MODULE 1

CHAPTER I
INTRODUCTION TO BIOCHEMISTRY

INTRODUCTION
Living things are composed of lifeless molecules. When these molecules are considered
individually, they are found to conform to all the physical and chemical laws that describe the
behaviour of inanimate matter. Yet when put together in a particular manner, they start to exhibit
the different attributes of life.
The smallest collection of molecules that exhibits the attributes of life is the living cell. It
feeds, respires, digests, excretes, moves, and reproduces.
In this module, we shall acquaint ourselves with the structure and biochemical activities
of living cells. It appears to be a logical first activity in our attempt to understand the chemistry
of biomolecules and ultimately, the living state.

LEARNING OUTCOMES
At the end of this unit, you should be able to:
 enumerate the attributes of living matter
 distinguish between prokaryotes and eukaryotes
 identify the important organelles of the cell
 enumerate the biochemical systems present in each organelle
 correlate each part with its function
 name the common elements required by living organisms
 enumerate the building blocks of biopolymers
 describe the four classes of biopolymers

LEARNING CONTENTS
1. IDENTIFYING CHARACTERISTICS OF LIVING MATTER
 HIGH DEGREE OF ORGANIZATION
Living matter is complicated and highly organized. Living organisms possess intricate
internal structures and contain many types of complex molecules, that play specific functions. In
contrast, contains much simpler chemical compounds of random mixtures.

 ABILITY TO EXTRACT, TRANSFORM AND USE ENERGY FROM THEIR

ENVIRONMENT

Food as energy source

All living things need food as their source of energy for all body activities. Plants make
their own food from water and carbon dioxide with the aid of sunlight while animals get their
food by eating plants and other animals.
 Respiration
Living organisms respire to get energy from food. Usually, this process involves taking in
oxygen and giving out carbon dioxide.

Waste disposal
Feeding and respiration also produce waste substances. Getting rid of them is called
excretion. Plants excrete through their leaves. Animals do it in various ways.

Movement
All living things move, though some, like plants, usually move too slowly for us to see.
Most animals can move their whole bodies so that they can go from place to place. This is called
locomotion.

 GROWTH
All living things grow. Trees keep on growing throughout their lives while others, like us,
reach a certain size and then stop. Inanimate objects are not capable of growth.

 REPRODUCTION
Perhaps the most extraordinary attribute of living organisms that differentiates them from
non-living things is their capacity to self-replicate, that is, to produce new versions of
themselves.

2. DIVERSITY AMONG CELLS

Cells are the smallest units that are capable of life. The smallest organisms consist of single cells,
while the human body is believed to contain at least 1014 cells, which are grouped into tissues and
organs. There are many different types of cells that are usually highly specialized. One type may
carry messages, another tense a muscle, one may deliver oxygen, another gobble bacteria. These
specialized cells cannot maintain themselves independently. Each cell depends on its neighbors
for some of its own needs. The miracle of the human body, or of any complex organism, is the
coordination of this fantastic number of cells.

The Cell Theory states that:

1. All living things are composed of a cell or cells. Fig
1-1.
2. Cells are the basic unit of life. The cells
3. All cells come from preexisting cells.

Cells within the same organism show Enormous Diversity in:

 Size
 Shape
 Internal Organization
1. Cell Size
 Female Egg - largest cell in the human body; seen without the aid of a microscope
 Most cells are visible only with a microscope.
Reason 1:
 limited in size by the ratio between their outer surface area and their volume. 
 a small cell has more surface area than a large cell for a given volume of cytoplasm. 
This is important because the nutrients, oxygen, and other materials a cell requires
must enter through its surface.  As a cell grows larger at some point its surface area
becomes too Small to allow these materials to enter the cell quickly enough to meet the
cell's need.
Reason 2:
 The cell's nucleus (the brain) can only control a certain amount of living, active
cytoplasm

2. Cell Shape
 Diversity of form reflects a diversity of
function.
 The shape of a cell depends on its function.

Fig. 1-2. Cell

shapes

3. Internal Organization

Two Basic Types Of Cell

Living cells exist in two basic patterns: prokaryotes and eukaryotes. These two terms are
derived from the Greek word karyon, “nut” or “kernel”, i.e. nucleus. Prokaryotic means “before
the nucleus” while eukaryotic “well formed nucleus”.
The characteristics that distinguishes one cell type from the other is the complexity of
their cellular organization. The eukaryotic cell possesses a membrane-bound nucleus while
prokaryotic cell does not.
1. PROKARYOTES
Prokaryotes are usually smaller and are
considered the first type of cells to arise in
biological evolution. They include bacteria,
blue-green algae, rickettsiae, and spirochetes
within the cell membrane of prokaryote is the
cytoplasm where the nuclear material,
ribosomes, and other nutrients are indistinctly
spread out. There is, therefore, little that could
be called internal structure in prokaryotic cells.
 Fig. 1-3. The Bacterial Cell
(Not all bacteria have capsule)

2. EUKARYOTE
Eukaryotes, on the other hand, are much larger than prokaryotes. Their volume is 1,000
to 10,000 times greater. The eukaryotes include green algae, fungi, protozoans and all other
plants and animals. They exhibit a high degree of organization by way of membrane enclosed
subcellular structures called organelles which have distinct features, composition, and its
functions.

Two Kinds:
Plant and Animal Cells

Compare and Contrast

Table 1-1 Summary of the features of cell organelles including their functions and composition.

Schematic drawing Molecular composition Properties and

functions
The nucleus, about 4 mm During mitosis,
in diameter, is surrounded chromosomes undergo
by a perinuclear envelope. replication of their DNA
The DNA within is and separation into
combined with histones daughter chromosomes.
and organized into
chromosomes. The
Nucleus nucleolus is rich in RNA.

There are about 800 The mitochondria are the

mitochondria in each power plants of the cell,
hepatocyte. They are where carbohydrates,
globular and a little over 1 lipids, and amino acids
mm in diameter, are oxidized to CO2 and
occupying about 20% of H2O by molecular
the cytoplasmic volume. oxygen, and the energy
Mitochondrion Their outer and inner set free is converted into
membranes differ in lipid the energy of ATP. The
composition and in enzymes of electron
enzymatic activity. The transport and energy
matrix is rich in enzymes. conversion are located in
the inner membrane.
Chloroplast The cells of higher plants Chloroplast are receptors
characteristically contain of light energy, which
plastids, membrane- they convert into the
surrounded organelles chemical energy of ATP
some of which possess a for the biosynthesis of
distinctive DNA. Those glucose and other organic
containing chlorophyll are biomolecules from
called chloroplasts. carbon dioxide, water,
Chloroplast are relatively and other precursors.
large compared to Oxygen is generated
mitochondria. There may during plant
be one, several, or many photosynthesis.
chloroplasts per cell, Chloroplast are the main
depending on the species; source of energy of
they may assume different photosynthetic cells in the
forms. light.

Ribosomes
Each E. Coli bacterial cell Ribosomes are the sites
contains about 15,000 of protein synthesis.
ribosomes. Each ribosome Messenger RNA binds in
has a large and a small sub the groove between the
unit. Each subunit subunits and specifies the
contains about 65% RNA sequence of amino acids
and 38% protein. in the growing
polypeptide chains.
Golgi complex The Golgi complex A series of flattened sacs
consists of flattened, that modifies, packages,
single-membrane vesicles, stores, and transports
which are often stacked. materials out of the cell.
Small vesicles arise Works with the
peripherally by a ribosomes and
pinching-off process.
Endoplasmic Reticulum.
Some become vacuoles in
which secretory products The Golgi apparatus
are concentrated. functions in the secretion
of cell products, such as
proteins, to the exterior.
Lysosomes Lysosomes are single- Lysosomes function in
membrane vesicles, 0.25- the digestion of materials
0.5 mm in diameter brought into the cell by
containing hydrolytic phagocytosis or
enzymes, such as pinocytosis. They also
ribonuclease and serve to digest cell
phosphatase. components after cell
death.
Cell wall and membrane The plant cell wall is The cell wall protects the
thick, rigid, and fibrils cell membrane from
encased in a cement of mechanical or osmotic
polysaccharides and rupture, firmly fixes the
proteins. position of the cell, and
confers physical shape
and strength upon plant
tissue.
The cell membrane or The cell membrane of
plasma membrane is the plant cell is selective in
boundary of the cell. permeability, containing
Composed of three active-transport systems
distinct layers - 2 layers for specific nutrients and
of fat and 1 layer of inorganic ions and also
protein certain enzymes.

Two types:
Complex network of 1. Smooth- ribosome
transport channels. free and functions in
poison detoxification.
2. Rough - contains
ribosomes and releases
newly made protein
from the cell

Centrioles Found only in animal Role in building cilia and

cells flagella
Paired organelles found Play a role in cellular
together near the nucleus, reproduction
at right angles to each
other.

Vacuoles
Found mostly in plants
and protists Sacs that help in food
Tonoplast also called digestion or helping the
vacuolar membrane is cell maintain its water
the cytoplasmic balance.
membrane surrounding
the vacuole separaing
the vacuolar contents
from the cell’s
cytoplasm.
 Cytoskeleton Framework of the cell They support the cell,
Contains small giving it its shape and
microfilaments and help with the movement
larger microtubules. of its organelles.

By way of an analogy, try to imagine a cell as a sort of factory. Figure 1-3 illustrates
the various cell organelles and their respective counterparts in a factory in operation.
Each part has a special job to do.

Figure 1-4. The Living Factory

3. CHEMICAL MAKEUP OF LIVING CELLS
The chemical makeup of all organisms appears to have been determined by the
availability of raw materials in the environment and by the fitness of the atoms for specific roles.

 Elemental Composition
Most cells and for that matter, most organisms are composed of only sixteen chemical elements
as shown in Table 1-2.

Table 1-2. Elements Found In Organisms

Major element Atomic number Trace elements Atomic number

(all organisms)
H 1 Mn 25
C 6 Fe 26
N 7 Co 27
O 8 Cu 29
P 15 Zn 30
S 16
Monoatomic ions (all organisms) Trace elements (some organisms)
Na+ 11 B 5
Mg++ 12 Al 13
Cl 17 Si 14
K+ 19 V 23
Ca++ 20 Mo 42
I 53

About 99 percent of the mass of most cells is provided by Hydrogen (H), Oxygen (O),
Carbon (C), and Nitrogen (N). Two other elements often found in organic matter are
Phosphorous (P) and Sulfur (S). Besides these six elements, five monoatomic ions and at least
eleven trace elements are known to be required for life processes.

 Fitness considerations
To answer the question, “only the aforementioned sixteen, and not the other elements?”,
the following merits of the bio-elements may be considered:

1. H, O, N and C are the smallest atoms so that they form more stable covalent bonds than
any other elements. Moreover, O, N, and C readily form multiple bonds C with four
valence electrons and the ability to form both C=C bonds, has the most versatile
 combining properties. With H, O, and N, C can form a tremendous variety of stable
molecules.
2. Bonds formed by P and S on the other hand are often unstable in the presence of water so
that considerable energy is required to form them. When these bonds are hydrolyzed P-
and S- containing molecules such as adenosine triphosphate (ATP) and coenzyme A
release considerable amounts of energy so that they are aptly called energy carriers of
living systems.
3. The ions like Na+, K+ , Ca++ and Mg++ are responsible for maintenance of osmotic balance,
the formation of ionic gradients in nerve conduction and active transport.
4. Fe and Cu can exist as stable ions in either of two oxidation states and are therefore well
suited in biological redox reactions.

 Noncovalent Bonds Of Importance In Biological Structures

In addition to the covalent bonds that predominate in biomolecules, 4 kinds of non-

covalent interactions are important in biological systems.

Ionic bonds resulting from oppositely charged groups such as carboxyl (-COO-) and
amino (-NH3+) in proteins.
Hydrogen bonds (H-bonds) a residual intermolecular force between a H atom that is
covalently bonded to electronegative atom (N or O) and another N or O either in the same
molecule or one nearby.
Van der Waal’s forces (London forces) are short-range attractive forces between
chemical groups in contact. They are much weaker than H-bonds, but they contribute
significantly to the stability of biological structures because of the abundance of Van der Waal’s
contacts.
Hydrophobic interactions the association of nonpolar groups with each other in aqueous
systems because of the tendency of the surrounding water molecules to seek their most stable
state.

 The Macromolecule of Life

More than 90% of the dry weight of most organisms are macromolecules. These are
giant molecules having molecular weights in the range of a few thousands to many millions. This
is so because they are in fact large polymers of one or a few similar kinds of precursor molecules
as building block units linked together into large repeating structures. The four major classes of
macromolecules are.

Proteins are polymers of amino acids, linked by peptide bonds. They are also called
polypeptide. They play a variety of important roles in organisms.
Nucleic acids, RNA and DNA, are polymers of nucleotides linked by phosphodiester
bonds. The nucleotide sequence in these polymers spells out the genetic information that directs
growth, development, and reproduction.
Carbohydrates also known as polysaccharides are polymers of monosaccharides or
simple sugars linked by glycosidic bonds. They serve primarily as storage sources of energy in
plants (starch) and animals (glycogen), and as structural elements in plants.
 Lipids are water-insoluble biomolecules that can be extracted by non-polar solvents. In a
strict sense, lipids cannot be categorized among the three other classes, since they are
heterogenous assembles of very dissimilar units like fatty acids, glycerol, choline, nitrogenous
bases, steroids, and many more. They are only lumped together by virtue of their solubility.
Lipids are principal sources of energy (triacylglycerols or neutral fats), responsible for the
integrity of cellular membranes (phospholipids), hormones (sex hormones, progesterone) and
vitamins (A, D, E, and K).

These biomolecules appear to be most versatile and most fitted for their functions in
cells. Their size, shape, and surface characteristics are important in the specificity of their
biological interactions as well as in their role as building blocks of structural machineries of
cells. Hence, they give cells superior survival value.

SUMMARY
Cells are the simplest structural and functional units of living organisms. The two basic
classes of cells are called prokaryotic and eukaryotic. The characteristics distinguishing the
two cell types is the complexity of their cellular organization, with the prokaryote having simpler
features.
Living matter requires only a few of the common chemical elements. The four elements
carbon, hydrogen, nitrogen, and oxygen make up 99 percent of the total mass of most living
organisms. These four elements together with phosphorous and sulfur are the constituents of
the building block molecules such as amino acids, nucleotides, sugars, and also fatty acids.
They in turn are linked together to form various macromolecules, the proteins, nucleic acids,
carbohydrates and lipids.

KEY TERMS/CONCEPTS

1 mm (millimeter) = 10-3m (meter) Biomolecules

1 μm (micrometer) = 10-6m macromolecules
1 nm (nanometer) = 10-9m proteins
1 A (angstrom) = 10-8cm or 10-10m peptide bonds
ionic bonds nucleic acids
covalent bonds carbohydrates
Hydrogen bonds polysaccharides
Van der Waal’s forces lipids
hydrophobic interaction

FLEXIBLE TEACHING LEARNING MODALITY (FTLM)

 Module, Edmodo, Google Meet, Exercises

TEACHING AND LEARNING ACTIVTIES

CELL EXPLORATION ACTIVITIES

This worksheet contains different activities that are all about cells. Cells are the basic unit
of living matter because they perform all the processes collectively called life. Although most
individuals’ cells are visible only with the aid of a microscope, while some maybe a meter long
(e.g., Nerve cells) or as large as small orange. Despite these differences, all cells are designed
similarly and share a variety of features.

HOW BIG IT IS?

Part A. Here you will look at objects by searching the INTERNET. Your job is to rank
them in order of size on the chart below and estimate the length of each (in nanometers,
micrometers or millimeters). In comparing, see to it that all of them have the same unit

OBJECT SKETCH SIZE RANK

(1-smallest,
7- largest)
Human hair

Dust mite

Red blood cells

E. coli

Staphylococcus

Ebola virus

Rhinovirus

Part B. BACTERIAL CELL MODEL. Label the numbered parts on each line.
LEARNING MATERIALS AND RESOURCES
 Videos
 Introduction to biochemistry https://www.youtube.com/watch?v=tpBAmzQ_pUE
 Types of Cells
https://study.com/academy/lesson/eukaryotic-and-prokaryotic-cells-
similarities-and-differences.html
 Transport in Cells: Diffusion and Osmosis https://www.youtube.com/watch?
v=PRi6uHDKeW4

 Molecular Models

ASSESSMENT TASK
On the lines below, write about what you’ve learned by doing the activities in this packet. Be
as specific as possible and use COMPLETE SENTENCES.

1. Let me tell you about some of the important things I’ve learned about cells. First, I’ll start
with….
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2. Next, I’ll tell you about….
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__________________________________________________________

3. Something else I learned was……

______________________________________________________________________________
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______________________________________________________________________________
______________________________________________________________________________
__________________________________________________________

4. Lastly, I now really know about and understand ……………

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
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REFERENCES
Berg, J.M., Tymoczko, J.L. and Stryer, L. (2011) Biochemistry. Freemann, 7th edition, retrieved
at http://www.whfreeman.com

Brown, P. (2009). Quick Reference to Wound Care, James and Bartelt. Publishing

Chulay, M. (2011).ACCN Essentials of Critical Care Nursing. McGraw-Hill Publishing

Hein, Morris (2005). Introduction to General, Organic and Biochemistry, John Wiley and Sons

Jones, Evangeline. (2011). Manual of Practical Medical Biochemistry.

Moore, John (2008). Chemistry: The Molecular Science . Thomson Brooks

Nelson, D.L. & Cox, M.M. Lehninger. ( ). Principles of Biochemistry. Freeman, 6th edition
http://bcs.whfreeman..com./lehninger6e/#t_824263/

Silberberg, M. (2010). Principles of General Chemistry. Mc Graw Hill

Voet, J. and Judith Voet. (2011) Biochemistry, 4th Edition. Wiley and Sons