Mechanism of DNA Replication

Mechanism of DNA Replication

DNA replication involves four important stages. These are

1. Initiation of DNA replication
2. Unwinding of DNA helix
3. Formation of Primer strand
4. Elongation of new strand

1.Initiation of DNA replication:-

Replication of DNA always begins at a definite site called replication origin. In virus and bacteria there is only one such replication origin present. e.g E-coli.But in eukaryotes there are several thousands of replication origins are present. These linearly arranged units are known as replicons.e.g-

                               Organisms                                      No. of replicons
                                Yeast                                                    500
                                 Drosophila                                          3500
                                 Toad                                                    1500
                                 Mouse                                                 25000
                                 Bean                                                    35000

In Escherichia coli replication is due to multienzyme complex known as replication apparatus or repliosome.

2.Unwinding of DNA helix:-

Now unwinding occurs in the  parental DNA molecule in such a manner that its internal bases are exposed to the replication enzymes.Unwinding  occurs due to a specific enzyme called Helicase or rep protein. This leads to formation of super coils which are then removed by the action of another enzyme called DNA gyrase or Topoisomerase.

Unwinding of DNA molecule separates the two strands to form a Y-shaped structure called replication fork.Then the exposed single strands ae stabilised by a protein called single stranded binding protein (SSB) or the helix destabilizing protein. The SSB proteins holds open the two separated strands to form replication fork.

3.Formation of Primer strand:-

After that opposite to each of the parental strand a new strand is synthesized. The parental strand acts as a template strand. The enzyme which is meant for replication is DNA Polymerase. In prokaryotes it is of three types i.e DP-I ,DP-II  and DP-III. Out of which DP-I and DP-II are concerned with DNA repair where DP-III takes part in actual DNA replication .But in eukaryotes  DNA polymerase is of five types i.e- DP-𝞪, DP-𝜷  ,DP-𝛄, DP-𝞭 and DP-Ɛ. Out of which  DP-Ɛ  takes part in DNA replication.However in both the cases DNA polymerase is incapable of initiating DNA synthesis. It is unable to deposit the first nucleotide in a daughter strand. For that reason another enzyme primase is initiating the synthesis by producing a short primer strand of RNA . Some other enzymes are also involved in this process and are collectively known as primasomes.

This primer strand then elongates and removed enzymatically once the initiation of DNA synthesis is completed. In E.coli DP-I helps in removal of RNA primer. In eukaryotes DP-𝛂 synthesizes primer strand.

4.Elongation of new strand:-

DNA replication takes place in 5'-3' direction. It occurs after the formation of primer strand. At this time deoxyribonucleotides are  added only to the 3'OH end of the new strand. These are ATP,GTP,CTP and TTP. In each of the addition a molecule of pyrophosphate is simultaneously released. Thus the nucleotide at 3' carbon of sugar is always the most recently added nucleotide to the chain.

As proceeds of the two parental strands synthesis of daughter or new strand occurs continuously along the upper strand in 5'-3'OH direction initially  known as leading strand. Similarly synthesis of another daughter strand along the lower parental strand in 3'OH-5'P direction occurs in the form of short pieces known as lagging strand. These pieces are called as okasaki fragments. Those are 1000 to 2000 in number (nucleotide pieces). Later on they joined together by the enzyme DNA ligase to form a continuous daughter strand.

So at the end two DNA molecules are formed from one molecule where each of the daughter DNA is made of one parental or old strand and other new or complementary strand.

Replication of DNA

Replication of DNA

DNA replication means synthesis of DNA.It occurs during the S-phase (synthesis phase) of cell cycle. DNA molecule performs 2 major functions i.e   Autocatalytic  function and Heterocatalytic function.

Whenever a DNA molecule synthesizes another DNA molecule similar to  it at that time it is called autocatalytic function. It is the replication of DNA.But whenever the DNA molecule directs the synthesis of protein, dissimilar in structure compared  to its own structure involving different types of RNAs it is called heterocatalytic function.

There are three possible ways of DNA replication i.e Dispersive,Conservative and Semiconservative.In the dispersive and conservative methods of DNA replication there is no experinmental proof available. In dispersive method of replication the two strands of mother DNA break at several points resulting in several pieces of  DNA.Each piece replicates and pieces are reunited randomly ,so the 2 copies of DNA  molecules are formed from single copy The new DNA molecules are hybrid which have  old and new DNA in patches .In conservative method of replication two DNA molecules are formed. One molecule has both parental strands and the other contains both newly synthesized strands.

Semiconservative method of DNA replication was proposed by Watson and Crick.It  states at the time of DNA replication the two parental strands are seperated.

Then opposite to each of the parental strand a new strand a new strand is synthesized.At this time the separated parental strand serves as a template or guide or model for the formation of new but  complementary strand.So at the end of the DNA replication  from a parent DNA molecule. Two daughter  DNAs  are synthesized where each one contains one parental strand or old strand and other newly formed complementary strand.

This semiconservative mode of DNA replication was experimentally proved by Meselson  and stahl in 1958, from E.coli.

Telome Theory

Telome Theory

It is now widely accepted that the  present day plants with green leaves and branches have evolved from the axial sporophyte of the earliest and most primitive land plants. Devinian Psilophytales which are considered to be the earliest vascular land plants, had a simple dichotomously branched axis with leaves and roots. Some of their terminal branches bore sporangia while other were sterile.The Telome Theory was 1st proposed by the German palaeobotanist Walter Zimmermann in his1930 book entitled "Die Phylogenic de  Pflanzen.

What is Telome?

The name telome has been given to the simple ultimate terminal portions of a dichotomously branched axis. These axes are undifferentiated and single nerved.Two telomes of a dichotomizing axis are united below the point of dichotomy to form a fused structure, called mesome. There are two types of telomes on the basis of their function.

1. Vegetative or sterile telomes-These telomes are without sporangia and they are also called phylloids.

2. Fertile telomes- Those telomes which bore terminal sporangia are called fertile telomes.

During the time of evolutionary development, telomes become grouped together and form a complex structure,is called syntelome or telome truss. When a syntelome consisted of only sterile telomes is called phylloid truss and a fertile truss if it consisted of only fertile telomes and a mixed telome truss or mixed syntelome when it consisted of both sterile and fertile telomes.

Process of  Telome Theory-

Zimmermann suggested that the following five elementary process were responsible for the development of higher vascular plants from the early vascular criptogams.

1. Overtopping
2. Planation
3. Syngenesis
4. Reduction
5. Curvation

1.Overtopping:

In this process one of the two dichotomizing brnches of an axis become laarger, stronger and grew vertically upward as the main axis. The shorter dichotomy was displaced laterally and it served as precursor of megaphylls.

Thus in this process the weaker branch was overtopped by the stronger branch. It resulted in the development of monopodial branches from equal dichotomies. Evolutionary studies have also shown that dichotomous branching is frequent in primitive pteridophytes and monopodial in advanced forms.

2.Planation-:

The equal dichotomies of a system,(cruciate dichotomy) which were in more than one plane come to lie in a single plane (fan-shaped dichotomy).This process, known as planation, helps in the interpretation of the development of organs of bilateral symmetry from those of radial symmetry. Thus, planation must have led to the evolution of leaf.

3.Syngenesis:

In this process, telomes and mesomes came to lie within a common parenchymatous tissue. This process is also known as fusion or webbing. Syngenesis also involves the fusion of vascular strands of telomes. It is an important process which explains the formation of (i)leaves with open dichotomous,pinnatified and reticulate venation and(ii)polystelic condition found in Selaginella and some fossil members of the Devonian and Lower Carboniferous period.

4.Reduction:

It involved transformation of a syntelome into a single needle like leaf. This process thus accounts for the evolution of simple microphyllous leaves of the lycopods.

5.Curvation:

It is brought about by unequal growth of tissues on two opposite flanks of the telome. There are two types of curvation process have been recognized.

• Recurvation:

When telomes bent downwards, it is called recurvation. It is believed that recurved position of sporangia in the Sphenopsida is the result of this process.

• Incurvation:

This process accounts for the shifting of sporangia to the ventral surface of the leaf in ferns.

Merits of Telome Theory:

Telome theory provids an excellent interpretation of the origin and evolution of sporophyte of land plants. It is based on phyletic relationship between the various groups of plants,both living and fossils. The Elementary processes proposed by Zimmermann provide a basis  of interpretation which remove outstanding morphological difficulties in the lower vascular plants.According to Eames (1936),though the theory is built upon structure in the lowest known vascular plants, higher plants can also be safely interpreted in this way. Bierhorst (1971) is of the view that the theory is too simple and too easily applicable but unfortunately its excessive use has greatly diminished its value.

Demerits of Telome Theory:

1. An important drawback of the telome concept is that Zimmermann has taken telome as a ready-made structural unit, without explaining as to how such a structure really came into existence.Although this problem was later realized by Zimmermann himself and he put forward several other elementary processes, but they do not satisfy plant morphologists.
2. Many fossil plants of much greater compllexity than Rhynia have been discovered in the beds of the same age. They bore whorled or lateral sporangia instead of terminal sporangia. The telome theory does not explain such arrangements of sporangia.
3. According to the telome theory ,all leaves in plants are telomic in nature. But Bower(1935) condidered that microphyllous leaves are simply outgrowths of the stem, i.e, they are not the end product of reduction.
4. According to the telome theory,the polystelic condition , such as found in the stem of Selaginella, has developed due to syngenesis and siphonostelic and actinostelic conditions are supposed to be the products of tangential or redial fusion of vascular systems of polystelic axis. Such an explanation is opposed to the widely accepted concept of stelar theory.

Bacteria-Discovery,characters,shape and size

Discovery of bacteria

Bacteria were 1st discovered by a Dutch botanist,Antony von Leeuwenhoek in 1676. He observed them in a rain drop with the help of  a simple microscope designed by him He also gave illustrated account of these microscopic organism from his own teeth scum. These were called 'animalcules' by the early microbiologists. It was Linnaeus (1758) who placed them under the genus vermes.The name Bacteria was given  by a German biologist Christian G. Ehrenberg (1828).However Bacteria as a group were recognised by German botanist, Karl Wilhelm von Nageli (1857) who proposed the name Schizomycetes for this group.

Antony von Leeuwenhoek

Louis Pasteur, a French chemist, observed that bacteria are the cause of   some diseases. This fact was called 'Germ Theory of  Disease". He also discovered bacteria causing chicken cholera. Almost at the same time Robert Koch discovered  bacteria causing anthux and tuberculosis.

General characters of Bacteria

1. Bacteria are the  simplest and the most primitive organisms. They are cosmopolitan and are found in all the places wherever life is possible.
2. Bacteria are considered to be the plants because they have a rigid cell wall.
3. Bacteria are prokaryotes like blue-green algae.
4. Bacteria are strictly unicellular and generally occur singly.Some of them are founds in groups.
5. Bacteria also lack membrane bound organelles like endoplasmic reticulum, golgi bodies,mitochondria,plastids etc.
6. Bacteria lack nuclear membrane and ,therefore, distinct nucleus and nucleoli absent.
7. Most of the bacteria lack chlorophyll,hence they are heterotrophic. However, few bacteria possess chlorophyll and are autotrophic.The chlorophyll  remains scattered in the cytoplasm.
8. Genetic material is represented by histone free DNA.
9. They commonly reproduce vegetatively by  fission.
10. Variations in the genetic characters are due to genetic recombinations brought about by conjugation, transformation and transduction.Flagellated gametes are, however not produced.

Shape of  Bacteria

There are have more than 2000 species of bacteria. and there have 4 fundamental shape are present.

[I]  Bacillus or rod-shaped

These are small stick or rod-shaped bacteria. This shape is the commonest of all the bacterial shapes. Bacilli may occurs in two form.

1. Diplobacillus- In this form two or more bacilli occur in a pair.    e.g,  Corynebacterium diphtheriae.
2. Streptobacillus-In this type many  bacilli occurs in a chain,     e.g,  Bacillus tuberculosis, Bacillus anthracis, etc.

[II]  Coccus or spherical

These  bacteria are  oval or spherical in shape .Cocci are generally non-motile and are the smallest bacteria.Cocci occur in 6 forms.

1. Micrococci-In this type each coccus is a free individual;  e.g,  Micrococcus luteus.
2. Diplococcus-Here cocci remain attached, mostly in pairs,  e.g,  Diplococcus pneumoniae.
3. Streptococcus-In this type cocci form chain;  e.g,  Streptococcus lactis.
4. Tetracoccus-Here four cocci form a characteristic group,  e.g,  Neisseria.
5. Staphylococcus-Cells form irregular groups or bunches, e.g,  Staphylococcus aureus.
6. Sarcinae-This is a type where 8-64 cocci are arranged in cubes, e.g,  Sarcina lutea.

 [III]   Spiral or helical

These bacteria are helical or cork screw shaped or coiled.  e.g,  Spirillum volutans.

[IV]Some other shapes

1. Comma shaped-These are short, incomplete spirals and look like comma (,). They are also known as Vibrio.  e.g,  Vibrio cholerae.
2. Stalked road- These are rod-shaped with a distinct stalk,  e.g,  Caulobacter.
3. Branched filament- The bacterium is long and thread-like,  e.g,  Streptomyces.






4. Pleomorphic-The shape of many bacteria changes according to time, habitat and medium. This characters of existance of different shapes in the same species is called pleomorphism, e.g,  Azotobacter.

Size of Bacteria

Bacteria vary considerably in size. The average size of a bacteria cell  is 0.5-1.0 ×2.0-5.μm Beggiatoa mirabilis is the largest bacterium.(16-45  μm). Bacillus butschlii, with a length of approximately 80  μm is considered to be the longest bacterium. Dialister pneumosintes is probably the smallest bacterium (length  0.15-0.31  μm).

Cell- Defination, Discovery, types and example of cell

Cell

All living bodies on earth are composed of a complex living substance, called protoplasm, which is the physical basis of life.It is found in all living bodies in a small organised morphological form rather than in large mass.These minute organised morphological forms are termed as cells.A living organism under the microscope shows to be composed of either a single cell or numerous cells. Therefore the cells are the structural unit of living body.

The word cell is derived from the greek word kytos, which means a vessel or container.A cell is the smallest unit of life that can replicate independently and cell are often called the "building blocks of life". The science which deals with the cell is called cytology.Cytology may also defined as the branch of science which deals with the study of morphology and internal structure of cells.

Definition of a cell:

A cell may be defined as a piece of nucleated cytoplasm surrounded by a cell wall or a membrane existing singly or in group and containing structures of various kinds.

                                                                         OR

Cell consist of cytoplasm  enclosed within a membrane which contain many biomolecules such as proteins and nucleic acids.

Discovery of the cell

The speculations about the existence of cell in living bodies can be traced back to the time of ancient Greek philosophers. The possibility for a scientific approach on cell arose in the 16th century, after the discovery of microscope by Janssen and Janssen in 1590.

In the year 1665, Robert Hooke, an Englishman, was able to visualise the cells under microscope for the first time. He designed and built an improvised compound microscope and examined the section of  a bottle cork under it. He found that the cork is not a compact mass. It consisted of a number of empty vassels or cavities bounded by definite walls, and thus giving an appearance of a honey-comb.Hooke named each of these cavities as  cell, the term derived from a latin word cellula, means a little room.

Robert Hooke

Types of cell

On the basis of presence and absence of organised nucleus ,two types of cells have been recognized.These are prokaryotic cells and eukaryotic cells.

Prokaryotic cell

(Gr. pro=primitive, karyon=nucleus)

This cell have a well organised nucleus. Organism composed of prokaryotic cells are commonly referred to as prokaryotes. Prokaryotes are considered to be primitive.In prokaryotes the protoplasm is relatively rigid,usually non-vacuolate gel; relatively resistant to desiccation, osmotic shock and thermal denaturation.True nucleus is absent in prokaryotic cell. The membrane bound organelles like  Golgi bodies, plastids, mitochondria ,Endoplasmic Reticulum, etc are absent in these cells. In prokaryotes 70S type of ribosomes is present.Mostly amitotic cell division is occur in prokaryotic cell.Mitotic apparatus is absent.

Examples:Cells of mycoplasma, bacteria, blue -green algae.

Eukaryotic cell

(Gr. Eu=good, karyon=nucleus)

The cell has a well organised nucleus. Organisms made of eukaryotic cell are known as eukaryotes. Eukaryotes are phylogenetically advanced.In eukaryotes the protoplasm is tipically more fluid, generally vacuolate, more sensitive to desiccation, osmotic shock and thermal denaturation. True nucleus is present in eukaryotic cell.Organelles like Golgi bodies, plastids, mitochondira,ER, etc are present  in these cell.In eukaryotes 80S type of ribosomes is present.In these cell tipically mitotic cell division is occur.Mitotic apparatus is present.

Examples:Cells of all the higher organisms, except  mycoplasma, bacteria and blue-green algae.

Function of Nucleus

Function of the Nucleus

The Nucleus is regarded as the centre of many vital activities of the cell.

1. It is concerned with the synthesis of enzymes which catalyze many metabolic reactions.
2. The hereditary factors which influence the characters of plants exist mainly in the nucleus.
3. The nucleus plays an important role in cell division.During cell division it divides first and then the cell divides in to two.Thus by repeated divisions the number of cells increases in the plant body.
4. The nucleus is directly connected with sexual reproduction.The nuclei of male and female gametes fuse together and give rise to the zygote or oospore , from which the embryo develops.
5. Cell nucleus is to control gene expression and mediate the replication of  DNA during the cell cycle.
6. Nucleus contains all the genetic information in its chromatin.
7. Nucleus forms ribosomes  on its nucleolus.
8. The main function of the nucleus is to supports and protects the cell
9. The metabolic reaction is occur in to the nucleus.
10. The nucleus directs all the activities of the cell,controls the growth and reproduction of the cell and contains the blueprints of the cell in the DNA.

Nucleus

What is nucleus?

Nucleus is the most prominent and largest cell organelle present roughly in center of animal cell and on side in a plant cell. It is found in most eukaryotic cells, the exception being red blood cells. It is the small bright body in the head of comet.

structure

Nucleus is a spherical body present inside the cell, surrounded by the cytoplasm.It is bound by a membrane, called  the nuclear membrane, which separates the inner content of the nucleus from the cytoplasm. Nuclear membrane is a double-layered membrane made up of lipo-protein. It is not a continuous membrane as some pores are present at place. These pores are called nuclear pores.Through this pores exchange of various substances takes place  between  the nuclear content and cytoplasm. The inner content of nucleus consists of undifferentiated protoplasm and ground substance known as nuclear sap or nucleoplasm or karyolymph. Inside the nuclear sap a net work of some dark staining thread like structures are present, called the nuclear reticulum or chromatin reticulum. Each of these threads is known as chromatin or chromosome.Chromatin is a characteristic substance in the nucleus.Besides the chromosomes a deeply stained small spherical body is present inside the nucleus, called the Nucleolus.
Each chromosome has a covering,called the matrix, which encloses two identical,spirally twisted, delicate threads known as chromatids. These two chromatids lie very close to each other and are attached to each other only at some points or constriction, called the kinetochore or centromere.


Along the length of the chromatids there are some granular bodies known as chromomeres.Again each chromatids consists of fine thread like structures, called chromonemata.The chromosome is differenciated into some darker staining regions and lighter staining regions,alternating with each other along its length. The darker stained region is called the heterochromatin or the heterochromatic region. The lighter stained region is called the euchromatin or euchromatic region.

Chromosomes consists of nucelic acids and proteins. Nucleic acids are of two types; deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).When these nucleic acids combine with proteins they form deoxyribonucleo-protein and ribonucleo-protein.

Chromosomes are the bearers of all the hereditary characters, and consists of hereditary units or genes. Each gene forms a part of the DNA chain present in the chromosomes. These genes control  all the activities and characters of plants and animals. Therefore, nucleus is the vital part of the cell.
Generally one nucleus is present in each cell of a living organism.But in case of some algae and fungi more than one nucleus  are present. In bacteria and few lower plants (algae) the nucleus is not covered by any membrane and remains undifferentiated inside the protoplast. Such a nucleus is often called incipient nucleus..

cell

cytoplasm

CYTOPLASM

           Within the cell wall the inner content of the cell is the protoplast, which is differentiated in to the cytoplasm and the nucleus. Cytoplasm remains surrounding the nucleus, and thereby it is known as the extranuclear part of protoplast. Optically it appears to be clear and hyaline in nature, consisting of somewhat viscous fluid. It embeds many granular bodies known as organelles. The viscous fluid of the cytoplasm is also termed as hyaloplasm, due to its hyaline appearence. The external surface layer of the cytoplasm lying against the cell wall is called the ectoplasm,while the internal layer around the vacuoles  are called tonoplasm. The granular cytoplasmic substances inbetween these two layers are called the endoplasm.

                                                                                  
         



                  Recent studies with the help of electron microscope reveales that the outermost part of the cytoplasm  i.e, the ectoplasm from a membrane or a bounding wall, also called as plasmamembrane. It remain close to the cell wall and  thus sarves as a boundary layer inbetween  the outer non living wall and internal cytoplamic ground substance or cytoplasmic matrix. Chemically plasmamembrane is  composed of protein and phospholipid, in such a way  that a layer of phospholipid is enclosed  on either  sides by two layears of protein. This lipo-protein  composition of the membrane offers it a semipermeable nature i.e, it allows only few selective compounds to pass through it. Therefore, it is otherwise known as semipermeable membrane or selectively permeable membrane. Some authors refers it also as unit membrane, and regard that lipo-protein composition is a characteristic of all the cell membranes.
             
                The various components of the  cytoplasm distributed over  the hyaloplasm are mainly vacuoles,organelles, and other living and non-living substances.

Vacuoles

               Vacuoles are the greatly expanded cavities inside the cytoplasm, filled with watery fluid or the sap. In matured cells two or three vacuoles may be present, and their size increase with the increase of the size and age of the cell. In meristematic cells the vacuoles are minute or even absent. Each vacuole is bounded by a plasmamembrane, known as  tonoplasm or tonoplast.
                                                                                           

 Organelles or Subcellular particles

                Organelles are the living bodies of different structures having some definite functions, and found suspended inside the cytoplasm. The chief organelles present inside the plant celles are plastids, mitochondria, endoplasmic reticulum, ribosomes, golgi bodies, lysosomes, spherosomes and centrosomes.
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branches of botany

26 branches of botany

1. Morphology (morphe=form, logos=science):Under this branch we study the form and structure of plant.That branch of morphology which is based upon the external form and  structure of plant is called External Morphology.
2. Anatomy:The study of internal structure of the plant with the help of section cutting, is called Internal Morphology.    
3. Cytology:Detailed study of the cell is called cytology. It includes structure, function of  different cell organelles, nucleus and cell inclusions.
4. Histology: The study of cell and tissues with the help of microscope is called histology.
5. Plant Physiology: This branch includes the study of various vital activities of the plant.
6. Taxonomy: In this branch the plants are classified according to their characteristics and interrelationship. With the help of taxonomy we are able to identify the plants and known their characters.
7. Ecology(Oikos=house, logos=science): The study of environment of plants and their communities and vice-versa. This branch also includes the studies of soil erosion, soil conservation and pollution.
8. Plant geography: This branch deals with the distribution of plants on the earth and reasons thereof.
9. Genetics: Study of heredity and variations. What are the laws of inheritance and why the offspring resembles or differs  for the parents are studies under this group.
10. Plant breeding: dealing with the development of improved varities of plants.
11. Embryology:Study the parental development of gametes,fertilization, and development of embryos and fetuses.
12. Paleobotany: the study of fossil plant.
13. Economic botany: The study of the relationship between people (individuals and cultures) and plant.
14. Plant pathology: The scientific study of diseases in plants caused by pathogens and environmental conditions.
15. Biochemistry: The study of chemical processes within and relating to living organisms.
16. Biophysics: This is an interdisciplinary science that applies the approaches and methods of physics to study biological systems.
17. Organic evolution: The study of the evolution of complex organisms from simple ones and the principles involved in it.
18. Microbiology: Study of microorganisms.
19. Molecular biology: Study of biochemistry at molicular level.
20. Palynology: Study of pollen grains in relation to taxonomy and evolution etc.
21. Biometrics: Statistical analysis of different results of biological experiment.
22. Genetic Engineering: Adding,removing or repairing part of genetic meterial, thereby changing the phenotype of organism and desired.
23. Agronomy: Is the science which deals with the crop plants.
24. Horticulture: Is the science which deals with the  study of  flowering fruiting plants.
25. Pharmacognosy: Dealing with the medical plants.
26. Pedology: Dealing with the  study of soils.