NMAT-Org-Chem - Biochem Lecture (1-JD

ORGANIC CHEMISTRY
Learnfast NMAT Review

Prepared by: Adrian Jonathan D. Velasco, MD-PhD (C)
LEWIS THEORY
•  Electronegativity!
o  The tendency of an
atom to attract a
bonding pair of
electrons.
•  Electron Affinity!
o  Energy released
when an electron is
added to an atom
LEWIS THEORY
•  Ionic Bonding!
o  When one atom is much more
electronegative than the other
LEWIS THEORY
•  Covalent Bonding!
o  When both atoms have more or less the
same electronegativities.
LEWIS THEORY
•  Drawing Lewis Dot Structure!

o  Count the number of valence electrons
o  Arrange the elements in a basic outline
o  Least electronegative element goes in the
middle
o  Hydrogen is almost always outside
o  Connect the atoms
o  Ensure that each atom has an octet, and the
valence electrons tallies with the original
LEWIS THEORY
CH4 CO2

o  Total valence electrons?
o  Arrange the elements in a basic outline
o  Connect the atoms
o  Ensure that each atom has an octet, and the
valence electrons tallies with the original
ORBITALS IN BOND
FORMATION
s, p, d & f orbitals
Probability where electrons can be found.
ORBITALS IN BOND
FORMATION
s, p, d & f orbitals hybridization
Mixture of qualities of different orbitals
ORBITALS IN BOND
FORMATION
σ-bond & π-bond
Head-to-head and side-to-side overlap respectively.
CHARACTERISTICS OF A
COVALENT BOND
Polarity
Two atoms of different electronegativities form a covalent bond.
COVALENT BOND
Bond Length
Average distance separating the nuclei of bonded atoms

Decreases with decreasing atomic size

C–I>C–C>C–H
Decreases with increasing polarities

C–C>C–N>C–O
Decreases with increasing bond order

C–C>C=C
COVALENT BOND
Bond Energy / Strength
Energy needed to disrupt a covalent bond.

Decreases with decreasing polarity

C – F > C – Cl > C – I
Decreases with decreasing character of s orbital

sp-sp > sp 2-sp > sp2-sp2
Decreases with decreasing bond order

C–C>C=C
STRUCTURAL EFFECTS
Resonance
Because electrons can’t just sit tight at one position.

STRUCTURAL EFFECTS
Inductive Effects
Distortion of electron distribution due to electron-donating
groups or electron-withdrawing groups.

STRUCTURAL EFFECTS
Stearic Effects
Bulky groups repel other groups.

STRUCTURAL EFFECTS
Intra- and Intermolecular Forces
Attractive forces that keep molecules close together.

ORGANIC FORMULAE
ORGANIC FORMULAE
ORGANIC FORMULAE
FUNCTIONAL GROUPS
HYDROCARBONS
•  Organic compounds that

contain only hydrogen and
carbons
•  Simplest organic
compounds.
HYDROCARBONS
•  Four bonds results in a

tetrahedral molecular
geometry.
•  Chiral center – when all
four species attached to
an atom are different.
•  Chirality determines
optical activity of a
molecule.
ALIPHATIC HYDROCARBONS
•  Presence of single bonds, double bonds

or triple bonds
AROMATIC HYDROCARBONS
NOMENCLATURE
•  Number of carbons at the longest

possible chain.
NOMENCLATURE
hexane isohexane cyclohexane

•  Is it linear, branching or cyclic?
NOMENCLATURE
•  Name of branch: prefix + yl

EXAMPLES: NAMING
Ball and stick model (left) and Skeletal model (right) of

the same molecule: C7H16
EXAMPLES: NAMING
Structural model (left) and Skeletal model (right) of the

same molecule: C8H18
EXAMPLES: NAMING
Structural model (left) and ball and stick model (right) of

EXAMPLES: NAMING
Structural model (left) and ball and stick model (right) of

HALOALKANE (ALKYL HALIDES)
•  Haloalkane – contains a
halogen
•  Nomenclature is
designated by an halo
prefix

ALCOHOLS
•  Alcohols – contains
hydroxyl functional
group (-OH)
•  Nomenclature is
designated by an –ol
suffix

NAME?
Name this compound.

ALDEHYDE & KETONES
•  Aldehydes – derived from

dehydration of alcohols
•  Aldehydes contain a
carbonyl group (C=O)
with at least one
hydrogen atom.
•  Ketones contain a
carbonyl group bonded
to two carbon atoms.
ALDEHYDE & KETONES
•  Nomenclature for
aldehydes:–al suffix, while
for ketone:–one suffix.
NAME?
Name this compound.

CARBOXYLIC ACID
•  Carboxyl group is composed

of two functional groups:
carbonyl group (C=O) and
hydroxyl group (-OH).
•  In condensed form, it is
represented as -CO2H or
-COOH
CARBOXYLIC ACID
•  Naming is designated by –oic

acid.
NAME?
Name this compound.

ETHERS
•  Ethers contain two

hydrocarbon groups attached
to a central O atom.
•  Nomenclature: substituents -
oxy + parent chain.
AMINES
•  Amines are derivatives of

ammonia (NH3) in which one
ore more of the hydrogen
atoms has been replaced by
a hydrocarbon.
•  Naming: amino- prefix or –
amine sufffix.
NAME?
Name this compound.

ISOMERS
ISOMERS
hexane isohexane cyclohexan

e
Same molecular formula, different structural
or spatial arrangements of the atoms.
ISOMERS
•  Varying structure translates to differences

in chemical and physical properties
STRUCISOMERS
STRUCTURAL ISOMERS
•  Chain isomers have different

arrangement of the carbon
skeleton.
•  Also known as skeletal
isomers.
STRUCTURAL ISOMERS
•  Position isomers are based

on the movement of the
same functional group in
the molecule.
STRUCTURAL ISOMERS
•  Functional isomers based

on different types of
functional groups.
•  Example: re-arrangement of
carbons in alkane can form
cycloalkanes.
STEREOISOMERS
Conformational isomerism
connected by single bonds that allow inter-conversion.
STEREOISOMERS
•  Geometric isomerism is also

known as cis-trans or E-Z
isomerism.
•  Involves double bonds.
Rotation of these bonds is
restricted.
•  Trans (E) – opposite side
•  Cis (Z) – same side
STEREOISOMERS
•  Optical isomers are so name

due to their effect on plane-
polarised light.
•  Also known as enantiomers.
•  Non-superimposable mirror
images – only possible for
chiral molecules.
STEREOISOMERS
•  Functional groups are arranged

depending on priority.
•  Priority is based on the atomic
weight of the constituents.
•  Point the functional group with the
least priority away from you.
•  If the remaining functional groups
are arranged counterclockwise: S
or L isomer
•  Clockwise: R or D isomer
STEREOISOMERS
Which molecule is chiral?

BIOCHEMISTRY
MAJOR CLASSES OF
BIOMOLECULES
CARBOHYDRATES
Monosaccharides
Polyhydroxy-aldehydes or ketones: Cn(H2O)n
CARBOHYDRATES
Disaccharides and Polysaccharides

Monosaccharides form more complex carbohydrates.
CARBOHYDRATES
General Functions:
•  Structural – cell wall, membrane function
•  Metabolic – energy storage and energy
source

•  Informational – cell-to-cell recognition
PROTEINS
PROTEINS
Amino Acids
(1)  Amino Group, (2) Carboxyl Group,
(2)  (3) H-atom and (4) R-group.
PROTEINS
•  Classification of Amino Acids:

•  Based on Polarity: Non-polar, Polar
(uncharged), Polar (charged)
•  Based on Source: essential vs non-
essential
•  Based on the functional groups present on
the side chain
•  Based on acidity / alkalinity
PROTEINS
Peptide Bond
Covalent bond
between the carbon of
the carboxyl group of
one amino acid to the
nitrogen of the amino
group of next
monomer (C–N)
LEVELS OF
PROTEIN
ORGANIZATON
Primary Structure (1°)
•  Order/sequence of amino
acids in a polypeptide chain

LEVELS OF
PROTEIN
ORGANIZATON
Secondary Structure (2°)
•  Steric/spatial relations
between amino acids (in the
polypeptide chain) that are
close to each other
•  Maintained by noncovalent
H-bonding
•  Includes: alpha-helix, beta
pleated sheet, random coil
LEVELS OF
PROTEIN
ORGANIZATON
Secondary Structure (2°)
•  Steric/spatial relations
between amino acids (in the
polypeptide chain) that are
close to each other
•  Maintained by noncovalent
H-bonding
•  Includes: alpha-helix, beta
pleated sheet, random coil
LEVELS OF
PROTEIN
ORGANIZATON
Tertiary Structure (3°)
•  3D arrangement
•  globular or elongated/fibrous
•  Held by hydrophobic and
electrostatic/salt linkage
interactions (non-covalent)
LEVELS OF
PROTEIN
ORGANIZATON
Quaternary Structure (4o)
•  Two or more polypeptide
chains (subunits / monomers)
arranged in 3D complexes
•  Multimer: protein with

multiple subunits
LIPIDS
A heterogeneous class of
biomolecules mostly
associated with fatty acids
that are hydrophobic,
amphipathic, and dissolves
widely in organic, non-polar
solvents.

No structural definition that will
define the entirety of lipids
LIPIDS
General Functions:
•  Storage Lipids - stores energy and allows insulation
•  Membrane Integrity - gives hydrophobic layer and
affects fluidity and melting point
•  Cell Signaling or Bioeffectors - includes hormones
and local mediators
•  Lipid as secondary messenger
•  Development - role of omega fats
LIPIDS
SIMPLE LIPIDS
Esters of fatty acids with
alcohol
•  Fats: Esters of fatty acids
and glycerol in semi-solid to
solid state
•  Oils: Fats in liquid state
•  Waxes: Esters of fatty acids
with high molecular weight,
monohydric alcohols
NUCLEIC ACIDS
The building blocks of nucleic acids are nucleotides.

NUCLEIC ACIDS
Parts of a nucleotide
Nitrogenous base
Purines
•  Guanine & Adenine
Pyrimidines
•  Cytosine, Thymine &
Uracil
Sugar
•  Ribose
•  Deoxyribose
A closer look. Phosphate

NUCLEIC ACIDS
Properties of DNA
•  Double-helix
•  Complementary
base-pairing
•  Anti-parallel
A closer look.
NUCLEIC ACIDS
DNA RNA
Nitrogenous Bases GATC GAUC
Number of Strands 2 1
Sugar Component Deoxyribose Ribose
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ORGANIC CHEMISTRY

Learnfast NMAT Review

• Drawing Lewis Dot Structure!

Decreases with decreasing bond order

• Organic compounds that

• Four bonds results in a

• Presence of single bonds, double bonds

• Number of carbons at the longest

hexane isohexane cyclohexane

• Name of branch: prefix + yl

Ball and stick model (left) and Skeletal model (right) of

Structural model (left) and Skeletal model (right) of the

Structural model (left) and ball and stick model (right) of

Structural model (left) and ball and stick model (right) of

Name this compound.

• Aldehydes – derived from

Name this compound.

• Carboxyl group is composed

• Naming is designated by –oic

Name this compound.

• Ethers contain two

• Amines are derivatives of

Name this compound.

hexane isohexane cyclohexan

• Varying structure translates to diﬀerences

• Chain isomers have diﬀerent

• Position isomers are based

• Functional isomers based

• Geometric isomerism is also

• Optical isomers are so name

• Functional groups are arranged

Which molecule is chiral?

Disaccharides and Polysaccharides

• Classification of Amino Acids:

The building blocks of nucleic acids are nucleotides.

A closer look. Phosphate

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•  Drawing Lewis Dot Structure!

•  Organic compounds that

•  Four bonds results in a

•  Presence of single bonds, double bonds

•  Number of carbons at the longest

•  Name of branch: prefix + yl

•  Aldehydes – derived from

•  Carboxyl group is composed

•  Naming is designated by –oic

•  Ethers contain two

•  Amines are derivatives of

•  Varying structure translates to diﬀerences

•  Chain isomers have diﬀerent

•  Position isomers are based

•  Functional isomers based

•  Geometric isomerism is also

•  Optical isomers are so name

•  Functional groups are arranged

•  Classification of Amino Acids: