BIOLOGY 111

(Cellular and Molecular Biology)

Lecture Notes 1

Biology as a Science
Biology is coined from two Greek words: ‘Bios’ – meaning life, and ‘Logos’ – meaning study. In short,
biology is the science or study of life. It is central to our lives and the earth as a whole. Thus, learning
about biology helps you to understand much more about the world. For instance, concepts such as
nutrition, HIV/AIDs, global climate change, water quality, endangered species, spread of drug
resistant bacteria and many other matters have their foundation in biology.
What is life?
All humans have an intuitive sense of life. For e.g., if you see a fish in a pond, you will know that the
fish is living, while the water is not living. But it is just difficult to say what makes the fish alive. On the
other hand, after an individual dies, you may wonder what invisible essence has transformed the
living into the dead. Based on these concepts of “living and dead”, scientists were faced with a
difficult question of defining what life is.
In the 18th century, a French physician, Marie Francois Xavier Bichat, poetically but imprecisely
defined life as “the ensemble of functions that resist death”. Other people suggested that life is a kind
of “black box” that endows a group of associated biochemicals with the qualities of life”.
But one way to define life is to list its basic components:
- cell is the basic unit of life
- every organism consists of one or more cells
- every cell has an outer membrane that separate it from its surrounding
- inside the membrane of every cell, are water and other chemicals that carry out the cell’s
functions
- one such biochemical is the DNA – the informative molecule of life
- cells use instructions coded by DNA to produce proteins
- proteins enable cells to specialize and to function in tissues, organs and systems.

However, a list of life’s biochemicals provides an unsatisfying definition of life because if the proteins,
DNA, water and cell membrane are placed in a test tube, they will not create an artificial life. Also, an
insect that is crushed to death contains all the biochemicals it had.
A concise definition that has been put forward contains five (5) qualities which in combination make
up life.
1. Life is organized
- living matter consists of parts organized in a 3-dimensional relation: Anterior-posterior, dorsal-
ventral and laterals.
- organization follows a hierarchical pattern of structures within structures within structures
- beyond the levels of the individual organization, life is organized into population, community,
ecosystem, and biosphere.

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 2. Life requires energy
- all living organisms require a constant supply of energy to maintain the many organized
biochemicals
- energy comes from the environment and is used to build new structures, repair old ones, and
reproduce
- based on the energy source, organisms are classified as producer, consumer and decomposer
- energy requirement link life into chains and webs
3. Life maintains internal constancy
- living organisms have the ability to sense and react to changes in their environment (stimuli).
- thus, conditions inside cells must remain within a constant range irrespective of any drastic
changes in the surrounding environment (hemostasis)

4. Life reproduces itself, grows and develop

- organisms reproduce others of their kind
- reproduction transmits DNA from parents to offspring, and from generation to generation
- offspring then grow and develop to maturity and then reproduce themselves
- reproduction is both asexual and sexual
- organisms have a life span
5. Life evolves
- organisms inherit characteristics or behaviours that enable them to survive and reproduce –
adaptation
- adaptive traits come from natural selection – one mechanism of evolution, which is the change
in the genetic makeup of a population
The Discovery of Cells
Many cells are too small to be seen with the unaided eye. The development of the compound
microscope in the 17th century gave biologists the opportunity to study cells. The 1 st compound
microscope magnified an object 270 times. The recent microscope magnifies an object 2,000 times,
while the electron microscope magnifies an object 200,000 times.
An English scientist Robert Hooke made a simple microscope and used it to observe a thin slice or
section of cork from an oak plant stem. He saw irregular pores which looked like honeycomb, and he
named these structures cells. Even though he was not looking at living cells, but what he saw on the
nonliving outer walls of the cork which had once lived shows a significant discovery about the
structure of living things.
With improvement in the development of the microscope and their lenses in the 18 th century, parts of
many plants and animals were now examined. In 1820s a French Botanist Rene’ Dutrochet was one
of the first scientists to make a generalized statement about the structure of living things. He
concluded that various parts of organisms are composed of cells, i.e., the leaves of a tree, and the
skin of animals are made of cells.
In 1830s, there was much use of the microscope to study pieces of all sorts of organisms. Robert
Brown announced in Scotland that a cell contains a large central part called the nucleus. A French
scientist Felix Dujardin later reported that cells are not hollow, empty structures, but are full of clear
jellylike fluid (cytoplasm). By the late 1830s, two German scientists working separately revealed
similar facts like other scientists and began to lay the basis for the formulation of the cell theory.
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Mathias Schleiden worked with plants and concluded that all plants and plant parts are composed of
living cells. Theodore Schwann worked with animals and also concluded that animals and animal
parts are composed of living cells. These conclusions meant that all living things are composed of
cells. Cells are the basic building g blocks of living things. The German physician Rudolf Virchow
stated that all cells arise from already existing cells.
Postulates of the Cell Theory
- all organisms are composed of cells
- cells are the basic, structural and functional unit of living organisms
- all cells arise from preexisting cells

Exceptions of cell Theory

- if every cell comes from a parent cell, where did the first cell come from? Since the environmental
conditions of the earth were much different than they are today, could those conditions at that time
have enabled the first living cell to form from non-living material?

- viruses are exceptions to the cell theory. Each virus is a package of nucleic acid wrapped in a
protein coating. A virus must enter and occupy a cell in order to reproduce. Therefore, without a cell,
a virus is lifeless. Is a virus alive or it is somewhere between living and nonliving?
Sizes and Shapes of Cells
Cells exist in a great variety of sizes and shapes. Cells range in size from the smallest bacteria like
organisms (Mycoplasmas) measuring about 0.1 to 0.3 µm in diameter to the largest ostrich egg cell
which measures about 100 mm (4 in) in diameter.
Cells exhibit much greater variety of shapes than in size. Some unicellular organisms such as
paramecium or euglena have a definite shape, while others, such as amoeba are constantly changing
in shape. Even within the human body, cells exhibit a great variety of shapes. Cells of the skin are flat
and irregularly shaped, while nerve cells are long, thin and stringlike. Skin cells function as a covering
for the body, while nerve cells function in transmitting impulses throughout the body. Thus, the shape
of a cell is related to its function.
Types of Cells
In spite of the extreme variety among cells, two fundamental types of cells exist: prokaryotic cells
represented by the bacteria, and eukaryotic cells which is found in the great majority of organism
(protists, fungi, plants and animals). However, some organisms do not have a nucleus, rather they
contain nucleic acid (DNA/RNA) enclosed in a protein coat, and called akaryotic. The most striking
difference between prokaryotic cells and eukaryotic cells is that eukaryotic cells have their genetic
material contained within a membrane structure, the nucleus, whereas, the genetic material of
prokaryotic cells is not enclosed within a unit membrane. A number of other features differ between
the two main cell types. **Tabulate these differences.
Structure and Functions of Eukaryotic Cells
A typical eukaryotic cell can be divided into two basic parts: an outer, nonliving cell membrane (or
outer boundary of the cell) and the inner living protoplasm. The protoplasm is composed of the
nucleus and cytoplasm.

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1. Structure and Function of Cell Membrane
The cell (or plasma) membrane encloses every cell. The cell membrane is thin a thin layer of protein
and lipid that separate the cell’s content from its environment. Cell membranes are 5-10 nanometers
(nm) thick. The cell membrane maintains the integrity of the cell, and offers physical protection to the
cell by acting as a barrier between its living protoplasm and the surrounding environment. It also
regulates the flow of molecules into and out of the cell (physiological function). Some surface
molecules such as glycoproteins play a role in recognizing specific pathogens and are involved in
immune responses. Membranes inside the cell surround a variety of organelles.

The main ingredients of membranes are lipids and proteins, but carbohydrate is also present.
Membranes are made mostly of phospholipids. Each phospholipid molecule has two ends (head and
tail) with different properties in water. The phospholipid head is hydrophilic (water loving) and can
dissolves easily in water, while the phospholipid tail is hydrophobic (water fearing) that does not
dissolve in water. The phosphate heads of both sides of the bilayer lipid face water fluids inside and
outside the cell. The phosphate tails are sandwiched inside the bilayer. In addition to phospholipids,
glycolipids and cholesterol are found in membranes. Two main types of proteins are found in
membranes: integral and peripheral proteins. Integral proteins penetrate far into the membrane to
reach the lipid layer, and peripheral proteins do not penetrate but lie superficial. Both glycolipid and
glycoproteins form a carbohydrate coat that envelopes the outer surface of the plasma membrane.

Two models have been proposed to describe the arrangement of protein and lipid molecules in
membranes: the Unit membrane model and the Fluid mosaic model.
In the 1940s, H Davidson and J. Danielli proposed the unit membrane model to describe the structure
of the plasma membrane. According to them, the membrane is something like a sandwich consisting
of a bilipid enclosed by two layers of proteins. With advancement in electron microscope, J. D.
Roberts observed the plasma membrane and found it to contain an outer dark layer of protein plus
the hydrophilic head and an inner hydrophobic tail of the phospholipids. He then suggested that all
membranes in various eukaryotic cells have basically the same components. This model was
accepted for only few years, and was later challenged by other scientists on the basis that not all
membranes have the same appearance in the electron micrographs and certainly do not have the
same function. For example, the inner membrane of a mitochondrion is coated with rows of enzyme
particles which function in respiration, and therefore appears a little different from the plasma
membrane.

In 1972, S. Singer and G. Nicolson proposed the fluid mosaic model of membrane structure.
According to this model, the membrane is a fluid phospholipid bilayer in which protein molecules are
either partially or wholly embedded. The proteins are scattered throughout the membrane in an

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irregular pattern that can vary from

2. The Protoplasm
The protoplasm is composed of the cytoplasm and the nucleus. The cytoplasm is the region between
the cell membrane and the nucleus. It is a semifluid medium (called cytosol) in which several
organelles are suspended. The cytosol is a watery solution of salt, sugar, amino acids, proteins, fatty
acids, nucleotides, and other substances. Organelles are small subcellular units with specific
structure and function.

With a few rare exceptions, all eukaryotic cells contain the following organelles, each with its own
structural and functional specialization: nucleus, endoplasmic reticulum, Golgi apparatus,
cytoskeleton, mitochondrion, ribosomes, and vacuoles. Other organelles are chloroplast, lysosomes,
microbodies, centrosome etc.

Most organelles in eukaryotic cells are part of an endomembrane system, where internal membranes
partition the cell into compartments so that each compartment provides a separate environment in
which specific metabolic functions can take place. Endomembrane system makes possible for two or
more incompatible processes to go on simultaneously in separate subcellular compartments, within a
particular cell. Membranous organelles include the nucleus, endoplasmic reticulum, Golgi apparatus,
mitochondrion, chloroplast, lysosomes, microbodies and vacuoles. The first five (5) organelles have
double membranes and the remaining three (3) have single membrane.

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The Nucleus
In many cells, the nucleus is the most prominent internal structure. It varies in size, shape, position
and chemical composition from cell to cell. Many nuclei are spherical but some are cylindrical, and
others are disk like. The nucleus is bounded by a double membrane (nuclear envelope) that forms a
boundary with the cytoplasm. The nuclear membrane has openings (or nuclear pores) to allow some
materials to pass between the cytoplasm and the nucleus. Within the nucleus is a fluid matrix, the
nucleoplasm, containing chromatin which is the cell’s genetic material. Chromatin is composed of the
nucleic acid DNA, and with proteins, is formed into rod-shaped structures called chromosomes. The
nucleus of most cells has one or more spherical bodies called nucleoli (sing: nucleolus). Nucleoli are
made up of DNA, RNA and proteins. Nucleoli manufacture ribosomal RNA (rRNA) and assemble
ribosomes. The nucleus performs the following functions:
- controls the activities of the cell by regulating protein and enzyme synthesis
- involved in the formation of ribosomes and RNA
- involves in the process of cell division
- contains the genetic material that carries the hereditary information.

The Mitochondrion
Mitochondria (sing: mitochondrion) are found in the cytoplasm of all eukaryotic cells, but may be
absent in highly specialized cells such as mature red blood cells. They are spherical or highly
elongated in shape, and are typically 5µm long and 0.2 µm wide. Each mitochondrion is enclosed by
a double membrane; the outer membrane is a smooth continuous boundary and it controls the entry
and exit of chemicals. The inner membrane is highly folded to form cristae, which contain enzymes
that catalyze the biochemical reactions of cellular respiration. They occur in large numbers in highly
active cells. They are the site of cellular respiration, and of some protein synthesis and fatty acids.

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The Endoplasmic Reticulum (ER)
It is an extensive network of sacs and tubes that extends throughout the cell from the nucleus to the
cell membrane. The structure of ER is adapted to its function which is transportation of materials
throughout the internal region of the cell. The ER is of two general types: smooth and rough. Smooth
ER does not have ribosomes on its external surface, while the rough ER has ribosomes on its
exterior.
The smooth ER has many unique enzymes embedded on its surface. Its functions are:
- production of membrane phospholipids and cellular lipids
- production of sex hormones such as testosterone and oestrogen
- detoxification of drugs in the liver
- aids the liver cells in releasing glucose into the bloodstream when needed
The rough ER has ribosomes which are involved in protein synthesis; thus, rough ER are involved in
protein development and transport.

The Golgi Apparatus

The Golgi apparatus is made of flattened sacs called cisternae, which are stalked on top of one
another. These sacs are fluid filled that pinch off as tiny sacs (called vesicles) at their ends. Each
stalk consists of two faces: the ‘cis’ face which usually located near the ER from which it receives
materials, and the ‘trans’ face that is directed towards the plasma membrane. Materials from the ER
move into the cisternae of the Golgi apparatus and continues to the trans end. Small sacs called
vesicles come off from the trans side carrying modified materials they are needed inside or outside
the cell. Golgi apparatus is especially prevalent in glandular cells such as pancreas which

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manufacture and secrete substances. The organelle functions in collection, packaging, modification
and distributing of materials within and outside the cell.

The Chloroplast
Chloroplasts belong to a larger group of organelles known as plastids. They occur in algae and
plants. In higher plants, most chloroplasts are 5 - 10µm long and are bounded by double membranes.
The interior of the chloroplast includes the grana (sing, granum), the thylakoids, and the stroma. A
granum is made up of numerous closed flattened stalks called the thylakoids. The thylakoids of some
grana are interconnected with adjacent grana by tubular extensions. Within the thylakoids are located
the photosynthetic pigments such as chlorophyll. The stroma is a colourless gelatinous matrix
containing ribosomes, lipid droplets and small starch grain in which the grana are suspended. Like
the mitochondrion, chloroplast contains its own DNA and ribosomes, and are capable of reproducing
independently of the cell. The chloroplasts serve as the site of photosynthesis.

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Lysozymes
Lysozymes are small spherical vesicles (0.1 – 1.0 µm in diameter) originating from the Golgi
apparatus or directly from the ER. They are bounded by a single membrane, and contain a mixture of
hydrolytic digestive enzymes. These enzymes are isolated from the rest of the cell by being enclosed
in sac to prevent them from acting upon other chemicals and organelles within the cell. Lysozymes
function in
- digesting materials the cell consumes from the environment
- digesting parts of the cell, such as worn-out cells – a process called autophagy
- digesting the remains of a cells after death – a process called autolysis
- releasing their enzymes outside the cell (exocytosis) to break down other cells, for e.g., in the
absorption of the tadpole tail during development.
Vacuoles
Vacuoles are fluid filled sacs bounded by a single membrane. Vacuoles are formed either by the
infolding and pinching off of the cell membrane, or by enlargement of a vesicle cut off from the Golgi
apparatus. Within matured plant cells, there is usually one large central vacuole enclosed by a single
membrane called the tonoplast. The plant vacuole is filled with sap, a solution of mineral salts,
sugars, amino acids, waste products and pigments such as anthocyanins. In animals, vacuoles are
much smaller but may occur larger in numbers. Animal types include food vacuoles and phagocytic
vacuoles. Vacuoles function in the following ways:
- in plants, vacuoles are temporary food store
- anthocyanins in plants give various colours to petals to attract insect pollinators and fruits to
attract animals for dispersal
- provide support to herbaceous plants and parts by creating pressure potential
- animal vacuoles play important roles in feeding and defense of the animals
- act as temporary store for organic waste such as tannins, which may accumulate in the
vacuoles and are removed when the leaves fall

Microbodies (Peroxisomes)
Microbodies are small spherical organelles bounded by a single membrane, and measures
between 0.5 to 1.5 µm in diameter. They are slightly granular and contain a number of
metabolically important enzymes, in particular, the enzyme catalase, which catalyzes the
breakdown of hydrogen peroxide (a harmful by-product to harmless products (water and oxygen).
Peroxisomes are particularly abundant in actively metabolizing cells (such as cells of the liver).

Non-Membranous Organelles
Ribosomes
Ribosome are minute cytoplasmic granules found in all cells. Each ribosomes measures 20nm in
diameter and consists of two unequal subunits. They lack exterior membranes, but contain protein
and RNA (ribosomal RNA) in roughly equal quantities. They may occur in groups called
polysomes, and may be associated with RER or occur freely within the cytoplasm. Free ribosomes
are the site of synthesis of proteins retained within the cell, while ribosomes bound to RER
produce proteins that are subsequently secreted outside of the cell. Ribosomes occur inside the

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mitochondria and chloroplasts of eukaryotic cells are usually smaller than the cytoplasmic
ribosomes.

Cytoskeleton
This is a network of interconnected protein fibers that extend from the nucleus to the plasma
membrane of eukaryotic cells. It is composed of three (3) elements: microtubules, microfilaments
and intermediate filaments. Microtubules occur in both plant and animal cells. They are straight,
unbranched hollow cylinders 25nm wide and usually quite short in length. Microtubules are made
of globular proteins called tubulin. Microfilaments are thin solid rods about 7 nm in diameter, and
are usually made of the protein actin, and small proportions of myosin. The cytoskeleton functions
as follows:
- provides an internal skeleton that support the cell and maintains its shape
- aids transport of materials within the cell
- form the spindle fiber during cell division, and in pulling chromosomes to opposite poles
- are involved in cytoplasmic movements
- form major parts of cilia and flagella, and so contribute to their movement

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