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

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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

please view this site.

http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

Biodiversity

BIODIVERSITY
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.

COMPOSITION:
Animals 70%
(Insects constitutes major-
70% of animal composition)
Plants (including algae, fungi, 22%
Bryophytes, pteridophytes,
Gymnosperms and angiosperms)
Prokaryotes leftovers

COMPOSITION OF ORGANISMS IN INDIA:
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

PATTERNS OF BIODIVERSITY
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?
Ans.
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.