SOUTHERN BAPTIST COLLEGE

MLANG, COTABATO
REGION XII

TABLE OF CONTENTS

GENERAL CONCEPTS AND STS HISTORICAL DEVELOPMENTS

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 INTRODUCTION TO THE
CHAPTER STUDY OF CELL AND
MOLECULAR BIOLOGY
1

1.1 DISCOVERIES OF CELL

1.2 BASIC PROPERTIES OF CELL

1.3 TWO FUNDAMENTALLY DIFFERENT CLASSES OF CELL

1.4 VIRUSES

ACTIVATING PRIOR KNOWLEDGE

Using the Venn Diagram, identify the similarities and differences of Eukaryotic Cell
and Prokaryotic Cell.

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 Learning Competencies

After studying this chapter, you should be able to:

a. Define what is cell.

b. Identify the basic properties of Cell.
c. Discuss the two fundamental classes of cell.
d. Explain the characteristic of Virus.
e. Relate the importance of Cell in the totality of living organism.

PRE-ASSESSMENT

Direction: Complete the following table by writing the name of the cell part or organelle
in the right-hand column that matches the structure or function in the left-hand
column. A cell part may be used more than once.

Structure Cell Organelle

Produces a usable form of energy for the
cell.
Digest excess or worn-out cell parts, food
particles, and invading viruses or bacteria.
Packages proteins for transport out of the
cell.
Provides temporary storage of food,
enzymes, and waste products.
The membrane surrounding the cell.

CONCEPT MAP

INTRODUCTION TO THE STUDY OF CELL AND MOLECULAR BIOLOGY

BASIC
DISCOVERY OF PROPERTIES OF CLASSES OF
CELLS CELL CELLS

VIRUSES

LEARNING ACTIVITY SEQUENCE

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 LESSON 1.1: THE DISCOVERY OF CELLS

A cell is the basic structural and functional unit of all life forms. Moreover,
all living things on Earth are made up of one or more cells. Organisms with a single
cell are known as unicellular organisms, such as bacteria. Furthermore, most
unicellular organisms are classed as microorganisms. In comparison, organisms
with two or more cells are called multicellular organisms, such as plants and
animals. The number of cells in plants and animals can vary from species to
species.

WHO DISCOVERED THE CELL?

In 1665, a scientist named Robert

Hooke made the first discovery of cells. He
was able to discover the cell because of
the invention of the microscope. Robert
Hooke’s microscope was a recreation of
Anton van Leeuwenhoek’s microscope
with 300 times magnification. After he
invented the microscope, he made
numerous observations, and one
observation was from very thin slices of a bottle cork. During Hooke’s observation of
thin slices of a bottle cork, he discovered a multitude of tiny pores. He named
them cells. The name ‘cell’ came from the Latin word ‘Cella’, meaning ‘a small
room’. Furthermore, it resembles cells inhabited by Christian monks in a
monastery. The name also came from the word ‘Cellulae’, which meant the six-sided
cell of a honeycomb.

CELL THEORY

Theodor Schwann and Matthias Jakob Schleiden are two scientists who first
developed the cell theory in 1839. Although one more scientist named Rudolf

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Virchow also contributed to the theory. However, his contribution to the theory was
not recognized.

Schleiden suggested that every structural part of a plant was made up of cells.
In addition, he also suggested that a crystallization process either within other cells
or from the outside made cells. On the other hand, Theodor Schwann states that
the structures of animals are also composed of cells. From these conclusions
about plant and animal cells, two principles of the cell theory were postulated. They
are:
 All living organisms are made up of one or more cells.
 The cell is the basic unit of structure and organization in organisms.
Later in 1855, Rudolf Virchow added the third principle to the cell theory, i.e.,

 All cells arise from pre-existing cells.

LESSON 1.2: BASIC PROPERTIES OF CELL

Cells have a life of their own, much like plants and animals do. Cells are the
smallest units to demonstrate life, which is the most fundamental characteristic of all
living things. Whole cells from a plant or animal can be taken out and grown in a lab,
where they will thrive and multiply for a long time, unlike the portions of a cell that
simply degrade if isolated. Neglecting them could result in death. The fact that only
living things experience death makes it one of life's most fundamental characteristics.

THE FIRST CULTURE OF HUMAN CELL

George and Martha Gey of Johns Hopkins University started the first human cell
culture in 1951. The cells were taken from a cancerous tumor and were given the
moniker HeLa cells in honor of the donor, Henrietta Lacks. HeLa cells, which
descended from this initial cell sample through cell division, are still being produced in
labs all over the world today. Cells cultivated in vitro, or in culture, outside the body,
have become a crucial tool for cell and molecular biologists because they are so much
easier to examine than cells found inside the body.

BASIC PROPERTIES OF CELL

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  Cells Are Highly Complex and Organized.

- Every level exhibits a high degree of uniformity. When seen under a powerful
electron microscope, each type of cell has a consistent look; that is, each
individual member of a species has a unique set of organelles with a specific
form and location. Similarly, the composition of macromolecules within each
type of organelle is constant and organized in a known manner.

 Cells Possess a Genetic Program and the Means to Use it.

- The information contained in a group of genes, which are made of DNA, is used
to build organisms. Without any known exception, every living cell on Earth
stores its genetic material in double-stranded DNA molecules. In multicellular
organisms, DNA directs the growth, development, and maintenance of tissues
and organs. The act of reproduction allows DNA instructions to be passed down
(inherited) from one generation to the next. Genes serve as the instructions for
carrying out cellular functions, the blueprints for building cellular structures,
and the recipe for self-replication. Genetic information can undergo changes
(mutations) due to the molecular structure of genes, which results in individual
variety and serves as the foundation for biological evolution.

 Cells are capable of Producing More of Themselves.

- Individual cells are created by reproduction, just like individual creatures are.
When a cell divides, the contents of the "mother" cell are divided between the
two "daughter" cells. The genetic material is duplicated before division, and each
daughter cell receives an exact and equal share of the genetic material.

 Cells Acquire and Utilize Energy

- Energy is a necessary input for all creatures to sustain the life process. For an
organism to grow and maintain itself, it must be able to absorb and transform
energy from its environment. This phenomenon is referred to as metabolism in
biology. The cells spend a tremendous amount of energy merely disassembling
and reassembling the macromolecules and organelles that make them up during
metabolism. This ongoing "turnover," as it is known, keeps cell parts intact
despite unavoidable wear and tear and enables the cell to react quickly to
changing circumstances.

 Cells Carry Out a Variety of Chemical Reactions

- The way that cells work is similar to a little chemical plant. A bacteria cell can
undergo hundreds of various chemical transformations, even in its most basic
form. All of these chemical alterations occur within cells where enzymes are
present. The molecules known as enzymes significantly speed up the rate at
which a chemical reaction takes place. The totality of a cell's chemical processes
is that cell's metabolism.

 Cells Engage in Mechanical Activities

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 - The interior of cells is a hive of activity. Materials are moved from one location
to another, molecules and structures are quickly put together and taken apart,
and in many instances, the entire cell moves itself from one location to another.
These processes entail dynamic mechanical adjustments within cells, many of
which are triggered by modifications in the structure of "motor" proteins. Motor
proteins are just one of many different kinds of molecular "machines" that cells
use to perform mechanical tasks.

 Cells Are Able to Respond to Stimuli

- Organisms continually detect changes in their environment and respond to

them in a controlled way. Through their receptors, they sense the environment
and react accordingly. Homeostasis is the term for this interaction between cells
and their surroundings. A single-celled protist, such as an amoeba, travels away
from obstacles in its path or in the direction of a food source. The majority of
cells are covered in receptors, which respond to environmental elements in very
particular ways. Cells have receptors for chemicals on the surfaces of other cells
as well as for hormones, growth factors, and extracellular materials. Target cells'
receptors offer channels through which external stimuli might elicit certain
responses. Cells may change their metabolic processes or relocate in response to
particular stimuli.

 Cells Are Capable of Self-Regulation

- Cells are strong because they are shielded from harmful changes in behavior
and composition. When there is a change, the feedback circuits kick in and help
the cell get back to where it should be. Energy is needed, but regular regulation
is also necessary to sustain a complex, organized state.

 Cells Evolve

- Cells are said to have originated from a type of precellular life form that itself
descended from nonliving organic substances that were present in the first
oceans. It is possible to study the evolution of cells by looking at currently
existing species. Modern biology holds that all living things descended from a
single, common ancestral cell that existed more than three billion years ago.
Evolution is a process that continues to alter the characteristics of cells that will
be found in organisms that have not yet materialized; it is not only a historical
occurrence.

LESSON 1.3: TWO FUNDAMENTALLY DIFFERENT CLASSES OF CELLS

Once the electron

microscope became widely
available, biologists were able
to examine the internal
structure of a wide variety of
cells. It became apparent from
these studies that there were
two basic classes of cells—
prokaryotic and eukaryotic—
distinguished by their size and
the types of internal structures,
or organelles, they contain. The
existence of two distinct classes of cells, without any known intermediates, represents
one of the most fundamental evolutionary divisions in the biological world. The

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structurally simpler, prokaryotic cells include bacteria, whereas the structurally more
complex eukaryotic cells include protists, fungi, plants, and animals.

CHARACTERISTICS THAT DISTINGUISH PROKARYOTIC AND

EUKARYOTIC CELLS

The following brief comparison between prokaryotic and eukaryotic cells reveals
many basic differences between the two types, as well as many similarities. The
similarities and differences between the two types of cells are listed below. The shared
properties reflect the fact that eukaryotic cells almost certainly evolved from prokaryotic
ancestors.

FEATURES HELD IN COMMON BY THE TWO TYPES OF CELLS:

 Plasma membrane of similar construction
 Genetic information encoded in DNA using identical genetic code
 Similar mechanism for transcription and translation of genetic information,
including similar ribosomes
 Shared metabolic pathways (e.g., glycolysis and TCA cycle)
 Similar apparatus for conservation of chemical energy as ATP (located in the
plasma membrane of prokaryotes and the mitochondrial membrane of
eukaryotes)
 Similar mechanism of photosynthesis (between cyanobacteria and green
plants)
 Similar mechanism for synthesizing and inserting membrane proteins
 Proteasomes (protein digesting structures) of similar construction (between
archaebacteria and eukaryotes).

FEATURES OF EUKARYOTIC CELLS NOT FOUND IN PROKARYOTES:

 Division of cells into nucleus and cytoplasm, separated by a nuclear envelope

containing complex pore structures
 Complex chromosomes composed of DNA and associated proteins that are
capable of compacting into mitotic structures
 Complex membranous cytoplasmic organelles (includes endoplasmic
reticulum, Golgi complex, lysosomes, endosomes, peroxisomes, and
glyoximes)
 Specialized cytoplasmic organelles for aerobic respiration (mitochondria) and
photosynthesis (chloroplast)
 Complex cytoskeletal system (including microfilaments, intermediate filaments,
and microtubules) and associated motor proteins
 Complex flagella and cilia
 Ability to ingest fluid and particulate material by enclosure within plasma

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 membrane vesicles (endocytosis and phagocytosis)
 Cellulose-containing cell walls (in plants)
 Cell division using a microtubule-containing mitotic spindle that separates
chromosomes
 Presence of two copies of genes per cell (diploidy), one from each parent
 Presence of three different RNA synthesizing enzymes (RNA polymerases)
 Sexual reproduction requiring meiosis and fertilization

 Earth’s biological clock.

A portrait of the past five billion years of Earth’s history showing a proposed time of
appearance of major groups of organisms. Complex animals (shelly invertebrates) and
vascular plants are relatively recent arrivals. The time indicated for the origin of life is
speculative. In addition, photosynthetic bacteria may have
arisen much earlier, hence the question mark. The geologic
eras are indicated in the center of the illustration.

 The
structure of a eukaryotic cell.
This epithelial cell lines the male reproductive
tract in the rat. A number of different organelles
are indicated and depicted in schematic
diagrams around the border of the figure.

 The cytoplasm of a eukaryotic cell

is a crowded compartment.
This colorized electron micrographic image
shows a small region near the edge of a
single-celled eukaryotic organism that had
been quickly frozen prior to microscopic
examination. The three-dimensional
appearance is made possible by capturing
two-dimensional digital images of the
specimen at different angles and merging the
individual frames using a computer.
Cytoskeletal filaments are shown in red,
macromolecular complexes (primarily
ribosomes) are green, and portions of cell
membranes are blue.

 Cell division in eukaryotes

Requires the assembly of an elaborate
chromosome-separating apparatus called
the mitotic spindle, which is constructed
primarily of microtubules. The microtubules

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in this micrograph appear green because they are bound by an antibody that is linked
to a green fluorescent dye. The chromosomes, which were about to be separated into
two daughter cells when this cell was fixed, are stained blue.

TYPES OF PROKARYOTIC CELLS

Prokaryotes are divided into two major taxonomic groups, or domains: the Archaea
(or archaebacteria) and the Bacteria (or eubacteria). Members of the Archaea are more
closely related to eukaryotes than they are to the other group of prokaryotes (the
Bacteria).

 Domain Archaea
The domain Archaea includes
several groups of organisms whose
evolutionary ties to one another are
revealed by similarities in the
nucleotide sequences of their
nucleic acids. The best known
Archaea are species that live in
extremely inhospitable
environments; they are often
referred to as “extremophiles.”
Included among the Archaea are
the methanogens [prokaryotes
capable of converting CO2 and H2 gases into methane (CH4) gas]; the halophiles
(prokaryotes that live in extremely salty environments, such as the Dead Sea or certain
deep sea basins that possess a salinity equivalent to 5M MgCl2); acidophiles (acid-
loving prokaryotes that thrive at a pH as low as 0, such as that found in the drainage
fluids of abandoned mine shafts); and thermophiles (prokaryotes that live at very high
temperatures). Included in this last-named group are hyperthermophiles, which live in
the hydrothermal vents of the ocean floor. The latest record holder among this group
has been named “strain 121” because it is able to grow and divide in superheated water
at a temperature of 121°C, which just happens to be the temperature used to sterilize
surgical instruments in an autoclave.

 All other prokaryotes are

classified in the domain
Bacteria.
This domain includes the smallest
known cells, the mycoplasma (0.2
µm diameter), which are the only
known prokaryotes to lack a cell
wall and to contain a genome with
as few as 500 genes. Bacteria are
present in every conceivable habitat
on Earth, from the permanent ice
shelf of the Antarctic to the driest
African deserts, to the internal
confines of plants and animals.
Bacteria have even been found living in rock layers situated several kilometers beneath
the Earth’s surface. Some of these bacterial communities are thought to have been cut

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off from life on the surface for more than one hundred million years. The most complex
prokaryotes are the cyanobacteria.

 Cyanobacteria
Cyanobacteria contain elaborate arrays of
cytoplasmic membranes, which serve as sites
of photosynthesis. The membranes of
cyanobacteria are very similar to the
photosynthetic membranes present within
the chloroplasts of plant cells. As in
eukaryotic plants, photosynthesis in
cyanobacteria is accomplished by splitting
water molecules, which releases molecular
oxygen. Many cyanobacteria are capable not
only of photosynthesis, but also of nitrogen
fixation, the conversion of nitrogen (N2) gas into reduced forms of nitrogen (such as
ammonia, NH3) that can be used by cells in the synthesis of nitrogen containing
organic compounds, including amino acids and nucleotides. Those species capable of
both photosynthesis and nitrogen fixation can survive on the barest of resources—light,
N2, CO2, and H2O. It is not surprising, therefore, that cyanobacteria are usually the
first organisms to colonize the bare rocks rendered lifeless by a scorching volcanic
eruption.

TYPES OF EUKARYOTIC CELLS: CELL SPECIALIZATION

The most complex eukaryotic cells are

not found inside of plants or animals, but
rather among the single-celled
(unicellular) protists. All of the
machinery required for the complex
activities in which this organism engages
—sensing the environment, trapping
food, expelling excess fluid, evading
predators—is housed within the confines
of a single cell.

MODEL ORGANISM

Escherichia coli is a rod-shaped

bacterium that lives in the digestive tract of
humans and other mammals. Much of what
we will discuss about the basic molecular
biology of the cell, including the mechanisms
of replication, transcription, and translation,
was originally worked out on this one

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prokaryotic organism. The relatively simple organization of a prokaryotic cell is
illustrated in this electron micrograph (compare to part of a eukaryotic cell).

Saccharomyces cerevisiae, more commonly

known as baker’s yeast or brewer’s yeast. It is the
least complex of the eukaryotes commonly
studied, yet it contains a surprising number of
proteins that are homologous to proteins in
human cells. Such proteins typically have a
conserved function in the two organisms. The
species has a small genome encoding about 6200
proteins; it can be grown in a haploid state (one
copy of each gene per cell rather than two as in
most eukaryotic cells); and it can be grown under either aerobic (O2-containing) or
anaerobic (O2-lacking) conditions. It is ideal for the identification of genes through the
use of mutants.

Arabidopsis thaliana, a member of a genus of

mustard plants, has an unusually small genome (120
million base pairs) for a flowering plant, a rapid
generation time, and large seed production, and it
grows to a height of only a few inches.

Caenorhabditis elegans, a microscopic sized

nematode, consists of a defined number of cells
(roughly 1000), each of which develops according
to a precise pattern of cell divisions. The animal is
easily cultured, has a transparent body wall, a
short generation time, and facility for genetic
analysis. This micrograph shows the larval nervous
system, which has been labeled with the green
fluorescent protein (GFP). The 2002 Nobel Prize
was awarded to the researchers who pioneered its
study.

Drosophila melanogaster, the fruit fly, is a

small but complex eukaryote that has been a
favored animal for genetic study for nearly 100
years. The organism is also well suited for the
study of the molecular biology of development
and the neurological basis of simple behavior.

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Certain larval cells have giant chromosomes, whose individual genes can be identified
for studies of evolution and gene expression.

Mus musculus, the common house mouse, is easily kept

and bred in the laboratory. Thousands of different genetic
strains have been developed, many of which are stored
simply as frozen embryos due to lack of space to house the
adult animals. The “nude mouse” pictured here develops
without a thymus gland and, therefore, can accept human
tissue grafts that are not rejected.

THE SIZES OF CELLS

The figure above shows the relative size of a number of structures of interest in cell
biology. Two units of linear measure are most commonly used to describe structures
within a cell: the micrometer (µm) and the nanometer (nm). One µm is equal to 10^-6
meters, and one nm is equal to 10^-9 meters. The angstrom (Å), which is equal to one-
tenth of a nm, is commonly employed by molecular biologists for atomic dimensions.
One angstrom is roughly equivalent to the diameter of a hydrogen atom. Large biological
molecules (i.e., macromolecules) are described in either angstroms or nanometers.
Myoglobin, a typical globular protein, is approximately 4.5 nm X 3.5 nm X 2.5 nm;
highly elongated proteins (such as collagen or myosin) are over 100 nm in length; and
DNA is approximately 2.0 nm in width. Complexes of macromolecules, such as
ribosomes, microtubules, and microfilaments, are between 5 and 25 nm in diameter.
Despite their tiny dimensions, these macromolecular complexes constitute remarkably
sophisticated “nanomachines” capable of performing a diverse array of mechanical,
chemical, and electrical activities. Cells and their organelles are more easily defined in
micrometers. Nuclei, for example, are approximately 5–10 µm in diameter, and
mitochondria are approximately 2 µm in length. Prokaryotic cells typically range in length from
about 1 to 5 µm eukaryotic cells from about 10 to 30 µm. There are a number of reasons
most cells are so small.

LESSON 1.4: VIRUSES

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 Viruses Small, obligatory intracellular pathogens that are not considered to be
alive because they cannot divide directly, which is required by the cell theory of life.
Viruses are tiny infectious agents that rely on living cells to multiply. They may use an
animal, plant, or bacteria host to survive and reproduce. As such, there is some debate
as to whether or not viruses should be considered living organisms. A virus that is
outside of a host cell is known as a virion.

Louis Pasteur.

During the mid- to late 19th century

Pasteur demonstrated that microorganisms
Dmitri Ivanovsky cause disease and discovered how to make
vaccines from weakened, or attenuated,
Ivanovsky, a Russian biologist, forced theHe
microbes. sapdeveloped the earliest vaccines
from a damaged plant through filters with pores so
against fowl cholera, anthrax, and rabies.
small that they prevented the passage of the tiniest
known bacterium in order to get more
understanding of the size and nature of the
infectious agent. Since the filtrate was still
infectious, Ivanovsky came to the conclusion that
some diseases were brought on by pathogens that
were smaller and more likely simpler than the
smallest known bacteria. These germs were later
dubbed viruses.

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  Wendell Stanley of the Rockefeller Institute discovered that the tobacco mosaic
disease virus could crystallize and that the crystals were contagious in 1935.
Crystal-forming substances have a highly organized, clearly defined structure
and are considerably less complex than the most basic cells. Stanley believed
the tobacco mosaic virus (TMV) to be a protein, which was incorrect. TMV is
actually a rod-shaped particle with a single RNA molecule inside of a helical
shell made of protein components.

 Numerous human diseases,

including AIDS, polio, influenza,
cold sores, measles, and a few
types of cancer, are brought on by
viruses. The shapes, sizes, and
structures of viruses vary greatly,
yet they all share a few
fundamental characteristics. Since
all viruses must exist inside of a
host cell in order to proliferate,
they are all necessary intracellular
parasites. Depending on the virus,
the host could be a bacterial cell,
plant, or animal. The virus only
exists as a particle, or virion, which
is essentially a macromolecular bundle, outside of a living cell.

A little quantity of genetic material, either single-stranded, double-stranded, RNA, or

DNA, depending on the virus, is present in the virion. Surprisingly, whereas some
viruses may only have three or four distinct genes, others may have several hundred. A
protein capsule, or capsid, surrounds the virion's genetic material. Virions are
macromolecular aggregates, inert particles incapable of reproducing, metabolizing, or
engaging in any of the other life-related functions on their own. Because of this, viruses
are not regarded as beings and are not referred to as being alive.

Bacteriophages, also known as phages, are

viruses that infect and replicate only in bacterial
cells. They are ubiquitous in the environment
and are recognized as the most abundant
biological agent on earth. They are
extremely diverse in size, morphology, and
genomic organization. However, all consist of a
nucleic acid genome encased in a shell of phage-

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encoded capsid proteins, which protect the genetic material and mediate its delivery
into the next host cell. Electron microscopy has allowed the detailed visualization of
hundreds of phage types, some of which appear to have "heads," "legs", and "tails".
Despite this appearance, phages are non-motile and depend upon Brownian motion to
reach their targets. Like all viruses, bacteriophages are very species-specific with regard
to their hosts and usually only infect a single bacterial species or even specific strains
within a species. Once a bacteriophage attaches to a susceptible host, it pursues one of
two replication strategies: lytic or lysogenic. During a lytic replication cycle, a phage
attaches to a susceptible host bacterium, introduces its genome into the host cell
cytoplasm, and utilizes the ribosomes of the host to manufacture its proteins. The host
cell resources are rapidly converted to viral genomes and capsid proteins, which
assemble into multiple copies of the original phage. As the host cell dies, it is
either actively or passively lysed, releasing the new bacteriophage to infect another host
cell. In the lysogenic replication cycle, the phage also attaches to a susceptible host
bacterium and introduces its genome into the host cell cytoplasm. However, the phage
genome is instead integrated into the bacterial cell chromosome or maintained as an
episomal element where, in both cases, it is replicated and passed on to daughter
bacterial cells without killing them. Integrated phage genomes are termed prophages,
and the bacteria containing them are termed lysogens. Prophages can convert back to a
lytic replication cycle and kill their host, most often in response to changing
environmental conditions.

LEARNING EXERCISES:

Instruction: Define the following terms.

1. CELL
_______________________________________________________________________________
_______________________________________________________________________________
______________

2. EUKARYOTIC CELL
_______________________________________________________________________________
_______________________________________________________________________________
______________
3. PROKARYOTIC CELL
_______________________________________________________________________________
_______________________________________________________________________________
______________
4. VIRUSES
_______________________________________________________________________________
_______________________________________________________________________________
______________

APPLICATION

I. Explain the importance of cell in an organism and discuss why is it important to

study cell until now.
______________________________________________________________________________________
______________________________________________________________________________________
______________________________________________________________________________________
______________________________________________________________________________________

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______________________________________________________________________________________
______________________________________________________________________________________
______________________________

II. Instructions: In a long size bondpaper, draw the eukaryotic cell, prokaryotic cell
and a bacteriophage virus. Label each part of the cell, and write a short
desccription about each cell.

GENERALIZATION

 The cell theory has three tenets. (1) All organisms are composed of one or
more cells; (2) the cell is the basic organizational unit of life; and (3) all cells
arise from preexisting cell.
 A number of characteristics can be used to characterize the characteristics
of life as shown by cells. The substructure of cells is highly ordered and
predictable, and they are incredibly complicated. A cell's genes contain the
instructions needed to develop the cell. Cells divide to create new cells, are
powered by chemical energy, carry out chemical reactions that are controlled by
enzymes, perform a variety of mechanical tasks, respond to stimuli, and exhibit
an impressive degree of self-regulation.
 Eukaryotic or prokaryotic are the two types of cells. Only archaebacteria
and eubacteria have prokaryotic cells; all other types of life, including protists,
fungi, plants, and animals, are made up of eukaryotic cells. Numerous
similarities exist between prokaryotic and eukaryotic cells, including their
cellular membranes, systems for storing and utilizing genetic information, and
metabolic processes. Prokaryotic cells are the less complex form because they
lack the complex membrane organelles, chromosomes, and cytoskeleton seen in
eukaryotic cells, such as the endoplasmic reticulum, Golgi complex,
mitochondria, and chloroplasts. The two types of cells can also be separated
based on how they divide, how they move, and what kind of cell wall they make,
if one is there. Complex plants and animals have a wide variety of cells, each
specialized for different functions.
 The size of cells is almost universally tiny. Eukaryotic cells normally measure
10 to 30 µm, but bacterial cells typically measure 1 to 5µm. For several reasons,
cells are minuscule in size: their nucleus only contain a certain number of
copies of each gene; the surface area, which serves as the cell's exchange
surface, becomes constrained as a cell enlarges, and the space between the cell
surface and interior gets too large for the needs of the cell to be satisfied by
basic diffusion.
 As noncellular pathogens, viruses can only procreate when existing inside a
live cell. The virus resides in the outside world as a Virion, a large molecular
package. Viruses can be found in several shapes and sizes, but they are all
made up of encased viral nucleic acid. in an envelope made of viral proteins.
Viral infections could result in Either (1) the host cell is destroyed together with
the production of viral offspring, or (2) viral nucleic acid is integrated entering
the host cell's DNA, which frequently modifies the functions of that cell. Viruses
are not thought of as living things.

BIBLE INTEGRATION

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 John 14:6 – “Jesus saith unto him, I am the way, the truth, and the life: no man
cometh unto the Father, but by me.”

EVALUATION

I. Instructions: Label the parts of the animal cell and plant cell.

II. Instructions: Answer the following questions briefly.

1. What are the three principles of cell theory?

_______________________________________________________________________________
_______________________________________________________________________________
______________
2. Are viruses regarded as non-living or living organisms?
_______________________________________________________________________________
_______________________________________________________________________________
______________

REFERENCES

Fechheimer, M. (2000b). Cell and Molecular Biology: Concepts and Experiments. Gerald
Karp. The Quarterly Review of Biology, 75(4), 454. https://doi.org/10.1086/393652

Patra, S. (2023b, January 25). Discovery of Cell: History, Cell Theory and Types Embibe.
Embibe Exams. https://www.embibe.com/exams/discovery-of-cell/

More, H. (2019b, June 20). 9 Important Characteristics of Cell with explanations. The
Fact Factor. https://thefactfactor.com/facts/pure_science/biology/characteristics-of
cell/1529/

Viruses. (n.d.-b). https://education.nationalgeographic.org/resource/viruses/

Kasman, L. M. (2022b, September 26). Bacteriophages. StatPearls - NCBI Bookshelf.

https://www.ncbi.nlm.nih.gov/books/NBK493185/

AUTHOR 18
Prepared by:
Kyla C. Alcosaba, BSED Gen. Science

CHECKED AND APPROVED BY

Checked and Approved by:

Prof. Joscel P. Enardecido M.Sc.

19
 CHAPTER THE CHEMICAL

2 BASIS OF LIFE

2.1 COVALENT BOND

2.2 NONCOVALENT BOND

2.3 ACIDS, BASES, AND BUFFERS

2.4 NATURE OF BIOLOGICAL MOLECULES

2.5 FOUR TYPES OF BIOLOGICAL MOLECULES

2.6 FORMATION OF COMPLEX

ACTIVATING PRIOR KNOWLEDGE

WORD SCAPE: Encircle the words you found inside the box.

W D M O L E C U L E S P
D A U H I O L Q R B N O
K C T S A W F S M A L L
Learning Competencies
L I F E D A E W V X P A
Y D W Q R G B B D A U R
After studying E
this Schapter,
W HyouJshould
R beA able
U to:
I O T I
W Q E T C S S U Y S E T
a. Define
F covalent
Q Y I bondsK and
O E noncovalent
P L Ebonds.
W Y
I R Y acids,
b. Differentiate T W Q and
bases, S G H J
buffers. S T
c. Discuss the nature of biological molecules.Y W
O C O V A L E N T T
P Q W R F C A F N Y M Q
d. Identify the four types of biological molecules.
e. Discuss the formation of complex macromolecular structures. 20
IDENTIFICATION: Identify what is being asked in the following sentences.

1. The type of chemical bond in which electron pairs are shared

between two atoms.
2. A relatively weak chemical bond based on attractive forces
between oppositely charged regions within a molecule or between
two nearby molecules.
3. A molecule that is capable of releasing a hydrogen ion.
4. Compounds that can interact with either free hydrogen or
hydroxyl ions, minimizing a change in pH.
5. Any molecule that is capable of accepting a hydrogen ion.

CONCEPT MAP

LEARNING ACTIVITY SEQUENCE

LESSON 2.1: COVALENT BOND

A particular kind of
chemical bond is a polar bond.
It might be regarded to be the
boundary between the

21
development of an electrovalent bond and a pure chemical bond. A polar chemical
bond, on the other hand, is a link that exists between two atoms and is made up of
electrons that are scattered unevenly, if we were to define it more precisely. This state
causes the molecules to have an electrical moment where the two ends are slightly
positive or negative. The many kinds of covalent bonds are mostly determined by the
electronegativity of the bond. An atom's propensity to pull a shared pair of electrons
toward itself is known as electronegativity. It is not a unit. It is known as a polar
chemical bond when two atoms in a molecule with an electronegative difference come
into contact with one another. Let's first go over the characteristics of covalent bonds
before talking about the polar covalent bond.

Two nonmetal atoms with various electronegativity levels produce polar covalent
bonds. Let's take into account A and B, which have a chemical link between them and
an electronegativity difference that is not equal to zero. The common pair of electrons
that connect A and B migrate in the direction of electronegative B. B then receives a
partial charge and reaches "A." A becomes partially charged, acquiring two charges
(forming poles and known as a dipolar molecular, dipole, or polar covalent molecule),
similar to how H and Cl are charged. The shared pair of electrons in this molecule
travels towards a chlorine atom with a high electronegative potential. A dipole is created
as a result of the H-atom receiving a partial positive charge and the Cl-atom receiving a
partial negative charge.

PROPERTIES OF COVALENT BOND

 Covalent bonds are very powerful chemical bonds that exist between atoms.
 Covalent bonds do not form new electrons. The bond only pairs electrons.
 Covalent bonds very rarely break spontaneously after being formed.
 Covalent bonds are directional where the atoms that are bonded showcase
specific orientations relative to at least one another.
 Most compounds that have covalent bonds have relatively low melting points
and boiling points.

 Compounds with covalent bonds usually have lower enthalpies of vaporization

and fusion.

 Covalent compounds don’t conduct electricity due to the shortage of free

electrons.

 Covalent compounds are not soluble in water.

TYPES OF COVALENT BOND

 SINGLE BONDS

A single bond is formed when only one pair of electrons is shared between the
two participating atoms. It is represented by one dash (-). Although this form of covalent
bond has a smaller density and is weaker than a double and triple bond, it is the most
stable. For example, the HCL molecule has one hydrogen atom with one valence
electron and one chlorine atom with seven valence electrons. In this case, a single bond
is formed between hydrogen and chlorine by sharing one electron.

22
  DOUBLE BONDS

When two pairs of electrons are shared by the two participating atoms, a double
bond is created. The symbol for it is two dashes (=). Although less stable, double
covalent bonds are substantially more powerful than single ones. A carbon dioxide
molecule, for instance, comprises two oxygen atoms with four valence electrons each
and one carbon atom with six valence electrons. Carbon shares two of its valence
electrons with one oxygen atom and two with another oxygen atom to complete its octet.
There are two double bonds in carbon dioxide because each oxygen atom shares its two
electrons with a carbon atom.

Oxygen Molecule: In the formation of the oxygen molecule, each oxygen atom has six
electrons in its valence shell. Each atom requires two more electrons to complete its
octet. Therefore, the atoms share two electrons each to form the oxygen molecule. Since
two electron pairs are shared, there is a double bond between the two oxygen atoms.

Ethylene Molecule: In ethylene, each carbon atom shares two of its valence electrons
with two hydrogen atoms and the remaining two electrons with the other carbon atom.
So, there is a double bond between the carbon atoms.

 TRIPLE BONDS

23
 When three pairs of electrons are shared by the two participating atoms, a triple
bond is created. The least stable type of covalent bonds are triple bonds, which are
denoted by three dashes (≡). For instance, each nitrogen atom, which has five valence
electrons, contributes three electrons to form three electron pairs, which are then
shared during the construction of a nitrogen molecule. The two nitrogen atoms thus
create a triple bond.

LESSON 2.2: NONCOVALENT BOND

The bond in which no sharing of electron pairs

takes place is called a non-covalent bond. It occurs
mostly between the macromolecules and is weaker than
the covalent bond. When two atoms share electrons
evenly, a type of chemical bond known as a non-polar
covalent bond is created. The number of electrons
shared by the neighboring atoms in an atom will
therefore be equal. Because of the largely insignificant
difference in electronegativity, the covalent bond is also
referred to as nonpolar. It also implies that there is no
charge gap between the two atoms or that their
electronegativity is similar. A similar kind of link is
created when atoms that are connected by a polar bond arrange themselves so that
their electric charges tend to cancel one another out. A non-polar covalent bond can
form between two non-metal atoms that are the same or different.

TYPES OF NONCOVALENT BOND

HYDROGEN BOND: An electronegative atom with a lone pair of electrons and a

hydrogen atom that are bound together create a hydrogen bond, an intermolecular force
that creates a dipole-dipole attraction. For instance, the water molecule's V-bent form
causes nearby positive hydrogen atoms to be drawn to slightly negative oxygen atoms.

24
IONIC BOND: The strongest noncovalent connection is an ionic bond, which is formed
between two ionic groups of molecules with opposing charges. Ionic bonds can be
divided into two categories: ion-dipole interactions and dipole-dipole interactions, which
include charged ions and polar molecules, respectively. As an illustration, the ionic link
between sodium cation and chloride anion forms salt.

VANDER WAALS BOND: This is a weak bond formed by the shifting of the electron
density between two nonpolar molecules.

POLAR VS. NON-POLAR

PROPERTIES OF WATER

 POLARITY

The electron density is unevenly distributed because water is a polar molecule. Water
has partial positive charges (+) close to the hydrogen atoms and partial negative charges
(-) close to the oxygen atoms because there are unshared pairs of electrons in the water.
Electrical attraction between the partial positive charge close to the hydrogen atoms
and the partial negative charge close to the oxygen atoms results in the formation of a
hydrogen bond. Because of their polarity, ions and other compounds can dissolve in
water.

 UNIVERSAL SOLVENT

The fact that water dissolves more compounds than any other chemical has earned it
the moniker "universal solvent." The polarity of each water molecule is the cause of this.
Each water molecule has an electric charge on the side of the hydrogen atom that is
slightly positive and one on the side of the oxygen atom that is slightly negative. Ionic
chemicals are split up into positive and negative ions in water thanks to this. Ionic

25
compounds have positive and negative halves that are drawn to opposite sides of water:
the positive halves to the oxygen side and the negative halves to the hydrogen side.

 HIGH BOILING POINT

The ability of water molecules to form hydrogen bonds. Despite having a low molecular
weight, its 100°C boiling point is very high. This is due to the fact that water must first
waste additional energy to dissolve its hydrogen bonds before it can begin to boil.

 HIGH FREEZING POINT

Water ecosystems rely on the extraordinarily slow boiling and freezing rates of water
molecules, which are made possible by the high boiling and low freezing temperatures
of water. Extreme environmental changes would destroy water bodies like oceans and
lakes and lead to the extinction of all aquatic life if freezing or boiling water were a fairly
simple process. Sweat can also help our bodies cool off for this reason. Let's look at how
water's boiling and freezing points differ from those of the majority of other substances.

 HIGH SPECIFIC HEAT

Compared to other common materials, water has a substantially larger specific heat
capacity. The earth's temperature is kept temperate by the high specific heat of water
because it absorbs heat during the day and releases it gradually at night. The result is
that the temperature on the surface of the globe does not change significantly, with
extremes of 134°F and -129°F.

 HIGH DENSITY

Less dense items feel lighter and tend to float, whereas denser objects feel heavier and
tend to sink. Density is defined as the ratio of mass to volume. Most items' densities
alter slightly as temperature changes.

 HIGH CAPILLARITY

Without capillary action, trees and plants would not be able to survive. It aids in raising
water to the roots. Water can move all the way up to the branches and leaves with the
aid of adhesion and cohesion. You should still care about capillary action in your life
even if you've never heard of it. Water (and everything dissolved in it) can be moved
around thanks to capillary action. It is described as the movement of water caused by
the forces of adhesion, cohesion, and surface tension within the pores of a porous
material.

 HIGH SURFACE TENSION

Due to the cohesive nature of its molecules, surface tension is a property of a liquid's
surface that enables it to resist an external force. Each solution exhibits different
surface tension qualities because these forces differ depending on the type of liquid (for
example, water vs. gasoline) or solutes in the liquid (surfactants like detergent).

 COHESION

26
The ability of water molecules to hold themselves together in a drop is due to cohesion,
which is the intermolecular forces between like molecules.

 ADHESION

Water molecules are drawn together by cohesion, but they are also attracted to the
walls of a narrow vessel. The outcome is capillary action, where the fluid is drawn
higher by the force of adhesion.

LESSON 2.3: ACID, BASE, AND BUFFERS

Atomic nuclei contain protons, but they are also expelled into the surrounding space if
a hydrogen atom loses a shared electron. Consider acetic acid, the key component of
vinegar, which can experience the dissociation detailed below.

ACID AND BASE

An acid is a molecule that has the ability to release (donate) a hydrogen ion. In the
previous process, the proton produced by the acetic acid molecule does not stay in the
free state; instead, it reacts with another molecule. A proton's possible responses
include the following:

 Combination with a water molecule to form a hydronium ion (H3O+).

 Combination with a hydroxyl ion (OH-) to form a molecule of water.

 Combination
with an amino group (ONH2) in a
protein to form a charged
amine.

 THE pH SCALE

27
The pH scale is used to rank solutions in terms of acidity or basicity (alkalinity). Since
the scale is based on pH values, it is logarithmic, meaning that a change of 1 pH unit
corresponds to a ten-fold change in H++start superscript, plus, end superscript ion
concentration. The pH scale is often said to range from 0 to 14, and most solutions do
fall within this range, although it’s possible to get a pH below 0 or above 14. Anything
below 7.0 is acidic, and anything above 7.0 is alkaline, or basic.

BUFFERS

The majority of species, including humans, require a pH range that is quite small in
order to exist. For instance, even when acidic or basic chemicals enter or exit the
bloodstream, human blood must maintain a pH of 7.4 and avoid moving noticeably
higher or lower. Buffers, solutions that can resist changes in pH, are key to
maintaining stable H+ ion concentrations in biological systems. When there are too
many H+ ions, a buffer will absorb some of them, bringing pH back up; and when there
are too few, a buffer will donate some of its own H+ ions to reduce the pH. Buffers
typically consist of an acid-base pair, with the acid and base differing by the presence
or absence of a proton (a conjugate acid-base pair). For instance, one of the buffers
that maintain the pH of human blood involves carbonic acid (H2CO3) and its conjugate
base, the bicarbonate ion (HCO3-). Carbonic acid is formed when carbon dioxide enters
the bloodstream and combines with water, and it is the main form in which carbon
dioxide travels in the blood between the muscles (where it’s generated) and the lungs
(where it’s converted back into water and CO2, which is released as a waste product).

If too many H+ ions build up, the equation above will be pushed to the right, and
bicarbonate ions will absorb the H+ to form carbonic acid. Similarly, if H+
concentrations drop too low, the equation will be pulled the left and carbonic acid will
turn into bicarbonate, donating H+ ions to the solution. Without this buffer system, the
body’s pH would fluctuate enough to put survival in jeopardy.

LESSON 2.4: THE NATURE OF BIOLOGICAL MOLECULES

Biological molecules are the massive molecules required for life that are constructed
from smaller organic components. Carbohydrates, lipids, proteins, and nucleic acids are
the four main types of biological macromolecules. Each is a vital part of the cell and
carries out a variety of tasks. These molecules make up the vast bulk of a cell's dry
mass when combined. Organic macromolecules, such as those found in living things,
include carbon atoms bound to hydrogen, as well as possible tiny amounts of oxygen,
nitrogen, and other elements.

FUNCTIONAL GROUPS

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Many of the crucial organic compounds for biology include carbon atom chains similar
to hydrocarbons, but certain hydrogen atoms have been substituted by other functional
groups. Functional groups are specific collections of atoms that frequently act
collectively and give organic compounds their physical properties. characteristics,
chemical reactivity, and solubility in water.

29
Ester bonds, which form between carboxylic acids and alcohols, and amide bonds,
which form between carboxylic acids and amines, are two of the most frequent
couplings between functional groups.

A CLASSIFICATION OF BIOLOGICAL MOLECULES BY FUNCTION

Based on their function in metabolism, the organic compounds that are frequently
found inside living cells can be categorized into a number of categories.

1. MACROMOLECULES

Large, intricately organized molecules known as

macromolecules, which can have a large number of carbon
atoms (dozens to millions), are what give cells their structure
and function. Some of these molecular giants are incredibly
precise and efficient at carrying out difficult tasks due to
their size and the diverse shapes that they can adopt. More
than any other feature, the presence of macromolecules gives
organisms their ability to function as living things and
chemically differentiates them from the non-living
environment. The four main groups of macromolecules are
proteins, nucleic acids, polysaccharides, and specific lipids. The first three varieties are made up
of a many monomers, or small-molecule building units. These macromolecules are made from
monomers using a polymerization process that is similar to attaching railroad cars to a train. All
creatures share the same fundamental macromolecular structure and function. The diversity
across species is not readily apparent until you examine the particular sequences of monomers
that make up individual macromolecules.

2. THE BUILDING BLOCKS OF MACROMOLECULES

With the exception of the cell's DNA, the majority of the

macromolecules within a cell have a short lifespan relative to
the cell itself; they are continuously degraded and replaced by
new macromolecules. Therefore, a supply (or pool) of low-
molecular-weight precursors that are prepared to be integrated
into macromolecules is present in the majority of cells. These
include fatty acids, which are integrated into lipids, sugars,
which are the precursors of polysaccharides, amino acids,
which are the precursors of proteins, and nucleotides, which
are the precursors of nucleic acids.

3. METABOLIC INTERMEDIATES (METABOLITES)

Since the molecules in a cell have intricate chemical

structures, they must be created step-by-step from particular
starting elements. Each chain of chemical processes that takes place
within a cell is known as a metabolic pathway. Compound A is first
transformed by the cell into compound B, which is then compound B
to compound C, and so forth, until a functional end product is
created, such as the amino acid building blocks of proteins.

30
Metabolic intermediates are substances that form along the pathways that lead to the final
products but may not necessarily have any purpose.

4. MOLECULES OF MISCELLANEOUS FUNCTION

This is obviously a broad category of molecules but not

as large as you might expect; the vast bulk of the dry weight of
a cell is made up of macromolecules and their direct
precursors. The molecules of miscellaneous function include
such substances as vitamins, which function primarily as
adjuncts to proteins; certain steroid or amino acid hormones;
molecules involved in energy storage, such as ATP; regulatory
molecules such as cyclic AMP; and metabolic waste products
such as urea.

LESSON 2.5: FOUR TYPES OF BIOLOGICAL MOLECULES

Biological molecules are the massive molecules required for life that are constructed from smaller
organic components. Carbohydrates, lipids, proteins, and nucleic acids are the four main types of
biological molecules. Each is a vital part of the cell and carries out a variety of tasks. These
molecules make up the vast bulk of a cell's dry mass when combined. Organic molecules, such as
those found in living things, include carbon atoms bound to hydrogen, as well as possible tiny
amounts of oxygen, nitrogen, and other elements.

CARBOHYDRATES

The majority of consumers have

some familiarity with the
macromolecules known as
carbohydrates. Some people follow
"low-carb" diets to lose weight.
Contrarily, athletes frequently "carb-
load" before significant contests to
make sure they have the energy to
compete at a high level. In truth, we
need carbohydrates in our diet; they
may be found naturally in grains,
fruits, and vegetables. The body
uses carbohydrates for energy,
especially the simple sugar glucose. Additionally essential roles for humans, animals, and plants
are played by carbohydrates. Carbohydrates can be represented by the formula (CH 2O)n,
where n is the number of carbon atoms in the molecule. In other words, the ratio of
carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are
classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides are simple sugars, of which glucose is the most prevalent (mono- =
"one"; sacchar- = "sweet"). Three to six carbon atoms are typically seen in
monosaccharides. Names of monosaccharides typically end in -ose. They may be
referred to as trioses (three carbon atoms), pentoses (five carbon atoms), or hexoses (six
carbon atoms), depending on how many carbon atoms are present in the sugar. In
aqueous solutions, monosaccharides are typically found as ring-shaped molecules but
can also exist as a linear chain.

The chemical formula for glucose is C6H12O6. In most living species, glucose is an
important source of energy. During cellular respiration, energy is released from glucose,
and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize

31
glucose using carbon dioxide and water by the process of photosynthesis, and the
glucose, in turn, is used for the energy requirements of the plant. The excess
synthesized glucose is often stored as starch that is broken down by other organisms
that feed on plants. Other typical monosaccharides include fructose (found in fruit) and
galactose, which are both components of lactose, or milk sugar. Although all three
sugars share the same chemical formula (C6H12O6), glucose, galactose, and fructose
differ structurally and chemically (and are referred to as isomers) due to different
groupings of atoms in the carbon chain.

Disaccharides (di- = “two”) form when two

monosaccharides undergo a dehydration reaction (a
reaction in which the removal of a water molecule
occurs). During this process, the hydroxyl group (–
OH) of one monosaccharide combines with a
hydrogen atom of another monosaccharide, releasing
a molecule of water (H2O) and forming a covalent
bond between atoms in the two sugar molecules. The
disaccharides lactose, maltose, and sucrose are
typical examples. The monomers glucose and
galactose combine to form the disaccharide known
as lactose. It naturally occurs in milk. Maltose, often
known as malt sugar, is a disaccharide that results
from the dehydration of two molecules of glucose. Sucrose, or table sugar, which is
made up of the monomers glucose and fructose, is the most popular disaccharide.

A polysaccharide is a lengthy chain of monosaccharides joined together by covalent

bonds (poly- meaning "many"). The monosaccharides in the chain could be of different
sorts and could be branched or unbranched. Molecular sizes of polysaccharides can be
enormous. The polysaccharides starch, glycogen, cellulose, and chitin are examples of.

Plants store carbohydrates as starch, which is

composed of the glucose polymers amylose and
amylopectin. Glucose can be produced by plants, and
any extra glucose is stored as starch in various plant
components, including the roots and seeds. Animals
ingest starch, which is broken down into smaller
molecules like glucose. The glucose can subsequently
be absorbed by the cells.

32
 In humans and other vertebrates, glucose is stored in
the form of glycogen, which is composed of glucose
monomers. Glycogen, a very branched molecule that is
often retained in muscle and liver cells, is the animal
analogue of starch. Glycogen is broken down to release
glucose whenever blood glucose levels drop.

One of the most prevalent natural biopolymers

is cellulose. Plants' cell walls, which provide
the cell its structural support, are primarily
formed of cellulose. The majority of wood and
paper's makeup is cellulosic. Glucose
monomers that are connected by bonds
between certain carbon atoms in the glucose
molecule make up cellulose.

In various species, carbohydrates have additional

purposes. Exoskeletons, which are found on
arthropods like insects, spiders, and crabs, serve
to protect the internal body sections of these
creatures. A nitrogenous carbohydrate called
chitin, a biological macromolecule, makes up this
exoskeleton. It is composed of nitrogen-containing
modified sugars in repeating units.

LIPIDS

Lipids are made up of a wide range of different molecules that share a characteristic.
Due to the nonpolar nature of lipids, which are hydrophobic ("water-fearing") molecules,
lipids are insoluble in water. They are hydrocarbons that solely include nonpolar
carbon-carbon or carbon-hydrogen bonds, which explains why. In a cell, lipids serve
numerous purposes. Cells store energy as lipids termed fats for long-term use. Lipids
also insulate plants and animals from their surroundings. Because they repel water, for
instance, they aid in keeping aquatic creatures and birds dry. Lipids are a crucial
component of the plasma membrane and the building blocks of numerous hormones.
Steroids, phospholipids, oils, and waxes are examples of lipids.

33
Glycerol and fatty acids are the two primary parts of a fat molecule, like a triglyceride.
Three carbon atoms, five hydrogen atoms, and three hydroxyl (-OH) groups make up the
organic molecule glycerol. The term "fatty acid" refers to a lengthy chain of
hydrocarbons to which an acidic carboxyl group is connected. Fatty acids can have
anywhere between 4 and 36 carbons; the most frequent have between 12 and 18
carbons. Each of the three oxygen atoms in the -OH groups of the glycerol molecule has
a covalent interaction with a fatty acid to form a fat molecule.

Three water molecules are released as this covalent bond forms. The three fatty acids in
the fat could be identical or different from one another. Due to the fact that they
contain three fatty acids, these fats are also known as triglycerides. Some fatty acids
are known by names that indicate where they are from. For instance, the palm tree is
the source of the saturated fatty acid palmitic acid. Arachis hypogaea, which is the
scientific name for peanuts, is the source of arachidic acid.

 Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are
only single bonds between neighboring carbons in the hydrocarbon chain, the
fatty acid is saturated.

Saturated fatty acids are saturated with hydrogen; in other words, the number of
hydrogen atoms attached to the carbon skeleton is maximized. When the hydrocarbon
chain contains a double bond, the fatty acid is an unsaturated fatty acid. Most
unsaturated fats are liquid at room temperature and are called oils. If there is one
double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil),
and if there is more than one double bond, then it is known as a polyunsaturated fat
(e.g., canola oil).

Solid at room temperature, saturated fats have a tendency

to pack firmly. Saturated fats include, for example,
butter's butyric acid-containing fat as well as the animal
fats with stearic and palmitic acid found in meat. In
specialized cells called adipocytes, which make up the
majority of the cell in mammals, fat globules are used as a
form of energy storage. When a plant is developing its
embryos, oil or fat is stored in its seeds and used as a
source of energy.

Unsaturated fatty acids are found in unsaturated fats and oils,

which are often derived from plants. The fatty acids are prevented
from packing securely by the double bond, which creates a bend
or "kink" that keeps them liquid at normal temperature.
Unsaturated fats include, for instance, olive oil, corn oil, canola
oil, and cod liver oil. Saturated fats may lead to the production of

34
arterial plaque, which raises the risk of a heart attack, whereas unsaturated fats aid to
lower blood cholesterol levels.

The primary component of the plasma

membrane is phospholipids. They are
made up of fatty acid chains joined to a
glycerol or other similar backbone, just like
fats. The glycerol backbone's third carbon
is bonded to a phosphate group, hence
there are only two fatty acids connected as
opposed to three. An alcohol is added to
the phosphate group to change it.

Both hydrophilic and hydrophobic areas

can be found in phospholipids. While the phosphate is hydrophilic and interacts with
water, the fatty acid chains are hydrophobic and keep themselves away from it. A
membrane with a bilayer of phospholipids surrounds each cell. The phosphate group
can face either the outside environment or the inside of the cell, both of which are
watery, as opposed to the fatty acids of phospholipids, which face within, away from

water.

STEROID AND AXES

Steroids have a ring structure, unlike the phospholipids and fats we've already talked
about. They are categorized alongside other lipids despite not resembling them since
they are hydrophobic. All steroid molecules contain four connected carbon rings, and
some of them, like cholesterol, also have a short tail.

Steroids include cholesterol. As a precursor to

numerous steroid hormones, including
testosterone and estradiol, cholesterol is
primarily produced in the liver. The vitamins E
and K are also made from it. Bile salts, which
aid in the digestion of lipids and their
subsequent absorption by cells, are precursors
to cholesterol and are thus produced first.
Despite the bad connotations sometimes
attached to cholesterol, it is essential to the
body's healthy operation. It has a significant role in the plasma membranes of animal
cells.

A hydrocarbon chain with an alcohol (-OH) group

and a fatty acid make up waxes. Beeswax and

35
lanolin are a couple of examples of animal waxes. Wax is another substance found in
plants that helps keep them from drying out. An example of this is the coating on
leaves.

PROTEINS

One of the most prevalent organic molecules in

biological systems, proteins perform the widest
variety of roles among all macromolecules.
Proteins might be poisons or enzymes, or they
can be structural, regulatory, contractile, or
protective elements that function in transport,
storage, or membranes. There could be
thousands of different proteins in each cell of a
living organism, each serving a specific
purpose. Their structures differ substantially
from their functions. However, they are all linearly ordered polymers of amino acids.

The 20 separate, chemically

unique amino acids that make
up proteins can be arranged in
any order to produce lengthy
chains with a wide variety of
functions. For instance, proteins
can act as hormones or
enzymes. Enzymes are typically
proteins that are created by
living cells and act as catalysts
in biological reactions (such as
digestion). Every enzyme has a unique action on a certain substrate (a reactant that
binds to an enzyme). Molecular bonds can be broken, rearranged, or new bonds can be
created by enzymes. Salivary amylase, an enzyme that breaks down the starch
component amylose, is one such instance.

In order to manage or regulate particular

physiological processes, such as growth,
development, metabolism, and reproduction, an
endocrine gland or set of endocrine cells secretes
hormones, which are chemical signaling molecules
that are typically proteins or steroids. For instance,
the protein hormone insulin regulates blood sugar
levels.

The monomers that make up proteins are amino acids.

The basic building block of every amino acid is a core
carbon atom connected to an amino group (-NH2), a
carboxyl group (-COOH), and a hydrogen atom. The R
group, a second variable atom or set of atoms bound to the
central carbon atom in every amino acid, is also present.
The R group is the only structural variation among the 20
amino acids; otherwise, they are all the same.

36
  PROTEIN STRUCTURE

NUCLEIC ACID

In the continuation of life, nucleic acids are important macromolecules. They include
the genetic code for a cell and the rules for how the cell should operate. The two
primary forms of nucleic acids are ribonucleic acid (RNA) and deoxyribonucleic acid
(DNA). All living things, from single-celled bacteria to multicellular animals, include
DNA as their genetic material.

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38
 Protein synthesis is primarily carried out by RNA, the
other kind of nucleic acid. The DNA molecules never
leave the nucleus; instead, they communicate with
the rest of the cell through an RNA bridge. The
regulation of protein production and other forms of
RNA are also involved.

DNA and RNA are made up of monomers known

as nucleotides. The nucleotides combine with each
other to form a polynucleotide, DNA or RNA. Each
nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon)
sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a
sugar molecule, which is attached to a phosphate group.

DNA is made up of two helices. It is made up of two

nucleotide strands, or polymers. Bonds between the
phosphate and sugar groups of neighboring
nucleotides help to create the strands. The term
"double helix" refers to a double spiral because the
strands are joined at their bases by hydrogen bonds
and coil around one another throughout their length.
The DNA's backbone is made up of alternating sugar
and phosphate groups that are located outside of
each strand. The inside of the nitrogenous bases is
stacked like a staircase, and these bases couple; the
pairs are connected by hydrogen bonds. The bases
pair so that the distance between the two strands'
backbones is constant throughout the entire
molecule.

LESSON 2.6: THE FORMATION OF COMPLEX

MACROMOLECULE STRUCTURES

 THE ASSEMBLY OF TOBACCO MOSAIC VIRUS

The tobacco mosaic virus (TMV) particle was the first macromolecular structure that
was shown to self-assemble in vitro, allowing in-depth investigations of the
mechanism. A unique stem-loop of the single-stranded viral RNA binds to the
central hole of a two-ring subassembly of the coat protein, referred to as the "disk,"
to start TMV self-assembly. The loop binds to its unique binding site between the
two rings of the disk, causing the stem to melt and opening up more RNA for
binding. The interaction between the protein subunits and the RNA causes the disk
to dislocate into a proto-helix. The axial space between the rings at the inner radii
closes as a result of the rearrangement of the protein subunits, trapping the RN

39
  RIBOSOMAL SUBUNITS

We isolated cytoplasmic ribosomes from TMV-

infected tobacco leaf tissue. Rapidly tagged
RNA-associated ribosomes were stable in
3x104 Mg2+ and could be readily extracted
from the bulk using sucrose density gradients.
When annealed with TMV-specific double-
stranded RNA but not with TMV-RNA, some
RNA isolated from these ribosomes became
resistant to ribonuclease. When quickly tagged
RNA was separated from ribosomes in diluted
EDTA and annealed with double-stranded
RNA specific to TMV, the same outcomes were
attained. TMV-specific RNA was found in the
ribosome complex independently of contamination by whole or fragmented virus
particles. Additionally, the potential for unincorporated nascent viral RNA to associate
with ribosomes during extraction was looked into. The incorporation of radioactive
amino acids into the two capsid polypeptides of the cowpea mosaic virus was studied in
relation to ribosome-specific inhibitors. The effects of the inhibitors on the incorporation
of amino acids into the two polypeptides made by ribulose diphosphate carboxylase
(RuDPCase), which was also recovered from the infected tissue, and the capsid
polypeptides were directly compared. Incorporation into RuDPCase polypeptides served
as a crucial control because the short polypeptide is synthesized on 80 S ribosomes and
the large polypeptide on 70 S ribosomes. Cycloheximide had very similar dose-
dependent inhibitions of incorporation into capsid polypeptides and the RuDPCase
short polypeptide, but it was a weak inhibitor of incorporation into the RuDPCase large
polypeptide. The incorporation of amino acids into the big enzyme polypeptide was
blocked by chloramphenicol, but not into the small enzyme polypeptide or the capsid
polypeptides. Thus, 80 S cytoplasmic ribosomes are likely the primary or sole site of
capsid polypeptide synthesis for cowpea mosaic virus.

LEARNING EXERCISES:

I. Instructions: Differentiate the following terms.

1. Covalent Bond vs. Noncovalent Bond

2. Polar Bond vs. Non-polar Bond
3. Acid vs. Base vs. Buffers

II. Instructions: Answer the following questions briefly.

1. What are the properties of water?

2. Discuss the 4 types of biological molecules.

APPLICATION

Instructions: In a long size bondpaper, draw the chemical structures of the four major
biological molecules.

40
 GENERALIZATION

 Atoms are held together by covalent bonds to form molecules. Covalent

Atoms share their outer shell electrons to create bonds, which are stable
unions where each partner receives a full outer shell. Depending on how
many pairs of shared electrons there are, covalent bonds can be single,
double, or triple. If a bond's electrons are distributed unevenly by the
component atoms, the one that attracts electrons the most while the other
atom has a partial positive charge, (the more electronegative atom) carries a
partial negative charge.
 Weak attractive forces between positively and negatively charged areas of the
same molecule or between two neighboring molecules cause noncovalent
bonds to form. In preserving the structure of biological molecules and
mediating their dynamic activities, noncovalent connections are essential.
Ionic bonds, hydrogen bonds, and van der Waals forces are examples of
noncovalent bonding. Van der Waals forces form between two atoms
exhibiting a transient charge because of a brief asymmetry in the
distribution of electrons around the atoms. Ionic bonds form between fully
charged positive and negative groups. Hydrogen bonds form between a
covalently bonded hydrogen atom (which bears a partial positive charge) and
a covalently bonded nitrogen or oxygen atom (which bears a partial negative
charge). Nonpolar molecules or parts of bigger molecules that are nonpolar.
In watery settings, molecules have a propensity to join together to create
interactions between hydrophobic. Examples of these various noncovalent
interactions include the formation of the hydrophobic core of soluble
proteins because of hydrophobic interactions and van der Waals forces, the
association of DNA and proteins by ionic bonds, the association of DNA
strand pairs by hydrogen bonds, and more.
 Life depends on the special qualities that water possesses. A water molecule
is made up of highly polarized covalent connections. Water is a great solvent
because it can create hydrogen bonds with almost any polar molecule. The
structure of biological molecules and the kinds of interactions they can
engage in are both significantly influenced by water. A solution's pH serves
as a gauge for hydrogen (or hydronium) ions present. Because the ionic state
of biological molecules is altered by variations in hydrogen ion concentration,
most biological processes are extremely sensitive to pH. Buffers—compounds
that react with hydrogen or hydroxyl ions—protect cells from pH changes.
 When biological compounds are created, carbon atoms are crucial. Up to
four additional atoms, including other carbon atoms, can form bonds with a
single carbon atom. This characteristic enables the development of massive
molecules with a carbon-atom chain as their backbone. Hydrocarbons are
molecules that only contain hydrogen and carbon. Most biologically
significant compounds have functional groups with one or more
electronegative atoms, which increases the molecule's polarity, water
solubility, and reactivity.
 The four different categories of biological molecules are carbohydrate, lipid,
protein, and nucleic acid molecules. Simple sugars and bigger molecules
(polysaccharides) made of sugar monomers are examples of carbohydrates.
The main roles of carbohydrates are as a source of chemical energy and as
strong building blocks for biological structures. Simple biological sugars
have a backbone made up of three to seven carbon atoms, with all but one of
them connected to hydroxyl groups. The remaining carbon bears a carbonyl
group. Sugars with five or more carbon atoms self-react to create molecules
with a ring shape. Stereoisomerism occurs at the four distinct groups-linked
carbon atoms along the sugar backbone, resulting in pairs of isomers that
cannot be superimposed. The distance of the sugar's farthest asymmetric
carbon from the carbonyl determines whether it is D or L. To create
disaccharides, oligosaccharides, and polysaccharides, sugars are joined

41
 together by glycosidic linkages. Sugar is generally stored as the branched
polysaccharide glycogen in mammals, which serves as a quickly accessible
energy source. Plants retain their remaining glucose as starch, which is a
combination of branched and unbranched amylopectin. In both glycogen and
starch, (1 n 4) connections connect the majority of the sugar molecules.
Plant cells produce cellulose, a structural polysaccharide that is a significant
part of the cell wall. Cellulase, an enzyme that is lacking in almost all
animals, cleaves the (1 n 4) links that connect the glucose monomers in
cellulose. A structural polysaccharide made up of N-acetylglucosamine
monomers is chitin.
 A large variety of hydrophobic molecules with a wide range of structural and
functional diversity make up lipids. Glycerol molecules that have been
esterified to three fatty acids make up fats. Different fatty acids have
different chain lengths, double bond counts, and double bond positions
(sites of unsaturation). A gram of fat has more than twice the amount of
chemical energy per calorie as a gram of carbohydrate. A class of lipids
known as steroids has a distinctive hydrocarbon skeleton with four rings.
Cholesterol is a component of steroids, as are several hormones (such as
progesterone, estrogen, and testosterone) that are produced from cholesterol.
Phospholipids, which are phosphate-containing lipid molecules with
hydrophilic and hydrophobic ends, are crucial to the composition and
operation of cell membranes.
 Proteins are large, multifunctional molecules made of amino acids connected
by peptide bonds to form polypeptide chains. The wide variety of proteins
includes enzymes, building blocks, membrane receptors, gene regulatory
elements, hormones, transporters, and antibodies. The sequence of
nucleotides in DNA encodes the order in which the 20 distinct amino acids
are added to proteins. The structural arrangement of all 20 amino acids is
the same and consists of an -carbon bound to an amino group, a carboxyl
group, and a side chain with a variety of structures. The side chains in the
current approach are divided into four groups: those fully charged at
physiological pH; those polar but uncharged and able to establish hydrogen
bonds; and those that interact by van der Waals interactions and are
nonpolar; Proline, cysteine, and glycine are three distinctive amino acids
properties.
 There are four progressively more complicated stages at which the structure
of a protein can be defined. The amino acid sequence of a polypeptide serves
as a description of its primary structure, while the conformation of the entire
polypeptide, its tertiary structure, and, if a protein contains more than one
polypeptide chain, the arrangement of its subunits serve as descriptions of
its secondary, tertiary, and quaternary structures, respectively. The  helix
and β-pleated sheet are both stable, maximally hydrogen bonded secondary
structures that are common in many proteins. The tertiary structure of a
protein is highly complex and unique to each individual type of protein. The
majority of proteins have a general globular shape in which the polypeptide
is folded to form a small molecule in which certain residues are placed in a
precise order to enable the protein to perform a particular function. Most
proteins have two or more domains, each of which is structurally and
functionally distinct from the others. By creating precise substitutions,
researchers can use the site-directed mutagenesis approach to understand
the function of particular amino acid residues. Recent years have seen the
emergence of the field of proteomics, which makes use of cutting-edge tools
like mass spectrometry and high-speed computing to research numerous
protein properties on a thorough and extensive scale.
 A polypeptide chain's fundamental structure contains the instructions needed to
adopt its native conformation. Some proteins can fold independently into their final
structure, whereas others need non-specific chaperones to help avoid the aggregation
of partially folded intermediates.
 Nucleic acids, which are made up of strands of nucleotide monomers, are principally
informative molecules. Each nucleotide in a strand is made up of a nitrogenous base,
phosphate, and sugar. The 3 hydroxyl group of the sugar in one nucleotide forms
bonds with the 5 phosphate group of the neighboring nucleotide, connecting the two

42
 nucleotides. Nucleotides are characterized by their bases, which can be either a
pyrimidine (cytosine or uracil/thymine) or a purine (adenine or guanine), and both
RNA and DNA are constructed from four distinct nucleotides. While RNA is typically
single stranded, it is frequently folded back on itself to form double stranded regions,
whereas DNA is a double stranded nucleic acid. The precise order of nucleotides that
make up a strand is how nucleic acids encode information.

BIBLE INTEGRATION

Do not conform any longer to the pattern of this world, but be transformed by
the renewing of your mind. Then you will be able to test and approve what God’s will is
—his good, pleasing and perfect will. ~ Romans 12:2

EVALUATION

REFERENCES

43
Fechheimer, M. (2000b). Cell and Molecular Biology: Concepts and Experiments. Gerald
Karp. The Quarterly Review of Biology, 75(4), 454. https://doi.org/10.1086/393652

Admin. (2023). Covalent Bond - Definition, Types, Properties, and Examples. BYJUS.
https://byjus.com/jee/covalent-bond/

Admin. (2023b). Non-polar Covalent Bond - Definition, Examples, Formation. BYJUS.

https://byjus.com/jee/non-polar-covalent-bond/

Byju’s. (2022b). What are the Types of Noncovalent Bonds - Different Mechanisms.
byjus.com. https://byjus.com/question-answer/what-are-the-types-of-noncovalent
bonds/

Vedantu. (n.d.). Polar Covalent Bond. VEDANTU. https://www.vedantu.com/iit

jee/polar-covalent-bond

Diksha. (2015, August 13). Difference between Polar and Non-Polar. Polar Vs Non-Polar.

Biological Molecules - Concepts of Biology | OpenStax. (n.d.).

AUTHOR

Prepared by:
Kyla C. Alcosaba, BSED Gen. Science

CHECKED AND APPROVED BY

Checked and Approved by:

Prof. Joscel P. Enardecido M.Sc.

44
 BIOENERGETICS,
CHAPTER ENZYMES, AND
3 METABOLISM

3.1 BIOENERGETICS
3.2 ENZYMES AS BIOLOGICAL CATALYSTS
3.3 METABOLISM

ACTIVATING PRIOR KNOWLEDGE

INSTRUCTIONS: Discuss what does energy conversion means based on the picture.

_____________________________________________

_____________________________________________

_____________________________________________

_____________________________________________

_____________________________________________

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 Learning Competencies

After studying this chapter, you should be able to:

a. Define what is bioenergetics.

b. Discuss enzymes as biological catalyst.
c. Define what is metabolism.

PRE-ASSESSMENT

IDENTIFICATION: Identify what is being asked in the following sentences.

1. The study of the various types of energy transformations that occur in living
organisms.
2. The vitally important protein catalysts of cellular reactions.
3. The total of the chemical reactions occurring within a cell.
4. The capacity to do work, it exists in two forms: potential and kinetic.
5. The study of the changes in energy that accompany events in the universe.

CONCEPT MAP

46