NOTES

Molecular biology notes

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BIOLOGICAL CLASSIFICATION

The purpose of biological classification is to organize the vast number of known plants and animals into categories that could be named and easily remembered and studied. As a result the study of one organism of a group gives us the idea about the rest of the members of that particular group.

Two Kingdom Classification

•          It was given by Linnaeus.

•           All the organisms are divided into two kingdoms namely Animalia & Plantae.

•          Major criterion of classification- Presence/ absence of cell wall.

•          Other Criteria – locomotion, mode of nutrition, response to external stimuli etc.

•           This system does not distinguish between eukaryotes and prokaryotes, unicelled and multicelled organisms and photosynthetic and non photosynthetic organisms.

•          Few organisms like Chlamydomonas, Euglena and slime moulds share characteristics of both plants and animals and it was proposed that a new kingdom is to be established to accommodate such organisms.

Three Kingdom Classification

•          It was given by Haeckel, a German zoologist (1866).

•           All the organisms are divided into three kingdoms namely Animalia, Plantae and Protista.

•           Kingdom Protista includes a wide variety of unicellular, mostly aquatic eukaryotes.

•           Protista includes Fungi, Protozoa, Algae, Bacteria and Slime moulds.

         Four Kingdom Classification

•          It was given by Copeland (1956).

•           All the organisms are divided into four kingdoms namely Animalia, Plantae, Protista and Monera.

•           Kingdom Monera includes all the prokaryotic organisms like eubacteria ( including cyanobacteria), archaebacterial and actinomycetes.

•           Copeland called Monera as ‘Mychota’. It was called as Monera by Daugherty and Allen.

Five Kingdom Classification

It was proposed by R.H. Whittaker. (1969).

•           All the organisms are divided into five kingdoms namely Monera, Protista, Fungi, Plantae and Animalia.

•          Basis of Five Kingdom Classification:

(i) Complexity of cell structure: Prokaryotic and Eukaryotic

(ii) Complexity of body organization: Unicellular and Multicellular

(iii) Mode of nutrition: Autotrophic and Heterotrophic ( Major Criteria)

(iv) Reproduction and (V) Phylogenetic or evolutionary interrelations.

Characters	Five Kingdoms
	Monera	Protista	Fungi	Plantae	Animalia
Cell Type	Prokaryotic	Eukaryotic	Eukaryotic	Eukaryotic	Eukaryotic
Cell wall	Noncellular (Polysaccharide+ amino acid)	Present in some	Present  ( Without  cellulose)	Present ( with cellulose)	Absent
Nuclear Membrane	Absent	Present	Present	Present	Present
Body Organisation	Cellular	Cellular	Multicellular/ loose tissue	Tissue/ organ	Tissue/ organ/ organ system
Mode of nutrition	Autotrophic and Heterotrophic	Autotrophic and Heterotrophic	Heterotrophic	Autotrophic	Heterotrophic

Six Kingdom Classification

It was proposed by Carl Woese.

•           All the organisms are divided into six kingdoms namely Archaebacteria, Eubacteria, Protista, Fungi, Plantae and Animalia.

•           Carl Woese separated the archaebacteria from eubacteria on the basis of some major differences which include:

•          (a) Absence of peptidoglycan in the cell walls

•          (b) Occurrence of branched chain lipids in the membrane.

KINGDOM: MONERA

•          Includes all Prokaryotes

•          Includes most primitive forms of life originating from more ancient living stock termed progenote.

•          Includes Eubacteria and Archaebacteria.

•          Eubacteria includes Cyanobacteria, Actinomycetes, mycoplasma, Rickettsiae, Chlamydiae, Spirochaetes etc.

•          Characters Of Monera

•          1. These are unicellular, colonial, multicellular prokaryotic organisms without nuclear membrane, nucleolus, chromatin and histone proteins.

•          2. Cell wall is made up of peptidoglycan.

•          3. Membrane bound organelles are absent.

•          4. Cyclosis is absent and ribosomes are of 70 S type.

•          5. Respiratory enzymes are found associated with plasma membrane.

•          6. Nucleoid/ prochromosome is composed of naled DNA, RNA and non-histone proteins.

•          7. Reproduction is by asexual method.

•          8. Cell division is amitotic type and lacks spindle formation.

•          Monera

•          Bacteria are the sole members of the Kingdom Monera.

•           Bacteria are cosmopolitan and  occur almost everywhere.

•            They also live in extreme habitats such as hot springs, deserts, snow and deep oceans where very few other life forms can survive.

•           Many of the bacteria live in or on other organisms as parasites.

•           The smallest bacteria is Dialister pneumosintes and Beggiatoa mirabilis is the largest filamentous bacteria.

•           Anton von Leeuwenhook discovered bacteria. 

•           Bacteria are photosynthetic autotrophic or chemosynthetic autotrophic or heterotrophs.

•          Types Of Bacteria

•          Cocci

•          Includes Spherical or nearly spherical, aflagellate bacteria.

•          Example: Micrococcus luteus, Gonococcus, Streptococcus etc.

•          Bacilli

•          Includes rod like, flagellated bacteria.

•          Most Common type of bacteria.

•          Example: Lactobacillus, Streptobacillus, Bacillus anthracis etc.

•          Vibrio

•          Includes comma-shaped bacteria.

•          Example: Vibrio Cholerae

•          Spirilla

•          Includes coiled forms of bacteria exhibiting twists with one or more turns.

•          Example: Spirillum volutans

MONERA - Archaebacteria

v  Archeabacteria  live in harsh habitats such as extreme salty areas (halophiles), hot springs (thermoacidophiles) and marshy areas (methanogens).

v   Posses different cell wall structure which facilitate the survival in extreme conditions.

v   Methanogens are present in the guts of several ruminants (cows and buffaloes) and are responsible for the production of methane.

v  MONERA – Eubacteria (True Bacteria)

v  Eubacteria are characterised by the presence of a rigid cell wall. They are motile or non motile and if motile, they posses flagellum.

v  Eubacteria include heterotrophs, autotrophs and chemotrophs.

v  Bacteria reproduce mainly by fission. Under unfavourable conditions, they produce spores.

v  They also reproduce by a sort of sexual reproduction by adopting a primitive type of DNA transfer from one bacterium to the other.

v  Heterotrophs absorb organic materials down in both living and dead organisms. Autotrophs can make their food by photosynthesis.

v  Chemotrophs get their food by breaking down inorganic substances.

v  The cyanobacteria are unicellular, colonial or filamentous, marine or terrestrial algae.

v  The cyanobacteria (blue-green algae) have chlorophyll a similar to green plants and are photosynthetic autotrophs.

v  The colonies are generally surrounded by gelatinous sheath. They often form blooms in polluted water bodies.

v  Some of these organisms can fix atmospheric nitrogen in specialised cells called heterocysts, e.g., Nostoc and Anabaena.

v  Chemosynthetic autotrophic bacteria oxidise various inorganic substances such as nitrates, nitrites and ammonia and use the released energy for their ATP production.

v   They play a great role in recycling nutrients like nitrogen, phosphorous, iron and sulphur.

v  Heterotrophic bacteria are the most abundant in nature.

v  The majority are important decomposers.

v  They are helpful in making curd from milk, production  of antibiotics, fixing nitrogen in legume roots, etc.

v  Some are pathogens causing damage to human beings, crops, farm animals and pets.

v  Cholera, typhoid, tetanus, citrus canker are well known diseases  caused by different bacteria.

v  The Mycoplasmas are organisms that completely lack a cell wall.

v   They are the smallest living cells known and can survive without oxygen.

v  Many mycoplasma are pathogenic in animals and plants.

Kingdom - Protista

v  Includes single-celled eukaryotes.

v  They are primarily aquatic.

v  The protistan cell body contains a well defined nucleus and other membrane-bound organelles.

v  Locomotion is by flagella or cilia.

v  Reproduction occurs sexually and sexually.

v  Includes Chrysophytes, Dianoflagellates, Euglenoids, Slime moulds and Protozoans.

Protista- Chrysophytes

v  1. Includes diatoms and golden algae (desmids).

v  2. They are found in fresh water as well as in marine environments.

v  3. They are microscopic and float passively in water currents (plankton).

v  4. Most of them are photosynthetic.

v  Diatoms:

v  * Diatoms are the chief ‘producers’ in the oceans.

v  *  The cell walls form two thin overlapping shells, embedded with silica and thus the walls are indestructible.

v  * Accumulation of cell wall is referred to as ‘diatomaceous earth’ and is used in polishing, filtration of oils and syrups.

Protista- Dianoflagellates

v  1. Dianoflagellates are mostly marine and photosynthetic.

v  2. They appear yellow, green, brown, blue or red depending on the main pigments present in their cells.

v  3. The cell wall has stiff cellulose plates on the outer surface.

v  4. Most of them have two flagella; one lies longitudinally and the other transversely in a furrow between the wall plates.

v  5. Red Tides: Red dianoflagellates like Gonyaulax undergo rapid multiplication and make the sea appear red. Toxins released by such large numbers may even kill other marine animals such as fishes.

Protista- Euglenoids

v  Mostly they are fresh water organisms found in stagnant water.

v  Instead of a cell wall, they have a protein rich layer called pellicle which makes their body flexible.

v  Posses two flagella, a short and a long one.

v  They are photosynthetic, when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms.

v  Pigments are identical to those present in higher plants. Example: Euglena

v  Slime moulds are saprophytic protists.

v  Under suitable conditions, they form an aggregation called plasmodium which may grow and spread over several feet.

v  During unfavourable conditions, the plasmodium differentiates and forms fruiting bodies bearing spores at their tips with true walls.

v  Spores are extremely resistant and survive for many years and are dispersed by air currents.

Protista-  Protozoans

1. Protozoans are heterotrophs and live as predators or parasites.
2. They are believed to be primitive relatives of animals.
3. There are four major groups of protozoans. They include:

1. Amoeboid protozoans
2. Flagellated protozoans
3. Ciliated protozoans
4. Sporozoans

Amoeboid protozoans

1.Live in fresh water, sea water or moist soil.

2.Locamotion is by  pseudopodia.

3.Marine forms have silica shells on their surface.

4.Some of them such as Entamoeba are parasites.

Flagellated protozoans

1.They are either free-living or parasitic.

2.Locamotion is by flagella.

3.The parasitic forms cause diaseases such as sleeping sickness.

Example: Trypanosoma.

•          Ciliated protozoans

•          1. These are aquatic, actively moving organisms. 2. Locomotion is by cilia. 3.They have a cavity (gullet) that opens to the outside of the cell surface. 4.The coordinated movement of cilia facilitates food to enter the gullet.

•           Example: Paramoecium

Sporozoans

•           1. This includes diverse organisms that have an infectious spore-like stage in their life cycle.

•          Example: Plasmodium (malarial parasite)

KINGDOM: FUNGI

•          Includes achlorophyllous, eukaryotic, heterotrophic, spore producing, thalloid organisms.

•          Based on the morphology of the mycelium, mode of spore formation and fruiting bodies this kingdom is divided into various classes namely  Phycomycetes, Ascomycetes, Basidiomycetes and  Deuteromycetes.

Characters Of Fungi

              1. They are cosmopolitan and occur in air, water, soil and on animals and plants.

2. The body is haploid and thalloid ( not differentiated into root, stem and leaves)

3. The fungal body is made up of thread like structures called hyphae which cris-cross with one another to form a network known as mycelium.

4. The hyphae may be aseptate and multinucleate and is termed as coenocytic. However in most of the fungi the mycelium is septate.

5.The cell wall is made up of chitin or fungal cellulose.

6. Reserve food material is stored in the form of oil and glycogen.

7. Cells have unicisternal golgi bodies.

8. Mitosis in somatic cells is by karyochorisis type (mitosis followed by intracellular spindle formation).

9. In most of the fungi, there are two distinct phases in the life cycle namely vegetative or assimilative phase and the reproductive phase

10. Reproduction in fungi can take place by vegetative means – fragmentation, fission and budding.

11. Asexual reproduction is by spores called conidia or sporangiospores or zoospores.

12. Sexual reproduction is by oospores, ascospores and basidiospores.

13. The various spores are produced in distinct structures called fruiting bodies.

14. The sexual cycle involves the following  three steps:

(i) Fusion of protoplasms between two motile or non-motile gametes called plasmogamy.

(ii) Fusion of two nuclei called karyogamy.

(iii) Meiosis in zygote resulting in haploid spores.

15. Most fungi are heterotrophic and absorb soluble organic matter from dead substrates and hence are  called saprophytes. Those that depend on living plants and animals are called parasites.

16. Fungi can also live as symbionts – in association with algae as lichens and with roots of higher plants as mycorrhiza.

Fungi :Class Phycomycetes  

1. Members of phycomycetes are found in aquatic habitats and on decaying wood in moist and damp places or as obligate parasites on plants.
2. The mycelium is aseptate and coenocytic.
3.  Asexual reproduction takes place by zoospores (motile) or by aplanospores (non-motile). These spores are endogeneously produced in sporangium.
4. Zygospores are formed by fusion of two gametes. These gametes are similar in morphology (isogamous) or dissimilar (anisogamous or oogamous).

Examples: Mucor , Rhizopus and Albugo.        

Fungi :Class Ascomycetes ( sac fungi)

1. Ascomycetes  are unicellular  ( yeast ) or multicellular (Penicillium).
2. They are saprophytic, decomposers, parasitic or coprophilous (growing on dung).
3. Mycelium is branched and septate.
4.  The asexual spores are conidia produced exogenously on the special mycelium called conidiophores.
5. Sexual spores are called ascospores which are produced endogenously in sac like asci which are arranged in fruiting bodies called ascocarps.

Examples: are Aspergillus, Claviceps and Neurospora, Morels ( edible), Buffles (edible) etc.

Fungi :Class Basidiomycetes

1. They grow in soil, on logs and tree stumps and in living plant bodies as parasites.
2. The mycelium is branched and septate.
3. No asexual spores. Vegetative reproduction is by fragmentation.
4. The sex organs are absent, but plasmogamy is by fusion of two vegetative or somatic cells of different strains or genotypes.
5. The resultant structure is dikaryotic which ultimately gives rise to basidium.
6. Karyogamy and meiosis take place in the basidium producing four basidiospores exogenously.
7.  The basidia are arranged in fruiting bodies called basidiocarps.
8. Includes  mushrooms, bracket fungi or puffballs. Examples: Agaricus (mushroom) , Ustilago (smut) and Puccinia (rust fungus)

Fungi :Class Deuteromycetes

1. Commonly known as imperfect fungi because only the asexual or vegetative phases of these fungi are known. 
2. Perfect (sexual) stages of members of dueteromycetes were discovered and were moved to ascomycetes and basidiomycetes.
3. The deuteromycetes reproduce only by asexual spores known as conidia.
4. The mycelium is septate and branched.
5. Some members are saprophytes or parasites while a large number of them are decomposers of litter and help in mineral cycling.

Examples: Alternaria, Colletotrichum and Trichoderma

Exceptions of Fungi

1. Yeast and synchytrium are unicellular members of Fungi.

2.  In sexual reproduction, in ascomycetes and basidiomycetes an intervening dikaryotic stage occurs;  such a condition is called a dikaryon and the phase is called dikaryophase of fungus.

         KINGDOM: PLANTAE

v  Includes all eukaryotic chlorophyll containing organisms commonly called plants. Cell wall is made of cellulose.

v   Few members are partially heterotrophic such as the insectivorous plants (Bladderwort and Venus fly trap) or parasites (Cuscuta).

v  Plantae includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms.

v  Life cycle of plants has two distinct phases – the diploid sporophytic and the haploid gametophytic that alternate with each other. This phenomenon is called alternation of generation.

              KINGDOM: ANIMALIA

v        Animalia is characterised by heterotrophic eukaryotic organisms that are multicellular and their cells lack cell walls. They directly or indirectly depend on plants for food.

v  They digest their food in an internal cavity and store food reserves as glycogen or fat.

v  Their mode of nutrition is holozoic ( ingestion of food ).

v  The sexual reproduction is by copulation of male and female followed by embryological development.

Viruses, Viroids and Lichens

In the five kingdom classification of Whittaker there is no mention of acellular organisms like viruses and viroids, and lichens.

Viruses: The viruses are non-cellular organisms that are characterised by having an inert crystalline structure outside the living cell. They are  smaller than bacteria

The name virus was given by Pasteur. D.J. Ivanowsky.

Viruses are obligate parasites and are inert outside their specific host cell.

Viruses contain  proteins and genetic material (RNA or DNA).

Viruses cause diseases like  mumps, small pox, herpes and influenza.

Bacterial viruses or bacteriophages (viruses that infect the bacteria) are usually double stranded DNA viruses. Aids in humans is caused by virus.

             Viroids: 

1. T.O. Diener (1971) discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease.
2. It was found to be a free RNA which was of low molecular weight.
3. It lacked the protein coat that is found in viruses, hence named viroid.

           Lichens :

1. Lichens are symbiotic associations between    algae and fungi. The algal component is known as phycobiont (autotrophic) and fungal component as mycobiont (heterotrophic).
2. Algae prepare food for fungi and fungi provide shelter and absorb mineral nutrients and water.
3. Lichens are very good pollution indicators – they do not grow in polluted areas.