BIO462

CHAPTER 1:
INTRODUCTION, BIOMOLECULES,
THERMODYNAMICS & PROPERTIES
OF WATER
Introduction & Biomolecules
 LEARNING OUTCOMES

Students should be able to :

 Define biochemistry, biomolecules

 Recognize various form of biomolecules

 Identify functional groups for specific biomolecules

 Understand thermodynamics

 Distinguish between two different laws of thermodynamics

 INTRODUCTION

 How does biochemistry describe life processes?

 Living things are diverse
 But, they have two things in common

 Their cells ALL use the same types of biomolecules

 They ALL use energy

WHAT IS BIOCHEMISTRY ?
METABOLIC PATHWAY
 BIOMOLECULES

 Biomolecules are organic molecules that make up living

things.
 Protein - amino acid

 Nucleic acid – nucleotide

 Carbohydrate - monosaccharide

 Lipid- fatty acid & glycerol

 Polymer??
 Monomer??
 FUNCTIONAL GROUP OF BIOMOLECULE ?

 Functional groups are specific groups of atoms within

molecules that responsible for the characteristic of
chemical reactions of those molecules.
 Number and arrangement of the groups help give each
molecule its unique properties
 Most important functional groups in biological
processes:
 Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and
phosphate
CHEMICAL
Hydroxyl
GROUP
In a hydroxyl group (-OH), a hydrogen atom is bonded to an
oxygen atom, which in turn is bonded to the carbon skeleton of
the organic molecule.
STRUCTURE

NAME OF
Alcohols
COMPOUND

EXAMPLE Ethanol, the alcohol present in alcoholic beverages

Is polar as a result of the electrons spending more time near

FUNCTIONAL the electronegative oxygen atom.
PROPERTIES Can form hydrogen bonds with water molecules, helping

dissolve organic compounds such as sugars

CHEMICAL
Carbonyl
GROUP
The carbonyl group (C=O) consist of a carbon atom joined to an
oxygen atom by a double bond

STRUCTURE

1. Ketones if the carbonyl group is within a carbon skeleton

NAME OF
2. Aldehydes if the carbonyl group is at the end of the carbon
COMPOUND
skeleton

Acetone, the simplest ketone

EXAMPLE
Propanal, an aldehyde

FUNCTIONAL
???
PROPERTIES
CHEMICAL
Carboxyl
GROUP
When an oxygen atom is double bonded to a carbon atom that is
also bonded to an -OH group, the entire assembly of atoms is called a
carboxyl group (-COOH).
STRUCTURE

NAME OF
Carboxylic acids, or organic acids
COMPOUND

EXAMPLE Acetic acid, which gives vinegar its sour taste

FUNCTIONAL
???
PROPERTIES
CHEMICAL
Amino
GROUP
The amino group (-NH2) consists of a nitrogen atom bonded to two
hydrogen atoms and to the carbon skeleton

STRUCTURE

NAME OF
Amines
COMPOUND

Because it also has a carboxyl group, glycine is both an amine and

EXAMPLE a carboxylic acid; compounds with both groups are called amino
acids.

FUNCTIONAL
???
PROPERTIES
CHEMICAL
Sulfhydryl
GROUP
The sulfhydryl group consists of a sulfur atom bonded to an atom of
hydrogen; resembles a hydroxyl group in shape.

STRUCTURE

NAME OF
Thiols
COMPOUND

EXAMPLE Cysteine is an important sulfur-containing amino acid.

FUNCTIONAL
???
PROPERTIES
CHEMICAL
Phosphate
GROUP
Phosphate group, a phosphorus atom is bonded to four oxygen
atoms; one oxygen is bonded to the carbon skeleton; two oxygens
carry negative charges.
STRUCTURE

NAME OF
Organic phosphates
COMPOUND

In addition to taking part in many important chemical reactions in

EXAMPLE cells, glycerol phosphate provides the backbone for phospholipids,
the most prevalent molecules in cell membranes.

FUNCTIONAL
???
PROPERTIES
 METABOLISM OVERVIEW

 Metabolism ?????
 Catabolic reaction are energy yielding: the
breakdown of larger molecules into smaller ones

 Anabolic reaction are energy requiring: the

synthesis of larger molecules from smaller ones
Thermodynamic
 BIOENERGETIC

• BIOENERGETICS: study of energy transformation

that occur in living organism
• Describe transfer and utilization of energy in
biological system

• Energy (E) – capacity to do work

2 FORM OF ENERGY
BASIC CONCEPTS OF THERMODYNAMIC

 important in thermoD  distinction of system and

surrounding
 The system  the portion of the universe with
which are concerned
 The surroundings  everything else in universe
BASIC CONCEPTS OF THERMODYNAMIC

 3 basic systems:
 Isolated system (cannot exchange matter /
energy with its surrounding
 Closed system (can exchange energy)
 Open system (can exchange either or both)
 Matter nutrient and waste product
 Living things are ‘open system’
 Absorb energy (light and chemical)
 Release heat and metabolic waste
 2 law of thermodynamic govern energy
transformation in organism
1st LAW OF THERMODYNAMIC
 Energy can be transferred and transformed but cannot
be created or destroyed

 Therefore, energy generated in any system is energy

that has been transformed from one state to another
(eg: chemically stored energy transformed to heat)
HEAT, WORK, INTERNAL ENERGY,
ENTALPHY
 The increase in the internal energy of the system is
equal to the amount of energy added by heating
the system minus the amount lost as a result of
the work done by the system on its surroundings

∆E = q - w
E=internal energy
q=heat absorb by the system
w=work done by the system
 HEAT, WORK, INTERNAL ENERGY,
ENTALPHY

 Enthalpy (H) is a measure of the total energy of a

thermodynamic system.
 +∆H indicates that heat is being absorbed in the
reaction (it gets cold) endothermic
 -∆H indicates that heat is being given off in the
reaction (it gets hot)exothermic
 2nd LAW THERMODYNAMIC
 Expresses concept that events in universe have
direction
 Systems tend to proceed from ordered to
disordered states
ENTROPY (S)
 Every energy transfer / transformation increase the
entropy of the universe
 Entropy (S) = measure of disorder or randomness
(dispersal of energy or matter in a system)
 Entropy increases as one goes from a solid to a liquid, or
more dramatically, a liquid to a gas
 SPONTANEITY
 Concept of entropy help us understand why certain
processes occurs on its own without outside help
 Spontaneous  process occurs without input of energy
 Eg: gradual decay of unmaintained building
 CHANGE OF ENERGY
 Initial state --> ??
 Final state --> ??
 Equilibrium state --> ??
FREE ENERGY
 The direction and extent to which chemical
reaction proceed  determined by 2 factors

 Entalphy (∆H), measure of the change in heat content

of the reactants and products

 Entropy (∆S), measure of the change in randomness

or disorder of reactant and products
 FREE ENERGY
 However mathematically, ∆H and ∆S can be used to
defined FREE ENERGY, which predict in which a reaction
proceed spontaneously.
 Free energy = G = Gibbs free energy
 Free energy, ∆G = ∆H -T ∆S
 ∆G = free energy change, energy available to do work
 When ∆G is negative, it indicates that a reaction or process is
spontaneous.
 A positive ∆G indicates a non-spontaneous reaction.
 ∆G = 0, reaction at equilibrium
EXERGONIC REACTION

spontaneous
ENDERGONIC REACTION

Non-spontaneous
Properties of Water, Acid & Base
 LEARNING OUTCOMES

Students should be able to :

 Recognize structure of molecule water

 Describe electronegativity and polarity

 Distinguish between hydrophilic and hydrophobic

 Compare acid and base

 Understand Henderson-Hesselbach equation

 Describe dissociation of carbonic acid in blood

Properties of water
 Water is essential to living organism

 No water = no life on earth

 Why is water important?
 Most biochemical processess essential for living
organism takes place in presence of water
 Water is the best solvent known – universal solvent
 Why is water the best solvent?

 It is due to the POLARITY of water molecule.

 So, the question is: what is polarity?
 STRUCTURE OF WATER

H H

1 molecule of water is
made up of 2 hydrogen atoms
bonded with 1 oxygen atom
Millions of molecules of water
make up 1 raindrop
 STRUCTURE OF WATER

The bond that forms water

is a covalent bond
Covalent Bonds

 A covalent bond is the sharing of a pair of valence

electrons by two atoms
 If electrons in a covalent bond are shared equally,
then this is a non-polar covalent bond
 If the electrons in a covalent bond are not equally
shared by the two atoms, then this is a polar
covalent bond
 Why is water called a polar compound?

 Water is polar because of the difference in

electronegativity between hydrogen and oxygen
 Electronegativity  tendency of an atom to attract electrons
to itself in a chemical bond.
 The highly electronegative oxygen atom attracts electrons or
negative charge to it, making the region around the oxygen
more negative than the areas around the two hydrogen
(uneven distribution of charge)  dipole
 Bent structure and uneven distribution of charge make it
polar
Hydrogen Bond

 Hydrogen bonds form when a hydrogen atom that is

already covalently bonded to a strongly electronegative
atom is attracted to another strongly electronegative
atom

 These strongly electronegative atoms are typically

nitrogen or oxygen
In the water molecule, the hydrogen atoms have partial positive
charges and oxygen atom partial negative charges

Areas with opposite charges are attracted

Hydrogen bonds have a significant effect on the physical
properties of hydrogen-bonded compounds
Water molecules have a strong tendency to stick
to one another, a property known as cohesion.
This is due to the hydrogen bonds among the
molecules, which gives water a high surface
tension. The molecules at the surface of the water
"stick together" to form a type of "skin" on the
water, strong enough to support very light objects.
 SOLVENT PROPERTIES OF H20
 Three types of molecules characteristics when mixed
with water

 Hydrophilic
 Hydrophobic

 Amphipathic
 SOLVENT PROPERTIES OF H20
 Ionic compound and polar compound tend to dissolve in water
 H20 can interact with and dissolve other polar compounds and
compounds that ionize
 Eg: NaCl dissolve in H20
Each dissolved Na+ attracts the –ve ends of H20 molecule, wherease Cl-
attracts the +ve ends
 SOLVENT PROPERTIES OF H20
• Micelle: a spherical arrangement of organic molecules in water
solution clustered so that:
– Their hydrophobic parts are buried inside the sphere

– Their hydrophilic parts are on surface of sphere and in contact

with the water environment

Why do oil and water mixed together
separate into layers?
Acid & Base
 ACIDS AND BASES
 An acids is a molecule that acts as a proton donor
(hydrogen ion)
 Strong acid: an acid that is completely ionized in aqueous
solution
(E.g: HCl, HBr, HI, HNO3, HCLO4, H2SO4 )

 A base is a molecule that acts as proton acceptor

 Strong base: a base that is completely ionized in aqueous
solution
(E.g: LiOH, NaOH, KOH, Ca(OH)2)
 WEAK ACIDS AND BASES

 An acid or base that

is incompletely
ionized in aqueous
solution
 E.g: acetic acid
 What is a pH?
 a measure of the hydrogen ion, or
proton [H+] concentration in a
solution
 pH is defined as negative logarithm
(to base 10) of the hydrogen ion
concentration in mol/L or M

pH = - log10 [H+]

 [H+] increase, the pH decrease

 [H+] decrease, the pH increase
Calculate acid

 Calculate pH of 1 x 10-3 M HCl

pH = - log [H+]
= - log (1o-3)
=3
 ACIDS DISSOCIATION
 Acid – proton donor
 Base – proton acceptor
 Acid and base always come in pair – every proton donor
must have proton acceptor
 Both sides of dissociation reaction will contain acid and
base
conjugate acid-base pair
O O
+
CH3 COH + H2 O CH3 CO - + H3 O
Acid Base Conjugate base Conjugate acid
of acetic acid of water

conjugate acid-base pair

ACIDS DISSOCIATION CONSTANT, Ka

 Ka, the acid dissociation constant is an equilibrium constant

that refers to the dissociation of an acid.
 The ionization of an acid in water is a reversible reaction.
 For the reaction in which the acid HA dissociates to form the ions
H+ and A-

Bracket refer to
molar concent. =
moles per liter
ACIDS DISSOCIATION CONSTANT, Ka

 Ka provides a measure of the equilibrium position

 if Ka is large, the products of the dissociation reaction
are favoured
 if Ka is small, undissociated acid is favoured

 Ka provides a measure of the strength of an acid

 if Ka is large  stronger acid
 if Ka is small  weak acid
The Ion Product Constant of Water

 The ionization of pure water produces equal concentration of

H+ and OH-
Calculate base

 Calculate pH of 1 x 10-4 M NaOH

In 1 x 10-4 M NaOH, [OH] = 10-4

Because Kw = [H][OH]= 10-14

[H]=(10-14)/(10-4)
=10-10
pH = -log[H] = 10
Henderson-Hasselbalch equation

 Ka value are numerically small and inconvenient in

calculation, more easier in logarithmic scale
 Thus, Henderson-Hasselbalch equation is derived:

Henderson-
Hasselbalch
equation
Henderson-Hasselbalch equation

 Handerson-Hasselbalch equation:

 From this equation, we see that

 When the concentration of weak acid and its conjugate base are
equal, the pH of solution equals the pKa of the weak acid
 When pH<pKa, the weak acid predominates
 When pH>pKa, the conjugate base predominates
 From this equation it can be seen that the smaller the pKa value,
the stronger is the acid
Calculate the pH of a buffer solution made from
0.20 M HC2H3O2 and 0.50 M C2H3O2 - that has an
acid dissociation constant for HC2H3O2 of 1.8 x 10 -
5 . Solve this problem by plugging the values into

the Henderson-Hasselbalch equation for a weak

acid and its conjugate base.
 TITRATION CURVES
 Titration: an experiment which measured amounts
of acid (or base) are added to measured amounts
of base (or acids)
 TITRATION CURVES
 From titration curve, the most effective buffering, indicated by the
region of minimum slope on the curve.
 Equivalence point / mid point: the point in an acid-base titration
at which enough acid has been added to exactly neutralize the
base (or vice versa)

Equivalence point
Polyprotic acids

 Polyprotic acids  specific acids that are capable of losing more

than a single proton per molecule in acid-base reaction
 E.g: Diprotic  release two proton, 2 equivalence points
 Monoprotic?? Triprotic??
 BUFFERS
 Buffer: a solution whose pH resists change upon
addition of either more acid or more base
 Why are buffers important?

 Body is very sensitive to its pH level

 Outside the acceptable range of pH, proteins are denatured
and digested, enzymes lose their ability to function, and death
may occur.
 Whenever arterial blood pH rises above 7.45 a person is said to
have alkalosis. A drop on arterial pH to below 7.35 results in
acidosis.
 Buffers are needed to stabilize pH changes in organism
 H2PO4, HPO4 is principal buffer in cells
 Bicarbonate buffering system

 carbon dioxide (CO2) can be shifted through carbonic acid (H2CO3) to

hydrogen ions and bicarbonate (HCO3-) as shown below.

 If the blood gained excess hydrogen ions (acidosis), some of those

hydrogen ions would shift to carbon dioxide, minimizing the increased
acidity.
 If the blood pH drops too low, the body will compensate by increasing
breathing, expelling CO2, and shifting the above reaction to the right
such that less hydrogen ions are free; thus the pH will rise back to
normal.
 Normal ventilation can
maintain blood pH  a
state of acid-base balance

 Hyperventilation can
result in increased blood
pH (more basic) 
alkalosis

 Hypoventilation can
result in decreased blood
pH (more acidic)
acidosis
END OF THIS CHAPTER