Ministry of Higher Education and

Scientific Research
University of Baghdad
College of Science
Department of Biology

General Zoology
2022-2023

‫ الدراستين الصباحيت والمسائيت‬- ‫المرحلت األولى‬

‫الفصل الدراسي األول‬

: ‫تدريسي المادة‬
‫ فاضل دمحم لفتت‬.‫د‬.‫م‬.‫ ركاد دمحم خماس ا‬.‫د‬.‫م‬.‫أ‬
‫ زينب حسين خضير‬.‫د‬.‫م‬

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 Lecture one: Introduction to Biology

What is Biology?
Biology is the natural science that studies life and living organisms,
including their physical structure, chemical processes, molecular
interactions, physiological mechanisms, development and evolution.
Biology recognizes the cell as the basic unit of life, genes as the basic unit
of heredity, and evolution as the engine that induce
the creation and extinction of species.

Characteristics of living organisms:

An individual living thing, such as an animal or a plant, is called an
organism. The term ‗living organism‘ is usually used to describe something
which displays all the characteristics of living things. There are seven
activities which make organisms different from non-living things, they are:
1- Nutrition: Living things take in materials from their surroundings that
they use for growth or to provide energy. Nutrition is the process by which
organisms obtain energy and raw materials from nutrients such as proteins,
carbohydrates and fats.
2- Respiration: Respiration is the release of energy from break down food
substances in all living cells to carry out the following processes.
3- Movement: All living things move, even plants move in various
different ways. The movement may be so slow that it is very difficult to see.

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4-Excretion: Excretion is defined as the removal of toxic materials, the
waste products of metabolism and substances in excess from the body of an
organism.
5- Growth: The permanent increase in cell number and size is called
growth. It is seen in all living things. It involves using food to produce new
cells.
6– Reproduction: All living organisms have the ability to produce
offspring.
7- Sensitivity: All living things are able to sense and respond to stimuli
around them such as light, temperature, water, gravity and chemical
substances.

Elements of Life
An element is one of the basic building blocks of matter; an element
cannot be broken down by chemical means. Considering the variety of living
and nonliving things in the world, it‘s remarkable that there are only 92
naturally occurring elements. It is even more surprising that over 90% of the
human body is composed of just four elements: carbon, nitrogen, oxygen,
and hydrogen.
Even so, other elements, such as iron, are important to our health. Iron-
deficiency anemia results when the diet doesn‘t contain enough iron for the
making of hemoglobin. Hemoglobin serves an important function in the
body, because it transports oxygen, another element, to our cells.
Each element has a name and a symbol. For example, carbon has been
assigned the atomic symbol C, and iron has been assigned the symbol Fe.
Some of the symbols we use for elements are derived from Latin. For

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example, the symbol for sodium is Na because natrium, in Latin, means
―sodium.‖ Likewise, the symbol for iron is Fe because ferrum means ―iron.‖
Chemists arrange the elements in a periodic table, so named because all the
elements in a column show periodicity, meaning that all the elements in each
column behave similarly during chemical reactions.

Molecules and Compounds

Atoms often bond with one another to form a chemical unit called a
molecule. A molecule can contain atoms of the same type, as when an
oxygen atom joins with another oxygen atom to form oxygen gas.
Or the atoms can be different, as when an oxygen atom joins with two
hydrogen atoms to form water. When the atoms are different, a compound
is formed.

Oxygen gas Water (H2O)

Water
Water is the most abundant molecule in living organisms, usually
making up about 60–70% of the total body weight. Furthermore, the
physical and chemical properties of water make life as we know it possible.
In water, the electrons spend more time circling the oxygen (O) atom than
the hydrogens, because oxygen has a greater ability to attract electrons than
do the hydrogen (H) atoms. The negatively charged electrons are closer to
the oxygen atom, so the oxygen atom becomes slightly negative. In turn, the

4
hydrogens are slightly positive. Therefore, water is a polar molecule; the
oxygen end of the molecule has a slight negative charge, and the hydrogen
end has a slight positive charge.

Properties of Water
1. Water is a liquid at room temperature. The hydrogen bonding between
water molecules keeps water a liquid and not a gas at room temperature.
2. Water is the universal solvent for polar (charged) molecules and
thereby facilitates chemical reactions both outside of and within our
bodies.
Ions and molecules that interact with water are called hydrophilic.
Nonionized and nonpolar molecules that do not interact with water are called
hydrophobic.
3. Water molecules are cohesive or union, so they stay together because of
hydrogen bonding, and yet, water flows freely. This property allows
dissolved and suspended molecules to be evenly distributed throughout a
system (e.g.; blood).
4. The temperature of liquid water rises and falls slowly, preventing
sudden or severe changes, therefore, water protects us and other organisms
from rapid temperature changes and helps us maintain our normal internal
temperature. Since the many hydrogen bonds that link water molecules
cause water to absorb a great deal of heat before it boils.
The control of body temperature is an example of homeostasis, which is the
maintenance of the internal environment within normal limits.
Frozen water is less dense than liquid water so that ice floats on water. As
water cools, the molecules come closer together and hydrogen bonding
becomes more rigid.
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 Lecture Two: The chemistry of cell

Molecules of Life

Four categories of organic molecules:

 Carbohydrates.
 Lipids.
 Proteins.
 Nucleic acids.
In biology, ―organic‖ doesn‘t refer to how food is grown; it refers to a
molecule that contains carbon (C) and hydrogen (H) and is usually
associated with living organisms. Each type of organic molecule in cells is
composed of subunits. When a cell forms a macromolecule, a molecule that
contains many subunits, it uses a dehydration reaction, a type of synthesis
reaction. During a dehydration reaction, a -OH (hydroxyl group) and a -H
(hydrogen atom), the equivalent of a water molecule, are removed as the
molecule forms.

 Carbohydrates

Carbohydrates are almost universally used as an energy source for living

organisms, including humans. In some organisms, such as plants and
bacteria, carbohydrates have a structural function. Carbohydrate molecules
all have carbon, hydrogen, and oxygen atoms grouped H-C-OH, which is
why they are often abbreviated as CHO. The ratio of hydrogen atoms (H) to
oxygen atoms (O) is approximately 2:1. This ratio is the same as the ratio in
water (hydros in Greek means ―water,‖ so the name ―hydrates of carbon‖
seems appropriate).

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 1- Simple Carbohydrates: Monosaccharides

Monosaccharides (mono, one; saccharide, sugar) consist of only a single

sugar molecule and are commonly called simple sugars. A monosaccharide
can have a carbon backbone of three to seven carbons. For example,
pentoses with five carbons (Ribose), and hexoses with six carbons. The
most common monosaccharide, and the one that our bodies use as an
immediate source of energy, is the hexose glucose. There are several
different ways a glucose molecule may be presented in figure (1) below:

Figure 1: Ribose and Glucose molecules

2-Disaccharides
A disaccharide (di, ―two‖; saccharide, ―sugar‖) is made by joining only two
monosaccharides together by a dehydration reaction. Maltose is a
disaccharide formed by a dehydration reaction between two glucose
molecules (Figure 2). When our hydrolytic digestive juices break down
maltose, the result is two glucose molecules. When glucose and fructose
join, the disaccharide sucrose forms, Sucrose, ordinarily derived from
sugarcane and sugar beets, is commonly known as table sugar. You may also
have heard of lactose, a disaccharide found in milk. Lactose is glucose
combined with galactose. Some people are lactose intolerant because they

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cannot break down lactose. This leads to unpleasant gastrointestinal
symptoms when they consume dairy products.

Figure 2: Disaccharide molecules (Maltose)

3-Complex Carbohydrates: Polysaccharides

Long polymers such as starch, glycogen, and cellulose are polysaccharides
(poly, many) that contain long chains of glucose subunits. Due to their
length, they are sometimes referred to as complex carbohydrates. The
polysaccharides starch and glycogen are long polymers of glucose that are
found in plants and animals, respectively. These chains may vary in length,
but may contain several thousand glucose molecules.
Both starch and glycogen are used to store glucose to meet the energy needs
of the cell. Starch and glycogen have slightly different structures, starch has
fewer side branches, or chains, than does glycogen. Because starches are the
storage form of carbohydrates in plants, we typically find them in roots
(such as potatoes) and in seeds, (such as wheat). After we eat these starchy
foods, the digestive system breaks down the starch into glucose, which then
enters the blood stream. The release of the hormone insulin from the
pancreas promotes the storage of glucose as glycogen in the liver (and to a
lesser extent, in muscle tissue). In between eating, the hormone glycogen
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instructs the liver to release glucose; this maintains the normal blood glucose
concentration at about 0.1%.
The polysaccharide cellulose, commonly called fiber, is found in plant cell
walls. In cellulose, the glucose units are joined by a slightly different type of
linkage than that in starch or glycogen. Though this might seem to be a
technicality, it is important, because we are unable to digest foods containing
this type of linkage; therefore, cellulose largely passes through our digestive
tract as fiber, or roughage.

 Lipids

Lipids are diverse in structure and function, but they have a common
characteristic: They do not dissolve in water. Their low solubility in water is
due to an absence of hydrophilic polar groups. They contain little oxygen
and consist mostly of carbon and hydrogen atoms. Lipids contain more
energy per gram than other biological molecules; therefore, fats in animals
and oils in plants function well as energy storage molecules. Others
(phospholipids) form a membrane so that the cell is separated from its
environment and has inner compartments as well. Steroids are a large class
of lipids that includes, among other molecules, the sex hormones.
Phospholipids have a phosphate group. They are constructed like fats,
except that in place of the third fatty acid, there is a phosphate group or a
grouping that contains both phosphate and nitrogen. These molecules are not
electrically neutral, as are fats, because the phosphate and nitrogen-
containing groups are ionized. They form the polar (hydrophilic) head of the
molecule, and the rest of the molecule becomes the nonpolar (hydrophobic)
tails. Phospholipids are the primary components of the plasma membranes in

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cells. In a water environment, they spontaneously form a bilayer (a sort of
molecular ―sandwich‖) in which the hydrophilic heads (the sandwich
―bread‖) face outward toward watery solutions, and the tails (the sandwich
―filling‖) form the hydrophobic interior .

 Proteins
Proteins are macromolecules with amino acid subunits. The central carbon
atom in an amino acid bonds to a hydrogen atom and to three other groups of
atoms. The name amino acid is appropriate because one of these groups is an
-NH2 (amino group) and another is a -COOH (carboxyl group, an acid). The
third group is the R group for an amino acid (figure 3).

Figure 3: The structure of the amino acid

The covalent bond between two amino acids is called a peptide bond. When
three or more amino acids are linked by peptide bonds, the chain that results
is called a polypeptide.

Proteins are of primary importance in the structure and function of cells.

Some of their many functions in humans include:

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1-Support: Some proteins are structural proteins. Keratin, for example,
makes up hair and nails. Collagen lends support to ligaments, tendons, and
skin.

2-Enzymes: Enzymes bring reactants together and thereby speed chemical

reactions in cells. They are specific for one particular type of reaction and
only function at body temperature.

3-Transport: Channel and carrier proteins in the plasma membrane allow

substances to enter and exit cells. Some other proteins transport molecules in
the blood of animals; hemoglobin in red blood cells is a complex protein that
transports oxygen.

4-Defense: Antibodies are proteins. They combine with foreign substances,

called antigens. In this way, they prevent antigens from destroying cells and
upsetting homeostasis.

5-Hormones: Hormones are regulatory proteins. They serve as intercellular

messengers that influence the metabolism of cells.

6-Motion: The contractile proteins actin and myosin allow parts of cells to
move and cause muscles to contract. Muscle contraction facilitates the
movement of animals from place to place.

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 Lecture Three: Structure and function of cell
The cell
All organisms, including humans, are composed of cells. From the
single-celled bacteria to plants and complex animals such as human, the cell
is the fundamental unit of life. Despite their importance, most cells are small
and can be seen only under a microscope. The small size of cells means that
they are measured using the smaller units of the metric system, such as the
micrometer (μm). Most human cells are about 100 μm in diameter, about the
width of a human hair. The internal contents of a cell are even smaller and,
in most cases, may only be viewed using microscopes. Because of this small
size, the cell theory, one of the fundamental principles of modern biology,
was not formulated until after the invention of the microscope in the
seventeenth century.

The Cell Theory

A cell is the basic unit of life. According to the cell theory, nothing
smaller than a cell is considered to be alive. A single-celled organism
exhibits the basic characteristics of life. There is no smaller unit of life that
is able to reproduce and grow, respond to stimuli, remain homeostatic, take
in and use materials from the environment, and become adapted to the
environment.
All living organisms are made up of cells. While many organisms, such as
the bacteria, are single-celled, other organisms, including humans and plants,
are multicellular. In multicellular organisms, cells are often organized as
tissues, such as nervous tissue and connective tissue. Even bone consists of
cells (called osteocytes) surrounded by the material that they have deposited.

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The prokaryotes and eukaryotes
Biologists classify cells into two broad categories the prokaryotes and
eukaryotes. The primary difference between a prokaryotic cell and a
eukaryotic cell is the presence or absence of a nucleus, a membrane-bound
structure that houses the DNA. Prokaryotic cells lack a nucleus, whereas
eukaryotic cells (Fig. 1) possess a nucleus.
The prokaryotic group includes two groups of bacteria, the eubacteria and
the archaebacteria. Within the eukaryotic group are the animals, plants, and
fungi, as well as some single-celled organisms called protists. Despite their
differences, both types of cells have a plasma membrane, a membrane that
regulates what enters and exits a cell.

Figure (1): Eukaryotic cell

Cell contents:
Plasma membrane
The plasma membrane is a phospholipid bilayer ―sandwich‖ made of
two layers of phospholipids. Their polar phosphate molecules form the top
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and bottom surfaces of the bilayer, and the nonpolar lipid lies in between.
The phospholipid bilayer is selectively permeable, which means it allows
certain molecules-but not others-to enter the cell. Proteins scattered
throughout the plasma membrane play important roles in allowing
substances to enter the cell. All cells are surrounded by an outer plasma
membrane (Fig. 2). The plasma membrane marks the boundary between the
outside and the inside of the cell. The function of the plasma membrane is
necessary to the life of the cell.
When phospholipids are placed in water, they naturally form a spherical
bilayer. The polar heads, being charged, are hydrophilic (attracted to water).
They position themselves to face toward the watery environment outside and
inside the cell. The nonpolar tails are hydrophobic (not attracted to water).
They turn inward toward one another, where there is no water. At body
temperature, the phospholipid bilayer is a liquid. It has the consistency of
olive oil. The proteins are able to change their position by moving laterally.
The fluid-mosaic model is a working description of membrane structure. It
states that the protein molecules form a shifting pattern within the fluid
phospholipid bilayer.

Figure 2: Organization of the plasma membrane

Cell wall
A cell wall is a structural layer surrounding some types of cells, just
outside the cell membrane. It can be tough, flexible, and sometimes rigid. It

14
provides the cell with both structural support and protection, and also acts as
a filtering mechanism. Cell walls are present in
most prokaryotes (except mollicute bacteria),
in algae, fungi and eukaryotes including plants but are absent in animals. A
major function is to act as pressure vessels, preventing over-expansion of the
cell when water enters. The composition of cell walls varies between species
and may depend on cell type and developmental stage. The primary cell wall
of land plants is composed of the
polysaccharides cellulose, hemicelluloses and pectin. Often, other polymers
such as lignin, suberin or cutin are anchored to or embedded in plant cell
walls. Algae possess cell walls made of glycoproteins and polysaccharides
such as carrageenan and agar that are absent from land plants. In bacteria,
the cell wall is composed of peptidoglycan. Fungi possess cell walls made of
the N-acetylglucosamine polymer chitin. Unusually, diatoms have a cell wall
composed of biogenic silica.

Cytoplasm
All types of cells contain cytoplasm, which is a semi-fluid medium that
contains water and various types of molecules suspended or dissolved in the
medium. The presence of proteins accounts for the semi-fluid nature of the
cytoplasm. The cytoplasm of a eukaryotic cell contains organelles, internal
compartments that have specialized functions. Eukaryotic cells have many
types of organelles. Organelles allow for the compartmentalization of the
cell. This keeps the various cellular activities separated from one another.
The Nucleus
The nucleus, a prominent structure in cells, stores genetic information
(Fig. 3). Every cell in the body contains the same genes. Genes are segments

15
of DNA that contain information for the production of specific proteins.
Each type of cell has certain genes turned on and others turned off. DNA,
with RNA acting as an intermediary, specifies the proteins in a cell. Proteins
have many functions in cells, and they help determine a cell‘s specificity.

Figure 3: The nucleus and endoplasmic reticulum

a. Nuleolus, b. nuclear envelope

Chromatin is the combination of DNA molecules and proteins that make up

the chromosomes. Chromatin can coil tightly to form visible chromosomes
during meiosis (cell division that forms reproductive cells in humans) and
mitosis (cell division that duplicates cells). Chromatin is immersed in a
semifluid medium called the nucleoplasm. A difference in pH suggests that
nucleoplasm has a different composition from cytoplasm. There were one or
more dark regions of the chromatin, these are nucleoli (sing., nucleolus),
where ribosomal RNA (rRNA) is produced. This is also where RNA joins
with proteins to form the subunits of ribosomes. The nucleus is separated

16
from the cytoplasm by a double membrane known as the nuclear envelope.
This is continuous with the endoplasmic reticulum. The nuclear envelope
has nuclear pores of sufficient size to permit the passage of ribosomal
subunits out of the nucleus and proteins into the nucleus.

Lecture Four: Structure and function of cell

Ribosomes
Ribosomes are organelles composed of proteins and rRNA. Protein
synthesis occurs at the ribosomes. Ribosomes are often attached to the
endoplasmic reticulum; but they also may occur are digested by lysosomal
enzymes into simpler subunits that then enter the cytoplasm. In a process
called autodigestion, parts of a cell may be broken down by the lysosomes.
Mitochondria
Mitochondria (sing., mitochondrion) are often called the powerhouses of
the cell. Just as a powerhouse burns fuel to produce electricity, the
mitochondria convert the chemical energy of glucose products into the
chemical energy of ATP molecules. In the process, mitochondria use up
oxygen and give off carbon dioxide. Therefore, the process of producing
ATP is called cellular respiration.
The inner membrane is folded to form little shelves called cristae. This
project into the matrix, an inner space filled with a gel-like fluid (Fig. 1).
The matrix of a mitochondrion contains enzymes for breaking down glucose
products. ATP production then occurs at the cristae. Protein complexes that

17
aid in the conversion of energy are located in an assembly-line fashion on
these membranous shelves.
The structure of a mitochondrion supports the hypothesis that mitochondria
were originally prokaryotes that became engulfed by a cell. Mitochondria
are bound by a double membrane. Mitochondria have their own genes—and
they reproduce themselves ATP-ADP Cycle. The ATP resembles that of a
rechargeable battery. The breakdown of glucose during cellular respiration is
used to produce ATP from ADP and inorganic phosphate P.

Figure 1: The structure of mitochondria

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) has two portions. Rough ER is
studded with ribosomes on the side of the membrane that ribosomes enter
the interior of the ER for additional processing and modification. Some of
these proteins are incorporated into the plasma membrane (for example,
channel proteins), whereas others are packed into vesicles and sent to the
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Golgi apparatus. The smooth ER is continuous with the rough ER, but it
does not have attached ribosomes (fig. 2). Smooth ER synthesizes the
phospholipids and other lipids that occur in membranes. It also has various
other functions, depending on the particular cell.

The Golgi apparatus

The Golgi apparatus is named for Camillo Golgi, who discovered its
presence in cells in 1898. The Golgi apparatus consists of a stack of slightly
curved saccules, whose appearance can be compared to a stack of pancakes.
Here proteins and lipids received from the ER are modified. The vesicles
that leave the Golgi apparatus move to other parts of the cell. Some vesicles
proceed to the plasma membrane, where they discharge their contents. In all,
the Golgi apparatus is involved in processing, packaging, and secretion.

Figure 2 : Endoplasmic reticulum

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Lysosomes
Lysosomes, membranous sacs produced by the Golgi apparatus, contain
hydrolytic enzymes that can break down many kinds of biomolecules. A
lysosome has a specific composition, of both its membrane proteins, and
its luminal proteins. The lumen's pH (~4.5–5.0) is optimal for the enzymes
involved in hydrolysis. Lysosomes are found in all cells of the body but are
particularly numerous in white blood cells that engulf disease-causing
microbes.
Cilia and Flagella
Cilia (sing., cilium) and flagella (sing., flagellum) are involved in
movement. The ciliated cells that line our respiratory tract sweep back up the
throat the debris trapped within mucus. Similarly, ciliated cells move an egg
along the uterine tube, where it may be fertilized by a flagellated sperm cell
(Fig. 3). Motor molecules, powered by ATP, allow the microtubules in cilia
and flagella to interact and bend and, thereby, move.

Figure 3 : Structure of cilia and flagella

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Centriole
In cell biology a centriole is a cylindrical organelle composed mainly of
a protein called tubulin. Centrioles are found in most eukaryotic cells. A
bound pair of centrioles, surrounded by a shapeless mass of dense material,
called the pericentriolar material (PCM), makes up a structure called
a centrosome. Centrioles are typically made up of nine sets of short
microtubule triplets, arranged in a cylinder (figure 4). The main function of
centrioles is to produce cilia during interphase and the aster and
the spindle during cell division. Centrioles are involved in the organization
of the mitotic spindle and in the completion of cytokinesis. The centrioles
can self-replicate during cell division. Centrioles are a very important part
of centrosomes, which are involved in organizing microtubules in
the cytoplasm. The position of the centriole determines the position of the
nucleus and plays a crucial role in the spatial arrangement of the cell.

Figure 4: The centriole structure

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Lecture Five: The Cytoskeleton
Movement and Cell Junctions
It took a high-powered electron microscope to discover that the cytoplasm
of the cell is containing by several types of protein fibers, called the
cytoskeleton. The cytoskeleton helps maintain a cell‘s shape and either
anchors the organelles or assists in their movement, as appropriate. In the
cytoskeleton, microtubules are much larger than actin filaments. Each is a
cylinder that contains rows of a protein called tubulin(Figure5).
Microtubules help maintain the shape of the cell and act as tracks along
which organelles move. During cell division, microtubules form spindle
fibers, which assist in the movement of chromosomes.
Actin filaments, made of a protein called actin, are long; extremely thin
fibers that usually occur in bundles or other groupings. Actin filaments are
involved in movement. Microvilli, which project from certain cells, contain
actin filaments.
Intermediate filaments, as their name implies, are intermediate in size
between microtubules and actin filaments.

Figure 5: Cytoskeleton

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Vacuole
A vacuole is a membrane-bound organelle which is present in all plant
and fungal cells and some protist, animal, and bacterial cells. Vacuoles are
essentially enclosed compartments which are filled with water containing
inorganic and organic molecules including enzymes in solution, though in
certain cases they may contain solids which have been engulfed. Vacuoles
are formed by the fusion of multiple membrane vesicles and are effectively
just larger forms of these. The organelle has no basic shape or size.

Vacuole Functions
The function of vacuoles varies according to the type of cell in which
they are present. In general, the functions of the vacuole include:
1) Isolating materials that might be harmful or a threat to the cell.
2) Containing waste products.
3) Containing water in plant cells.
4) Maintaining internal hydrostatic pressure within the cell.
5) Maintaining an acidic internal pH.
6) In protists, vacuoles have the function of storing food which has been
absorbed by the organism and assisting in the digestive and waste
management process for the cell. In animal cells, vacuoles assist in processes
of exocytosis and endocytosis, (there are some animal cells that do not have
any vacuoles).

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Figure 6: Food vacuole

24
 Lecture Six: Genetics

Cell reproduction

Cell reproduction is the process by which cells divide to form new

cells. Each time a cell divides, it makes a copy of all of its chromosomes,
which are tightly coiled strands of DNA, the genetic material that holds
the instructions for all life, and sends an identical copy to the new cell that is
created.

Chromosome
Chromosomes: the microscopic threadlike part of the cell that carries the
hereditary information in the form of genes consisting of DNA and
associated proteins in the nucleus (Figure 7).
Bacteria (prokaryotes) typically have one circular chromosome,
while eukaryotes usually have linear chromosomes and vary widely in their
sizes and numbers of chromosomes.
The compactness of chromosomes plays an important role in helping to
organize genetic material during cell division and enabling it to fit inside
structures such as the nucleus of a cell, the average diameter of which is
about 5 to 10 μm.

The chromosomes of a eukaryotic cell consist of two types of ribonucleic

acids , primarily DNA attached to a protein core and RNA in the cytoplasm.
Every eukaryotic species has a characteristic number of chromosomes
(chromosome number). In species that reproduce asexually, the chromosome
number is the same in all the cells of the organism.

25
Among sexually reproducing organisms, the chromosomes in the body
consists of two types according to the type of the cells, in the somatic cells
the chromosomes called somatic or autosomes chromosomes control the
inheritance of all the characteristics except the sex-linked ones each somatic
cells have diploid set of chromosomes so called diploid with 2n; a pair of
each chromosome, the gametes (sex cells) contain each one have the half
number of the somatic chromosomes therefore each gametes contain sex
chromosomes which are controlled the sex-linked characteristics therfore
called haploid cells with 1n.

Figure 7: Chromosomes

Cell division
All cells arise from the division of preexisting cells of the multicellular
organisms originated from the division of single cell, zygote, which is
formed from the union (fertilization) of an egg and sperm. Cell division
provides the bases for one form of growth for both sexual and asexual

26
reproduction , and for transmission of hereditary qualities from one cell
generation to another. The division of the cells include two types : nuclear
division (karyokinesis) and cytoplasmic division (cytokinesis)
the nuclear material of the living body cells both somatic and reproductive
cells requires division before the division of the cytoplasm ,therefore there
are two types of nuclear division mitosis and meiosis
all living somatic cells require mitosis division, each daughter cells receiving
a complete set of genetic material, thus all the somatic cells which number in
hundreds and billions in large animals, have the same genetic content
because all are result by reproduction of the original zygote by mitosis.
In animals that reproduce asexually, mitosis is the only mechanism for
transverse the genetic information from parent to progeny, while the animals
that reproduce sexually, the parent must produce sex cells (gametes) that
contain only half number of chromosomes, so that the offspring formed by
union of the gametes during fertilization will contain double content of
parental genetic material, therefore the gametes require a special type of
division called meiosis.

Cell cycle (cell division cycle)

The cells undergo cycles of growth and replication as they repeatedly
divide. A cell cycle is mitosis-to-mitosis cycle that is the interval between
one cell generation and the next i.e. between two nuclear divisions. We can
define the cell cycle is series of events that take place in a cell leading to
duplication of its DNA (DNA replication) and division of cytoplasm and
organelles to produce two daughter cells.

27
Stages of the cell cycle
The two main parts of the cell cycle are mitosis and interphase. Mitosis is
the phase of cell division, during which a ―parent cell‖ divides to create two
―daughter cells‖
The longest part of the cell cycle is called ―interphase‖ – the phase of growth
and DNA replication between mitotic cell divisions.
In bacteria, which lack a cell nucleus, the cell cycle is divided into the B, C,
and D periods. The B period extends from the end of cell division to the
beginning of DNA replication. DNA replication occurs during the C period.
The D period refers to the stage between the end of DNA replication and the
splitting of the bacterial cell into two daughter cells.
In eukaryotic cells, or cells with a nucleus, the stages of the cell cycle are
divided into two major phases: interphase and the mitotic (M) phase.
The eukaryotic cell cycle consists of four distinct phases:
- G1 phase (Growth phase 1)
- S phase (synthesis phase)
- G2 phase (Growth phase2) , collectively known as interphase
- M phase (mitosis and cytokinesis).
M phase is itself composed of two tightly coupled processes: mitosis, in
which the cell's nucleus divides, and cytokinesis, in which the cell's
cytoplasm divides forming two daughter cells. To divide a cell must
complete several important tasks: it must grow, copy its genetic material
(DNA), and physically split into two daughter cells. Cells perform these
tasks in an organized, series of steps that make up the cell cycle. The cell
cycle is a cycle, rather than a linear pathway, because at the end of each go-
round, the two daughter cells can start the exact same process over again
from the beginning.
28
 During interphase, the cell grows and makes a copy of its DNA. While in
the mitotic (M) phase, the cell separates its DNA into two sets and divides
its cytoplasm, forming two new cells.
G1 , also called the first gap phase, the cell grows physically larger, copies
organelles, and makes the molecular building blocks it will need in later
steps.
In the great majority of cases, cells do indeed grow before division.
However, in certain situations during development, cells may split
themselves up into smaller and smaller pieces over successive rounds of cell
division.
S phase. In S phase, the cell synthesizes a complete copy of the DNA in its
nucleus. It also duplicates a microtubule-organizing structure called the
centrosome. The centrosomes help separate DNA during M phase.
G2 also called the second gap phase, the cell grows more, makes proteins
and organelles, and begins to reorganize its contents in preparation for
mitosis, phase ends when mitosis begins.
The G, S, and G2 phases together are known as interphase. The prefix
inter- means between, reflecting that interphase takes place between one
mitotic (M) phase and the next (figure 8).

29
Figure 8 : Cell cycle

30
Lecture Seven: Mitosis
Mitosis
Is a part of the cell cycle when replicated chromosomes are separated into
two genetically identical new nuclei? In mitosis, the nuclear DNA of the cell
condenses into visible chromosomes and is pulled apart by the mitotic
spindle, a specialized structure made out of microtubules. Mitosis takes
place in four stages:
1- prophase (sometimes divided into early prophase and prometaphase)
2- metaphase 3-anaphase 4-telophase
Followed by a process known as cytokinesis, which begins in telophase,
In cytokinesis, the cytoplasm of the cell is split in two, making two new
cells. Cytokinesis usually begins just as mitosis is ending. Importantly,
cytokinesis takes place differently in animal and plant cells (figure 9).
Mitosis occurs only in eukaryotic cells. Prokaryotic cells, which lack a
nucleus, divide by a different process called binary fission. Mitosis is carried
out by somatic cells. Every somatic cell that undergoes mitosis produces two
genetically identical diploid daughter cells, meaning that the cell
chromosome number remains the same during cell division. Mitosis can be
divided into four phases - prophase, metaphase, anaphase and telophase,

 Prophase involves the condensing of chromatin into chromosomes, the

movement of the centrioles to opposite poles of the cell and the synthesis
of the mitotic spindle apparatus, the deterioration of the nuclear
membrane and the disappearance of the nucleoulus, and the synthesis of
the kinetochores on each chromosome. The two chromatids are joined at
the centromere. Close to the nucleus of animal cells are structures called

31
 centrosomes, consisting of a pair of centrioles surrounded by a loose
collection of proteins The centrosome is the coordinating center for the
cell's microtubules.

 Metaphase, the centrioles are now on opposite poles and have attached
their spindle fibers onto the kinetochores. They also align all the
chromosome pairs along the center of the cell.
 Anaphase, disjunction takes place. Disjunction is the separation of the
chromosome pairs by the pulling of the spindle fibers, which separate the
chromosomes to opposite poles.
 telophase, is a reversal of prophase and prometaphase events the
chromosomes have been separated and the nuclear membrane begins to
reform around both sets, thereby forming two nuclei. The spindle
apparatus deteriorates and the chromosomes begin to decondense into
chromatin in preparation for interphase.
Cytokinesis, Cytokinesis is not a phase of mitosis but rather a separate
process, necessary for completing cell division, the end of cytokinesis marks
the end of the M-phase. The process, by which the cell divides the cell
membrane and cytoplasm into two cells, begins and continues after
telophase ends. Once the cell undergoes mitosis, it produces two genetically
identical diploid cells. Mitosis is complete. Each daughter nucleus has an
identical set of chromosomes. Cell division may or may not occur at this
time depending on the organism. There are many cells where mitosis and
cytokinesis occur separately, forming single cells with multiple nuclei. The
most notable occurrence of this is among the fungi, slime molds, and some
algae, but the phenomenon is found in various other organisms.

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 Figure 9 : Mitosis

Function of mitosis
1- Development and growth
The number of cells within an organism increases their numbers by
mitosis. This is the basis of the development of a multicellular body
from a single cell ( zygote) and the growth of a multicellular body.

2- Cell replacement
In some parts of body, e.g. skin cells and endothelium of digestive tract,
cells are constantly sloughed off and replaced by new ones, red blood
cells have short lifespan (only about 4 months) and new RBCs are
formed by mitosis.

3- Regeneration

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Some organisms can regenerate body parts. The production of new cells
in such instances is achieved by mitosis. For example, starfish regenerate
lost arms through mitosis and tail of some lizards also regenerate by
mitosis

4- Asexual reproduction
Some organisms produce genetically similar offspring through asexual
reproduction. For example, the hydra reproduces asexually by budding.
The cells at the surface undergo mitosis and form a mass called a bud.
Mitosis continues in the cells of the bud and this grows into a new
individual. The same division happens during asexual reproduction or
vegetative propagation in plants.

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 Lecture Eight: Evolution

Evolution

Evolution is change in the heritable characteristics of biological

populations over successive generations. Or Change in the gene pool of a
population from generation to generation by such processes as DNA
mutation, natural selection, and genetic drift.

Source of variation
1-Genetic drift:
Genetic drift is a cause of allelic frequency change within populations of
a species. Alleles are different variations of specific genes. They determine
things like hair colour, skin tone, eye colour and blood type; in other words,
all the genetic traits that vary between individuals. Genetic drift does not
introduce new alleles to a population, but it can reduce variation within a
population by removing an allele from the gene pool.

2- Modern synthesis:

The modern evolutionary synthesis is based on the concept that

populations of organisms have significant genetic variation caused by
mutation and by the recombination of genes during sexual reproduction. It
defines evolution as the change in allelic frequencies within a population
caused by genetic drift, gene flow between sub populations, and natural
selection. Natural selection is emphasized as the most important mechanism
of evolution; large changes are the result of the gradual accumulation of
small changes over long periods of time.

35
Evidence for evolution comes from many different areas of
biology:

 Anatomy. Species may share similar physical features because the

feature was present in a common ancestor (homologous structures).
 Molecular biology. DNA and the genetic code reflect the shared
ancestry of life. DNA comparisons can show how related species are.
 Biogeography. The global distribution of organisms and the unique
features of island species reflect evolution and geological change.
 Fossils. Fossils document the existence of now-extinct past species
that are related to present-day species.
 Direct observation. We can directly observe small-scale evolution in
organisms with short lifecycles (e.g., pesticide-resistant insects).
Homology
In biology, homology (homologous), similarity of the structure,
physiology, or development of different species of organisms based upon
their ancestry from a common evolutionary ancestor. Homology is
contrasted with analogy.

Thus the forelimbs of such widely differing mammals as humans, bats,

and deer are homologous; the form of construction and the number of bones
in these varying limbs are practically identical, and represent adaptive
modifications of the forelimb structure of their common early mammalian
ancestors.

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Analogy

Analogous which is a functional similarity of structure based not upon

common evolutionary origins but upon mere similarity of use?

Analogous structures, on the other hand, can be represented by the wings of

birds and of insects; the structures are used for flight in both types of
organisms, but they have no common ancestral origin at the beginning of
their evolutionary development.

 Morphological homology - species (correctly) placed in the same

taxonomic category show anatomical similarities.
 Ontogenetic homology - species placed in the same taxonomic
category show developmental (embryonic) similarities.
 Molecular homology - species placed in the same taxonomic
category show similarities in DNA and RNA and in their proteins.

Morphological Homology

A structure found in two (or more) different species, but derived from a
common ancestral structure is said to be Homologous in those species. The
structure may or may not be used for the same function in the species in
which it occurs.

37
 Homology Analogy

In contrast, a structure that serves the same function in two species, but is
not derived from a common ancestral structure is said to be Analogous.
Examples of Analogous structures:

 wings of bat, bird (though the BONES are homologous!), insect:

 camera eye of the vertebrate and the cephalopod (squid & octopus):
 walking limbs of insects and vertebrates
 cranium of vertebrates and exoskeletal head shield of insects
 fusiform shape of fish and cetaceans (whales & dolphins)

Natural selection

Natural selection is the differential survival and reproduction of

individuals due to differences in phenotype. It is a key mechanism of
evolution, the change in the heritable traits characteristic of a population
over generations. Charles Darwin popularized the term "natural selection",
contrasting it with artificial selection, which in his view is intentional,
whereas natural selection is not.

38
Population: All the members of a single species living in a defined
geographic area. Though Darwin's idea (natural selection) was probably the
most important and powerful one in the history of Biological Science, he
didn't consider some of the other mechanisms by which evolution also can
take place, most of which have to do with Random Processes.

39
 Lecture Nine: The evolutionary history of biological
diversity

Phylogenetic tree

A phylogenetic tree or evolutionary tree is a branching diagram or

"tree" showing the inferred evolutionary relationships among various
biological species or other entities based upon similarities and differences in
their physical and/or genetic characteristics. The taxa joined together in the
tree are implied to have descended from a common ancestor.

In a rooted phylogenetic tree, each node with descendants represents

the inferred most recent common ancestor of the descendants, and the edge
lengths in some trees may be interpreted as time estimates. Each node is
called a taxonomic unit. Internal nodes are generally called hypothetical
taxonomic units, as they cannot be directly observed. Trees are useful in
fields of biology such as bioinformatics, systematics, and comparative
phylogenetics.

A phylogenetic tree of living things based on RNA data and proposed by

Carl Woese, showing the separation of bacteria, archaea, and eukaryotes.
Trees constructed with other genes are generally similar, although they may
place some early-branching groups very differently, thanks to long branch
attraction. The exact relationships of the three domains are still being
debated, as is the position of the root of the tree. It has also been suggested
that due to lateral gene transfer, a tree may not be the best representation of
the genetic relationships of all organisms. For instance some genetic

40
evidence suggests that eukaryotes evolved from the union of some bacteria
and archaea (one becoming an organelle and the other the main cell).

Bacteria: Bacteria are a type of biological cell. They constitute a large

domain of prokaryotic microorganisms. Typically a few micrometers in
length, bacteria have a number of shapes, ranging from spheres to rods and
spirals. Bacteria were among the first life forms to appear on Earth, and are
present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs,
radioactive waste, and the deep biosphere of the earth's crust. Bacteria also
live in symbiotic and parasitic relationships with plants and animals. Most
bacteria have not been characterized, and only about 27 percent of the
bacterial phyla have species that can be grown in the laboratory (specifically
uncultivable phyla, known as candidate phyla, make up 103 out of
approximately 142 known phyla). The study of bacteria is known as
bacteriology, a branch of microbiology.

41
Archaea: Archaea (singular archaeon): constitute a domain of single-celled
organisms. These microorganisms are prokaryotes, and have no cell nucleus.
Archaea were initially classified as bacteria, receiving the name
archaebacteria (in the Archaebacteria kingdom), but this classification is
outmoded. Archaeal cells have unique properties separating them from the
other two domains, Bacteria and Eukaryota. Archaea are further divided into
multiple recognized phyla. Classification is difficult because most have not
been isolated in the laboratory and have only been detected by analysis of
their nucleic acids in samples from their environment.

Eukaryotes: Eukaryotes are organisms whose cells have a nucleus enclosed

within membranes, unlike prokaryotes (Bacteria and Archaea), which have
no membrane-bound organelles. Eukaryotes belong to the domain
Eukaryota or Eukarya. Eukaryotic cells also contain other membrane-
bound organelles such as mitochondria and the Golgi apparatus, and in
addition, some cells of plants and algae contain chloroplasts. Unlike
unicellular archaea and bacteria, eukaryotes may also be multicellular and
include organisms consisting of many cell types forming different kinds of
tissue. Animals and plants are the most familiar eukaryotes.

Protist: Protist is any eukaryotic that is not an animal, plant, or fungus. The
protists do not form a natural group, or clade, since they exclude certain
eukaryotes with whom they share a common ancestor; [a] but, like algae or
invertebrates, the grouping is used for convenience. In some systems of
biological classification, such as the popular five-kingdom scheme proposed
by Robert Whittaker in 1969, the protists make up a kingdom called
Protista, composed of "organisms which are unicellular or unicellular-
colonial and which form no tissues‖ protista was first used by Ernst Haeckel
42
in 1866. Protists were traditionally subdivided into several groups based on
similarities to the "higher" kingdoms such as:

Protozoa:
These unicellular "animal-like" (heterotrophic, and sometimes
parasitic) organisms are further sub-divided based on characteristics
such as motility, such as the (flagellated) Flagellata, the (ciliated)
Ciliophora, the (phagocytic) amoeba, and the (spore-forming)
Sporozoa.
Protophyta
These "plant-like" (autotrophic) organisms are composed mostly of
unicellular algae. The dinoflagelates, diatoms and Euglena-like
flagellates are photosynthetic protists.
Molds
Slime molds and water molds are "fungus-like" (saprophytic)
organisms. These are consumer-decomposer protists. Two separate
types of slime molds exist, the cellular and acellular forms.

Plant Diversity : How Plants Colonized Land

Land plants evolved from green

algae

Morphological and Molecular Evidence

1. Rings of cellulose-synthesizing
proteins

43
2. Peroxisome enzymes
3. Structure of flagellated sperm
4. Formation of a phragmoplast

Derived Traits of Plants

Four key traits appear in nearly all land plants but are absent in the
charophytes

1. Walled spores produced in sporangia

2. Apical meristems
3. Embryophytes
4. Alternation of generations and multicellular, dependent embryos

Walled Spores Produced in Sporangia

 The sporophyte produces spores in organs called sporangia

 Diploid cells called sporocytes undergo meiosis to generate haploid
spores
 Spore walls contain sporopollenin, which makes them resistant to
harsh environments

Multicellular Gametangia

 Gametes are produced within

organs called gametangia
 Female gametangia, called
archegonia, produce eggs
and are the site of fertilization

44
  Male gametangia, called antheridia, produce and release sperm

Apical Meristems

 Plants sustain continual growth in their apical meristems

 Cells from the apical meristems differentiate into various tissues

Additional derived traits include:

1-Cuticle, a waxy covering of the epidermis

2-Mycorrhizae, symbiotic associations between fungi and land plants that
may have helped plants without true roots to obtain nutrients
3-Secondary compounds that deter herbivores and parasites

Plant Diversity: The Evolution of Seed plants:

Common traits of all seed plants:

1. Gametophyte reduction in size
2. Heterospory
3. Ovules and production of eggs
4. Pollen and production of sperm
5. Seeds
1. Reduced gametophytes can be microscopic:
Advantages of reduced gametophyte:
a. protection of female gametophytes from environmental changes
b. help prevent drought
c. protect from UV radiation
d. can obtain nutrients from sporophytes

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2. Heterospory

 each megasporangia produces 1 megaspore (spore from a

heterosporous plant species that develops into a female gametophyte)
 each microsporangia produces many microspores (a spore from a
hetersporous plant species that develops into a male gametophyte).
3. Ovules and production of eggs

Layers of integument enclose megaspore gymnosperms 1 integument

angiosperms two integuments whole structure = ovule

4. Pollen and production of sperm

o microspores become pollen grains (male gametophytes)

o protected by sporopollenin (tough coat polymer)
o carried by wind, animals for pollination
o Purpose: reproduction over long distances
o advantages: long distance, no motility needed

46
5. Evolution of seeds Advantages:
-multicellular layer of tissue (seed coat) extra protection for
embryo can resist harsh conditions
-Supply of food within can remain dormant for years
-disperse widely

Fungi: A fungus is any member of the group of eukaryotic organisms that

includes microorganisms such as yeasts and molds, as well as the more
familiar mushrooms. These organisms are classified as a kingdom, fungi,
which is separate from the other eukaryotic life kingdoms of plants and
animals.
A characteristic that places fungi in a different kingdom from plants,
bacteria, and some protists is chitin in their cell walls. Similar to animals,
fungi are heterotrophs; they acquire their food by absorbing dissolved
molecules, typically by secreting digestive enzymes into their environment.
Fungi do not photosynthesize.

Growth is their means of mobility, except for spores (a few of which are
flagellated), which may travel through the air or water. Fungi are the
principal decomposers in ecological systems. These and other differences
place fungi in a single group of related organisms, named the Eumycota
(true fungi or Eumycetes), which share a common ancestor (form a
monophyletic group), an interpretation that is also strongly supported by
molecular phylogenetics. This fungal group is distinct from the structurally
similar myxomycetes (slime molds) and oomycetes (water molds).

47
 Lecture Ten: The evolutionary history of biological
diversity
An Overview of Animal Diversity

Animal evolution began in the ocean over 600 million years ago with tiny
creatures that probably do not resemble any living organism today. Since
then, animals have evolved into a highly diverse kingdom. Although over
one million extant (currently living) species of animals have been identified,
scientists are continually discovering more species as they explore
ecosystems around the world. The number of extant species is estimated to
be between 3 and 30 million.
But what is an animal? While we can easily identify dogs, birds, fish,
spiders, and worms as animals, other organisms, such as corals and sponges,
are not as easy to classify. Animals vary in complexity—from sea sponges to
crickets to chimpanzees—and scientists are faced with the difficult task of
classifying them within a unified system. They must identify traits that are
common to all animals as well as traits that can be used to distinguish among
related groups of animals. The animal classification system characterizes
animals based on their anatomy, morphology, evolutionary history, features
of embryological development, and genetic makeup. This classification
scheme is constantly developing as new information about species arises.
Understanding and classifying the great variety of living species help us
better understand how to conserve the diversity of life on earth

48
Classification & the Animal Kingdom

How is Organisms Classified?

Classification: the grouping of anything according to its similar

characteristics. The science of classifying organisms is known as taxonomy.

How is Organisms Classified?

There are eight classification groups of living things:

Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
What is an Animal?

We will be focusing specifically on the Kingdom Animalia and its 9

phyla. Vertebrates: animals with backbones Invertebrates: animals
without a backbone97% of all animal species are invertebrates!
What is Symmetry?

To classify animals, scientists also look at symmetry, or how the body

parts are arranged.
1. Radial symmetry: body parts are arranged in a circle around a center
point.
2. Bilateral symmetry: body can be divided into two mirror image halves.

49
3. Asymmetry: no pattern of symmetry

What are
the Characteristics of all Animals?

 Animals cannot make their own food (consumers).

 Animals digest their food.
 Many animals move from place to place.
 Animals have many cells.
 Animal cells have nuclei and organelles (eukaryotic cells).
What are the nine Different Phyla in Kingdom Animalia?

Phylum Porifera
Phylum Cnidaria
Phylum Platyhelminthes
Phylum Nematoda
Phylum Mollusca
Phylum Annelida
Phylum Arthropoda
Phylum Echinodermata
Phylum Chordata
 Phylum Porifera

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 Aquatic organisms lack tissues and organs asymmetrical, mostly sessile
(do not move) Example: sponges. This is a ―real‖ sponge are Aquatic
organisms, lack tissues and organs Asymmetrical, mostly sessile (do not
move).
 Phylum Cnidaria
Aquatic organisms, radial symmetry, digestive cavity with one opening,
tentacles with stinging cells; Examples: jellyfish, corals, hydra, sea
anemones.

Phylum Platyhelminthes

Bilaterally symmetrical worms, flat

bodies, digestive system with one
opening; Examples: parasitic and
free-living species Examples: Flat
worms.
 Phylum Nematoda
Round, smooth worms, Bilateral symmetry Digestive system with two
openings free living and parasitic forms Examples: roundworms.
 Phylum Mollusca

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 Soft-bodies, many with a hard shell or foot-like appendage, aquatic or
terrestrial; Examples: clams, snails, squid, octopuses.

 Phylum Annelida
Round worms with segmented bodies, bilateral symmetry, Terrestrial
and aquatic; Examples: earthworms, leeches, and marine polychaetes.


Phylum Arthropoda
Largest animal group, bilateral symmetry, Have an exoskeleton,
segmented bodies, and pairs of jointed appendages, Land and aquatic;
Examples: insects, crustaceans, and spiders.
 Phylum Echinodermata

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 Marine organisms, Radial symmetry Spiny/leathery skin, Water-vascular
system with tube feet; Examples: sea stars, sand dollars, sea urchins.

 Phylum Chordata
Organisms with internal skeletons and specialized body systems, At some
point all have a backbone (or notochord), gill slits, and a tail; Examples:
fish, amphibians, reptiles, birds, and mammals.

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