Saturday, November 15, 2008

Biodiversity ---2

Loss of Biodiversity
The colonization of Tropical Island by humans is said to have led to extinction of more than 2,000 species of native birds. According the IUCN Red last (2004) 784 species of organisms are extinct in the last 5 years such as vertebrates (338), invertebrates (359), and 87 plants. Some recent examples are the dodo( Mauritius), quagga (Africa) thylacine (Australia).teller’s Sea Cow(Russia) and three subspecies( Bali, Javan, Caspian) of tiger. Recently in last 20 years 27 species disappeared.
Species facing the threat of Extinction are 12%of all bird species, 23% of all mammal species, 32% of all amphibian species and 31% of all gymnosperm species in the world.
Consequences of loss of Biodiversity
1. Decline in plant production
2. lowered persistence to environmental perturbations such as drought
3. Increased variability in certain ecosystems processes such as plant productivity, water use, and pest and disease cycles.
Causes of biodiversity losses
Habitat loss and fragmentation

This is the most important cause of extinction of plant and animals. When the habitat is lost the organisms either dies or moves to new habitats. Rain forest were covering 14% of earth’s land surface but now it is only 6%.The Amazon rain forest (it is so huge that it is called the ‘lungs of the planet’)millions of species cut and cleared for cultivating for growing Soya beans or for conversion to grasslands for raising beef cattle. Pollution is also one of the causes of threatening of many species. When large habitats are broken into small fragments due to various human activity, mammals and birds which needs large areas to live and certain animals with migratory habitats are badly affected, leading to populations declines.
Over-exploitation: Many species in the last 500 years (Steller’s sea cow, passenger pigeon) were extinct due to overexploitation by humans.
Alien species invasions: Sometimes introduction of alien species cause disappearance of native species.
· The Nile perch, an exotic predatory fish was introduced in Lake Victoria in east Africa resulted in elimination of more than 200 species of small Cichlid fish that were endemic in Lake Victoria.
· Invasive weed species like Carrot grass (Parthenium), Lantana threat posed to our native species.
· Water Hyacinth (Eicchornia) has resulted in Chogged Rivers and lakes which has threatened the survival of many aquatic species in lakes and ponds.
· The recent illegal introduction of the African catfish Clarias gariepinus for aquaculture posing a threat to the indigenous catfishes in our rivers.
Co-extinctions: When a species becomes extinct. The plant animal species associated with it an obligatory way also become extinct. When a host fish species becomes extinct its parasites also get extinct. Another example is the case of a coevolved plant- pollinator mutualism where extinction of one invariably leads to the extinction of the other.
Biodiversity Conservation
Why we should conserve Biodiversity?

a. The Narrowly utilitarian reasons: Human get benefits directly from nature such as Food-Cereals pulses fruits, firewood, fibers, construction material industrial products (tannins, lubricants, dyes, resins, perfumes) products of medicinal importance. More than 25% drugs sold in the market are derived from the plants and 25,000 species of plants are used by native people around the world.
b. The broadly utilitarian reasons: Biodiversity plays a major role in many ecosystems services that nature provides. Amazon forest is estimated to produce 20% of the total oxygen in the earth’s atmosphere. Pollination without (which plants cannot give us fruits or seeds)is another service, ecosystems provide through pollinators layer- bees, bumble bees, birds and bats.
c. Ethical: We also derive the aesthetic pleasures of walking through thick woods, watching spring flowers in full bloom or walking up to a bulbul’s song in the morning. This is our moral duty to care for their well being and pass on our biological legacy n good order to future generations.
How do we conserve Biodiversity?
Ex situ Conservation:
1. Hotspots
· To protect the organism biodiversity hot spots regions are identified. Hot spots are the richest and the most threatened reservoirs of plant and animal life. There are two criteria’s for determining the hot spot.
· Number of endemic species.
· Degree of threat, which is determined in terms of habitat loss.
· Initially 25 bio diversity hot spots were identified but now the total number of bio diversity hot spots in the world is 34.

.Three of these hot spots are Western Ghats and Sri Lanka, Indo- Burma and Eastern Himalayas.
· Though the area of bio diversity hot spots cover less than 2% of the total earth’s area but because of strict protection of these hot spots reduce the extinctions rate to 30%.
Bio sphere reserves are the protected area of land. In India there are 14 bio sphere reserves such as Nanda Devi, Sunder Vans. In India 19 National Parks and 448 Wild Life Centuries are present. In our country many plants and animals are sacred and worshiped by local peoples, so trees and wild life within are venerated and given total protection. Such sacred groves are found in Khasi and Jaintia hills in Meghalaya, Aravalli Hills of Rajasthan, and Western Ghats regions of M.P. In Meghalaya, the sacred groves are the last refuges for a large number of rare and threatened plants.
In this conservation threatened animals and plants are taken out from their natural habitat and placed in a place where they can be protected and given special care. Such as Zoological Parks, Botanical Garden, and wild life safari parks.
CRYOPRESERVATION –Gametes OF threatened species can be preserved in viable and fertile condition for long periods using CRYOPRESERVATION techniques. It is a technique by which plants and animals parts can be preserved in liquid nitrogen at a temperature of -196 0C
Eggs can be fertilized in vitro, and plants can be propagated tissue culture methods.
Seed Banks
Seeds of different genetic strains of commercially important plants can be kept for long periods in seed banks.

The historic Convention on Biological Diversity (‘The Earth Summit’) held in Rio de Janeiro in 1992., called upon all nations to take appropriate measures for conservation of biodiversity and sustainable utilization of its benefits. In a follow up, the World Summit on Sustainable Development held in Johensberg, South Africa, 190 countries pledged their commitment to achieve by 2010, to reduce the current rate of biodiversity loss at global, regional and local levels.

Saturday, June 28, 2008

DNA Replication

Origin of replication
For a cell to divide, it must first replicate its DNA. It occurs at S phase of the cell cycle. This process is initiated at particular points within the DNA, known as origin of replication or ‘Ori’. In a bacterium or virus DNA has only one origin of replication. Eukaryotic DNA is a giant molecule so they have number of origins of replication because of its large size and association with proteins. Origins contain DNA sequences recognized by replication initiator proteins (e.g. DNAA in E coli' and the Origin Recognition Complex in yeast).
Initiator proteins recruit other proteins to separate the DNA strands at the origin, forming a bubble. Origins tend to be "AT-rich" (rich in adenine and thymine bases) to assist this process because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair)—strands rich in these nucleotides are generally easier to separate.
Replication actually precedes bidirectional in both prokaryotes and eukaryotes except in coli phage P2 chromosome
Steps of Replication
1. Unwinding of DNA- The two strands of DNA separate. There are enzymes Helicases which unwind the DNA and separate the two strands. It involves breaking the weak Hydrogen bonds present in between the two strands of DNA. Now the two strands are free to act as template. Single stranded DNA binding proteins (SSBS) selectively bind to the single stranded DNA strands to stabilize this condition. Unwinding also creates a coiling of tension. This tension is released by topoisomerase. In prokaryotes topoisomerase and helicases are replaced by DNA gyrases.

2. The replication fork
Whole of DNA does not open in one stretch, due to very high energy requirement, the point of separation proceeds slowly from one end to another, it gives the appearance of Y shape structure called the replication fork
3. DNA strands serve as template. The enzyme DNA polymerase III in E. coli play an important role in adding the buildings blocks (nucleotides) it is a very fast process and the building blocks of DNA are not present in the form of deoxyribonucleotides but in the form of deoxyribonuclesides triphosphates. It is an energy consuming process. Deoxyribonuclesides triphosphates have two roles in DNA replication. It acts as a substrate; it also provides energy for polymerization reaction. As the two terminal phosphates are high energy molecules as in ATP.

4. The enzyme is active only in presence of Mg2+ and preexisting DNA.

5. DNA polymerase cannot initiate the synthesis of DNA. It needs RNA primer, which is a short stretch of RNA formed on the DNA template. The enzyme which polymerizes the RNA building blocks (AUCG) into the primer is known as primase, it contains free 3’OH.
6. DNA polymerase needs a free 3’OH on DNA. After start of nucleotide chain RNA primer is removed by a 5’→ 3’. Exonuclease enzyme.

Leading strand synthesis
The two separated DNA strand in the replication fork function as template. The DNA polymerase can polymerize the nucleotides only in the 5’ → 3’ direction.
Since the two strands of DNA are in ant parallel orientation (opposite direction), One is in 5’ → 3’ direction and the other is in 3'→5' direction. Replication of the two templates proceeds in two opposite direction. The synthesis is continuous in 3’→5' strand as its 3’ end is open for elongation. This strand is known as leading strand.

Lagging strand synthesis
The lagging strand is the DNA strand of replication fork running in the 3' to 5' direction. Because DNA polymerase cannot synthesize in the 3'→5' direction, the lagging strand is synthesized in short segments known as Okazaki fragments. Along the lagging strand's template, primase builds RNA primers in short bursts. DNA polymerases are then able to use the free 3' OH groups on the RNA primers to synthesize DNA in the 5'→3' direction. The RNA fragments are then removed (different mechanisms are used in eukaryotes and prokaryotes) and new deoxyribonucleotides are added to fill the gaps where the RNA was present by DNA polymerase I. DNA ligase then joins the deoxyribonucleotides together, completing the synthesis of the lagging strand.
Proof Reading and DNA repair
A wrong base is sometimes introduced during replication. The frequency is one in ten thousand. DNA polymerase I and III are able to sense the same. It goes back removes the wrong base and allows addition of proper base and then proceeds forward in the 5'→3' direction

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Thursday, June 12, 2008


The occurrence of different kinds of organisms reflects the biological diversity. The term biodiversity refers to the totality of genes, species and ecosystems of a region.
Biodiversity is a term given by sociobiologist Edward Wilson to describe the combined diversity at all the levels of biological organization.
Biological diversity includes three hierarchical levels:
1. genetic diversity
2. species diversity
3. ecological diversity
Genetic diversity:
It refers to the variations of genes, the difference could be in alleles (different variant of the same genes), in entire genes (the traits determining particular characteristic) or in chromosomal structures. The genetic diversity enables a population to adapt to its environment and respond to natural selection. If a species has more genetic diversity it can adapt better to the changed environmental conditions. The genetic variation shown by the medicinal plant Rauolfia vomitora, found in different Himalayan regions, is in terms of potency and concentration of the active chemical (reserpine) that the plant produce. India has more than 50000 genetically different strains of rice and 1000 varieties of mango.

Species diversity:
It refers to the variety of species in the region. Simplest measure of species diversity is species richness i.e. the number of species per unit area. If there are many unrelated species in any sample area then species diversity would be higher. In India for e.g. Western Ghats have greater amphibian species diversity than the Eastern Ghats.

Ecological diversity:
India has deserts, rain forests, mangroves, coral reefs, wet lands, estuaries and alpine meadows which have greater Ecosystem diversity than a Scandinavian country like Norway.
How many species are there on earth and how many species are there in India?
According to IUCN (2004) the total no. of plant and species described on the earth is between 1.5 million which is fewer than 15% of the actual no.
The total no. of species existing on earth ranges from 20-50 million. According to Robert May global species diversity is about 7 million.
Animals 70%
(Insects constitutes major-
70% of animal composition)
Plants (including algae, fungi, 22%
Bryophytes, pteridophytes,
Gymnosperms and angiosperms)
Prokaryotes leftovers
India has only 22.4% of the worlds land area. It shares 8.1% of the global species diversity.
Plant species: 1 lakh
Animal species: more than 3 lakh
Recorded species of plants 45000
Recorded species of animals 90000

Latitudinal Gradients
Bio diversity varies with change in latitude or altitude as we move from high to low latitudes i.e. from the poles to the equator the biological diversity increases in the temperate region the climate is sever with short growing period for plants. In tropical rainforests the conditions are favorable for growth throughout the year so larger no. of species is present. Tropics (latitudinal range of 23.5o N to 23.5o S) have more species then temperate or polar areas.
Colombia located near the equator has nearly 1,400 species of birds
New York at 41o N has 105 species
Greenland at 71o N has 56 species
A forest in a tropical region like Equator has up to 10 times as many species of vascular plants as a forest of equal area in a temperate region like the Mid west of the USA.
Amazonian Rain Forest in South America has the greatest biodiversity on earth.
Q. What is so special about tropics that might account for their greater biological diversity?
1. In temperate regions frequent glaciations are present in the past. In tropical regions latitudes have remained undisturbed for million of years had a long evolutionary time for species diversification.
2. Tropical environments are more constant, less seasonal than temperate that is also responsible foe greater species diversity.
3. There is more solar energy available in the tropics so higher productivity, indirectly one of the cause of greater diversity.
Species diversity decreases from lower to higher altitudes, mountain. With 1000m increase in altitude results in temperature drops of about 6.5 0C this drop in temperature and greater seasonal variability at higher altitudes is major factor that reduces Bio diversity.
Species Area Relationship
German naturalist and geographer Alexander von Humboldt while exploring the wilderness of South American jungles found that within region the species richness increased with increasing area but up to a certain limit. The relationship between species richness and area turned out to be rectangular hyperbola for a wide variety of texa whether they are birds, bats, fresh water fishes or flowering plants. On a logarithmic scale it is a straight line.
Log S = log C + Z log A
Here S is species richness, Z is a slope of line or regression coefficient,
C is intercept while A is area.
The value of regression coefficient (Z) is generally 0.1 to 0.2.regardless of taxonomic group or region e.g. plants in Britain birds in California, or mollusks in New York. If the species area relationship is considered for a very large area like a whole continent regression coefficient or slope of the line comes to have Z value of 0.6 to 1.2, e.g., frugivores and mammals of tropical forests of different continents the slope is found to be 1.15.
The importance of species diversity to the ecosystem
Ecologist believed that communities with more species are more stable than those with less species.
What exactly is stability for a biological community?
A stable community should not show too much variation in productivity from year to year. It must be either resistant or resilient to occasional disturbances (natural or man made) and it must also be resistant to invasions by alien (foreign) species.
David Tillman’s did long term ecosystem experiments using outdoor plots provide some tentative answers. Tillman found that plots with more species showed less year to year variation in total biomass. He also showed that in his experiments more species diversity results in higher productivity.
Does it really matter to us if a few species become extinct?
The Rivet popper hypothesis used by Stanford ecologist Paul Ehrich. In an aero plane (ecosystem) all parts are joined together using thousands of rivets (species). If every passenger traveling in it starts popping a rivet to take home (causing a species to become extinct), I may not affect flight safety (proper functioning of the ecosystem) initially, but as more and more rivets are removed.
Than it also matters which rivet is removed? Removal of key tone species causes serious disruption in the functioning of the community. For Example, in the tropical rain forest, the different species of figs are the key stone species as these produce large quantity of fruits. During the time of food scarcity, these fruits are eaten by monkeys, birds, bats and other vertebrates. So by protecting the fig trees, the animals dependent on them are also conserved.

Thursday, May 29, 2008

Energy Flow

· Plants and photosynthetic and chemosynthetic bacteria (autotrophs) fix sun’s radiant energy to make food from simple inorganic materials. Plants fix only 2-10% of the photosynthetic ally active radiation and this small amount of energy sustain the entire living world. All organisms are depended for their food on producers either directly or indirectly there is unidirectional flow of energy from the sun to producers then to consumers.
· Producers are herbaceous and woody plants in a terrestrial ecosystem. Primary producers in an aquatic ecosystem are various specious like phytoplanktons. Algae and higher plants

Food Chain
· All animals depend on plants directly or indirectly for their food so they are called consumers or hertrotrops. If they feed on the producers, plants, they are called primary consumers. And if the animals eat other animals then they are called as secondary consumers then tertiary consumers and so on.
· Primary consumers – herbivores for e.g. insects, birds, and mammals in terrestrial ecosystem and mollusks in aquatic ecosystem
· Primary Carnivores or secondary consumers- They fed on herbivores. Secondary carnivores feed on primary carnivores.
· Grass…………….Goat…...............................Man
· (Producer) (Primary consumer) (Secondary consumer)
· Organisms occupy a specific place in the food chain is that is known as trophic levels. Producers…I trophic level, Herbivores….II trophic level
· .Each trophic level has a certain mass of living material, at a particular time called as the standing crop. The standing crop is measured as the mass of living organisms (biomass)or the number n a unit area. The biomass of a species is expressed in terms of fresh or dry weight. Measurement of biomass in terms of dry weight is more accurate.
· Detritus food chain begins with dead organic matter. It includes decomposers which feed on dead and decaying matter or detritus. Decomposer is mainly saprotrophs including fungi and bacteria. Decomposers secrete digestive enzymes that break organic matter into simple inorganic material.
· In an aquatic food chain Grazing food chain is the major source of energy flow. In terrestrial ecosystem a much larger fraction of energy flows through the detritus food chain than through GFC. Detritus food chain may be connected with the GFC at some levels. Some of the organisms of DFC are prey to the GFC animals, and in a natural ecosystem some animals like cockroaches, crows, etc are omnivores. These natural interconnections of food chains make it a food web.

· The number of trophic levels in the GFC is not more than 4 or 5.As the transfer of energy follows 10 percent law –only 10 % of the energy is transferred to each trophic level from the lower trophic level. After 4 or 5 trophic levels energy which is left not sufficient to sustain life.

Wednesday, May 28, 2008

Ecological pyramids

Graphical representation of trophic levels of food chain is known as Ecological pyramids.
•The base of each pyramid represents the producers or the first trophic levels, mid herbivores and the apex represents tertiary or top level consumers.
•Common parameters used for constructing ecological pyramids are no. of individuals (pyramid of no.), dry weight (pyramid of biomass), or rate of energy flow (pyramid of energy)

Cycling of nutrients

Standing state: The amount of nutrients such as C,N,P, Ca,etc.,present in the soil at any given time is known as standing crop.
• The movement of nutrient elements through the various components of an ecosystem is called nutrient cycling or biogeochemical cycle.
• Types of Nutrient cycles- 1. Gaseous and 2. Sedimentary. The reservoir for gaseous type of nutrient cycle present in the atmosphere.

The reservoir for Sedimentary type of nutrient cycle present in the earth’s crust. Environmental factors such s soil, moisture, pH, temperature etc., regulate the rate of release of nutrients into the atmosphere.

· Carbon is essential component of all major organic compounds of protoplasm as carbohydrates, fats, proteins and nucleic acids.
· Carbon constitute 49% of the dry weight of the organisms and is next only to water
· In atmosphere .032% CO2 is present. out of the total quantity of global Carbon 71% Carbon is found dissolved in oceans
· CO2 is fixed in the biosphere by the process of photosynthesis by plants. The plans are able to fix carbon by the process of photosynthesis ranging from 4-9 x 1013 per year.
· Carbon fixed by producers enters the food chain and passed to herbivores, carnivores, decomposers.
· CO2 is released in atmosphere by respiration of producers and consumers.
· It is also released by the decomposition of waste materials and dead organic matter by decomposers in land or oceans
· Another source of CO2 is burning of wood, forest fire & combustion of organic matter fossil fuel. Volcanic activities are additional sources for releasing CO2 in the atmosphere.
· Some amount of fixed CO2 is lost to sediments and is removed from circulation. In oceans CO2 remains stored as bicarbonates as lime stone and marble rocks.
Phosphorous is the major constituent of biological membranes nucleic acid and cellular energy transfer systems (ATP). Many animals also need large quantities of this element to make shells, bones and teeth.
· The natural reservoir of phosphorous is rock which contains phosphorous in the form of phosphates.
· The inorganic phosphorous is added to the soil as a result of weathering of phosphate rock. It is absorbed by the roots of the plants.
· Herbivores and other animals take this element from plants.
· After death and decay of organisms phosphorous is recycled due to action of decomposers especially by phosphate - solubilising bacteria releasing phosphorous.
· Phosphorous cycle is different from carbon cycle in two ways :
o There is no respiratory release of phosphorous into atmosphere as in carbon cycle.
o Atmospheric inputs of phosphorous through rainfall are much smaller than carbon

Tuesday, May 27, 2008

Ecosystem -Ecological Succession

Ecological Succession
The successive replacement of communities in an area over a period of time is known as ecological succession.
Types of succession
Primary succession: succession occurring on previously unoccupied sites, such as a bare rock, newly cooled lava, newly created pond or reservoir.
Secondary succession: It occurs in an area where the natural vegetation has been destroyed or removed e.g. the forests destroyed by fire. The reappearance and establishment of communities in such areas is called secondary succession.

Pioneer community- The first biotic community which develops in a bare area is called pioneer community. This stage takes the longest time to change the environment for invasion of the next community.
Pioneer species-The species that invade the bare land initially are called pioneer species.
Seral communities- The pioneer community is replaced by another community. This second community is replaced by a third community, and so on. The different communities or stage like mosses, herbs, shrubs, and trees replacing one another during succession are called seral stages or seral communities.
Climax community- is the stable, self perpetuating and final biotic community that develops at the end of biotic succession and is in perfect harmony with the physical environment. It is termed as climatic climax community. The climax community is stable and does not show changes in species composition, as long as the environmental conditions remain the same.
Sere- The entire sequence of development stages of biotic succession from pioneer to a climax community is known as sere.
Biotic Succession on Bare Rock (Xerarch)
v Lichen and Moss stage
Lichens are the first species to invade the bare rock. They secrete acids to dissolve rock. Helping in weathering and soil formation.
Lichens are normally followed by small plants like mosses (Bryophytes) which can thrive in the small amount of soil. Lichens and mosses speed up the process of soil accumulation by trapping wind blown particles. Mosses grow in bunch, and together with lichens, make a mat over the substratum. Lichens and Mosses are the pioneer species forming he pioneer community
Annual Herb Stage
The mat formed by mosses on the partially fragmented rock provides suitable substratum for the germination of seeds of annual herbaceous plants. These plants have more sand binding properties. Their death and decomposition accumulate more soil so the annual grasses are replaced by perennial grasses.
Shrub Stage
Due to further weathering of rocks and death of the herbs, more soil is accumulated. So the habitat becomes suitable for the growth of shrubs. The shrubs are large in size and their roots penetrate more deeply in the rocky substratum causing more weathering and soil formation. This favours the invasion of the area by next seral stage.
Forest Stage
It is the climax community. Further weathering of rocks and increasing humus content of the soil favors the growth of more trees. Type of climax community depends upon the climate e.g. a rain forest in a moist tropical area; a coniferous forest or deciduous forest in temperate area; grassland in area with less rainfall.
Xerophytic habitat gets converted into a mesophytic one.

Biotic Succession on Water Body (Hydrarch)
In water bodies silting is done as a result of soil erosion from surrounding areas.
In a pond the phytoplankton and zooplankton makes the pioneer community.
Submerged aquatic plants, with their roots are present in the mud.
The dead remains of these organisms settle at the bottom .Floating plant species invade the pond.
Stages of Hydrarch
Phytoplankton and zooplankton stage
Submerged plant stage
Submerged free floating plant stage
Reed swamp stage
Marsh- meadow stage
Shrub stage
Forest with trees
With the continued situation, the pond bottom is gradually raised and water layer becomes shallow and rich in nutrients.
As a result rooted, emergent plants with aerial leaves, such as reeds, are able to live in the pond.
This is followed by the invasion of Dragonflies, crustaceans and more rooted species of plants.
With increasing settling of silt and decomposition of dead organic mater the pond becomes shallower until it gets transformed into a terrestrial habitat. Finally terrestrial species like grasses ,bushes and trees colonies the
pond area and a climax community is established.