BONIFACIO LUZ NATIVIDAD EDUCATIONAL FOUNDATION, INC.
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Government Recognition No. E-022 s.2013, E-034 s.2013, S-018 s.2015
Tel. No. 611-09-63, 0925-617-29-14
INTRODUCTION
The study of Chemistry need not be boring.
From the definition of matter to the properties and behavior of different chemical
compounds to common calculations encountered in chemistry, this module, General
Chemistry 1, introduces the reader to the core topics covered in an Introductory Chemistry
class for senior high school students.
This module delivers comprehensive but concise introduction to chemistry. The topics
and discussions were carefully chosen and crafted to be easily understood by a first-learner,
while being thorough enough to create a solid foundation of higher-level learning.
In this module, you are expected to read and understand carefully all the lessons
instruction before answering the exercises and activities given on each learning outcomes
and also this module contain more comprehensive lessons about the Biology based on the
curriculum of Senior High School
Chemistry 1 also helps you to achieve your 21st century skills such as Creativity, and
Critical Thinking Skills which enable you to understand the world of life science.
After completing this module, you are expected to take an Assessment given by your
teacher to check the mastery of the subject matter by identifying some important properties
of each lessons. By this, you are expected to enhance and discover the core values that the
BLUN offers which is Sensible, Motivated, Industrious, Loving, and Excellence.
Enjoy the ride and welcome to the world of Chemistry BLUNians!
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TABLE OF CONTENTS
Introduction…………………………………………………………………..............................1
Learning Competencies…………………………………………………...............................4
Lesson 1. Electronic Structure and Quantum Numbers..………..……………………..…5
Reflection………………………………………………………………………………11
Lesson 2. Lewis Structure and Molecular Geometry ………………..............................12
Reflection…………………………………………………………………………..….25
Lesson 3. Organic Compounds……………………………………………………………….26
Reflection…………………………………………………………………………..….40
Lesson 4. Biomolecules…………..…………………………………………………………..…41
Reflection…………………………………………………………………………....57
References……………………………………………………………….………………………58
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INSTRUCTION FOR THE LEARNERS
This Module “Atomic Structure, Chemical Reaction and Gases” contains the
whole lesson and necessary information in order to complete this course.
The unit of competency “Atomic Structure, Chemical Reaction and Gases” contains
knowledge, attitudes and skills required for completing General Chemistry 1.
This module contains the whole topic of every lesson that you need to know. The lesson
in this module is made easy for your grade level, so read carefully the whole topic on each
lesson because it will help you answer all the series of learning activities on your Learning
Activity Sheets.
Reflection is the part where the learners connects the lesson learned to real-life values
and other disciplines.
Be sure that you answer this module in an “Honest way.”
If you have questions, don’t hesitate to ask your teacher for assistance.
3
CONTENT STANDARDS






The learners demonstrate understanding of…
The quantum mechanical description of the atom and its electronic structure.
Ionic bond formation in terms of atomic properties.
Covalent bond formation in terms of atomic properties.
The properties of molecular covalent compounds in relation to their structure.
The properties of organic compounds and polymers in terms of their structure.
PERFORMANCE STANDARDS
Illustrate the reactions at the molecular level in any of the following:



Enzyme action.
Protein denaturation.
Separation of components in coconut milk.
LEARNING COMPETENCIES
At the end of this quarter learners are expected to:
1.
2.
3.
4.
5.
6.
use quantum numbers to describe an electron in an atom.
determine the magnetic property of the atom based on its electronic configuration.
draw an orbital diagram to represent the electronic configuration of atoms.
draw the Lewis structure of ions.
apply the octet rule in the formation of molecular covalent compounds.
Write the formula of molecular compounds formed by the nonmetallic elements of
the representative block.
7. draw Lewis structure of molecular covalent compounds.
8. determine the polarity of simple molecules.
9. describe the different functional groups
10. describe some simple reactions of organic compounds: combustion of organic fuels,
addition, condensation, and saponification of fats.
11. describe the formation and structure of polymers.
12. explain the properties of some polymers in terms of their structure.
13. describe the structure of proteins, nucleic acids, lipids, and carbohydrates, and
relate them to their function.
14. describe the preparation of selected organic compounds.
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LESSON 1: Electronic Structure and Quantum Numbers
LEARNING OBJECTIVES




Trace the development of the atomic model from the plum pudding model to the currently
accepted quantum mechanical model.
Describe the quantum mechanical model of the atom.
Use quantum numbers to describe electrons in atoms.
Write the electron configuration of atoms.
Imagine climbing a ladder and
trying to stand between the
rungs. Unless you could stand on
air, it would not work. When
atoms are in various energy
states, electrons behave in much
the same way as What
a person
happens
climbing up the rungs of
a
ladder.
to a person
attempting to
step on the next
level with
insufficient
energy?
Introduction
Models are used to help provide mental
images of things that we cannot actually
see like the subatomic particles. Based on
experiments done, theories have been
proposed by several scientists which
helped develop mental models of atomic
structure. These give us an idea of what
scientists believe individual atoms would
look like if they could be seen. The
electron
configuration
gives
a
representation of how the electrons are
distributed in an atom.
What are the principal sub atomic particles?
How are these subatomic particles arranged
in the atom?
Thomson’s Plum Pudding Model in which the
electrons were supposed to be embedded in a
positive cloud.
Rutherford’s Nuclear Model which presents the
atom as having a small nucleus where the positive
charge and mass of the atom is concentrated.
The Bohr Model Another concept of atomic
structure came in 1913 when Niels Bohr, a Danish
physicist, proposed a planetary model of the atom.
The electrons were supposed to move in orbits
around the nucleus, but they could orbit only in
certain specified energy levels, they cannot exist
between energy levels.
5
What is the present concept of atomic structure?
Schrodinger’s Model
The theory was supported by Erwin Schrodinger in
1926, who showed that if an electron within an atom is
treated as a wave rather than as a particle, the various
allowable energies (Bohr’s stationary states) could be
described by the mathematics of three dimensional wave
behavior. This new view came to be called quantum
mechanics (quantum theory + wave mechanics) as
Schrodinger wrote and solved mathematical equations to
describe the energy and the location of electrons in atoms.
The position of an electron within an atom cannot
be pinpointed. Using Schrodinger’s wave mechanics, we
can only specify regions around the nucleus of an atom in
which there is a large probability of finding the electrons.
Quantum Numbers
From the mathematical solutions of the Schrodinger Equations, certain numbers were derived
that can describe the distribution of electrons in a given atom. These numbers, called quantum
numbers, labels a wave function and can even be used to compute for certain properties.
There are four quantum numbers, namely; the principal quantum numbers, the angular
momentum quantum number, the magnetic quantum number and, the spin quantum number. Each
electron in an atom has its own set of quantum numbers that can describe its behavior and even the
atomic orbital it belongs to.
Principal Quantum Number
How is the principal quantum number determined?
The principal quantum number (n) describes the main energy level or shell that contains the
electron. The shells describe regions where there is a high probability of finding an electron. It is
approximately equivalent to the energy level introduced by Bohr. The allowed values for are only
positive integers.
n = 1, 2, 3, 4…
The value of n also relates to the average value of the distance from the nucleus and its size.
The higher the value of n, the larger the shell and the farther it is from the nucleus. For example, a n =
3 shell is larger than a n= 1 shell. Furthermore, an electron in n = 3 shell is farther than an electron in n
= 1 shell.
Also, each shell contains a number of sublevel or subshells equal to the value of n. For example,
one subshell can be found in n= 1 shell, two subshells for n = 2 and so on.
Angular Momentum Quantum Number
How is angular quantum number related to shape
of orbitals?
The angular momentum quantum
number (𝒍) describes the shape of the orbitals in a subshell. The allowed values of the 𝑙 are dependent
on the value of the principal quantum numbers n. For a given value of n, the values of 𝑙 are integers
that range from 0 to n-1.
𝒍 = 𝟎, 𝟏, 𝟐, 𝟑, 𝟒 … ( 𝒏 − 𝟏)
For example, for n = 3 shell, it can have three subshells designated by 𝑙 values that range from
0 to 2 (n- 1 = 2 – 1 = 2). Thus, the subshells of n = 3 shell have 1 values of 0, 1, and 2.
Aside from the numbers, other letters symbols are more commonly used to describe a subshell,
and later on, an orbital.
6
𝑙 = 0, 1, 2, 3, 4, 5 … … ..
𝑛𝑜𝑡𝑎𝑡𝑖𝑜𝑛 = 𝑠, 𝑝, 𝑑, 𝑓, 𝑔, ℎ … ..
An s-orbital is spherical in shape with the electron cloud becoming less dense as it moves
farther from the nucleus. A p-orbital is dumb bell in shape that consists of two lobes on the opposites
side of the nucleus separated by a planar region called a node, which is an area where there is no
probability of finding an electron. Because of the nature of the shape of the p-orbital, it can assume
three possible orientations in space. The d-orbitals mostly look like a four-leaf clover and can assume
five possible orientations in space. Orbitals from f and beyond have more complex shape.
Each subshell in an energy level can be designated by the combined symbols of 𝑛 and 𝑙. For
example, the subshell with n = 3 and l = 0 can be called the 3s subshell. The other two subshells of n =
3 shell are the, called 3p and 3d.
Magnetic Quantum Number
How does magnetic quantum number work?
The magnetic quantum number (ml) describes the orientation of each orbital in space with
the values dependent on the value of angular momentum quantum numbers l. For a given subshell,
the allowed values of ml are integers that range from - l to + l. Also, for each given subshell, the number
of values of ml = is equal to 2 l + 1.
For example, for 1 = 2 subshell, there are 5 (2 l + 1 = 2(2) + 1 = 5) possible ml values which are 2, -1, 0 ,1 and 2. The number of ml values is also indicative of the number of orbitals a given subshell
can hold. Thus, an s subshell with l = 0 can contain 1 orbital while a p subshell with l = 1 can contain 3
orbitals and so on.
What are the two possible spin quantum numbers?
Spin Quantum Number
Electrons can be thought of as rotating charges. This rotational motion is called a spin and can
have two possible opposing directions. Since a spinning charge can generate a magnetic field, the
direction of an electron’s spin can be determined by its response to a magnetic field. This apparent
spin of an electron is described by the spin quantum number (𝒎𝒔 ) and can have one of two values:
𝒎𝒔 = +
Name
Principal
Angular Momentum
Magnetic
Spin QN
Symbol
n
l
𝑚ℓ
𝑚𝑠
𝟏
𝟏
𝒐𝒓 −
𝟐
𝟐
Allowed Values
1, 2, 3, 4……
0 to (n-1)
-ℓ to +ℓ
1
1
+ 𝑜𝑟 −
2
2
Meaning
Energy level or shell
Subshell and shape of orbital
Orbital and orientation in space
Spin state
7
Electronic Configuration
Know More
As a student board a bus, they each sit
in a separate bench seat until they are
all full. Then, they begin sharing seats.
Electrons fill atomic orbitals in a similar
way.
Where are electrons supposed to be found in the atom?
How is the arrangement of electrons in an atom?
With the use of quantum numbers, you can now label the orbital location of any given
electron. In a way, the set of quantum numbers of an electron serves as its “address” in the atom of
being the more general location to l and 𝑚𝑙 giving specifics.
Aside from the orbital location of an electron, the quantum numbers are also used in defining
the arrangement of electrons in any given atom. This arrangement is called the Electronic
Configuration.
Pauli’s Exclusion Principle
This principle of Wolfgang Pauli (1900-1958), a Swiss physicist, states that no two electrons in the
same atom can have the same four quantum numbers. If two electrons both reside in the orbital, they
will both have quantum numbers n= 1, l = 0, and ml =0. However, one electron must have 𝑚𝑠 = +1/2
while the other has 𝑚𝑠 = -1/2. Therefore, each orbital can only contain a maximum of 2 electrons of
opposite spins.
n
1
2
3
Aufbau Build-Up Principle
l
0
0
1
0
1
2
𝒎𝓵
0
0
-1, 0,1
0
-1, 0, 1
-2, -1, 0, 1, 2
𝒎𝒔
+
1
1
𝑜𝑟 −
2
2
How electron orbitals are filled in accordance with Aufbau
principle?
Electrons do not just randomly occupy orbitals. According to the Aufbau Build-Up Principle,
electrons of an atom will occupy orbitals from the orbitals with the lowest energy to orbitals of the
highest energy. The relative energies of these orbitals are determined by the values of and quantum
numbers following the n + 1 rule
𝑬𝒓𝒆𝒍𝒂𝒕𝒊𝒗𝒆 = 𝒏 + 𝟏
The higher the value of n+1, the higher the energy of the orbital. For example, an orbital in the
3s subshell has n =3 and ℓ = 0 with an n + 1 = 3. An orbital in the 4p subshell, on the other hand, has n
= 4 and ℓ = 1 with an n + 1 = 5. Thus, a 3s orbital has a lower relative energy than a 4p orbital and will
come first in the arrangement of orbitals in the electronic configuration.
In addition, for orbitals with the same value for 𝑛 + ℓ, the orbital with the lower value for n has
a lower relative energy. For example, a 4p orbital has n =4 and ℓ= 1 with 𝑛 + 𝑙 = 5 but since the 3d
orbitals has a lower value of n, it has the lower relative energy.
8
Here is a sample arrangement for the first few subshells and their corresponding orbitals in an
electronic configuration based on their relative energies:
𝟏𝒔 < 𝟐𝒔 < 𝟐𝒑 < 𝟑𝒔 < 𝟑𝒑 < 𝟒𝒔 < 𝟑𝒅 < 𝟒𝒑 < 𝟓𝒔 < 𝟒𝒅 < 𝟓𝒑 < 𝟔𝒔 < 𝟒𝒇 < 𝟓𝒅 < 𝟔𝒑 … …
Thus, in accordance with the Aufbau Build-up Principle, it follows that electrons must first fill-up
the orbitals of a 1s subshell before the orbitals of 2s subshell and so on.
Recall that the number of orbitals contained in a given subshell is dependent on the number
of possible ml values in that subshell before the orbitals of 2s subshell and so on.
Recall that the number of orbitals contained in a given subshell is dependent on the number
of possible ml values in that subshell. For example, a 2p orbital has ℓ = 1 with three possible 𝑚ℓ values
which are -1, 0, and 1. Thus, in a 2p subshell, there are three 2p orbitals. These orbitals, which belong
to the same energy level and are with the same energy, are called degenerate orbitals. Thus, p
subshells contain three orbitals, d subshells contain five orbitals, and so on.
Each orbital can contain a maximum of two electrons. Since a 2p subshell contains three
orbitals, it can contain a maximum of 6 electrons. Furthermore, in accordance with the Pauli’s
Exclusion Principle, the two electrons in each orbital must be of opposite spin. A common notation of
the electronic configuration is as follows
𝒏𝒍# 𝒐𝒇𝒆−
Where nl denotes the subshell including combined description of the main energy level and the shape
of orbital and the superscript denotes the number of electrons in that subshell.
Let’s take a neutral 4Be atom as an example. Beryllium has 4 electrons which must each be
assigned to orbitals. Following the Aufbau Build-up Principle, the electronic configuration of Beryllium
can be written as such:
1s22s2
The electronic configuration can also be represented by an orbital diagram such as:
1s2 2s2
Each box in the orbital diagram represents a single orbital while the arrows represent the
electrons. Also, the direction of the narrow represents the spin of the electron. As a convention, the
up arrow represents an electron with 𝑚𝑠 = +1/2 while the down arrow represents an electron with 𝑚𝑠
9
= -1/2. Notice that the electronic configuration also follows the Pauli’s Exclusion Principle, with each
orbital containing a maximum of two electrons with opposite spins.
Hund’s Rule of Maximum Multiplicity
What is the importance of Hund's rule?
Let’s try another example such as 6C. Since the carbon has 6 electrons, its electronic distribution
will be as follows:
1s22s22p2
But since the subshell 2p has three orbitals, how will the two electrons of the 2p subshell be
distributed? Will the two electrons belong in a single orbital or distributed in two different orbitals?
When distributing electrons in a subshell with multiple degenerate orbitals, the Hund’s rule of
Maximum Multiplicity, named after German physicist Frederic Hund, must apply. Hund’s Rule states
that the most stable arrangement of electrons in subshells is the one with the greatest number of
parallel spin. Parallel spins mean electrons of the same spin quantum number.
Therefore, for the case of 6C, electrons must be distributed.
1s2
2s2
2p2
Notice that in order for the electrons of the 2p subshell to achieve maximum multiplicity, the
two electrons of the same spin must occupy two separate orbitals. In general, to follow the Hund’s
rule, in a subshell, electrons of the same spin must first fill degenerate orbitals before electrons of
opposite spin can pair up with another orbital.
In addition, it doesn’t matter which of the three orbitals of the 2p subshell will be occupied first
since all three have the same energies because they are degenerate orbitals and only differ in
orientation.
Let’s have this Sample Problem
Write the electronic configuration of 8O and draw its orbital diagram.
Required:
Electronic Configuration of 8O.
Given:
Z = 8 = # of Proton
8O
Since atom is neutral, the number of electrons must be equal to the number of protons which is 8.
Strategy:
For the electronic configuration, simply follow the Aufbau Build-up Principle and fill subshells
from the lowest energy to lowest energy.
Solve the Problem:
1s22s22p4
As for the orbital diagram:
O
1s2 2s2
2p4
Since there is only orbital for the 1s and 2s, each orbital just has
to be filled with two electrons of the opposite spin. However, for the 2p subshell, the first three electrons
of the same spin and first fill all three degenerate orbitals. The remaining electron of the opposite spin
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can, then, pair up with any of the 2p orbitals already occupied by a single electron. This is in
accordance with the Hund’s Rule.
For most cases, electronic configurations following the Aufbau Build-up Principle are effective
in describing the most stable electronic distribution of the electrons, also called the ground state
electronic configuration. However, there are actually some exceptions.
Take
must be:
24Cr,
for example. Following the Aufbau Build-up Principle, the electronic configuration
1s22s22p63p64s23d4
However, a more accurate electronic configuration for
24Cr
is actually:
1s22s22p63s24s13d5
This is due to the higher stability of a half-filled d-subshell, where all orbitals contain a single
electron, in the second configuration than a partially filled d-subshell of the first configuration. Since a
half-filled d-subshell is preferred, one of the electrons from the 4s subshell will go down a main energy
level back to the 3d-subshell.
Another exception applies to electronic configuration of elements with electrons that can form
full d-subshells such as in the case of 29Cu with the ground state electronic configuration of:
1s22s22p63s23p64s13d10
For elements with many electrons, it is jot that efficient to write a very long electronic
configuration so as short-hand notation, some of the electrons of lower energy can be represented
by a Noble Gas Core, wherein the symbol of the noble gas that precedes the element the closest is
placed in a bracket. This is then, followed by the symbol for electronic configuration of the electrons
of higher energy.
For example, in the case of the previous example 29Cu, the electronic configuration can be
written as:
[Ar]4s13d10
Since the noble gas argon is the noble gas that precedes copper.
Gain better Understanding about the Electron Configuration and Quantum
Numbers by visiting this link.
https://www.youtube.com/watch?v=2AFPfg0Como
https://www.youtube.com/watch?v=Aoi4j8es4gQ
REFLECTION
Optimism. Electron configuration describes the orbitals occupied by electrons in an
atom. In life, no matter how we imbibe negativity we must not be affected by it
because life is a series of positive and negative experiences. And like what we
always say, “Think like a proton, always positive.”
REMINDERS
For your activity, check your Learning Kits for the required assessment for this
week. If you have any question or clarification regarding the lesson don’t
hesitate to ask, there is a space on your learning kit where you can write your
concerns. Remember, answer all the activities in an honest way. Good luck!
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LESSON 2: Lewis Structure and Molecular Geometry
LEARNING OBJECTIVES






Draw the Lewis structure of ion.
Apply the octet rule in the formation of molecular covalent compounds.
Write the formula of molecular compounds formed by the nonmetallic elements of the
representative block.
Draw Lewis structure of molecular covalent compounds.
Describe the geometry of simple compounds.
Determine the polarity of simple molecules.
Have you ever run in a three-legged
race? Each person in the race shares
one of their legs with a teammate to
form a single three- legged team. In
some ways, three-legged race
mirrors how atoms share electrons
and join together as a unit.
Introduction
From knowing the structures of the
atoms, we move on to learning about why
and how they react, the nature of the
bonds formed between them, the forces
that makes the bonding possible, and the
structure and properties of the resulting
combinations of atoms.
Atoms have the natural tendency to
go to a state of stability comparable with
the noble gases and the number and
arrangement of valence electrons of the
atoms of noble gas lead us to an
understanding of why and how atoms
interact or form chemical bonds with one
another.
Why do atoms form bonds?
Understanding the bonding in compounds is essential to developing new chemicals and
technologies. Atoms react with each other by way of their valence electrons which result into some
changes in the distribution of electrons in their outermost energy levels.
LEWIS STRUCTURE
For easier analysis of chemical bonding of different elements and the compound they form,
the American chemist Gilbert Lewis devise a system to represent different elements. The Lewis Dot
Symbol representing an atom is comprised of the element’s chemical symbol surrounded by dots
representing the valence electrons.
For example, the elements iodine can be represented by the following Lewis Dot Symbol:
12
Since iodine has seven valence electron, it is surrounded by seven dots: one for each valence
electrons. Furthermore, the arrangement of the dots also reflects the orbital assignment of the
electrons. With the electronic configuration of iodine. ([Kr]5s24d105p5), the pair of dots represents the
pair of electrons are in the 5s orbitals and the two 5p while the single dot represent the electron singly
occupying one of the 5p orbitals.
The Lewis Dot Symbols of the first 20 elements. Notice that the elements belonging to the same
group have same valence electrons and have similar Lewis Dot Symbols. The Group 2A elements (Be,
Mg, Ca), for example, have two valence electrons and have a two dots surrounding their chemical
symbols.
Lewis Dot Symbols are generally not used for transition metals, lanthanides and actinides since
they all have incompletely filled inner shells. In addition, Lewis symbols are not only used to represent
elements but can also be used to represent ionic and covalent compounds.
Lewis Dot Symbol of the First 20 Elements of the
Periodic Table
Writing Lewis Structures
How to Draw a Lewis Structure?
Some combinations of atoms may be difficult to arrange in order to construct a favorable
Lewis Structure. In case like this, it may be difficult to identify which atom bonds to which or the number
of covalent bond a certain pair can form. The table below details a step-by-step process to guide you
in the construction of Lewis Structures for different molecules. The polyatomic anion SCN - will be used
as an example.
STEPS IN WRITING LEWIS STRUCTURE
1. Identify the central atom – the atom surrounded by other atoms
In most molecules, the construction of the Lewis Structure starts with the atom at the center
structure. This atom can either be the different atom, such as sulfur in SO 2, or the atom with the
lowest electronegativity, such as carbon in COCl 2.
In SCN-, since carbon is the least electronegative, it will be the central atom.
13
2. Determine the total number of available electrons for the structure (NA). This includes the
total number of valence electrons for all atoms. Furthermore, if the molecule is a polyatomic
ion.
a. For the anion, increase the number of available electrons by the charge of anion.
b. For a cation, decrease the number of available electrons by the charge of the cation.
The total number of valence electrons can be computed as follows:
S- 1 x 6 = 6
C- 1 x 4 = 4
N- 1 x 5 = 5
Total = 15
Since it is anion, add 1 for the negative charge. Thus, NA = 16
3. Determine the number of electrons needed (NN) to satisfy the Octet Rule for each atom.
Note that although most atoms follow the Octet Rule and will require eight electrons, there are
some exceptions such as hydrogen, which required only two electrons and Group 3A
elements, which require only six electrons.
Each atom will require eight electrons. Thus,
NN = 3 x 8 = 24
4. Determine total number of bonds (B) which can be computed as follows:
𝑁𝑁 − 𝑁𝐴
𝐵=
2
24 − 16
=4
2
5. Arrange the bonds around the central atom and the surrounding atoms. This can have
multiple possible structures.
𝐵=
6. Complete the structure by adding lone pairs to complete the octet for each structure.
The number of lone pair for each atom (NLP) can be computed as follows:
NLP =
8−𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑏𝑜𝑛𝑑𝑠 𝑎𝑡𝑡𝑎𝑐ℎ𝑒𝑑 𝑡𝑜 𝑎𝑡𝑜𝑚𝑠
2
7. Indicate formal charges to each element.
𝐹𝐶 = 𝑉 − 𝐿 +
1
𝑆
2
8. Choose the most favored structure on the basis of the formal charges.
Among the three structures, structure C has the most formal charges and is the least
stable. Between structure A and B, B is more stable since the negative formal charge
belongs the nitrogen which is the more electromagnetic element.
CHEMICAL BONDS
Chemical bond is a force that holds atoms together. It is all about the electrons. Electrons that
are attracted to positively charged nucleus of the other atom.
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How are chemical bonds formed?
CLOSER LOOK
Linus Pauling
In the 1930s, Pauling used
new mathematical theories
to
enunciate
some
fundamental principles of the
chemical bond. By 1932,
Paulling’s interest turned to
biological molecules, and he
was awarded the 1954
Nobel Prive in Chemistry for
his work on protein structure.
Linus Pauling was one of the
most influential chemists of
the 20th Century.
Ionic Bonding
What changes happen to atoms of elements when ions are formed?
An ionic bond is formed when there is an electron transfer between atoms. The compounds
that are formed using ionic bonds are called ionic compounds. In the formation of an ionic
compound, the individual atom transfers electrons leading to formation of ions which is isoelectronic
to noble gases.
When elements become isoelectronic, or have the same electronic configuration, with a
noble gas, they acquire a certain similar stability. Recall that noble gases are inherently stable
compounds and this can be attributed to their shells being completely filled. The general valence shell
electronic configuration of the noble gases is ns 2 np6, with the exception of He which has a valence
shell electronic configuration of 1s2.
Since most noble gases have eight electrons in their valence shells, two in the s-orbital and six
on the p-orbital, elements will lose or gain electrons to have eight electrons in their filled outer energy
level simply known as the Octet Rule. This rule supplies to the formation of ions that make up different
ionic compounds.
Take, for example, the previously mentioned ionic compound sodium chloride (NaCl). It is
formed using an ionic bond and is represented by the following Lewis symbols:
15
Lewis Dot Symbol for Sodium Chloride
Since Na has one valence electron, in order to become isoelectronic with a noble gas, it will
have to either lose one electron or gain seven more electrons. Since sodium is a metal, it will prefer
losing electrons and forming a cation.
On the other hand, since cl has seven valence electrons, it can either lose seven electrons or
gain one electron. But since it is a non-metal, it will prefer gaining electrons and forming an anion.
In the case, the electron lost by sodium is gained by chlorine forming the compound sodium
chloride and the ionic compound can be represented as follows:
Another example is the formation of the ionic compound magnesium chloride which is made
up of magnesium and chloride. The Lewis symbol of the compound is as follows:
Lewis Dot Symbol for Magnesium Chloride
Since magnesium has two valence electrons, it will have to lose two electrons in order to be
isoelectronic with a noble gas. However, since chlorine has seven valence electrons, it can only
accept one electron. Thus, two chloride atoms are required in order to accommodate the two
electrons lost by a single magnesium atom.
It is important to note that in the formation of ionic compounds, the total number of electrons
lost to form the cation must be equal to the total number of electrons gained to form the anions.
Covalent Bonding
How are covalent bonds differ from ionic bonds?
While ionic compounds are formed with ionic bonds, covalent compounds, also known as
molecular compounds, are formed with the covalent bonds. Covalent bonds are formed though
electron sharing which means that some electrons in a covalent compound belong to more than one
element. Like the ionic compounds, most covalent compounds share electrons in order to achieve
an octet for the outer energy levels of each component atom as required by the Octet Rule.
The Lewis diagram of two hydrogen atoms sharing electrons looks like this:
This depiction of molecules is simplified further by using a dash to represent a covalent bond.
The hydrogen molecule is then represented as follows:
Remember that the dash, also referred to as a single bond, represents a pair of bonding
electrons.
Fluorine is another element whose atoms bond together in pairs to form diatomic (two-atom)
molecules. Two separate fluorine atoms have the following electron dot diagrams:
Each fluorine atom contributes one valence electron, making a single bond and giving each
atom a complete valence shell, which fulfills the octet rule:
The circles show that each fluorine atom has eight electrons around it. As with hydrogen, we
can represent the fluorine molecule with a dash in place of the bonding electrons:
16
Each fluorine atom has six electrons, or three pairs of electrons, that are not participating in
the covalent bond. Rather than being shared, they are considered to belong to a single atom. These
are called nonbonding pairs (or lone pairs) of electrons.
Single Covalent Bonds Between Different Atoms
Now that we have looked at electron sharing between atoms of the same element, let us
look at covalent bond formation between atoms of different elements. Consider a molecule
composed of one hydrogen atom and one fluorine atom:
Each atom needs one additional electron to complete its valence shell. By each contributing
one electron, they make the following molecule:
In this molecule, the hydrogen atom does not have nonbonding electrons, while the fluorine
atom has six nonbonding electrons (three lone electron pairs). The circles show how the valence
electron shells are filled for both atoms (recall that hydrogen is filled with two electrons).
Larger molecules are constructed in a similar fashion, with some atoms participating in more
than one covalent bond. For example, water, with two hydrogen atoms and one oxygen atom, and
methane (CH4), with one carbon atom and four hydrogen atoms, can be represented as follows:
Multiple Covalent Bonds Between Different Atoms
In many molecules, the octet rule would not be satisfied if each pair of bonded atoms shares
only two electrons. Consider carbon dioxide (CO2). If each oxygen atom shares one electron with
the carbon atom, we get the following:
17
This does not give either the carbon or oxygen atoms a complete octet; The carbon atom
only has six electrons in its valence shell and each oxygen atom only has seven electrons in its
valence shell. Thus, none of the atoms can reach the octet state in the current configuration. As
written, this would be an unstable molecular conformation.
Sometimes more than one pair of electrons must be shared between two atoms for both
atoms to have an octet. In carbon dioxide, a second electron from each oxygen atom is also
shared with the central carbon atom, and the carbon atom shares one more electron with each
oxygen atom:
In this arrangement, the carbon atom shares four electrons (two pairs) with the oxygen atom
on the left and four electrons with the oxygen atom on the right. There are now eight electrons
around each atom. Two pairs of electrons shared between two atoms make a double bond
between the atoms, which is represented by a double dash:
Some molecules contain triple bonds, covalent bonds in which three pairs of electrons are shared by
two atoms. A simple compound that has a triple bond is acetylene (C2H2), whose Lewis diagram is as
follows:
In general, multiple bonds are stronger than single bonds, such that the double bond between
two carbon and oxygen in carbon dioxide is stronger than the single bond between two fluorine atoms
in the fluorine molecule. This also means that multiple bonds are shorter than single bonds.
18
Comparison of Single, Double and Triple Bond
VALENCE SHELL ELECTRON PAIR REPULSION THEORY (VSEPR THEORY)
The 3D arrangement of the atoms in a molecule is usually defined by the relative locations of
atoms and lone pairs surrounding a central atom. These arrangements usually resemble common
geometric figures; wherein you can imagine the central atom at the center of the figure and the
atoms and lone pairs attached to the central atom lying at the corners.
Geometric Figures
Take, for example, the molecule phosphorous pentachloride PCl 5. The Lewis Structure of this
molecule reveals that the central atom, phosphorus, surrounded by five chlorine atoms. In the 3d
arrangement, three of these five chloride atoms lie in a single plane separated by 120 o angles while
the other two forms an axis perpendicular to the previously mentioned plane. If you imagine the
chloride atoms to be corners, you get a figure that looks like two triangular-based pyramids stacked
together; thus the trigonal bipyramidal geometry.
Lewis Structure and Geometry of
Phosphorus Pentachloride
According to the Valence Shell Electron Pair Repulsion Theory or VSEPR, a valence shell
electrons of the central atom tend to take up position that maximize their separation to attain stability.
In the VESPR model, the focus is on the valence shell electrons of the central atom. These
valence shell electrons can either be a bonding pair or a lone pair. When these groups of electrons
But what is the basis for the selected locations of these bonding atoms and lone pairs?
are situated close to each other, they tend to repel each other until repulsion is weakened with
distance and the molecule become stable. Thus, the geometric structure acquired by any given
molecule is actually a consequence of the electron repulsion of the different electron pairs that fill the
valence shell of the central atom.
19
MOLECULAR GEOMETRIES
The geometry followed by a molecule is dependent on the total number of groups surrounding
the central atom. These groups include atoms attached to the central atom with bonding electron
pairs or lone pairs of the central atom. The bonding electron pairs and lone pairs are made up of the
central atom’s valence electrons.
Each molecular geometry can be distinguished from one another by the number of
surrounding groups and their arrangement around the central atom. Remember that these
arrangements are based on the VSEPR theory which states that electron groups must be as far apart
as possible to attain stability. For simple molecules such as those with only one central atom, there are
five general molecular geometries: linear, trigonal planar, tetrahedral, trigonal bipyramindal, and
octahedral.
A parameter called the bond angle is often used to describe the arrangement of the
surrounding groups. A bond angle is the angle between two surrounding groups with the central atom
as the vertex. Each of the two molecular geometries mentioned have ideal bond angles which are
usually followed when all surrounding groups are the same while deviations occur when there are two
or more different surrounding groups.
Linear Geometry
The linear geometry is usually assumed by molecules with two groups surrounding the central
atom. In order for the electron groups to be as afar apart as possible, the group must be on opposite
sides of the central atom with an ideal 180o separation and, thus, forming a linear shape. One example
of this is the carbon dioxide molecule.
Trigonal Planar
For molecules with three surrounding groups, the molecular geometry is a trigonal planar. This
is named so because the three surrounding groups from the vertices of a triangle. They are oriented
in a plane separated by roughly 120o as can be seen in a molecule of boron hydride:
20
Tetrahedral
In another example, molecules with four groups surrounding the central atom will assume a
tetrahedral geometry. In this arrangement, the groups are located in the corners of tetrahedron to
make 109.5o ideal angles in between any two groups. One example is the methane molecule:
Trigonal Bipyramidal
For molecules with five surrounding groups, the geometry assumed is that of a trigonal
bipyramidal. The surrounding groups are either placed in an equatorial plane (equatorial region) or
an axis perpendicular to the equatorial plane (axial region). The three groups located on the
equatorial plane are separated from each other by 120 o ideal angles while the two groups on the axis
are separated by a 180o ideal angle. The phosphorus petachloride is an example of this geometry.
Octahedral
Octahedral geometry which is common for molecules with six groups surrounding the central
atom. In this molecular geometry, four groups separated by 90o ideal angles lie along a plane
(equatorial region) while the other two groups lie on both ends of an axis perpendicular to the plane
(axial region). Like the trigonal bipyramidal geometry, the octahedral geometry looks like two
pyramids stacked together. However, instead of triangular-based pyramids, it has squared-based
ones.
Sulfur
hexafluoride
follows
this geometry:
21
Whereas molecular geometry is defined by the total number of surrounding groups, the
molecular shape is described in terms of surrounding atoms and not the surrounding lone pairs. Thus,
it is possible for some molecules to have the same molecular geometries but have different shapes.
Nevertheless, the shape of a molecule, just like the molecular geometry, can be determined on the
basis of the Lewis Structure.
Molecules can be assigned to be specific shape category with the use of a simple formula
which includes the bonded atoms (B) and lone pairs (L) attached to the central atom (A). Each shape
category is defined by the formula ABxLy where X represents the number of bonded atoms and L
represents the number of lone pairs. Molecules belonging to the same shape category share the same
general shape. A summary of the different molecular geometries and shapes along with their
description can be seen in Table.
With the use of table, geometry and shape of any given molecule can easily be identified.
Details a step-by-step guide in identifying the geometry and shape of a molecule on the basis of its
Lewis Structure. The molecule NCl3 will be used as a working example.
Identifying Molecular Geometry and Shape
Step
1. Write the Lewis Structure
2. Identify the molecular Geometry by
counting the total number of groups
surrounding the central atom.
3. Identify the number of bonded atoms
X and number of lone pairs Y
surrounding the central atom.
Since NCl3 has four surrounding groups, it is of
a tetrahedral geometry.
X = 3 (three chlorine atoms)
Y = 1 (one lone pair)
22
4. Identify the shape category using the
formula ABxLY and predict shape. Since
the shape category is AB3L 1 the shape
is a trigonal pyramidal.
How molecules are classified as polar and non-polar?
Polarity of Molecules
Molecules can also be classified as polar or non-polar based on the distribution of electrons in
the entire structure. In general, the polarity of a molecule is based on the resultant dipole moment.
Since dipole moment is a vector quantity, to determine the resultant dipole moment of a molecule, it
is important to consider both magnitude and direction of the dipole moment. Because of this, the
arrangement of the bonds or the molecular geometry of a molecule is an important consideration in
determining its polarity. For certain molecules, even if polar bonds are present, the molecule may not
necessarily be a polar molecule.
For example, carbon dioxide (CO2) molecule has two polar bonds. Because the oxygen atom
is more electronegative than carbon, a partial negative charge is formed on oxygen and a partial
positive charge is formed on a carbon creating a dipole moment.
The two polar bonds are equal in magnitude since they are both C = 0 bonds. However, since
carbon dioxide has a linear geometry, the two dipole moments in the two bonds point in opposite
directions and cancels out. Thus, the whole molecule has a zero resultant dipole moment and is nonpolar despite having polar bonds
Carbon Dioxide Dipole Moment
In another example, the water (H2O) molecule also has two polar bonds with the partial
negative charge on oxygen and partial positive on hydrogen. Thus, the dipole moment of each O –
H bond points towards the oxygen molecule.
Like that of carbon dioxide, the two polar bonds are equal in magnitude since it involves the
same pair of elements. However, unlike carbon dioxide, the dipole moments of the two polar bonds
do not cancel each other. Looking at the bent geometry of the water molecule, there is a clear
resultant dipole moment pointing towards oxygen. Thus, water is a polar molecule.
Water Dipole Moment
Polarity is one of the key properties that define a molecule’s physical and chemical properties.
Gain better Understanding about the Lewis Structure and Molecular Geometry by
visiting this link.
https://www.youtube.com/watch?v=Sk7W2VgbhOg
https://www.youtube.com/watch?v=Q9-JjyAEqnU
https://www.youtube.com/watch?v=_Cw0_cJzkSI
23
REFLECTION
Sharing is caring. Just like chemical bonding they share what they have to balance
things in their environment. In life, we should share what we have to others who really
need a help. Sharing is caring, and caring is love.
REMINDERS
For your activity, check your Learning Kits for the required assessment for this
week. If you have any question or clarification regarding the lesson don’t
hesitate to ask, there is a space on your learning kit where you can write your
concerns. Remember, answer all the activities in an honest way. Good luck!
24
LESSON 3: Organic Compounds
LEARNING OBJECTIVES





Describe the different functional groups.
Describe structural isomerism.
Describe some simple reactions of organic compounds: combustion of organic fuels, addition,
condensation, and saponification of fats.
Describe the formation and structure of polymers.
Explain the properties of some polymers in terms of their structure.
Introduction
If you have ridden in a car or a bus,
you have used hydrocarbons. The
gasoline and diesel fuel that are
used in cars, trucks, and buses are
hydrocarbons.
Organic compounds abound in nature.
They are of great importance because of their
practical value in everyday life.
Organic substances make up the prime
necessities of man-not only food, but also
clothing and shelter. From absolute necessities,
through all the gradations to absolute luxuries,
organic substances are utilized by man. If a man
is followed through his daily life from morning to
night, it is not surprising to find that 90 percent
or more of all the materials he uses are organic
in nature.
Organic chemistry is essentially the
study carbon and its compounds, its combination
with a relatively small number of other elements,
principally hydrogen, oxygen, nitrogen, sulfur,
chlorine, phosphorus, and bromine.
HYDROCARBONS
The simplest organic compounds are hydrocarbons, which contain only the elements carbon
and hydrogen. How many different com- pounds do you think two elements can form? You might
guess that only a few compounds are possible. However, thousands of hydrocarbons are known, each
containing only the elements carbon and hydrogen. The simplest hydrocarbon molecule, CH4, consists of
a carbon atom bonded to four hydrogen atoms. This substance, called methane, is an excellent fuel and
is the main component of natural gas.
Models of Methane
25
How are hydrocarbons classified?
Hydrocarbon having only single bonds is defined as
Carbon can bond to other carbon
atoms in double and triple bonds.
These Lewis structures and structural
formulas show two ways to denote
double and triple bonds.
a saturated hydrocarbon. A hydrocarbon that has at least one
double or triple bond between carbon atoms is an unsaturated
hydrocarbon.
Aliphatic Hydrocarbons
How are various compounds formed by carbon?
Know More
Have you ever used a Bunsen burner
or an outdoor gas grill? If so, you have
used an alkane. Natural gas and
propane are the two most common
gases used in these applications, and
Alkanes
are alkanes.
hydrocarbons that contain only singlebonds.
both are
Straight-Chain Alkanes
Methane is the smallest member of a series of hydrocarbons known as alkanes. It is used as a
fuel in homes and science labs and is a product of many biological processes.
The models for ethane (C2H6), the second member of the alkane series, are shown in table.
26
Ethane consists of two carbon atoms bonded together with a single bond and six hydrogen atoms
sharing the remaining valence electrons of the carbon atoms.
The third member of the alkane series, propane, has three carbon atoms and eight hydrogen
atoms, giving it the molecular formula C3H8. The next member, butane, has four carbon atoms and
the formula C4H10. Compare the structures of ethane, propane, and butane in Table.
Propane, also known as LP (liquified propane) gas, is sold as a fuel for cooking and heating.
Butane is used as fuel in small lighters and in some torches. It is also used in the manufacture of synthetic
rubber.
SIMPLE ALKANES
Naming straight-chain alkanes
By now, you have likely noticed that names of alkanes end in -ane. Also, alkanes with five or
more carbons in a chain have names that use a prefix derived from the Greek or Latin word for the number
of carbons in each chain.
For example, pentane has five carbons just as a pentagon has five sides, and octane has eight
carbons just as an octopus has eight tentacles. Because methane, ethane, propane, and butane were
named before alkane structures were known, their names do not have numerical prefixes. Table shows the
names and structures of the first ten alkanes. Notice the underlined prefix representing the number of
carbon atoms in the molecule.
Condensed structural formulas, save space by not showing how the hydrogen atoms branch off
from the carbon atoms.
In the table, you can see that –CH2– is a repeating unit in the chain of carbon atoms. Note, for
example, that pentane has one more –CH2– unit than butane. You can further condense structural
formulas by writing the –CH2– unit in parentheses followed by a subscript to show the number of units, as
is done with octane, nonane, and decane.
A series of compounds that differ from one another by a repeating unit is called a homologous
series. A homologous series has a fixed numerical relationship among the numbers of atoms. For alkanes,
the relationship between the numbers of carbon and hydrogen atoms can be expressed as CnH2n+2, where
n is equal to the number of carbon atoms in the alkane. Given the number of carbon atoms in an alkane,
27
you can write the molecular formula for any alkane. For example, heptane has seven carbon atoms, so
its formula is C7H2(7)+2, or C7H16.
FIRST
TEN
OF
THE
ALKANE SERIES
28
Alkyl groups
An alkyl is a functional group of an organic chemical that contains only carbon and
hydrogen atoms, which are arranged in a chain.
Branched-Chain Alkanes
A branched chain alkane or branched alkane is an alkane which has alkyl groups bonded to
its central carbon chain. Branched alkanes contain only carbon and hydrogen (C and H) atoms, with
carbons connected to other carbons by single bonds only, but the molecules contain branches
(methyl, ethyl, etc.)
Now look at the two structures. If you count the carbon and hydrogen atoms, you will discover
that both structures have the same molecular formula, C4H10. If you think that the structures represent
two different substances, you are correct. The structure on the left represents butane, and the structure
on the right represents a branched-chain alkane known as isobutane—a substance whose chemical
and physical properties are different from those of butane. Carbon atoms can bond to one, two,
three, or even four other carbon atoms. This property makes possible a variety of branched-chain
alkanes.
You
have seen that
both
a
straight-chain
and
a
branchedchain alkane
can have the
same
molecular
formula. This
fact illustrates
a
basic
principle
of
organic
chemistry: the
order
and
arrangement
of atoms in an
organic
molecule
determine its
identity.
Therefore, the
name of an
organic
compound
must
also
29
—
accurately describe the molecular structure of the compound.
COMMON ALKYL GROUPS
When naming branched-chain alkanes, the longest continuous chain of carbon atoms is called
the parent chain. All side branches are called substituent groups because they appear to substitute for a
hydrogen atom in the straight chain. Each alkane-based substituent group branch- ing from the parent
chain is named for the straight-chain alkane that has the same number of carbon atoms as the substituent.
The ending -ane is replaced with the letters -yl. An alkane-based substituent group is called an alkyl group.
Naming branched-chain alkanes
To name organic structures, chemists use the following systematic rules approved by the
International Union of Pure and Applied Chemistry (IUPAC).
Step 1. Count the number of carbon atoms in the longest continuous chain. Use the name of the straightchain alkane with that number of carbons as the name of the parent chain of the structure.
Step 2. Number each carbon in the parent chain. Locate the end carbon closest to a substituent group.
Label that carbon Position 1. This step gives all the substituent groups the lowest position numbers possible.
Step 3. Name each alkyl group substituent. Place the name of the group before the name of the parent
chain.
Step 4. If the same alkyl group occurs more than once as a branch on the parent structure, use a prefix (di, tri-, tetra-, and so on) before its name to indicate how many times it appears. Then, use the number of
the car- bon to which each is attached to indicate its position.
Step 5. When different alkyl groups are attached to the same parent structure, place their names in
alphabetical order. Do not consider the prefixes (di-, tri-, and so on) when determining alphabetical
order.
Step 6. Write the entire name, using hyphens to separate numbers from words and commas to separate
numbers. Do not add a space between the substituent name and the name of the parent chain.
Example Problem:
Naming Branched-Chain Alkanes
Name the alkane shown.
30
Analyze the Problem
You are given a structure. To determine the name of the parent chain and the names and locations of
branches, follow the IUPAC rules.
Solve for the Unknown
Step 1. Count the number of carbon atoms in the longest continuous chain. Because structural formulas
can be written with chains oriented in various ways, you need to be careful in finding the longest continuous
carbon chain. In this case, it is easy. The longest chain has eight carbon atoms, so the parent name is
octane.
Step 2. Number each carbon in the parent chain. Number the chain in both directions, as shown below.
Numbering from the left puts the alkyl groups at Positions 4, 5, and 6. Numbering from the right puts alkyl
groups at Positions 3, 4, and 5. Because 3, 4, and 5 are the lowest position numbers, they will be used in the
name.
Step 3. Name each alkyl group substituent. Identify and name the alkyl groups branching from the
parent chain. There are one-carbon methyl groups at Positions 3 and 5, and a two-carbon ethyl group
at Position 4.
Step 4. If the same alkyl group occurs more than once as a branch on the parent structure, use a prefix (di-, tri-,
tetra-, and so on) before its name to indicate how many times it appears. Look for and count the alkyl groups
that occur more than once. Determine the prefix to use to show the number of times each group appears. In this
example, the prefix di- will be added to the name methyl because two methyl groups are present. No prefix is
needed for the one ethyl group. Then show the position of each group with the appropriate number.
31
Step5.Whenever different alkyl groups are attached to the same parent structure, place their names
in alphabetical order. Place the names of the alkyl branches in alphabetical order, ignoring the
prefixes. Alphabetical order puts the name ethyl before dimethyl.
Step 6. Write the entire name, using hyphens to separate numbers from words and commas to
separate numbers. Write the name of the structure, using hyphens and commas as needed. The name
should be written as 4-ethyl-3,5-dimethyloctane.
Evaluate the Answer
The longest continuous carbon chain has been found and numbered correctly. All branches have
been designated with correct prefixes and alkyl-group names. Alphabetical order and punctuation
are correct.
Cycloalkanes
One of the reasons that such a variety of organic compounds exists is that carbon atoms can form
ring structures. An organic compound that contains a hydrocarbon ring is called a cyclic hydrocarbon.
To indicate that a hydrocarbon has a ring structure, the prefix cyclo- is used with the hydrocarbon name.
Thus, cyclic hydrocarbons that contain only single bonds are called cycloalkanes.
Cycloalkanes can have rings with three, four, five, six, or even more carbon atoms. The name for
the six-carbon cycloalkane is cyclohexane. Cyclohexane, which is obtained from petroleum, is used in paint
and varnish removers and for extracting essential oils to make perfume.
Note that cyclohexane (C6H12) has two fewer hydrogen atoms than straight-chain hexane (C6H14) because
a valence electron from each of two carbon atoms is now forming a carbon-carbon bond rather than a
carbon-hydrogen bond.
Cyclohexane can berepresented in several ways.
32
Naming substituted cycloalkanes
Like other alkanes, cycloalkanes can have substituent groups. Substituted cycloalkanes are
named by following the same IUPAC rules used for straight-chain alkanes, but with a few modifications.
With cycloalkanes, there is no need to find the longest chain because the ring is always considered
to be the parent chain. Because a cyclic structure has no ends, numbering is started on the carbon
that is bonded to the substituent group. When there are two or more substituents, the carbons are
numbered around the ring in a way that gives the lowest-possible set of numbers for the substituents.
If only one group is attached to the ring, no number is necessary. The following Example Problem
illustrates the naming process for cycloalkanes.
Example Problem:
Naming Cycloalkanes
Name the cycloalkane shown.
Analyze the Problem
You are given a structure. To determine the parent cyclic structure and the location of branches,
follow the IUPAC rules.
Solve for the Unknown
Step 1. Count the carbons in the ring, and use the name of the parent cyclic hydrocarbon. In this
case, the ring has six carbons, so the parent name is cyclohexane.
Step 2. Number the ring, starting from one of the CH3— branches. Find the numbering that gives the
lowest possible set of numbers for the branches. Here are two ways of numbering the ring.
Numbering from the carbon atom at the bottom of the ring puts the CH3— groups at Positions 1, 3,
and 4 in Structure A. Numbering from the carbon at the top of the ring gives Positions 1, 2, and 4. All
other numbering schemes place the CH3— groups at higher position numbers. Thus, 1, 2, and 4 are
the lowest possible position numbers and will be used in the name.
Step 3. Name the substituents. All three are the same—carbon methyl groups.
33
Step 4. Add the prefix to show the number of groups present. Three methyl groups are present, so you
add the prefix tri- to the name methyl to make trimethyl.
Step 5. Alphabetical order can be ignored because only one type of group is present.
Step 6. Put the name together using the name of the parent cycloalkane. Use commas between
separate numbers, and hyphens between numbers and words. Write the name as 1,2,4trimethylcyclohexane.
Evaluate the Answer
The parent-ring structure is numbered to give the branches the lowest possible set of numbers. The
prefix tri- indicates that three methyl groups are present. No alphabetization is necessary because all
branches are methyl groups.
Alkenes
Unsaturated hydrocarbons that contain one or more double covalent bonds between carbon
atoms in a chain are called alkenes. Because an alkene must have a double bond between carbon
atoms, there is no 1-carbon alkene. The simplest alkene has two carbon atoms double bonded to
each other. The remaining four electrons—two from each carbon atom—are shared with four
hydrogen atoms to give the molecule ethene (C2H4).
EXAMPLE OF ALKENES
Naming alkenes
Alkenes are named in much the same way as alkanes. Their
names are formed by changing the -ane ending of the
corresponding alkane to -ene. An alkane with two carbons is
named ethane, and an alkene with two carbons is named ethene.
Likewise, a three-carbon alkene is named propene. Ethene and
propene have older, more common names: ethylene and
propylene, respectively.
To name alkenes with four or more carbons in the chain, it is
necessary to specify the location of the double bond, as shown in
the examples in Figure a. This is done by numbering the carbons
in the parent chain, starting at the end of the chain that will give
the first carbon in the double bond the lowest number. Then, use
only that num- ber in the name.
Note that the third structure is not “3-butene” because it is
identical to the first structure, 1-butene. It is important to recognize
that 1-butene and 2-butene are two different substances, each
with its own properties.
34
Naming branched-chain alkenes
When naming branched- chain alkenes, follow the IUPAC rules for naming branched-chain
alkanes, but with two exceptions. First, in alkenes, the parent chain is always the longest chain that
contains the double bond, whether or not it is the longest chain of carbon atoms. Second, the position
of the double bond, not the branches, determines how the chain is numbered.
Note that there are two 4-carbon chains in the molecule shown in Figure 21.13a, but only the
one with the double bond is used as a basis for naming. This branched-chain alkene is 2-methylbutene.
Some unsaturated hydrocarbons contain more than one double (or triple) bond. The number
of double bonds in such molecules is shown by using a prefix (di-, tri-, tetra-, and so on) before the
suffix -ene. The positions of the bonds are numbered in a way that gives the lowest set of numbers.
Which numbering system would you use in the example in Figure 21.13b? Because the molecule has
a seven-carbon chain, you would use the prefix hepta-. Because it has two double bonds, you would
use the prefix di- before -ene, giving the name heptadiene.
Adding the numbers 2 and 4 to designate the positions of the double bonds gives the name
2,4-heptadiene.
Example Problem:
Naming Branched-Chain Alkenes
Name the alkene shown.
Analyze the Problem
You are given a branched-chain alkene that contains one double bond and two alkyl groups. Follow
the IUPAC rules to name the organic compound.
Solve for the Unknown
Step 1. The longest continuous-carbon chain that includes the double bond contains seven carbons.
The 7-carbon alkane is heptane, but the name is changed to heptene because a double bond is
present.
Step 2. Number the chain to give the lowest number to the double bond.
35
Step 3. Name each substituent.
Step 4. Determine how many of each substituent is present, and assign the correct prefix to
represent that number. Then, include the position numbers to get the complete prefix.
Step 5. The names of substituents do not have to be alphabetized because they are the same. Apply
the complete prefix to the name of the parent alkene chain. Use commas between numbers, and
hyphens between numbers and words. Write the name 4,6-dimethyl-2-heptene.
Evaluate the Answer
The longest carbon chain includes the double bond, and the position of the double bond has the
lowest possible number. Correct prefixes and alkyl-group names designate the branches.
Alkynes
Unsaturated hydrocarbons that contain one or more triple bonds between carbon atoms in
a chain are called alkynes. Triple bonds involve the sharing of three pairs of electrons. The simplest
and most commonly used alkyne is ethyne (C2H2), which is widely known by its common name
acetylene.
Naming alkynes
Straight-chain alkynes and branched-chain alkynes are named in the same way as alkenes.
The only difference is that the name of the parent chain ends in -yne rather than -ene. Alkynes with
one triple covalent bond form a homologous series with the general formula CnH2n-2.
36
Properties and uses of alkynes
Alkynes have physical and chemical properties similar to those of alkenes. Alkynes undergo
many of the reactions alkenes undergo. However, alkynes are generally more reactive than alkenes
because the triple bonds of alkynes have even greater electron density than the double bonds of
alkenes. This cluster of electrons is effective at inducing dipoles in nearby molecules, causing them to
become unevenly charged and thus reactive.
Hydrocarbon Isomers
Know More
Have you ever met a pair of identical
twins? Identical twins have the same
genetic makeup, yet they are two
separate individuals with different
personalities. Isomers are similar to
identical twins- they have the same
Isomers are two or more compounds that have the same molecular formula but different
molecular formula, but different
molecular structures.
molecular structures and properties.
Structural isomers
Structural isomers have the same chemical formula, but their atoms are bonded in different
arrangements. Structural isomers have different chemical and physical properties despite having the same
formula.
37
Stereoisomers
Stereoisomers are isomers in which all atoms are bonded in the same order but are arranged
differently in space. The arrangement in which the two methyl groups are on the same side of the
molecule is indicated by the prefix cis-. The arrangement in which the two methyl groups are on
opposite sides of the molecule is indicated by the prefix trans-. These terms derive from Latin: cis means
on the same side, and trans means across from. Because the double-bonded carbon atoms cannot
rotate, the cis- form cannot easily change into the trans- form.
Isomers resulting from different arrangements of groups around a double bond are called
geometric isomers. Note how the difference in geometry affects the isomers’ physical properties, such
as melting point and boiling point. Geometric isomers differ in some chemical proper- ties as well. If
the compound is biologically active, such as a drug, the cis- and trans- isomers usually have very
different effects.
Aromatic Hydrocarbons
Know More
What do bright, colorful fabrics and
essential oils for perfumes have in
common? They both contain aromatic
hydrocarbons.
Aromatic hydrocarbons are unusually stable compounds with ring structures in which electrons are
shared bymany atoms. Organic compounds that contain benzene rings as part of their struc- tures are
called aromatic compounds. The term aromatic was originally used because many of the benzenerelated compounds known in the nineteenth century were found in pleasant-smelling oils that came
from spices, fruits, and other plant parts.
38
Naming Aromatic Compounds
Namethe aromatic compound shown.
Analyze the Problem
You are given an aromatic compound. Follow the rules to name the aromatic compound.
Solve for the Unknown
Step 1. Number the carbon atoms to give the lowest numbers possible.
As you can see, the numbers 1 and 3 are lower than the numbers 1 and 5. So the numbers
used to name the hydrocarbon should be 1 and 3.
Step 2. Determine the name of the substituents. If the same substituent appears more than
once, add the prefix to show the number of groups present.
39
Step 3. Put the name together. Alphabetize the substituent names, and use commas
between numbers and hyphens between numbers and words. Write the name as 1,3dipropylbenzene.
Evaluate the Answer
The benzene ring is numbered to give the branches the lowest possible set of numbers. The
names of the substituent groups are correctly identified.
Polymerization
Polymers are very different than the other kinds of organic molecules that you have seen so
far. Whereas other compounds are of relatively low molar mass, polymers are giant molecules of very
high molar mass. Polymers are the primary components of all sorts of plastics and related compounds.
A polymer is a large molecule formed of many smaller molecules covalently bonded to one another
in a repeating pattern. The small molecules that make up the polymer are called monomers. Polymers
are generally formed by either addition or condensation reactions. Teflon (see figure below) is a nonreactive, non-stick coating used on cookware as well as in containers and pipes for reactive or
corrosive chemicals.
Polytetrafluoroethylene (also known as Teflon) is formed from the polymerization of
tetrafluoroethylene.
Polymers
Plastic pipes usually used for plumbing are made up polyvinyl chloride, more commonly known
as PVC. It is highly durable and is resistant to fires. Because of this and its other sought after properties,
it is among the most widely used plastic materials.
PVC is an example of polymer. A polymer is a molecular compound unique for its high
molecular mass and repeating structure and can have varying physical and chemical properties.
Structure and properties
When polymeric materials were first studied, they were generally observed to display unusual
properties that can be attributed to very high molar masses. At that time, scientist thought that small
molecules formed aggregates via the use of intermolecular forces.
It was not until 1920, when Hermann Staudinger extensively studied these materials and proved
that they are not simply made up of aggregates of small molecules but rather molecules of repeating
units that are covalently bonded together and were eventually coined polymers from the Greek
words polus which means “many” and “meros” which mean “parts.”Polymers, by definition, are long
chained molecules made up of small, covalently bonded molecular units called monomers.
40
Common Synthetic Polymer and their Use
Gain better Understanding about the Organic Compounds by visiting this link.
https://www.youtube.com/watch?v=sMsNulRKViU
https://www.youtube.com/watch?v=yixbP3KPDtg
https://www.youtube.com/watch?v=_c84jxTo5bw
REFLECTION
Environmentalist. In familiarizing the common functional groups, you can explore
their properties. As part of the future generation you have to help in preserving and
conserving the environment in using these examples of functional groups in a
manner of protecting the mother Earth.
REMINDERS
For your activity, check your Learning Kits for the required assessment for this
week. If you have any question or clarification regarding the lesson don’t
hesitate to ask, there is a space on your learning kit where you can write your
concerns. Remember, answer all the activities in an honest way. Good luck!
41
42
LESSON 4: Biomolecules
LEARNING OBJECTIVES


Describe the structure of proteins, nucleic acids, lipids, and carbohydrates, and relate them
to their function.
Describe the preparation of selected organic compounds.
Introduction
Have you ever wondered how plants
process and produce food? How the
components of food help us to live
a healthy life? How the doctors and
nurses detect and cure our diseases
that, at occasions, can be life
threatening?
Biochemistry is the study of the molecular basis of
life, it studies the chemical process involved in
living organisms. It is the application of the
methods of chemistry to the fields of biology and
physiology. It is the language of biology basic to
the understanding of the different phenomena
both on the biological and medical sciences.
Biochemistry focuses on the activities that are
happening inside our cells and studies components
like proteins, lipids, and organelles.
Proteins
Know More
Some cleaning products, such as
contact lens cleaning solution, contain
enzymes. Did you ever wonder what
an enzyme
was?of chemical reaction takes place in all living organisms. These reactions are vital
A wide variety
for the survival of living things. Coordinating these intricate reactions of life are large molecules called
proteins. The word protein came from the Greek root word protos, meaning first, proteins are
macromolecules present in all living cells. About 50% of your body’s dry weight is proteins.
Proteins have many functions in living organisms. For example, proteins are the major structural
components of animal tissues. They are the key parts of the skin, nails, cartilages, and muscles. Other
proteins act as catalysts in biological reaction. Some can transport other substances like oxygen. Other
proteins serve as hormones to regulate specific process in the body. Proteins are also important in the
immune system and in tissue differentiation. Although their functions vary, all proteins are chemically
similar in that they composed of the same building blocks called amino acids. The amino acids in a
protein are joined by linkages called peptide bonds. Proteins are not just chains of amino acids that
are randomly connected. For a protein to function properly, it must be folded into a specific threedimensional structure.
43
a
b
c
d
(a)The red cell contains the protein hemoglobin that carries oxygen throughout the
body; (b) the horn of the rhinoceros is made up of keratin, a protein which is also present
in hair and nails; (c) the strength of the spider web is due to the presence of a protein
called fibroin; (d) a firefly glows because of the presence of a protein called luciferin.
Amino Acids
Amino acids are the building blocks of protein. There are at least 20 different amino acids
found in proteins. As their name imply, these compounds contain both an amino group and a
carboxylic group. The general structure of an amino acids is shown:
An amino acid has four different group attached to a central carbon atom. The four groups
are: an amino group (-NH2), a carboxylic group (-COOH), a hydrogen atom, and an R group which
represents a variable side chain group. Amino acids differ mainly on this side chain group. The R group
range from a single hydrogen atom to a complex double-ring structure. Notice that some amino acids
have nonpolar side chains, polar side chains, acidic, or basic side chains, and aromatic rings. Also,
take note of abbreviations used for these amino acids. Amino acids vary greatly in their physical and
chemical properties due to their differences in their side chains. The wide variety of the side chains of
the amino acids enables proteins to carry out so many different functions.
The 20 Common Amino Acids
44
Peptide Bond
In protein structures, the amino acids are joined together by peptide bonds. A peptide bond
is formed from the reaction between the carboxyl group of one amino acids and the amino group of
another amino acid. A peptide bond is actually an amide group.
When two amino acids form a peptide bond, the resulting molecule is called a dipeptide. The
structure of two dipeptides formed from the same amino acids – tyrosine and serine. Take note of the
order in which amino acids tyrosine and serine are linked by peptide bonds in these dipeptides. The
sequence of amino acids in protein structure is very important in determining its three-dimensional
structure.
45
Functions of proteins
Proteins are very vital for the survival of a living organism. They play major role in living cells.
Proteins can act as catalysts in biological reactions, transporters of substance, and regulatory
molecules for cellular processes. They can also serves as structural materials and energy sources when
other sources become limited.
Enzymes
One of the major functions of proteins is catalyzing biological or biochemical reactions that
occur inside a living cell. Proteins that catalyze biological reactions are called enzymes. As catalysts,
enzymes speed up the rate of a reaction without being consume in the process.
How do enzymes function? In an enzymes-catalyzed reaction, the substance that is acted
upon by an enzyme is called substrate. A substrate binds to a specific site of an enzyme called the
active site of the enzyme. The active site is usually a pocket or a crevice in the three-dimensional
structure of an enzyme. The substrate must fit into the active site in a manner similar to a key that fits a
lock for catalysis to occur. In some cases, the active site can change its shape slightly to fit more tightly
around the substrate. This recognition process is called induced fit. A molecule that cannot fit to the
active site of an enzyme is not good substrate and cannot undergo the catalyzed reaction.
When the substrate binds to the active site of the enzyme, an enzyme-substrate complex is
formed. The amino acid on the active site are very important in the formation of several intermolecular
forces of attraction between the substrate and the enzymes. These intermolecular forces lower energy
needed for the reaction to occur, thus making the reaction proceed at a faster rate.
Proteases are enzymes that catalyze the breakdown of proteins. One good example of
protease is the enzyme papain found in papayas, pineapples, and other plant sources. Papain is
utilized as meat tenderizer. When papain sis sprinkled on moist meat, it breaks down the protein
present in the meat making the meat tenderer.
The reaction between a substrate
and an enzyme. The active site of
an enzyme is like a pocket or a
crevice. The enzyme
accommodates a certain substrate
that can fit in its active site like a key
fits into a lock. An enzyme-substrate
complex is then formed and
dissociates to form the products
leaving the enzyme unchanged.
Transport Proteins
Other proteins act as transporter of small molecules throughout the body. The protein
hemoglobin carries oxygen from your lungs to the rest of your body. Myoglobin, similar to hemoglobin,
is a transporter of oxygen in the skeletal muscles. Transport proteins can also combine with other
biological molecules called lipids to transport them to different parts of the body from the
bloodstream.
46
Structural Proteins
Proteins that form structures that are necessary for living organisms are called structural
proteins. One of the most abundant structural protein found in animals is collagen. Collagen is the
major protein found in muscles, skin, ligaments, tendons, and bones. Another protein called keratin is
a structural protein found in hair, nails, fur, wool, hooves, and feathers. The protein silk produced by
silkworms and fibroin that found webs are also example of structural proteins.
Hormones
Proteins can also function as hormones. Hormones are substance that carry signals from one
part of the body to another. Some hormones are protein in nature. An example of a polypeptide
hormone is insulin. Insulin is a small protein (51 amino acids) that is produced by the cells of the
pancreas. When insulin is released into the bloodstream, it signals the body cells that the amount of
sugar in the blood is high, thus, the sugar must be stored. Lack of insulin results to a disease called
diabetes. A person with diabetes will have an elevated blood sugar level which can be very harmful.
Another example of a peptide hormone is the human chorionic gonadotropin (HCG). HCG is
produced by a developing embryo. Release of this hormone causes the development of a placenta
that gives nourishment to the embryo. The hormone is also present in the urine of a pregnant woman.
Detection of this hormone is the basis of most pregnancy test kits.
The pregnancy test kit tests for the
presence of the human chorionic
gonadotropin. A positive result is
indicated by the red bands while
single red bands indicates a
negative result.
Nucleic Acids
Know More
DNA testing is becoming more routine
in
medicine,
forensic
science,
genealogy, and identification of
victims
in
disasters.
Modern
techniques have made it possible to
get a useful DNA sample from
surprising sources, such as a strand of
hair or dried saliva on a postage
47
Nucleic acids are a class of biopolymers that serve as carrier of genetic information of
organisms. This group of nitrogen-containing compounds obtained its name from the cellular location
where they are usually found – the nucleus. Two types of nucleic acids exists, namely:
deoxyribonucleic acid (DNA) and, ribonucleic acid (RNA). DNA molecules are very large molecules
having molecular weights ranging from 6 to 16 million amu. RNA molecules is found both in the nucleus
and in the cytoplasm. Genetic information is necessary for the synthesis of proteins are stored in the
DNA. RNA carries these information stored by the DNA out of the nucleus into the cytoplasm where
proteins synthesis take place. The flow of information from DNA to RNA to protein is called is called the
central dogma of genetics.
Structure of Nucleic Acids
Nucleic are polymers whose building blocks are called nucleotides. In the structure of nucleic acids,
these nucleotides are joined together by phosphodiester bonds. A nucleotide consists of: (1) a five-carbon
sugar, (2) a phosphate group, and (3) a nitrogen containing organic base. The sugar components can be ribose
or deoxyribose. RNA contains ribose as its sugar component while DNA has deoxyribose. The nitrogenous base
can be a purine or a pyrimidine. Examples of purine bases are adenine (A) and guanine (G) while pyrimidine
bases include cytosine (C), thymine (T), and uracil (U). Aside from the sugar component, DNA and RNA also
differ in terms of the pyrimidine bases present in structures. In DNA the pyrimidine bases found are cytosine
and thymine while for RNA cytosine and uracil are found.
The structure of nucleotides showing
its three components.
The structure of ribose and
deoxyribose. The only difference is the
absence of –OH group at carbon 2 on
deoxyribose.
The structure of the purine bases
Adenine and Guanine and the Pyrimidine
bases Cytosine, Uracil and Thymine.
48
In structure of nucleic acids, the sugar of one nucleotide is connected to the phosphate group
of another nucleotide. These nucleotides from a chain or strand containing alternating sugar and
phosphate groups. The nitrogen-containing base is attached to each sugar and sticks out from the
chain. The nitrogen-containing bases on adjoining nucleotides are stacked one above the other in a
slightly slanted position which is similar to the steps in staircase.
Sugar components
Nitrogenous bases
Cellular location
DNA
Deoxyribose
A,G, C, T
Nucleus and mitochondria
RNA
Ribose
A, G, C, U
Nucleus and cytoplasm
Formation of phosphodiester bond
between the –OH groups of one nucleotide
and phosphate group of another
nucleotide. A polynucleotide showing
alternating sugar-phosphate backbone and
stacking of nitrogenous bases similar to
staircase.
Structure of the DNA: The Double Helix
DNA molecules consist of two strands of polynucleotides that are wound together in the form
of a double helix. The double helical structure of DNA was proposed by Watson and Crick. The
alternating sugar and phosphate groups in each chain are found outside and make up the backbone
of the helix. The nitrogenous bases are found inside the helix. The double helical structure of the DNA
is similar to a zipper whose two ends are twisted in opposite directions. The teeth of the zipper are the
nitrogenous bases found inside the helix. The two strand are held by hydrogen bonding interactions
among the nitrogenous bases is specific, that is purine base can only pair up with a pyrimidine base.
For example, guanine can only pair up with cytosine while adenine can only pair up with thymine. In
RNA, adenine pairs up with uracil. The G – C and A – T pairs are called complementary base pairs.
Because of this base complementarity, the amount of adenine in a molecule of DNA is the same as
the amount of thymine. Also, the amount of guanine equals the amount of cytosine in a given helical
DNA molecule. The pairing of these bases is the result of hydrogen bond formation.
49
The ribbon structure of
DNA and the space
filling model of the
double helical DNA as
proposed by Watson
and Crick.
Hydrogen bond formation
between adenine and thymine
and guanine and cytosine.
The function of DNA
The double helical model of the DNA molecule as proposed by Watson and Crick was used to
predict hoe DNA’s chemical structure enables it to carry out its function. Genetic information is stored
as specific sequence of nucleotides in the DNA molecule. Before the cell divides, copying of DNA
molecules occur so that the new generation of cells gets the same genetic information. This process
is called replication. Since the two strands making up the DNA molecule are complementary, Watson
and Crick realized that complementary base pairing provides a mechanism by which genetic
information stored in the DNA coped. Genetic information store in the DNA are like sentences. The
specific sequence of these bases represents an organism’s master instruction, similar to the sequence
of letters in a sentence that conveys a specific meaning. The sequence of bases differs from organisms
to organism, allowing for an enormous diversity of life forms. It is fascinating that in the language of the
cell only four letters are use! In a human cell it is estimated that the DNA has about three billion
complementary base pairs, arranged in a sequence unique to humans.
Ribonucleic Acid (RNA)
Another type of nucleic acid is ribonucleic acid (RNA). RNA, in contrast to DNA, is usually found
as a single stranded molecule. Whereas DNA’s main function is to store genetic information, RNA
allows cell to use information found in DNA. There are three types of RNA, namely: messenger RNA
(mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). The mRNA serves as the template for protein
50
synthesis, Amino acids are brought at the site of protein synthesis by tRNA molecules. Together with
other proteins, the rRNA molecules make up the ribosomes which are the actual sites of protein
synthesis.
You have learned that genetic information are contained in specific sequences of nucleotides
in the DNA molecule. Cells use this sequence of bases to produce RNA with a corresponding base
sequence in a process called transcription. The RNA, specifically the mRNA, is used to make proteins
through a process called translation. The amino sequence of the protein is dictated by the sequence
of bases found in the mRNA. The translation of the base-sequence of nucleic acids into the amino
acids sequence of proteins is known as the genetic code.
Carbohydrates
Know More
A lot of media attention has been
focused on carbohydrates. Low-carb
diets have become a popular way of
controlling
weight.
However,
carbohydrates are an important
energy source for the body.
Carbohydrates are important class of biomolecules that are abundantly found in plants and
animals. The name carbohydrates (hydrates of carbon) is derived from their empirical formulas:
Cn(H2O)n. For example, glucose, the most abundant carbohydrates in nature has the molecular
formula C6H12O6 or C6(H2O)6. However carbohydrates are not actually hydrates of carbon but are
polyhydroxy aldehydes or ketones or compounds that can be hydrolyzed to these compounds.
Glucose, for example, is a six-carbon aldehyde while fructose, carbohydrate found in fruits, is a sixcarbon aldehyde while fructose, a carbohydrate found in fruits, is a six-carbon ketone.
Carbohydrates are used mainly by living organisms as energy sources. This is the reason why
marathon runners eat large quantities of pasta before a big race. Our cell used glucose mainly as
immediate source of energy. Excess carbohydrates in our bodies are stored in the liver in the form of
glycogen. Starch, another example of a carbohydrate, is the storage form of glucose in plants.
Glucose
Fructose
Aldose
Ketose
51
Kinds of Carbohydrates
Monosaccharide
Monosaccharide are the simplest type of carbohydrates. They are also called simpler
sugars. The most common monosaccharide that are found in nature contain five or six
carbon atoms. These compounds contain carbonyl groups making them aldehydes or
ketones depending on the location of their carbonyl groups. Monosaccharides containing
the aldehyde group are called aldoses while those that contain the ketone group are called
ketoses. They are also characterized by the presence of hydroxyl groups (-OH) in most of their
carbon atoms. These functional groups make carbohydrates polar, water soluble, and give
them high melting point.
Glucose is an example of an aldose that contains six carbon atoms. It is found in large
concentration in the blood because it serves as the immediate source of energy in the body,
it is for this reason why glucose is oftentimes called blood sugar another example of an aldose
is galactose which is present in moist dairy products. In terms of structure, galactose differ
from glucose only in the position of the –OH group at the fourth carbon atom. The
monosaccaride fructose is an example of ketose. It is also called fruit sugar because it is
found in great quantities in fruits. Similar to glucose and galactose, fructose also contains six
carbon atoms. Glucose and fructose are functional isomers, that is, they differ in functional
group, glucose being an aldehyde and fructose being a ketone.
The structure of glucose and galactose
showing the difference in the position of –OH
group at carbon 4. Carbon 2, 3 and 5 of both
glucose and galactose have the same
arrangement of –OH and –H groups.
When monosaccharides are dissolved in water, they exits both in the open-chain structure and
in cyclic structures. Cyclization of glucose for example, occurs when the –OH group at the 5th carbon
atom (C5) of glucose reacts with the carbonyl group. This reaction is called hemiacetal formation.
Notice that in the cyclic structure, the carbonyl group, carbon 1 (C1), is converted to –OH group.
During the formation of the ring structure of glucose, the –OH group on C1 can be on the same side
of the ring as the –OH group of C2. This cyclic structure of glucose is called the 𝛼 form. The –OH group
at C1 can also be on the side of the ring giving the cyclic 𝛽 form of sugar of glucose. Although the
difference between the 𝛼 and the 𝛽 forms might seem small, it has enormous biological
consequences. As you shall soon see, this minimal change in structure accounts for the vast difference
between the structure and biological functions of starch and cellulose.
52
Disaccharides
Disaccharides are formed from the condensation reaction of two monosaccharide.
The bond between these monosaccharide is called glycosidic bond which is an ether
functional group (C – O – C).
One common disaccharide is sucrose, also known as table sugar. Sucrose is formed
by joining together glucose and fructose. Maltose, a disaccharide composed of two glucose
units, is also called mal sugar. Lactose, the disaccharide found in milk and other dairy
products, composed of the monosaccharide glucose and galactose. It is also called milk
sugar.
Disaccharides are too large to be absorbed into the bloodstream from the human
digestive system. They must be hydrolyzed to monosaccharide before they can absorbed.
Enzymes responsible for the breakdown of these disaccharides are present in the small
intestine. For example, sucrose is the enzymes that hydrolyzes sucrose to glucose and
fructose. Lactose is degraded by the enzyme lactase. Some individuals do not produce
lactase or their lactase is defective. They cannot hydrolyze lactose from their diet. When they
eat dairy products containing lactose, they suffer from bloating, flatulence, and diarrhea as
a result of accumulation of lactose in the large intestines. This condition is called lactose
intolerance.
The Structure of disaccharides sucrose, lactose, and maltose.
Polysaccharides
53
Polysaccharides are made up of several monosaccharide joined together by glycosidic bond.
Polysaccharides composed only of one type of monosaccharide are called homopolysaccharides.
Glucans are homopolysaccharides composed of glucose units only. Exam of glucans are starch,
glycogen, and cellulose. When polysaccharides are compose of more than one type of
monosaccharide, they are called heteropolysaccharides.
Starch refers to a group of polysaccharides found in plants. It is not a pure substance. Starch
serve as a major storage form of carbohydrates in plant seeds and tubers. Corms, potatoes, rice and
wheat are foods containing large amounts of starch. These plant products serve as major sources of
food energy for humans.
In terms of structure, starch is made up of two subunits – amylose and amylopectin. Amylose
is the linear subunit of starch where in the glucose units are joined by 𝛼- 1, 4-glycosidic bonds. The
glycosidic bond 𝛼- 1, 4 means that the glucose units in amylose are all in the 𝛼 form. The numbers 1
and 4 show the connection between glucose units, that is, C1 of one glucose to C4 of another
glucose. Amylopectin is the branched subunit of starch. In amylopectin, the glucose units are joined
by both 𝛼-1, 4- and 𝛼- 1, 6-glycosidic bonds. The presence of 𝛼-1, 6-glycosidic bonds gives rise to
branching. The branch points in the structure of amylopectin occurs for every 25-30 glucose units.
The structures of amylose
and amylopectin showing the
α-1, 4- and α- 1, 6-glycosidic
bonds.
Glycogen is another example of a polymer of glucose. It is the storage form of carbohydrates
in animals and humans. For humans, glycogen is found in the liver. The structure of glycogen is similar
to amylopectin, meaning it is also a branched polymer. The only difference of glycogen from
amylopectin is the degree of branching. In glycogen, the 𝛼-1, 6-glycosidic bonds occur for every 8-12
glucose units making it more branched than amylopectin.
Cellulose is a glucan which is found mainly in the cell wall of plants. It is a structural
polysaccharide whose main function is to give rigidity to plant cells. Wood and cotton fibers are
principally made up of cellulose. The structure of cellulose is similar to amylose in that they are both
linear polymers of glucose. However, in cellulose, the glucose units are joined by 𝛽-1, 4-glycosidic
bonds.
Another example of a homopolysaccharide is chitin. Chitin is a polymer of Nacetylglucosamine, a compound derived from glucose. Chitin is found in the exoskeleton of insects
54
and crustaceans. In medicine, chitin is used to make surgical thread because its flexibility and strength.
Chitin is also biodegradable, thus, it wears away as the wound heals.
The structure of cellulose showing the 𝛽-1, 4-glycosidic bonds
Structure of cellulose and starch showing the arrangement of
glucose units in space. These representation show geometrical
arrangements of bonds about each carbon atom. Notice the
difference in the orientation of glucose units in both structures.
Heteropolysaccharides are also abundant in nature as structural materials of cell and
tissues. Example of these are hyaluronic acid which is found as a lubricant in the synovial
fluid, chondroitin sulfate in cartilages, dermatan sulfate in the skin, keratin sulfate in nails and
hooves, and heparin
sulfate
How
do
fats
compare
with
oils
chemically
and
physically?
which is used as
The oily liquid that drips out your
burger, the wax that you use to polish
your shoes, and the vitamin D that
fortifies the milk you are drinking.
anticoagulant.
Lipids
Know More
The oily liquid that drips out your burger, the wax that you use to polish your shoes, and the
vitamin D that fortifies the milk you are drinking.
55
Lipids are group of compounds that are insoluble in water but are soluble in nonpolar solvents
such hexane and ether. In living organisms lipids function as secondary sources of immediate and
stored energy and they also make up of the most of the structure of the cell membrane. Unlike proteins
and carbohydrates, lipids are not polymers with repeated monomer subunits.
The grease in burger, shoe polish and Vitamin D in milk all contain lipids.
Fatty Acids
Although lipids are not polymers of specific subunits, most lipids are composed of a major
building block called fatty acids. Fatty acid are long chain carboxylic acids having the general
formula CH3(CH2)nCOOH. Most fatty acids are even chain, which is they contain even number of
carbon atoms. They can be classified as based on the presence or absence of double bonds. Fatty
acids without double bonds are called saturated fatty acids. Unsaturated fatty acids are those that
contain double bonds.
Palmitic acid is the most abundant saturated fatty acids in animals and humans. Oleic acid
is monounsaturated fatty acid which means that it contains one double bond. Linoleic acid, linolenic
acid, arachidonic acid are examples of polyunsaturated fatty acids. They are also called essential
fatty acids because they cannot be synthesized by the body. We can only obtain them from the diet.
Fatty acids can be named using shorthand notations. For example, the shorthand notation for
palmitic acid is 16:0. In this notation, the number 16 represents the number of carbon atoms of palmitic
acid. The number 0 refers to the number of double bonds, meaning palmitic acid has no double or it
is saturated. For oleic acid, the shorthand notation is 18: 1Δ9 . This notation tells you that oleic acids
contains 18 carbon atoms with one double bond. The superscript of number (Δ9) corresponds to the
position of the double bond, that is, oleic acid contains a double bond joining C9 an C10.
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Fatty acids are used as secondary sources of energy when glucose and other carbohydrates
are depleted. The oxidation of these compounds that occurs inside the mitochondrial matrix liberates
high amount of energy that can be used by the cells.
Triglycerides
Triglycerides can exist in the liquid or solid at room temperature. Fixed oils are triglycerides that
exist in the liquid state at room temperature. An exception to this Cocoa butter, also known as
theobroma oil. Cocoa butter is classified as affixed oil but it is solid at room temperature. This oil is
extracted from cocoa beans and is used to make chocolate, ointments, and other pharmaceutical
products. It is mainly composed of a triglyceride derived from plamitic acid, stearic acid, and oleic
acid. Triglycerides that exist in the solid state at room temperature are called fasts. Cod liver oil is an
exception to this. It is classified as fat but it is liquid at room temperature. This fat is derived from cod
fish. It is widely used as a food supplement because it also contains A and D.
Cocoa butter or theobroma oil is a pale-yellow vegetable fixed oil obtained from cocoa
beans. It is composed mainly of the triglycerides made from the three fatty acids
palmitic, stearic, and oleic acids.
Triglycerides are the storage forms of fatty acids in humans. In humans, stored triglycerides are
found in the adipose tissues. When energy is abundant, fats cells store the excess energy in the fatty
acids of triglycerides. During starvation or when other sources of energy are scarce, the cells break
down the triglycerides, forming free fatty acids and glycerol. Lipases are enzymes that hydrolyze
triglycerides.
The hydrolysis of triglycerides by a strong base is called Saponification. The product of this reactions
are glycerol and the salts of fatty acids. Saponification is used to make soaps. Soaps are actually
sodium salts of the fatty acids components of the triglyceride. A soap has both a polar end and a
non-polar end. Because of this structural feature, soap can be used to clean nonpolar dirt and oil with
water. The oily dirt to the polar end of the soap molecule is soluble in water. Thus, the dirt-laden soap
molecules can be rinsed with water.
Phospholipids
Phospholipids are important types of lipids that are found in large quantities of cell membranes. The
structure of a phospholipid is very similar to that of a triglyceride only that one of the fatty acids in
triglyceride is replaced by a polar phosphate group. In a phospholipid, the polar part of the molecule
forms a polar “head”, and the nonpolar fatty acids look like tails. Phospholipids make up the most
portion of the cell membrane. The cell membrane is said to be composed of a lipid bilayer wherein
the phospholipids are arranged such their nonpolar tails associate to form an inner layer and their
polar heads forming an outer layer. The lipid bilayer structure acts a barrier for the cell. It regulates the
movement of compounds in and out of the cell.
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How do waxes compare with fats in chemical composition?
Waxes
Structure of a phospholipid with its
polar head and non-polar tail.
Another type of lipid which also contains fatty acid is wax. Waxes are made up of fatty acids
combined with long-chain alcohols. Waxes are soft, solid fats low melting points.
General structure of a wax. Wax is an ester
of a fatty acid and a long-chain alcohol.
Plants as well as animals produce waxes. The honeycomb of bees is made up was called
beewax. It is made up of the 16-carbon fatty acid, palmitic acid and a 30-carbon alcohol. Beewax is
commonly used in making candles because it burns slowly and evenly. Leaves of plants are coated
with wax to prevent water loss.
The honeycomb of bees is made up of a wax commonly known as beewax. Raindrops “bead
up” on the leaves of a plant indicating the presence of the waxy layer.
Steroids
Steroids are lipids that do not contain fatty acids. They are characterized by the presence of
four-ring system in their structure. Steroids are important class of compound with many biological
functions. One common example of a steroid is cholesterol, an important component of the cell
membrane. It is also used as a precursor for the synthesis of bile acids and steroid hormones. Vitamin
D also contains the steroid ring and plays a role in calcium absorption and bone formation. Some
hormones, such as sex hormones, are steroids that function to regulate metabolic processes.
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What are the classes of biomolecules-their nature and properties?
Why are they said to be biological importance?
How are the functions of biomolecules related to their structure?
Structures of common steroids. Cholesterol is found in the cell membrane.
Too much of cholesterol in the blood can lead to heart disease. Testosterone
is a male sex hormone while progesterone is a female sex hormone.
Polarity is one of the key properties that define a molecule’s physical and chemical properties.
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Gain better Understanding about the Biomolecules by visiting this link.
https://www.youtube.com/watch?v=YO244P1e9QM
https://www.youtube.com/watch?v=H8WJ2KENlK0
REFLECTION
Physically-sound individual. God lend us a healthy life, we must take good care of
it. In studying biomolecules we explore particularly our lifestyle. We must keep
ourselves physically stable and with a balanced lifestyle.
REMINDERS
For your activity, check your Learning Kits for the required assessment for
this week. If you have any question or clarification regarding the
lesson don’t hesitate to ask, there is a space on your learning kit
where you can write your concerns. Remember, answer all the
activities in an honest way. Good luck!
REFERENCES

General Chemistry 1,2016. Rex Book Store

General Chemistry 1, 2019. Vibal

Science, 2017.Flexible Open And Distance Education Private Mail Bag


https://www.unf.edu/~michael.lufaso/chem2045/index.html
https://boisestate.pressbooks.pub/chemistry/chapter/1-3-physical-and-chemicalproperties/
https://mydigitalkemistry.com/stoichiometry-notes-full-chapter-important-questionsclass-11-chemistry-notes/
https://www.mcvts.net/cms/lib/NJ01911694/Centricity/Domain/136/chap11.pdf
https://byjus.com/chemistry/daltons-law-of-partial-pressure/
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