51

CHEMISTRY NOTES
GENERAL CHEMISTRY
Dalton’s Atomic Theory
Main postulates of Dalton atomic theory are as follows:
Matter is composed of very tiny or microscopic particles
called "atom".
1. Atom is an indivisible particle.
2. Atom can neither be created nor destroyed.
3. Atoms of an element are identical in size, shape, mass,
and in other properties.
4. Atoms of different elements are different in their
properties.
5. Atoms combine with each other in small whole
numbers.
6. All chemical reactions are due to the combination or
separation of atoms.
Defects in Dalton’s Theory
Postulates 2, 3, 4 and 6 are incorrect as described below:
> Atom can be divided into a number of sub-atomic
particles: electron, proton, and neutron.
> Atoms of an element may be different in their masses.
(1H1, 1H2, 1H3)
> Not all compounds have small number of atoms.
(Decane C10H22, Sugar C10H22O11)
> Atoms can be destroyed by fission process (atom bomb,
nuclear reactor)
On the basis of above defects, Dalton's atomic theory has
failed now.
Matter: anything that has mass and occupies space
Law of Conservation of Mass: The total mass of the
products of a chemical reaction is the same as the total
mass of the reactants (mass remains constant during
chemical reaction)
Law of Definite Composition (Law of Definite
Proportions): The elemental composition of a pure
compound is always the same, regardless of its source
Law of Multiple Proportions: When two elements form
more than one compound, the masses of one element in
these compounds for a fixed mass of the other element
are in ratios of small whole numbers
Atomic Number: number of protons in the nucleus
Mass Number: number of protons + number of neutrons
Isotopes: atoms of the same element with different mass
numbers (carbon-12 and carbon-13)
Atomic Mass Unit (amu): exactly one-twelfth the mass
of a carbon-12 atom
Atomic Mass (weight): average mass of the atoms of
an element in amu: mass in g of one mol of the element
Mole (mol): quantity of a given substance that contains
as many molecules or formula units as the number of
atoms in exactly 12 g of carbon-12; consists of 6.02 x 1023
particles

Mixtures: combinations of two or more substances in Molar Mass: mass of one mol of substance; in g it is
which each substance retains its own chemical identity numerically equal to the formula mass (weight) in atomic
and hence its own properties mass units

Physical Change: change of state or phase Mass % of A = (

𝑚𝑎𝑠𝑠 𝑜𝑓 𝐴 𝑖𝑛 𝑡ℎ𝑒 𝑤ℎ𝑜𝑙𝑒
) × 100%
𝑚𝑎𝑠𝑠 𝑜𝑓 𝑡ℎ𝑒 𝑤ℎ𝑜𝑙𝑒

Chemical Change: transformation in which substances

Molecule: definite group of atoms that are chemically
are converted into other substances
bonded together
Compound: substance composed of two or more
Ion: electrically-charged particle obtained from an atom
elements chemically combined in fixed proportions
or chemically bonded group of atoms by adding or
removing electrons
Element: substance that cannot be decomposed by any
chemical reaction into simpler substances.
Chemical Formula: notation that uses atomic symbols
Matter with numerical subscripts to convey the relative
proportions of atoms of the different elements in the
substance
Heterogeneous
by physical Homogeneous
Matter
means into Matter Empirical Formula (Simplest Formula): formula with
(variable
composition) the smallest integer subscripts

Molecular Formula: chemical formula that gives the

exact number of different atoms of an element in a
Homogeneous by physical Pure Substances molecule
Matter means into (fixed composition)
(variable Molecular Empirical
Substance
composition) Formula Formula
water H2O H2O
hydrogen
Compounds by chemical Elements H2O2 HO
means into peroxide
ethane C2H6 CH3
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Molecular Mass / Weight (MW): the sum of the atomic
masses/weights of all the atoms in a molecule
Formula Mass / Weight (FW): the sum of the atomic
masses/weights of all atoms in a formula unit of the
compound, whether molecular or not
Empirical Formula Mass or Empirical Formula
Weight (EFW): the sum of the atomic masses divided
by the weights of all the atoms in an empirical formula
Molecular Formula = 𝑛 × 𝐸𝑚𝑝𝑖𝑟𝑖𝑐𝑎𝑙 𝐹𝑜𝑟𝑚𝑢𝑙𝑎
Pauli’s Exclusion Principle: No two electrons in the
same atom may have the same set of all four quantum
numbers.
Hund’s Rule of Multiplicity: In the ground state of an
atom, electrons are distributed among the orbitals of a
subshell in a way that gives the maximum number of
unpaired electrons with parallel spins.
Aufbau Principle (Building-up Principle): A scheme
used to reproduce the electronic configurations of atoms
by successively filling subshells with electrons in a specific
order (orbitals with lower energy first).

where: 𝑛 =
𝒎𝒐𝒍𝒆𝒄𝒖𝒍𝒂𝒓 𝑜𝑟 𝑓𝑜𝑟𝑚𝑢𝑙𝑎 𝑤𝑒𝑖𝑔ℎ𝑡 Periodic Properties of the Elements
𝑒𝑚𝑝𝑖𝑟𝑖𝑐𝑎𝑙 𝑓𝑜𝑟𝑚𝑢𝑙𝑎 𝑤𝑒𝑖𝑔ℎ𝑡

Atomic Size: within a period, decreases from left to

Stoichiometry: Calculation of the quantities of reactants
right; within a group, increases from top to bottom
and products involved in a chemical reaction:
Size of Cation: within a period, decreases from left to
chemical right; within a group, increases from top to bottom
N2(g) + 3H2(g)  2NH3(g)
reaction
1 3 2 Size of Anion: within a period, decreases from left to
molecular
molecule + molecules  molecules right; within a group, increases from top to bottom
interpretation
N2 H2 NH3
1 mole 3 moles 2 moles molar Ionization Energy (energy needed to remove an
+ 
N2 H2 NH3 interpretation electron from a gaseous atom in the ground state): within
3 X 2.02g 2 X 17.0g mass a period, increases from left to right; within a group,
28.0g N2 + 
H2 NH3 interpretation decreases from top to bottom

Limiting Reactant or Limiting Reagent (LR): reactant
that is entirely consumed when a reaction completes
Theoretical Yield: Quantity of product that is calculated
to form when all of the LR reacts
Actual Yield: Amount of product actually obtained in a
reaction
Electron Affinity (energy change when an electron is
added to a gaseous atom in the ground state): within a
period, increases negative value from left to right; within a
group, no clear trend
Basicity of Metal Oxides: within a period, decreases
from left to right; within a group, increases from top to
bottom

Percentage Yield =
𝒂𝒄𝒕𝒖𝒂𝒍 𝒚𝒊𝒆𝒍𝒅
𝑥 100% Acidity of Non-metal Oxides: within a period, increases
𝒕𝒉𝒆𝒐𝒓𝒆𝒕𝒊𝒄𝒂𝒍 𝒚𝒊𝒆𝒍𝒅
from left to right; within a group, decreases from top to
bottom
Atomic Structure and Periodic Table
Metallic Property (reducing property): within a period,
The Nuclear Atomic Model: Protons and neutrons in
decreases from left to right; within a group, increases
the nucleus; electrons outside the nucleus
from top to bottom
The Quantum Mechanical Model
Non-metallic Property (oxidizing property): within a
Quantum numbers: n, l, ml, ms
period, increases from left to right; within a group,
> Principal Quantum Number: n = 1(K), 2(L), 3(M)…;
decreases from top to bottom
identifies the shell or level to which the electron belongs
> Azimuthal Quantum Number: l = 0(s), 1(p), 2(d), 3(f)…;
Electronegativity (measure of the ability of an atom in a
n-1 identifies the subshell
molecule to draw bonding electrons to itself): within a
> Magnetic Quantum Number: ml = +1…0…-1 gives the
period, increases from left to right; within a group,
shape of the subshell: orientation of atomic orbital spin
decreases from top to bottom
quantum number
1 1
> Spin Quantum Number: ms =+ , − Chemical Bond
2 2

Heisenberg’s Uncertainty Principle: It is impossible to Electrovalent Bond (ionic bond): formed by transfer of
determine simultaneously the exact position and the exact electrons to form ions
momentum of a fast moving body like an electron.
Covalent Bond: formed by sharing of electrons between
atoms
> Lewis or electron-dot formulas

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> Normal and coordinate covalent bonds INORGANIC CHEMISTRY

> Formal charge and oxidation number
> Formal Charge (FC) = Group No. minus No. of
unshared e’s minus No. of covalent bonds
> The higher the bond order, the shorter the bond length
and the greater the bond strength
Increasing bond length:
triple bond < double bond < single bond
Decreasing bond length:
triple bond > double bond > single bond
Metallic Bond: a crystal of the metal consists of a
regular arrangement of the positive ions, and the valence
electrons move throughout the crystal attracted to the
positive cores of all the positive ions.
Polar and Non-Polar Bonds
Non-Polar Covalent Bond: equal sharing of a pair of e’s
in diatomic molecules consisting of identical atoms in
identical atoms with identical neighbors
Polar Covalent Bond: unequal sharing of a pair of e’s in
identical atoms with different neighbors when two bonded
atoms are dissimilar
Polar and Non-Polar Molecules: consider polarity of
bonds, then geometry of molecule
> Non-polar bonds  non-polar molecules
> Polar bonds but symmetrical  non-polar molecules
> Polar bonds and not symmetrical  polar molecules
Bonding Non-bonding Shape of
e-pairs e-pairs molecule
6 0 octahedral
5 1 square pyramidal
4 2 square planar
3 3 T-shaped
2 4 linear
Hybrid Orbitals: mixing of atomic orbitals to form a
hybrid (e.g., sp, sp2, sp3). The number of hybrid orbitals is
equal to the number of pure atomic orbitals that mixed.
Phases of Matter: consider intermolecular forces of
attraction
1. Ion-dipole
2. Dipole-dipole
3. London forces / Van der Waals forces
4. H-bonding
Gases
Kinetic Molecular Theory
1. tiny molecules, far apart
2. constant, random, straight line motion: elastic collisions
3. average KE increases with increase in T
4. attractive forces are negligible
Ideal Gas Law
PV=nRT
“Carefree Boys & Girls Play Tennis & Volleyball”
Law Constant Relationship
Charle’s Law Pressure ↑ V= ↑T
Boyle’s Law Temperature ↑P=↓V
Gay-Lussac’s Law Volume ↑ P= ↑T
Liquids
Vapor Pressure: pressure of vapor in equilibrium with a
liquid at a given temperature
Boiling Point: temperature at which the vapor pressure
of a liquid is equal to the external pressure
Viscosity: resistance of fluid to flow
Surface Tension: measure of the inward force on the
surface of the liquid caused by intermolecular forces of
attraction
Solids
Molecular Solids: atoms or molecules held together by
intermolecular forces
Metallic Solids: positive cores of atoms held together by
a “sea” of electrons (metallic bonding)
Ionic Solids: cations and anions held together by the
electrical attraction of opposite charges (ionic bonds)
Covalent Network Solids: atoms held together in large
networks or chains by covalent bonds
Thermodynamics
> Tells whether the reaction is spontaneous or not
First Law of Thermodynamics: Energy can be
converted from one form into another, but it can neither
be created nor destroyed.
Second Law of Thermodynamics: Every spontaneous
change is accompanied by an increase in entropy.
Gibb’s Free Energy: Reactions tend to seek a minimum
in energy and a maximum in randomness.
Third Law of Thermodynamics: At absolute zero the
entropy of a perfect crystalline substance may be taken as
zero.

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EXERGONIC ENDERGONIC Strong Acid Weak Acid

Spontaneous Non-spontaneous HCl HClO4 HClO3 HClO2 HClO
ΔS=+ (positive) ΔS =- (negative) HBr HBrO4 HBrO3 HBrO2 HBrO
↑ entropy (disorderliness) ↓ entropy (disorderliness) HI HIO4 HIO3 HIO2 HIO
ΔG = - (negative) ΔG = + (positive) H2SO4 H2SO3
Gibb’s Free energy Gibb’s Free energy HNO3 HNO2 HNO
ΔH = - (negative) ΔH = + (positive)
exothermic endothermic CH3COOH
Acetic Acid (HAc)
Ea = Activation Energy
Ea exergonic < Ea endergonic
Strong Base Weak Base Amphoteric Base
Solutions
IA IIA NH4OH Heavy Metal
Molarity, M: Number of moles of the solute per liter of (ammonium
the solution Li Ca hydroxide) Pb As
Molality, m: Number of moles of the solute per kilogram
of the solvent Na Mg R- NH2 (amines) Al Au
Mole Fraction, X
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑚𝑜𝑙𝑒𝑠 ∆ K Sr Hg Ag
𝑋∆ =
𝑇𝑜𝑡𝑎𝑙 𝑚𝑜𝑙𝑒𝑠 𝑜𝑓 𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛
Ba
Equivalent Point: point in a titration when an equivalent
amount of titrant has been added to the analyte solution Nuclear Chemistry
Balancing Nuclear Reactions - Types of Nuclear
Colligative Properties: depend on the number of Reactions:
particles and not on the kind of particle
1. Radioactive Decay: process in which an unstable
Raoult’s Law: Pertains to ideal solutions in which the nucleus is changed by the emission of radiation
intermolecular forces between molecules are all essentially
238 234 4
the same. a. alpha decay 𝑈 → 𝑇ℎ + 𝐻𝑒
92 90 2
1. Boiling Point Elevation, Tb = Kb m where: Kb for
water is 0.520C per molal solution 125 125
b. gamma radiation [ 𝑇𝑒] ∗ → 𝑇𝑒 + 𝛾
52 52
2. Freezing Point Depression,Tf = Kf m where: Kf for
water is 1.860C per molal solution excited state  ground state

Buffers: solutions capable of maintaining their pH at c. -decay

131
𝐼 →
131
𝑋𝑒 +
0
𝑒
some fairly constant value even when small amounts of 53 54 −1
acid or base are added; could be a mixture of a weak acid
and the salt of its conjugate base (e.g. HOAc-OAc-) or a
11 11 0
mixture of a weak base and the salt of its conjugate acid d. positron decay 𝐶 → 𝐵+ 𝑒
6 5 1
(e.g. NH3-NH4-)
e. electron capture
Henderson-Hasselbalch Equation:
[𝐴− ] 81 0 81
𝑝𝐻 = 𝑝𝐾𝑎 + log 𝑅𝑏 + 𝑒(𝑜𝑟𝑏𝑖𝑡𝑎𝑙 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛) → 𝐾𝑟
[𝐻𝐴] 37 −1 36
where pH = -log [H+] and pKa = - log Ka
[A-] = molar concentration of a conjugate base 2. Transmutation: process in which one nucleus is
[HA] = molar concentration of weak acid transformed into another through bombardmen by various
subatomic particles or ions
The equation can be rewritten to solve for pOH: 14 4 17 4
𝑁 + 𝐻𝑒 → 𝑂 + 𝐻𝑒
[𝐻𝐵 + ] 7 2 8 2
𝑝𝑂𝐻 = 𝑝𝐾𝑏 + log
[𝐵]
3. Nuclear Fission: process in which a heavy nucleus is
[HB+] = molar concentration of the conjugate acid
split into lighter ones
[B] = molar concentration of a weak base 1 235 142 91 1
𝑛+ 𝑈 → 𝐵𝑎 + 𝐾𝑟 + 3 𝑛
0 92 56 36 0
SALT STRUCTURE
+(BASE) - (ACID ) 4. Nuclear Fusion: process in which light nuclei are fused
pH = 7 Strong Base Strong Acid into heavier one
pH > 7 Strong Base Weak Acid 1 1 2 0
𝐻+ 𝐻 → 𝐻+ 𝑒
pH < 7 Weak Base Strong Acid 1 1 1 1

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ORGANIC CHEMISTRY
Organic chemistry is the study of the compounds of
carbon, their structure, chemical and physical properties,
as well as their preparation and source.
Despite the limited number of atoms that consist
organic compounds (C, H, O, N, S, P, and the halogens),
their number is much greater than the inorganic ones.
This is due to the unique versatility of carbon.
Organic chemistry developed from one of the most
fundamental theories, the structural theory which
proposes that carbon has a valence of four and thus
tetravalent, and that carbon can use one or more of its
valences to form bonds with other atoms including carbon
itself. The nature of chemical bonds in organic compounds
is covalent (resulting from the sharing of electrons).
Covalent bonds are formed by overlapping orbitals of two
atoms in different ways:
1. Head-to-head overlap – leading to sigma (σ) bond
formation.
- by atomic orbitals (s, p, d) and/or hybrid orbitals
(sp, sp2, sp3 and sp3d)
2. Side-to-side overlap – leading to pi (π) bond
formation
- by p and d orbitals only
Knowledge of the orbitals used in bond formation is
needed to identify the types of bonds formed and the
location of lone pairs of electrons (if any).
Characteristics of Covalent Bonds
1. Polarity – results when two atoms of different
electronegatives (EN) form a covalent bond such that the
electrons are not equally shared between them
e.g. H - Cl or H – Cl
δ+ δ- I - moderate EWG include: -CN, -(C=O)OH, -(C=O)OR,
- a dipole moment results from the partial positivity and
partial negativity of a polar covalent bond
- a molecule with no net dipole moment is a nonpolar
molecule; a molecule with a net dipole moment is a polar
molecule
e.g. C - F > C - Cl > C - Br > C - I
- there is also such thing as bond polarity (even if the
two atoms held by the bond are the same) due to the
difference in hybridization between the two atoms such
as in the sp-sp3 and sp2-sp3 hybrid orbitals resulting to
electron-withdrawing property due to the greater s-
character of one of the atoms.
e.g. H–CC–CH3 > CH2  CH – CH3 >CH3 – CH2 – CH3
2. Bond Length – the average distance separating the
nuclei of bonded atoms
- bond length decreases with decreasing atomic
radius/size:
C–I > C–C > C–H
- bond length decreases with increasing polarities:
C–C > C–N > C–O > C–F
- bond length decreases with increasing s character of
the hybrid orbitals:
H–CH2–CH2–CH3 > H–CHCH–CH3 > H–CC–CH3
- bond length decreases with increasing π bond electron
density: H3C – CH3 > H2C = CH2 > HC  CH
3. Bond Energy/Strength – the energy needed to
disrupt a covalent bond (in kJ/ mol)
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55
- bond strength increases with increasing polarity:
C–F > C – Cl > C – Br > C–I
- bond strength increases with increasing s character of
the hybrid orbitals:
sp–sp > sp2 – sp > sp2 – sp2 > sp3 – sp2 > sp3 – sp3
- bond strength increases with increasing π bond
electron density: C  C > C=C > C–C
198 kcal 163 kcal 88 kcal
Structural Effects – show how electrons are distributed
in organic molecules and how they affect the physical and
chemical properties of the molecule
1. π -Electron Delocalization or Resonance
- this concept generally applies to conjugated systems
and is used to explain strengthening and shortening of
bonds, nucleophilicity/electrophilicity of sites, and
thermodynamic stability
2. Inductive Effects
- results in the distortion of electron distribution due to
the effect through sigma bond/s by strong electron-
donating (EDG) or electron-withdrawing (EWG)
atoms/ group of atoms
- strong EDG which release electrons by resonance
effect include: - NH2, -NHR and –NR2
- moderate EDG whose nonbonding electron pairs are
less free include: -NH(C=O)R, -NR(C=O)R,-OH and -OR
- other EDG which release electrons by
hyperconjugative effect include: -CH3, -CH2R, -CHR2,
-CR3 and –C6H5 (the phenyl ring)
- in organic compounds, EDG makes the electron pair
more available, leading to ENHANCED BASICITY
- strong EWG are due to electronegative atoms/ group
of atoms: -NO2, -CX3 (where X = F, Cl, Br, I)
-(C=O)H, -(C=O)R, -SO3H
- weak EWG include the halides: -F, -Cl, -Br, -I
- in organic compounds, EWG enhance both the
positivity of H and the dispersal of the negative charge
(upon removal of the protonic H atom) stabilizing the
conjugate base thus leading to ENHANCED ACIDITY
3. Steric effects
- the presence of bulky substituents may result in the
crowding of other substituents or atoms that may lead
to weakening of bonds leading to acceleration of bond
cleavage
- steric effect near an acidic group favors the removal of
protons regardless of whether the groups present are
EDG or EWG (i.e. ENHANCED ACIDITY)
- steric effect near the lone pair of electrons makes
them less accessible or available for donation, thus
DECREASING BASICITY
4. Intra- and Intermolecular Forces of Attraction
(IMF)
- boiling and melting substances involve disrupting IMFs
existing between its particles
- on the other hand, dissolution involves breaking of
IMFs between similar molecules AND forming of IMFs
between dissimilar molecules (solute and solvent)
- the boiling point (Tb) of an organic compound is
affected by several factors:
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a. Tb increases with increasing molecular size This involves the rupture of C-H bonds by homolysis to
(due to larger surface area) form free radicals. Halogenation is another similar
b. Tb increases with decreased branching process to give monohalogenated products:
(branching decreases molecular surface area) CH4 + Cl2  CH3Cl + HCl
c. Tb increases with increasing polarity of the The order of reactivities is: tertiary (3O) > secondary (2O)
molecule > primary (1O) > methane
(strong dipole-dipole IMFs) CH3 H H H
d. Tb increases with decreasing molecular symmetry l l l l
e. Tb increases with less intramolecular H-bonding H3CC–H H3CC–H H3CC–H H3CC–H
(this minimizes IMF with the solvent) l l l l
- the solubility of an organic compound in water is CH3 CH3 H H
affected by several factors:
a. it increases with decreasing carbon chain length B. ALKENES – contain at least one carbon-carbon double
b. it increases with branching bond
c. it increases with increasing capacity to form IUPAC Nomenclature
intermolecular H-bonding (substituents) + root + -ene

Functional Groups Physical Properties

Alkenes are relatively nonpolar molecules. However, in
Organic compounds are characterized by the presence the presence of alkyl substituents like the methyl group
of a certain arrangement of atoms called a functional which is an electron-donating group, the π-bond electrons
group. This is the site in a molecule where a chemical are slightly pushed creating a slight polarization.
reaction is most likely to occur and where physical Electronegative atoms like the halogens also affect the
properties are also determined. Organic compounds may dipole moment, this time by withdrawing electrons from
be classified into aliphatic and aromatic compounds. the π-bond.
Alkenes possessing larger dipole moments have
I. ALIPHATIC HYDROCARBONS relatively higher boiling point than the lower on zero
A. ALKANES and CYCLOALKANES- contains only C–C dipole moment isomer. This is due to larger dipole-dipole
single bonds besides the C-H bonds IMF that holds the molecules together. On the contrary,
alkenes with lower or zero dipole moments have higher
IUPAC Nomenclature melting point than isomers with higher dipole moment. A
(substituents) + root + -ane structure with zero dipole moment reflects its higher
Linear: also represented symmetry and therefore better and tighter packing in the
as solid crystal lattice together with more efficient IMF.
CH4 methane Alkenes are relatively soluble in nonpolar solvents and
CH3CH3 ethane insoluble in polar solvents.
CH3CH2CH3 propane
CH3CH2CH2CH3 butane Chemical Properties
CH3CH2CH2CH2CH3 pentane The reactions of alkenes are mainly centered on the π
CH3CH2CH2CH2CH2CH3 hexane bond which is a site of high electron density. They can
therefore be considered as nucleophiles (seeking a
Physical Properties positively-charged center, symbolized as Nu-) and the
Alkanes are nonpolar molecules. The C-H bond can be attacking reagents as electrophiles (seeking a negatively-
considered a nonpolar bond due to the almost equal EN of charged center, symbolized as E+). One of the most
H and C (2.1 and 2.5 respectively). Alkanes are in the common reactions of alkenes is catalytic
liquid state due to van der Waal’s attractive forces. hydrogenation
Branching decreases the surface area of alkanes and Ni/Pd/Pt CH2 = CH2 + H2  CH3CH3
results to lesser van der Waal’s interaction and thus Electrophilic addition on alkenes is governed by
lowers the leading to lower boiling point. Markovnikov’s rule, which says that the hydrogen of an
Alkanes because of their weak intermolecular forces attacking E+ will add to the alkene carbon containing the
(IMF) can only be dissolved by similar nonpolar solvents greater number of H substituents.
with weak IMF of attraction. They are thus insoluble in
water which possess strong IMF of attraction between C. ALKYNES – contain at least one carbon-carbon triple
them molecules. bond
IUPAC Nomenclature
Chemical Properties (substituents) + root + -yne
Alkanes do not react with bases nor with acids because Linear: also represented as
it has no H atom attached to an EN atom like oxygen and HCCH ethyne =
does not have an electron pair for donation. But it can HCC-CH3 propyne
easily catch fire, by the combustion reaction process: HCC-CH2CH3 1-butyne -
CH4 + 2O2  CO2 + 2H2O H3C-CC-CH3 2-butyne

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Physical Properties
Alkynes have similar boiling and melting points to those of
corresponding alkenes. They are soluble in nonpolar
solvents but more soluble in water than alkenes or
alkanes.
Chemical Properties
Alkynes are reduced (i.e. lower bond order) via the
following reactions.
Terminal alkynes are also characterized by acidity of the H
atom.
II. AROMATIC HYDROCARBONS
Aromatic hydrocarbons are cyclic conjugated
hydrocarbons which are specially stabilized and react by
substitution instead of addition. According to Hückel’s
Rule, a compound is aromatic if it satisfies all of the
following: (1) it is planar, (2) fully conjugated, (3)
monocyclic and (4) has (4n+2) electrons where n = 0, 1,
2, 3, etc. Application of this rule to reveals that the
following are examples of aromatic compounds:
H δ+ δ-
+ l :- +
benzene cyclopropenyl cyclopentadienyl tropylium
cation cation cation
IUPAC Nomenclature
Common names of frequently occurring parent
compounds such as benzene are also considered IUPAC
names. For monosubstituted benzene derivatives:
substituent + benzene. For disubstituted benzene
derivatives: positions of substituents relative to parent
functional group are indicated by numbers. When the
benzene ring is a substituent instead, the prefix phenyl- is
used to indicate its presence.
For common names, the positions of substituents
relative to the parent functional group are indicated by the
prefixes ortho- (o-) for groups on adjacent C atoms on the
ring, meta- (m-) for groups separated by one C atom and
para- (p-) for groups on C atoms directly opposite each
other.
Physical Properties
Benzene is not as polar as the alkenes, and is soluble in
relatively nonpolar to moderately polar solvents like
hexane, ether, chloroform and ethyl acetate.
EWG except for the weakly deactivating halides are meta-
directors. The halides though they withdraw by inductive
effect can also denote electrons by resonance effect and
are thus ortho- and para- directors.
III. ALKYL HALIDES – halogenated derivatives of
alkanes with the general formula CnH2n+1X. Alkyl halides
are usually prepared by halogenations of alkanes, alkenes
or alkynes.
Physical Properties
Alkyl halides are slightly more polar than alkanes due to
the C – X bond. Alkyl halides have higher boiling point
than corresponding alkanes due to larger molecular weight
and stronger dipole-dipole interactions. In terms of
density, the order is
R – I > R – Br > H2O > R – Cl > R – F
Alkyl halides like alkanes are insoluble in water,
although some alkyl fluorides exhibit slight solubility due
to the occurrence of H-bonding:
R – F...... H – OH
δ+ δ-
Chemical Properties
Alkyl halides can either undergo nucleophilic substitution
or elimination reactions, Nu:- +R – X  R – Nu + X –
H X
l l
–C–C– + :B- >C=C< + HB: + X–
l l
H H
IV. ALCOHOLS and PHENOLS – hydrocarbon
compounds with at least one of its hydrogens replaced by
a hydroxyl group, and phenyl rings with a hydroxyl
substituent
IUPAC Nomenclature
(substituents)+parent chain+ -ol
The common way to name alcohols consist of identifying
the parent chain: alkyl + alcohol
Primary (1o):
CH3CH2CH2CH2OH 1-butanol (n-butyl alcohol)
OH
Secondary (2o): l 2-butanol (2-butyl alcohol)
OH 3-methyl-1,4-pentadiol

Chemical Properties l OH
Benzene reacts by electrophilic aromatic substitution to
maintain the highly stabilized phenyl ring in the following
general manner Tertiary (3o):
H E OH
l
+ E+ + 3,4-dimethyl-3-hexanol
H+

The orientation of further substitution reactions of OH 2-ethyl-3-methyl-1-penten-3-ol

substituted benzene derivatives are also affected by the l
groups already attached to the phenyl ring. All EDG from
weak to strong are ortho- and para- directors while all

LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER


Physical Properties
Alcohols have relatively higher boiling points than
corresponding hydrocarbons because they are involved in
intermolecular H-bonding. Since H-bonding is also possible
with water, low-molecular weight alcohols (i.e. with C: OH
ratio below 5) are soluble in water. Alcohols with more
than one hydroxyl group may be involved in intra- and
intermolecular H-bonding.
Chemical Properties
Generally, alcohols are more acidic than terminal
alkynes but less acidic than water, with the decreasing
acidity going from 1o to 3o alcohols. Phenols are much
more acidic than alcohols, and even more acidic than
water because of the large stabilization of the phenolate
anion. EWG on the ortho- and para- positions especially
enhance its acidity.
Most of the reactions of alcohols consist of their
conversions into aldehydes (with a special reagent called
pyridinium chlorochromate, PCC) or carboxylic acids (from
1o alcohols), or ketones (from 2o alcohols) with oxidizing
agents such as chromic acid (H2CrO4), KMnO4 and K2Cr2O7
in acid.
O corresponding alcohols (stronger H-bonds due to more EN
ll
RCH2OH RCH aldehydes
O
ll
RCH2OH RC – OH carboxylic acids
O In the aqueous phase, 3o < 2o < 1o < NH3 because the
ll
R2CHOH RCR ketones
V. ETHERS – contain two hydrocarbon groups attached
to a central oxygen atom, R – O – R’
IUPAC Nomenclature
(substituents)+ -oxy- + parent chain
Ethers may be named as alkyl group1+alkyl group2+ ether.
Physical Properties
Ethers contain polar C – O bonds are therefore more
polar than alkanes. Ethers have higher boiling points than
corresponding alkanes and alkenes, but much lower than
alcohols due to absence of H-bonding. They are, however,
as soluble in water as alcohols of the same molecular
weight. As the alkyl groups of the ether increase in size,
the ether becomes relatively more nonpolar.
Chemical Properties
The oxygen of ethers has free electron pairs available
for proton donors or Lewis acids. Protonation of this
oxygen will weaken the C – O bond and result in the
partial positivity of the  - C which will be a good site for
nucleophilic attack. The -H atoms are also readily
abstracted by free radicals.
H Aldehydes and ketones have lower boiling points than
l H+ l corresponding alcohols, since they do not participate in H-
–C– O – C–
l l
Nu:-
LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER
58
VI. AMINES – nitrogen-containing organic compounds
that can be considered as alkyl or aryl (aliphatic or
aromatic) derivatives of ammonia, NH3. Since ammonia
contains three hydrogen atoms, there are three classes of
amines.
RNH2: 1o amines, characterized by an –NH2 group
attached to one alkyl/ aryl group
R2NH: 2o amines, characterized by an –NH group attached
to two alkyl/ aryl groups
R3N: 3o amines, characterized by full substitution of all H
atoms by alkyl/ aryl groups
IUPAC Nomenclature
(substituents) + root + suffix –amine
Amines can also be commonly named by placing the prefix
amino- before the name of the parent chain.
Physical Properties
Amines are moderately polar compounds due to their C
– N bond. In addition to this, the possibility of H-bonding
(for 1o and 2o amines only) causes amines to have higher
boiling points than alkanes of similar molecular weight.
They have, however, lower boiling points than
O atoms). All classes of amines can form H-bonds with
water such that all low-molecular weight amines are very
soluble in water.
Chemical Properties
Amines can act as Lewis bases due to the lone pair on
N. However, the trend in basicity depends on the medium.
bulky and nonpolar alkyl/aryl groups on substituted
amines hinder access to the lone pair, besides decreasing
solvation of the amine. However in the gas phase, the
trend is reversed because the alkyl groups can now
enhance the amine’s basicity by inductive effect (EDG).
The three classes of amines can form salts with mineral
acids:
CH3CH2NH2 + HCl CH3CH2NH3Cl
VII. CARBONYL COMPOUNDS – a family of compounds
whose chemical properties are predominated by the
reactivity of the carbonyl moiety, a C atom doubly bonded
to an O atom. Carbonyl compounds are also characterized
by the acidity of the -H (even though bonded to C)
A. ALDEHYDES and KETONES
-aldehydes are organic compounds that are characterized
by the formula O
ll
R–C–H
- ketones have the remaining hydrogen substituted with
the general formula O
ll
R–C–R
Physical Properties
bonding with similar molecules. However, they have
higher boiling points that corresponding ethers and
alkanes because of the more polar carbonyl group.
 59

Aldehydes and ketones are as soluble as their alcohol Unsaturated:

counterparts since they can form H-bonds with water. The palmitoleic acid CH3(CH2)5CH = CH(CH2)7COOH
same solubility restriction (i.e. C:O ratio should be less oleic acid CH3(CH2)7CH = CH(CH2)7COOH
than 5) holds. linoleic acid CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH
linolenicacid
Chemical Properties CH3(CH2)4CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH
Most of these compounds’ reactions involve simple
nucleophilic addition to the carbonyl bond wherein the C – Physical Properties
O bond is reduced to a single bond: Only carboxylic acids with five or fewer carbons are
Aldehydes and ketones also undergo oxidation with soluble in water. They are soluble because they can form
KMnO4, H2CrO4 and K2Cr2O7 into carboxylic acids: H-bonds with water. As the alkyl portion of the acid
O O increases, the nonpolar property and hydrophobicity of the
ll ll compound predominate. Due to intermolecular H-bonding,
RCH RC – OH carboxylic acids such as acetic acid are found as dimmers
in the gas state and in nonpolar solvents.
O
ll Chemical Properties
=O C – OH Carboxylic acids react with bases to form the
carboxylate salts, RCOOH+ NaOH RCOO-Na+ + H2O
C – OH The presence of EWG on the R substituent enhances
ll the acidity of carboxylic acids because of dispersion of
O electron density and consequent stabilization of the –COO-
B. CARBOXYLIC ACIDS and DERIVATIVES – organic group. On the other hand, substituents on the -C (-
compounds containing a hydroxyl group attached to a branched acids) are usually less acidic than the
carbonyl O unbranched acids since their – COO- groups are shielded
ll from solvent molecules and cannot be stabilized by
R – C – OH solvation as effectively.
Carboxylic acids can be readily derivatized to give other
IUPAC Nomenclature functional groups:
(substituents) + root + suffix –oic + word “acid”
The carbonyl C is assigned as C1 of the parent chain. They 1. Formation of ESTERS (esterification)
may also be identified with common names such as formic - reaction with alcohols in the presence of an acid catalyst
acid, butyric acid and caproic acid (found in ants, butter lower rates are
and goats, respectively). Carboxylic acids can also be
named as derived from acetic acid. Examples are phenyl O O
acetic acid and trimethyl acetic acid: ll ll
O O RC – OH + R’ – OH RC – OR’ + OH2
ll ll
CH2C – OH C – OH IUPAC Nomenclature
(substituents) + parent chain + suffix –oate

Illustrations: The chain to which the carbonyl group belongs is

CH3CH2COOH propanoic acid considered as the parent chain, with the carbonyl C as C1.
(also methyl acetic acid) The other group R’ attached to O is considered as the
O substituent, with the O- linked C as C1.
ll O
C – OH 2,2-dimethylpropanoic acid ethyl ethanoate
O (also called ethyl acetate)
ll OCH2CH3
CH2C – OH phenylethanoic acid
O
Long-chain carboxylic acids are called fatty acids. They
usually contain an even number of C atoms along the methyl benzoate
parent chain which may or may not contain a double OMe
bond.
Saturated:
CH3(CH2)4COOH caproic acid Physical Properties of Carboxylic Acid Derivatives
CH3(CH2)6COOH caprylic acid Esters, anhydrides and acyl chlorides do not form H-
CH3(CH2)8COOH capric acid bonds with themselves unlike carboxylic acids and
CH3(CH2)10COOH lauric acid alcohols. They, therefore, have lower boiling points than
CH3(CH2)12COOH myristic acid carboxylic acids and alcohols for comparable molecular
CH3(CH2)14COOH palmitic acid weight. Their boiling points are similar to those of
CH3(CH2)16COOH stearic acid aldehydes and ketones of corresponding molecular weight.

LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER


They are soluble in water as long as they have 5 C or less
because of H-bonding for the esters; and because of
reaction with water (hydrolysis) leading to the formation
of carboxylic acids for the acyl chlorides and anhydrides.
Amides can form H-bonds with themselves and thus
have high boiling points as well as melting points. The
N,N-disubstituted amides, however, do not form H-bonds
with themselves and therefore have lower boiling and
melting points. Amides with 5 C or less are soluble in
water due to formation of H-bonds between solute and
solvent.
Chemical Properties of Carboxylic Acid Derivatives
The reactions undergone by these families of
compounds are predominantly centered on the partially
positive carbonyl carbon being attacked by nucleophiles.
The relative reactivities of the carbonyl compounds is in
the order
O O O O O disappears) in the FEHLING’S and Benedict’s tests.
ll ll ll ll ll
RC – Cl > RC – O – CR’ > RC – OR’ > RC – NH2
most reactive least reactive
The relative reactivity depends on (1) relative electron
density or withdrawing effect of a group –X towards the
carbonyl C, (2) the relative ability of –X as a leaving
group, and (3) both the electronic and steric effect of the
R-group. Nucleophilic substitution takes place readily if the
incoming group (Nu:-) is a stronger base than the leaving
group (-X) or if the final product is resonance-stabilized
BIOCHEMISTRY
1. Carbohydrates are polydroxy aldehydes and ketones
(called aldose and ketose) or, compounds yielding these
substances upon hydrolysis; they include sugars, starches
and cellulose.
2. Carbohydrates can be monosaccharides, (containing
one sugar unit) or polysaccharides (containing two or
more units); those containing two units are often called
disaccharides.
M.S. + M.S. + energy D.S.
(dehydration synthesis involving removal of water)
hydrolysis
D.S. M.S. + M.S. + energy
Lactose glucose + galactose
Maltose 2 glucose
sucrose glucose (C6H12O6) + fructose (C6H12O6)
3. Glucose is one of the most common
monosaccharides; it is the sugar found in the blood and
hence is often referred to as blood sugar. (also known as
dextrose or grape sugar)
4. Sucrose: (table sugar) most common disaccharides;
it consists of a glucose unit and a fructose unit.
5. Starch (an important nutrient for man) is a
polysaccharide made up of many glucose units.
a. starch: storage carbohydrate found in plants
b. glycogen: storage carbohydrate of animals
LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER
60
c. cellulose: insoluble CHO abundant in the tough
outer wall of plant cells. In humans, cellulose does not serve as f
6. Carbohydrates are formed from CO2, H2O and
chlorophyll, in the presence of sunlight, by the process of
photosynthesis.
chlorophyll : sunlight
6 CO2 + 6 H2O C6H12O6 + 6 O2
7. Hydrolysis of a polysaccharide yields the
monosaccharides that is made up of.
8. Carbohydrates undergo fermentation to produce
alcohols. Sucrose and maltose will ferment with yeast but
not lactose.
9. Reducing sugars are identified by becoming oxidized
by Cu2+ (which is reduced and hence blue color
Maltose and lactose show reducing properties except
sucrose. Polysaccharides: (-) tests for reducing sugars.
10. Proteins are the main constituents of living cells.
They are made up of amino acids (acids that contain the
amine group as well as the carboxyl group) linked through
the nitrogen atom to form very large molecules with
molecular weights as high as 50 million.
11. All the amino acids that have been isolated from
proteins are alpha amino acids and hence have the
general formula however, they can also have another
NH2 O
R – CH – C – OH; -NH2 or –COOH as part of the R
group. Also, the R group can contain an –OH group S
atoms, and it can be aliphatic or aromatic.
12. The essential amino acids are those required by
man but cannot be synthesized by the body.
13. The amino acids in a protein are joined together
through the nitrogen atom on one amino acid and the
carboxyl group on another, to form a peptide linkage.
Hence proteins are sometimes called polypeptides.
14. The kind and order of amino acids in a protein
determine the primary structure, and the type of chain
and hydrogen bonding within the molecule determines the
secondary structure. The tertiary structure has to do
with the overall shape of the molecule, and the
quaternary structure refers to interaction between
protein molecules.
15. Since proteins contain both an amine group (-NH2,
which is basic) and the acid or carboxyl (-COOH) also form
a type of double ion, called a Zwitterion. The pH value
where it is neutral is called the isoelectric point.
16. Proteins undergo hydrolysis to yield the amino acids
that the protein is composed of; they can be denatured
by heat, acid, base, or alcohol. This breaks the hydrogen
bonds and thus changes the structure and reactivity of the
protein.

17. Proteins can be simple (only contain amino acids) or
conjugated protein (contain phosphoric acid,
carbohydrates, or nucleic acids). They can be classified
according to their function as enzymes, hormones,
antibodies, structural (in skin, hair and so on),
contractile (in skeletal muscles), or blood proteins.
18. Lipids are fatlike substances that are esters, acids or
alcohols. Fats, oils and waxes are examples of lipids.
19. Fatty acids are long chain monocarboxylic acids that
can be saturated or unsaturated.
20. Fats and oils are esters of glycerol and fatty acids; all
R groups (from the acids) are the same in a simple
glyceride, and they are different in a mixed glyceride.
Fats have saturated R group and oils the R groups contain
multiple bonds; an oil can be converted to a fat by
hydrogenating it to form saturated R groups.
21. The number of double bonds in a fat or oil can be
determined by the iodine number, which tells how many
grams of iodine will react with 100 grams of fat or oil. The
saponification number is used to determine the
molecular weight of a fat; by measuring the number of
milligrams of KOH that will react with one gram of fat, to
form a soap (an alkali metal salt of a fatty acid).
22. Waxes are esters of high molecular weight
monohydroxy alcohols.
23. Simple lipids are esters of fatty acids; compound
lipids contain other groups (such as phosphoric acid,
carbohydrates, and nitrogen compounds) along with the
acid and alcohol; derived lipids are obtained by the
hydrolysis of simple or compound lipids – for example,
fatty acids and sterols (high molecular weight cyclic
alcohols – such as cholesterol) are derived lipids.
24. Most enzymes are proteins and will undergo all the
reactions of proteins. The enzymes in the body function
best about 400C. Temperatures above or below body
temperature will decrease the activity of enzymes. Each
enzymes has a certain pH at which it can function best.
An increase in the amount of enzyme will
increase the rate of reaction. An increase in the
amount of substrate will increase the rate of
reactions.
Compounds that increase the activity of an enzyme are
called activators. Compounds that interfere with the
activity of an enzyme are called inhibitors.
Enzymes contain an “active site” that binds to the
substrate to form an enzyme substrate complex. This
complex yields the products and regenerates the enzyme.
Many enzymes contain two parts – a protein and a non-
protein part. The protein part of an enzyme is called the
apoenzyme.
Some enzymes require the presence of a substance
called a coenzyme before they can act effectively.
Coenzymes frequently contain the B vitamins or
compounds derived from the B vitamins.
Under the older system of naming enzymes the
substrate was not mentioned, the newer system indicates
the substrate being acted on. The names of enzymes
LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER
61
under this system end in-ase. Enzymes can be classified
as oxidoreductases (enzymes that catalyze oxidation –
reduction reactions between two substrates),
transferases (which catalyze the transfer of a functional
group between substrates), hydrolases (which catalyze
hydrolysis reactions), lyases (which catalyze the removal
of groups from substrates by means other than
hydrolysis), isomerases (which catalyze the
interconversion of cis-trans isomers), and ligases (which
catalyze the coupling of two compounds with the braking
of pyrophosphate bonds).
Some hydrolytic enzymes are found in the lysosomes of
the cytoplasm. The cytoplasm also contains mitochondria.
These structural and functional units contain most of the
oxidative enzymes and are deeply involved in the electron
transport system of oxidation reaction. The mitochondria
also produce ATP, the cells’ chief source of energy.
Abnormal plasma enzyme concentrations are of clinical
significance in the diagnosis of certain diseases.
Isozymes are enzymes with the same function but
slightly different structural features.
Allosteric enzymes are key metabolic enzymes whose
activity can be changed by molecules other than the
substrate.
Zymogens are the precursors of enzymes.
25. Enzymes are proteins that act as catalysts for the bio-
chemical reactions take place in the body. There is a
specific one for each reaction. Without these, the
biochemical reaction will not take place fast enough to
sustain life.
26. The main constituent of genes and viruses in the body
are nucleo-proteins, which consist of proteins and
nucleic acids. These are two classes of nucleic acids –
ribonucleic acids, RNA and deoxyribonucleic acids,
DNA. These are responsible for the genetic code;
transfer RNA’s (tRNA) select specific amino acids from
a cell and transfer them to messenger RNA’s (mRNA),
which transmit the genetic code from the DNA in protein
synthesis.
27. Food taken into the body first undergoes digestion.
which breaks up the complex molecules into simple ones,
and then metabolism, in which the digested food
undergoes chemical changes in the tissues. There are two
types of metabolism – catabolism produces energy from
the nutrients and anabolism either stores the nutrients
or produces proteins and other substances from them.
28. Carbohydrates, which usually consumed as starches,
are one of the main sources of energy in the body. By a
series of processes they are converted to glucose and
either used to produce energy (by forming carbon dioxide
and water, plus energy, in the Krebs or citric acid
cycle) or stored for later use.
29. In the metabolism of proteins, they are hydrolyzed to
amino acids, which are then either used for tissue building
or broken down to ammonia, carbon dioxide and water
with the production of energy. The ammonia, which is
toxic, is removed by converting it to urea in the liver. In
adults there is a nitrogen balance between the amount

taken in and amount excreted; however in children this is
not the case since some is used in tissue building.
30. Fats and oils are oxidized to produce energy in the
body, being an even richer source than carbohydrates.
Fats can also be stored in the body; these not only serve
as a source of reserve food but also cushion the body
organs.
31. The food we eat consists of carbohydrates, proteins,
fats, minerals, water, and vitamins (compounds that are
essential to an organism but cannot be synthesized by the
organism)
32. Nutrients can be classified as according to the
following functions;
 provision from energy
 body-building materials
 regulation of the body processes.
The three main food types
 carbohydrates, proteins and fats
 proteins, calcium, and phosphorus are used
 elements such as sodium, potassium, chlorine,
magnesium, sulfur and iron are necessary, along
with traces of copper, cobalt, iodine, zinc,
molybdenum, and fluorine.
33. Drugs fall into two categories: pharmacodynamic
agents, which alter body functions by acting on the
nervous system and chemotherapeutic agents, which
destroy organisms that are harmful to the body.
Additional Notes in Proteins
Colloidal Nature: Proteins form colloidal dispersions with
water. Being colloidal, protein will pass thru filter paper
but not membrane. Proteins present in the bloodstream
cannot pass through the capillaries and should remain in
the blood. Since proteins cannot pass through
membranes, there should be no protein material present
in the urine. The presence of protein in the urine indicates
damage to the membranes in the kidneys-possibly
nephritis.
Denaturation of a protein refers to the unfolding and
rearrangement of the secondary and tertiary structures of
a protein without breaking the peptide bonds. A protein
that is denatured loses it biological activity. Reversible
denaturation occurs when the conditions for denaturation
are mild, the protein can be restored to the original
conformation by carefully reversing the conditions that
caused their denaturation.
Reagents that cause denaturation
1. Alcohol coagulates (precipitates) all types of proteins
except prolamines. 70% alcohol is used as disinfectant
because its ability to coagulate the protein present in
bacteria. Alcohol denatures proteins by forming H-bonds
that complete with the naturally occurring H-bonds in the
protein.
2. Salts of heavy metals such as mercuric chloride or silver
nitrate, precipitate proteins. The antidote for mercuric
LEARNFAST REVIEW AND TUTORIAL HUB – NMAT REVIEWER
62
chloride when these poisons are taken internally is egg
white. The heavy metal will react with the egg white and
precipitate out. (The egg white colloid has a charge
opposite to that of the heavy metal ion and so attracts it).
The precipitate thus formed must be removed from the
stomach by an emetic or the stomach will digest the egg
white and return the poisonous material to the system.
3. Heat. Gentle heating causes reversible denaturation of
protein, whereas vigorous heating causes irreversible
denaturation by disrupting several types of bonds.
4. Alkaloidal Reagents such as picric acid or tannic acid
denature protein by disrupting the salt bridges and
hydrogen bonds. Tannic acid has been used extensively in
the treatment of burns. When the substance is applied to
the burned area, it causes the protein to precipitate as a
tough covering, thus reducing the amount of water loss
from the area.
5. Radiation. Proteins in cancer cells (rapidly dividing cells)
are more susceptible to radiation than those present in
normal cells so x irradiation is used to destroy cancerous
tissues.
6. pH. Changes in pH can disrupt H-bonds and salt
bridges, causing irreversible denaturation. Proteins are
coagulated by such strong acids as concentrated HCl,
sulfuric acids and nitric acids. Casein is precipitated from
milk as a curd when it comes in contact with the HCl of
the stomach. Heller’s ring test is used to detect the
presence of albumin in the urine. A layer of conc. nitric
acid is carefully placed in a sample of urine in a test tube.
If albumin is present, it will precipitate out as a white ring
at the interface of the two liquids. If acid or base remains
in contact with protein for long period of time, the peptide
bonds will break.
7. Oxidizing and reducing agents. Oxidizing agents such as
bleach and nitric acid and reducing agents such as sulfites
and oxalates denature protein irreversibly to disrupting
disulfide bonds.
8. Salting out. Most proteins are insoluble in saturated salt
solutions and precipitate out unchanged. To separate a
protein from a mixture of other substances, the mixture is
placed in a saturated salt solution (such as NaCl, or
Na2SO4. The protein precipitates out and is removed by
filtration. The protein can then be purified from the
remaining salt by the process of dialysis.
Biomolecules
A. Carbohydrates (L. “carbos” charcoal, “hydros” water)
 Most abundant organic molecule in nature
 Monomer is monosaccharide, polymer is
polysaccharide
 Majority of these compounds contain carbon,
hydrogen and oxygen with a common ration of
Cn(H2O)n “hydrate of carbon”
 Functions include energy sources and structural
elements
 They are classified as monosaccharides,
 63

disaccharides, oligosaccharides, and

polysaccharides according to the number of simple
sugars they contain.
 monosaccharides (glucose, fructose, galactose,
mannose)
 disaccharides (lactose, maltose, sucrose)
 oligosaccharides (3-10 monosaccharide units,
found in ER, GB)
 polysaccharides (starch, glycogen, cellulose, chitin,
pectin, gum, peptidoglycan)
 Monosaccharides are linked together by a process
called dehydration synthesis/ condensation
(removal of water).
 Polysaccharides are broken down to their component
monosaccharides through hydrolysis.
B. Proteins
 Monomer is amino acid, polymer is polypeptide
 There are currently 20 naturally-occurring amino acids
 Amino acids are linked together by peptide bonds
 Protein Denaturation=disruption of 3° structure
 Of all the molecules encountered in living systems,
proteins have the most diverse functions.
Function Examples
Enzymes (amylase,
1. catalysis
cellulose, papase/ papain)
Collagen (connective tissue
matrix)
2. structure Fibroin (silk), spider web
Keratin (hair, horns,
feathers, hooves)
Actin and tubulin (involved
in cell movements in
3. movement
Amoeba and sperm cells;
found in flagella and cilia)
Skin keratin (first line of
protection)
Fibrinogen and thrombin
(blood clot)
4. defense
Antibodies (secreted by
lymphocytes in response to
infection)
Spines of sea urchin
Hormones (insulin &
5. regulation
glucagon, growth hormone)
Hemoglobin (oxygen and
waste material transport)
Myoglobin (transport of
6. transport
oxygen to muscles)
Glucose transporters
Zein (corn), gliadin
(wheat), plastids,
7. storage
ovalbumin (egg white),
casein (milk)
* words in italics are specific names of proteins
There are four levels of protein structure:
 Primary (1°)
 Secondary (2°)
 Tertiary (3°)
 Quaternary (4°)
C. Lipids (L. “lipos” fat)
 Unlike other biological polymers, lipids are not defined
by specific, repeating monomeric units. Rather, they are
defined by their water-repelling property.
 They contain 3 fatty acids and 1 glycerol.
 They also contain non-polar hydrocarbon groups
(-CH3CH2)
 Functions include transport, storage, and insulation.
 3 types: oils (saturated and unsaturated), waxes,
phospholipids
 Oil is liquid at room temperature, while wax is solid.
 Phospholipids usually assume two forms in an aqueous
environment: micelle and phospholipids bilayer.
 Oil is usually plant-derived, while fat (wax) is animal-
derived.
 Lipids have the most amount of energy content:
Lipids>Carbohydrates> Proteins
D. Nucleic Acids
 There are two types: DNA and RNA.
 Monomer is nucleotide
 The sugar component is a pentose (Nucleotide is made
up of three components: nitrogenous base, sugar
(ribose, deoxyribose) and phosphate group.
 The nitrogenous bases are adenine, guanine,
cytosine, thymine, uracil.
 Types of bond found in Nucleic Acids: H-bonds
(between complementary nitrogenous bases);
Phosphodiester bond (connects nucleotides); and
N-glycosidic bond (connects bases and sugars).
 Main function is involved in heredity, protein synthesis,
and as energy carriers.
DNA RNA
Sugar Deoxyribose Ribose
Bases A, G, C, T A, G, C, U
Strand Double-stranded Single-stranded
Helix Helical Non-helical
mRNA, tRNA, rRNA,
Examples B-DNA, A-DNA, Z-DNA
hnRNA, snRNA

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PRIORITY TABLE OF FUNCTIONAL GROUPS OF ORGANIC CHEMISTRY

Suffix Prefix
Formula Function Example
(main function) (secondary function)
O
CH3-COOH
II Acid -oic acid carboxyl-
Ethanoic acid
R-C-OH
O
CH3-COO-CH3
II Ester -yl, -oate
Methyl ethanoate
R-C-O-R’
O
CH3-CH2-CONH2
II Amide -amide carboxamido-
Propanamide
R-C-NH2
CH3-CN
R-CN Nitrile -nitrile (cyanide) cyano- Ethanenitrile
Methyl cyanide
O
CH3-CH2-CHO
II Aldehyde -al oxo-
Propanal
R-C-H
O
CH3-CO-CH3
II Ketone -one oxo-
Propanone
R-C-R’
CH3-CH2OH
R-OH Alcohol -ol hydroxi-
Ethanol
CH3-CH2-NH2
R-NH2 Amine -amine amino-
Ethylamine
CH3-O-CH2-CH3
R-O-R’ Ether -y … yl ether oxa-
Ethylmethyl ether

C=C CH3-CH=CH2
Alkene -ene
Propene

CH3-CHCH
-CC- Alkyne -yne
Propyne
CH3-CH2-NO2
R-NO2 Nitro nitro-
Nitroethane
fluoro-, chloro-, CH3-CH2Br
R-X Halide
bromo-, iodo- Bromoethane
CH3
I
-R Radical yl-
CH3-CH-CH3
Methylpropane

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