OVERVIEW OF GENERAL AND

ORGANIC CHEMISTRY AND

INTRODUCTION TO
BIOCHEMISTRY
Christian Adam Espiritu, M.D., Ph.D.
BASIC CONCEPTS

 Organic Chemistry
 Study of carbon and its compounds
 Substances that are primarily composed of carbon have been
known as organic substances

 Biochemistry
 Chemistry of living organisms
 Study of biology at the cellular and molecular level
PRINCIPAL AREAS IN BIOCHEMISTRY
 Structure and function of biomolecules
 Metabolism – anabolic and catabolic processes

 Molecular genetics – how life is replicated, regulation of

protein synthesis
MOLECULES AND COMPOUNDS
 Formed when two or more atoms unite in the basis of
their electron structure

 Carbon
 Period 2 and Group IV of the Periodic Table of Elements
 Tetravalent
 Has the ability to participate in a wide variety of chemical
reactions and is able to form different compounds with other
elements
TYPES OF CHEMICAL BONDS
 Ionic Bond
 involves in the complete transfer of electrons from one atom
to another, resulting in the production of charged atoms,
known as ions
 these ions can be positively charged or negatively charged.

 Covalent Bond
 results
from the sharing of electrons between two atoms.
 covalent bonds can can be polar or nonpolar
CHEMICAL REACTIONS
 To be able to form new compounds, they have to participate
in chemical reactions. These chemical reactions
characteristically involve the disruption and formation of
chemical bonds.

 Site of organic chemical reactions

 Multiple Bonds
 Polar Groups
 Lewis Acid and Lewis Base Characteristics

 Reaction Intermediates
 Carbocation, Cabanions
 Free Radicals
GENERAL TYPES OF ORGANIC
REACTIONS
 Addition Reactions
 This is usually a characteristic of unsaturated compound and
usually result to disruption of multiple bonds
 Elimination Reactions
 Reverse of addition, formation of double bonds
 Substitution Reactions
 Replacement of one substituent by another
 Rearrangement Reactions
 Rearrangement of the structure of a compound
PROPERTIES OF ORGANIC COMPOUNDS
 The properties of organic compounds are largely
influenced by these factors:
 Intermolecular
forces of attraction
 Molecular geometry

 Structural effects:
 Orbital hybridization
 Steric effects
 Inductive effects – distortion of electron cloud
 Resonance – pi electron delocalization
 CH Hyperconjucation – sigma electron delocalization
BOND POLARITY AND
ELECTRONEGATIVITY
POLAR COVALENT BONDS

 A given bond is either ionic and covalent. However, the

shared electrons in covalent bonds tend to be attracted
somewhat more strongly by one atom by the other.

 We call such bonds with unsymmetrical electron

distribution as polar covalent bonds.
ELECTRONEGATIVITY

 Bond polarity is due to differences in electronegativity,

the intrinsic ability of an atom to attract electrons in
covalent bond.
BOND POLARITY

 As a rule, bonds between atoms with similar or almost

the same electronegativities (EN) are nonpolar covalent
bonds, bonds between atoms whose electronegativities
differ by less than 2 units are polar covalent, and bonds
between atoms whose electronegativities differ by more
than 2 units are ionic bonds.
MOLECULE POLARITY

 The polarity of a molecule is dictated by its geometry

AND the individual bonds existing within molecule.

 A molecule with polar bonds may not necessaily be

polar. Why?
MOLECULE POLARITY

 The Dipole Moment or the total or net product of

vectors or charges is considered through their molecular
geometry.

 For example: Ammonia and Carbon dioxide

 Take note of the symmetry.

INTERMOLECULAR FORCES OF
ATTRACTION
PHYSICAL PROPERTIES
 Solubility is one the most important properties of organic
compounds

 These properties of organic compounds is generally

related to the intermolecular forces of attraction or
IMFA. IMFA are the forces that must be overcome or
broken during melting, evaporation and sublimation.
IMFA
 Recall that atoms in molecules are associated with other
atoms by covalent bonds.
 These are relatively strong bonds and are called
intramolecular forces.
 We differentiate this from IMFA, which are forces
between molecules.
TYPES OF IMFA
 London dispersion forces (Ldf)
 Dipole-dipole forces
 Hydrogen Bond

Ldf and Dipole-dipole forces are collectivelly known as

van der Waals forces (vdW)

 Ion-Ion forces – of ionic organic compounds

LONDON DISPERSION FORCES
 Ldf are present in all substance, the only IMFA present
in non-polar substances and noble gases.
 Usually increase with molar mass (MM); the larger the
MM, the stronger the Ldf
 For example let us compare N2, Cl2 and F2
LONDON DISPERSION FORCES
 N2 < F2 < Cl2

Substance Boiling Point, K

N2 77.4
F2 85.0
Cl2 239.1
DIPOLE-DIPOLE FORCES
 Polar molecules exhibit dipole-dipole forces aside from
Ldf.
 The more polar molecule, the stronger the dipole-dipole
interaction.

 Let us consider: HI, HBr and HCl, which among the

three exhibits the strongest dipole-dipole interaction?
ASSESSING VAN DER WAALS FORCES
 HCl has stronger dipole-dipole forces but based on their
MM, HBr has stronger Ldf???

 Ifthe substances are of widely different MM, Ldf are

considered important than dipole-dipole interaction in
determining the relative strength of vdW forces

 Ifthe MM of are relatively close, the presence of dipole-

dipole interaction greatly contributes in determining the
relative vdW
HYDROGEN BONDING
 Hydrogen bonding is a strong IMFA and a special type
of dipole-dipole interaction.
 It is present among molecules which contain hydrogen
bound to a small, highly electronegative atom such as N,
O and F.
ION-ION FORCES
 Every ionic compound is held in a well-ordered
crystalline state.
 The forces that hold ions together are strong electrostatic
lattice forces, an adequate amount of energy is needed to
break the orderly structure of the crystal.
 In sodium acetate, an ionic organic compound, BP is
very high that it tends to decompose before it boils.
SOLUBILITY AND MISCIBILITY
BASED ON POLARITY
 “Like dissolves like”
 The overall solvation capacity of a solvent depends upon its
polarity
 Polar solvents like water dissolve polar solutes (hydrophilic)
 Nonpolar solvent dissolves nonpolar solutes (hydrophobic)
ISOMERISM
 Isomers are defined as compounds possessing the same
molecular formula but different structural formula
 Structural/constitutional
isomerism – variation in the bonding
arrangement of atoms or groups
 Skeletal
 Positional

 Functional

 Stereoisomerism – no variation in bonding arrangement, only

in orientation in space.
 Optical
 Conformational

 Geometric
ORIGINS OF LIFE
 Vitalism is the idea that substances and processes
associated with living organisms did not behave
according to the known laws of physics and chemistry.

 Evidence
 Biochemicalcan only be produced by living organisms
 Complex bioconversion of chemical substance require living
matter
BIOCHEMICAL EVOLUTION
• Urea was synthesized by heating the inorganic compound
ammonium cyanate (1828)
• This showed that compounds found exclusively in living
organisms could be synthesized from common inorganic
substances
ORGANIZATION OF LIFE
 Elements
 Simple organic compounds

 Macromolecules

 Supramolecular structures

 Organelles

 Cells

 Tissues

 Organism
 MANY IMPORTANT BIOMOLECULES ARE
POLYMERS

lipids proteins carbo nucleic acids

monomer fa tty a c id a m ino ac id g lu co se n uc leo tide

polymer p ho sp ho lip id p rote in su b un it c e llu lo se DNA

supramolecular
m em b rane p rote in c om plex c e ll w a ll c h ro m o s om e
structure
 BIOMOLECULES – STRUCTURE
Anabolic
 Building block  Macromolecule
 Simple sugar  Polysaccharide
 Amino acid  Protein (peptide)
 Nucleotide  RNA or DNA
 Fatty acid  Lipid

Catabolic
32
LINKING MONOMERS
Cells link monomers by a process
called dehydration synthesis
(removing a molecule of water)

Remove
H

H2O Forms

Remove OH

This process joins two sugar monomers

to make a double sugar 33
BREAKING DOWN
POLYMERS
 Cells
break down
macromolecules by
a process called
hydrolysis (adding
a molecule of
water)

Water added to split a double sugar

34
 LIPIDS

monomer fa tty a c id

polymer p ho sp ho lip id

supramolecular
m em b rane
structure
 PROTEINS

monomer amino acid

polymer protein subunit

supramolecular
structure Enzyme complex
 CARBOHYDRATES

monomer g lu co se

polymer c e llu lo se

supramolecular
structure c e ll w a ll
 NUCLEIC ACIDS

monomer n uc leo tide

polymer DNA

supramolecular
c h ro m a tin
structure
Common theme:

Monomers form
polymers through
condensations

Polymers are broken

down through
hydrolysis.
WATER
About 60-90 percent of
an organism is water

Water is used in
most reactions in
the body
Water is called
the universal
solvent 41
ACIDS AND BASES
DEFINITIONS
 Arrhenius
 acids are substances that increase the concentration of
hydronium ions when added to solutions, and base increases
the concentration of hydroxide ions.
 Bronsted-Lowry
 A Bronsted-Lowry acid is a substance that donates a proton
(hydrogen ion), and a Bronsted-Lowry base is a substance
that accepts a proton
 Lewis
 A Lewis acid is a substance that accepts an electron pair and
a Lewis base is a substance that donates an unshared electron
pair
PH AND POH
 Because of the enormous range in the concentrations of
hydronium and hydroxide ions, we usually use a
logarithmic scale to express this concentrations:
WEAK ACIDS AND BASES
BUFFERS
 Certain solutions can resist drastic changes in pH when
small quantities of acids and base are added to them.
 Such solutions are called BUFFERS.
 Mixtures of a weak acid and a salt containing its conjugate
base or a weak base and a salt containing its conjugate acid.
OXIDATION AND REDUCTION IN
ORGANIC MOLECULES