CHEM 105L

bioChemistry (LAB)

Rachelle C. Mendoza, RCh, MSc

College of Arts and Sciences

Batangas State University

 UNIT II
INTRODUCTION TO ORGANIC CHEMISTRY
INTRODUCTION
Organic chemistry, then, is the study of carbon compounds. As a group 4A element, carbon can
share four valence electrons and form four strong covalent bonds. Furthermore, carbon atoms can bond to
one another, forming long chains and rings. Carbon, alone of all elements, is able to form an immense
diversity of compounds, from the simple methane, with one carbon atom, to the staggeringly complex DNA,
which can have more than 100 million carbons.
INTENDED LEARNING OUTCOMES

At the end of this chapter, the students must be able to:

1. Draw structures in different ways;

2. Describe how the covalent bond is formed;
3. Identify the different classes of organic compounds;
4. Determine the common an systematic name of different types of organic compounds.

GENERAL CONCEPT

Drawing Chemical Structures

In condensed structures, carbon-hydrogen and carbon-carbon single bonds aren’t shown. If a
carbon has three hydrogens bonded to it, it is written as CH 3; if the carbon has two hydrigens bonded to it,
it is written as CH2; and so on.

Skeletal structure is simpler than condensed structure. Rules in drawing skeletal structures are as
follows:
1. Carbon atoms are not usually shown. Instead, a carbon atoms is assumed to be at each intersection
of two line (bonds) and at the end of each line. Occasionally, a carbon atom might be indicated for
emphasis or clarity.
2. Hydrogen atoms bonded to carbon are not shown. Because carbon always has valence of 4, the
correct number of hydrogen is mentally supplied for each carbon.
3. Atoms other than carbon and hydrogen are shown.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Table 2.2 Kekule and Skeletal Structures for Some Compounds

Functional Groups

Functional group is a group of atoms within a molecule that has a characteristic chemical
behaviour. The structural features of functional groups are used to classify compounds.

Table 2.3 Structures of Some Common Functional Groups

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L
 NOMENCLATURE
Alkanes
The system of nomenclature that is widely used is devised by the International Union of Pure and
Applied Chemistry (IUPAC). There are four parts in the IUPAC system of nomenclature:

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Table 2.4 Names of Straight-Chain Alkanes

Steps in Naming Complex Branched-Chain Alkanes

Step 1. Find the parent hydrocarbon.
a. Find the longest continuous chain of carbon atoms in the molecule, and use the name of that chain
as the parent name. The longest chain may not always be apparent from the manner of writing.

b. If two different chains of equal length are present, choose the one with the larger number of branch
points as the parent.

Step 2. Number the atoms in the longest chain.

a. Beginning at the end nearer the first branch point, number each carbon atom in the parent chain.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 The first branch occurs at C3 in the proper system of numbering, not at C4.
b. If there is branching an equal distance away from the both ends of the parent chain, begin
numbering at the end nearer the second branch point.

Step 3. Identify and number the substituents.

Table 2.5 Some Straight-Chain Alkyl Groups

a. Assign a number, or locant, to each substituent to locate its point of attachment to the parent chain.

b. If there are two substituents on the same carbon, give both the same number. There must be as
many numbers in the name as there are substituents.

Step 4. Write the name as a single word.

Use hyphens to separate the different prefixes, and use commas to separate numbers. If two or more
different substituents are present, cite them in alphabetical order. If two or more identical substituents are
present on the parent chain, use one of the multiplier prefixes di-, tri-, tetra-, and so forth, but don’t use
these prefixes for alphabetizing.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Step 5. Name a complex substituent as though it were itself a compound.
In some particularly complex case, a fifth step is necessary. It occasionally happens that a substituent on
the main chain has sub-branching. In the following case, for instance, the substituent at C6 is a three-carbon
chain with a methyl sub-branch. To name the compound fully, the complex substituent must be first named.

Number the branched substituent beginning at its point of its attachment to the main chain, and identify it,
in this case, a 2-methylpropyl group. The substituent is treated as a whole and is alphabetized according to
the first letter of its complete name, including any numerical prefix. It is set off in parentheses when naming
the entire molecule.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 For historical reasons, some of the simpler branched-chain alkyl groups also have nonsystematic, common
names as follows:

The common names of these simple alkyl groups can be used in IUPAC system of nomenclature, thus

When writing the alkane name, the nonhypenated prefix iso- is considered part of the
alkyl-group name for alphabetizing purposes, but the hyphenated and italicized prefixes sec- and
tert- are not.

Alkenes
Steps in Naming Alkenes
Step 1. Name the parent hydrocarbon.
Find the longest carbon containing the double bond, and name the compound accordingly, using the suffix
–ene.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Step 2. Number the carbon atoms in the chain.
Begin at the end nearer the double bond or, if the double bond is equidistant from the two ends, begin at
the end nearer the first branch point. This rule ensures that the double bond carbons receive the lowest
possible numbers.

Step 3. Write the full name.

Number the substituents according to their positions in the chain, and list them alphabetically. Indicate the
position of the double bond by giving the number of the first alkene carbon and placing that number directly
before the parent name. If more than one double bond is present, indicate the position of each and use one
of the suffixes –diene, -triene, and so on.

It should also be noted that IUPAC changed their naming recommendations in 1993 to place the
locant indicating the position of the double bond immediately before the –ene suffix rather than before the
parent name. However, it is not widely accepted so the older and more commonly used name.

Cycloalkenes are named similarly, but because there is no chain end to begin from, we number the
cycloalkane so that the double bond is between C1 and C2 and the first substituent has a low number as
possible. It’s not necessary to indicate the position of the double bond in the name because it’s always

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 between C1 and C2. As with open-chain alkenes, newer but not yet widely accepted naming rules place the
locant immediately before the suffix in diene.

There are few alkenes whose names are firmly entrenched in common usage but don’t conform to
the rules.

Table 2.6 Common Names of Some Alkenes

Alkynes
Steps in Naming Alkynes
Step 1. Name the parent hydrocarbon.
Alkyne nomenclature follows the general rules for hydrocarbons (alkanes and alkenes). The suffix –yne is
used, and the position of the triple bond is indicated by giving the number of the first alkyne carbon in the
chain.
Step 2. Number the carbon atoms in the parent chain and write the name.
Numbering the chain begins at the end nearer the triple bond so that the triple bond receives as low number
as possible.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Compounds with more than one triple bond are called diynes, triynes, and so forth; compounds containing
both double and triple bonds are called enynes. Numbering of an enyne chain starts from the nearer the first
multiple bond, whether double or triple. When there is a choice in numbering, double bonds receive lower
numbers than triple bonds.

As with alkyl and alkenyl substituents derived from alkanes and alkenes, respectively, alkynyl groups are
also possible.

Alkyl Halides or Organohalides

Steps in Naming Alkyl Halides
Step 1. Find the longest chain, and name it as the parent.
If a double or triple bond is present, the parent chain must contain it.
Step 2. Number the carbons of the parent chain beginning at the end nearer the first substituent,
whether alkyl or halo.
Assign each substituent a number according to its position on the chain.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 If different halogens are present, number all and list them in alphabetical order when writing the name.

Step 3. If the parent chain can be properly numbered from either end by step 2, begin at the end
nearer the substituent that has alphabetical precedence.

Aromatic Compounds

Figure 2.17 Some aromatic hydrocarbons found in coal tar.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Table 2.7 Common Names of Some Aromatic Compounds

Steps in Naming Aromatic Rings

Monosubstituted benzenes are named systematically in the same manner as other hydrocarbons,
with –benzene as the parent name.

Step 1. Find the parent chain.

Alkyl-substituted benzenes are referred to as arenes and are named in various ways depending on the size
of the alkyl group. The arene is named as an alkyl-substituted benzene if the alkyl substituent is smaller
than the ring (six or fewer carbons). The compound is named as phenyl-substituted alkane if the alkyl
substituent is larger than the ring (seven or more carbons).

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Step 2. Determine the substituents attached to the parent chain.
Disubstituted benzenes are named using one of the prefixes ortho (o), meta (m), or para (p).

Benzenes with more than two substituents are named by choosing a point of attachment as carbon 1 and
numbering the substituents on the ring so that the second substituent has a low number as possible. Number
so that the third or fourth substituent has a low number as possible, until a point of difference is found if
ambiguity still exists. The substituents are listed alphabetically when writing the name.

Alcohols and Phenols

Alcohols are classified as primary (1°), secondary (2°), an tertiary (3°), depending on the number
of organic groups bonded to the hydroxyl-bearing carbon.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Steps in Naming Alcohols
Step 1. Select the parent chain.
The parent chain is the longest carbon chain containing the hydroxyl group, and derive the parent name by
replacing the –e ending of the corresponding alkane with –ol. The –e is deleted to prevent the occurrence
of two adjacent vowels.
Step 2. Number the chain beginning at the end nearer the hydroxyl group.
Step 3. Number the substituents and write the name.
Number the substituent according to their position on the chain, and write the name, listing the substituents
in alphabetical order and identify the position to which the –OH is bonded. Also, just like in alkanes, newer
IUPAC naming recommendations place the locant immediately before the suffix rather than before the
parent.

Some simple and widely occurring alcohols have common names that are accepted by IUPAC.

Phenols are named as described in aromatic rings. Note that –phenol is used as the parent name
rather than –benzene.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Aldehydes
Steps in Naming Aldehydes
Step 1. Find the parent chain and number the carbons in the chain.
The parent chain must contain the –CHO group. Number the chain in a manner in which the –CHO carbon
is numbered as carbon 1.
Step 2. Write the name.
Aldehydes are named by replacing the terminal –e of the corresponding name with alkane name with –al.

For cyclic aldehydes, the –CHO group is directly attached to the ring. The suffix –carbaldehyde is used.

Table 2.8 Common Names of Some Simple Aldehydes

Ketones
Steps in Naming Ketones
Step 1. Find the parent chain and number the carbons in the chain.
The parent chain is the longest chain that contains the ketone group. Numbering begins at the end nearer
the carbonyl carbon.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Step 2. Write the name.
Ketones are named by replacing the terminal –e of corresponding alkane name with –one. The locant is
placed before the parent name in older rules but before the suffix in newer IUPAC recommendations.

Some ketones with common names are allowed by the IUPAC to be retained.

When it’s necessary to refer the R-C=O as a substituent, the name acyl group is used and the name ending
–yl is attached.

If other functional groups are present and the doubly bonded oxygen is considered a substituent on a parent
chain, the prefix oxo- is used.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Carboxylic Acids
Steps in Naming Carboxylic Acids
Step 1. Find the parent chain and number the carbons in the chain.
The parent chain is the longest chain that contains the -COOH group. The –COOH carbon atom is numbered
C1.
Step 2. Write the name.
Carboxylic acids are named by replacing the terminal –e of corresponding alkane name with –oic acid.

Compounds that have –COOH group attached to a ring are named using the suffix –carboxylic acid. The
COOH carbon is attached to C1 in this system and is not itself numbered. The COOH group is called a
carboxyl group, as a substituent.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Table 2.9 Common Names of Some Carboxylic Acids and Acyl Groups

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Amines
Amines can be either alkyl-substituted (alkylamines) or aryl-substituted (arylamines). Amines are
classified as primary (RNH2), secondary (R2NH) or tertiary (R3N).
Primary amines are named in the IUPAC system in several ways. For simple amines, the suffix
–amine is added to the name of alkyl substituent.

Alternatively, the suffix –amine can be used in place of the final –e in the name of the parent
compound.

Amines with more than one functional group are named by considering the –NH2 as an amino
substituent on the parent molecule.

Symmetrical secondary and tertiary amines are named by adding the prefix di- or tri- to the alkyl
group.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Unsymmetrical substituted secondary and tertiary amines are named as N-substituted primary
amines. The largest alkyl group is chosen as the parent name, and the other alkyl groups are considered N-
substituents on the parent chain.

Heterocyclic amines are compounds in which the nitrogen atom occurs as part of a ring, and are
also common. Each different heterocyclic ring system has its own parent name. The heterocyclic nitrogen
atom is always numbered as position 1.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 Chapter Exercise

1. Draw the line and skeletal structure of the following condensed structures.
a. CH3CH2CH2CH2CH2CH2CH3
b. CH3CH2CH2CH2(CH3)CHCH3
c. (CH3)2CHCH2CH3
d. CH3CH2CH2C(CH3)2CH2CH3
2. Identify the different functional group(s) present in the following compounds.

a.

b.

c.

d.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L

 3. Give the IUPAC name of the following compounds.

a.

b.

c.

d.

e.

f.

4. Give the structure of the following organic compounds:

a. 3-ethyl-5-isobutyldecane
b. 2-chloro-3-ethylpentane
c. 2,3-dibromo-2-methylbutane
d. 3-iodo-5-isopropyl-3,4-dimethylheptane

REFERENCES
Carey, Francis A. and Guiliano, Robert M. (2014). Organic Chemistry 9 th Edition. McGraw-Hill
Companies, Inc. New York USA.
Mc Murry, J (2019). Organic Chemistry, 9 th edition. John Wiley & Sons Inc.

RACHELLE C. MENDOZA │ BATSTATEU CAS CHEM 105L