LEVY MWANAWASA

MEDICAL UNIVERSITY

MEDICAL BIOCHEMISTRY
MCT 221

LECTURER 1
2019
 What is Biophysical chemistry?

— In Biochemistry we study physical properties of

biological macromolecules at either a chemical
sequence level or structural level.
— The study of the physical properties of biological
macromolecules at chemical sequence level or
structural level is called Biophysical chemistry.
— Biophysical chemistry is also used to describe
techniques suited to understanding the physical
properties of biological molecules.
— The goal of the biophysical chemistry is to provide
physical explanations for the ways in which important
biological systems function.
 What is Biophysical chemistry ?

— Cells of living organisms contain biomolecules such

protein, carbohydrates, lipids and nucleic acids
which are dissolved in water.
— Living organisms are about 70% water, therefore
constituents of living organisms are bathed in
water.
— This means that biochemical reactions occur in
aqueous solution, that is in water.
— Therefore water interacts with biomolecules and
this interaction determines the structure, stability,
properties and functions of these biomolecules.
 What is Biophysical chemistry ?

— Since water is the most abundant substance in

living systems, the study of physical and chemical
properties of water will help us understand the
properties of biomolecules in living organisms.

— To understand the properties of water we must

appreciate the structure of water.

— The first impression one has upon looking at water

H-O-H is that water is a linear compound but that
is not the case.
 What is the structure of water ?

— Water has two hydrogens attached to oxygen.

— And oxygen has two unshared pair of electrons.
— The two lone pair repel each other and also repel the
bond electrons between oxygen and hydrogen.
— This repulsion makes water forms a bent structure
or v-shaped structure.
— Consequently the H-O-H bond angle is 104.5o,
slightly less than the 109.5°.
What is the structure of water ?

H δ
+
Electropositive
region
δ– O δ+
H

Electronega δ–
tive region

• The green coloured regions are a pair of

electrons
• Water molecule forms a bent structure. 6
 What is the structure of water ?

— The oxygen atom has electronegativity of 3.0 and

hydrogen has electronegativity of 2.1.
— The strongly electronegative oxygen atom pulls
electrons away from the hydrogen nuclei, leaving
them with partial positivity while oxygen becomes
with partial negatively charged.
— As a result there is an electrostatic attraction
between the oxygen atom of one water molecule and
the hydrogen of another.
— The oxygen sort of donates a lone pair of electrons to
a hydrogen which is electron deficient forming a
physical bond called a hydrogen bond.
What is the hydrogen bond ?

H 104.5o H δ+
δ+

O
2δ−

Hydrogen bond 0.177nm

δ+

Covalent bond 0.0965 nm

δ+
2δ−

8
What are the consequences of
hydrogen bonds in water ?

— Hydrogen bonding makes various water molecules

in water to be tightly bound to each other.
— Therefore hydrogen bonds make water to have the
following properties:
— a high melting point,
— a boiling point,
— a high heat of vaporization
— a high heat of fusion
— a high dielectric constant
What are the consequences of
hydrogen bonds in water ?

— A high heat of vaporization ensures that less body

fluid is lost against more heat lost. This ensures
water bathes cells and makes them pliable.

— A high specific heat capacity of water ensures that

the production of heat or heat loss is minimized.
This ensures the body maintains a body temperature
at near constant which would consequently support
enzymatic processes.
— A high heat of fusion prevents contents of the cell
from freezing.
 What are the consequences of
hydrogen bonding –high heat of
vaporization

— Water has a high heat of vaporization - large amount

of heat is needed to evaporate water because
hydrogen bonds must be broken to change water
from liquid to gaseous state.

— A high dielectric constant ensures that more solute

or metabolites are dissolved and made available for
cellular metabolism.

— These properties described enable water to sustain

life.
What are bio-molecular forces ?

— Cells of living organisms contain biomolecules such

protein, carbohydrates, lipids and nucleic acids
which are dissolved in water.
— The various biomolecules interact with each other
and with the environment.
— These interactions determines the structure,
stability, properties and functions of these
biomolecules.
— The interaction biomolecules with each other are
called Biomolecular interactions
— The forces between biomolecules are called bio
molecular forces.
What are bio-molecular forces ?

— Biomolecular forces includes:

— Hydrogen bonding;

— Hydrophobic interaction;

— Van der waal’s forces;

— Pie-pie interaction
 Examples of bio-molecular
What is a hydrogen bond?
— Hydrogen bond is a weak non covalent
bond that occurs when a hydrogen bonded to a
highly electronegative element like oxygen bond to
a lone pair of electrons of a highly electronegative
element in an another molecule or of the same
molecule.
— Hydrogen bonding occurs when there is a hydrogen
donor and a hydrogen acceptor.
— Hydrogen bonding has a maximum strength when
the angle between the covalent bond to the hydrogen
atom and the hydrogen bond is 180°
What conditions are required for
formation of hydrogen bonding ?

— Note that there are two main conditions for

formation of hydrogen bond namely:
— There must be a hydrogen donor and
— There must be a hydrogen acceptor

— The hydrogen acceptor is a highly electronegative

atom such as oxygen or nitrogen and fluorine which
possesses a lone pair of electrons.

— The hydrogen donor is a hydrogen covalently

bonded to another electronegative atom.
What are features of hydrogen
bonding ?

— The Hydrogen bonds are weaker than covalent

bonds.
— The Hydrogen bonds in liquid water have a bond
dissociation energy of about 20 kJ/mol, compared
with 348 kJ/mol for the covalent C-C bonds.

— Hydrogen bonding is enthalpically driven.

— Although most of the molecules in liquid water are

engaged in hydrogen bonding, the life time of each
hydrogen bond is less than 1x10-9s.
What are features of hydrogen
bonding ?

— The Hydrogen bonds may be formed between

— Protein and another protein
— Carbohydrate and another carbohydrate
— Nucleic acid and another nucleic acid

— These interactions aid in formation of a biological

activity biomolecule.
 Examples of bio-molecular
What is a hydrophobic bond?

— When you introduce a fat or lipid in water, initially

water molecules surround the fat molecules
— However, later on the fat molecules which are called
hydrophobes start aggregating together excluding
water molecules from their space.
— This tendency of non polar molecules to aggregate
together excluding water molecules from their space
is called Hydrophobic effect
— The aggregating together non polar molecules
together excluding water molecules from their space
is called hydrophobic interaction.
 Examples of bio-molecular
What is a hydrophobic bond?

— The aggregating together non polar molecules

together excluding water molecules from their space
is called hydrophobic interaction.
— This interaction occur because when you introduce
nonpolar biomolecules in water the non-polar
molecules interfere with water-water interactions
which exist between water molecules but nonpolar
molecules are unable to form water-solute
interactions.
— As a result these nonpolar molecules aggregate
together
 What conditions are required for
formation of hydrogen interactions?

— Hydrophobic effect may be said to the tendency

of nonpolar molecules to become buried are
away from water because that leads to
increased entropy of water.
— This effect is a major driving force for instance
protein folding.
— Note that there are main conditions for
formation of hydrophobic interaction is the
presence of hydrophobic groups in the vicinity.
— The formation of hydrophobic interaction is
driven by increasing the entropy of water
molecules.
What is hydrophobic effect?
 What are features of
hydrophobic bonds ?

— The Hydrophobic bonds are weaker than covalent

bonds.

— The Hydrophobic bonds in liquid water have a bond

dissociation energy of about less than 10 kcal/mol

— Hydrogen bonding is entropically driven.

 What are features of
hydrophobic bonds?

— The Hydrophobic bonds may be formed between

— Protein and another protein
— lipid and another lipid
— Nucleic acid and another nucleic acid

— These interactions aid in formation of a biological

activity biomolecule.
 Examples of bio-molecular
What is a hydrophobic bond?
— Other examples of hydrophobic bonds are:
— Ionic –ionic interactions.

— Van der waal’s interactions.

— Pie-pie interactions.

— These forces are individually weak but collectively

have a significant influence on the three dimensional
structures of proteins, nucleic acids,
oligosaccharides, and membrane lipids
— These interactions aid in formation of a biological
activity biomolecule.
 Water as a universal solvent

— Uncharged but polar biomolecules such as sugars

dissolve readily in water because of they are able
to hydrogen bonds with water.
— That is hydroxyl groups or carbonyl oxygen of
the sugar can form hydrogen bond with oxygen
and hydrogen of water respectively.
— Therefore compounds such as alcohols,
aldehydes, ketones, and compounds containing
N-H bonds all form hydrogen bonds with water
molecules and tend to be soluble in water
 Water as a universal solvent

— Compounds that dissolve in water are called

hydrophilic compounds.

— Compound such as salts like sodium chloride

dissolve in water despite that they do not
hydrogen bond why?

— It should noted that Na+ and Cl- ions are held

together by an electrical force of attraction
which follows the coulomb’s law.
 What is dielectric constant of a
solvent?

— The force of electrostatic interactions between

charged ions in the ionic lattice is given by.

— F= Q1Q2
Er2
— Where F = force of ionic interactions in a solution
Q=magnitude of the charges
R=the distance between the charged groups
E=dielectric constant of the solvent in which
the interactions occur
 Water as a universal solvent

— Water dissolves such salts as NaCl by having the

oxygen of water which negatively charged
interacting with Na+ in the NaCl lattice thus
stabilizing the Na+ and by having the hydrogen of
water which positively charged interacting with Cl-
in the NaCl, this weakening the electrostatic
interactions between Na+ and Cl- and thus
counteracting their tendency to associate in a
crystalline lattice making the NaCl dissolve in water.
 Water may act as a solvent

— Water may interact with charged polar substances

such as
Sodium chloride thus dissolving it.
— Water dissolves such salts as NaCl by interacting with Na+ in the
NaCl lattice thus stabilizing the Na+ and by interacting with
Cl- in the NaCl, this weakening the electrostatic interactions between
Na+ and Cl- and thus counteracting their tendency to associate in a
crystalline lattice
 What is dielectric constant of a
solvent?

— What water molecules are doing is to effectively

screening the electrostatic interactions between
charged ions in the ionic lattice.
— The ability to diminish the strength of electrostatic
attractions in an ionic lattice is called dielectric
constant.
— The higher the dielectric constant of a solvent the
higher is the diminishing of strengths of electrostatic
attractions between ions.
— Water has a high dielectric constant of about 78.5,
— Water diminishes the strengths of electrostatic
attractions by a factor of 78.5, compared with the
same interactions in a vacuum.
 What is dielectric constant of a
solvent?

— How do compounds such the charged

biomolecules with a charged functional groups
such as COO-, NH3+ and phosphate esters and
anhydrides dissolve in water.
— These molecules interact with each other by
solute-solute hydrogen bonds.
— In presence of water, the water replaces these
solute-solute hydrogen bonds with water-solute
hydrogen bonds, thus screening or reducing the
electrostatic interactions between solute
molecules.