CHAPTER II

A Survey of Biologically-
important Molecules
A. Functional Groups
• Functional groups are a set of specific atoms
within a molecule that determines the molecule’s
overall reactivity and properties
• Compounds that have the same functional
groups will have the same type of reactivity,
though small deviances will result if other
substituents or functional groups are present on
the molecule
• There are 8 important functional groups in the
chemistry of life: hydroxyl, carbonyl, carboxyl,
amino, thiol, phosphate, aldehyde, and ketone
groups
Hydroxyl Group
• Consists of a hydrogen atom covalently bonded
to an oxygen atom
• The hydroxyl group is denoted by -OH in
chemical structures and has a valence charge of
-1 when in the hydroxyl ion form
• It is present in alcohols and carboxylic acid
molecules
Hydroxyl Group
Carbonyl Group
• Written as a covalent C=O
• It is a very polar molecule and the carbonyl
carbon can serve as a reaction site for many
reactions
• It is present in aldehydes, ketones, esters,
anhydrides, and carboxylic acids
Carbonyl Group
Carboxyl Group
• The monovalent group -COOH, consisting of a
carbonyl group bound to a hydroxyl group
• It is the main functional group in organic acids
(carboxylic acids)
• Its hydrogen can dissociate due to the strong
stabilizing resonance that forms between the two
oxygens when deprotonated
Carboxyl Group
Amino Group
• The amino group (–NH2) consists of one atom of
nitrogen attached by covalent bonds to two atoms
of hydrogen, and a spot where it is attached to an
alkyl group, or another hetero atom
• This leaves a lone valence electron pair on the
nitrogen which is available for bonding to another
atom
Amino Group
Thiol Group
• A functional group containing a sulfur atom
bonded to a hydrogen atom
• General formula: -SH
• Eg. the amino acid cysteine contains a thiol
group; it is the thiol derivative of a hydroxyl group,
and can undergo similar reactions
Thiol Group
Phosphate Group
• A functional group or radical comprised of
phosphorus attached to four oxygen (a diester),
and with a net negative charge, (PO43-)
• The phosphate group is important in living things
in varying ways:
• It is an important structural backbone component of nucleotides,
which is the basic structural unit of DNA and RNA
• It is used as an electron transfer component of energy-rich
molecules, such as ATP
• It is bound to coenzymes like NADP / NADPH involved in
anabolic reactions (such as photosynthesis in plants and lipid
synthesis in animals)
• It is also a part of the hydrophilic head of phospholipids in
biological membranes
Phosphate Group
Aldehyde Group
• Aldehydes are the second compound containing
the carbonyl group (C=0) wherein one of the two
groups attached to the carbonyl carbon is an alkyl
group, while the other is a hydrogen atom
(RCOH)
• Aldehyde carbonyl occurs at the end of a chain of
carbon atoms (i.e. in sugars, R-CHO is at the end
of a chain, while a carbonyl inside the chain
attached to two carbons is a ketone)
• They can form acetals and hemiacetals when
exposed to water, or in the presence of hydroxyl
groups
Aldehyde Group
Ketone Group
• With the structure RCOR', where R and R' can be
a variety of carbon-containing substituents
• Along with aldehydes, ketones are simple
compounds that contain a carbonyl group
because they do not have reactive groups like –
OH or –Cl attached directly to the carbon atom in
the carbonyl group
• Many ketones are known and many are of great
importance in industry and in biology.
• Examples include many sugars (ketoses) and the
industrial solvent acetone
Ketone Group
B. Physical and Chemical Properties of Water
• With chemical formula H2O and consists of two
hydrogen atoms covalently bonded to a single
oxygen atom
• Appears in nature in all three states of matter and
may take many different forms on Earth
• A tasteless, odourless liquid at standard
temperature and pressure
• Is transparent, allowing light to pass through and
enabling plants to survive in aquatic
environments
• A polar molecule
• Non-linear with the oxygen atom having a
higher electronegativity than hydrogen atoms
and thus carrying a slightly negative charge
whereas the hydrogen atoms are slightly
positive
• Has high surface tension and capillary forces
• Forms an unusually large number (four) of
intermolecular hydrogen bonds for a molecule
of its size, resulting into strong attractive forces
between molecules
• Often referred to as the universal solvent
• Dissolves the following substances: salts,
sugars, acids, alkalis, and some gases –
especially oxygen, carbon dioxide (through a
process known as carbonation) while unable to
mix with fats and oils
• Substances that dissolve in water are called
hydrophilic while those that do not mix with it
are called as hydrophobic
• Dissolves all the major components in cells
such as proteins, DNA, and polysaccharides
• Has a low electrical conductivity that increases
significantly with the dissolution of small amounts
of ionic material such as sodium chloride
• With boiling point that is dependent on the
barometric pressure
• For example, on the top of Mt. Everest, water
boils at 68 degrees Celsius, compared to 100
degrees Celsius boiling temperature at sea
level. Conversely hundreds of degrees when
found deep in the ocean near geothermal vents
• Has the second highest molar specific heat capacity
of any known substance, after ammonia, as well as a
high heat of vaporization (40.65 kJ / mol), due to the
extensive hydrogen bonding between its molecules
• The high specific heat capacity and high heat of
vaporization enables water to act as Earth’s thermal
regulator (moderating the climate and buffering large
fluctuations in temperature)
• Has a maximum density that occurs at at 3.98
degrees Celsius
• It has the anomalous property of becoming less dense
when it is cooled down to its solid form, ice
• Known as the anomalous expansion of water when frozen,
it expands to occupy 9 % greater volume in this solid state
which explains why ice floats on liquid water
C. Acids and Bases
1. General Properties
• Acids
• Substances which donate hydrogen and form H3O+
(hydronium) ions when dissolved in water
• Have a characteristic sour taste eg., acetic acid in vinegar
and citric acid in lemon
• Cause color change in certain plant dyes eg., turns blue
litmus into red
• React with certain metals such as Fe, Mg, and Zn to produce
H2
• 2HCl + Mg → MgCl2 + H2
• React with carbonates and bicarbonates such as Na2CO3,
Ca2(C03)2, and NaHCO3 to produce CO2
• 4HCl + Ca2(CO3)2 → 2CaCl2 + 2H20 + 2CO2
• Produce electrolytic aqueous solution
• Bases
• Substances which accept hydrogen and form OH-
(hydroxide) ions in solution
• Have a characteristic bitter taste
• Feel slippery eg., soaps
• Cause color change in certain plant dyes eg., turns red
litmus into blue
• Produce electrolytic aqueous solution
2. Definition / Classification
• Bronsted Definition
• An acid is a proton donor while a base is a proton
acceptor
• Eg. HCl is a Bronsted acid based on the following
reaction:
• HCl(aq) + H2O(l) → H3O+(aq) + Cl-(aq)
• H3O+ is a hydrated proton, also called as hydronium
ion, and is also represented as H+

• Eg. NH3 is a Bronsted base because it accepts

proton from H2O
• NH3(aq) + H2O(l) → NH4+ + OH-
• Conjugate Acid-Base Pairs
• Consist of an acid and its conjugate base or a base and its
conjugate acid
• The conjugate base of a Bronsted acid is the substance that
remains when one proton has been removed from the acid
• Conversely, a conjugate acid is the substance that forms when a
proton has been added to a Bronsted base
• Eg. In the following reaction:
• CH3COOH + H2O → CH3COO- + H3O+
• CH3COOH is the acid and CH3COO- is the conjugate base while
H20 is the base and H30+ is the conjugate acid
• In the reaction NH3 + HF → NH4+ + F-,
identify the acid and its conjugate base as well as the base and
its conjugate acid
• Acid-Base Neutralization Reaction
• A reaction between an acid and a base that
results into the formation of a salt (an ionic
compound) and water
• Eg.,
• HCl + NaOH → NaCl + H2O
• HF + KOH → KF + H2O
• H2SO4 + 2NaOH → Na2SO4 + 2H2O
• Lewis Definition
• A Lewis acid is a substance that accepts an electron pair
• A Lewis base is a substance that donates an electron pair
• Consider the reaction NH3(aq) + H2O(l) → NH4+ + OH-
• NH3 is a Lewis base because it donates an electron pair to
H+ to form NH4+
• H+ is a Lewis acid because it accepts an electron pair given
by NH3
3. Acid-Base Properties of Water
• H2O has the unique ability to act either as an acid
or as a base (it acts as acid when reacting with a
base and as a base when reacting with an acid)
• It is a weak electrolyte and undergoes a reaction
known as auto-ionization
• The ion product of water, given as K, is

• Since only a small fraction of H2O molecules are

ionized, the concentration of H2O remains
virtually unchanged; therefore

• where Kw is called as the ion product constant

which is equal to the product of the molar
concentration of the H3O+ or H+ and OH- at a
particular temperature
• In pure / distilled H2O at 20 to 250C, the
concentration of H+, [H+], and the
concentration of OH-, [OH-], are constant
and is each equal to 1 x 10-7 M
• In symbols, Kw = [H+] [OH-]
= (1 x 10-7 M) (1 x 10-7 M)
Kw = 1 x 10-14 M
• Given Kw = [H+] [OH-] , [H+] and [OH-]
can be computed
To solve for [H+], the formula is
[H+] = Kw / [OH-]
To solve for [OH-], the formula is
[OH-] = Kw / [H+]
• Therefore, in any solution,
• If [H+] = [OH-], the solution is neutral
• If [H+] > [OH-], the solution is acidic
• If [H+] < [OH-], the solution is basic
• SAMPLE PROBLEM 1.
The concentration of OH-, [OH-] in a
certain household ammonia cleaning solution is
0.0025 M. Calculate the concentration of the
H+, [H+] in this solution.
• SAMPLE PROBLEM 2.
Compute the concentration of OH- , [OH-]
in a HCl solution with a concentration of H+,
[H+] = 1.3 M.
4. pH – A Measure of Acidity
• pH is the negative logarithm of the hydrogen ion
concentration (in mol / L or M) of any solution
• In symbols, pH = - log [H+]
• Acidic and basic solutions at 250C can be
distinguished by their pH values:
• Acidic solutions: [H+] > 1.0 x 10-7, pH < 7.0
• Basic solutions: [H+] < 1.0 x 10-7, pH > 7.0
• Neutral solutions: [H+] = 1.0 x 10-7, pH = 7.0
Table 2.1. pH of Some Common Fluids
SUBSTANCE pH values
gastric juice in the stomach 1.0 – 2.0
lemon juice 2.4
vinegar 3.0
orange juice 3.5
urine 4.8 – 7.5
water exposed to air 5.5
saliva 6.4 – 6.9
milk 6.5
pure H2O 7.0
blood 7.35 – 7.45
tears 7.4
pOH – A Measure of Basicity
• pOH = - log [OH-]
• Basic solutions: [OH-] > 1.0 x 10-7, pOH < 7.0
• Acidic solutions: [OH-] < 1.0 x 10-7, pOH > 7.0
• Neutral solutions: [OH-] = 1.0 x 10-7, pOH = 7.0
Recall that [H+][OH-] = kw = 1.0 x 10-14 M
• Thus, if the negative log of both sides of the
equation shall be taken:
• -log [H+] – log [OH-] = -log 1.0 x 10-14 M
pH + pOH = 14.0
pH = 14.0 – pOH
pOH = 14.0 - pH
Sample Problems
1. The concentration of H+ in a bottle of wine was
3.2 x 10-4 M right after the cork was removed.
Only half of the wine was consumed while the
other half was left standing in the bottle. After a
month, the wine was found to have a concentration
of H+ = 1.0 x 10-3 M. Compute the pH of the wine
on these two occasions and account for the
difference.
2. Hydrogen nitrate (HNO3) is used in the
production of fertilizers, drugs, dyes, and
explosives. Calculate the pH of a HNO3 solution
with [H+] = 0.076 M
3. The pH of rainwater collected in a certain region was
4.82. Calculate its [H+].
4. Given that the pOH of a certain laboratory reagent is
11.08, what is its [OH-]?
ANSWER FOR SAMPLE PROBLEM NO. 3
Given:
pH of rainwater = 4.82
Unknown:
[H+]
Solution:
If pH = -log[H+], then [H+] = inv log –pH
= inv log – 4.82
= 1.51 x 10 -5 M
D. Biomolecules / Macromolecules
• Biomolecules are substances that are formed only
inside a living unit through a process known as
biosynthesis which occurs through a dehydration /
condensation mechanism
• They are composed of repeating units known as
building blocks or structural units that have been
chemically combined to form larger structures, thus,
they are also called as macromolecules
• Since they are primarily composed of Carbon and
Hydrogen, they are also called as organic molecules
• They are classified as four different groups namely,
carbohydrates, lipids, proteins, and nucleic acids