Biology With Tanveer Kurd Behramshahi Mastung.

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Introduction to Biology. Biology. Is the study of living things.It is a branch of science and like other sciences and it is a way of understanding nature.The word Biology is derived from the Greek word "Bios" meaning life and "Logos" meaning to study so the literal meaning of biology is the study of life. Biologist The person who study biology is biologist.Biologists deal with the living part of nature and with the non-living things which affect the living things in anyway which strive to understand explain, integrate and descrribe the natural word of living things. ................................................................. Aspects of Biology. Biology is the study of life but there are certain aspects of life that lie beyond the scope of the science of biology like the answers to the questions. What is the meaning of life? Why should there be life? These are the questions not usually taken up by biologists and are left to philosophers and theologiens.Biologists mainly deal with the matters relating to how life works. ................................................................. What is life? It is very difficult to define life.However, life for biologists, is a set of characteristics that distinguish living organisms from nonliving objects ( objects including dead organisms). ................................................... ............ Characteristics of living things.(living organisms). 1. Are high organized. 2. Are complex entities. 3. Are composed of one or more cells. 4. Contain genetic program of their Characteristics. 5. Can acquire and use energy. 6. Can carry out and control numerous chemical reactions. 7. Can grow in size. 8. Maintain fairly internal constant environment. 9.Produce offspring similar to themselves. 10. Respond to change in their environment. And objects possessing all these characteristics simultaneously can be declared as a living thing and is an object for biological studies. ................................................................. Why we classify the biology? The science of biology is a very wide based study. Itincludes very aspects of living things. Therefore, volumes and volumes of information are available under this major head. It is but natural divide this science into quite a number of branches for our convenience of comprehending studying biology. .................................. ............................ Some Major fields of Biology Embryology A branch of biology dealing with embryos and their development.It deals with process of development of an individual from the zygote to whole organism. Physiology The branch of biology that deals with the normal functions of living organisms and their parts. Morphology It is a branch of biology dealing with the study of form and the structure of organisms and their specific structural future. It may be. External morphology. This includes aspects of the external appearance ( shape,structure,colour, pattern,size) of an organism. Internal morphology or anatomy. It deals with internal gross structure of parts of an organism. ................................................. ............... Histology It is microscopic study of tissue of an organism. paleontology It is a branch of biology dealing with study of fossils. It is the way of getting information about history of early life. Evolution It is the process by which kinds of living organisms are thought to have developed from earlier forms during the history of the earth. Genetics The branch of biology that deals with heredity information especially the mechanism of heredity transmission from parents to offspring. Zoogeography The biological study of the geographic distribution of animals, on earth especially the causes of such and effects of such distribution. Taxonomy It is a branch of biology that deals with the description,identification,nomenclature, and classification of organisms. Cytology The branch of biology concerned with the structure and function of cells. Molecular Biology Molecular biology is a branch of biology which deals with the structure of organisms, the cells and their organelles rganic evolution. Evolution refers to the processes that have transformed life on earth from its earliest forms to the vast diversity which is observed today. Evolutionary change is based mainly on the interactions between populations of organisms and their environments. CONCEPT OF EVOLUTION VS SPECIAL CREATION In a bid to explain the cause of diversity of life and interrelationship among living organisms, two schools of thoughts emerged in the earlier 19th century. Creationists believed in the Theory of Special Creation, whereas evolutionists believed in the Theory of Natural Selection. Theory of creation According the theory of special creation, all living things came into existence in their present forms especially and specifically created by Nature. Among the scientists who believed in divine creation was Carolus Linnaeus (1707-1778). Theory of evolution. The idea that organism might evolve through time, with one type of organism giving rise to another type of organism, is an ancient one, existing from the days of Aristotle. Aristotle recognized that organisms ranged from relatively simple to very complex structures. However, the present day concept of evolution is based on a known history Darwin was the first person who argued from evidences that species were not specially created in their present forms, rather they had evolved from ancestral species. He also proposed a mechanism of revolution, which he termed Natural Selection. Carolus Linnaeus in the eighteenth century classified organisms. He grouped similar species in the same genus and similar genera in one family. But as a natural theologian, he believed that species were permanent creations. A century later, the taxonomic system of Linnaeus became of focal point in Darwin’s arguments for evolution. ENZYMES Definition Enzymes are the most important group of proteins which are biologically active. They tremendously increase the efficiency of a biochemical reaction and are specific for each type of reaction. Importance Without these enzymes the reaction would proceed at a very slow speed making life impossible. Composition Enzymes are composed of hundreds of amino acids. These amino acids are brought closer and are arranged in a specific way by coiling and folding of the polypeptide chain within the globular symmetry of the enzyme Active Site. The catalytic activity is restricted to a small portion of the structure known as the active site. Substrate. The reactant called substrate is attached to the active site and converted into product. Active site consisting of only a few amino acids. While rest of the bulk of the amino acids maintains the globular structure of the enzyme. ofactors Definition. Some enzymes consist solely of proteins. Others also have a non-protein part known as a co-factor, which is essential for the proper functioning of the enzymes. Functions. The cofactor usually acts as “bridge” between the enzyme and its substrate, It contributes directly to the chemical reactions which bring about catalysis. Sometimes the co-factor provides a source of chemical energy, helping to drive reactions which would otherwise be difficult of impossible. Fig. shows: Substrate molecules will not fit correctly at the active centre and there will be no catalytic action unless the cofactor molecule is also present. Activators Some enzymes use metal ions as co-factors and this detachable co-factor is known as an activator if it is an inorganic ion. Examples: DNA polymerase uses Mg2+ and Carbonic anhydrase uses Zn2+ Prosthetic Group If the non-protein part is covalently bonded, it is known as a prosthetic group. Example: Cytochrome enzymes use haem group. Coenzymes If it is loosely attached to the protein part it is known as coenzyme. It is closely related to vitamins, which represent the essential raw materials from which coenzymes are made. Only small quantities of vitamins are needed because, like enzymes, co-enzyme can be used again and again. Examples Nicotinamide Adenine dinucleotide (NAD). Flavin Adenine dinucleotide (FAD) Differentiate Holoenzyme and Apoenzyme? An enzyme with its coenzyme, or prosthetic group, removed is designated as apoenzyme.It is inactive enzyme, Adding the correct concentration of coenzyme to the apoenzyme will restore enzyme activity. It consists of only protein. Example: Pepsinogen An activated enzyme consisting of polypeptidechain and a cofactor is known as holoenzyme. It is an activated enzyme. It consists of both protein and non protein parts. Example: Pepsin Location of enzymes Many enzymes are simply dissolved in the cytoplasm. Other enzymes are tightly bound to certain sub cellular organelles. They are produced by living cells for use in or near the site of their production. The enzymes important in photosynthesis are found in the chloroplasts and Enzymes involved in cellular respiration are found in the mitochondria. Some of the enzymes involved in the synthesis of proteins are integral part of ribosomes. Why some enzymes secreted in inactive form? Some enzymes are potentially damaging if they are manufactured in their active from. For example, pepsin is a powerful protein – digesting enzyme and is quite capable of destroying cell’s internal structure and thus is produced in inactive pepsinogen form by the cell. It is converted in its active from only in the digestive tract where it is required to be active. Characteristics of enzymes. All enzymes are globular proteins. They increase the rate of reaction without themselves being used up. Their presence does not affect the nature of properties of end products. Small amounts of an enzyme can accelerate chemical reaction. They are very specific in their action; a single enzyme catalyzes only a single chemical reaction or a group of related reactions. They are sensitive to even a minor change in pH, temperature and substrate concentration. Some enzymes require a co-factor for their proper functioning. They lower the activation energy of the reactions. Why enzymes are specific in nature? An enzyme is a three dimensional globular protein that has specific chemical composition due to its component amino acids and a specific shape. Every enzyme by virtue of its specificity recognizes and reacts with a special chemical substance called substrate. Any enzyme, therefore, reacts only with its specific substrate and transforms it into products(s). It is then released unaltered and thus can be used again and again. Enzyme Chain to Chain Association In certain cases enzymes act in a series of chemical reactions in a particular order to complete a metabolic pathway such as respiration or photosynthesis. The successive enzymes containing these reactions are normally present together in a precise order of reaction such that substrate molecules can be literally handed on’ from one enzyme to another forming an enzyme to enzyme chain. In this way the products from one step in pathway are transferred to the enzyme. Feed Back Inhibition. Feedback inhibition, is inhibition of the activity of an enzyme, by end product of metabolic pathway when it exceeds the limits. Active site Definition An enzyme and its substrate react with each other through a definite charge-bearing site of an enzyme called active site. It may also be defined as The catalytic activity is restricted to a small portion of the structure known as the active site. Composition The charge and shape of the active site is formed by some amino acids present in polypeptide chain of enzyme. Regions The active site of the enzyme is made up of two definite regions i.e the binding site and the catalytic site. Binding site. The binding site helps the enzyme in the recognition in the recognition and binding of a proper substrate to produce an ES complex. This reaction activates the catalytic site. Catalytic site. It catalyzes the transformation of the substrate into product (s). Thus the enzyme after catalysis detaches itself from the products unchanged. Point To be Memorize Most enzymes do not float about in a kind of cytoplasmic ‘soup’ but are attached to membranes systems inside the cell in specific and orderly arrangements. Mitochondria and chloroplasts are good examples of this. Models of Enzymes Lock and key Model Proposed by Emil Fischer (1890) proposed a lock and Key model to visualize substrate and enzyme interaction. Statement According to this model, as one specific key can open only a specific lock, in the same manner a specific enzyme can transform only one substrate into products(s). Flexibility Active site is rigid structure. There is no modification or flexibility in the active site before. During or after the enzyme action and it is used only as a template. a template. Acceptance Later studies did not support this model in all reactions. Induce Fit Model Proposed by On the basis of new evidences Koshland (1959) proposed its modified form. This is known as induce fit Model. Statement According to this model when a substrate combines with an enzyme, it induces changes in the enzyme structure. The change in structure enables the enzyme to perform its catalytic activity more effectively. Flexibility Active site is flexible and may be modified during enzymatic actions. Acceptance This is most accepted model. Factors Affecting the Rate of Enzyme Action Factors The functional specificity of every enzyme is the consequence of its specific chemistry and configuration. Any factor that can alter the chemistry and shape of an enzyme can affect its rate of catalysis. Enzyme Concentration The rate of reaction depends directly on the amount of enzyme present at a specific time at unlimited substrate concentration. If the amount of enzyme is increased by two fold the reaction rate is doubled. rate is doubled. Reason By increasing the enzyme molecules an increase in the number of active sites takes place. More active sites will convert the substrate molecules into product(s), in the given period of time. After a certain limiting concentration, the rate of reaction will no longer depend upon this increase. Substrate Concentration At low concentration of substrate the reaction rate is directly proportional to the substrate available. At high concentration. If the enzyme concentration is kept constant and the amount of substrate is increased, a point is reached when a further increase in the substrate does not increase the rate of the reaction any more. This is because at high substrate in the substrate all the active sites of the enzymes are occupied and further increase does not increase the reaction rate. This is said to be saturation. Temperature The rate of enzyme controlled reaction may increase with increase in temperature but up to a certain limit. Every 10 C rise in temperature doubles the enzymatic reaction. Optimum Temperature All enzymes can work at their maximum rate at a specific temperature called as optimum temperature. For enzymes of human body 37°C is the optimum temperature. Effect of increase Heat provides activation energy and therefore, chemical reactions are accelerated at high temperatures. Heat also supplies kinetic energy to the reacting molecules, causing them to move rapidly. Thus the reactants move more quickly and chances of their collision with each other are increased. Denaturation. However, further increase in heat energy also increases the vibrations of atoms which make up the enzyme molecule. If the vibrations become too violent, globular structure essential for enzyme activity is lost and the enzyme is said to be denatured. Non competitive inhibitors Definition They form enzyme inhibitor complex at a point than the active site. They alter the structure of the enzyme in such a way that even if genuine substrate binds the active site, catalysis fails to take place. Examples Pyruvate kinase that catalyzes final step of glycolysis is non competitively inhibited by Alanine. Non-competitive Inhibition. ntroduction Humans, like other species, are part of the earth’s environment. The first humans were hunters and had low population. At the time, humans functioned as natural predators and herbivores. With the adoption of agriculture, some 10000 years ago human populations and conversion of land to agricultural production began to increase readily. Industrialization changed the nature of human interaction with the global environment. The demand for energy to run industry and the concentration of populations or urbanization brought environmental problems of great magnitude. Environment Surrounding of an organism including both living and living things is regarded as environment. Significance. It is a treasure of all types of resources essential to maintain life on earth. Environment is a direct or indirect source of food, shelter, clothing, fuel etc. for humans. Environmental Resources. Environmental resources are the primary sources for the existences of humans. These resources are either renewable or non-renewable. Renewable resources. Air, water, food, land, forests and wild life are renewable resources because they are never depleted. They are recycled in nature. Non-renewable resources These include various metals, non-metallic minerals and fossil fuels (coal, oil and natural gas). These resources are exhaustable and once consumed cannot be replaced. Nutrient Cycles. In nature, there is no such thing as waste; dead materials decay and become food for other living things. This food is consumed, or decays and becomes food again. This is the nutrient cycle, the process that supplies food to living things.All resources necessary for life form a part of natural cycles. These cycles have no beginning and no end. The driving force behind all of these cycles in the sun. Upsetting of cycle. The balance in the nutrient cycle can be upset when: not enough food is produced, Too much food is consumed, Decayed nutrients are not returned to the ground. The earth is a self-sustained unit. We are in our own space ship. There are no chances of bringing in more resources. We have to use wisely what we have. Renewable Resources Renewable resources are such type of resources, as you can use again and again. There is a natural cycle to make them reusable that is why they are called renewable resources. Some of the renewable resources are discussed below Air: It is several kilometers thick blanket of atmosphere surroundings the earth. Air is very important natural resources. Composition. It consists of nitrogen (79%), oxygen (20%), carbon dioxide (0.03%) and traces of inert gases called noble gases. Uses Oxygen is consumed in respiration and along with it, CO_2 and nitrogen are raw materials in a natural cycle for making food and other substances required by living systems. Air Pollution. Air is being polluted rapidly due to industrialization and automobiles. Polluted air contains certain gases, like carbon monoxide, hydrocarbons and oxides of nitrogen and Sulphur. Greenhouse effect and acid rains are global effects of the pollution. Water: About 70% of the earth surface is covered with water. It is also component of soil and air. It is also major constituent of living organisms, comprising 70-90% of their body weight. About 97% of the total water of planet earth is in ocean, 2 % water is in the form of frozen ice-caps and only 1% as available fresh water in lakes, streams and rivers. Use of Water: Main use of water is: (i) domestic/industrial use 10% (ii) Irrigation 90%. It is very important as raw material in making variety of food stuff, liquid drinks, detergents and many other products. From seawater, we obtain sodium chloride (table salt), which is used in cooking and manufacture of other useful chemicals such as chlorine and sodium hydroxide. Water Pollution . Industrial chemical wastes are extremely toxic. They inhibit the natural purification of water carried out by microorganisms. Chemical wastes degrade the river water and make it harmful for aquatic life. If pollution of fresh water resources continues, we will soon run out of fresh water supply. These measures should be taken to avoid or improve this. Land and Soil: Land is an important natural resource. Soil can be defined as “the upper layer of earth’s crust.” Constituents. The basic constituents of soil are soil particles, soil water, soil air and inorganic matter and soil organisms. Uses. Soil plays a very vital role in supporting life on land, land plants depend directly on soil to be anchored firmly. Soil provides water, organic and inorganic nutrients to the plants. Abuse of Land. Only 30% of earth is land. Man is terrestrial animal and his increasing population makes more use of land, 11% of the total area of the world is under cultivation. Soil is continuously being depleted of its mineral nutrients, due to vigorous crop production. Land may also be abused in many ways like erosion, poor agricultural practice, extensive grazing, leeching etc. Rapid urbanization is also a factor in disturbing the natural land conditions. Fertilizer, insecticides and pesticides are also polluting the soil. To conserve soil, proper awareness is required; farmers and general public may be educated through media. Wild Life: In general, wild life refers to all non-cultivated plants and non-domesticated animals. Human Intervention. All living organisms are interdependent. There is a delicate balance between living organisms and environment. Man has been disturbing this balance since very long. Man’s decisions regarding the usefulness or harmfulness of the wild life have led to severe disturbances in natural habitats. Extinction of Species. As result human intervention many animals and plants have either become extinct or else in their number as to be on the verge of extinction. These are known as the endangered species. Today there are thousands of endangered plants and animals. Wildlife is a renewable resource but it can become non-renewable under extreme conditions of human intervention. Importance of wild life. Games animals and plants have been major source of food for humans Wild life plays very important role in food chain. Without these, the food chain can be disturbed to such an extent that it will be very difficult to maintain the balance. Need of Conservation . The effects of changes in the environment brought about by man are becoming more and more apparent with the passage of time. He must keep the wild life balance; otherwise, it may also jeopardize his own existence. There are several ways to conserve the wild life, for examples: Water reserves where fishing is prohibited have also been set up to protect marine life. Rare species are sometimes kept in zoo, where they can safely breed. Introduction. Questions of origins of earth and life on it have been on the minds of humans since prehistoric times. Many of us are also concerned with questions of origin: How old is the planet earth? How long has life been on earth? How did life arise on earth? How did a certain animal species come into existence? Answers for these questions come from scientific inquiry. In this chapter we will study some aspects of organic evolution. Evolution. Evolution refers to the processes that have transformed life on earth from its earliest forms to the vast diversity which is observed today. Evolutionary change is based mainly on the interactions between populations of organisms and their environments. CONCEPT OF EVOLUTION VS SPECIAL CREATION In a bid to explain the cause of diversity of life and interrelationship among living organisms, two schools of thoughts emerged in the earlier 19th century. Creationists believed in the Theory of Special Creation, whereas evolutionists believed in the Theory of Natural Selection. Theory of creation According the theory of special creation, all living things came into existence in their present forms especially and specifically created by Nature. Among the scientists who believed in divine creation was Carolus Linnaeus (1707-1778). Theory of evolution. The idea that organism might evolve through time, with one type of organism giving rise to another type of organism, is an ancient one, existing from the days of Aristotle. Aristotle recognized that organisms ranged from relatively simple to very complex structures. However, the present day concept of evolution is based on a known history Darwin was the first person who argued from evidences that species were not specially created in their present forms, rather they had evolved from ancestral species. He also proposed a mechanism of revolution, which he termed Natural Selection. Carolus Linnaeus in the eighteenth century classified organisms. He grouped similar species in the same genus and similar genera in one family. But as a natural theologian, he believed that species were permanent creations. A century later, the taxonomic system of Linnaeus became of focal point in Darwin’s arguments for evolution. EVOLUTION FROM PROKARYOTES TO EUKARYOTES Vent Hypothesis. (Origin of life) One of the speculations trying to explain the origin of life is that it may have begun deep in the oceans, in underwater hot springs called hydrothermal vents. These vents could have supplied the energy and raw materials for the origin and survival of early life forms. Evidence. A group of bacteria, called archaeobacteria, that tolerate temperatures up to and seem to have undergone less evolutionary change than any other living species supports this vent hypothesis. Evolution of Photosynthesis. Need The nutrients produced in the primitive environment would have limited early life. If life were to continue, another source of nutrients was needed. Photosynthesis, probably freed living organisms from a dwindling supply of nutrients. Release of Oxygen The first photosynthetic organisms probably used hydrogen sulfide as a source of hydrogen for reducing carbon dioxide to sugars. Later, water served this same purpose, and oxygen liberated by photosynthetic reactions began to accumulate in the atmosphere. Formation of oxidizing Environment Earth and its atmosphere slowly began to change due to oxygen accumulation. Ozone in the upper atmosphere began to filter ultraviolet radiation from the sun, the reducing atmosphere slowly became an oxidizing atmosphere, and at least some living organisms began to utilize oxygen. About 420 million years ago, enough protective ozone had built up to make life on land possible. Ironically, the change from a reducing atmosphere to an oxidizing atmosphere also meant that life could no longer arise abiotically. Evolution of Eukaryotes The first cells were most likely very simple prokaryotic forms. The prokaryotes may have arisen more than 3.5 billion years ago. Eukaryotes are thought to have first appeared about 1.5 billion years ago. There are few hypothesis for evolution of eukaryotes. Endosymbiots Hypothesis. Evolution of eukaryotic membrane bound organelles was related with development of symbiotic relationship between organisms of past. This idea was first proposed by Lynn Margulis. According to this hypothesis, Mitochondria have evolved when a large anaerobic (living without oxygen) amoeboid prokaryote ingested small aerobic (living with oxygen) bacteria and stabilized them instead of digesting them. The aerobic bacteria developed into mitochondria, which are the sites of aerobic respiration and most energy conversion in eukaryotic cells. The possession of these mitochondria like endosymbionts brought the advantage of aerobic respiration of the host. Flagella (whip like structures) may have arisen though the ingestion of prokaryotes similar to spiral-shaped bacteria called spirochetes. Chloroplast have evolved when Ingestion of prokaryotes that resembled present-day cyanobacteria could have led to the endosymbiotic development of chloroplasts in plants Membrane invagination Hypothesis Another hypothesis for the evolution of eukaryotic cells proposes that the prokaryotic cell membrane invaginated (folded inward) to enclose copies of its genetic material this invagination resulted in the formation of several double membrane- bound entities (organelles) in a single cell. These entities could then have evolved into the eukaryotic mitochondrion, nucleus, chloroplast etc. Increase in Diversity Whatever the exact mechanism for the evolution of the eukaryotic cell might be the formation of the eukaryotic cell led to a dramatic increase in the complexity and diversity of life-form on the earth. Evolution of Multicellular organism. At first, these newly formed eukaryotic cells existed only by themselves. Later, however, some probably evolved into multicellular organisms in which various cells became specialized into tissues, which, in turn formed organs for many different functions. These multicellular forms then adapted themselves to life in a great variety of environments. INHERITANCE OF ACQUIRED CHARACTERISTICS Lamarckism. Toward the end of the eighteenth century, several naturalists suggested that life had evolved along with the evolution of earth. But only one of Darwin’s predecessors developed a comprehensive model that attempted to explain how life evolves. Jean Baptiste Lamarck (1744-1829) published his theory of evolution in 1809, the year Darwin was born. Lamarck was in-charge of invertebrate collection at the Natural History Museum in Paris. He presented a mechanism to explain how specific adaptations evolve. Jean Baptiste Lamarck (1744-1829) published his theory of evolution in 1809, the year Darwin was born. Lamarck was in-charge of invertebrate collection at the Natural History Museum in Paris. He presented a mechanism to explain how specific adaptations evolve. Lamarckism. This theory includes use and misuse of organs and inheritance of acquired characteristics. Use and misuse of organs. Lamarck argued that those parts of the body used extensively to cope with the environment become larger and stronger, while those that are not used deteriorate. Example 1. Among the examples Lamarck cited were the blacksmith developing a bigger bicep in the arm that works the hammer Example 2. Giraffe stretching its neck to new lengths is pursuit of leaves to eat. Inheritance of acquired characteristics. The second idea Lamarck adopted, was called the inheritance of acquired characteristics. In this concept of heredity, the modifications an organism acquires during its lifetime can be passed along to its offspring Example. , Lamarck reasoned, the long neck of the giraffe, evolved gradually as the cumulative product of a great many generations of ancestors stretching higher and higher. Dismissal of Lamarckism Weismann conducted the experiment of removing the tails of 68 white mice, repeatedly over 5 generations, and reporting that no mice were born in consequence without a tail or even with a shorter tail. These experiment clearly showed that acquired characteristics cannot be inherited. arwinism. Observations on American Coastline. He observed and collected thousands of specimens of diverse fauna and flora of South America. He noticed that the fauna and flora of the different regions of the continent had a definite South American stamp, very distinct from the life forms of Europe. Furthermore, the South American fossils that Darwin found, though clearly different from modern species, were distinctly South American in their resemblance to the living plants and animals of that continent. Observations on Galapagos Islands. A particularly puzzling case of geographical distribution was the fauna of the Galapagos Islands. Most of the animal species on the Galapagos live nowhere else in the world, although they resemble species living on the South American mainland. It was as though the islands were colonized by plants and animals that strayed from the South American mainland and then diversified on the different islands. Darwin finches. Among the birds Darwin collected on the Galapagos were 13 types of finches that, although quite similar, seemed to be different species. Some were unique to individual islands, while other species were distributed on two or more islands that were close togethe. Quetta library Fatima Jinnah road Quetta. 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