Chapter I

CELL

1
CELL THEORY
Cell Theory is one of the basic principles of biology. Credit for the
formulation of this theory is given to German scientists Theodor
Schwann, Matthias Schleiden, and Rudolph Virchow.
The Cell Theory states:
 All living organisms are composed of cells. They may be
unicellular or multicellular.
 The cell is the basic unit of life.
 Cells arise from pre-existing cells. (They are not derived
from spontaneous generation.)
The modern version of the Cell Theory includes the ideas that:
 Energy flow occurs within cells.
 Heredity information (DNA) is passed on from cell to cell.
 All cells have the same basic chemical composition.
In addition to the cell theory, the gene
theory, evolution, homeostasis, and the laws of
thermodynamics form the basic principles that are the foundation
for the study of life.
Proponents of Cell Theory
Robert Hooke
Robert Hooke 1635–1703, English
physicist, mathematician, and
inventor. He became curator of
experiments for the Royal Society
(1662), professor of geometry at
Gresham College (1665), and city
surveyor of London after the great
1666 fire. Considered the greatest
mechanic of his age, he made
many improvements in
astronomical instruments and in
watches and clocks, was the first to
formulate the theory of planetary
2
movements as a mechanical problem, and anticipated universal
gravitation. In 1684 he devised a practicable system of
telegraphy. He invented the spiral spring in watches and the first
screw-divided quadrant and constructed the first arithmetical
machine and Gregorian telescope. He also stated Hooke's law
and in his pioneering book Micrographia (1665) he described his
microscopic observations of plant tissues and coined the term
cell.

Anton Van
Leeuwenhoek
The father of microscopy, Anton Van
Leeuwenhoek of Holland (1632-1723),
started as an apprentice in a dry
goods store where magnifying glasses
were used to count the threads in
cloth. Anton van Leeuwenhoek was
inspired by the glasses used by drapers to inspect the quality of
cloth. He taught himself new methods for grinding and polishing
tiny lenses of great curvature which gave magnifications up to
270x diameters, the finest known at that time.

Matthias Schleiden
Matthias Schleiden was born in
Hamburg, Germany, in 1804. By
1838 his methods had led him to
propose the cell theory for plants.
Schleiden was the first to recognize
the importance of cells as
fundamental units of life. In his most
well-known article, Schleiden
described Robert Brown's 1832
discovery of the cell nucleus (which

3
he renamed cytoblast). Schleiden knew that the cell nucleus must
somehow be connected with cell division, but he mistakenly
believed that new cells erupted from the nuclear surface like
blisters. Even so, he made other accurate observations about
plant cells and cell activity and his conclusions marked the
beginning of plant cytology. In 1839, Theodor Schwann would
expand Schleiden's cell theory to include the animal world,
establishing cell theory as the fundamental concept in biology.
Schleiden included this article and others in a botany textbook--
one that introduced new teaching methods which would dominate
the instruction of botany for years. His approach to educating
students was very different, and his liberal views often put him at
odds with other scientists. However, his great abilities and his
introduction of improved techniques earned him the title "reformer
of scientific botany."

Theodor Schwann
The German biologist Theodor
Schwann (1810-1882) is
considered a founder of the cell
theory. In 1838 Schwann became
familiar with Matthias Schleiden's
microscopic research on plants.
Schleiden described plant cells
and proposed a cell theory which
he was certain was the key to plant
anatomy and growth. Pursuing this
line of research on animal tissues,
Schwann not only verified the
existence of cells, but he traced
the development of many adult tissues from early embryo stages.
This research and the cell theory which followed were
summarized in Mikroskopische Untersuchungen ueber die
Uebereinstimmung in der Struktur und dem Wachstum der Thiere
4
und Pflanzen (1839; Microscopical Researches on the Similarity
in the Structure and the Growth of Animals and Plants, 1847).
This work, which in Schwann's own words demonstrated that "the
great barrier between the animal and vegetable kingdoms, viz. the
diversity of ultimate structure, thus vanishes," established the cell
theory to the satisfaction of his contemporaries.

Rudolf Virchow
Rudolf Virchow was a scientist,
physician, anthropologist, social
scientist, and politician. His ideas were
very progressive and set the foundation
of not only cellular pathology, but also
the role of societal structures in health
and disease. Virchow is credited with
several very important discoveries. His
most widely known scientific contribution
is his cell theory, which built on the work
of Theodor Schwann. He also
hypothesized that cells divide to form new cells. He also proposed
that every cell came from a cell that already existed. His
observations and conclusions and those of others are
summarized in the cell theory.

5
CELL STRUCTURE AND FUNCTION
Cell Structure
Ideas about cell structure have changed considerably over the
years. Early biologists saw cells as simple membranous sacs
containing fluid and a few floating particles. Today's biologists
know that cells are infinitely more complex than this.
There are many
different types, sizes,
and shapes of cells in
the body. For
descriptive purposes,
the concept of a
"generalized cell" is
introduced. It includes
features from all cell
types. A cell consists of three parts: the cell membrane, the
nucleus, and, between the two, the cytoplasm. Within the
cytoplasm lie intricate arrangements of fine fibers and hundreds
or even thousands of miniscule but distinct structures called
organelles.

Cell membrane
Every cell in the body is
enclosed by a cell (Plasma)
membrane. The cell
membrane separates the
material outside the cell, extracellular, from the material inside the
cell, intracellular. It maintains the integrity of a cell and controls

6
passage of materials into and out of the cell. All materials within a
cell must have access to the cell membrane (the cell's boundary)
for the needed exchange.
The cell membrane is a double layer of phospholipid molecules.
Proteins in the cell membrane provide structural support, form
channels for passage of materials, act as receptor sites, function
as carrier molecules, and provide identification markers.

Nucleus and Nucleolus

The nucleus, formed by a nuclear
membrane around a fluid
nucleoplasm, is the control center of
the cell. Threads of chromatin in the
nucleus contain deoxyribonucleic
acid (DNA), the genetic material of
the cell. The nucleolus is a dense region of ribonucleic acid (RNA)
in the nucleus and is the site of ribosome formation. The nucleus
determines how the cell will function, as well as the basic
structure of that cell.
Chromatin - a complex of nucleic acid and basic proteins (as
histone) in eukaryotic cells that is usually dispersed in the
interphase nucleus and condensed into chromosomes in mitosis
and meiosis.

Cytoplasm
The cytoplasm is the gel-like fluid
inside the cell. It is the medium for
chemical reaction. It provides a
platform upon which other

7
organelles can operate within the cell. All of the functions for cell
expansion, growth and replication are carried out in the cytoplasm
of a cell. Within the cytoplasm, materials move by diffusion, a
physical process that can work only for short distances.

Cytoplasmic
organelles
Cytoplasmic organelles are
"little organs" that are
suspended in the
cytoplasm of the cell. Each
type of organelle has a
definite structure and a
specific role in the function of the cell. Examples of cytoplasmic
organelles are mitochondrion, ribosomes, endoplasmic reticulum,
Golgi apparatus, and [lysosomes.
Mitochondrion- any of various round or long cellular organelles
of most eukaryotes that are found outside the nucleus, produce
energy for the cell through cellular respiration, and are rich in fats,
proteins, and enzymes.
Ribosome – in biology, a structure found inside cells that is
involved in making proteins. Ribosomes help link amino acids
together to form proteins.
Endoplasmic Reticulum - a network of sac-like structures and
tubes in the cytoplasm (gel-like fluid) of a cell. Proteins and other
molecules move through the endoplasmic reticulum. The outer
surface of the endoplasmic reticulum can be smooth or rough.

8
The rough endoplasmic reticulum has many ribosomes on its
outer surface and makes proteins the cell needs. The smooth
endoplasmic reticulum makes other substances that the cell
needs, such as lipids (fats) and carbohydrates (sugars). The
endoplasmic reticulum is a cell organelle.
Golgi Apparatus - a stack of small flat sacs formed by
membranes inside the cell’s cytoplasm (gel-like fluid). The Golgi
apparatus prepares proteins and lipid (fat) molecules for use in
other places inside and outside the cell. The Golgi apparatus is a
cell organelle.
Lysosome - a sac-like compartment inside a cell that has
enzymes that can break down cellular components that need to
be destroyed.

Cell Function
The structural and functional characteristics of different types of
cells are determined by the nature of the proteins present. Cells of
various types have different functions because cell structure and
function are closely related. It is apparent that a cell that is very
thin is not well suited for a protective function. Bone cells do not
have an appropriate structure for nerve impulse conduction. Just
as there are many cell types, there are varied cell functions. The
generalized cell functions include movement of substances
across the cell membrane, cell division to make new cells, and
protein synthesis.

9
Movement of substances across the cell
membrane
The survival of the cell depends on maintaining the difference
between extracellular and intracellular material. Mechanisms of
movement across the cell membrane include simple diffusion,
[glossary term:] osmosis, filtration, active transport, [glossary
term:] endocytosis, and [glossary term:] exocytosis.
Simple diffusion is the movement of particles (solutes) from a
region of higher solute concentration to a region of lower solute
concentration. Osmosis is the diffusion of solvent or water
molecules through a selectively permeable membrane. Filtration
utilizes pressure to push substances through a membrane. Active
transport moves substances against a concentration gradient
from a region of lower concentration to a region of higher
concentration. It requires a carrier molecule and uses energy.
Endocytosis refers to the formation of vesicles to transfer particles
and droplets from outside to inside the cell. Secretory vesicles are
moved from the inside to the outside of the cell by exocytosis.

DNA replication and protein synthesis

Proteins that are synthesized in the cytoplasm function as
structural materials, enzymes that regulate chemical reactions,
hormones, and other vital substances. DNA in the nucleus directs
protein synthesis in the cytoplasm. A gene is the portion of a DNA
molecule that controls the synthesis of one specific protein
molecule. Messenger RNA carries the genetic information from
the DNA in the nucleus to the sites of protein synthesis in the
cytoplasm.

10
PROKARYOTIC AND EUKARYOTIC CELL

Prokaryotic Cells
Prokaryotic cells are cells
without a nucleus. The DNA
in prokaryotic cells is in the
cytoplasm rather than
enclosed within a nuclear
membrane. Prokaryotic cells
are found in single-celled
organisms, such as bacteria, like the one shown in Figure below.
Organisms with prokaryotic cells are called prokaryotes. They
were the first type of organisms to evolve and are still the most
common organisms today.

Eukaryotic Cells
Eukaryotic cells are cells that
contain a nucleus. A typical
eukaryotic cell is shown in
Figure below. Eukaryotic
cells are usually larger than
prokaryotic cells, and they
are found mainly in
multicellular organisms. Organisms with eukaryotic cells are
called eukaryotes, and they range from fungi to people.

11
CELL TYPES
Cells in the human body number in the trillions and come in all
shapes and sizes. These tiny structures are the basic unit of living
organisms. Cells comprise tissues, tissues comprise organs,
organs form organ systems, and organ systems work together in
an organism. There are hundreds of different types of cells in the
body and the structure of a cell is perfectly suited for the role it
performs. Cells of the digestive system, for instance, are different
in structure and function from cells of the skeletal system. No
matter the differences, cells of the body depend on each another,
either directly or indirectly, to keep the body functioning as one
unit. The following are examples of different types of cells in the
body.

Stem Cells
Stem cells are unique cells of the body in
that they are unspecialized and have the
ability to develop into specialized cells for
specific organs or to develop into tissues.
Stem cells are able to divide and replicate
many times in order to replenish and
repair tissue. In the field of stem cell
research, scientists are attempting to take advantage of the
renewal properties of stem cells by utilizing them to generate cells
for tissue repair, organ transplantation, and for the treatment of
disease.

Bone Cells
Bones are a type of mineralized
connective tissue and a major
component of the skeletal system.
Bone cells form bone, which is
composed of a matrix of collagen
and calcium phosphate minerals.
12
There are three primary types of bone cells in the body.
Osteoclasts are large cells that decompose bone for resorption
and assimilation. Osteoblasts regulate bone mineralization and
produce osteoid (organic substance of bone matrix), which
mineralizes to form bone. Osteoblasts mature to form osteocytes.
Osteocytes aid in the formation of bone and help maintain calcium
balance.

Blood Cells
From transporting oxygen throughout
the body to fighting infection, cells of
the blood are vital to life. The three
major types of cells in the blood are
red blood cells, white blood cells, and
platelets. Red blood cells determine
blood type and are also responsible
for transporting oxygen to cells.
White blood cells are immune system cells that destroy
pathogens and provide immunity. Platelets help to clot blood and
prevent excessive blood loss due to broken or damaged blood
vessels. Blood cells are produced by bone marrow.

Muscle Cells
Muscle cells form muscle tissue,
which is important for bodily
movement. Skeletal muscle tissue
attaches to bones enabling voluntary
movement. Skeletal muscle cells are
covered by connective tissue, which
protects and supports the muscle
fiber bundles. Cardiac muscle cells form involuntary cardiac
muscle found in the heart. These cells aid in heart contraction and
are joined to one another by intercalated discs, which allow for
synchronization of the heartbeat. Smooth muscle tissue is not
striated like cardiac and skeletal muscle. Smooth muscle is
13
involuntary muscle that lines body cavities and forms the walls of
many organs (kidneys, intestines, blood vessels, lung airways,
etc.).

Fat Cells
Fat cells, also called adipocytes, are
the major cell component of adipose
tissue. Adipocytes contain droplets of
stored fat (triglycerides) that can be
used for energy. When fat is being
stored, fat cells swell and become
round in shape. When fat is being
used, these cells shrink in size.
Adipose cells also have an endocrine function as they produce
hormones that influence sex hormone metabolism, blood
pressure regulation, insulin sensitivity, fat storage and use, blood
clotting, and cell signaling.

Skin Cells
The skin is composed of a layer of
epithelial tissue (epidermis) that is
supported by a layer of connective
tissue (dermis) and an underlying
subcutaneous layer. The outermost
layer of the skin is composed of flat,
squamous epithelial cells that are
closely packed together. The skin protects the internal structures
of the body from damage, prevents dehydration, acts as a barrier
against germs, stores fat, and produces vitamins and hormones.

Nerve Cells
Nerve cells or neurons are the basic unit of
the nervous system. Nerves send signals
among the brain, spinal cord, and other

14
body organs via nerve impulses. A neuron consists of two major
parts: a cell body and nerve processes. The central cell body
contains the neuron's nucleus, associated cytoplasm, and
organelles. Nerve processes are "finger-like" projections (axons
and dendrites) that extend from the cell body and are able to
conduct and transmit signals.

Endothelial Cells
Endothelial cells form the inner lining of
cardiovascular system and lymphatic system
structures. These cells makes up the inner
layer of blood vessels, lymphatic vessels,
and organs including the brain, lungs, skin,
and heart. Endothelial cells are responsible for angiogenesis or
the creation of new blood vessels. They also regulate the
movement of macromolecules, gases, and fluid between the
blood and surrounding tissues, and help to regulate blood
pressure.

Sex Cells
Sex cells or gametes are reproductive
cells produced in male and female
gonads. Male sex cells or sperm are
motile and have a long, tail-like projection
called a flagellum. Female sex cells or ova
are non-motile and relatively large in comparison to the male
gamete. In sexual reproduction, sex cells unite during fertilization
to form a new individual. While other body cells replicate by
mitosis, gametes reproduce by meiosis.

Pancreatic Cells
The pancreas functions as both an
exocrine and endocrine organ.
Exocrine acinar cells produce and

15
secrete digestive enzymes that are transported by ducts to the
small intestine. A very small percentage of pancreatic cells have
endocrine function and secrete hormones. Pancreatic endocrine
cells are found in small clusters called islets of Langerhans.
Hormones produced by these cells include insulin, glucagon, and
gastrin. Pancreatic cells are important for regulating blood
glucose concentration levels as well as for the digestion of
proteins, carbohydrates, and fats.

Cancer Cells
Cancer results from the
development of abnormal
properties in normal cells that
enable them to divide
uncontrollably and spread to other
locations. Cancer cell development
can be caused by mutations that
occur from factors such as chemicals, radiation, ultraviolet light,
chromosome replication errors, or viral infection.

16
CELL CYCLE
The cell cycle is a cycle of stages that cells pass through to allow
them to divide and produce new cells. It is sometimes referred to
as the “cell division cycle” for that reason.
New cells are born through the division of their “parent” cell,
producing two “daughter” cells from one single “parent” cell.
Daughter cells start life small, containing only half of the parent
cell’s cytoplasm and only one copy of the DNA that is the cell’s
“blueprint” or “source code” for survival. In order to divide and
produce “daughter cells” of their own, the newborn cells must
grow and produce more copies of vital cellular machinery –
including their DNA.
Mitosis
Mitosis is a process where a
single cell divides into two
identical daughter cells (cell
division).
 During mitosis one cell
divides once to form two
identical cells.
 The major purpose of mitosis is for growth and to replace
worn out cells.
 If not corrected in time, mistakes made during mitosis can
result in changes in the DNA that can potentially lead to
genetic disorders.

17
Mitosis is divided into five phases:

1. Interphase:
 The DNA in the cell is copied in preparation for cell division,
these results in two identical full sets of chromosomes.
 Outside of the nucleus are two centrosomes, each
containing a pair of centrioles, these structures are critical for
the process of cell division.
 During interphase, microtubules extend from these
centrosomes.

2. Prophase:
 The chromosomes condense into X-shaped structures that
can be easily seen under a microscope.
 Each chromosome is composed of two sister chromatids,
containing identical genetic information.
 The chromosomes pair up so that both copies of
chromosome 1 are together; both copies of chromosome 2
are together, and so on.
 At the end of prophase the membrane around the nucleus in
the cell dissolves away releasing the chromosomes.
 The mitotic spindle, consisting of the microtubules and other
proteins, extends across the cell between the centrioles as
they move to opposite poles of the cell.

3. Metaphase:
 The chromosomes line up neatly end-to-end along the
center (equator) of the cell.

18
  The centrioles are now at opposite poles of the cell with the
mitotic spindle fibres extending from them.
 The mitotic spindle fibers attach to each of the sister
chromatids.

4. Anaphase:
 The sisters’ chromatids are then pulled apart by the mitotic
spindle which pulls one chromatid to one pole and the other
chromatid to the opposite pole.

5. Telophase:
 At each pole of the cell a full set of chromosomes gather
together.
 A membrane forms around each set of chromosomes to
create two new nuclei.
 The single cell then pinches in the middle to form two
separate daughter cells each containing a full set of
chromosomes within a nucleus. This process is known as
cytokinesis.

Meiosis
Meiosis is a process where a single cell
divides twice to produce four cells
containing half the original amount of
genetic information. These cells are our
sex cells – sperm in males, eggs in
females.
 During meiosis one cell divides twice
to form four daughter cells.

19
  These four daughter cells only have half the number of
chromosomes of the parent cell – they are haploid.
 Meiosis produces our sex cells or gametes (Eggs in females
and sperm in males).
Meiosis can be divided into nine stages. These are divided
between the first time the cell divides (meiosis I) and the second
time it divides (meiosis II):
Meiosis I

1. Interphase:
 The DNA in the cell is copied resulting in two identical full
sets of chromosomes.
 Outside of the nucleus are two centrosomes, each
containing a pair of centrioles, these structures are critical for
the process of cell division.
 During interphase, microtubules extend from these
centrosomes.

2. Prophase I:
 The copied chromosomes condense into X-shaped
structures that can be easily seen under a microscope.
 Each chromosome is composed of two sister chromatids
containing identical genetic information.
 The chromosomes pair up so that both copies of
chromosome 1 are together; both copies of chromosome 2
are together, and so on.
 The pairs of chromosomes may then exchange bits of DNA
in a process called recombination or crossing over.
 At the end of Prophase I the membrane around the nucleus
in the cell dissolves away, releasing the chromosomes.
20
  The meiotic spindle, consisting of microtubules and other
proteins, extends across the cell between the centrioles.

3. Metaphase I:
 The chromosome pairs line up next to each other along the
center (equator) of the cell.
 The centrioles are now at opposites poles of the cell with the
meiotic spindles extending from them.
 The meiotic spindle fibers attach to one chromosome of
each pair.

4. Anaphase I:
 The pair of chromosomes are then pulled apart by the
meiotic spindle, which pulls one chromosome to one pole of
the cell and the other chromosome to the opposite pole.
 In meiosis I the sister chromatids stay together. This is
different to what happens in mitosis and meiosis II.

5. Telophase I and cytokinesis:

 The chromosomes complete their move to the opposite
poles of the cell.
 At each pole of the cell a full set of chromosomes gather
together.
 A membrane forms around each set of chromosomes to
create two new nuclei.
 The single cell then pinches in the middle to form two
separate daughter cells each containing a full set of
chromosomes within a nucleus. This process is known as
cytokinesis.

21
  Meiosis II

6. Prophase II:
 Now there are two daughter cells, each with 23
chromosomes (23 pairs of chromatids).
 In each of the two daughter cells the chromosomes
condense again into visible X-shaped structures that can be
easily seen under a microscope.
 The membrane around the nucleus in each daughter cell
dissolves away releasing the chromosomes.
 The centrioles duplicate.
 The meiotic spindle forms again.

7. Metaphase II:
 In each of the two daughter cells the chromosomes (pair of
sister chromatids) line up end-to-end along the equator of
the cell.
 The centrioles are now at opposites poles in each of the
daughter cells.
 Meiotic spindle fibers at each pole of the cell attach to each
of the sister chromatids.

8. Anaphase II:
 The sister chromatids are then pulled to opposite poles due
to the action of the meiotic spindle.
 The separated chromatids are now individual chromosomes.

9. Telophase II and cytokinesis:

22
 The chromosomes complete their move to the opposite
poles of the cell.
 At each pole of the cell a full set of chromosomes gather
together.
 A membrane forms around each set of chromosomes to
create two new cell nuclei.
 This is the last phase of meiosis; however cell division is not
complete without another round of cytokinesis.
 Once cytokinesis is complete there are four granddaughter
cells, each with half a set of chromosomes (haploid):
 in males, these four cells are all sperm cells
 in females, one of the cells is an egg cell while the other
three are polar bodies (small cells that do not develop into
eggs).

23
TRANSPORT MECHANISMS
It is of seminal importance to the cell that it be able to
transport molecules in and out of itself. Imagine that a protein
having multiple transmembrane domains is structured so that
these domains are arrayed in the plane of the membrane in a
circle, thereby forming a cylinder, or, better yet, a barrel when
viewed from the outside of the cell, with each of the staves of the
barrel being one of the transmembrane domains. The center of
the barrel could constitute a hole in the plasma membrane that is
isolated from the lipid bilayer by an array of transmembrane
domains around it. This hole could be used to transport
substances into the cell or out from the cell. In fact, this hole can
be a relatively hydrophilic environment if hydrophilic side chains
from the membrane-spanning chains surrounding the hole
protrude into the hole itself.

Simple Diffusion
Simple diffusion means that the
molecules can pass directly
through the membrane.
Diffusion is always down a
concentration gradient. This
limits the maximum possible
concentration of the molecule
inside the cell (or outside the cell
if it is a waste product). The effectiveness of diffusion is also
limited by the diffusion rate of the molecule (see Purves box 5.B).
Therefore, though diffusion is an effective enough transport
mechanism for some substances (such as H2O), the cell must
utilize other mechanisms for many of its transport needs.

24
 Facilitated
Diffusion
Facilitated diffusion utilizes
membrane protein channels
to allow charged molecules
(which otherwise could not
diffuse across the cell
membrane) to freely diffuse
in and out of the cell. These
channels come into greatest use with small ions like K+, Na+, and
Cl-. The speed of facilitated transport is limited by the number of
protein channels available, whereas the speed of diffusion is
dependent only on the concentration gradient.

Active Transport
Active transport requires the
expenditure of energy to
transport the molecule from
one side of the membrane
to the other, but active
transport is the only type of
transport that can actually
take molecules up their
concentration gradient as
well as down. Similarly to facilitated transport, active transport is
limited by the number of protein transporters present.

25
Chapter II
BIOMOLECULES

26
STRUCTURES AND FUNCTIONS OF
BIOMOLECULES

Biomolecule
Biomolecule, also called biological molecule, any of numerous
substances that are produced by cells and living organisms.
Biomolecules have a wide range of sizes and structures and
perform a vast array of functions. Biomolecules include large
macromolecules (or polyanions) such as proteins, carbohydrates,
lipids, and nucleic acids, as well as small molecules such as
primary metabolites, secondary metabolites, and natural products.
A more general name for this class of material is biological
materials. Biomolecules are usually endogenous but may also be
exogenous. For example, pharmaceutical drugs may be natural
products or semisynthetic (biopharmaceuticals) or they may be
totally synthetic.

27
CARBOHYDRATES
Carbohydrates are the most abundant
biomolecule on Earth. Living organisms
use carbohydrates as accessible energy
to fuel cellular reactions and for
structural support inside cell walls. Cells
attach carbohydrate molecules to
proteins and lipids, modifying structures
to enhance functionality. For example,
small carbohydrate molecules bonded to
lipids in cell membranes improve cell identification, cell signaling,
and complex immune system responses. The carbohydrate
monomers deoxyribose and ribose are integral parts of DNA and
RNA molecules. To recognize how carbohydrates function in
living cells, we must understand their chemical structure. The
structure of carbohydrates determines how energy is stored in
carbohydrate bonds during photosynthesis and how breaking
these bonds releases energy during cellular respiration.
Monosaccharides consist of a
carbon chain of three or more
carbon atoms containing a hydroxyl
group attached to every carbon
except one. The lone carbon atom
is double-bonded to an oxygen
atom, and this carbonyl group may
be in any position along the carbon chain. Therefore, one oxygen
atom and two hydrogen atoms are present for every carbon atom
in a monosaccharide. Consequently, we can define
monosaccharides as possessing the molecular formula (CH2O)n,

28
where n equals the number of carbon atoms and must be greater
than or equal to three.
Monosaccharides (Greek, meaning “single sugar”) are simple
sugars and are frequently named using the suffix –ose. Sugars
with the carbonyl group attached to a carbon at the end of the
chain are aldoses (“aldehyde sugar”) such as glucose. When the
carbonyl group is located anywhere other than the end of the
carbon chain, the monosaccharide is a ketose (“ketone sugar”)
such as fructose.

Because the position of individual

atoms within a sugar molecule
varies, many monosaccharides are
isomers of one another. For
example, glucose and fructose
share the molecular formula
C6H12O6, but are structurally
different. Differences between
isomers are not always as readily apparent as in structural
isomers like glucose and fructose. More subtle stereoisomers
share the same order of covalent bonds between atoms, but differ
in the three-dimensional positions of the atoms around one or
more individual carbon atoms. For example, glucose and
galactose are stereoisomers, and appear very similar in drawings.
Small details such as whether an – OH extends from the right or
left side of each carbon atom are extremely important to taste,
chemical reactivity, and human health.

29
LIPIDS
Unlike other biomolecule
groups, lipids are not
defined by the presence of
specific structural
characteristics. Lipids are
insoluble biomolecules,
defined by an overall lack
of polarity necessary for solubility in water-based solutions. In
popular culture, fats are synonymous with lipids, giving lipids a
negative role in diet and health. However, lipids play vital roles in
many cellular processes including energy storage, structural
support, protection, and communication. Common lipid groups
include waxes, steroids, fats, and phospholipids.

One type of lipid monomer, a fatty acid, consists of one carboxyl

group at the end of a linear hydrocarbon containing at least four
carbon atoms. Because hydrocarbon chains are nonpolar, fatty
acids with long hydrocarbon chains are mainly hydrophobic
(insoluble in water) despite having one polar functional group.
Unlike other biomolecule groups, fatty acid monomers are not
directly bonded to each other in polymer chains. Dehydration
synthesis reactions in lipids form an ester linkage between the
carboxyl group of a fatty acid and the hydroxyl group of an alcohol
monomer such as glycerol. Monomer and polymer structures vary
widely depending on the type of lipid, and not all lipid groups
contain fatty acids.

Fatty acids can be saturated or unsaturated. We determine

saturation level by identifying the types of covalent bonds present

30
 in the hydrocarbon chain of a fatty
acid. Before examining the
hydrocarbon chain of a fatty acid,
first identify the one oxygen-to-
carbon double bond in the carboxyl
functional group, which is present in
all fatty acids and does not affect
saturation. If all carbon-to-carbon
bonds in the hydrocarbon chain are
single covalent bonds, the fatty acid is saturated with as many
hydrogen atoms as possible. Therefore, the fatty acid is
saturated. When one or more carbon-to-carbon double bonds are
present, the fatty acid is not saturated with hydrogen atoms and is
called unsaturated. The carbon atoms involved in each double
bond are bonded to one less hydrogen atom than the carbon
atoms involved in each single bond. This is an unsaturated state
because changing a double bond into a single bond would
increase the number of hydrogen atoms.

The degree of saturation of each fatty acid in a fat or other lipid

polymer affects the structure and function of that biomolecule. In
particular, saturated and unsaturated fatty acids have significant
effects on dietary fat appearance, taste, digestion and human
health.

cis and trans fatty acid structural

modelsLike many biomolecules,
fatty acids form isomers when a
double bond is present because
the double bond locks the atoms
around it into a fixed position. The

31
specific isomers present in a particular lipid have significant
effects on the lipid’s structure and function in living organisms.
Almost all living organisms synthesize and incorporate cis-fatty
acids into their lipids. Cis-fatty acids are isomers in which the
continuing carbon chains on each end of the double bond face the
same direction. A cis-isomer is bent or “kinked,” preventing cis-
fatty acids from packing closely together.

Trans-fatty acids are isomers often created during commercial

food production. In trans-fatty acids, the continuing carbon chains
face opposite directions around a double bond. Trans-isomers are
structurally similar to saturated fatty acids because the
hydrocarbon chain does not contain a “kink.” Both saturated and
trans-fatty acids pack closely together as monomers and when
they are present in fats.

Waxes are bees making

honeycomb class of lipids that
contain two monomers, one fatty
acid bonded through an ester
linkage to one alcohol (a
hydrocarbon containing a hydroxyl
group). The hydrocarbon chain in
the alcohol monomer of waxes varies from a short linear chain to
complex carbon ring structures. Waxes provide protective barriers
to prevent water loss and protect cells. Waxes protect seeds and
nutrients inside plant fruits and coat the surface of plant leaves,
forming a cuticle to prevent water loss. Bees synthesize beeswax
honeycombs for storing food and protecting offspring. Waxes
prevent dehydration from body surfaces of many insects and
repel water on the surface of bird feathers and some animal furs.

32
 Steroids are a class of
lipids containing four fused
(directly attached) carbon
rings. Although steroids can
bond to fatty acids, steroid
molecules do not contain a
fatty acid chain, and the
monomer of a steroid
biomolecule is difficult to
define. Steroid rings usually contain one or a few small functional
groups including hydroxyls, carbonyls, or carboxyls. Cholesterol
and other steroids containing a hydroxyl group are called sterols.
Cholesterol and related sterols are present in animal cell
membranes and are precursors for the synthesis of many vital
steroids and other sterol derivatives.

Many steroids and their derivatives perform vital cellular functions.

Steroid hormones such as estrogen and testosterone control
reproductive processes and development. Bile salts and fat-
soluble vitamins are lipids derived from cholesterol and related
lipid molecules. Scientists modify steroids in laboratories,
synthesizing medical drugs that work by mimicking natural
compounds in the human body. Anabolic steroids, a specific class
of artificially manufactured steroid drugs, stimulate muscle growth
and increased development of secondary sex characteristics. In
individuals with metabolic diseases, anabolic steroids can
improve health by restoring normal signals, but anabolic steroid
use by otherwise healthy individuals can be extremely harmful to
internal organ function.

33
PROTEIN
Proteins are the most diverse
biomolecules on Earth, performing
many functions required for life.
Protein enzymes are biological
catalysts, maintaining life by
regulating where and when cellular
reactions occur. Structural proteins
provide internal and external support
to protect and maintain cell shape.
For example, keratins are an important class of structural proteins
found in the hair, skin, nails, and feathers of animals. Motility
proteins provide the basis for cellular and whole organism
movement, including muscle motor proteins that can move entire
animals! Membrane proteins transmit signals during cell-to-cell
communication, transport molecules into and out of cells, and
protect living organisms by identifying and flagging invaders.

Protein functions are so diverse because of the many unique

three-dimensional structures protein polymers form. Despite such
variety, proteins also share several specific structural
characteristics in their monomers, the amino acids. Structural
similarities among amino acids make protein synthesis a uniform
and regulated process; however, each amino acid contains a
unique structural component as well. Specific differences between
each amino acid interact to create unique three-dimensional
protein structures. Combined, the similarities and differences
between amino acids explain how cells can build a diverse pool of
proteins from the same set of building blocks.

34
 In every amino acid, one
central carbon atom exists -
the alpha-carbon (α-carbon).
Of the four atom groups
covalently bonded to the α-
carbon, three are the same in
all amino acids. The α-carbon
is always directly bonded to
one amino group and to one
carboxyl group (carboxylic
acid). The name amino acid derives from the presence of these
two functional groups (amino + acid). All amino acids share a third
common covalent bond to a hydrogen atom, but the fourth atom
(or atomic group) bonded to the α-carbon is unique in each amino
acid.
The fourth α-carbon bond may link to another single hydrogen
atom, as in glycine, or to a group of atoms. Atom groups range in
both size and polarity or charge. For example, lysine contains a
large and ionic atom group. For simplicity, when a specific amino
acid is not identified, biologists use the term “R-group” to refer to
the fourth atom or group bonded to the α-carbon. The term “R”
signifies the rest of the molecule and is used when discussing
general structure and reactivity of amino acids without
complicating a structure by inclusion of R-group details.
Protein synthesis involves building
a polymer of amino acids with
complex three-dimensional
structure. Dehydration synthesis
forms a peptide bond between
amino acids and releases a water
molecule. A dipeptide forms when
a peptide bond is created between
two individual amino acids, connecting the carboxyl-group carbon

35
of one amino acid and the amino-group nitrogen of another amino
acid. As additional amino acids are bonded through dehydration
synthesis, a short chain (peptide) grows. Polypeptides are
formed as peptide chain lengths reach one hundred or more
amino acids. Proteins form as amino acids in one or more
polypeptides chemically interact to create a complex three-
dimensional structure.
Living organisms synthesize almost all
proteins using only twenty different
amino acids. Polypeptides form a
unique three-dimensional structure
based on the type and position
(sequence) of these amino acids. Within
the sequence, amino acid R-groups
form chemical interactions that create a
specific three-dimensional structure.
These R-groups are commonly called
“side chains” because they are not involved in the peptide bonds.
The R-groups stick out on the side of a polypeptide, freeing them
to chemically interact with one another. Side chain interactions
form each protein’s specific structure, a structure uniquely
capable of performing that protein’s cellular function.
Unlike polysaccharides, polypeptide chains are assembled with a
wide variety of amino acids in each polymer. The set of twenty
amino acids commonly found in biological proteins is directly
responsible for the diversity of protein structures in living cells.
Each protein differs in several aspects that determine structure
and, therefore, function. A protein may be composed of one or
more polypeptide strands. A cell’s genes determine the length of
each polypeptide strand, as well as the type and position of each
amino acid in the sequence. Together, these factors determine
protein structure, which determines the function a protein can
perform.

36
ENZYMES
Enzymes are large biomolecules
that are responsible for many
chemical reactions that are
necessary to sustain life.
Enzymes are a protein molecule
and are biological catalysts.
Enzymes increase the rate of the
reaction. Enzymes are specific;
they function with only one
reactant to produce specific
products. Enzymes have a three-dimensional structure and they
utilize organic molecules like biotin and inorganic molecules like
metal ions (magnesium ions) for assistance in catalysis.
Substrate is the reactant in an enzyme catalyzed reaction. The
portion of the molecule that is responsible for catalytic action of
enzyme is the active site.

Enzyme Classification
The current system of nomenclature of enzymes uses the name
of the substrate or the type of the reaction involved, and ends with
"-ase". Example:'Maltase'- substrate is maltose. 'Hydrolases'-
reaction type is hydrolysis reaction.

Classification of enzymes
Enzymes are classified based on the reactions they catalyze into
6 groups: Oxidoreductases, transferases, hydrolases, lyases,
isomearses, ligases.
Oxidoreductases - Oxidoreductase are the enzymes that
catalyze oxidation-reduction reactions. These emzymes are

37
important as these reactions are responsible for the production of
heat and energy.
Transferases - Transferases are the enzymes that catalyze
reactions where transfer of functional group between two
substrates takes place.
Hydrolases - Hydrolases are also known as hydrolytic enzymes,
they catalyze the hydrolysis reactions of carbohydrates, proteins
and esters.
Lyases - Lyases are enzymes that catlayze the reaction
invvolving the removal of groups from substrates by processes
other than hydrolysis by the formation of double bonds.
Isomerases - Isomerases are enzymes that catalyze the
reactions where interconversion of cis-trans isomers is involved.
Ligases - Ligases are also known as synthases, these are the
enzymes that catalyze the reactions where coupling of two
compounds is involved with the breaking of pyrophosphate bonds.

Structure of Enzymes
Enzymes are proteins, like the proteins the enzymes contain
chains of amino acids linked together. The characteristic of an
enzyme is determined by the sequence of amino acid
arrangement. When the bonds between the amino acid are weak,
they may be broken by conditions of high temperatures or high
levels of acids. When these bonds are broken, the enzymes
become nonfunctional. The enzymes that take part in the
chemical reaction do not undergo permanent changes and hence
they remain unchanged to the end of the reaction.
Enzymes are highly selective, they catalyze specific reactions
only. Enzymes have a part of a molecule where it just has the
shape where only certain kind of substrate can bind to it; this site

38
of activity is known as the 'active site'. The molecule that reacts
and binds to the enzyme is known as the 'substrate'.
Most of the enzymes consist of the protein and the non-protein
part called the 'cofactor'. The proteins in the enzymes are usually
globular proteins. The protein part of the enzymes is known
'apoenzyme', while the non-protein part is known as the cofactor.
Together the apoenzyme and cofactors are known as the
'holoenzyme'.

Cofactors may be of three types: prosthetic groups, activators

and coenzymes.
Prosthetic groups are organic groups that are permanently
bound to the enzyme. Example: Heme groups of cytochromes
and bitotin group of acetyl-CoA carboxylase.
Activators are cations- they are positively charged metal ions.
Example: Fe - cytochrome oxidase, CU - catalase, Zn - alcohol
dehydrogenase, Mg - glucose - 6 - phosphate, etc.
Coenzymes are organic molecules, usually vitamins or made
from vitamins. they are not bound permanently to the enzyme, but
they combine with the enzyme-substrate complex temporarily.
Example: FAD - Flavin Adenine Dinucleotide, FMN - Flavin Mono
Nucleotide, NAD - Nicotinamide Adenine Dinucleotide, NADP -
Nicotinamide Adenine Dinucleotide.

39
Function of Enzymes
Biological Functions of Enzymes:
 Enzymes perform a wide variety of functions in living
organisms.
 They are major components in signal transduction and cell
regulation, kinases and phosphatases help in this function.
 They take part in movement with the help of the protein
myosin which aids in muscle contraction.
 Also other ATPases in the cell membrane acts as ion pumps in
active transport mechanism.
 Enzymes present in the viruses are for infecting cell.
 Enzymes play a important role in the digestive activity of the
enzymes.
 Amylases and proteases are enzyme sthat breakdown large
molecules into absorbable molecules.
 Variuos enzymes owrk together in a order forming metabolic
pathways. Example: Glycolysis.

Industrial Application of Enzymes:

Food Processing - Amylases enzymes from fungi and plants are
used in production of sugars from starch in making corn-syrup.
Catalyze enzyme is used in breakdown of starch into sugar, and
in baking fermentation process of yeast raises the dough.
Proteases enzyme help in manufacture of biscuits in lowering the
protein level.
Baby foods - Trypsin enzyme is used in pre-digestion of baby
foods.
Brewing industry - Enzymes from barley are widely used in
brewing industries.
40
NUCLEIC ACID
Possibly the first biomolecules to
support life, acids store and
transfer cellular information and
transfer energy in all living
organisms. Deoxyribonucleic
acid, better known as DNA,
stores hereditary information in
small segments called genes inside long polymer strands.
Ribonucleic acid (RNA) delivers gene information from DNA to
create functional products. Other RNA molecules are active,
three-dimensional products that provide enzymatic or regulatory
functions inside cells. An enormous body of evidence suggests
that RNA was the original molecule of life due to RNA’s ability to
both store hereditary information and provide functional activity as
enzymes.
Each component of nucleic acid structure plays an important role
in DNA and RNA’s ability to store and transmit information during
a cell’s life and to deliver a copy into offspring. Nucleic acids are
polymers of individual nucleotide monomers. Each nucleotide is
composed of three parts: a 5-carbon sugar, a phosphate group,
and a nitrogenous base. Only two 5-carbon sugars are found in
nature: ribose and deoxyribose. Deoxyribose is a ribose derivative
in which an oxygen atom is missing from one carbon; the carbon
was deoxygenated. DNA contains deoxyribose nucleotides while
RNA contains ribose nucleotides. DNA is more stable than RNA
because of the reduction in reactive oxygen atoms.

41
 A 5-carbon sugar (ribose or
deoxyribose) forms the central
molecule in a nucleotide. By
convention, the carbon atoms in the
sugar are numbered from the
original carbonyl position on the
chain using a number plus the prime
symbol (‘). For example, a
nitrogenous base is attached to the
1’ (pronounced “one prime”) carbon position, which was originally
the sugar’s carbonyl group. A phosphate group is attached to the
5’ carbon position, the carbon atom that is outside the sugar ring.
Each nucleotide includes one nitrogenous base, attached to the 1’
carbon of the sugar. A nitrogenous base is an organic molecule
containing both carbon and nitrogen atoms. The name
nitrogenous base signifies that several nitrogen atoms act as
bases in solution. In nucleic acids, nitrogenous bases contain
either one ring or two fused rings. Purines are double-ring
nitrogenous bases found in nature and include adenine and
guanine. Thymine, cytosine and uracil are pyrimidines, single-ring
nitrogenous bases found in nature.
The sugar and nitrogenous
base present in a nucleotide
define the nucleotide and its
functional role. Because the
sugar and phosphate are
similar structural components
in all nucleotides, scientists
frequently use a shorthand
notation to identify a nucleotide by naming only the unique
nitrogenous base present. For example, “adenine” may refer to
the nitrogenous base alone or to a nucleotide containing adenine,
depending on the context. Similarly, a nucleotide is often called a

42
“base,” a shorthand reference to the presence of a nitrogenous
base in the nucleotide structure.
Like monosaccharaides, nucleotides and short nucleotide chains
perform important cellular functions. Adenosine triphosphate
(ATP) is an important energy carrier in living organisms. ATP is
composed of adenine, a ribose sugar, and three phosphate
groups bonded sequentially. The bonding of three anionic
phosphate groups in a row forces several negative ions into close
proximity, an unfavorable state. Reactions that remove the
outermost phosphate group (forming adenosine diphosphate, or
ADP) release energy for use in other chemical reactions.
Dinucleotides such as NAD+, NADP+, and FAD act
as coenzymes, delivering energy by transferring electrons from
one reaction to another.
DNA polymers store hereditary
information for each living organism.
The unique structure of a DNA
polymer provides a template for
identification and delivery of the
information inside each gene and for
accurate replication of DNA during
cell division. RNA polymers perform a
variety of cellular functions, including
delivering DNA messages to
synthesize proteins and acting as
enzymes or regulatory molecules in
many cellular processes. Although less complex than protein
structure, RNA polymers frequently form three-dimensional
structures specific to their function. Interactions between the
nitrogenous bases in DNA and RNA polymers form the basis for
the structure, function, and accurate replication of nucleic acids.

43
Chapter III
ENERGY
TRANSFORMATION

44
ATP-ADP CYCLE
The ATP-ADP cycle has everything to do with the storage and
use of energy in living things. Energy is defined as the ability to do
work. There are two types of energy:
Potential Energy is stored energy that is currently not in use, but
it is available and can be released at a later point. Chemical
bonds contain potential energy because when they are broken
their energy stored within them is released.
Kinetic Energy is also called free energy. This is energy that is
being used now and it is doing work. Synthesis is a type of work
that is done within cells, and in this process it creates molecules
or organelles.

45
 Adenosine
triphosphate, also
known as ATP,
contains stored
energy. A single
molecule of ATP
contains ten carbon
atoms, sixteen
hydrogen, five nitrogen, thirteen oxygen and 3 phosphorus atoms.
The shorthand formula is C10H16N5O13P3. Note in the diagram
that there are three phosphate groups attached to a
conglomeration we call adenosine. The last two bonds on the
phosphate groups contain especially high energy and therefore
are very useful for doing work within living cells.

To take advantage
of the high energy
bonds in ATP there
are within many
cells a substance
called ATPase. This
is really an ATP
splitter. It cuts off
the last phosphate group of the ATP molecule turning it into
adenosine diphosphate. (Note the "di-" prefix means "two".) In
the process of this splitting a great deal of energy is released and
used in the cell to do work, move things and build things.

When carbohydrates and other foods are consumed by the body,

they also contain energy. When they are broken down, the energy
is released and, in many cases, the energy is used to reattach the

46
phosphate molecule to the ADP, turning it back into ATP. Then
the cycle of bond-breaking and bond-making begins all over
again, alternately releasing and storing energy, as needed. A
convenient way to remember the cycle is ATP = ADP + P +
antomaEnergy1.

The adding and subtracting

of a phosphate to ADP is a
metabolic process.
Metabolic processes can be
separated into two phases;
catabolism is the process
of breaking down (breaking
down food to make ATP),
and anabolism is the
process of building up
(using the energy created in
converting ATP to ADP to build up cells or move molecules
around the cell). The ATP - ADP cycle occurs in plants (in
photosynthesis) and animals.

47