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
Identify the differences between 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
BIOCHEMISTRY ?
Study of chemical and chemical interaction/processes
in any living organism
Metabolism = all chemical reaction occurs in the body
Millions of chemical reaction for living things to survive
~40,000 reaction / seconds
Deals with function and structure of cellular
component (CHO, protein, lipid, nucleic acids, other
biomolecules)
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??
LEVEL OF ORGANIZATION
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, methyl, carbonyl, carboxyl, amino, sulfhydryl, and
phosphate
TYPES OF FUNCTIONAL GROUP
TYPES OF FUNCTIONAL GROUP
METABOLISM OVERVIEW
Metabolism = the chemical reactions of
biomolecules
Catabolism + Anabolism
Catabolic reactions are energy yielding: the
breakdown of larger molecules into smaller ones
Anabolic reactions are energy requiring: the
synthesis of larger molecules from smaller ones
Thermodynamics
BASIC CONCEPTS OF THERMODYNAMICS
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 THERMODYNAMICS
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
Isolated system Closed system
Open system
BASIC CONCEPTS OF THERMODYNAMICS
Living things are ‘open system’
Absorb energy (light and chemical)
Release heat and metabolic waste
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
All cells require energy for various purposes;
◼ Synthesis of large molecule
◼ Cell division (mitosis and meiosis)
◼ Active transport in cells, etc.
TYPES OF ENERGY
Chemical energy – stored in chemicals bond of molecules, (e.g
glucose)
Heat energy – flow of the thermal energy from a hotter object to a
colder one
Solar energy - is the transport energy from the sun as
electromagnetic waves
Electrical energy – the flow of charged particles
Mechanical energy – the movement of body
2 FORM OF MECHANICAL ENERGY
Potential energy – type of
stored energy, that is the
energy of position
Kinetic energy – the energy of
movement/motion
1st LAW OF THERMODYNAMICS
Energy can be transferred and transformed but cannot
be created or destroyed
‘ Plant converting energy from sunlight into chemical
energy, plant as energy transformer not producer’
Therefore, energy generated in any system is energy
that has been transformed from one state to another
(eg: chemically stored energy transformed to heat)
The total energy of an isolated system is conserved
The 1st law explains that the total
‘quantity’ of energy in the universe
stays the same
HEAT, WORK & INTERNAL ENERGY
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
ENTHALPY
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
Endothermic reaction
The reactants have less
potential energy than do
the products.
Energy must be input in
order to raise the
particles up to the higher
energy level.
Non-spontaneous : process occurs
with an input of energy
Exothermic reaction
The reactants have
more potential energy
than the products have.
The extra energy is
released to the
surroundings.
Spontaneous : process occurs without
input of energy
2nd LAW THERMODYNAMICS
When energy is converted from one form to another (energy
available to do work) is degraded into a less-usable form (heat)
that disperses into the environment.
Less-usable energy is more diffuse or disorganized
Expresses concept that events in universe have direction
Systems tend to proceed from ordered to disordered
states/randomness
The 2nd law is about the direction which the process
can take place and the ‘quality’ of the energy
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
CHANGE OF ENERGY
Total energy content of system before chemical or
physical process takes place: initial state
After the process has taken place: final state
As system proceed from initial to equilibrium state, it
may absorb energy from/deliver energy to its
surroundings
Equilibrium state: condition in which no further
change is occurring within system or between
surroundings and system
CHANGE OF ENERGY
The direction and extent to which chemical
reaction proceed → determined by 2 factors
Enthalpy (∆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
3rd LAW THERMODYNAMICS
The entropy of any crystalline, perfectly ordered
substance must approach zero as the temperature
approaches 0 K
At T = 0 K, entropy is exactly zero
“Absolute zero”
FREE ENERGY
However mathematically, Enthalpy (∆H) and Entropy (∆S)
can be used to defined FREE ENERGY which predict in
which a reaction proceed.
Free energy = G = Gibbs free energy
∆G = free energy change, energy available to do work
∆G = ∆H – T∆S (* T: temp measured in Kelvin)
-∆G → indicates a spontaneous reaction
+∆G → indicates a non-spontaneous reaction
∆G = 0 → reaction at equilibrium
ENERGY TRANSFER
Energy acquired from sunlight or food must be
used to drive endergonic (energy-requiring)
processes in the organisms.
Two classes of biomolecules do this:
Reduced coenzymes (NADH, FADH2)
High-energy phosphate compounds (ATP)
ATP
PEP (phosphoenolpyruvate) and 1,3-BPG (1,3 bis-
phosphoglycerate) are created in the course of
glucose breakdown.
Their energy (and phosphates) are transferred to
ADP to form ATP.
But ATP is only a transient energy carrier – it
quickly passes its energy to a host of energy
requiring processes
Properties of Water, Acid & Base
LEARNING OUTCOMES
Students should be able to :
Understand water and polarity
Define hydrogen bond
Compare acid and base
Understand Henderson-Hesselbach equation
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
A LOT OF MOLECULES
OF WATER
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
Covalent Bonds
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 : water-loving (tend to dissolve in water)
Hydrophobic : water-fearing (tend not to dissolve in
water)
Amphipathic : contain both polar (hydrophilic) and
nonpolar (hydrophobic) portion
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?
Why do oil and water mixed together
separate into layers?
Oil and water don't mix because oil is made up of
non-polar molecules while water molecules are
polar in nature.
Because water molecules are electrically charged,
they get attracted to other water molecules and
exclude the oil molecules.
This eventually causes the oil molecules, or lipids, to
clump together.
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 (10-3)
=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
+
CH 3 COH + H2 O CH 3 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, 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
Has the ability to maintain the pH
and bring it back to its optimal value
by addition or removal of
hydrogen ions.
Components of a buffer
The components of a buffer solution are acid-base
conjugate pairs
Can be a weak acid and a salt of its conjugate base –
typically have equal concentrations of the weak acid
and its salt
Can also be a weak base and a salt of its conjugate
acid
Components of a buffer
Example of acid-base buffers are solutions containing
CH3COOH (acetic acid) and CH3COONa (sodium acetate)
H2CO3 an (carbonic acid) and NaHCO3 (sodium carbonate)
Human blood contains a buffer of carbonic acid (H 2CO 3)
and bicarbonate anion (HCO 3 -) in order to maintain
blood pH
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
Bicarbonate, phosphate and plasma protein are 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.
When hydrogen ions increased or decreased from the reactions, the system
shifts to counteract the disturbance and to maintain a relatively constant
hydrogen ion concentration
Bicarbonate buffering system
If the blood gained excess hydrogen ions → the blood pH drops too low
(acidosis), some of those hydrogen ions would shift to carbon dioxide
(drive the equation to the left), minimizing the increased acidity.
The excess hydrogen ions combine with the HCO3–(bicarbonate ion) to
form H2CO3 (carbonic acid), the body will compensate by increasing
breathing, expelling CO2.
Due to the shift, the concentration of hydrogen ions decreases which
therefore the pH will rise back to normal.
Bicarbonate buffering system
If the pH of the blood suddenly goes up, there are less H+ ions present in
the blood (alkalosis) → the equation will shift to the right to produce
more H+ to compensate for the decrease in hydrogen ions
More H+ are produced, decreasing the pH, which counteracts the initial
increase in pH. By doing so, the system is able to regulate the pH of your
blood
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