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.
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.

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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 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.

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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 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.

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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 life

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

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 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 instructs the liver to release glucose; this maintains the
normal blood glucose concentration at about 0.1%.

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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 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 .

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  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:

1-Support: Some proteins are structural proteins. Keratin, for example,

makes up hair and nails. Collagen lends support to ligaments, tendons,
and skin.

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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.

Lecture Three: The chemistry of life

 Nucleic Acids

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Nucleic acids, which are polymers of nucleotides, store information,
include instructions for life, and conduct chemical reactions. The general
structure of a nucleotide is shown in Figure (1).

Figure 1: The general structure of a nucleotide

Two types of nucleic acids are important in the storage and processing of
the genetic information. DNA (deoxyribonucleic acid) is the type of
nucleic acid that not only stores information about how to copy, or
replicate, itself but also specifies the order in which amino acids are to be
joined to make a protein.

Nucleotide Structure
Each nucleotide is a molecular complex of three types of subunit
molecules phosphate (phosphoric acid), a pentose (5-carbon) sugar, and a
nitrogen-containing base. The nucleotides in DNA contain the sugar
deoxyribose, and the nucleotides in RNA contain the sugar ribose; this
difference accounts for their respective names, also, there are four
different types of bases in DNA:
adenine (A), thymine (T), guanine (G), and cytosine (C) (Table 1).
The base can have two rings (adenine or guanine) or one ring (thymine or
cytosine). In RNA, the base uracil (U) replaces the base thymine. These
structures are called bases because their presence raises the pH of a
solution.

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The nucleotides link to make a polynucleotide called a strand, which has
a backbone made up of phosphate-sugar-phosphate-sugar. The bases
project to one side of the backbone.
DNA (deoxyribonucleic acid)
DNA is double-stranded, with the two strands twisted about each
other in the form of a double helix (Figure 2). In DNA the two strands are
held together by hydrogen bonds between the bases. When coiled, DNA
resembles a spiral staircase. When unwound, it resembles a stepladder.
The uprights (sides) of the ladder are made entirely of phosphate and
sugar molecules, and the rungs of the ladder exhibit complementary base
pairing.

Figure 2: DNA structure

Thymine (T) always pairs with adenine (A), and guanine (G) always pairs
with cytosine (C). Complementary bases have shapes that fit together.
Complementary base pairing allows DNA to replicate in a way that
ensures that the sequence of bases will remain the same. This is important
because it is the sequence of bases that determines the sequence of amino

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acids in a protein. RNA is single-stranded. When RNA forms,
complementary base pairing with one DNA strand passes the correct
sequence of bases to RNA. RNA is the nucleic acid directly involved in
protein synthesis.

RNA (ribonucleic acid) is a diverse type of nucleic acid that has multiple
uses, RNA main types contains:
1-Messenger RNA (mRNA) is a temporary copy of a gene in the DNA
that specifies what the amino acid sequence will be during the process of
protein synthesis.

2-Transfer RNA (tRNA) is also necessary in synthesizing proteins and

helps translate the sequence of nucleic acids in a gene into the correct
sequence of amino acid during protein synthesis.

3-Ribosomal RNA (rRNA) is the RNA component of the ribosome, it

works as an enzyme to form the peptide bonds between amino acids in a
polypeptide.

Not all nucleotides are made into DNA or RNA polymers. Some
nucleotides are directly involved in metabolic functions in cells. For
example, some are components of coenzymes, nonprotein organic
molecules that help regulate enzymatic reactions.
ATP (adenosine triphosphate) is a nucleotide that stores large amounts
of energy needed for synthetic reactions and for various other energy-
requiring processes in cells.

Differences in the Structures of DNA and RNA

Though both DNA and RNA are polymers of nucleotides, there are some
small differences in the types of subunits each contains and in their final

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structure. These differences give DNA and RNA their unique functions in
the body.

Table 1: Comparison between DNA and RNA Structure

DNA RNA
Sugar Deoxyribose Ribose Ribose

Bases Adenine, guanine, thymine, Adenine, guanine, uracil, cytosine

cytosine
Strands Double-stranded with base pairing Single-stranded

Helix Yes No

Lecture Four: 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

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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.

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

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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 structure:
Plasma membrane
The plasma membrane is a phospholipid bilayer ―sandwich‖ made of
two layers of phospholipids. Their polar phosphate molecules form the
top 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

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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 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

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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 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.

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 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 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.

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 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

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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 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

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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
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.

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 Figure 2 : Endoplasmic reticulum

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.

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 Figure 3 : Structure of cilia and flagella
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.

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 Figure 4: The centriole structure
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. 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.
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

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 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).
Lecture Six: Structure and function of cell
Plasma Membrane Functions
The plasma membrane keeps a cell intact. It allows only certain
molecules and ions to enter and exit the cytoplasm freely. Therefore, the
plasma membrane is said to be selectively permeable (Figure 1). Small,
lipid-soluble molecules, such as oxygen and carbon dioxide, can pass
through the membrane easily. The small size of water molecules allows
them to freely cross the membrane by using protein channels called
aquaporins.

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 Figure 1: Selective permeability of the plasma membrane

Plasma membrane contributes in different activities:

1-Diffusion
Diffusion is the random movement of molecules from an area of
higher concentration to an area of lower concentration, until they are
equally distributed. Diffusion is a passive way with no cellular energy is
needed (Figure 2). Oxygen diffuses across the plasma membrane, and the
net movement is toward the inside of the cell. This is because a cell uses
oxygen when it produces ATP molecules for energy purposes.

Figure 2: Diffusion across the plasma membrane

2-Osmosis
Osmosis is the net movement of water across a semipermeable
membrane, from an area of higher concentration to an area of lower
concentration. The membrane separates the two areas, and solute is
unable to pass through the membrane. Water will tend to flow from the
area that has less solute (and therefore more water) to the area with more
solute (and therefore less water). Tonicity refers to the osmotic
characteristics of a solution across a particular membrane, such as a red
blood cell membrane. Normally, body fluids are isotonic to cells. There is
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the same concentration of non-diffusible solutes and water on both sides
of the plasma membrane.
Therefore, cells maintain their normal size and shape. Intravenous
solutions given in medical situations are usually isotonic. Solutions that
cause cells to swell or even to burst due to an intake of water are said to
be hypotonic. A hypotonic solution has a lower concentration of solute
and higher concentration of water than the cells. If red blood cells are
placed in a hypotonic solution, water enters the cells. They swell to
bursting. Lysis is used to refer to the process of bursting cells. Bursting of
red blood cells is termed hemolysis. Solutions that cause cells to shrink or
shrivel due to loss of water are said to be hypertonic. A hypertonic
solution has a higher concentration of solute and lower concentration of
water than do the cells. If red blood cells are placed in a hypertonic
solution, water leaves the cells; they shrink. These changes have occurred
due to osmotic pressure which control water movement in our bodies. For
example, in the small and large intestines, osmotic pressure allows us to
absorb the water in food and drink. In the kidneys, osmotic pressure
controls water absorption as well.

Osmosis and Diffusion Similarities

Osmosis and diffusion are related processes that display similarities:

 Both osmosis and diffusion equalize the concentration of two

solutions.
 Both diffusion and osmosis are passive transport processes, which
means they do not require any input of extra energy to occur. In
both diffusion and osmosis, particles move from an area of higher
concentration to one of lower concentration.

Osmosis and Diffusion Differences

28
  Diffusion can occur in any mixture, including one that includes a
semipermeable membrane, while osmosis always occurs across
a semipermeable membrane.
 Osmosis in biology, it always refers to the movement of water. In
chemistry, it's possible for other solvents to be involved. In
biology, this is a difference between the two processes.
 One big difference between osmosis and diffusion is that both
solvent and solute particles are free to move in diffusion, but when
we talk about osmosis, only the solvent molecules (water
molecules) cross the membrane.

3-Facilitated Transport
Many solutes do not simply diffuse across a plasma membrane. They
are transported by means of protein carriers within the membrane. During
facilitated transport, a molecule is transported across the plasma
membrane from the side of higher concentration to the side of lower
concentration (Figure 3). This is a passive means of transport because the
cell does not need to expend energy to move a substance down its
concentration gradient. Each protein carrier, sometimes called a
transporter, binds only to a particular molecule, such as glucose.

Figure 3: Plasma membrane facilitated transport

29
4- Active Transport
During active transport, a molecule is moving from a lower to higher
concentration. One example is the digestive tract; sugar is completely
absorbed from the gut by cells that line the intestines. Active transport
requires a protein carrier and the use of cellular energy obtained from the
breakdown of ATP. When ATP is broken down, energy is released. In
this case, the energy is used to carry out active transport. Proteins
involved in active transport often are called pumps. Just as a water pump
uses energy to move water against the force of gravity, energy is used to
move substances against their concentration gradients.
5-Endocytosis and Exocytosis
During endocytosis, a portion of the plasma membrane invaginates, or
forms a pouch, to envelop a substance and fluid. Then the membrane
pinches off to form an endocytic vesicle inside the cell (Figure 4). Some
white blood cells are able to take up pathogens (disease-causing agents)
by endocytosis. Here the process is given a special name: phagocytosis.
Usually, cells take up molecules and fluid, and then the process is called
pinocytosis. During exocytosis, a vesicle fuses with the plasma
membrane as secretion occurs. This is the way that signaling molecules,
called neurotransmitters, leave one nerve cell to excite the next nerve cell
or a muscle cell.

30
 A. Endocytosis (Phagocytosis) B. Pinocytosis
Figure 4: Movement of large molecules across the membrane
Cell communication

Individual cells, like multicellular organisms, need to sense and

respond to their environment. A free-living cell—evens a humble
bacterium—must be able to track down nutrients, tell the difference
between light and dark, and avoid poisons and predators. And if such a
cell is to have any kind of ‗social life,‘ it must be able to communicate
with other cells.
In a multicellular organism, things are much more complicated. Cells
must interpret the multitude of signals they receive from other cells to
help coordinate their behaviors. The signals that pass between living cells
are simpler than the sorts of messages that humans ordinarily exchange.
In a typical communication between cells, the signaling cell produces a
particular type of signal molecule that is detected by the target cell. As in
human conversation, most animal cells both send and receive signals, and
they can therefore act as both signaling cells and target cells. Target
cells possess receptor proteins that recognize and respond specifically to
the signal molecule. Signal transduction begins when the receptor
protein on a target cell receives an incoming extracellular signal and
converts it to the intracellular signals that alter cell behavior. Cells in
multicellular organisms use hundreds of kinds of extracellular molecules
to send signals to one another. The signal molecules can be proteins,
peptides, amino acids, nucleotides, steroids, fatty acid derivatives, or
even dissolved gases.

31
 Lecture Seven: Structure and function of cell
The cell and the lows of thermodynamics

The laws of thermodynamics are important unifying principles

of biology. These principles govern the chemical processes (metabolism)
in all biological organisms. The First Law of Thermodynamics, also
known as the law of conservation of energy, states that energy can neither
be created nor destroyed. It may change from one form to another, but
the energy in a closed system remains constant.

The Second Law of Thermodynamics states that when energy is

transferred, there will be less energy available at the end of the transfer
process than at the beginning. Due to entropy, which is the measure of
disorder in a closed system, all of the available energy will not be useful
to the organism. Entropy increases as energy is transferred.

In addition to the laws of thermodynamics, the cell theory, gene theory,

evolution, and homeostasis form the basic principles that are the
foundation for the study of life.

First Law of Thermodynamics in Biological Systems

All biological organisms require energy to survive. In a closed system,

such as the universe, this energy is not consumed but transformed from
one form to another. Cells, for example, perform a number of important
processes. These processes require energy. In photosynthesis, the energy
is supplied by the sun. Light energy is absorbed by cells in plant leaves
and converted to chemical energy. The chemical energy is stored in the

32
form of glucose, which is used to form complex carbohydrates necessary
to build plant mass.

The energy stored in glucose can also be released through cellular

respiration. This process allows plant and animal organisms to access the
energy stored in carbohydrates, lipids, and other macromolecules through
the production of ATP. This energy is needed to perform cell functions
such as DNA replication, mitosis, meiosis, cell movement, endocytosis,
exocytosis, and apoptosis.

Second Law of Thermodynamics in Biological Systems

As with other biological processes, the transfer of energy is not 100

percent efficient. In photosynthesis, for example, not all of the light
energy is absorbed by the plant. Some energy is reflected, and some is
lost as heat. The loss of energy to the surrounding environment results in
an increase of disorder or entropy. Unlike plants and other photosynthetic
organisms, animals cannot generate energy directly from the sunlight.
They must consume plants or other animal organisms for energy.

The higher up an organism is on the food chain, the less available

energy it receives from its food sources. Much of this energy is lost
during metabolic processes performed by the producers and primary
consumers that are eaten. Therefore, much less energy is available for
organisms at higher trophic levels. (Trophic levels are groups that help
ecologists understand the specific role of all living things in the
ecosystem.) The lower the available energy, the less number of organisms
can be supported. This is why there are more producers than consumers
in an ecosystem.

33
 Living systems require constant energy input to maintain their highly
ordered state. Cells, for example, are highly ordered and have low
entropy. In the process of maintaining this order, some energy is lost to
the surroundings or transformed. So while cells are ordered, the processes
performed to maintain that order result in an increase in entropy in the
cell's/organism's surroundings. The transfer of energy causes entropy in
the universe to increase.

Reduction–oxidation reaction

34
 Reduction–oxidation reaction (Redox) is a type of chemical reaction
in which the oxidation states of atoms are changed. Redox reactions are
characterized by the transfer of electrons between chemical species, most
often with one species (the reducing agent) undergoing oxidation (losing
electrons) while another species (the oxidizing agent) undergoes
reduction (gains electrons).

Oxidation is the loss of electrons or an increase in the oxidation state of

an atom by a molecule, an ion, or another atom.

Reduction is the gain of electrons or a decrease in the oxidation state of

an atom by a molecule, an ion, or another atom.

Redox Reactions in Cellular Respiration

During cellular respiration, the fuel glucose is being consumed to

generate energy in a long series of enzyme‐catalyzed reactions; in simple
words, electrons can be transferred from glucose to molecular oxygen,
oxidizing the carbon molecules to carbon dioxide and reducing O2 to
water.

This aspect of redox reactions in living organisms is called cellular

respiration by which cells break down molecules of food (glucose) in a
series of chemical reactions to produce energy, carbon dioxide, and
water; the process depends heavily on the reduction of NAD+ to NADH
and the reverse oxidation reaction of NADH to NAD+ as intermediate
steps.

Oxidation–reduction reactions exist in all cells and are critical for cell
homeostasis and signalling, including energy metabolism, gene
expression, cell cycle regulation, immune response, cell growth, and cell

35
apoptosis. In addition, this redox couple also function in rhythms,
apoptosis, aging, development, and carcinogenesis.

Other biological processes that involve the redox reaction is the

production of free radicals, which can be produced by detaching electrons
from certain type of molecules and react to another type of molecule
instantaneously; free radicals play an important role for the programmed
cell death (apoptosis), and any uncontrolled production of free radicals
may lead to cause cancer.

Co enzyme

Aerobic cellular respiration made up of 3 parts: glycolysis, the Krebs

cycle, and oxidative phosphorylation. In glycolysis, glucose is
metabolized into 2 molecules of pyruvate, with an output of ATP and
nicotinamide adenine dinucleotide (NADH). The pyruvate is oxidized
into acetyl CoA and NADH and carbon dioxide (CO2). The acetyl CoA is
then used in the Krebs cycle, also known as the citric acid cycle, which is
a chain of chemical reactions that produce CO2, NADH, flavin adenine
dinucleotide (FADH2), and ATP. In the final step, the NADH, FADH2
amassed from the previous steps is used in oxidative phosphorylation, to
make water and ATP.

Lecture Eight: Structure and function of cell

36
Cellular Respiration

Plants, algae, and some bacteria harvest the energy of sunlight through
photosynthesis, converting radiant energy into chemical energy. These
organisms are called autotrophs. All other organisms live on the energy
autotrophs produce and are called heterotrophs. At least 95% of the
kinds of organisms on earth (all animals and fungi, and most protists and
bacteria) are heterotrophs.
Most foods contain a variety of carbohydrates, proteins, and fats,
all rich in energy-laden chemical bonds. Carbohydrates and fats, for
example, possess many carbon-hydrogen (C—H), as well as carbon-
oxygen (C—O) bonds. The job of extracting energy from this complex
organic mixture is tackled in stages. First, enzymes break the large
molecules down into smaller ones, a process called digestion. Then, other
enzymes dismantle these fragments a little at a time, harvesting energy
from C—H and other chemical bonds at each stage. This process is called
catabolism.
Cellular respiration
When oxygen gas (O2) accepts the hydrogen atom, water forms,
and the process is called aerobic respiration. When an inorganic
molecule other than oxygen accepts the hydrogen, the process is called
anaerobic respiration. When an organic molecule accepts the hydrogen
atom, the process is called fermentation.
Stage One: Glycolysis
This process occurs in the cytoplasm and involves a sequence of 10
reactions that convert glucose into 2 three carbon molecules of pyruvate.
For each molecule of glucose that passes through this transformation, the
cell nets two ATP molecules by substrate-level phosphorylation.
The first half of glycolysis consists of five sequential reactions that
convert one molecule of glucose into two molecules of the three-carbon
37
compound, glyceraldehyde 3-phosphate (G3P). These reactions demand
the expenditure of ATP, so they are an energy-requiring process. This
process generates two ATP molecules.
Because each glucose molecule is split into two G3P molecules, the
overall reaction sequence yields two molecules of ATP, as well as two
molecules of NADH and two of pyruvate.

Stage Two: The Oxidation of Pyruvate

In the presence of oxygen, the extraction of additional energy from
pyruvate takes place inside mitochondria. The cell harvests pyruvate‘s
energy in two steps: first, by oxidizing pyruvate to form acetyl-CoA, and
then by oxidizing acetyl-CoA in the Krebs cycle.

38
Stage Three: The Krebs cycle
In this third stage, acetyl-CoA is oxidized in a series of nine
reactions called the Krebs cycle. These reactions occur in the matrix of
mitochondria. In this cycle, the two-carbon acetyl group of acetyl-CoA
combines with a four-carbon molecule called oxaloacetate. The resulting
six-carbon molecule then goes through a sequence of electron-yielding
oxidation reactions, during which two CO2 molecules split off, restoring
oxaloacetate. The oxaloacetate is then recycled to bind to another acetyl
group. In each turn of the cycle, a new acetyl group replaces the two CO2
molecules lost, and more electrons are extracted to drive proton pumps
that generate ATP.

39
Stage Four: The Electron Transport Chain
The NADH and FADH2 molecules formed during the first three
stages of aerobic respiration each contain a pair of electrons that were
gained when NAD+ and FAD were reduced.
The NADH molecules carry their electrons to the inner mitochondrial
membrane, where they transfer the electrons to a series of membrane
associated proteins collectively called the electron transport chain.

Moving Electrons through the Electron Transport Chain

The first of the proteins to receive the electrons is a complex enzyme

called NADH dehydrogenase. A carrier called ubiquinone then passes
the electrons to a protein-cytochrome complex called the bc1 complex.
Cytochromes are respiratory proteins that contain heme groups. The
electron is then carried by another carrier, cytochrome c, to the
cytochrome oxidase complex. This complex uses four such electrons to
40
reduce a molecule of oxygen, then each oxygen combines with two
hydrogen ions to form water:
O2 + 4 H+ + 4 e-  2 H2O
This series of electron carriers is collectively called the electron transport
chain.
The electron transport chain uses electrons harvested in aerobic
respiration to pump a large number of protons across the inner
mitochondrial membrane. Their subsequent re-entry into the
mitochondrial matrix drives the synthesis of ATP.

Anaerobic Respiration
In the absence of oxygen to accept the electrons, some organisms
can still respire anaerobically, using inorganic molecules to accept the
electrons. For example, many bacteria use sulfur, nitrate, or other
inorganic compounds as the electron acceptor in place of oxygen.

41
Methanogens. These bacteria use CO2 as the electron acceptor; reducing
CO2 to CH4 (methane) and they called methanogens.
Sulfur Bacteria. These bacteria derived energy from the reduction of
inorganic sulfates (SO4) to H2S. They do the same thing methanogens
do, but they use SO4 as the oxidizing agent in place of CO2.

Lecture Nine: Structure and function of cell

Photosynthesis
Introduction:
Photosynthesis is considered the most important process for
all living organisms except anaerobic bacteria, which can fix CO2
without using hydrogen of H2O as a source of protons. In addition,
the process is essential for life in terms of energy transfer. The
42
photosynthetic organisms produce about 50 million ton of sugar
annually by this process and this amount of sugar require transfer
of 1021 calories of sun energy to chemical energy. Photosynthesis is
sometimes called as carbon assimilation (assimilation: absorption
into the system). This is represented by the following traditional
equation.

During the process of photosynthesis, the light energy is converted

into chemical energy and is stored in the organic matter, which is
usually the carbohydrate. One molecule of glucose for instance,
contains about 686 K Calories energy. CO2 and water constitute
the raw material for this process and oxygen and water are formed
as the byproduct during photosynthesis.
Photosynthesis needs the following essential requirements:
1. Source of light energy
2. Source of energy capture
3. Means for energy storage

Photosynthesis pigments:
Studied conducted by plant physiologists indicated that the
pigments absorbed light energy and transfer it to chemical energy
are the chlorophylls which occurred in the plastids. The pigments
are classified as follow:
1. Chlorophyll
The quantity of chlorophyll is 10 times more than carotenoids and
it includes the following types:

43
 a. Chlorophyll a: occurred in all photosynthetic plants and
maximum absorption of light appeared at 430 and 660 nm
wavelengths.
b. Chlorophyll b: occurred in all higher plants and green algae and
maximum absorption of light appeared at 450 and 640 nm
wavelengths.
c. Chlorophyll c: Occurred in brown algae
d. Chlorophyll d: Occurred in red algae
e. Chlorophyll e: Occurred in some plant species
The chemical structure of chlorophyll a and chlorophyll b are well
established. The molecular formula for chlorophyll a: C 55H72O5N4
Mg and chlorophyll b: C55H70O6N4 Mg. Both of them consist of
Mg porphyrin head, which is hydrophilic, and a phytol tail, which
is lipophilic. The two chlorophylls differ because in chlorophyll b
there is a –CHO group instead of CH3 group at the 3rd C atom in
pyrrole ring II.

Figure1. Chlorophyll structure

44
 2-Other pigments: It consists of two groups:
a. Carotenoids
Carotenoids are lipid compounds that are distributed widely in both
animals and plants and range in color from yellow to purple.
Carotenoids are present in variable concentrations in nearly all
higher plants and in many microorganisms (e.g., red and brown
algae, photosynthetic bacteria and fungi). It includes α-carotene, β-
carotene and lycopene .
b- Xanthophylls
The xanthophylls are more abundant in nature than carotenes and
located in chloroplast. Xanthophylls are carotenes containing
oxygen.
Functions of Carotenoids:
a- Protect chlorophylls against photooxidation in excessive light.
b- Absorption of light and transfer it to chlorophylls.
c- Causes phototropism in plants.
Location of photosynthetic pigments in chloroplast
The photosynthetic pigments are located in grana portions of the
chloroplast. They are present in the thylakoid membrane or
membrane of grana lamella. The membrane of thylakoid is made
up of proteins and lipids or the membrane consists of both lipid
layer and protein layer. The hydrophilic heads of the chlorophyll
molecules remain embedded in the protein layer while lipophilic
phytol tail in the lipid layer.

45
 Grana portions of the chloroplast
Light
The chief source of light energy for photosynthesis is sun. The
solar radiation or solar energy passes through the space and reaches
the earth in the form of electromagnetic radiation with waves of
varying lengths. The various portions of electromagnetic spectrum
are gamma rays, ultraviolet rays, visible rays and infrared rays. The
wavelength of these rays ranges from 280 nm to 1000 nm.
Photosynthetic pigments absorb light energy only in the visible part
of the spectrum. The earth receives only about 40% of the total
solar energy. Only about 1% of the total solar energy received by
the earth is absorbed by the pigments and utilized in
photosynthesis.
Mechanism of Photosynthesis
Photosynthesis process is a chain of successive redox-reactions,
which requires sunlight at early stages (Robin Hill phase), while
subsequent steps can occur in the dark (F.F. Blackman phase).
In the light phase of photosynthesis absorption of light occurs by
chlorophyll molecules ―a‖ with the participation of auxiliary
pigments (chlorophyll ―b‖, carotenoids, phycobilins) and
transformation of solar energy into ATP and NADPH +H+. All
these processes are carried out in photochemically active
chloroplasts membranes, and represent a complex system of

46
photophysical, photochemical and chemical reactions. In the dark
phase of photosynthesis carbon fixation by the primary acceptor
(ribulose-1,5-diphosphate) happens, involving enzymes located in
the chloroplast stroma and with energy consumption in the form of
ATP and NADPH+H+ which are the final products of the light
phase.
Light Phase of Photosynthesis
The processes occurring during the light phase of photosynthesis
can be related to:
(1) Absorption of carbon dioxide;
(2) Absorption of solar energy and its transformation into
chemical energy.
(1) Absorption of carbon dioxide from the external environment
happens through the open ostiole (photoactive physiological
reaction). Carbon dioxide enters the sub substomatal cavity, from
where it diffuses through the free intercellular spaces to directly
contact the cellulose membranes of palisade assimilatory
parenchyma, situated on the upper side of the leaf blade, or the
cells of the spongy parenchyma from the inferior side.
In the envelopes of assimilatory cells are continuously irrigated
with water absorbed from the soil, the CO2 from the air that
circulates in the intercellular spaces, possessing a high
hydrosolubility, dissolves and forms carbonic acid (H2CO3), which
dissociates in H+, HCO3-, CO 3-2. In the ionic form carbon dioxide
enters the cytoplasm and reaches chloroplasts. Consequently, it
results that the first condition of photosynthesis is the degree of
osteole opening and the presence of a sufficient amount of water in
foliar tissues. At night, when stomata are closed (photoactive
closure) as well as in drought conditions (hydroactive closure),

47
when the cellular membranes of the leaf mesophyll cells are dry,
photosynthesis is blocked and plant growth stagnates.
(2) Absorption of solar energy and its transformation into
chemical energy
Happens via several successive stages:
• Solar energy absorption and excitation energy migration to the
system of pigments.
• Oxidation of the reaction centre and stabilization of the separated
charges.
• Electron transfer through the electron transport chain (ETC).
• Water photooxidation and molecular oxygen elimination.
• Conjugation of electron transport with proton transfer and the
synthesis of ATP.
These processes are carried out in granal and stromal thylakoids
with the participation of different molecules that make up two
specific structures in superior plants—photosystem I (PS I) and
photosystem II (PS II), which differ in their protein components,
pigments and optical properties. Each photosystem is formed of a
reaction center conjugated with electron donors and acceptors
together with the ―antenna‖ pigments.
Chromoproteids of the antenna-complexes have no photochemical
and enzymatic activity. Their role is reduced to the accumulation
and transmission of energy quanta to a limited number of
molecules, which carry out photochemical reactions.

48
 Photorespiration

Photorespiration presents in all plants and takes place in the

presence of light. The reactions of photorespiration are completed
in 3 cellular structures namely chloroplast, perexisome and
mitochondria. The process is important for biosynthesis of the
amino acids (glycine and serine) which are essential for protein
biosynthesis. The Photorespiration occurs as in follow conditions:
1. Occurs on hot, dry, bright days
2. Stomates close
3. Fixation of O2 instead of CO2
4. Produces 2-C molecules instead of 3-C sugar molecules
5. Produces no sugar molecules or no ATP
49
 Because of photorespiration, plants have special adaptations to limit
the effect of photorespiration in C4 plants and CAM plants.

Lecture Ten: 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.
Bacteria (prokaryotes) typically have one circular chromosome,
while eukaryotes usually have linear chromosomes and vary widely in
their sizes and numbers of chromosomes.

50
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.
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.
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 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)

51
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.
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.

52
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.
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

53
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 2).

Figure 2 : Cell cycle

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:

54
 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 3).
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 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.

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 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 3 : 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
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

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 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.

Lecture Eleven: Genetics

Meiosis
Meiosis is reduction division that takes place in the germ cells to
generate male and female gametes, sperm and egg cells, respectively.
Meiosis requires two cell division, meiosis I and meiosis II, to reduce the
number of chromosomes from diploid (2n) to haploid number (1n). The
end products of meiosis are 4 haploid (1n) cells.

Meiosis in males is called (Spermatogenesis) and produce sperm

Meiosis in females is called (Oogenesis) and produce egg or ovum

(pleural =ova)

- Diploid cells (2n) have double structured chromosomes (46

chromosomes).

- Haploid cells (1n) have single stranded chromosomes (23

chromosomes).

- Fertilization is the fusion of a sperm (1n) and egg cell (1n) to produce a
zygote.

-Zygote has a diploid chromosome (2n) number, one set from each
parent.

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In human, somatic cells (body cells) have 23 pairs of homologous
chromosomes.

Homologous chromosomes
- Pair of chromosomes (one from each parent) that are similar in length,
gene position, and centromere location .Human has 23 pairs of
homologous chromosomes:-
22 pairs of autosomes + 1 pair of sex chromosomes
(XX in female, or XY in male)
Meiosis has two distinct stages:
1- Meiosis I 2- Meiosis II

Meiosis I consist of 4 phases

1- Prophase I 2-Metaphase I 3-Anaphase I 4-Telophase I
Male germ cells (primary spermatocytes) and female germ cells (primary
oocyte) at the beginning of meiosis I similar to mitosis interphase, the
gametes replicate their DNA so that each chromosome consists of two
sister chromatids held together at a centromere. Centrioles pairs also
replicate.
2- Meiosis II
- No interphase occurs (no need for more DNA replication)
- Meiosis II is similar to mitosis
Meiosis II consist of 4 phases
1- Prophase II 2- Metaphase II 3- Anaphase II 4- Telophase II
Comparison between meiosis I with meiosis II

meiosis I meiosis II

1- Interphase I No interphase II
DNA replication

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2- Prophase I Prophase II
Pairing of homologous No pairing of chromosomes
chromosomes
3- Metaphase I Metaphase II
Homologous duplicated haploid number of duplicated
chromosomes at equator chromosomes at equator

4- Anaphase I Anaphase II
Homologous chromosomes Sister chromatids separate,
separate to the poles becoming daughter chromosomes
that move to the poles

5- Telophase I Telophase II
Two haploid daughter cells Four haploid daughter cells

Gene Expression
RNA (ribonucleic acid)
RNA (ribonucleic acid) is made up of nucleotides (nt)
containing the sugar ribose. This sugar accounts for the scientific name of
this polynucleotide. The four nucleotides that make up the RNA molecule
have the following bases: adenine (A), uracil (U), cytosine (C), and
guanine (G). One of the differences between RNA and DNA is the
replacement of thymine with uracil. As with DNA, complementary base
pairing may occur in RNA; cytosine pairs with guanine and adenine pairs
with uracil. However, unlike the double-helix structure of DNA, most
RNA is single-stranded.
RNA is divided into coding and noncoding RNAs. The coding RNA is
messenger RNA (mRNA), which is translated into protein. Noncoding
RNAs are divided into ribosomal RNA (rRNA), transfer RNA (tRNA),
and the small RNAs. The small RNAs are involved in the expression of
the genes that code for mRNA and rRNA.

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Messenger RNA (mRNA) is produced in the nucleus, where DNA
serves as a template for its formation. This type of RNA carries genetic
information from DNA to the ribosomes in the cytoplasm, where protein
synthesis occurs. Messenger RNA is a linear molecule.
Ribosomal RNA (rRNA) is produced using a DNA template in the
nucleolus of the nucleus. Ribosomal RNA joins with specific proteins to
form the large and small subunits of ribosomes. The subunits then leave
the nucleus and either attach themselves to the endoplasmic reticulum or
remain free within the cytoplasm. During the process of protein synthesis,
the large and small ribosomal subunits combine to form a complex (the
ribosome) that acts as a workbench for the manufacture of proteins.
Transfer RNA (tRNA) is produced in the nucleus, and a portion of DNA
also serves as a template for its production. Appropriate to its name,
tRNA transfers amino acids to the ribosomes. At the ribosomes, the
amino acids are bonded together in the correct order to form a protein.
There are 20 different types of amino acids used to make proteins. Each
type of tRNA carries only one type of amino acid; therefore, at least 20

61
different tRNA molecules must be functioning in the cell to properly
make a protein.

Transcription
During transcription, a strand of DNA acts as a template upon which a
strand of RNA is assembled from RNA nucleotides. A nucleotide can be
added to a growing strand of RNA only if it is complementary to the
corresponding nucleotide of the parent strand of DNA: G pairs with C,
and A pairs with U. Thus. each new RNA is complementary in sequence
to the DNA strand that served as its template.

Translation
Protein synthesis is accomplished through a process called translation.
After DNA is transcribed into a messenger RNA (mRNA) molecule
during transcription, the mRNA must be translated to produce a protein.
In translation, mRNA along with transfer RNA (tRNA)
and ribosomes work together to produce proteins.

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Once mRNA has been modified and is ready for translation, it binds to a
specific site on a ribosome. Ribosomes consist of two parts, a large
subunit and a small subunit. They contain a binding site for mRNA and
two binding sites for tRNA located in the large ribosomal subunit.
Mutations
Mutations are changes in the sequence of a cell‘s DNA. If a mutation
changes the genetic instructions encoded in the DNA, an altered gene
product may be the result. More than one codon can specify the same
amino acid, so cells have a certain margin of safety. For example, a
mutation that changes a UCU codon to UCC in an mRNA may not have
further effects, because both codons specify serine.
Types of mutations:
1- Base-pair substitution: Type of mutation in which a single base-pair
changes.
2- Deletion Mutation in which one or more base pairs are lost.
3- Insertion Mutation in which one or more base pairs become inserted
into DNA.

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 Lecture Twelve: 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

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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.

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

65
adaptive modifications of the forelimb structure of their common early
mammalian ancestors.

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.

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 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.

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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.

Lecture Thirteen: 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

68
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 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

69
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.

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

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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 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

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1. Rings of cellulose-synthesizing proteins
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

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  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
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o advantages: long distance, no motility needed

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

75
structurally similar myxomycetes (slime molds) and oomycetes (water
molds).

Lecture Fourteen: 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

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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.

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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.
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

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 Phylum Echinodermata
Phylum Chordata

 Phylum Porifera
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

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 Round, smooth worms, Bilateral symmetry Digestive system with two
openings free living and parasitic forms Examples: roundworms.
 Phylum Mollusca
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.

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 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
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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