F.Sc Biology Part 1 Complete Notes

NAMS PATTOKI

01 Introduction to Biology

Biology is the branch of science that studies living organisms and all the processes, phenomena and characteristics associated with them. Biologists also study the non-biological factors of earth that influence living things directly or indirectly.

Living things or organisms are complex objects in nature that have following characters:

·         made up of cells,

·         contain genetic material,

·         acquire and use energy from nature,

·         carry out and control chemical reactions in their bodies,

·         grow and reproduce,

·         maintain constant internal environment,

·         Detect and respond to changes in the environment.

Branches of Biology

Ecology is the branch of biology that studies interaction of organisms with other organisms and with their environment.

Embryology is the branch of biology that studies the formation and early development of complete living organisms from a single fertilized egg (zygote).

Physiology is the branch of biology that studies the functioning of organisms in relation to their structure.

Morphology is the branch of biology that studies the structure of animals and plants. External morphology deals with the outer structure of organisms. Internal morphology or anatomy studies the shape of internal organs.

Paleontology is the study of fossils. Fossils are the remains of organisms that existed in the distant past that were buried in soil and have now become part of earth crust.

Histology is the branch of biology that studies microscopic structure of animal or plant tissues.

Evolution is the branch of biology that studies how organisms existed in the past and what changes have occurred in their structure over time.

Genetics is the branch of biology that studies heredity (how traits are passed from one generation to the next) and variation in organisms.

Zoogeography is the study of distribution of organisms over different parts of earth and the processes behind distribution patterns.

Molecular Biology is the branch of biology that studies the structure and processes of macromolecules (mainly nucleic acids and proteins) essential to life and the role played by genetic information.

Environmental Biology is the study of relationship between organism and their environment. It also studies how changes in environment affect living things as well as the changes in the environment caused by human activities.

Microbiology is the study of organisms which are too small to be seen by naked eye and require microscope for their study. These include bacteria and viruses and certain groups of protozoa, algae and fungi.

Freshwater Biology is the branch of biology that deals with the organism living in freshwater bodies (rivers, lakes, streams and ground water) as well as physical and chemical properties of these water bodies.

Marine Biology is the study of organism living in seas and oceans as well as physical and chemical properties of these water bodies.

Parasitology is the branch of biology that studies parasites (organisms that live in or on other organisms and obtain food from them). Structure, mode of transmission, life cycle, and host-parasite relationship are studied in parasitology.

Human Biology is the branch of biology that studies all aspects of human life. This includes form and structure (anatomy), function (physiology), histology, evolution, genetics and ecology of human beings.

Social Biology is the branch of biology which deals with the study of social interactions of human beings and aspects of their communal life.

Biotechnology is the use of organisms or part of organisms for the benefit of mankind. It utilizes systems or processes of living beings for manufacturing and industries.

Levels of Biological Organization

Atoms and Molecules

Out of 92 naturally occurring elements, only 16 are usually required for the formation of bodies of living things. These 16 and a few other (rarely found) elements are called bioelements.

Element	Percentage	Element	Percentage
Oxygen	65%	Potassium	0.35%
Carbon	18%	Sulfur	0.25%
Hydrogen	10%	Chlorine	0.15%
Nitrogen	3%	Sodium	0.15%
Calcium	2%	Magnesium	0.05%
Phosphorus	1%	Iron	0.004%

Elements that are present in small amounts in the body are called trace bioelements. These include Manganese, Iodine, Zinc and Copper.

Atoms of two or more elements combine to form molecules. Molecules can be divided into two types on the basis of molecular weight.

·   Micro-molecules are those molecules which are small and have low molecular weight, e.g., CO₂ and H₂O.

·   Macro-molecules are large molecules with high molecular weight and are usually made up of small repeating subunits. For example starch and cellulose are made up of thousands of subunits of glucose, proteins are made up of subunits of different amino acids, DNA and RNA are made up of nucleic acid subunits.

Organelles and Cells

Organelles are organized structures found in cells that are usually bounded by membranes. Each type of organelle has a definite structure and carries out specific function,e.g., mitochondria, chloroplasts, nucleus.

Cells are structural and functional units of life. A unicellular organism is composed of only one cell, while multicellular organisms have many cells in their body. On the basis of structure, cells can be of two types:

·   Prokaryotic cells do not contain a definite membrane--bound nucleus.Their genetic material is present in the cytoplasm.

·   Eukaryotic cellshave definite membrane-bound nucleus in their cells, which contains genetic materials.

Tissues are assemblages of structurally similar cells that perform a specific function together. For example

·   Parenchyma tissues in leaves carry out photosynthesis

·   Muscles in animals are responsible for contraction.

Organ and Organ Systems

An organ is usually composed of more than one distinct type of tissues. It is a fully differentiated structural and functional unit in an organism that is specialized for some particular function. For example heart pumps blood in animals and leaves are specialized for photosynthesis in plants.

An organ system is formed when two or more organs work together to carry out a general function, such as digestion or movement.

Different organs and organ systems combine to form an individual. Each individual is similar to other members of its species in some respects while it is also unique at the same time.

A population is a group of individuals of the same species living in the same area at the same time.

Community and Ecosystem

A community is formed when several populations of different species (animals and plants) inhabit the same area and interact with each other in different ways.

All living organisms in a given area plus all of the nonliving matter and energy constitute an ecosystem.

Biome

A Biome is a large regional community primarily determined by climatic conditions. It usually has a distinct flora and fauna,e.g., desert and tropical rain forest.

The number and variety of organisms in a specific area is called biodiversity. There are nearly 2,500,000 known species of organisms. It is estimated that about 30 million species are still unknown.

Organisms	Percentage
Insects	53%
Animals (except insects)	19.9%
Vascular Plants	17.6%
Fungi, Algae, Protozoa, Prokaryotes	9.4%

Era	Period	Age (mya)	Plants	Animals
Cenozoic	Quaternary	70	Angiospersm (flowering plants) became dominant
	Tertiary			Birds, mammals and insects become dominant
Mesozoic	Cretaceous	135		Dinosaurs become extinct
	Jurassic	180	Gymnosperms became dominant	Dinosaurs become dominant
	Triassic	255		Dinosaurs, birds and mammals evolved
Paleozoic	Permian	270		Diversification of reptiles
	Carboniferous	350	Deposits of oil, coal and gas Origin of seed plants	First reptiles evolved
	Devonian	400		First amphibians and insects evolved
	Silurian	440	Origin of vascular plants	Origin of arthropods
	Ordovician	500		First vertebrates (jawless fishes) evolved
	Cambrian	600		Origin of all major animal phyla
Proterozoic		2000	Age of fungi and algae Origin of animal and plant ancestors from Protista First prokaryotic organisms arose (about 3000 million years ago) Origin of earth

Living World in Time

Fossils are organisms that existed in the past but later became extinct and their remains became part of earth crust.

Phyletic Lineage is an unbroken series of species arranged in ancestor to descendant sequence. Each later species evolved from the one immediately before it.

Biological Method

Science is a systematic way of obtaining knowledge. The scientific method is based on observations, hypothesis, experiment, and results.

Observation is the first step of biological method. Observations are usually made with five senses. An observation can be qualitative or quantitative.

·   Qualitative observations are based on the quality of an object like color, taste or smell. They are not very useful for scientific inquiry.

·   Quantitative observations are based on quantity of an object like size, length, or volume, which can be expressed in the form of numbers. Different instruments can be used to measure these parameters.

Hypothesis is a proposed explanation for a natural phenomenon that is not yet verified. It is based on previous observations or experimental studies.A hypothesis is tested by repeated experiments.

A scientific hypothesis that survives thoroughexperimental testing becomes a scientifictheory. A good theory has explanatory power and is predictive.

Scientific law is a uniform or constant fact of nature that cannot be refuted. It is derived from a theory which has been tested in all possible ways. It is usually more general.

Deductive reasoning involves drawing specific conclusions from some general principles.

Inductive reasoning involves discovering general principles on the basis of specific observations.

Biology in theServiceof Mankind

Food Problem

Artificial selection or selective breeding is the procedure of selecting desired traits in organisms and allowing only those individuals to breed that show the trait. Next generation therefore has more individuals with that specific trait.

Direct manipulation of genes by recombinant DNA technology is called genetic engineering. It allows new or improved traits to be introduced in organisms.

Plants and animals in which foreign genes have been incorporated are called transgenic organisms.

Cloning is the production of genetically identical copies of organisms or cells by asexual reproduction.

A clone is a cell or individual and all its asexually produced offspring. All members of a clone are genetically identical to each other.

Plant tissue culture is the process of growing a plant in the laboratory from cells rather than seeds. This technique is used in traditional plant breeding as well as in agricultural biotechnology.

Pesticides are chemicals that are used to kill insect or fungal pests.

Biological control is the use of biological agents (natural enemies) to control pests. These agents usually include parasites and predators of pest species.

Integrated disease/pest management is the use of all appropriate techniques of controlling diseases/pests in a coordinated manner that enhances, rather than destroys, natural controls.A combination of biological, cultural, and genetic control methods are usually employed.

Bio-pesticides are substances used for pest control that are derived from natural materials such as plants, animals, bacteria, fungi and some minerals. Unlike chemical pesticides, these are not broad-spectrum poisons.

Hydroponic culture technique allows growing plants directly in a solution of nutrients, without the requirement of soil. It allows experimentation on nutrient requirements of plants.

Pasteurization is a process of heating a food (usually liquid) to a specific temperature for a definite length of time, and then cooling it immediately. This process kills microbes and prevents spoilage.

Fighting Diseases

Vaccination is the process of protecting the body from infection by inoculating killed or weakened infectious agents or their parts in the body. It results in increased immunity against the particular disease.

Antibiotics are chemicals (usually synthesized by microorganisms) that can kill or inhibit the growth of certain other microorganisms. These are commonly used for curing infections.

Use of high-energy radiation from radioactive materials to kill cancer cells is calledRadiotherapy. The cancer tissue is usually exposed to small doses of radiation at regular intervals for this purpose.

Chemotherapy involves the use of anti-cancer drugs for the treatment of cancer. It usually results in killing or halting the replication or spread of cancer cells in the patient.

Eugenics is the study of methods for improving genetic qualities by selective breeding (especially when applied to humans).

Gene therapy is the insertion of functional copy of a gene into an individual's cellsto treat disease. It is usually employed when the person has mutation in that particular gene and does not function properly.

Protection and Conservation ofEnvironment

Contamination of environment with harmful and unwanted chemicals is called pollution. Itcauses instability, disorder, harm or discomfort to the ecosystem and directly affects living organisms.

Bioremediation is the removal or degradation of environmental pollutants or toxic substances by the use of living organisms (microorganisms, fungi, green plants or their enzymes).

Endangered species is a population of organisms which is at risk of becoming extinct because it is either few in numbers or threatened by disease or habitat destruction.

02 Biological Molecules

Biochemistry is the branch of biology, which studies the chemical components and chemical processes of living systems. Basic understanding for biochemistry is essential for understanding the structure and function of living systems.

All the chemical reactions occurring in the body or a cell are called metabolism. Metabolic reactions are of two types.

Reactions in which simpler substances are combined to form complex substances are called anabolic reactions. These reactions usually require energy (e.g. photosynthesis).

Reactions in which complex substances are broken down in simple substances are called catabolic reactions. These reactions usually produce energy (e.g. glycolysis).

Role of Carbon and Water

Properties of Carbon

Carbon is the most important element in organic substances and has many properties that are unique, making many processes of life possible.

Carbon is a tetravalentelement (tetra=four; valent=valency), meaning that it can form four covalent bonds with many different elements. Due to this ability, carbon can make many complex molecules like branched or unbranched chains or rings which are highly stable.

The carbon-carbon (C–C) bonds are strong, making the chains or rings highly stable.

Carbon also forms covalent bond with hydrogen (C–H) bond which serves as source of energy in biological systems.

Carbon combines with Nitrogen (C–N) to form peptide bond present in proteins.

Carbon combines with oxygen (C–O) to form glycosidic bond present in carbohydrates.

Small compounds of carbon (called micromoleculeslike ATP, glucose, and amino acids) can further join together to form large polymers or macromolecules(like DNA, Starch, and proteins respectively).

Properties of Water

Water is the medium of life.Almost all reactions of the cell occur in aqueous environment. Human body contains about 70-90% water and its amount varies in different types of cells. It is also involved in many chemical reactions directly (e.g. hydrolysis) and is used as raw material in photosynthesis.

Water is highly polarin nature. Polar substances can dissolve in it very easily. When ionic substances are placed in water, they become dissociated in positive and negative ions. Non-ionic substances with charged groups also become dispersed in water. In solution form, the ions and molecules have kinetic energy due to which they can combine with each other easily. Non-polar substances (e.g. lipids) do not dissolve in water.

Heat capacity is the amount of heat energy required to raise the temperature of a substance. Water has an unusually high heat capacity. Specific heat capacity of water (to raise its temperature from 15 to 16 ^oC) is 1.0, far greater than other liquids. This is because water has a lot of hydrogen bonds and energy is required to break these bonds. This property makes water a good temperature stabilizer and protects living things from change in environmental temperature.

Heat of vaporization is the heat required to convert one gram liquid into gas. Water has unusually high heat of vaporization. Specific heat of vaporization of water is 574 Kcal/kg. When water evaporates, the remaining water becomes cool. This property helps to cool our body (by evaporation of sweat) and also the plants (by transpiration).

Water molecules ionize to form H⁺ and OH^- ions. At 25°C the concentration of each of H⁺ and OH^- ions in pure water is about 10^-7 mole/liter. These ions help in various reactions and processes of the body.

Water is an excellent lubricant that provides protection against friction. Tearsprotectthesurfaceofeyefromthe rubbingofeyelids and water also forms afluid cushion around important organs.

Carbohydrates

Carbohydrates are composed of carbon, hydrogen and oxygen. The word carbohydrate literally means “hydrated carbons”. Chemically, carbohydrates are defined as polyhydroxy aldehydes or kentones, or complex substances which on hydrolysis yield polyhydroxy aldehyde or ketone subunits.Hydrolysis is the breakdown of complex molecules with addition of water.

Their general formula is C_x(H₂O)_y where x can be any number from 3 to several thousands and y can be equal to x or smaller.The ratio of hydrogen and oxygen is the same as in water.

Carbohydrates play both structural and functional roles in the body. They are found in all organisms and in all parts of the cell. Simple carbohydrates are main source of energy in all types of cells. Some make up cell wall in plants and bacteria. Cellulose of wood, cotton and paper, starches present in cereals, root tubers, cane sugar and milk sugar are all examples of carbohydrates.

The main source of carbohydrates is green plants which make glucose during photosynthesis. Plants can make all other biological molecules from glucose. Carbohydrates combine with other types of compounds to produce conjugated molecules. For example, they combine with lipids and proteins to form glycolipids and glycoproteins which play important role in making extracellular matrix, plasma membrane, and bacterial cell wall.

Carbohydratesarealsocalled'saccharides' (saccharon=sugar). They can be divided into three groups: monosaccharides, oligosaccharides, and polysaccharides.

Monosaccharides

Monosaccharides are simple sugars which cannot be hydrolyzed. They are sweet in taste and easily soluble in water. Chemically they are either polyhydroxy aldehydes or ketones.

All carbon atoms in a monosaccharide have a hydroxyl group except one. The remaining carbon atom is either a part of an aldehyde group or a keto group. The sugar with aldehyde group is called aldo-sugar; and with the keto group as keto-sugar.

A monosaccharide may contain from 3 to 7 carbons. Trioses (3C) are formed during respiration and photosynthesis. Tetroses (4C) are relatively rare and are found in some bacteria. Pentoses (5C) and hexoses (6C) are very common and provide energy (like glucose).

In aqueous solution, pentoses and hexoses are in the form of rings rather than straight chains. Ribose forms a five-cornered ring called ribo-furanose. Glucose forms a six cornered ring called gluco-pyranose.

Glucose is a hexose found in all fruits like grapes, figs and dates. Blood contains about 0.08% glucose. It is also present in combined form in disaccharides and polysaccharides. Starch, glycogen and cellulose yield glucose on complete hydrolysis.

Plants produce glucose during photosynthesis using energy in the form of sunlight. For the synthesis of 10g of glucose 717.6 Kcal of solar energy is used. This energy is stored in chemical bonds and later utilized by living organisms.

Oligosaccharides

Oligosaccharides are formed by joining of two to ten monosaccharides.The covalent bond between two monosaccharides is called glycosidic bond (C–O–C).These are relatively less sweet and less soluble in water. Oligosaccharides that yield two monosaccharides on hydrolysis are called di-saccharides, those yielding three are known as tri-saccharides and so on.

Sucrose (cane sugar) is the most commonly known disaccharide. Its general formula is C₁₂H₂₂O₁₁. Sucrose yields glucose and fructose upon hydrolysis.Maltose is another disaccharide present in fruits. Lactose is another disaccharide present in milk.

Polysaccharides

Polysaccharides are very complex sugars made up of long chains of thousands of monosaccharide subunits. They are usually branched, tasteless and insoluble in water. Their molecular weight is very high. Important polysaccharides include starch, glycogen, cellulose, dextrins, agar, pectin, and chitin.

Starch is a polysaccharide found in fruits, grains, seeds and tubers. All animals consume starch in their diet for energy. Upon hydrolysis, it produces glucose subunits. Starch gives blue color in iodine solution. It is of two types.

1.       Amylose starch has long unbranched chains of glucose and is somewhat soluble in hot water.

2.       Amylopectin starch contains highly branched chains of glucose and is insoluble in water.

Glycogen is called animal starch. Excess glucose in the animal body is stored in the form of glycogen in liver and muscles.It also yields glucose upon hydrolysis. It is insoluble in water. It gives red color with iodine.

Cellulose is the most abundant carbohydrate in nature. Cell walls of plants are made up of cellulose. Cotton is the purest form of cellulose. It is highly insoluble in water. It also yields glucose upon hydrolysis.It gives no color with iodine solution. Humans cannot digest cellulose. Special micro-organisms (bacteria, yeasts and protozoa) present in the digestive tract of herbivores secrete an enzyme cellulase, which helps to digest cellulose in them.

Lipids

Lipids are diverse group of compounds related to or derived from fatty acids. These are nonpolar substances that do not dissolve in water but readily dissolve in organic solvents like ether, alcohol, chloroform and benzene.

All Lipids are hydrophobic(hydro=water; phobic=fearing) in nature. They play both structural and functional roles in the cell.

·   They are major part of membranes in the cell.

·   They also store excess amount of energy. Since the proportion of C–H bonds is higher in lipids, they can store double energy as compared to carbohydrates.

·   Lipids provide insulation against hot and cold environments.

·   Theyalso help to make water-proof surfaces e.g. waxes on the surface of exoskeleton of insects and cutin on the surface of leaves and fruits.

Chemically, lipids are of several types.

Fatty Acids

Fatty acids are long molecules containing straight chains of carbon bonded with hydrogen atoms. A carboxylic (–COOH) group is attached at one end of the chain. The number of carbon atoms in the chain is usually even, from 2 to 30.Fatty acids in plants may have branches or rings in them.

Their solubility (in organic solvents) and melting point increase with increasing chain length.They are usually lighter than water with a specific gravity of 0.8. They are usually not crystalline, but some can be crystallized in special conditions. Fatty acids are of two types:

1.       Saturated fatty acids do not contain any double bond and are usually present in animals. They are usually solid at room temperature (like animal fats).

2.       Unsaturated fatty acids contain double bonds and are usually derived from plants. They are usually liquid at room temperature (like plant oils).

Acyl-glycerols

Acyl-glycerols are formed by combination of fatty acids and glycerol. Most common acylglycerol is triacyl glycerol, also called triglyceride or neutral lipids.

Chemically, they are esters of fatty acids and alcohol. An ester is formed when an alcohol combines with a carboxylic acid and a water molecule is released. During this reaction, alcohol provides OH while acid provides H to produce a water molecule.

Phospholipids

Phospholipids are formed by the combination of glycerol, fatty acids and phosphoric acid. Nitrogenous bases like choline, ethanolamine and serine may also be present in phospholipids. They are widely present in membranes and are found in all groups of organisms.Phosphatidyl-choline is an example of phospholipid.

Waxes

Waxes are mixtures of long chain alkanes and alcohols, ketones and esters of long chain fatty acids. Alkanes in waxes have odd number of carbon atoms ranging from 25 to 35. They are present in protective coating of leaves and fruits. They prevent water loss and abrasive damage.

Terpenoids

Terpenoids are important molecules made up of repeating isoprenoid units. After combining in different ways, they produce compounds like rubber, carotenoids, steroids, and terpenes.

Proteins

Proteins are polymers of amino acids containing carbon, nitrogen, hydrogen, and oxygen. A single protein can have a few to thousands of amino acids. These are most abundant (50% of dry weight) biological molecules in the cell and are present in all cells.

Amino Acids

Amino acids contain a central carbon atom (called alpha carbon) bonded to four different functional groups. An amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom are present in all amino acids. The fourth functional group is denoted by R and can be –H, –CH₃ or some other group. Twenty different types of amino acids are commonly found due to different R groups. Human proteins may also contain 5 rare amino acids. About 170 different amino acids have been found so far in living organisms.

Polypeptides

Amino acids join together to form polypeptides or proteins. The amino group of one amino acid reacts with carboxyl group of the other to form peptide bond (C–N). A water molecule is released during the process. The resulting molecule is called a dipeptide and has a free carboxyl group on one side and amino on the other. Therefore, it can combine with more amino acids to form long chains or polypeptides.

Function of Proteins

Proteins play both structural and functional roles in the cell.

·   Many structures of the cell are made up of proteins.

·   Enzymes are globular proteins that control all chemical reactions in a cell.

·   Some proteins (e.g. hemoglobin) act as carriers for transport of important substances like oxygen, lipids and metal ions.

·   Antibodies are proteins that defend the body against pathogens.

·   Blood clotting proteins prevent the loss of blood in case of an injury.

·   Muscles contain special proteins that help in locomotion of entire organism or organs.

·   Some proteins help in movement of organelles and chromosomes within cells (e.g. during cell division).

Structure of Proteins

Function of all proteins depends on their structure. Any change in structure affects the shape and function of proteins.Arrangement of amino acids is very important for proper functioning of the protein. For example, when only one amino acid of hemoglobin gets changed, it results in sickle cell anemia. Due to this change, hemoglobin cannot carry oxygen, leading to death of patient.

There are four levels of organization of the structure of proteins, which will be discussed below.

Primary Structure

The number and sequence of amino acids present in a protein make its primary structure. Size of a protein molecule depends on the number and type of amino acids present in it. There are about 10,000 different proteins in humans, each with a distinct amino acid sequence. This sequence is controlled by DNA.

F. Sanger was the first person to determine the sequence of a protein. He determined that insulin is composed of two chains. One chain contains 21 amino acids while the other contains 30 amino acids. These two chains are joined by disulfide bonds. Hemoglobin is composed of four chains, two are called alpha chains and two are called beta chains. Alpha chains contain 141 amino acids while beta chains contain 146 amino acids.

Secondary Structure

Polypeptide chains usually do not remain straight, but rather form one of two definite shapes: an alpha helix or a beta pleated sheet. Together, these two structures make the secondary structure of proteins. An alpha helix is a spring like structure in which each complete turn is made up of 3.6 amino acids. Amino acids of different turns bond with each other by hydrogen bonds and maintain the spiral structure.Beta pleated sheet is a flat structure formed by folding of polypeptide chain.

Tertiary Structure

The polypeptide chain further bends and folds onto itself to give rise to its tertiary structure. It is usually globular structure which is maintained by ionic bonds, hydrogen bonds, and disulfide bonds (–S–S–). In aqueous environment, most of the hydrophobic amino acids of proteins are buried deep inside, while hydrophilic amino acids are on surface.

Quaternary Structure

Quaternary structure is formed when different polypeptide chains come together to give rise to a single large structure. These chains usually join by hydrophobic, ionic or hydrogen bonds. In hemoglobin, for example, four separate chains are combined together to make a single protein molecule.

Types of Proteins

There are many different types of proteins in a cell. On the basis of structure they can be divided into two groups.

Fibrous Proteins

Polypeptide chains in fibrous proteins assemble together in the form of long fibrils.Secondary structure of fibrous proteins is important. They are usually insoluble in water. They are usually non-crystalline and elastic in nature. Their main role is making important structures like silk (in silkworm and spiders), myosin (of muscles), fibrinogen (for blood clotting) and keratin (hair and nails).

Globular Proteins

Globular proteins are spherical or ellipsoid in shape. Tertiary structure is important in them as folding of polypeptide chain gives them their shape. Their structure is adversely affected by change in physical conditions (temperature, pH etc.). They are usually soluble in water and can be crystallized. Examples of globular proteins are enzymes, antibodies, hormones, and hemoglobin.

Nucleic Acids

Nucleic acids are polymers of nucleotides. They were first discovered by F. Miescher in 1869 from nuclei of pus cells. Nucleic acids are of two main types: RNA (Ribo nucleic acid) and DNA (Deoxyribo nucleic acid).

Nucleotides are building blocks of nucleic acids and also play other important roles in cell (e.g. ATP is energy currency of cell). Each nucleotide is composed of three basic subunits: a pentose sugar, a phosphate group and a nitrogenous base. The nitrogenous base is attached to carbon number 1 of pentose sugar, while phosphate group is attached to carbon 3 by ester linkages.

1. The pentose sugar in RNA is ribose while in DNA it is Deoxy-ribose (meaning that it has one less oxygen at carbon number 2; an –OH is replaced by –H).

2. Nitrogenous bases are of four different types, namely: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). RNA contains Uracil (U) instead of thymine.

3. When only nitrogenous base and pentose are present (and phosphate is absent), the molecule is called nucleoside. When a phosphate is added to nucleoside, it forms a complete nucleotide.

Deoxyribo Nucleic Acid (DNA)

DNA is present in the nucleus of the cell. It is the hereditary material that controls all structures and functions of the cell. It is synthesized by polymerization of A, T, G, and C in the form of long chains called polynucleotide chains.

When two nucleotides join together, a dinucleotide is formed. Some dinucleotides, like nicotine-amine dinucleotide plays important role in oxidation-reduction reactions in the cell.

The amount of DNA present in each cell is fixed for a given species and depends on number of chromosomes. The amount of DNA in germ cells (sperms and eggs) is half that of somatic cells.

The sequence of bases in a polynucleotide chain can be divided into several units called genes. Gene is the basic unit of inheritance and directs the synthesis of a specific protein for performing a specific function. The genome of E. coli contains 4,639,221 base pairs which codes for 4,288 different proteins. Haemophilus influenzae was the first organism whose entire genome was sequenced in 1995.

Structure of DNA

The structure of DNA was first determined by J. Watson, and F. Crick in 1953. They built the first model of DNA on the basis of work of two other scientists.

Erwin Chargaff had proposed in 1951 that amount of adenine is always equal to amount of thymine while amount of guanine is always equal to amount of cytosine. This is called Chargaff’s rule.

Maurice Wilkins and Rosalind Franklin used X-ray diffraction to determine the structure of very pure crystals of DNA. Their data suggested that DNA is a double helix.

From both of these observations, Watson and crick built a model of DNA. Salient features of their model are:

·         Each molecule of DNA is composed of two polynucleotide strands.

·         These two strands are coiled around each other in the form of a spiral or double helix.

·         The coiling of these strands is opposite in direction (i.e. each strand is anti-parallel to the other).

·         Both of these strands are held together by hydrogen bonds.

·         The two strands are made up of phosphate and deoxy-ribose sugar while nitrogenous bases lie between them and form “base pairs”.

·         Adenine is always present opposite to Thymine of the other strand and two hydrogen bonds are present between them.

·         Guanine is always present opposite to Cytosine of the other strand and three hydrogen bonds are present between them.

·         Each turn of the double helix contains ten base pairs and is 34 angstrom (34 x 10^-10 meter) in length.

Ribonucleic Acid (RNA)

RNA is a polymer of ribo-nucleotides. RNA molecules are usually single stranded, which may sometimes fold onto themselves. Uracil (U) is present in RNA instead of thymine (T) and can base pair with Cytosine (C). Synthesis of RNA from DNA is called Transcription. There are three types of RNA.

Messenger RNA(mRNA) takes the genetic message from nucleus and brings it to cytoplasm. This information is carried to ribosomes in the cytoplasm where it can be processed to produce amino acid chains (proteins). Length of mRNA is usually variable and depends on the size of the gene from which it was copied. It makes up 3-4% of the total RNA in the cell.

Transfer RNA (tRNA) is present in cytoplasm and transfers amino acids to the site of protein synthesis. There are at least 20 different types of tRNA in a cell for 20 different amino acids. tRNA moleculesare usually short with only 75-90 nucleotides. They make up 10-20% of total RNA of the cell.

Ribosomal RNA (rRNA) is present in cytoplasm where it is associated with ribosomal proteins to form ribosomes. It acts as factory for production of new proteins. The message of mRNA is read by ribosomes and amino acids brought by tRNA are joined accordingly to produce proteins. rRNA is most abundant type of RNA and makes up about 80% of total RNA of the cell.

Conjugated Molecules

There are four basic types of biological molecules. Sometimes two different types of biological molecules combine to form conjugated molecules.

·   Carbohydrates combine with proteins to form glycoproteins. Most secretions of cells are glycoproteins. They are also present in plasma membrane.

·   Carbohydrates combine with lipids to form glycolipids. These are also important component of plasma membrane.

·   Lipoproteins are formed when lipids combine with proteins. They also form basic framework of plasma membrane.

·   Nucleic acids combine with basic proteins to form nucleo-proteins. Nucleo-histones make up chromosomes and play important role in regulation of gene expression.

·   RNA combines with proteins to form ribonuleo-protein particles in ribosomes.

·   Short polypeptide chains combine with long carbohydrate chains to form peptido-glycan which forms bacterial cell wall.

03 Enzymes

Enzymes are a group of biologically active proteins that catalyze chemical reactions in the cells. These are composed of hundreds of amino acids joined together and arranged to form a three dimensional globular structure.

Acceleration of a chemical reactions induced by the presence of molecules that are not directly used in the reaction is called catalysis. A catalyst is a molecule that can increase the rate of reactions without being used up. Enzymes are the major biological catalysts.

The reactants of a chemical reaction, upon which enzymes can act, are called substrate.

Cofactors

Some enzymes require a non-protein molecule for their proper functioning. This molecule is called co-factor. Co-factors usually provide chemical groups responsible for catalysis or are a source of energy for the reaction.

Some enzymes require metal ions as co-factors (like Mg⁺², Fe⁺², Zn⁺²) which are usually detachable. These are called activators.

Prosthetic group is the non-protein part of a protein molecule which is attached to the main molecule by covalent bond.

Coenzyme is the non-protein part of a protein that is loosely attached to the main protein molecule. These are usually derived from vitamins.

Vitamins are small organic molecules required in small amounts for the body. These are used to synthesize coenzymes and play important part in metabolism.

An enzyme without its coenzyme or prosthetic group is designated as apoenzyme. An apoenzyme cannot work alone to catalyze a reaction.

The main protein molecule and cofactor combine to form holoenzyme which is activated and can catalyze chemical reactions.

Pepsin is a powerful protein-digesting enzyme present in stomach. It is synthesized in its inactive form called Pepsinogen.

Enzyme Action

In most cases, enzymes act in a series of chemical reactions in a particular order in which products of one reaction are used as substrate for the next reaction. This series of reactions, catalyzed by enzymes, is called a biochemical pathway.

The catalytic activity of an enzyme is usually present in a small part of the structure, called the active site. The substrates bind to this region and are then converted to products by the enzyme.

Binding site is a specific region within the active site of enzyme with which the substrate binds. It is responsible for recognizing and attaching the proper substrate molecule with the enzyme and activating the catalytic site.

Catalytic site is a specific region within the active site of enzyme that is responsible for carrying out the chemical reaction and converting the substrate into product.

Lock and Key Model of enzyme action was proposed by Emil Fischer in 1890. According to this model an enzyme is a rigid structure that has a specifically shaped active site which can accept only a specific substrate just like a lock which can be opened by a specific key.

Koshland proposed a modified model for explaining enzyme activity in 1959 called Induced Fit Model. According to this model, attachment of substrate in the active site of enzyme brings about (induces) certain changes in the structure of enzyme. This change in structure allows the catalytic site to perform its action more effectively.

Factors Affecting the
Rate of Enzyme Action

Any factor, that can change the chemistry or shape of the enzyme, is capable of affecting the rate of catalysis. Some important factors are concentration of enzyme, concentration of substrate, temperature, and pH of the medium.

Most enzymes can work over a narrow range of temperature. The temperature at which enzymes can work at maximum rate is called its optimum temperature (usually 37°C). Any large change in temperature can have drastic effect on the structure of enzyme due to which its efficiently is reduced.

Most enzymes can work over a narrow range of pH. The pH at which enzymes can work at maximum rate is called its optimum pH. Any change in pH can have drastic effect on the charges of amino acids due to which the shape of enzyme is affected.

Rate of enzyme catalyzed reaction increases with increasing enzyme concentration. However, after a certain limit, increasing the enzyme concentration does not increase the rate. This concentration is called inhibitory concentration.

At very low levels of, increasing the substrate concentration also increases the rate of reaction. However, after a certain limit, all the active sites are occupied and increasing the substrate concentration does not further increase the rate of reaction.

Inhibitors

Inhibitors are chemical substances that react (in place of substrate) with the enzyme but are not transformed into products. They can block the active site temporarily or permanently and therefore stop the reaction. Poisons, antibiotics and some drugs show their effects by acting as inhibitors of specific enzymes.

An irreversible inhibitor binds to the enzyme permanently (e.g., by covalent bonds) or destroy the shape of active site, thereby permanently stopping the reaction.

Reversible inhibitors form weak linkages with the enzyme. Their effect can be neutralized by increasing the concentration of substrate.

Competitive inhibitorsare similar in shape to the substrate molecule. These can bind to the active site of the enzyme and block it. Therefore the substrate cannot bind to it and the reaction is blocked.

Non-competitive inhibitors bind to some part of the enzyme other than active site. The structure of enzyme is changed due to their binding and the enzyme fails to bind and transform the original substrate.

04 The Cell

Cells are defined as functional and structural units of life. All activities of life are carried out at the levels of cells. Multicellular organisms are made up of many cells.

Cell Theory

Many scientists contributed in the development of cell theory.

Robert Hook was the first scientist who discovered small box-like chambers in thin slices of cork in 1665. He called them cells in his famous book “micrographia”.

Robert Brown discovered nucleus in the cell in 1831.

Schleiden and Schwann found that all cells have certain common features in 1838. These include a single large nucleus, a fluid around the nucleus called cytoplasm, and an outer covering of the cell called plasma membrane.

Rudolph Virchow (1855) hypothesized that all cells arise from division of pre-existing cells. IN his book he wrote his famous phrase “omnis cellula e cellula”.

Louis Pasteur (1862) provided the experimental proof of Virchow’s hypothesis by showing that bacteria arise from pre-existing bacteria.

These ideas and observations were combined into a single theory, called the cell theory. According to this theory:

1. All organisms are composed of one or more cells.

2. All cells arise from pre-existing cells.

3. Cell is the basic structural and functional unit of life.

Studying Cells

Resolution is the minimum distance between two points that can be differentiated by human eye (or an instrument like lenses or microscope). Resolution of human eye is 1.0mm.

Cell fractionation is the process of separating different components of a cell by homogenizing tissues and centrifugation.

During homogenization the contents of a tissue are disrupted by crushing or chemical agents to produce homogenous mixture of cells.

During centrifugation the contents of a homogenized tissue are placed in a test tube and spun at high speed. Different components of the mixture arrange in different layers due to differences in their density.

Plasma Membrane

Plasma Membrane is the outermost boundary of the cell. It is mainly composed of lipids and proteins and a small amount of carbohydrates.

Unit membrane model proposes that cell membrane is composed of lipid bilayer sandwiched between inner and outer layers of proteins.

The fluid mosaic model proposes that the membrane is composed of a fluid “sea” of lipids in which protein molecules can float freely. The proteins in lipid membrane make a mosaic pattern on the lipid bilayer. The membrane contains charged pores through which materials can pass by active or passive transport.

Differential (or selective) permeability refers to the ability of plasma membrane to allow some types of molecules to pass freely while acting as a barrier to others. Lipid soluble substances can cross the membrane freely while polar or charged molecules (and ions) have difficulty in passing through the membrane.

Diffusion is the movement of molecules from an area of higher concentration to an area of lower concentration. It does not require energy.

Passive transport is the movement of molecules from area of higher concentration to area of lower concentration across a membrane.It does not require energy.

Active transport is the movement of molecules from an area of lower concentration to an area of higher concentration. This requires energy in the form of ATP. Special proteins in plasma membrane usually perform this function.

Endocytosis is the intake of materials by infolding of plasma membrane to form vacuoles. It is of two types: phagocytosis or pinocytosis.

1.       Phagocytosis is the intake of solid food particles by infolding of plasma membrane.

2.       Pinocytosis is the intake of liquid material by infolding of plasma membrane.

Cell Wall

Cell wall is an extra boundary around the cell, outside the plasma membrane. It is found in plants, fungi and prokaryotes. It provides strength and shape to the cells.

Plant cell wall is made up of cellulose. It is composed of three main layers: primary wall, secondary wall and the middle lamella.

Middle lamella is the first layer of cell wall to be formed after cell division.

Primary wall is formed after middle lamella and is composed of cellulose, pectin and hemicellulose. It is the true wall and develops in newly growing cells.

Secondary wall is formed on the inner side of primary wall and is comparatively thick and rigid. It is composed of inorganic salts, silica, waxes, cutin, lignin etc.

Prokaryotic cell wall does not contain cellulose. It is made up of peptidoglycan. Long chains of carbohydrates are linked by short chains of peptides.

Fungal cell wall is made up of chitin.

Cytoplasm

Protoplasm is the living material of the cell made up of cytoplasm and the nucleoplasm.

Cytoplasm is composed of clear aqueous ground substance containing all organelles, inclusions and soluble materials.

Cytosol is the soluble part of cytoplasm that forms the ground substance. It contains about 90% water and contains true solutions and colloidal solutions.

The cytoplasm is continuously moving and flowing within the cell like a river. This is called cytoplasmic streaming or cyclosis.

Endoplasmic Reticulum

Endoplasmic reticulum is a network of channels extending throughout the cytoplasm. These channels are sometimes in contact with the nuclear membrane on one side and plasma membrane on the other and may appear smooth or rough.

The endoplasmic reticulum is composed of spherical or tubular membranes which are connected with each other to form a network. These membranes are called cisternae.

The surface of rough endoplasmic reticulum appears granular due to attached ribosomes. It is involved in synthesis of proteins.

The surface of smooth endoplasmic reticulum does not have any ribosomes attached and usually functions in metabolism of lipids and detoxification of drugs. It is also responsible for transmission of impulses in muscles and neurons.

Ribosomes

Ribosomes are small granular structures dispersed throughout cytoplasm. They are composed of RNA and proteins and function in synthesis of new proteins.Sometimes many ribosomes are attached to a single mRNA molecule in cytoplasm. These are called polysomes.

Golgi Apparatus

Golgi apparatus (also called Golgi complex) consists of a stack of flattened membrane bound sacs. These sacs are called cisternae. Many small vesicles are also associated with Golgi apparatus. Golgi complex is concerned with cell secretions and protein packaging.

The outer (convex) surface of the Golgi complex is called forming face and the inner (concave) surface is called maturing face.

Lysosomes

Lysosomes are membrane bound vesicles that contain hydrolytic enzymes for digestion of many types of molecules. Lysosomes are involved in digestion of food particles that enter the cell through phagocytosis.

Primary lysosomes are those lysosomes that are freshly budded off from Golgi complex and have not yet fused with any phagosome. Upon fusion with phagosome they form phago-lysosomes.

Autophagy is the process during which lysosomes fuse with old, worn-out organelles of the cell to recycle their components.

Storage diseases are diseases that are caused by accumulation of substances like glycogen or glycolipids in the cell. The cells lack the enzymes for their breakdown which are normally present in lysosomes. Accumulation of these substances leads to abnormal functioning or death of the cell.

Tay Sach’s disease is a storage disease caused by the absence of an enzyme involved in catabolism of lipids. Accumulation of these lipids in the brain cells causes mental retardation and death in childhood.

Peroxisomes

Peroxisomes are organelles found in liver cells and other tissues and contain oxidative enzymes. They contain enzymes like peroxidase, catalase and glycolic acid oxidase. They are responsible of formation and decomposition of hydrogen peroxide (H₂O₂) in the cell. They are also found in protozoa, yeast and many cell types of higher plants.

Glyoxisomes

Glyoxisomes are plant organelles that contain many oxidative enzymes usually not found in animal cells. They are abundant in plant seedlings and are responsible for releasing energy from stored fatty acids. They convert fatty acids into carbohydrates necessary for the formation of a new plant. These organelles are usually present for a short period during early growth and germination.

Vacuoles

Vacuoles are organelles that store water, nutrients and waste materials in cells. In plant cells, there is a single large vacuole in the center while in animal cells many small vacuoles are usually present. Vacuoles in plants also provide support to cells by turgor pressure.

Cytoskeleton

Cytoskeleton is a network of tubules and fibers in a cell responsible for providing structural support and motility. It also maintains the shape of the cell. The proteins that form cytoskeleton include tubulin, actin, myosin, and tropomyosin.

Microtubules are long, unbranched, slender structures made up of tubulin protein. They form structures like cilia, flagella, basal bodies and centrioles.

Intermediate filaments have a diameter in between that of microtubules and microfilaments. They play a role in maintaining the shape of the cell.

Microfilaments are relatively thinner cylinders made up of contractile protein called actin. They are connected to inner surface of plasma membrane. They are responsible for movement of organelles with the cells, cyclosis and amoeboid movements.

Centriole is a cylindrical array of nine microtubules. A pair of two perpendicular centrioles is usually present near the outer surface of nucleus. Their main function is the formation of spindle fiber during cell division. They are found in animals, some microorganisms and lower plants while absent in higher plants.

Mitochondria

Mitochondria are double membrane bounded organelles of eukaryotic cells that are involved in manufacture and supply of energy. They are also known as the powerhouse of the cell. They are vesicle, rod or filament shaped. Their number and shape varies widely. They contain their own DNA and ribosomes. These are self-replicating organelles and synthesize their own proteins.

The outer membrane of mitochondria is smooth while inner membrane forms infoldings into the inner chamber. These infoldings are called cristae. The inner chamber of mitochondria is called mitochondrial matrix.

The inner surface of cristae of mitochondrial matrix contains knob-like structures called F₁ particles.

Mitochondria contain large number of enzymes, coenzymes and salts to carry out many metabolic pathways. The energy extracted from organic foods is extracted in these pathways and stored in the form of ATP.

ATP(adenosine tri-phosphate)is the energy currency of the cell.It provides energy for all chemical reactions of a cell on demand. The spent energy which is in the form of ADP is converted to ATP by mitochondria.

Plastids

Plastids are membrane bounded pigment containing bodies present in plant cells. These are of three types: chloroplasts, chromoplasts and leucoplasts.

Chloroplast

Chloroplasts are double membrane bound organelles found in plants that contain green pigment (chlorophyll) in them. The size and shape of chloroplasts is variable. Their diameter is about 4 to 6 µm. They are self-replicating organelles.

Chlorophyll is an organic compound that can absorb light energy and utilize it for the synthesis of food. Chlorophyll molecules are similar to heme group of blood. The major difference is that chlorophyll contains Mg⁺⁺ ions while heme contains Fe⁺⁺.

The envelope of chloroplasts consists of a double membrane. The fluid filled inside the envelope is called stroma. Stroma contains proteins, ribosomes and small circular DNA. Chloroplasts synthesize their own proteins. CO₂ is fixed to form sugars in stroma.

Small granules are embedded in stroma of chloroplasts, called grana.

Thylakoid membranes are flattened vesicles stacked on each other, like coins, to form grana. 50 or more thylakoids are stacked in a single granum. Chlorophyll molecules are present on thylakoid membranes, that is why they appear green. Sunlight energy is trapped by chlorophyll molecules present on thylakoid membrane.

Grana are interconnected with each other by non-green membranes called inter-granum.

Chromoplast

Chromoplasts are organelles that give color to different parts of plants. They are present in petals of flowers and in ripened fruit. They attract insects and other animals to help in pollination of flowers and dispersal of seeds.

Leucoplast

Leucoplasts are colorless organelles that have tubular, triangular or other shape. They are present in underground parts of the plant and store food.

Nucleus

Nucleus is the most prominent organelle of the cell that controls all its activities. It can be irregular or spherical in shape. It is usually present in the center of the cell in animals while in plants it is present close to cell membrane due to presence of a large vacuole in the center.

Cells usually have only one nucleus and are called mono-nucleate. Cells that have two or more nuclei are called bi-nucleate or multinucleate respectively. Nucleus is visible only when the cell is not dividing.

The nucleus is surrounded by a nuclear membrane that folds upon itself to form a double membrane envelope. The outer membrane is at places continuous with endoplasmic reticulum.

Nucleus contains chromatin material which is responsible for all properties and activities of the cell. The soluble part of nucleus is called nucleoplasm. When a cell is dividing, the chromatin material condenses to form chromosomes and the nucleus disappears.

Chromosomes

During cell division, the chromatin material condenses and forms darkly staining thread-like structures called chromosomes. It consists of DNA and proteins. Number of chromosomes in cells of a species remains constant generation after generation.

The arms of a chromosome are called chromatids. Genes are located at the chromatids that control the properties and activities of the cell. Chromatids are joined together by a centromere. Centromere is the point of attachment of spindle fibers during mitosis.

Nuclear Pore

The outer and inner membranes of nuclear envelope are continuous at certain points resulting in the formation of pores called nuclear pores. Nuclear pores allow movement of materials in and out of the nucleus.

Nucleolus

Nucleolus is a darkly stained region within the nucleus that is not covered by any membrane. More than one nucleoli are sometimes present in a single nucleus. Nucleolus is the place for synthesis of ribosomes. Nucleolus has two regions:

·   Outer granular region contains ribosomal subunits

·   Innerfibrillar region contains ribosomal RNA and rDNA.

Prokaryotes & Eukaryotes

Prokaryotic cells do not have a distinct membrane bound nucleus. Their genetic material is suspended in the cytoplasm. These include bacteria and blue-green algae.

Eukaryotic cells have a distinct membrane bound nucleus. Their genetic material is present in the nucleus. These include all animals, plants, fungi and protists.

·   Prokaryotic cells do not contain any membrane bound organelles while eukaryotic cells contain many membrane bound organelles like Golgi complex, mitochondria, endoplasmic reticulum and vacuoles.

·   Cell wall of prokaryotes is composed of peptidoglycan (carbohydrate chains linked by short peptides) while in eukaryotes it consists of cellulose (in plants) or chitin (in fungi).

·   Prokaryotes have smaller ribosomes (70S) as compared to eukaryotes (80S).

·   Prokaryotes divide by binary fission while eukaryotes divide by mitosis.

·   Prokaryotes are primitive life forms while eukaryotes are more advanced creatures.

05 Variety of Life

A species is a group of natural population which can interbreed freely among themselves and produce fertile offspring, but are reproductively isolated from all other such groups in nature. However, interbreeding is not considered a valid criterion for species that reproduce asexually.

Nomenclature is the process of giving names to biological species. Conventionally, scientific names were given on the basis of morphology. However, nowadays names are given based on information from cytology, genetics, biochemistry, physiology etc.

Binomial nomenclature is a method of assigning unique “scientific” names to each species. This method was proposed by Carlous Linnaeus. Name of a species consists of two words. The first word starts with a capital letter and represents the genus to which the species belongs. The second word starts with a small letter and describes certain character of the species. The entire name is italicized (in print) or underlined (when handwritten).

Two to Five Kingdom Classification

Plants are eukaryotic, autotrophic, sessile, and multicellular life forms that can synthesize their own food using energy from the sun.

Animals are multicellular, eukaryotic, heterotrophic, and usually motile life forms that cannot synthesize their own food and depend on other animals, plants or dead matter for their nutrition. Animals obtain food by ingestion and have special cavities in their bodies where the food is digested.

Fungi are multicellular, eukaryotic, heterotrophic, and sessile life forms that depend on dead, decaying organic matter for nutrition. The obtain nutrition by absorption. They grow on decaying matter upon which they secrete digestive enzymes and absorb the digested molecules.

Protista include all eukaryotic organisms that do not fit the definition of plants animals or fungi. These are mostly unicellular or simple multicellular organisms and are considered direct descendants of unicellular prokaryotes.

Prions

Prions are infectious proteins that can promote synthesis of more proteins like them in host cells without the involvement of nucleic acids. They cause diseases of nervous system in mammals like mad-cow disease in cows and a mysterious brain infection in man.

Viruses

Viruses are non-cellular infectious agents made up of protein and nucleic acids (DNA or RNA). Some viruses may also contain lipids and small amount of carbohydrates. Most viruses are so small that they can pass through porcelain filters through which bacteria cannot pass.They can only be seen under electron microscope.The reproduction of viruses in a host cell is called replication. During replication they cause disease in the host cell. They are resistant to broad range antibiotics like penicillin.

Viruses cannot live and multiply outside the host cell. They do not have the machinery for synthesis of proteins or DNA and depend on host cells for this function.Therefore, they are called obligate intracellular parasites.

The branch of biology that studies the properties, characteristics and diseases associated with viruses is called virology.

Structure of Viruses

A complete and mature infectious particle of a virus is called virion.

The virions contain nucleic acid genome (either DNA or RNA) which is surrounded by a protein coat called capsid. Capsid is made up of protein subunits called capsomeres and gives definite shape to the virion. The nucleic acid genome and capsid together are referred to as nucleocapsid.

Some animal viruses are covered in a lipid membrane derived from the host cell’s plasma membrane. This membrane is called envelope. Viruses that lack envelope are called naked viruses.

The shape of viruses is highly variable. Animal and plant viruses may be polyhedral (with many sides), helical (rod shaped) or complex.

Viruses are classified on the basis of their genomes and morphology. The genome can be either DNA or RNA. The virus can be naked, enveloped or complex. The shape of the virus can be rod-like, spherical or tadpole-like.

Vaccination is the process of protecting the body from infection by inoculating killed or weakened infectious agents or their parts in the body. This results in enhanced immune system that protects from disease if the infectious agents enter the body in later life.

Bacteriophages

Bacteriophages(bacterio: bacteria; phage: eater) are viruses that infect bacteria. They can be cubical or helical in shape. Many phages contain a head (which is icosahedral) and a tail (which is rod-shaped).

Twort (1915) and D’Herelle (1917) discovered bacteriophages. They observed that bacteria grown on artificial media undergo lysis producing clear areas on the plate. This lytic effect can be transferred from one plate to another and the sample can cause lysis even when it is filtered or diluted.

Most well studied bacteriophages are those that infect the bacterium E. coli. These are called T phages. T₂ and T₄ phages are very well understood.

Structure of Bacteriophages

The shape of T₄ bacteriophage resembles a tadpole (having a head and a tail). The head is icosahedral, to which a tubular tail is attached. Head contains the double stranded DNA genome. The inner core of phage tail is formed of protein which is covered in another protein sheath. There is a collar on one side of sheath and end plate on the other. Six long tail fibers are attached to the end plate, which help in attachment with the host cell.

Lytic Cycle of Bacteriophage

The bacteriophage replicates only in bacterial cell. The first step is theattachment or adsorption of phage to a specific receptor site on the host cell wall by weak chemical bonding. The next step is penetration during which tail releases the enzyme lysozyme to digest and dissolve a small region of cell wall. The tail sheath then contracts and the core is injected across the cell wall and plasma membrane. The DNA leaves the viral head through the core tube and enters the bacterial cell. Only DNA enters the cell while remaining structure remains out of the cell.

Upon entering the cell, the viral genome takes control of the cell’s machinery and directs synthesis of its own proteins. The genome of virus is also copied and new mature virus particles are synthesized. In about 25 minutes more than 200 copies of phage are formed and the host cell then bursts to release the phage particles. This is called lysis and the life cycle is called lytic cycle. Viruses that cause lysis of their host cell are called lytic phages or virulent phages.

Lysogenic Cycle of Bacteriophage

In lysogenic cycle, the genome does not take control of the host cell immediatelyand becomes part of the bacterial chromosome. The phage genome in this state is called a prophage and the process is called lysogeny. The viral genome is duplicated whenever host cell divides. Sometimes however, the viral genome detaches itself from host’s chromosome and restarts the lytic cycle. This process is called induction. The phage that causes lysogeny is called temperate or lysogenic phage.

Diseases Caused by Viruses

Smallpox is caused by pox virus which is an enveloped virus with DNA genome.Smallpox is characterized by formation of raised fluid filled vesicles on the skin which become pustules and form permanent pitted scars (called pocks). It was a common disease throughout the world but has now been eradicated from the world.

Herpes simplex virus is a DNA virus that causes vascular lesions in epithelial layers of the skin. These vesicles are usually formed in mouth, on lips and other parts of the skin.

Influenza viruses are viruses with RNA genome that cause epidemics of flu in humans.

Mumps and measles viruses are large enveloped viruses with RNA genome that belong to the group paramyxoviruses. Mumps is a contagious disease but is not fatal. It causes swelling of salivary glands. About 60% adults have immunity against this virus. Measles is also a common disease of childhood. It is characterized by high fever and red spots on skin. This disease also produces immunity in its victims.

Poliomyelitis is caused by polio virus which is a spherical virus with RNA genome. It is among the smallest known viruses. This virus usually infects in early childhood. Polio has been eradicated from most parts of the world and is only found in Pakistan, Afghanistan and some parts of Africa.

Retroviruses

Retroviruses are also called tumor viruses (or oncoviruses) because they cause tumors in infected tissues. They are spherical in shape, contain single stranded RNA genome, and are enveloped in lipid membrane. They are commonly found in fowl, rodents and birds in which they cause tumors.

The human immunodeficiency virus (HIV) is a commonly known retrovirus that causes AIDS (acquired immune deficiency syndrome).White blood cells (leukocytes) are the host of AIDS virus. These cells have a special receptor on their surface. This receptor protein allows attachment and entry of the virus in the cell.

Retroviruses contain a special enzyme called reverse transcriptase that converts single stranded RNA genome into double stranded DNA. This DNA is called provirus, whichintegrates in the host genome and takes control of the cell. This integration also results in cancer.

Acquired Immune Deficiency Syndrome (AIDS)

AIDS was first discovered in a group of young homosexual patients who suffered from complex symptoms like severe pneumonia, a rare vascular cancer, sudden weight loss, swelling in lymph nodes, and loss of all functions of immune system. The disease was later found in non-homosexual patients like those who had received multiple blood transfusions in the past. The virus responsible for the disease was discovered in1984 by researchers at Pasteur Institute in France and National Institute of Health in USA.

Mechanism of infection

HIV mostly infects T lymphocytes which are a type of white blood cells and play important role in immune system. When the number of T lymphocytes decreases due to virus, the immune system gradually fails and body becomes susceptible to infections from other bacteria and viruses. Some cells of central nervous system can also be infected by HIV. HIV can also infect and multiply in monkeys but does not cause disease in them, meaning that HIV is host specific.

Transmission

HIV is transmitted by intimate sexual contact, and contact with blood and breast milk. Healthcare workers may acquire HIV accidentally during professional activities. Avoiding direct contact with HIV is important measure for preventing the disease. Prevention of intra-venous drugs with common syringes and use of sterile needles, syringes and medical equipment is important.

Hepatitis

Hepatitis means inflammation of liver. Hepatitis is commonly caused by infectious agents, toxic chemicals or drugs. Symptoms of hepatitis include jaundice, abdominal pain, liver enlargement, fatigue, and fever. It can be mild or acute but sometimes may lead to liver cancer. It can be controlled by adopting hygienic measures, vaccination and screening of blood / organs / tissue. There are different types of hepatitis.

Hepatitis A is transmitted by contact with feces from infected individuals or contaminated water. It was previously called infectious hepatitis. HAV is a non-enveloped virus that contains an RNA genome. It causes mild, short term, less virulent disease symptoms. A vaccine is available against HAV.

Hepatitis B is transmitted by contact with body fluids like serum, breast milk, and saliva. Sexual contact, pregnancy or breast feeding also spread the disease. It was previously called serum hepatitis. It is the second major cause of hepatitis. Its symptoms include fatigue, loss of appetite and jaundice. Infected persons recover completely and become immune to later infections. HBV is caused by a DNA virus which is common in Asia, China, Philippines, Africa and Middle East. Genetically engineered vaccines are available against HBV.

Hepatitis Cspreads from one person to other mainly by use of contaminated syringes, blood or blood products, and reuse of razors etc. It was previously called non-A non-B hepatitis or transfusion hepatitis.HCV is an enveloped virus that contains RNA genome. It causes long term chronic infection and leads to serious liver damage. It is less severe than hepatitis A and B. No vaccine is available against HCV.

The causative agents of hepatitis F and G are not yet identified.

06 Kingdom Prokaryotae (Monera)

Kingdom Prokaryotae includes organisms with prokaryotic cells. Prokaryotic cells lack nucleus and membrane bound organelles. Bacteria are categorized into two major divisions: eubacteria (true bacteria) and archaeobacteria (ancient bacteria).

Microorganisms were first reported by Antone van Leeuwenhoek (1673) who used his self-made microscope to see bacteria and protozoa in rain water, saliva, vinegar, infusions and other substances. He named these organisms “animalcules” (small animals) and gave accurate descriptions and drawings.

The existence of microorganisms was confirmed by Louis Pasteur. He made many discoveries in the field of microbiology and medicine. His main achievement was the development of vaccines for diseases like anthrax, fowl cholera, and rabies. He also made significant contributions in development of pasteurization technique and fermentation industries. His work proved that microorganisms are usually responsible for disease.

Germ Theory

Robert Koch formulated the germ theory of disease. The four postulates of germ theory are used to find whether the organism found in disease lesions is the causal agent of the disease or not.

1.       A specific organism can always be found in association with a given disease.

2.       The organism can be isolated and grown in pure culture in the laboratory.

3.       The pure culture will produce the disease when inoculated into susceptible animal.

4.       It is possible to recover the organism in pure culture from experimentally infected animal.

Koch discovered bacteria from the blood of sheep that had died of anthrax. He also discovered bacteria that caused tuberculosis and cholera. Koch and his colleagues developed many techniques concerning inoculation, isolation, media preparation, maintenance of pure cultures, and preparation of specimens for microscopic examinations.

Occurrence of bacteria

Bacteria are found almost everywhere in air, land, water, oil deposits, food, decaying organic matter, on plants, man and animals. Their type and number varies according to locality and environmental conditions.

Some bacteria are always present and contribute towards the natural flora. Others are present in specific environments such as hot springs, alkaline / acidic soils, highly saline environments, in highly polluted soils and waters.

Structure of Bacteria

All bacteria cells have cell membrane, cytoplasm, ribosome, and chromatin bodies. The majority of bacteria have a cell wall, which gives shape to the bacteria cell. Specific structures like capsule, slime, flagella, pili, fimbriae and granules are also present in some bacteria.

Size of Bacteria

Bacteria range in size from about 0.1 to 600 µm in one dimension. The smallest bacteria (members of genus Mycoplasma) are about 100-200 nm in diameter (which is the size of pox viruses). E. coli is about 1.1-1.5 µm wide and 2-6 µm long. Some spirochetes reach 500µm in length whereas Staphylococci and Streptococci are 0.75 – 1.25 µm in diameter. Some bacteria may grow as large as 600x80 µm, a little smaller than a printed hyphen.

Shape of Bacteria

Bacteria are grouped into three categories on the basis of shape: cocci, bacilli, and spiral. Most bacteria have a constant shape but some are pleomorphic. Pleomorphic bacteria can exist in different shapes.

Cocci are spherical or oval bacteria. Diplococcuspneumoniae (that causes pneumonia) and Staphylococcus aureus (that causes respiratory tract infections) are example of cocci. Cocci can exist in a number of different arrangements.

·         When two cocci exist together, the arrangement is called diplococcus.

·         When cocci form long chains, the arrangement is called streptococcus.

·         Tetrad is a group of four cocci that is formed when the division of cells is in two planes.

·         When division is in three planes, a cube of 8 cells is formed, called sarcina.

·         When division occurs randomly, the cells are present irregularly like bunch of grapes, called staphylococcus.

Bacilli are rod shaped bacteria with squarish ends. All bacilli divide in one plane.Examples of rod-shaped bacteria are Escherichia coli, Bacillus subtilis, and Pseudomonas.

·         When two bacilli are present together, the arrangement is called diplobacillus.

·         When long chains of bacilli are present, the arrangement is called streptobacillus.

Spiral bacteria are spirally coiled like a spring. Examples of spiral bacteria are Vibrio (that cause cholera) and Hyphomicrobium. These bacteria can exist in one of three forms.

·         Vibrio are slightly curved or coma shaped.

·         Spirillum is a thick, rigid spiral.

·         Spirochete is a thin, flexible spiral.

Exceptions to above mentioned shapes are trichome forming, sheathed, stalked, square, star-shaped, spindle shaped, lobed, and filamentous bacteria.

Parts of Bacterial Cell

Flagella

Flagella are very thin, hair-like structures. Flagella originate from basal body which is present in cytoplasm, just below the plasma membrane. They are made up of protein flagellin. Most bacilli and spiral bacteria have flagellum. Cocci do not usually have flagellum.

Bacteria can be divided into many groups on the basis of presence, number, and arrangement of flagella.

·      Atrichous bacteria do not have any flagellum.

·      Monotrichous bacteria have a single flagellum present on one pole of the cell.

·      Lophotrichous bacteria have a tuft of flagella on one pole of the cell.

·      Amphitrichous bacteria have two tufts of flagella, one on each pole of the cell.

·      In peritrichous bacteria, the whole cell is surrounded by flagella.

The main function of flagella is to help in motility. Bacteria can detect and move in response to chemicals in their environment with the help of flagella. Movement in response to chemical signalsis called chemotaxis.

Pili

Pili are hollow, non-helical, filamentous structures present on the wall of many bacteria. They are made up of a special protein called pilin. True pili are only present on Gram-negative bacteria. These are usually shorter than flagella and do not help in motility.

Pili are mainly involved in mating process of bacteria, called conjugation. Some pili may help in attachment of bacteria to different surfaces.

Cell Envelope

The structure of bacterial cell surface is very diverse. The layers that are present outsidecell membrane are collectively called as the cell envelope. These layers include capsule, slime and cell wall.

Some bacterial cells are covered in a capsule. It is made up of repeating units of polysaccharides, proteins or both. The capsule is tightly bound to the cell. It has a thick, gummy nature due to which colonies of these bacteria appear “sticky”.

Some bacteria are covered with loose, soluble shield of macromolecules, called slime. Capsule and slime provide greater pathogenicity to bacteria because it protects them from immune system.

Cell Wall

Cell wall is present outside the plasma membrane, beneath capsule and slime. It is a rigid structure. It determines the shape of bacterium. It protects the cells from osmotic lysis.

Christian Gram developed the method of Gram staining. Bacteria can be divided into two groups on the basis of their staining properties. In this staining procedure, the Gram positive bacteria are stained purple (due to primary dye). Gram negative bacteria are stained pink (due to secondary dye). This difference is due to difference in the structure of cell wall.

·   Cell wall of Gram positive bacteria consists of one major layer while that of Gram negative bacteria consists of two layers.

·   Overall thickness of Gram positive bacteria is 20-80nm while that of Gram negative bacteria is 8-11nm.

·   Cell wall of Gram positive bacteria is more permeable than Gram negative bacteria.

·   The cell wall of Gram positive bacteria contains 50% peptidoglycan while the cell wall of Gram negative bacteria contains only about 20% peptidoglycan.

Cell wall of most bacteria is made up of a macromolecule called peptidoglycan. It consists of long carbohydrate chains cross-linked with short peptides. The amount of peptidoglycan is different in different bacteria. The cell wall may also contain sugar molecules, teichoic acid, lipoproteins, and lipopolysaccharides.

Cell wall of some bacteria is different from that of Gram negative or Gram positive bacteria. Some bacteria do not have a cell wall at all (like Mycoplasma).

Cell wall of archeobacteria is also different as they do not contain peptidoglycan. Their cell walls are composed of proteins, glycoproteins and polysaccharides.

Cell Membrane

Cell membrane is present just below the cell wall. It is very thin and flexible and completely surrounds the cytoplasm. It is very delicate and any damage to it results in the death of the cell. Bacterial membranes are different from eukaryotic membranes because they do not have sterols like cholesterol.

The plasma membrane regulates the transport of proteins, nutrients, sugar, electrons and other metabolites. The plasma membrane of bacteria also contains enzymes for respiration.

Cytoplasmic Matrix

The cytoplasm of prokaryotic cells does not contain any membrane bound organelles and cytoskeleton (microtubules). The cytoplasmic matrix is the substance between plasma membrane and nucleoid. It has gel like consistency. Small molecules can move through it easily.

The plasma membrane and everything present in it is called protoplast. Therefore, cytoplasmic matrix is a major part of protoplast. Other large, discrete structures like chromatin, ribosomes, mesosomes, granules and nucleoid are present in this matrix.

Nucleoid

Bacterial cells do not contain any membrane bound nucleus. The nuclear material is present near the center of the cell. It consists of a large, single, circular, double stranded DNA molecule. It aggregates as an irregular shaped dense area called nucleoid. This is in fact an extremely long molecule of DNA that is tightly folded to fit inside the cell. Since bacteria have a single chromosome, they are haploid.

Nucleoid is also called nuclear body, chromatin body or nuclear region. It is visible under light microscope after staining with Feulgen stain.

Plasmid

Many bacteria contain extra DNA molecules in addition to chromosome. These are small, circular, double stranded DNA molecules called plasmids. They are self-replicating and are not essential for bacterial growth and metabolism.

Plasmids often contain genes for resistance against drugs, heavy metals, insects and genes for causing disease. They are very useful in modern genetic engineering techniques.

Ribosomes

Prokaryotic ribosomes consist of RNA and proteins, like eukaryotic ribosomes. Some ribosomes are loosely attached to plasma membrane. They are protein factories. Thousands of ribosomes are present in each cell. Prokaryotic ribosomes are small (70S) while eukaryotic ribosomes are large (80S).

Mesosomes

Plasma membrane of bacteria sometimes folds (invaginates) inwards to form small pockets called mesosomes. These are in the form of vesicles, tubules, or lamellae.

Mesosomes are involved in DNA replication and cell division whereas some mesosomes are also involved in export of exo-cellular enzymes. Respiratory enzymes are also present on mesosomes.

Granules and Storage Bodies

Bacteria usually live in harsh environments where nutrients are not easily available. Bacteria store extra nutrients in storage bodies or granuleswhenever possible. These nutrients include glycogen, sulfur, fats, and phosphates.

Cells may also contain waste materials which are later excreted. Common waste materials of bacteria include alcohol, lactic acid, and acetic acid.

Spores

Spores are metabolically dormant bodies produced by some bacteria. These are produced when a cell has completed its life and conditions are unfavorable. These spores can be present outside the vegetative cells (exospores) or within vegetative cells (endospores).

Spores protect bacteria from adverse environmental conditions such as light, desiccation, pH and chemical agents and especially heat. Underfavorable conditions spores germinate and form vegetative cells.

Cysts

Cysts are dormant, thick-walled, desiccation resistant forms. They are not heat resistant. They develop during differentiation of vegetative cells and germinate under suitable condition.

Nutrition of Bacteria

Like all living organisms, bacteria need energy for their growth, maintenance, and reproduction. Most bacteria are heterotrophic (they cannot synthesize their own food from simple inorganic substances).

Parasitic bacteria depend on host species for their nutrition. Some bacteria live as saprophytes meaning that they get their food from dead organic material.

Soil is full of organic compounds in the form of humus. Humus is the material resulting from the partial decay of plants and animals. Saprophytic bacteria that live in soil have extensive enzyme system that breaks down the complex substances of humus to simple compounds and extract energy.

Some bacteria are autotrophic. They can synthesize complex organic molecules necessary for their survival from inorganic substances. There are two categories of autotrophic bacteria: photosynthetic autotrophic bacteria and chemosynthetic autotrophic bacteria.

Photosynthetic autotrophicbacteria have chlorophyll which is different from chlorophyll of plants. Plant chlorophyll is present in chloroplasts while chlorophyll of bacteria is dispersed within the cytoplasm. During photosynthesis, these bacteria use hydrogen sulfide (H₂S) instead of water as hydrogen provider and liberate sulfur instead of oxygen.

Green sulfur bacteria, purple sulfur bacteria and purple non-sulfur bacteria are photosynthetic bacteria. The overall reaction of photosynthesis in photosynthetic bacteria can be written as:

CO₂ + 2H₂S à (CH₂O)_n + H₂O + 2S

Chemosynthetic autotrophic bacteria oxidize inorganic compounds like ammonia, nitrate, nitrite, sulfur, or ferrous ions and trap the energy produced during oxidation for their own reactions. Nitrifying bacteria are chemosynthetic.

Respiration in Bacteria

Respiration in bacteria may be aerobic or anaerobic. Bacteria that can grow in the presence of oxygen are called aerobic bacteria. Pseudomonas is an aerobic bacterium. Bacteria that can grow in the absence of oxygen are called anaerobic bacteria. Spirocheta is an anaerobic bacterium.

Facultative bacteria can grow either in the presence or absence of oxygen. E. coli is a facultative anaerobic bacterium. Micro-aerophilic bacteria require very low concentration of oxygen for their growth.Campylobacter is a micro-aerophilic bacterium.

Growth and Reproduction

Bacterial growth generally refers to increase in number of bacterial cells. Bacteria increase in number by an asexual method of reproduction called binary fission. In binary fission, the parent cell increases in size, its chromosome duplicates and plasma membrane pinches inwards at the center of the cell. When the nuclear material has been evenly distributed, the cell wall grows inward to separate cell into two daughter cells.When the division is complete, the bacteria grow and develop their unique features.

This sequence is repeated at intervals by each new daughter cell which in turn increases the population of cells. The interval of time from one division to the next division is known as generation time. A graph showing different stages of bacteria growth is called a bacteria growth curve. Bacterial growth shows four distinct phases.

1.       Lag phase is the period of no growth. Bacteria prepare themselves for division during lag phase.

2.       Log phase is the period of rapid growth. Bacteria grow at exponential rate.

3.       In stationary phase, the death rate of bacteria becomes equal to rate of multiplication. Therefore, the number of cells becomes constant.

4.       In death or decline phase, the bacteria start dying. The death rate becomes more than multiplication rate.

Conjugation in Bacteria

Bacteria lack sexual reproduction and mitosis. However, some bacteria can transfer genetic material from one individual (donor) to another (recipient). This process is called conjugation.

Some conjugating bacteria have special sex pili for transfer of genetic material. Conjugation produces new genetic combinations that may allow the bacterium to survive in a variety of conditions.

Importance of Bacteria

Ecological Importance

Bacteria are ecologically very important. They are highly adaptable and are found nearly everywhere. They are able to decompose organic matter and play a significant role in the completion of cycles of nitrogen, phosphorus, sulfur and carbon.

Economic Importance

Bacteria are used in a number of industries including food, drugs and in biotechnology. They are used for production of vaccines and antibiotics in medicine. Bacteria are also responsible for spoilage of food and vegetables. Many plant pathogens adversely affect agriculture.

Bacteria are very common pathogens of humans. Approximately 200 species are known to cause disease in humans. Many bacteria also inhabit the bodies of man and other animals normally and do not cause any disease.

Control of Bacteria

Control of microorganisms is essential in home, industry, as well as in medical fields. Diseases can be prevented and treated by controlling microorganisms. Spoilage of foods and other industrial products can be prevented by controlling microorganisms. There are many methods for the control of microorganisms.

Different chemical and physical agents have different mode of action. They may disrupt the cell wall, membranes, enzymes or nucleic acids of the cell.

Physical Methods

Use of physical agents to control bacteria or microorganisms is called sterilization. Physical methods include use of steam, dry heat, filters and radiation to control bacteria. It results in destruction of all life forms.

High temperature is often used in microbiology labs for control of microbes. Both dry heat and moist heat are effective. Moist heat causes coagulation of proteins and kills the microbes. Dry heat causes oxidation of chemical components of microbes and kills them.

Electromagnetic radiation below 300nm wavelength is effective in killing microorganisms. Gamma rays are also commonly used for sterilization.

Membrane filters can be used to sterilize heat sensitive things like antibiotics, serum, hormones, etc. These filters have very fine pores that do not allow bacteria to pass through them.

Chemical Methods

Antiseptics, disinfectants and chemotherapeutic agents can be used for microbial control. Agents that kill microbial cells immediately are called microbicidal. Agents that do not kill microorganisms but inhibit their reproduction are called microbistatic.

Chemical substances used on living tissues to kill microorganisms are called antiseptics.

Disinfectants are used to kill or inhibit growth of microbes on non-living surfaces and materials. Important chemical agents used for disinfection are oxidizing and reducing agents. For example halogen gases, phenols, hydrogen peroxide, potassium permanganate, alcohol and formaldehyde are commonly used disinfectants.

Chemotherapeutic agents and antibiotics work in the body with natural defense mechanisms and stop the growth of bacteria and other microbes. These are sulfonamides, tetracycline, penicillin, etc. They also kill or inhibit the growth of microbes inside the body.

Immunization and Vaccination

Different measures are usually undertaken to prevent and treat microbial diseases. These include immunization (vaccination), antisepsis (eliminate or reduce chances of infection), chemotherapy, and public health awareness (e.g., water purification, sewage disposal, and food preservation).

Vaccination is the process of protecting the body from infection by inoculating killed or weakened infectious agents or their parts in the body. It results in increased immunity against the particular disease, therefore it is also called immunization.

Edward Jenner was the first to successfully vaccinate people against small pox by inoculating them with cow pox virus. The tested individuals developed immunity against small pox because the two viruses are structurally related. Pasteur later used the same technique to develop vaccines against fowl cholera, hydrophobia (rabies) and anthrax.

Use and Misuse of Antibiotics

Antibiotics are chemotherapeutic chemical substances used for the treatment of infectious diseases. Antibiotics are synthesized and secreted by certain bacteria, actinomycetes, and other fungi. Today some antibiotics are synthesized in laboratory, however, their origin are living cells.

Misuse of antibiotics has resulted in a lot of problems.

·   Microorganisms become resistant due to excessive use of antibiotics producing more virulent strains which are difficult to treat.

·   Misused antibiotics may interfere with human metabolism and may prove fatal in extreme cases.

·   Misuse of penicillin may cause allergic reactions.

·   Streptomycin can affect auditory nerve thus causing deafness.

·   Tetracycline and related compounds cause permanent discoloration of teeth in young children.

Cyanobacteria

Cyanobacteria is the largest and most diverse group of photosynthetic bacteria. These were previously known as “blue-green algae”.

Cyanobacteria are prokaryotes that vary greatly in shape and appearance.They range in diameter from about 1-10µm and may be unicellular, colonial or filamentous surrounded by mucilaginous sheath.

Colonial bacteria form small colonies of different shapes. Filamentous bacteria make long filaments made up of trichomes or long chains of cells. They lack flagella and often use gas vesicles to move in water. Many filamentous species have gliding motility.

Their photosynthetic system closely resembles that of eukaryotes. They have chlorophyll and photosystem II. They carry out oxygenic photosynthesis (i.e., they produce oxygen during photosynthesis using water).

Cyanobacteria use phycobilins as accessory pigments. Photosynthetic pigments and electron transport chain components are located in thylakoid membranes linked with particles called phycobilisomes. Phycocyanin pigment (blue) is their predominant phycobilin and CO₂ in them is assimilated through Calvin cycle.

Cyanobacteria store extra food in the form of glycogen. Cyanobacteria reproduce by binary fission and fragmentation. Hormogonia, akinetes and heterocysts are specialized structures in cyanobacteria.

Importance of Cyanobacteria

·    Cyanobacteria help in bioremediation of alkaline soils.

·    Cyanobacteria have heterocysts, which are helpful in fixation of atmospheric nitrogen.

·    They release O₂ in the environment due to their photosynthetic activity.

·    Oscillatoria and a few other cyanobacteria can be used as pollution indicators.

·    They form symbiotic relationship with protozoa and fungi.

·    Nitrogen fixing species form association with angiosperms.

·    They are photosynthetic partners in most lichen associations.

·    Many species of cyanobacteria form water blooms where they often impart unpleasant smell. Due to large amount of suspended organic matter water becomes unfit for consumption.

·    Some species produce toxins that kill livestock and other animals that drink the water.

·    “Super blue green algae” are expensive pond scum having cyanobacteria. It produces its own food through photosynthesis. It serves as a complete “whole food” which contains 60% protein with all essential amino acids in perfect balance.

Nostoc

Habitat and Occurrence

Nostoc is a common terrestrial and subaerial cyanobacterium. It is widely distributed in alkaline soils and on moist rocks and cliffs. Nostoc forms a jelly like mass in which numerous filaments are embedded.

Structure

Trichomes of Nostoc are unbranched and appear beaded. Individual cells are mostly spherical but sometimes barrel shaped or cylindrical.

All cells in trichome of Nostoc are mostly similar in structure.Slightly large, round, light yellowish thick walled cells are present at intervals, called as heterocysts. Trichome mostly breaks near heterocyst and forms hormogonia and thus helps in fragmentation.

Reproduction

There is no sexual reproduction in Nostoc. It reproduces asexually by formation of hormogonia. Hormogonia are formed when filament breaks at different points into smaller pieces. This is due to death and decay of an ordinary cell. A heterocyst may also serve as a breaking point.

Nostoc can also reproduce by Akinete formation. Akinetes are thick walled, enlarged vegetative cells which accumulate food and become resting cells. On arrival of favorable conditions they form normal vegetative cells.

07 Kingdom Protista

Kingdom Protista includes eukaryotic organisms which are aquatic in habitat and are difficult to characterize. Any eukaryotic organism that cannot be placed into other kingdoms is placed in Protista.

Protists have diverse body forms, size and structure, means of locomotion, types of reproduction, modes of nutrition, habitat, interactions with other organisms, and lifestyle.

They are mostly unicellular, colonial or simple multicellular organisms. Like plants and animals, they are also eukaryotic and are more complex than prokaryotes. Unlike plants or animals, they do not develop from embryo or blastula.

Kingdom Protista can be divided into four major groups: animal-like protista(protozoa), unicellular algae (plant like), multicellular algae (plant like), slime molds and oomycetes (fungus like).

Biologists consider Protista a polyphyletic group (a group that does not share a single common ancestor, but arose from many different organisms). Kingdom Protista arose from prokaryotes while kingdoms Fungi, Plantae and Animalia arose from protists.

Protozoa – Animal Like Protists

Protozoa are animal-like Protists. They are unicellular and ingest food by endocytosis. They are further divided into many groups.

Amoebas

Amoebas are free-living freshwater, marine and soil dwelling organisms. Amoebas do not have flagella and move by forming special cytoplasmic projections called pseudopodia.

·   Some amoebas are also parasites of animals and humans. Entamoeba histolytica is an intestinal parasite of humans and causes amoebic dysentery.

·   Giant amoeba (Pelomyxa palustris) is found in the bottom of freshwater ponds. It is the most primitive of eukaryotes. It has many nuclei in its cells but lacks other organelles. Its cells have many methanogenic bacteria that provide it energy.

Zooflagellates

Zooflagellates are unicellular (or colonial) organisms with spherical or elongated bodies and a single central nucleus. They may be free living, symbiotic or parasites.

·   They have one or more long, whip-like flagella for locomotion. The flagella are usually located at anterior end of the body and allow fast movement.

·   Flagellates obtain food by ingesting living or dead organisms or by absorbing nutrients from dead or decaying organic matter.

·   Trichonymphas are complex, specialized flagellates having many flagella. They live in the guts of termites and help in the digestion of dry wood.

·   Parasitic flagellates cause diseases. Trypanosoma is a human parasite that causes “African Sleeping Sickness”. It is transmitted by the bite of tsetse fly.

·   Choanoflagellates is a group of sessile marine or freshwater flagellates. They are attached to substrate by a stalk and their flagellum is surrounded by a delicate collar. They are of special interest because similar “collar” cells are also present in sponges.

Ciliates

Ciliates are unicellular organisms with a flexible outer covering called pellicle that gives them a definite shape.

·   In Paramecium the surface of the cell is covered with thousands of fine, short, hair like cilia. Coordinated beating of cilia helps the organism to go not only forward but also in reverse direction.

·   Some ciliates are sessile and remain attached to rock or other surface. Their cilia create water currents that draw food towards them e.g. stentor.

·   Most ciliates ingest bacteria or other small protists.

·   Water balance in the cell is maintained by a special organelle called a “contractile vacuole”.

·   They have two types of nuclei:

o   One or more small diploid micronuclei function in sexual process.

o   A large polyploidmacronucleus that controls metabolism and growth.

Most ciliates reproduce sexually by conjugation. During conjugation two individuals come together and exchange genetic material.

Foraminifera and Actinopoda

Foraminiferans and Actinopods are marine protozoa that produce shells. These shells are called tests.

·   The tests of foraminifera are made up of calcium.

·   Tests of actinopoda are made up of silica.

·   The shell contains small pores through which cytoplasmic projections can be extended. These projections are sticky and form a net to entangle prey.

·   Dead foraminiferans sink to the bottom of the ocean where their shells form a grey mud that is gradually transformed into chalk. Foraminiferans of the past have created vast limestone deposits.

Apicomplexa

Apicomplexans are a group of parasitic protozoa and cause serious diseases.

·   They do not have any specific locomotory structure and move by flexing.

·   Most apicomplexans spend part of their life in one host and part in a different host species.

·   Many apicomplexans form spores in their life cycle which helps in spreading from one host to the other.

Plasmodium is an apicomplexan that causes malaria in humans.

·   It enters the human body through the bite of an infected female Anopheles mosquito.

·   Plasmodium first enters liver cells and then in red blood cells.

·   It multiplies in red blood cells and new parasites are produced.

·   The blood cell bursts due to these parasites and the released parasites infect new cells.

·   The bursting of millions of red blood cells causes the symptoms of malaria: a chill, followed by high fever. It is caused by toxic substances produced by the parasite.

Algae – Plant Like Protists

Algae is a group of protists that can carry out photosynthesis and produce their own food like plants. They carry out about 50-60% of all photosynthesis on earth. Algae are different from plants in many respects.

Almost all algae live in water (aquatic). They are restricted to damp or wet environments like ocean, freshwater ponds, lakes and streams, hot springs, polar ice, moist soil, trees and rocks.

Cellular Organization

They show a remarkable range of diversity. Some are unicellular, others are multicellular. Multicellular algae can be of three types.

·   Filamentsof filamentous algaeare usually made up of distinct cells but sometimes form coenocytes.Coenocytes are multinucleated structures that lack cross-walls.

·   Some algae are colonial

·   Some multicellular algae (like sea-weeds) are branched or arranged in leaf-like structures. But their body is called thallus because it lacks definite roots, stems and leaves. Xylem and phloem are also absent.

Photosynthetic Pigments

All types of algae contain chlorophyll a. Some species also containaccessory pigments. Pigment composition is helpful in classification into phyla.

Yellow and orange caroteniodsare present in all algal phyla.Xanthophyll and Phycoerythrin (red) are also involved in photosynthesis.

Life Cycle

Life cycle of algae is also very diverse. Almost all algae (except Rhodophyta) have a motile stage in their life cycle.

Their sex organs are unicellular and the zygote is not protected by the parent body. The sex organs of plants are multicellular and the zygote is also multicellular which is protected by the parental tissue.

Importance of Algae

Algae have great economic and environmental importance.

·   Some algae (like kelps) are edible and may be used to overcome food shortage in the world.

·   Marine algae are also a source of valuable substances like algin, agar, carrageenan, and antiseptics.

·   They are major producers in aquatic ecosystems. Therefore, they provide food and oxygen to other organisms.

Euglenoids (Euglenophyta)

These are unicellular organisms with flagella for locomotion. They have photosynthetic pigments like chlorophyll and carotenoids.

Scientists in the past have classified euglenoids with plants (in algae) or animals (in protozoa). Recent molecular data suggests that they are closely related to zooflagellates.They are like plants due to presence of photosynthetic pigments.

Some euglenoids lose their chlorophyll when grown in dark and obtain their food hetertrophically (by ingesting organic matter). Some species are always heterotrophic and colorless.

Dinoflagellates (Pyrrophyta)

It is a very unusual group of Protista. Most dinoflagellates are unicellular. They have flagella for locomotion. They have cholorophyll, carotenoids and fucoxanthins for photosynthesis. Their cells are covered with shells of interlocked plates of cellulose with deposition of silicates.

They are ecologically very important group of producers (organisms that synthesize their own food). Sometimes their population increases suddenly in the water creating algal blooms. These blooms turn the water colored (orange, red, or brown) and are called “red tides”.

Diatoms (Chrysophyta)

These are unicellular organisms that have chlorophyll, carotenes and fucoxanthin for photosynthesis.

The cell wall of diatoms consists of two shells that overlap and fit together like a petri dish. The shell is made up of silica and it is deposited in an intricate pattern.

Diatoms are major producers in aquatic environment (both marine and freshwater). They are very important in aquatic food chain.

Brown Algae (Phaeophyta)

They are multicellular and range from a few centimeters to 75 meters. The largest brown algae, called kelps, are tough and leathery in appearance.

They possess leaf-like blades, stem-like stipes, and root-like anchoring holdfast.

Brown algae are common in cooler marine waters, especially along rocky coastlines in the intertidal zone.

Red Algae (Rhodophyta)

They are multicellular. The body is composed of interwoven filaments that are delicate and feathery. Some are flattened sheets of cells.

Most multicellular red algae attach to rocks or other substances by basal holdfast.

Some red algae incorporate calcium carbonate in their cell walls form the ocean and take part in building coral reefs with coral animals.

Green Algae (Chlorophyta)

Green algae are photosynthetic. They can be unicellular or multicellular. Their chloroplasts contain chlorophyll a, chlorophyll b and carotenoids like higher plants.

Green algae are similar to plants in many ways. Their pigments, food storage molecules, and cell walls are similar to plants. Because of these similarities it is generally accepted that plants evolved from green algae. RNA sequence also suggests that this hypothesis is true.

The extra food energy is stored in the form of starch.

Cell walls of most green algae are made up of cellulose.

·   Chlorella is a unicellular non-motile green algae found in freshwater. It has been used as a model organism in research on photosynthesis as well as being investigated as an alternate source of food.

Fungi-like Protists

Some protists are superficially similar to fungi. They are not photosynthetic. Their bodies are made up of long threads called hyphae.

However, they are different from fungi in many ways.

·   Cells of these organisms may contain centrioleswhile fungi do not have centrioles.

·   Their cell walls may also contain cellulose while cell walls of fungi are made up of chitin.

Slime Molds (Myxomycota)

Feeding stage of slime molds is called plasmodium. It is a multi-nucleate mass of cells that can grow up to 30cm. It is slimy in appearance and streams over damp, decaying logs and leaf litter. It often forms a large network of channels. It ingests bacteria, yeast, spores and decaying organic matter.

When conditions are unfavorable, they form resistant haploid spores by meiosis in stalked bodies called sporangia. When conditions are good again, spores germinate into bi-flagellated or amoeboid reproductive cells (also called swarm cells). Two swarm cells unite to form diploid zygote. Zygote then produces plasmodium again.

The slime mold Physarum polycephalum is a model organism that has been used to study many basic biological processes like growth and differentiation, cytoplasmic streaming, and function of cytoskeleton.

Water Molds (Oomycota)

They are similar to fungi and have a similar structure but they are now regarded as an ancient group. Their cell walls contain cellulose, not chitin. Their hyphae do not have cross walls (aseptate).Oomycetes include many pathogenic organisms.

Phytophthora infestans causes late potato blight in potatoes. It caused Irish potato famine in 19^th century when several rainy cool summers in 1840s encouraged its growth and the crops were completely destroyed.About 1 million people died due to food shortage. Many people migrated to other areas like USA.

08 Fungi – The kingdom of Recyclers

Fungi are multicellular, eukaryotic, heterotrophic, and sessile life forms that depend on dead, decaying organic matter for nutrition. The obtain nutrition by absorption. They grow on decaying matter upon which they secrete digestive enzymes and absorb the digested molecules.

They resemble plants because they are sessile and their cells lack centrioles and have cell walls. But unlike plants, they are heterotrophic. Their cell walls are made up of chitin which is present in the exoskeleton of arthropods.

They are different from animals as well because of presence of cell walls and absorptive mode of nutrition. Their DNA studies also confirmed that they are different from animals and plants, so they were placed in a separate kingdom.

Fungi have a special type of cell division called “nuclear mitosis”. During nuclear mitosis, nuclear envelope does not break, instead the mitotic spindle form within the nucleus and the nuclear membrane constricts to form two nuclei.

Body of Fungi

Body of a fungus is called a mycelium. Mycelium is composed of long, thread-like filaments called hyphae. Hyphae spread all over the surface of substrate to absorb nutrients.

Hyphae are sometimes divided by cross-walls called septa into smaller compartments. Such hyphae are called septate hyphae. Sometimes, the cross-walls are not present and the entire hyphae is like a single cell with many nuclei. Such hyphae are called aseptate or non-septate hyphae. These are also called coenocytic hyphae. The cytoplasm in these hyphae can move easily and nutrients can be distributed in the entire body. Sometimes the cross-walls are present but there are holes in the walls to allow flow of water and nutrients.

Sometimes are hyphae are packed together in the form of complex reproductive structures like mushrooms, puff balls, morels etc. Some fungi are non-hyphal like yeast.

The bodies of all fungi are haploid. Diploid stage is usually very brief when a zygote is formed. Fungi can withstand harsh conditions by forming spores.

They can tolerate wide range of pH (2-9) and temperature. They can also grow in environments with high osmotic pressure like in concentrated salt and sugars. That is why fungi can even grow in jelly and jams etc.They can store extra food in the form of lipids or glycogen.

Nutrition in Fungi

Fungi do not have photosynthetic pigments. They absorb nutrients from their surroundings and are therefore called absorptive heterotrophs. They usually grow in moist habitats where lots of organic matter is present. There are three modes of nutrition in fungi.

Saprophytes

Most fungi are saprophytes(or saprobes), i.e. they obtain their food by decomposing dead organic material (dead leaves, wood, or animals).

They secrete digestive enzymes on the substratum which digest the dead bodies. The simple organic molecules produced by digestion are absorbed by the hyphae. Most bacteria cannot decompose cellulose and lignin present in the wood. Therefore fungi are the principle decomposers of these substances.

Saprobic fungi use modified hyphae, called rhizoids, to attach to substrate. Along with bacteria, they are the major decomposers in the ecosystem and recycle important materials like C, N, P, O, and H etc.

Parasites

Some fungi are parasites, i.e. they get nutrients directly from a living host and therefore damage the host. They have special hyphal tips called haustoria that absorb nutrients from the host.

Some species are obligate parasites while others are facultative. Obligate parasites can grow only on a specific host. Various mildews and rust species are obligate parasites of plants. Facultative parasites can grow parasitically on their host as well as by themselves.

Predators

Some fungi are active predators. For example, the oyster mushroom paralyses the nematodes (that try to eat it), penetrates their body and absorbs their nutritional contents to fulfill its nitrogen requirements. It gets its glucose by decomposing the wood. Some species of Arthrobotrys trap soil nematodes by forming a constricting ring. Some species produce sticky substances to trap prey.

Symbiotic

Some fungi also live in mutualistic relationships (a relationship in which both partners get benefit).

Lichens

Lichens are mutualistic symbiotic relationship between fungi and algae (or sometimes cyanobacteria). Most of the body of the lichen is made up of fungus and algal partner is present embedded in the hyphae.

Fungus protects the algae from harsh environment and water shortage. Algae provides food by photosynthesis in return. This helps lichens grow on places where neither of the components alone could grow.

Lichens vary in their shape, color, appearance and growth forms. They are important bioindicators (i.e. they indicate the quality of air) as they are not present in polluted environments.

Mycorrhiza

Mycorrhizae are mutualistic association between fungi and vascular plants. Hyphae increase the surface area for absorption of phosphorus, zinc, copper and other nutrients from the soil. These hyphae are attached with the roots of the plants. Plants with attached hyphae can grow better due to this association. Plants supply glucose to the fungal hyphae.There are two types of mycorrhizae

·   In endomycorrhizae the fungal hyphae penetrate the cells of roots and from coils, swellings and branches.

·   In ectomycorrhizae the hyphae surround the cells but do not penetrate them. These are usually found in pines and firs.

Reproduction in Fungi

Most fungi can reproduce both sexually and asexually. Imperfect fungi (deuteromycota) cannot reproduce sexually.

Asexual Reproduction

Asexual reproduction can take place by means of spores, conidia, fragmentation and budding.

Spores

Spores are metabolically dormant (خوابیدہ)bodies that can withstand harsh environmental conditions. They are haploid, non-motile and do not need water for dispersal (پھیلاؤ). These are small, produced in very large number, and dispersed by wind to great distance.

They allow wide distribution of many types of fungi including many pathogens of plants. When spores reach a suitable place, they germinate and produce new hyphae. They are also dispersed by insects, animals and rain splashes.

Spores may be produced by sexual or asexual process.Spores are produced inside the reproductive structures called sporangia. Sporangia are cut off from the main hyphae by complete septa.

Conidia

Conidia are non-motile, asexual spores which are cut off at the end of specialized hyphae called conidiophores. They are not produced inside any special sporangia. They are usually produced in the form of chains or clusters. These are produced in very large numbers and can survive for many weeks. They allow rapid colonization of new food sources.

Fragmentation

Fragmentation is simple breaking of filaments and each broken filament gives rise to a new organism. It is a common mode of reproduction in fungal hyphae.

Budding

Some unicellular yeasts reproduce by budding. It is an asymmetric division in which a small outgrowth or “bud” is produced which may separate from the parent cell and grow. Some yeasts may divide by relatively equal cell division.

Sexual Reproduction

Different groups of fungi have different methods of sexual reproduction. But meiosis and fusion of haploid gamete is common in all groups.

During sexual reproduction, hyphae of two different but compatible “mating types” come together. Their cytoplasms fuse (fusion of cytoplasms is called plasmogamy) and the nuclei also fuse (called karyogamy). These fused hyphae produce sporangia in which spores are produced by meiosis.

In ascomycetes and basidiomycetes, the nuclei do not fuse immediately after plasmogamy. Instead, both nuclei live together in the same hyphae for most of the life of the fungus. Such fungal hyphae having two nuclei from different genetic types are called dikaryotic or heterokarytichyphae.

Different groups of fungi produce different types of haploid sexual spores after meiosis in zygote (basidiospores and ascospore). These spores may be produced in special fruiting bodies (basidia/basidiocarps in basidiomycota and asci/ascocarps in Ascomycota).

Classification of Fungi

Fungi are classified on the basis of type of sexual reproductive structures and method of reproduction. However, different groups also have different types of hyphae and other characters are also different.

Zygomycota (Conjugating fungi)

When hyphae of two different mating types fuse during sexual reproduction, a zygospore is formed. It is a dormant, thick walled, resistant structure. These fungi are called zygomycetes due to this zygospore.

Meiosis takes place in zygospore and it germinates. Haploid spores are produced by mitosis. When these new spores germinate, they produce the new mycelium.

Asexual reproduction by spores is also common. Hyphae are coenocytic. A common example is Rhizopus which is found on spoiling (سڑتی ہوئی)bread and fruit.

Ascomycota (Sac fungi)

It is the largest group of fungi that includes about 60,000 species. Many of them form lichens and mycorrhiza. Some species like morels are edible and highly valued. Most are terrestrial (زمینی) while some are found in marine and freshwater habitats. Small unicellular yeasts and large cup fungi are also members of this group.

They produce haploid sexual spores called ascospores. These are produced by meiosis in special sac-like structures called asci. An ascus is formed when two fungal hyphae fuse and then undergo meiosis. Eight ascospores are produced in each ascus. Microscopic asci are usually present inside large fruiting bodies called ascocarps.

Hyphae of sac fungi are septate. Their dikaryotic stage is lengthy. They reproduce asexually by forming conidia that are dispersed by wind.

Yeasts are microscopic fungi. They originated from all the three different groups of fungi but mostly Ascomycetes. They reproduce mostly asexually by budding. They may sometimes reproduce sexually by forming asci or basidia. They ferment carbohydrates (glucose) into ethanol and carbon dioxide. Saccharomyces cerevisiae is the most commonly used yeast in household and industry.

Basidiomycota (Club fungi)

These are the most commonly seen fungi. They include edible mushrooms, plant pathogens like rust and smut, puffballs, and bracket / shelf fungi.

They are named for their special, club-shaped sexual structures called basidia. A basidium is formed when two fungal hyphae fuse and then undergo meiosis. Four haploid sexual spores are produced on (not inside) the basidium.

During most part of the life, hyphae are septate. Cells are uninucleate during one phase while binucleate (dikaryotic) in remaining, lengthy phase. The visible mushrooms are made up of dikaryotic mycelium.

Rust Fungi

Puccinia species are most common rust fungi. They are called rust because of orange-yellow colored disease spots on leaves that resemble iron rust (زنگ).

Smut Fungi

Ustilago species are most common smut fungi. They are called smut due to black, dusty spores that resemble soot or smut. These spores replace the grain kernels such as those of wheat and corn.

Spores of Ustilago tritici (lose smut of wheat) are carried by wind from infected wheat ears (گندم کے خوشے) to healthy flowers, where they germinate. The hyphae penetrate flower ovaries. Inside the ovary mycelium spreads and becomes dormant. It remains dormant in the seed. When infected seeds are sown in the next season, the hyphae grow within the growing plant and form smut spores inside new kernels(بیج). The kernels are completely destroyed. The covering of the seed breaks and spores are exposed that may be dispersed by the wind.

Deuteromycota (Imperfect fungi)

It is a heterogeneous group that includes all fungi in which sexual phase is not present. Most of them are related the sexually reproducing relatives of Ascomycota, while others are related to other two phyla (zygomycota and basidiomycota).

If sexual structures are found in an imperfect fungi, then it is assigned to appropriate phylum. DNA sequence similarities are now being used to classify imperfect fungi even if sexual structures are not found.

Despite absence of sexual reproduction, imperfect fungi show special kind of genetic recombination called parasexuality. In this type of reproduction, parts of chromosomes of the two nuclei in the same hyphae are exchanged.

Penicillium, Aspergillus, Alternaria, Fusarium, Helminthosporium are some of the economically important genera of Deuteromycota.

Penicillium (blue green molds) are wide spread saprophytic species common on decaying fruit, bread, etc. They reproduce asexually by means of conidia, which are present in chains on conidiophores. Brush-like arrangement of its conidia is characteristic of Penicillium. These conidia give color to circular mycelial colony. Mature condia are easily dispersed.

Land Adaptation of Fungi

Fungi can grow best in moist environments. But they are present almost everywhere where organic material is present. They are a very successful group of land organisms. They possess several features in their body and reproduction strategies that help them survive in their habitat.

Extensive system of fast-spreading hyphae penetrates the substrate and enormously increases the contact and surface area for absorption. Cytoplasmic streaming in entire hyphae allows distribution of nutrients and rapid growth and spread. Chitin in their cell walls is more resistant to decay than cellulose and lignin found in plants. They can even break-down lignin to obtain nutrition. In saprobes, certain modified hyphae called rhizoids anchor the fungus to substrate and also digest and absorb food.

They are very well adapted to live on land due to lack of flagellated cells, thick walled zygote, non-motile spores, and conidia which allow rapid dispersal by wind. Hyphae are adapted to enable them to reproduce without depending on water.

Many fungi can tolerate osmotic pressure which even bacteria cannot tolerate. Many can tolerate temperature extremes of ­5^oC to 50^oC. That is why molds like Penicillium can grow on oranges and jelly kept in a refrigerator, while bacteria cannot.

Importance of Fungi

Ecological Importance

Fungi are ecologically very important. Some fungi act as decomposers while others are symbiotic like mycorrhiza and lichens.

Decomposers

Fungi are responsible for recycling of materials in the ecosystem. Nutrients and organic compounds would be locked up after the death of animals and plants if fungi are not present to recycle them.

Mycorrhizal fungi increase the growth of plants. 95% of all plants have fungi associated with their roots.

Lichens grow on bare rocks and make conditions favorable for other plants to grow there (this is called ecological succession). They are also bioindicators of air quality as they are sensitive to pollution. Some fungi are used for bioremediation (removal or degradation of environmental pollutants or toxic substances by the use of living organisms).

Economic Benefits of Fungi

Edible Fungi

Some fungi are edible. About 200 species of mushrooms (Agaricus), morels (Morchella), and truffles (Tuber), are edible.

Penicillium is used for flavoring, aroma (خوشبو) and characteristic color to some cheese.

Fermentation

Because of their ability to ferment glucose into ethanol certain fungi like Saccharomyces cerevisiae are used in production of bread and liquor.

Some species of genus Aspergillus are used for fermenting soya sauce and soya paste from soya beans. Citric acid is also produced from some species of Aspergillus.

Poisonous Fungi

Some fungi are poisonous however (called toadstools) such as death cap (Amanita) and jack O’ lantern.

Fodder for Animals

Reindeer moss (a lichen) is used as food for reindeers and other animals in arctic / subarctic / boreal region.

Drugs and Chemicals

·   Lovastatin is a drug used for lowering blood pressure.

·   Cyclosporine obtained from a soil fungus is used in organ transplantation to avoid organ rejection.

·   Ergotine is used to relieve one kind of headache calledmigraine.

·   Griseofulvin is used to inhibit fungal growth.

·   Some species are source of antibiotics. Penicillin was the first antibiotic discovered by Fleming in 1928.

·   Some natural dyes obtained from lichens are used in textile industry.

Use in Research

Yeasts are used as model organisms in genetics and molecular biology research due to their ease of manipulation and rapid growth. A lot of information is available about their genetics and biochemistry. Yeasts were the first organisms used by genetic engineers.

In 1983 an artificial chromosome was made in Saccharomyces cerevisae. It was also the first eukaryotic organism whose genome was completely sequenced in 1996. Yeasts are also being used for production of human hormones. Neurospora (pink bread mold) has also been used in genetics research.

Economic Losses due to Fungi

Fungi cause many serious plant and animal diseases.

Plant Diseases

Powdery mildew (on grapes, rose, wheat etc.) ergot of rye, red rot of sugar cane, potato wilt, cotton root rot, apple scab and brown rot of peaches, plum, apricot and cherries are some common plant diseases caused by fungi.

Rusts and smuts cause serious damage to rice, wheat and corn, resulting in mass displacement and starvation of people.

Human Diseases

Ringworm (داد) and athlete’s foot are skin infections caused by certain imperfect fungi.Candida albicansis a yeast that causes oral and vaginal thrush (candidiosis).

Histoplasmosis is a serious infection of lungs caused by inhaling spores of a fungus that is common in soil contaminated with bird feces. If infection spreads to blood stream, and to other organs, it can be very serious and even fatal.

Aspergillus fumigatus causes aspergillosis but only in persons with weakened immune system (like in AIDS patients).

Some species of Aspergillus produce most carcinogenic mycotoxins, called aflatoxins. It also contaminates improperly stored food gains such as peanuts and corn. Milk, eggs and meat may also have small traces of aflatoxins. Any moldy human food or animal forage product should be discarded.

Ergotism is caused by eating bread made from purple ergot-contaminated rye flour. The poisonous material in ergot causes nervous spasms, convulsions, psychotic delusions and even gangrene.

Damage to Household Items

Some saprobic fungi cause incalculable damage to food, wood, fiber, and leather by decomposing them. 15-50% of world fruit is lost each year due to fungal attack. Wood rotting fungi destroy not only living trees but also structural timber. Bracket / shelf fungi cause lot of damage to stored cut lumber as well as stands of timber of living trees.

A pink yeast (Rhodotorula) grows on shower curtains and other moist surfaces.

09Kingdom Plantae

The purpose of classification is to arrange organisms in groups which logically reflect their similarities and dissimilarities at various levels. Such groups foreshadow the natural relationships among living organisms and their origin. This system of classification is called phylogenetic system of classification.

Kingdom Plantae includes eukaryotic, autotrophic, multicellular and non-motile organisms which develop from embryos. Plant cells have cell walls around their plasma membrane, made up of cellulose. There are about 360,000 known species of plants.

Classification of Plantae

The organisms within Plantae are divided into two major groups: the bryophyta (non-vascular plants) and tracheophyta (vascular plants). This division reflects certain similarities and dissimilarities between the two groups. Each division is further divided into sub-divisions, classes, sub-classes and other taxonomic ranks.

Division Bryophyta

Bryophytes were the first plants that colonized land. They probably evolved from green algae. They are poorly adapted to land and are confined (محدود) to damp and shady places.

Bryophytes are flowerless plants. They do not have specialized conducting and strengthening tissues (vascular bundle made up of xylem and phloem). Therefore they are called non-vascular plants. The transport of water and minerals as well as prepared food and other substances takes place by osmosis and simple diffusion.

The body is covered in a proper cuticle but is usually very thin. Water is absorbed by the surface of plant. Bryophytes are sometimes called the amphibians of the plant world because they cannot live away from water. They are dependent on water for reproduction.

These plants show a regular alternation of heteromorphic generations. They have a dominant, free living gametophyte. The gametophyte is sometimes thallus like in appearance (as in many liverworts). Sometimes the body is differentiated into structures that resemble stem, leaves and rhizoids (like in mosses and some liverworts). Rhizoid is the root-like structure that absorbs water and anchors the plant on ground.

The gametophyte produces a sporophyte which is less conspicuous. It is partially or totally dependent upon the gametophyte for its nutrition. The sporophyte generally consists of foot, seta and capsule. It is usually diploid (2n) and produces haploid spores in sporangia. All spores are of one type, therefore, the sporophyte is homosporous.

The spores germinate to produce haploid (n) gametophytes. Multicellular male and female sex organs are produced on gamethophyte. Male sex organs are called antheridia while female sex organs are called archegonia. Male and female sex organs may be produced on same or on different plants. These sex organs are multicellular and are protected by a sterile covering of cells.

Gametes are produced by mitosis. Male gametes produced in antheridia are called antherozoids. They are motile and are always produced in large numbers. Female gametes are produced in archegonia and are called eggs. A single egg is produced in each archegonium.

Fertilization occurs in water. Antherozoids (n) are attracted towards archegonia (n) chemotactically. A single antherozoid fuses with an egg (n) to fertilize it. It results in the formation of the diploid zygote (2n). the zygote remains in the archegonium for some time. After a resting period the zygote develops into a diploid embryo by mitosis. The embryo produces a sporophyte which is also diploid.

The entire development of sporophyte takes place in the gametophyte plant body. Even when the sporophyte is fully developed, it remains attached to the gametophyte for nourishment and protection because it does not contain chloroplast and is unable to perform photosynthesis.

This life cycle therefore shows alternation of generation because multicellular haploid gametophyte generation alternates with multicellular diploid sporophyte generation. This is very important phenomenon because it provides continuous genetic variation. It is helpful in selection of the best genetic make up for survival and adaptation in the changing environments.

Important distinguishing features of bryophytes are:

·   Vascular system is absent

·   Gametophyte is dominant

·   Sporophyte attached to gametophyte

·   Homosporous.

Adaptation to Land Habitat

There are many features in bryophyte body that helped them in colonizing land.

·   Their body is a compact multicellular structure with small surface area. A cuticle is usually present, covering the body. Both of these features help in reducing loss of water by evaporation.

·   Photosynthetic tissue is present in special chambers for easy absorption of CO₂. This helps reducing water loss and protects from direct exposure to light.

·   Rhizoids help in anchoring the plant and absorbing water.

·   They produce two types of gametes (heterogamy). Egg is non-motile and has stored food. Sperm is small and motile.

·   Gametes are produced in special multicellular reproductive organs (antheridia and archegonia) which provide protection.

·   The multicellular embryo remains inside the female reproductive body for protection.

·   Alternation of generation allowed the plant to produce diversity and test the best genetic combinations for adapting to the versatile terrestrial conditions.

Classification of Bryophytes

Bryophytes are classified into three sub-divisions. Hepaticopsida, Bryopsida, and Anthoceropsida.

Hepaticopsida (Liverworts)

Liverworts are the simplest of all bryophytes. They include about 900 species. They are commonly found on moist rocks and on wet soil. They live near water to reduce chances of drying out.

The plant body is a gametophyte. It may be thalloid (i.e. flat) or ribbon-like (usually dichotomously branched). It is attached to soil by means of rhizoids (like Marchantia). Other species grow upright and falsely appear leafy (they have a false stem and leaves; like Porella) the sporophyte is dependent upon gametophyte for nourishment and protection.

Sex organs develop on the upper surface of the thallus near the tip of branches. Sometimes they develop on special branches on gametophyte called the antheridiophores and the archegoniophores as in Marchantia.

Bryopsida (Mosses)

They are also found in damp places. They may also grow in fairly dry places as well. However, water is essential for their reproduction. They usually grow to form cushions or mats.

Adult moss plant (gametophyte) is differentiated into two structures which resemble stem and leaves. Multicellular rhizoids are also present. Examples of mosses are Funaria and Polytrichum.

Archegonia and antheridia, develop on the tips of different branches on the same plant (as in Funaria) or on different plants (as in Polytrichum). The archegonia and antheridia form clusters and are mixed with sterile hairs, the paraphyses.

Formation of sporophyte and spores follow the same pattern as in liverworts. However, the spore of a moss develops into an alga like structure, called protonema. Small buds appear on protonema which give rise to haploid gametophytes.

Anthoceropsida (Hornworts)

This group is different in many ways and is slightly advanced than Bryopsida and Hepaticopsida. The gametophyte is highly lobed and irregular in outline.

The sporophyte is dependent on gametophyte for only a brief period of time during early development. Antheridia and archegonia are partially sunken in the gametophytic tissue. The sporophyte has many advanced characters due to which it can survive on land better than other groups. The sporophyte has stomata and chloroplasts in the epidermis and can thus photosynthesize its own food. It also has waxy cuticle to prevent water loss.

At the junction of foot and spore producing region, there is a band of meristematic tissue. This tissue keeps on adding cells towards the spore-producing region during the formation, maturation and dispersal of spores from the opposite end. Due to fast growth rate of this meristematic tissue the sporophyte keeps on increasing in length for an indefinite period of time.

Due to these characters, the sporophyte continues to survive as such even after the death and decay of the gametophyte. One good example of Anthoceropsida is Anthoceros which is also found in hilly areas of Pakistan.

Alternation of Generation

The life cycle of liverworts, mosses and hornworts has two distinct multicellular phases or generations. These are: haploid gametophyte and diploid sporophyte, which alternate with each other.

The gametophyte is dominant generation because it is more conspicuous. It produces gametes called spermatozoids or antherozoids and eggs, therefore called gamete-producing generation.

A haploid spermatozoid fuses with a haploid egg to produce diploid oospore. The oospore does not produce gametophyte directly but produces a totally different plant called sporophyte.

The sporophyte in bryophytes is a less conspicuous generation, which is usually differentiated into feet, seta, and capsule (also called sporogonium). Spores develop within the capsule by meiosis.

The sporophyte produces spores and is called spore producing generation. The spore does not develop into a sporophyte but gives rise to the gametophyte. Thus in the life-history of a bryophytic plant, the two generations, the gametophyte and the sporophyte, regularly alternate with each other. The phenomenon of alternation of gametophyte and sporophyte in the life history of a plant is called alternation of generation.

It should be noted that the gametophyte or haploid stage begins with spores and ends at gamete, whereas the sporophyte begins with oospore and ends at spore mother cells.

Significance of Alternation of Generation

Reshuffling of genes takes place during formation of spores. This results in numerous spores with different genetic makeup. These spores produce gametophytes with different genetic combinations. Those with better genes have more chances of survival in the environment. Gametophytes with less advantageous characters are eliminated. There is also reshuffling of genes during gametogenesis in the gametophyte as gametes are produced after mitosis.

The oospore that develops after fertilization has a different genetic makeup as compared to parents. This genetic variation passes to new sporophyte which on maturity once again produces more genetic recombination.

Therefore, during this process, large amount of diversity is produced and nature selects the best genetic combinations. This allows the population to become more adapted to their environment.

Division Tracheophyta

Tracheophytes are called vascular plants because they have a vascular (conducting) tissue i.e. xylem and phloem. These are very successful on land. They are successfully adapted to rough land habitat. Among them, flowering plants are the most dominant group of land plants.

Evolution of many complex vegetative and reproductive characters allowed vascular plants (especially flowering plants) to become dominant flora of land.

·   Body is divided into root, stem and leaves.

·   Vascular system is present in stems, roots and leaves.

·   Sporangia are protected, leading to evolution of seed.

·   A pollen tube is formed for the transmission of male gamete to female gamete. It allows safe and water-independent transmission.

·   Evolution of flower and fruit.

·   Heteromorphic alternation of generation.

Tracheophytes are further divided into four sub-divisions, Psilopsida, Lycopsida, Sphenopsida, and Pteropsida.

Psilopsida

The sporophyte of psilopsida does not have a root. The stem is differentiated into an underground rhizome and an aerial part. Both are dichotomously branched. The rhizome bears rhizoids, which function as root. The aerial branches are green, leafless and bear small vein-less outgrowths and carryout photosynthesis.

The reproductive organs of sporophyte are sporangia which develop at the tips of long or short branches, or on lateral sides of branches. Internal structures of stem are simple. Vascular tissue is narrow, central and solid without pith, with a broad cortex.

Psilopsida is considered to be the earliest group of vascular plants. Most of the representatives of this group have become extinct, for example, Horneophyton, Psilophyton, Cooksonia etc. There are only two living members, Psilotum and Tmesipeteris.

The gametophyte is thallus like. It is colorless and underground. Its cells contain a fungus (mycorrhiza) which provides food to the gametophyte and in return gets protection from it.

Lycopsida(Club/Spike mosses)

The sporophytes of Lycopsida are differentiated into roots, stems and leaves. The leaves are small and single veined, and are also called microphylls. The arrangement of leaves is spiral or opposite.

The sporangia develop singly on the upper side of the sporophylls, which may or may not be arranged to form strobili. Lycopsids are also called club mosses / spike mosses because their strobili are club or spike shaped, and their small leaves resembe mosses.

The sporophyte may have sporangia of one kind or of two kinds. Lycopodium produces one type of spores while Selaginella has two types of spores i.e. microsporangia and megasporangia. On the basis of types of spores produced in the sporophyte they are referred to as being “homosporous” or “heterosporous” respectively. This condition is called homospory and heterospory.

Selaginella resembles seed producing plants (spermatophytes) because of its heterosporic condition and some other characters. The gametophyte of Lycopsida is mainly underground.

Sphenopsida (Horsetails)

The sporophyte of Sphenopsida is differentiated into root stem and leaves in sphenopsida. The leaves may be expanded or scale-like and are always arranged in whorls.

They are sometimes called arthrophytes because the body is composed of large number of joints (arthro = جوڑ). Main stem is not smooth, it has large number of ridges and furrows. Each node has whorl of branches. The sporangia are born on structures called sporangiophores, aggregated to form strobili.

Each sporangiophore has a slender (پتلی)stalk and an expanded disc at its free end. The sporangia appear on the underside of the disc. The thalloid gametophytes grow in clayey soil and on mud, e.g. Equisetum.

Evolution of Leaves

Early vascular plants did not have true leaves and roots. They were usually small. Their aerial parts were dichotomously (دو شاخہ) branched, erect and smooth. Subterranean (زیرِ زمین) rhizome was strong and adapted for anchoring and absorption.

Cooksonia is a species that lived about 350 million years ago. It had the same structural layout. It had naked green stem without leaves.

The leaves arose on such plants in the form of small scale-like outgrowths. These outgrowths did not have vascular tissue. Therefore these are not considered true leaves.

Lycopsids were the first plants that formed the true leaves and roots. However, their leaves are small. Each leaf has a single undivided vein. Such a leaf is called microphyll.

Large leaves having divided veins and veinlets with an expanded leaf blade or lamina are known as megaphylls. Megaphylls are characteristic for ferns and seed plants. It is suggested that evolution of megaphylls started from a dichotomous branching system in some primitive psilopsids approximately 350 million years ago. It is assumed that evolution of a megaphyll included series of successive evolutionary steps.

The dichotomously branched aerial portion of the stem showed unequal branching. Some branches remained short while others grew and expanded at a much faster pace. All these branches grew in different planes. Such an unequal development of various branches is called overtopping.

Next important step was the arrangement of unequal dichotomies in one plane. This process is termed as planation.

Overtopping and planation was followed by a process known as fusion or webbing. The space between the overtopped dichotomous branches was occupied by a sheet of parenchyma cells which connected these branches forming a flat lamina or leaf blade type of structure, having many dichotomously branched veins.

During evolution, fusion of vascular strands resulted in net or reticulate venation pattern. The process of evolution of leaf was very slow and gradual which completed in more than 15-20 million years.

Pteropsida

Pteropsida is divided into three classes:

·   Class Filicineae (ferns)

·   Class Gymnospermae (naked seeds)

·   Class Angiospermae (enclosed seeds)

a) Class Filicineae

The class Filicineae contains seedless plants (called ferns) with foliar sporangia (attached to fronds). The leaves are called fronds. When the frond is immature, it is coiled. This pattern of development is called circinate vernation. It is an important character of this group.

The Filicineae or ferns are mostly shade and moisture loving plants. A very few are able to live under dry conditions. They grow on the hills and in plains. Some are epiphytic (grow on the bark of other trees).

Although ferns are worldwide in distribution, they are especially abundant in tropics. They vary greatly in size. Important ferns are Dryopteris, Pteridium, Adiantum and Pteris.

Adiantum (maiden hair fern)

Adiantum is a fern that grows along moist walls and water courses. It is a small herb consisting of stem, roots, and leaves. Stem is a short, thick and underground, usually unbranched horizontally growing rhizome. It is protected by brownish scales (ramenta) and covered by base of shed leaves. Fibrous adventitious roots arise from the lower side of the rhizome. Large, pinnately (feather-like) compound fronds arise from the upper side of rhizome. Young leaves (called fiddle heads) show circinate vernation. The stipe (stalk) and rachis (axis of leaf) are black, smooth, and shiny (hence called maiden’s hair). The leaflets show dichotomous venation. Sori (group of sporangia) are present on the underside of reflexed (مڑے ہوئے) lobesof the margins of leaflets. They are protected by bent margin of the leaflet, forming false indusium (membrane that protects spores).

Life cycle of Adiantum shows heteromorphic alternation of generation. Sporophyte is dominant and gametophyte is small and reduced but separate and independent. The diploid sporophyte produces large number of sori. They are green but become dark brown after ripening (پکنے کے بعد). Each sorus consists of a number of sporangia covered by false indusium. The leaves bearing sporangia are called sporophylls.

Each sporangium is slightly flattened, biconvex body born on a multicellular stalk. The capsular wall consists of a single layer of flat, thin walled cells. The edge of the capsule is made up of two parts, the annulus and the stomium. The annular cells have their radial and inner walls thickened. The stomial cells are thin walled. Inside the sporangia, haploid spores are formed by reduction division, from diploid spore mother cells. The annulus of the sporangium contracts in dry weather, the stomial cells being thin-walled rupture and spores are dispersed by wind. When a spore falls on a moist soil, it germinates at a suitable temperature and produces a haploid gametophyte or prothallus.

The prothallus (gametophyte) is an autotrophic, small flat, heart shaped structure. At the anterior end of the prothallus is a notch in which lies the growing point. Its size is about 8mm at its longest diameter. It is horizontally placed on the soil, and has unicellular rhizoids on its lower surface towards the posterior end. The rhizoids fix the prothallus to the soil and absorb nutrients for it. it is composed of rounded thin walled cells. The margin of the prothallus is one cell thick but the middle part is many cells and is cushion-like. The prothallus is monoecious (male and female sex organs appear on the under-surface of the same prothallus). In the mature prothallus, archegonia occur near the notch and the antheridia are scattered among the rhizoids.

Each antheridium produces numerous spermatozoids which are spirally soiled and multiciliated. The archegonium consists of a center and a neck. The venter contains the egg or oosphere and is embedded in the cushion of the thallus. The antherozoids reach the archegonium, by swimming in water. Fertilization occurs and an oospore is formed. The oospore forms the sporophyte. Young sporophyte is first attached to the gametophyte but later becomes independent.

Evolution of Seed Habit

Seed plants (called spermatophytes) are the most abundant plants in the plant kingdom. This important adaptation (starting about 390 million years ago) allowed these plants to better adapt on land. First complete seeds appeared about approximately 365 million years ago during late Devonian times.

Seed can be defined as fertilized ovule. An ovule is an integumented, indehiscent megasporangium. Integuments are specialized protective coverings around megasporangium.

Primitive (قدیم) vascular land plants were homosporous (produced only one type of spores). During early phase of evolution, some plant groups started producing two different types of spores, small microspores and large megaspores. This condition is called heterospory. Microspores originate in microsporangia and produce micro-gametophyte. Megaspores originate in megasporangia and produce mega-gametophyte.

In early land plants, the megaspores were shed from the sporophyte and dispersed. They germinated in wet soil and produced female gametophyte. In some plants (like Selaginella) the megaspore is not released immediately after formation. In other plants it is permanently retain within the megasporangia. The megaspore thus germinates within megasporangium.

Some branch-like structures surrounded the megasporangium and fused to form a protective covering, called integument. These coverings protected the megasporangium from water loss. This structure later became ovule which is an integumented indehiscent megasporangium.

In early plants each spore mother cell in a megasporangium produced four megaspores and four mega-gametophytes. There was intense (شدید) competition between then for space and nutrients. Vascular plants soon started producing only one megaspore and megagametophyte in one megasporangium. The remaining three are aborted during early stages and never produce gametophyte.

One megaspore germinates into one mega-gametophyte. This gametophyte then becomes embryo sac.

The megasporangium became specialized for capturing pollen grains (microspores containing micro-gametophyte). When pollens are trapped in the distal cavity of megasporangium, they germinate to form micro-gametophyte. This microgametophyte has a pollen tube. This tube leads the male gamete into the embryo sac to fertilize the egg. A zygote is formed after fertilization. The megasporangium (now called ovule) is transformed into seed. Integuments of megasporangium become seed coat. The seed protects the developing embryo under unfavorable terrestrial (زمینی) environment.

b) Class Gymnospermae (naked seed plants)

Gymnosperms are one of the most successful groups of seed plants. They are distributed all around the world. They constitute about one third of the world’s forests. The gymnosperms are heterosporous plants which produce seeds but no fruit (hence the term “naked seeds”). The ovules in these plants are usually borne on the exposed surfaces of fertile leaves (megasporophylls). These ovules, unlike those of angiosperms are not enclosed but lie naked on the surface of fertile leaves.

Like Filicinae, they show regular heteromorphic alternation of generations. They have independent, dominant sporophyte. The gametophyte is less conspicuous, and dependent on sporophyte. The female gametophyte is permanently retained within the ovule. The two kinds of spores are microspores and megaspores which develop on microsporophylls and megasporophylls respectively. The megasporophylls bearing ovules are not folded and joined at the margins to form an ovary. For this reason the seeds lie naked on the megasporophylls.

Life Cycle of Pinus

The pine is a conifer (having cones). The main plant body is sporophyte which produces spores after reduction division of spore mother cell in sporangia. Conifers are heterosporous. Microspores and megaspores are produced in microsporangia and megasporangia respectively. Sporangia (i.e. micro and megasporangia) are produced on respective cones (male cones and female cones) on the same plant.

The male cones are small in size and are produced in clusters on an axis. Each male cone consists of microsporaphylls which contain microsporangia. Microspore germinates to form a small inconspicuous male gametophyte (also called as microgametophyte) within the spore wall. Such a microspore of seed plants that contains microgametophyte including the gametes is called a pollen grain.

Pollen are produced in great numbers and are transported by wind. Pollen grain in Pinus has two wings attached to its lateral sides. Due to wings, pollen can float in air for a longer period of time and can travel long distances. The gymnosperms have successfully evolved this totally new mechanism of transfer of male gamete to the female gametophyte through wind which has made them independent of water for this purpose. This is an important improvement and evolutionary adaptation to survive in the harsh dry terrestrial environment.

The female cones are large and conspicuous. Each female cone is composed of large number of spirally arranged scales, the megasporophylls which are woody in texture. At the base of each scale two ovules are present. An ovule is actually a megasporanguim which is protected by an integument. Each megasporangium has a single diploid megaspore mother cell. The megaspore mother cell divides meiotically to produce four haploid megaspores. The functional megaspore (n) undergoes mitosis to produce female gametophyte or an embryo sac. The embryo sac contains one to several archegonia. The archegonia contain the female gamete or an egg.

During pollination the pollen directly land on the ovules. Only few pollen are able to germinate to form pollen tubes through which male gametes are transferred to the embryo sac for fertilization.

More than one egg can be fertilized to form several zygotes, but one zygote usually survives to form a single embryo. After fertilization the ovule becomes the seed. The seed now contains an embryo along with some stored food material. The seed upon germination gives rise to a new sporophyte.

In the life cycle of pinus, the dominant diploid sporophyte generation alternates with inconspicuous haploid gametophyte germination.

b) Class Angiospermae

The term angiosperm literally means enclosed seeds. Fertile leaves, bearing ovules, are folded and joined at the margins to form ovaries. The ovary after fertilization is changed into a fruit, containing seeds.

There are about 235,000 to 360,000 known species of plants. They are heterosporous, autotrophic plants. These are highly evolved of all the plants on the earth. These plants produce flowers, fruits and seeds.

Life Cycle of Angiosperms

The adult plant is a diploid sporophyte mostly differentiated into roots, stem and leaves. At maturity it produces flowers. A flower is a modified shoot which consists of a pedicel, thalamus or torus, and floral leaves (sepals, petals, stames and carpels). Thalamus and floral leaves, especially the stamens and the capels are modified and do not even look like stem and leaves (respectively). The sepals and petals are non-essential or non-reproductive parts, and stamens and carpels are the essential or reproductive parts.

The sepals and petals protect the stamens and carpels. They also attract insects for pollination. When the pollination is over, the sepals usually and the petals always fall off.

The anthers contain microspore mother cells which produce haploid microspores by meiosis. Each microspore germinates to produce male gametophyte. Such microspores containing male gametophytes are called pollen.

The carpel consists of a basal broader part, the ovary, the style and the terminal part of the style, the stigma. The ovary contains ovules. The ovule consists of an integument (covering) and a tissue, the nucellus present inside.

After pollination, the pollen grain is transferred to the stigma. Here it germinates to form a pollen tube. The nucleus of the microspore divides by meiotic divisions to form two male gametes and the tube nucleus. At this stage of development, the pollen grain is called male gametophyte. In the meantime certain changes occur in the ovule leading to the formation of female spore (megaspore). The megaspore develops into female gametophyte. This consists of seven cells only. One of these cells is the egg or oosphere.

The pollen tube grows through the style, enters the ovule and then reaches the female gametophyte. Here it discharges the male gametes. The egg and one of the two male gametes fuse to form the oospore. The second male gamete fuses with the secondary nucleus to form endosperm nucleus (double fertilization). The oospore develops into an embryo and endosperm nucleus develops into a multicellular nutritive tissue, the endosperm.