 20 times weaker than covalent
bonds.
• Non-covalent bonds may be
intra-molecular (occurring between different
atoms of the same molecule) or
inter-molecular molecular (occurring between
different molecules).
Non-covalent Bonds
• Intra-molecular week bonds cause
bends in the molecule and are
responsible for the molecular shape or conformation.
For example,
proteins though have a linear covalent structure, assume
three-dimensional conformation due to the intramolecular non-covalent bonds.
• Inter-molecular week bonds, on the other hand, are
responsible for supra-molecular aggregations (complex
formation) of molecules.
Examples of supra-molecular aggregations are – crystals;
complexes of protein molecules; complexes of protein
and nucleic acids (nucleoproteins – chromatin and
ribosome); complexes of lipid and proteins
(lipoproteins, biological membranes).
Non-covalent Bonds
• There are basically 4 types of non-covalent
bonds –
1) ionic bond,
2) hydrogen bond,
3) hydrophobic bonds/interactions and
4) van der Waals forces.
• Ionic and hydrogen bonds are electrostatic
bonds because
both are formed due to charge.