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MODULE 6
ORGANIC COMPOUNDS

MOST ESSENTIAL LEARNING COMPETENCIES (MELCs)

At the end of the module, you should be able to:
1. describe the different functional groups;
2. describe structural isomerism, give examples;
3. describe some simple reactions of organic compounds: combustion of organic fuels,
addition, condensation, and saponification of fats;
4. describe the formation and structure of polymers;
5. explain the properties of some polymers in terms of their structure;
6. describe the structure of proteins, nucleic acids, lipids, and carbohydrates, and relate
them to their function;
7. describe the preparation of selected organic compounds.

Specific Learning Objectives

After going through the lesson, you should be able to:

1. describe the special nature of carbon;
2. list general characteristics of organic compounds;
3. describe the bonding in ethane, ethene (ethylene), ethyne (acetylene) and explain
their geometry in terms of hybridization and sigma and pi carbon-carbon bonds;
4. describe the different functional groups;
5. cite uses of representative examples of compounds bearing the different functional
groups;
6. describe structural isomerism; give examples;
7. describe some simple reactions of organic compounds: combustion of organic fuels,
addition, condensation, and saponification of fats;
8. describe the formation and structure of polymers;

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9. give examples of polymers;

10. explain the properties of some polymers in terms of their structure;
11. describe some biomolecules: proteins, nucleic acids, lipids, and carbohydrates;
12. describe the structure of proteins, nucleic acids, lipids, and carbohydrates and relate
them to their function;
13. (LAB) perform exercises on the structure of organic compounds using of models;
14. (LAB) prepare selected organic compound and describe their properties;
15. (LAB) perform laboratory activities on enzyme action, protein denaturation,
separation of components in coconut milk.

In the living world, carbon, in combination with hydrogen, oxygen, nitrogen, and sulfur, forms
the basis for millions of organic compounds. Carbon compounds provide us with energy sources
in the form of hydrocarbons and their derivatives that allow us to heat and light our homes, drive
our automobiles to work, and fly off to some tourist vacation. Small substitutions in these carbon
molecules can produce chlorofluorocarbons, the compounds used in plastics and refrigerants. An
understanding of these molecules and their effect upon our global environment is vital in the
continuing search to find ways to maintain our lifestyles while preserving the planet.
Through delicately controlled mechanisms, a living cell oxidizes food for energy, maintains
the concentrations of thousands of aqueous components, interacts continuously with its environment,
synthesizes both simple and complex molecules and even reproduces itself. No man-made system
compares with the cell in terms of its complexity and elegant functions.
The cell, like a machine, consumes, creates and consists largely of organic compounds.
In addition, except for a few inorganic salts and water, nearly everything put into or on your body-
food, medicine, cosmetics and clothing- consists of organic compounds
Organic fuels warm our homes, cook our meals and power our vehicles. Major
industries are devoted to producing organic compounds, including plastics,
pharmaceuticals and insecticides.

DO YOU KNOW THAT:

Carbon is far from being among the most abundant elements in the
earth’s crust. Approximately 75% of the earth’s crust are oxygen and
silicon found in silicate minerals, clays, sand, rocks and soil.

It is not even one among the 10 most abundant elements

but one of the remaining 0.9% of the earth’s crust

Organic compounds can be obtained from inorganic materials. Friedrich Wohler disproved
the vital force theory i.e organic compounds comes only from living organisms but Wohler performed
an experiment where urea (a metabolic product found in urine) was synthetically produced in the
laboratory by reacting ammonium chloride and silver cyanate to form urea and silver chloride
- August Kekule proposed that carbon atoms can bond to one another to form extended
chains of linked atoms and chains can double back on themselves to form rings.

Organic compounds differ from inorganic compounds in many of their properties mainly because of
the type of bonding in organic compounds that are entirely covalent while inorganic compounds have
ionic bonds.

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Prior to our main discussion in understanding the properties of organic compounds and its polymers
in terms of their structure, it is good to recall:
- the concepts in chemical bonding and the existence of electrons that are concentrated in
certain regions of space around the nucleus called - the atomic orbitals – s, p, d and f.
- how the valence electrons play a fundamental role in chemical bonding- in the formation of
ionic or covalent compounds particularly- organic compounds and its polymers
- the Lewis theory, octet rule, molecular geometry or shapes, VSEPR theory
- the properties of ionic and covalent compounds in terms of its chemical reactions like:
o in a sense, the oppositely charged ions present in an ionic compound are attracted to
one another like the opposite poles of a magnet. In its crystalline structure, the ions are
packed in a definite arrangement but is not connected to another particular ion. So,
when the substance dissolve, the ions are able to move in the solutions freely.

o when two or more atoms are joined by covalent bonds- it constitutes a molecule.

o the bond formation in molecules can be characterized in terms of its:

bond length, bond energy, bond angle, bond polarity, type of bonds:
single, double, triple

EXERCISE: As a form of recall, do your best to answer the following:

1. Show the number of valence electrons in each of the following atoms.
Use Lewis symbols.

a. Calcium e. Carbon

b. Boron f. Bromine

c. Oxygen g. Nitrogen

d. Phosphorus h. sulfur

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2. Use the relative position of the elements in the periodic table to classify the
following substances as ionic or covalent:
a. F2 ____________ e. BaCl2 ____________
b. KI _____________ f. PCl3 ____________
c. P2O5 _____________ g. LiBr ____________
d. SiCl4 _____________ h. ClF ____________
3. Using the Lewis theory/ Lewis symbol/ Lewis structure, write the structural formula for
each compound. Then use the line structure to represent a single, double or triple bond
formed between the atoms.
a. CH3CH2OH

b. CH3F

c. C3H8

d. CH3NH2

e. C2H5Cl

f. CH2O

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1. The element carbon (6th element in group IVA in the periodic table) is very special. 99% of the
37 million + presently known chemical compounds contain carbon (also known as organic
compounds) since carbon can:

a) Share valence electrons to form strong covalent bonds

b) Bond to one another forming long chains and rings

c) Form diverse compounds from one carbon in methane to complex DNA having more
than 100 million carbons

d) Not only bond chiefly with H, O and N in most organic compounds but also with S, P,
and a halogen (F, Cl, Br or I)

2. The usual number of covalent bonds in compounds are made up of:

a) Carbon: with 4 covalent bonds & has no unshared pair of electrons

b) Nitrogen: 3 covalent bonds with one unshared pair of electrons

c) Oxygen: 2 covalent bonds with two unshared pair of electrons

d) Hydrogen: one covalent bond & has no unshared pair of electrons

e) A halogen (F, Cl, Br, I) forms one covalent bond with three unshared pair of
electrons

3. The characteristic strength of covalent bonds, its molecular shapes based on the interaction
of its atomic orbitals are explained by the valence bond theory. (refer to p298 of your
chemistry textbook).

4. In connection to their complex geometries, organic compounds are noted for their great
number and diverse chemical behavior (page 397 of your Chemistry textbook)

5. One of the most important ideas in organic chemistry is the presence of a functional group, a
specific combination of bonded atoms that reacts in a characteristic way, no matter what molecule
it occurs in. This is used to classify the organic compounds and behaves differently in chemical
reactions. The different classes may have the same molecular formula but different in structural
formulas, called isomers, giving rise to different chemical and physical properties.

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6. In order to be familiar with the different groups or classes of organic compounds is to also be
knowledgeable of naming the organic compounds and to understand its properties even with just
its structural formula. (refer to p400 – 417 of your Chemistry textbook)

7. Carbon’s ability to bond to many other elements, including O and N, creating polar bonds and
resulting to greater reactivity, leads to the chemical diversity of organic compounds.

8. Each class of organic compounds can undergo important oxidation-reduction reactions. There
are countless different carbon-containing molecules that exist but there are relatively few organic
reactions and only a few carbon atoms are involved in any common reaction. These are the
following (and specific examples will be given): Combustion, Addition, Condensation,
Substitution, Saponification

9. Polymers are manufactured from double-bonded (unsaturated) molecules like

polyethylene plastic bags and bottles, polystyrene styrofoam cups and plastic wrap;
acrylonitriles- a polymer found in clothings and superabsorbants (capable of retaining
2,000 times their mass of water).

10. There exists in nature some very large molecules (macromolecules) that contain tens of
thousands of atoms. Some of these such as starch, glycogen, cellulose, proteins, DNA have
molar masses in the millions and are central to many of our life processes.

11. Biochemistry is the study of molecules and chemical reactions of life. It makes use of the
principles and language of chemistry to explain biology at the molecular level. It includes the
study of carbohydrates, proteins & enzymes, lipids and nucleic acids (genetic materials).

ORBITAL HYBRIDIZATION

- explained by the valence bond theory, VB theory: a covalent bond forms when orbitals of
two atoms overlap and a pair of electrons occupy the overlapping region
- (refer to p298 of your chemistry textbook)
o VB theory use Lewis’ notion of electron pair and atomic orbitals

o In the Lewis theory: covalent bonding occurs when atoms share electrons, and in
such sharing, concentrates the electron density between the nuclei.

o VB theory explains that the building up of electron density between two nuclei is
visualized as occurring when a valence atomic orbital of one atom merges with that
of another atom

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▪
Orbitals are then said to share a region of space or to overlap allowing two
electrons of opposite spin to share the common space between the nuclei
forming a covalent bond.
▪
Merging of orbitals are called molecular orbitals
▪
Bonding molecular orbital: electrons are strongly attracted to both nuclei

▪
Anti-bonding molecular orbital: results when there is greater repulsion
between nuclei and in order for attraction to occur, higher energy is required
▪
Orbitals that overlap must be half-filled or with one electron and orbitals lie
symmetrically
▪
Molecular orbitals can form from various combinations of half-filled s and p
orbitals

- Types of molecular orbitals: (refer to p304-305 of your chemistry textbook)

o 1. Sigma molecular orbital, σ – head to head overlap
▪
Ex. between 2 s orbitals: s - s
▪
Between s-orbital and any p-orbital: s-px; s-py; s-pz
▪
Between 2 px orbitals: Px – Px

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o 2. Pi molecular orbital, π – side-to-side overlap of two p-orbitals

▪
Are generally weaker than sigma bonds

▪
Example: py – py ; pz - pz

Fig. s-s overlap s-px overlap px-px overlap σ bond py-py overlap

HYBRIDIZATION- mixing two or more atomic orbitals shapes in the bonded atom

o Introduced by Linus Pauling

o There is formation of new orbitals of different shapes and orientation

called hybrid orbitals (refer to p299 – 301 of chemistry textbook)
o Types of hybrid orbitals:

1) sp3 – s orbital mixing with 3 p orbitals in the same subshell

• central atom forms 4 equivalent bonds with terminal atoms

• characteristic of single bonds; tetrahedrally shaped

2) sp2 – mixing one s orbital with two p orbitals

• characteristic of double bonds; trigonally shaped

3) sp – mixing of one s-orbital

with 1 p-orbital

▪ characteristic of triple
bonds; linearly shaped

Lewis structure of acetylene or ethyne fig. conjugated structure of ethene

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Fig. Formation of the two pi bonds in acetylene

The study of organic compounds is called organic chemistry. Organic chemistry is better defined
as the study of carbon-containing compounds (except carbonates, cyanides, CO 2, CO and other ionic
compounds to which carbon is part of) in which carbon atoms are bonded to one another ( C – C), to
hydrogen (C – H) as well as to other non-metal atoms such as oxygen ( C – O ) and nitrogen (C -
N).Carbon has a total of four bonds, in contrast to hydrogen and fluorine that typically forms one bond,
oxygen forming two bonds, and nitrogen forming three bonds. Due to the greater number of bonds
found in carbon, it gives more possibilities for forming a diverse set of compounds.
A carbon compound that contains only carbon and hydrogen is called a hydrocarbon. In
hydrocarbons, carbon has the ability to bond to other carbon atoms to form long chains or rings of
carbon atoms with hydrogen atoms attached.

Different branching patterns are possible in many hydrocarbon molecules. Two compounds having the
same composition and formula (molecular) but with different arrangement of atoms in their molecular
structure (called structural formula) are isomers of one another.
Carbon can bond to another non-metal, such as nitrogen and oxygen, in a few defined ways,
giving a characteristic grouping of atoms called functional group- the reactive part of a
molecule that undergoes reactions. An example is when a hydroxide, OH- is present in propane,
C3H8 we have propyl alcohol or propanol, C3H7OH and in this case the -OH is characteristic of
alcohols (see p410 of Chemistry textbook)
How to represent the structure of organic compounds? These are the different models to
describe it. (see p397-403 of chemistry textbook)

a. Ball and stick

Fig. Types of hydrocarbon compounds and their structure

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b. Structural formula
i. Expanded structural formula
ii. Condensed structural formula

c. Line structure : 1. With single bonds (expanded structural formula)

2. with double bonds (partial condensed structural formula)

3. with triple bond

d. Zig-zag line structure- especially are used for longer chain hydrocarbons

Fig. Representing organic molecules skeletal structures

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e. Cyclic structure

Fig. first four cycloalkanes

Constitutional or structural isomers- same elements and number of atoms or compounds with
the same molecular formula but it shows the different arrangement of atom and bonds (see
p402 -403 chemistry textbook).
Stereoisomers - molecules with the same arrangement of atoms but different orientations of
groups in space.

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Types of stereoisomers (see p404 chemistry textbook)

a. Optical isomers – two objects are mirror images of each other but are not
superimposable

- An example: left and right hand seen on a mirror can be superimposed or if placed palm-
to-palm are imposable. What is non-superimposable is when stretching out your right
hand and putting your left hand with the palm of your left hand at the back of your right
hand.

- Organic compounds that are non-superimposable are also called asymmetric

molecules, i.e., they possess a chiral center – if it is carbon-called chiral carbon or
asymmetric carbon; it is the carbon that is bonded to 4 different groups.

- Classes of optical isomers are determined using a polarimeter; they can rotate the plane of
polarized light either to the left -are called levorotatory or if they rotate the plane of light to
the right – are called dextrorotatory.
o d-glucose; l-glucose; d-alanine; l-alanine

- Optical isomers have biological properties- as they differ in usability by an

organism
o An example: nearly all carbohydrates and amino acid are optically active but only one of
the isomers is biologically usable.

o You can metabolize d-glucose for energy but excrete l-glucose unused

o l-alanine (an amino acid) is incorporated naturally into your protein, but d-alanine is
not.

o An organism can utilize only one of a pair of optical isomers because of its
enzymes. A specific organic compound can only be catalyzed by a specific enzyme
-class of proteins; are biological catalysts that speed up virtually every reaction in a
cell
o Many drugs are chiral molecules; one optical isomer has a certain biological activity,
and the other has either a different type of activity or none at all

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2. Geometric isomers (see p405 chemistry textbook)

- also called cis- and trans- isomers; cause by rotational restriction between C=C in
Ethene and ethyne unlike in ethane where
all the hydrogens can rotate around
carbon.

- In ethene, only the two hydrogens in each carbon can rotate only around the carbon to which
they are attached. So if in a -C=C- have different atoms bonded aside from hydogen, the
location of these other atoms constitute a geometric isomer
- Example:

- For cis isomer -CHBr2 and CH3 bonded to – C=C- are on the same side
- For trans isomer -CHBr2 and CH3 bonded to -C=C-are on opposite side

CLASSIFICATION OF ORGANIC REACTIONS

Fig. addition reaction

Addition reactions occur when two reactants combine to give a single product

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Fig. condensation reactions

SUBSTITUTION REACTION – a replacement of one atom or group of atoms by a

second atom or group of atoms

Example 1

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Example 2:

Fig. The formation of ethanol from bromoethane through a substitution reaction with potassium hydroxide (KOHKOH)

COMBUSTION REACTION

Fig, Balanced chemical equations for the complete and incomplete combustion of methane

-Combustion products of organic compounds in excess or enough oxygen will always

produce carbon dioxide and water

Saponification reaction

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Trigylceride is a triester + sodium hydroxide forms an alcohol (glycerol) and soap

Fig. Saponification reaction

POLYMERS
A polymer- is an extremely large molecule or macromolecule consisting of covalently linked
chain of smaller molecules- called monomers. (see p418-419 of chemistry textbook)
- A monomer is the repeating unit of the polymer

- A typical polymer may have from hundreds to hundreds of thousands of repeating units. (see
examples of synthetic polymers and its uses on p420 chemistry book)

- There are many types of monomers and their chemical structure are brought about by different
kinds of intermolecular forces that stabilizes it.
o Synthetic polymers are created by chemical reactions in the laboratory
▪
Also known as synthetic macromolecules

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-
Naming polymers- add the prefix poly- to the monomer name

▪ Polyethylene or polystyrene; polyvinyl chloride or PVC o Formation

of synthetic polymers are of two major types
-
Addition polymers
▪ Undergoes addition reaction with one another

▪ Also called chain reaction polymers

Condensation polymers

• Monomers of condensation polymers must have two functional groups

Are also called copolymers- consisting of two or more different repeating unit

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o Natural polymers or biopolymers are created by chemical reactions within

the organism- ex. biomolecules- chemical compounds that sustain life
▪
Biological macromolecules (see p421-427 in your chemistry textbook)
▪
Are condensation polymers
▪
Natural polymers- examples: polysaccharides, proteins, nucleic acids

• The stuff of life

• Structures that make wood strong (cellulose); fingernails hard, wood

flexible

• Speeds up reactions in every cell or defends the body against

infection

• Possess the genetic information organisms need to bring other

biomolecules together

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CARBOHYDRATES
- Monosaccharides and
polysaccharides

- Simple sugars and more

complex sugars
- Monosaccharides:
glucose, fructose
- Disaccharide: sucrose
(table sugar- glucose + fructose); lactose (milk sugar)
- Polysaccharides: starch; cellulose

Properties of carbohydrates (see page 421 of chemistry textbook

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Fig. Carbohydrates

PROTEINS
- Polyamides of nature; unbranched polymers formed from two monomers
(amino acid) which has both a carboxyl group – COOH and an amine group –
NH2 attached to a central carbon atom (alpha carbon)
- Consists of many peptide chains (polypeptide)

- Made up of about 20 amino acids each with its own side chain that identifies the
specific amino acid (see p422 of your chemistry textbook)

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PROTEIN STRUCTURE (see p. 423 of

chemistry textbook)

- Each type of protein has its own amino

acid composition, specific
numbers and proportions of
amino acids

- It is not the composition that defines

the protein’s role in the cell but
the sequence of amino acids
will determine the
protein’s shape and function
- Proteins range from about 50 to
several thousand amino acids
fig. proteins

- Even a small protein molecule of 100 amino acids has a virtually

limitless number of possible sequence of the 20 types of amino acids
- An organism as complex as a human being have about 10 5 different types of
protein
-
- See the different structures of proteins on p424 of your chemistry textbook

NUCLEIC ACID
- Made up of nucleotides; are polynucleotides
- Unbranched polymers consisting of linked monomers called mononucleotides
- An organism’s nucleic acids construct its proteins

- A nucleotide consists of: a nitrogen-containing base- purine or pyrimidine; a sugar; and a

phosphate group
- Two types of nucleic acids
o RNA – ribonucleic acid
▪
Consists of ribose (sugar)

o DNA- deoxyribonucleic acid

▪
Consists of deoxyribose (ribose structure where one -OH in the
▪
second carbon of ribose is replaced by hydrogen)

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FUNCTIONS

Fig. main function of nucleic acid

LIPIDS
- Also known as fats provide a major way of storing chemical energy and carbon atoms
in the body.
- Fats surround and insulate vital organs
- Provides protection from mechanical shock
- Prevents excessive loss of heat energy
- Basic components of cell membranes: phospholipids, glycolipids and cholesterol

- Several cholesterol derivatives function as chemical messengers (hormones) within the body

STRUCTURE
Unlike carbohydrates, lipids do not have a common structural feature that serves as the basis
of defining such compounds.

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A lipid is an organic compound found in living organisms that is insoluble (or only
sparingly soluble) in water but soluble in non-polar organic solvents. When a biochemical
material (human, animal or plant tissue) is homogenized in a blender and mixed with a non-
polar organic solvent, the substances that dissolve in the solvent are lipids.
Lipids are structurally diverse- some are:
o Esters, amides, alcohols, cyclic, acyclic, polycyclic

o From its varied diverse composition and classes, solubility rather than structure is
common to them: they are all insoluble in water

Fig. Lipids – Introduction and classification

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Fig. Functions and effects of the major groups of lipids

- Saturated fats have all

its carbon single bonded;
unsaturated fats have
one or more double
bonds
- Lipids contain long
chains of fatty acids
(saturated or
unsaturated) connected
to glycerol
- Hydrogenation of fats-
conversion of
unsaturated fats to
saturated fats-a more
solid state- by adding
hydrogen. Example:
soybean or cottonseed
oil can be made into
margarine or other
shortenings used in
baking.

PREPARATION OF SELECTED ORGANIC COMPOUNDS

Fig. The Kolbe Synthesis

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aspirin is used to treat pain and fever; long-term use at low doses helps prevent heart attacks, strokes
and blood clot formation in people at high risk of developing blood clots, over the counter pain relief
especially for headaches

EXERCISES: on the structural formula of organic compounds

I. 1. Draw structural formulas for all possible isomers having the following molecular
formula.
a) C3H6

b) C3H7Cl

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c) C2H4F2

2. For each of the following abbreviated structural formulas, write a structural formula that
shows all of the bonds:
a) CH3(CH2)4CH3

b) CH3CH2SCH2CH3

3. For each of the following abbreviated structural formulas, write a structural

formula that shows all of the bonds.
a) ClCH2CH2OH

b) (CH3CH2)2NH

4. For each of the following abbreviated structural formulas, write a line

structural formula
a) CH3(CH2)4CH3

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b) (CH3)2CHCH2C CH2CH3

c) CH3CHCH2C(CH3)3

OH

5. Draw all possible skeletons for a 7-carbon compound with:

a) 6-C chain and 1 double bond

b) 5-C chain and 1 double bond

c) 5- C ring and no double bond

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6. Each of the following names is wrong. Draw structures based on these and correct the
names.
a) 4-methyhexane

b) 2-ethypentane

c) 2-methycyclohexane

d) 3,3 – methyl-4-ethyloctane

e) 3,3-dimethylbutane

II. Refer to page 431 of your Chemistry textbook, answer #15.45 (letters a to e)

a. ____________________________
b. ____________________________
c. ____________________________
d. ____________________________
e. ____________________________

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#15.46 (letters a to e)

a. _____________________________
b. _____________________________
c. _____________________________
d. _____________________________

e. _____________________________

Given the following examples of alkenes and alkynes, indicate for each (structure 1 & 2 ) the:
a) specific molecular orbital found in each bond, i.e., sigma or pi bonds
b) type of hybridization of each bond, i.e., sp3, sp2 or sp hybrid
c) copy each structure and answer a and b correctly

Ethene propene

ANSWER:

Propyne 2 - Butyne

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ANSWERS TO MODULE 6

FORMATIVE ASSESSMENT
1. a. Ca b. Carbon c. Boron d. phosphorus

e. Oxygen bromine nitrogen sulfur

2.a.covalent b. ionic c. covalent d. covalent e. ionic f. covalent

g. ionic h. covalent

3. a. CH3CH2OH

b.CH3F c.C3H8

d.CH3NH2 e.C2H5Cl H

EXERCISES

1. a) C3H6 or

b)C3H7Cl

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c) C2H4F2

2) a. CH3(CH2)4CH3

Condensed structural formula

CH3 CH2 CH2 CH2 CH2CH3
( repeating unit is -CH2-)
Expanded structural formula

b.CH3CH2SCH2CH3

FORMATIVE ASSESSMENT 2

σ σ
π ethene
σ σ σ

σ
σ π σ
σ σ
σ σ σ

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2-

ethene

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2-

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