KOLEHIYO NG LUNGSOD NG DASMARIÑAS

Course Module
Biochemistry

Prepared by:
Maria Edralin M. Leonisa
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MODULE 1
Organic Chemistry

Organic Chemistry encompasses an interdisciplinary field

integrating biological, physical, and chemical sciences. It focuses
on the structure, properties, and reactions of organic compounds,
which contain carbon. Carbon is fundamental to life and present in
all living organisms. Organic compounds are present in a wide
variety of materials including plastics, pharmaceuticals, fabrics, and
food.

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Learning Outcomes

1. Define organic chemistry and identify its importance and

application.

2. Investigate the physical properties of organic compounds and

identify the basic principles of organic reactions.

3. Differentiate organic compounds based on their functional groups,

structure, physical properties, and common source.

4. Apply the IUPAC system in naming compounds.

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OUTLINE OF TOPICS
1. Introduction to Organic Chemistry
2. Physical Properties and Basic Reactions of Organic Compounds
3. Hydrocarbons and Functional Groups
4. Nomenclature

LESSON PROPER
Development of the lesson:

Introductory Question

Have you ever wondered about the molecules that make up the materials around us? From
the air we breathe to the food we eat, there's a fascinating world of compounds that form
the building blocks of life.
Can you think of any everyday items or substances you encounter that might be composed
of unique molecules?

You may make a list of any everyday items or substance you encounter.

TOPIC 1: Introduction to Organic Chemistry

Defining Organic Compounds

Organic compounds are chemical compounds that contain carbon atoms. They are
molecules that are generally composed of hydrogen, oxygen, nitrogen, and other atoms such as
sulfur, phosphorus, and halogens. Organic compounds are molecules that are associated with life
and are found in all living organisms, including humans.
The majority of organic compounds contain carbon-carbon double bonds or carbon-
heteroatom bonds. Organic compounds are the basis of all life on earth and are essential for life
processes such as metabolism, respiration, and reproduction.

- As a nursing student, how does understanding the organic chemistry

Essential contribute to solving global challenges in pharmaceuticals and

medications on patients’ health?

Question - Research for the latest advancements in organic chemistry. In your

opinion, how might they shape the future of various industries?

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History of Organic Chemistry

The History of Organic Chemistry can be traced back to the 18th century when scientists
began to investigate the properties of organic compounds.

Organic chemistry has since flourished and today scientists are able to synthesize complex
organic molecules, study the biochemistry of living organisms, develop new pharmaceuticals, and
explore the chemistry of the universe. As the field continues to evolve,

Importance of Organic Chemistry

Organic chemistry plays a pivotal role in various scientific and practical, and industrial applications
due to its fundamental role in understanding and manipulating the behavior of carbon-containing
compounds.

1. Organic chemistry is essential for understanding the chemical makeup of living things. It is
the foundation for understanding the structure, function, and interactions of biological

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molecules such as proteins, nucleobases, carbohydrates, and lipids that are necessary for
life.
2. Organic chemistry plays a vital role in drug discovery and development, with medicinal
chemists creating and synthesizing compounds to target biological pathways, resulting in
pharmaceuticals that treat a wide range of conditions and improve human health.
3. Organic Chemistry is concerned with the study of pollutants, waste disposal, and the
environmental effects of chemicals. It contributes to the understanding of the degradation,
accumulation, and interaction of pollutants with ecosystems.
4. Organic compounds play a vital role in the creation of a variety of materials, from polymers
and plastics to textiles and coatings, where organic chemistry plays an essential role in the
formulation and synthesis of materials with unique properties for a variety of uses.
5. Organic chemistry plays a significant role in the chemical makeup of food and in the
influence of cooking and processing processes. Organic compounds play a role in the taste,
smell, and nutrition of food.
6. Organic chemistry helps create new energy sources, like biofuels or solar cells. Knowing
how organic materials react with each other is key to making the most of energy conversion.
7. Genetically engineering and manipulating organisms often necessitate an understanding
of organic reactions. Organic chemistry is an integral part of any biotechnology process,
such as the creation of enzymes and antibiotics, as well as biofuels.
8. Organic chemicals, such as pesticides, herbicides, and fertilizers, are commonly composed
of organic compounds intended to enhance crop productivity and reduce the risk of plant
damage caused by harmful organisms. Organic chemistry contributes to the development
of efficient and sustainable agricultural products.
9. Organic chemistry offers a basis for cutting-edge research across a wide range of
disciplines. Areas such as nano-technology, materials science and drug delivery are based
on organic chemical principles.
10. The use of organic compounds in personal care products such as cosmetic products,
perfumes and toiletries is based on their specific characteristics and effects.

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Topic 2: Physical Properties and Basic Reactions of Organic Compounds

A. Physical Properties
1. Solubility – It refers to the ability of a substance to dissolve in another substance to
form a homogeneous mixture, often called a solution. The ability of a substance to
dissolve in another substance to form a homogeneous mixture, often called a solution.
Organic compounds can be soluble in organic solvents (like dissolves like) and may show
varying degrees of solubility in water depending on their functional groups and polarity.
2. Melting and Boiling Points - The melting and boiling points of organic compounds are
key properties that reflect intermolecular forces and molecular structure. They are
affected by factors like molecular weight, shape, and types of intermolecular forces.
Larger, complex molecules tend to have higher melting and boiling points, showcasing
their interactions and compound nature.
3. Color and Smell - Certain organic compounds have unique colors and odors attributed
to chromophores and functional groups. Color results from electronic structure and
chromophores that absorb specific light wavelengths.
4. Density - Organic compounds can have densities either lower or higher than water,
influenced by molecular weight and structure. Density quantifies mass per unit volume
and is affected by factors like molecular arrangement and functional groups.
5. Electrical Conductivity - Electrical conductivity gauges a material's capacity to carry an
electric current. Organic compounds, mainly consisting of carbon and hydrogen, usually
demonstrate low electrical conductivity due to the absence of freely mobile charged
particles. This is primarily attributed to the absence of free ions necessary for conducting
electricity in most organic compounds.

B. Reactions of Organic
1. Substitution - A functional group is replaced by another functional group or atom. This
type of reaction is crucial in modifying organic compounds and creating new ones. An
example of this reaction is the chlorination of methane, which involves the substitution
of hydrogen atoms with chlorine atoms.
2. Addition – This happens when two or more reactants combine to form a single product
molecule. This type of reaction involves the breaking of multiple bonds and the creation
of new ones. A classic example is the hydrogenation of alkenes where the hydrogen gas
is added across a carbon-carbon double bond to form a saturated compound.

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3. Elimination – A molecule loses atoms or groups of atoms to form a new molecule. These
reactions often involve the removal of atoms from adjacent carbon atoms, resulting in
the formation of multiple bonds. A common example is the dehydration of alcohols
where the water is removed from the molecule to form an alkene.
4. Oxidation-Reduction (Redox) Reactions – This process involves the transfer of electrons
between reactants. These reactions play a crucial role in changing the oxidation states
of atoms within molecules.
a. Oxidation - In an oxidation process, an atom or molecule loses electrons, resulting
in an increase in its oxidation state. It may involve the addition of oxygen or the
removal of hydrogen.
i. Oxidizing Agent - a species that causes oxidation by accepting electrons
from another substance. Common oxidizing agents in organic
chemistry include peroxides, chromic acid, and potassium
permanganate (KMnO4).
b. Reduction - In a reduction process, an atom or molecule gains electrons, leading
to a decrease in its oxidation state. It may involve the removal of oxygen or the
addition of hydrogen.
i. Reducing Agent - a species that causes reduction by donating electrons
to another substance. Common reducing agents in organic chemistry
include hydrides like sodium borohydride (NaBH4) and metals like zinc.
5. Hydrolysis – This is a reaction when a molecule reacts with water, leading to the
breakdown of bonds and the formation of new compounds. This process is essential for
the decomposition of organic molecules and the creation of functional groups. Example
is the saponification reaction which involves the hydrolysis of an ester to form a
carboxylic acid and an alcohol. Saponification is the process used to produce soap from
fats and oils.
6. Condensation – This happens when two or more molecules combine to form a single,
larger molecule with the simultaneous release of a smaller molecule, typically water or
another simple compound. This process is essential for the synthesis of larger organic
compounds and the creation of new functional groups. Peptide bond formation is an
example of condensation reaction. It involves the reaction between two amino acids to
form a peptide bond, which is a covalent bond that connects amino acids in proteins.
7. Esterification – This reaction involves the formation of an ester by the reaction between
a carboxylic acid and an alcohol. Esters are versatile compounds commonly found in
various natural and synthetic substances, including fragrances, flavorings, and plastics.

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An example of this is the use of ethyl acetate with a fruity aroma that is often found in
fruits and used as a flavoring and fragrance agent. It is synthesized through the
esterification reaction between acetic acid and ethanol.

Topic 2: Hydrocarbon and Functional Groups

Hydrocarbon
Hydrocarbons are organic compounds made up of carbon (C) and hydrogen (H) only. There
are four general classes of them: alkanes, alkenes, alkynes and arenes.
Aromatic compounds derive their names from the fact that many of these compounds in
the early days of discovery were grouped because they were oils with fragrant odors.
Two main types of Hydrocarbons:
a. Saturated Hydrocarbons - These are hydrocarbons that only contain single bonds
between carbon atoms.
b. Unsaturated Hydrocarbons – These are hydrocarbons that contains at least one
carbon-carbon double bond or carbon-carbon triple bond.

1. Alkanes - Alkanes are saturated hydrocarbons. In other words, it has only one carbon-
carbon bond and is saturated with hydrogen. The general formula for alkanes is CnH2n+2.
Alkanes can be in straight chain or in branched structure. Because the carbon-carbon bond
is so strong, alkanes are relatively non-reactive. Their main reactions are combustion and
Halogenation. Example includes methane (CH4), ethane (C2H6), and propane (C3H8)
2. Alkenes - Alkenes are unsaturated hydrocarbons that has at least one double bond
between the carbon and the hydrogen (C = C). The general formula for alkene is CnH2n. An
alkene can also have a straight-chain structure or a branched structure. Alkene undergoes
addition reactions because the pi bond is present in the alkyl double bond. The most
common addition reactions are hydrogenation and halogenation. Other addition reactions
include hydration (forming alcohols). Examples include ethene (C2H4) and propene (C3H6).
3. Alkynes - Alkynes are unsaturated hydrocarbons that have at least one carbon to carbon
triple bond (C = C). Alkynes have a general formula of CnH2n-2 and are linear in structure.
Unlike alkenes, alkynes are more reactive and undergo addition reactions and
polymerization. Examples include ethyne (C2H2) and propyne (C3H4).
4. Arenes (Aromatic Hydrocarbons) - Arenes are a special class of hydrocarbons known for
their aromaticity, which arises from a resonance-stabilized ring of pi electrons. The most
common aromatic hydrocarbon is benzene (C6H6), with a hexagonal ring structure and

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alternating double bonds. Aromatic compounds exhibit unique stability and reactivity
patterns. They often undergo electrophilic aromatic substitution reactions. Example
includes benzene (C6H6), toluene (C₆H₅CH₃), and naphthalene (C10H8)

Figure 1. Basic structure of hydrocarbon

Image Source: https://chem.libretexts.org/@api/deki/files/142496/hydrocarbon_classification.png?revision=1&size=bestfit&width=616&height=269

Functional Group

Functional groups refer to the arrangement of atoms in a molecule that determines the
chemical reactivity of the molecule and its chemical behavior. Functional groups are, in essence,
the reactive “building blocks” that provide organic compounds with their unique characteristics
and functions. Functional groups in organic chemistry define the class of compounds and provide
information on the reactivity and chemical behavior of the compound.

Each functional group is made up of a collection of atoms, typically consisting of carbon, hydrogen,
oxygen, nitrogen, and occasionally other elements, that are arranged in a certain way. The types
and number of atoms in a functional group influence how a molecule interacts with others, reacts
in different chemical reactions, and plays a role in the properties of the compound.

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Here are some functional groups and their characteristics:

1. Hydroxyl Group (-OH)

Found in alcohols and phenols, it imparts polarity and the ability to form hydrogen bonds.
It consists of an oxygen atom (O) and a hydrogen atom (H) covalently bonded to a carbon
atom (C) in an organic molecule.
The hydroxyl group has the structure -OH, where the oxygen atom is bonded to the
carbon atom of the molecule and the hydrogen atom is bonded to the oxygen atom. Hydroxyl
groups introduce polarity and hydrogen bonding with other molecules, which makes
compounds with this group more water-soluble and gives them unique properties. Hydroxyl
groups also affect how quickly these compounds boil and melt.
Example
Here are some of the examples: of
a. Alcohol - The most common Alcohol
type of compound containing the
hydroxyl group. Example
b. Phenols - compounds where of
Phenol
the hydroxyl group is directly
attached to a benzene ring.
Figure 2. Example of Organic compounds with hydroxyl group
Phenols are less acidic than Image Source:
carboxylic acids but still exhibit Methanol and Ethanol: https://pscprep.com/ethanol-and-methanol/
Hydroquinone and Resorcinol: https://www.britannica.com/science/phenol
some acidity due to resonance
effects.
2. Carbonyl Group (C=O): A functional group characterized by a carbon atom (C) double-
bonded to an oxygen atom (O). The chemical structure of the carbonyl group is C=O.
Present in aldehydes, ketones, carboxylic acids, esters, and amides. It leads to varying
reactivity and properties depending on its location and surroundings.
Example of Compound with Carbonyl
Group
a. Aldehydes– the carbonyl group is
located at the terminal carbon of
the carbon chain. Example is
formaldehyde (HCHO).
Figure 3. Structure of Simplest Carbonyl Group
b. Ketones - the carbonyl group is
found within the carbon chain. Image Source:
Example is acetone (CH3COCH3). https://www.masterorganicchemistry.com/2010/10/06/functional-groups-
organic-chemistry/

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3. Carboxyl Group (-COOH): Present in carboxylic acids, it imparts acidity to the compound.
It consists of a carbonyl group (C=O) and a hydroxyl group (-OH) attached to the same
carbon atom (C) in an organic molecule. The chemical structure of the carboxyl group is -
COOH.
The carboxyl group introduces acidity to compounds due to the presence of the hydroxyl
group. Carboxylic acids are weak acids, capable of donating a proton (H+) in aqueous
solutions. This is responsible for the sour taste of many organic acids.
Example of Carboxylic Acid
a. Formic acid – the simplest carboxylic acid,
formic acid is found in ants and has various
industrial applications.
b. Acetic acid – the main component of vinegar,
used as a solvent, preservative, and starting
material for chemicals.
c. Butyric Acid - Known for its unpleasant odor,
butyric acid occurs naturally in dairy products Figure 4. Structure of Common Carboxylic Acid
and is used in food flavoring and chemical Image Source: https://www.nagwa.com/en/explainers/950189497046/

production.

4. Ester Group (-COO-): A functional group that consists of a carbonyl group (C=O) bonded
to an oxygen atom (O), which is then bonded to an alkyl or aryl group (R). Esters are known
for their pleasant and often fruity odors, making them important components in perfumes
and flavorings.
Example of Ester
a. Ethyl acetate – found in fruits like
bananas and is used as solvent in nail Isopentyl acetate

polish remover and glues. Figure 5. Structure of Common Carboxylic Acid

b. Isopentyl acetate – Contributes to the Image Source:
smell of bananas and is used in the Ethyl Acetate: https://www.nagwa.com/en/explainers/950189497046/
Isopentyl acetate: http://www.t3db.ca/toxins/T3D4851
production of artificial banana flavor.

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5. Ether Group (-O-): A functional group characterized by an oxygen atom (O) bonded to two
alkyl or aryl groups (R). The chemical structure of the ether group is typically represented
as -O-. Ether has low reactivity and is often used as a solvent or protective group.
Example of Ether
a. Diethyl Ether– a commonly used
solvent and was historically used as Diethyl Ether Methyl tert-Butyl Ether
an anaesthetic.
Figure 5. Structure of Compounds with Ether Group
b. Methyl tert-Butyl Ether – Used as an
Image Source:
additive in gasoline to improve octane Diethyl Ether: https://www.cdhfinechemical.com/diethyl-ether

ratings and reduce emissions. Methyl tert-Butyl Ether: https://www.scbt.com/it/p/tert-butyl-methyl-

ether-1634-04-4

6. Amino Group (-NH2): It consists of a nitrogen atom (N) bonded to two hydrogen atoms (H)
that can be attached to a carbon atom, forming an amine functional group. This group
imparts important characteristics to molecules and plays a vital role in the structure and
reactivity of amino acids, proteins, and many other organic compounds.
Example
a. Amino Acids - the building blocks of proteins, contain an amino group, a carboxyl
group, and a side chain. The amino group is responsible for the basic nature of
amino acids.

Figure 6. Structure of Compounds with Ether Group

Image Source: https://cdn1.byjus.com/wp-content/uploads/2023/07/Amino-Acid-Structures-Updated-1.png

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7. Amide Group (-CONH2): A functional group composed of a carbonyl group (C=O) bonded
to a nitrogen atom (N). The chemical structure of the amide group is typically represented
as -CONH2. Amides are found in various molecules, including proteins and peptides, and
play a crucial role in biochemistry and organic synthesis.
Example
a. Acetamide - is a primary amide.
It is a white crystalline solid and
has various applications in the
chemical and pharmaceutical
industries. It's used as a solvent,
Figure 6. Structure of Acetamide
in the production of other Image Source: https://www.researchgate.net/figure/Structure-of-
chemicals, and as a plasticizer in acetamide-showing-a-single-peptide-group-red_fig1_308698623

the manufacture of plastics.

8. Thiol Group (-SH): It comprises a sulfur atom (S) bonded to a hydrogen atom (H). This
functional group introduces distinct properties and reactivity into molecules, playing a vital
role in various biochemical processes and synthetic applications.
Example of Thiols
a. Methanethiol – simple thiol with methyl
group bonded to the sulphur atom. It
contributes to the characteristic smell
off food like garlic.
b. Cysteine – an amino acid contains a thiol Methanethiol Cysteine

group in its side chain. It plays a crucial Figure 7. Structure of Compounds with Thiol group
part in forming disulfide bonds in Image Source:
Methanethiol: https://en.wikipedia.org/wiki/Methanethiol
proteins which stabilize their structures. Cysteine: https://en.wikipedia.org/wiki/Cysteine

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9. Phosphate Group – A functional group composed of a phosphorus atom (P) bonded to four
oxygen atoms (O). The chemical structure of the phosphate group is usually represented as
-PO4. This group plays a central role in energy transfer, DNA structure, and various cellular
processes.
Examples
a. Adenosine Triphosphate (ATP) – a molecule that stores and transfers energy in cells.
It contains a chain of three phosphate groups linked together, forming a high-energy
bond that can be readily broken to release energy.

ATP

Figure 7. Structure of Adenosine Triphosphate

Image Source: https://en.wikipedia.org/wiki/Adenosine_triphosphate

b. DNA and RNA – The backbone of DNA and RNA consists of alternating sugar and
phosphate groups, forming a "sugar-phosphate backbone." This backbone
provides stability to the molecule's structure.

Figure 8. Structure of DNA and RNA

Image Source: https://www.geeksforgeeks.org/difference-between-dna-and-rna/

Organic Chemistry - https://youtu.be/PmvLB5dIEp8?si=ibDS83kJrnSn4pjN

Useful https://www.youtube.com/watch?v=UloIw7dhnlQ
Functional Group -

Links https://www.youtube.com/watch?v=nMTQKBn2Iss&t=15s
Reaction Mechanism of Organic Compounds -
https://www.youtube.com/watch?v=ORMUTUhYjvg

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Topic 3: Nomenclature

Nomenclature refers to the systematic naming of chemical compounds. Nomenclature

follows a set of rules to ensure unambiguous and unambiguous communication of chemical
compounds. In organic chemistry nomenclature offers a standardized way of naming and
describing the large number of organic compounds. Chemists use nomenclature to communicate
essential information about a compound’s structure and properties.
Nomenclature plays an important role in scientific communication. For example, in organic
chemistry, where there are many different types of compounds, the use of nomenclature allows
chemists to understand the structure, structure, and characteristics of molecules without having
to draw their structures.
The International Union of Pure and Applied Chemistry (IUPAC) is the international
authority responsible for developing and maintaining standardized nomenclature rules for
chemistry. IUPAC nomenclature aims to provide unambiguous names that reflect the compound's
structure, while also being concise and systematic.

According to IUPAC system, a chemical name has three parts, the prefix, parent, and suffix.

Table 1. Number of carbons in parent chain

Prefix – Parent – Suffix
and the corresponding root word or prefix

What are How many

What family?
substituents? carbons?

Parent Chain – This is usually the

longest continuous carbon chain, to
which functional groups and
substituents are attached.
Suffix – Reflects the type of functional
groups present.
Prefix – Reflects the substituents.
These are smaller groups or atoms
that branch off the parent chain and
can alter the compound's properties.

Table Source: https://img.brainkart.com/imagebk37/CISwzuE.jpg

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A. Naming Alkanes

Alkanes are saturated hydrocarbons with carbon (C) atoms attached by single bonds to
hydrogen (H). The nomenclature of alkanes follows the rules of the (IUPAC) nomenclature. The
general formula for alkane is CnH2n+2. The rule in naming alkanes should end with the suffix “ane”

Here is the systematic way of naming alkanes:

1. Locate the parent chain or the longest continuous chain of carbon.

2. Number the carbon atoms of the parent chain starting from whichever end of the chain
gives the location of the first branch.

Table 2. Names of Alkanes and Alkyl Groups

3. The branch is closer to the left end, so start the
number from left to right.

1 2 3 4 5 6
4. Name the parent chain. Since it has 6 carbon atoms,
therefore it is hexane.

5. Name the alkyl group attached to the branch. The

branch CH3 on the third carbon is named methyl.
Table Source:
https://useruploads.socratic.org/L3ZPqOKmTwWqOOTIG4vt_tumblr_myyt0
mgux01r8lpslo3_500.png

6. Attach the name of the alkyl group as a prefix of the parent chain.
methyl + hexane = methylhexane
7. Place the location number of the alkyl group in front of the resulting name.
8. Since it is on the third carbon, the name of the branched alkane would be
3-methylhexane
ethyl
“hyphen (-)” is used to separate the number from the word.
9. In cases where two alkyl groups, are attached to the
parent chain, name each and locate each with a number. 1 2 3 4 5 6 7

10. The alkyl names are assembled in alphabetical order. methyl

Again, use a hyphen to separate the number from the 2-ethyl-4-methylheptane

words.

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B. Naming Alkenes

Alkenes are unsaturated hydrocarbons containing at least one carbon-carbon double bond
(C=C). The nomenclature of alkenes follows the rules of the (IUPAC) nomenclature. The general
formula for alkane is CnH2n. The rule in naming alkanes should end with the suffix “ene”

Here is the systematic way of naming alkanes:

1. Locate the parent chain or the longest continuous chain of carbon.

2. The parent chain must include the double bond even if it takes shorter than the other.

3. Numbering of the parent chain starts from whichever end gives the double bonded
carbon. The location number should be given as to where the double bond is.

7 6 5 4 3 2 1
4. Name the parent chain. Since it has 7 carbon atoms, therefore it is heptane, and the
double bond is located on the 2nd carbon.

5. Name and locate the alkyl group attached to the branch. The branch CH3 on the 3rd
carbon is named methyl and on the 5th is ethyl.
Table 3. Number of atoms and Its Prefix
ethyl methyl

7 6 5 4 3 2 1

6. The name of the branched alkene would be:

3-methyl-5-ethyl-2-heptene

7. In cases where an
alkene has two or ethyl methyl
more double bonds,
the prefixes di, tri, 1 2 3 4 5 6
tetra, penta and so on
3-ethyl-5-methyl-1,4-hexadiene
are used as part of Table Source: https://wou.edu/chemistry/files/2017/04/prefix_names-
1.png

the parent’s name.

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C. Naming Alkynes

Alkynes are unsaturated hydrocarbon with at least one carbon-carbon triple bond (C≡C). The
nomenclature of alkynes follows the rules of the (IUPAC) nomenclature. The general formula for
alkyne is CnH2n-2. The rule in naming alkanes should end with the suffix “yne”.

Here is the systematic way of naming alkynes:

1. Locate the parent chain or the longest continuous chain of carbon.

2. The parent chain must include the triple bond and numbering of the parent chain starts
from whichever end gives the triple bonded carbon. Since it has 6 carbon atoms,
therefore it is hexyne and the triple bond is located on the 3rd carbon.

1 2 3 4 5 6

3. Name and locate the alkyl group attached to the branch. There are two CH3 (methyl)
attached to the 2nd carbon therefore the prefix “di” must be used. The branch will be
2-dimethyl.
1 2 3 4 5 6

4. The name of the branched alkyne would be:

2-dimethyl-3-hexyne
5. In cases where an alkyne has two or more triple bonds, the prefixes di, tri, tetra, penta
and so on are used as part of the parent’s name.

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D. Naming Cyclic Structure

In naming cyclic structures, it is often referred to as cycloalkanes or cyclic compounds, following

specific rules within the IUPAC nomenclature system.

Here is the systematic way of naming cyclic structures:

1. Determine the number of carbon atoms in the ring. In this case, there are six carbon
atoms, forming a six-membered ring. 6
5 1

4 2
3

2. Use the prefix "cyclo-" followed by the name of the alkane with the same number of
carbon atoms. For a six-membered ring, the corresponding alkane is "hexane." Therefore,
this is cyclohexane.
3. Name the substituents attached to the cyclic structure, name as alkyl groups and indicate
their positions on the ring. The CH3 (methyl) is on the 1st carbon. 6

Therefore, this is 1-methyl. 5 1

methyl

4 2
3

4. Combine the cycloalkane name and the substituent name using hyphen to separate numbers and
words.
1-methylcyclohexane

E. Basic Nomenclature for Some Functional Groups

Replace the -e ending of the Methane becomes

1. Alcohols Hydroxyl (-OH)
corresponding alkane with -ol. Methanol
Oxygen atom (-O-)
Name the groups attached to the
bonded to two
2. Ethers oxygen in alphabetical order Ethyl methyl ether
alkyl or aryl
followed by the word "ether."
groups.
Carbonyl group
Replace the -e ending of the Propane becomes
3. Aldehydes (C=O) at the end of
corresponding alkane with -al Propanal
a carbon chain
Carbonyl group
Replace the -e ending of the Butane becomes
4. Ketones (C=O) within a
corresponding alkane with -one Butanone
carbon chain
5. Carboxylic Carboxyl group (- Replace the -e ending of the Methane becomes
Acids COOH) corresponding alkane with -oic acid Methanoic acid

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Carbonyl group
(C=O) and oxygen Name the alkyl group attached to
6. Esters atom (O) bonded the oxygen followed by the -oate Ethyl ethanoate
to the same ending
carbon atom
Nitrogen atom (N)
Name the alkyl or aryl groups
bonded to one or
7. Amines attached to nitrogen in alphabetical Methylamine
more alkyl or aryl
order followed by the word "amine.
groups
Carbonyl group
(C=O) and nitrogen Replace the -oic acid ending of the Ethanoic acid
8. Amides atom (N) bonded corresponding carboxylic acid with - becomes
to the same amide Ethanamide
carbon atom

EXERCISES:

Name the following structure using the IUPAC system of Nomenclature.

Example: 1. Identify the parent chain or the longest 3. Identify and name any
chain. substituents (groups attached to
H 3C CH2
H 3C CH2
the parent chain) and its position
CH CH3 CH CH3
corresponding to the carbon
H 2C CH2 H 2C CH2
number. The methyl is attached to
the 3rd carbon.
CH3 CH3

2. Number the carbon atoms in the parent

H 3C CH2
chain consecutively, starting from the end
CH CH3
nearest to the first substituent methyl
H 2C CH2
encountered. Since it has 6 carbon chain,
therefore, its HEXANE. No double or triple CH3
4. Combine the parent chain
bond found. This belongs to Alkane.
name and substituent name.
H 3C CH2
1 2
3
CH CH3
5 3-methylhexane
H 2C CH2
4
6 CH3

Biochemistry
 Institute of Applied Sciences
Science Unit

CH2 CH2 CH3 H3C CH3

1. 2.
CH3 CH2 C CH2 C CH3
CH3
H3C
CH3

3.

KEY POINTS
• Organic chemistry is the branch of chemistry that focuses on the study of
compounds primarily composed of carbon and hydrogen, often with other elements
like oxygen, nitrogen, and halogens.
• Understanding the structure is crucial as it dictates the compound's behavior and
reactivity, including its physical and chemical properties.
• Organic compounds exhibit a wide range of physical properties, such as melting and
boiling points, density, solubility, color, and odor.
• Organic compounds undergo various basic reactions like substitution, addition,
elimination, hydrolysis, and oxidation-reduction (redox) reactions.

Biochemistry
 Institute of Applied Sciences
Science Unit

ASSESSMENT

1. Which element is the primary constituent of organic compounds?

A. Nitrogen C. Oxygen
B. Carbon D. Hydrogen

2. Which of the following is NOT a common functional group in organic compounds?

A. -OH (Hydroxyl) C. -CO2 (Carboxyl)
B. -NH2 (Amino) D. -Cl (Chlorine)

3. Which of the following structures shows the functional group ester?

A. B. C. D.

4. Aspirin works by reducing substances in the body that cause pain, fever, and
inflammation. Which of the functional groups below are presence in aspirin?
A. Carboxylic acid, ester, benzene ring
B. Carboxylic acid, phenol, benzene ring
C. Ketone, ester, hydroxyl group
D. Benzene ring, ether, alkene

5. Based on the structure below, what is it name following the IUPAC system?

A. 1,2-hexadiene
B. 1-2,hexadene
C. 5,6-pentadene
D. 4,5-hexadiene

OUTPUT-BASED ACTIVITY

1) Organic Compounds and Its Properties. In this activity you will explore hydrocarbons and
functional groups by creating an informative table that compares their properties and
characteristics.
2) Research examples of hydrocarbons and functional groups and create a table on a long bond
paper with the following columns:
• Compound Name

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• Chemical Structure
• Functional Group
• Physical Properties
• Common Sources

Reminders:
The output must be handwritten for more engaging experience.
You may use coloring materials. Be creative as you can.

RUBRICS / GRADING CRITERIA

In grading students’ output, the following rubric will be used.

Category 5 (excellent) 3 (average) 1 (poor)

Content Accurate identification of Mostly accurate Some inaccuracies in
Accuracy hydrocarbons and identification of identifying
functional groups. hydrocarbons and hydrocarbons and
Columns accurately filled functional groups. Most functional groups. Few
with complete and columns accurately columns may lack
relevant information. filled, with minor complete or relevant
omissions or information.
inaccuracies.
Functional Clear evidence of Good understanding of Basic understanding of
Group understanding the impact how functional groups functional groups' effect
Understanding of functional groups on influence properties and on properties and
properties and behavior. behavior. Patterns are behavior.
mentioned.
Presentation Neat handwriting and Neat handwriting with Handwriting is
Quality well-organized organized presentation. somewhat neat, but the
presentation. Content is Content is mostly presentation lacks
easily readable and readable and visually consistency. Content
visually pleasing. presentable. may be somewhat
difficult to read.
Demonstrates a strong Shows reasonable effort Reflects limited effort
Overall Quality effort, creativity, and and understanding. and understanding.
understanding. It appears
not to be rushed just to
comply.

Biochemistry
 Institute of Applied Sciences
Science Unit

REFERENCES
• Averill, B., & Eldredge, P. (2013). General chemistry: Principles, patterns, and applications.
Flat World Knowledge, Inc.
• Burrows, A., Holman, J. S., & Parsons, A. F. (2017). Chemistry 3: Introducing inorganic,
organic and Physical Chemistry (3rd ed.). Oxford University Press.
• Timberlake, K. C., & Orgill, M. K. (2019). General, organic, and Biological Chemistry:
Structures Of Life. Pearson.

Biochemistry