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Yvonne Choo Shuen Lann November 28, 2009 Photosynthesis Light Reaction During the light reaction, chlorophyll captures light energy which excites the electrons of chlorophyll molecules to higher energy levels. In the excited state, the electrons leave the chlorophyll molecules. Light energy is also ...

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Yvonne Choo Shuen Lann November 28, 2009 Photosynthesis Light Reaction During the light reaction, chlorophyll captures light energy which excites the electrons of chlorophyll molecules to higher energy levels. In the excited state, the electrons leave the chlorophyll molecules. Light energy is also used to split the water molecules into hydrogen ions and hydroxyl ions. This reaction is known as the photolysis of water. 24H2O → 24H++ 24OH(light and chlorophyll)

The hydrogen ions then combine with the electrons released by the chlorophyll to form hydrogen atoms. 24H++24e-→24H The energy from the excited electrons is used to form energy-rich molecules of ATP. At the same time, each hydroxyl ion loses an electron to form a hydroxyl group. This electron is then received by the chlorophyll. 24OH-→24OH+24eThe hydroxyl groups then combine to form water and gaseous oxygen. 24OH→12H2O+6O2 Oxygen is released into the atmosphere and used for cellular respiration. The ATP molecules provide energy while the hydrogen atoms provide reducing power for the dark reaction which takes place in the stroma.

Dark Reaction The dark reaction is also known as the Calvin cycle. It is light independent. During the dark reaction, the hydrogen atoms are used to fix carbon dioxide in a series of reactions catalysed by photosynthetic enzymes. The overall reaction results in the reduction of carbon dioxide into glucose. 6CO2+24H→6(CH2O)+6H2O (CH2O) is a basic unit of glucose. Six units of it combine to form one molecule of glucose. The glucose monomers then undergo condensation to form starch which is temporarily stored as starch grains in the chloroplast. The entire process can be represented by the following equation. 6H2O+6CO2→C6H12O6+6O2

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Yvonne Choo Shuen Lann November 28, 2009

Respiration Aerobic Respiration Aerobic respiration requires a continuous supply of oxygen from the air or water surrounding the organism. Oxygen that is taken in is delivered by the blood circulatory system to the body cells. In the cells, glucose molecules are oxidised by oxygen to release energy. Aerobic respiration can be summarised by the following chemical equation: C6H12O6+6O2→6CO2+6H2O+2898kJ Aerobic respiration involves the oxidation of glucose in the presence of oxygen to carbon dioxide, water and energy. Organisms that respire aerobically are called aerobic organisms. Aerobic respiration releases all the available energy stored within the glucose molecules. The entire process does not only involve a single chemical reaction, but also driven by a sequence of complex biochemical reactions which are catalysed by the respiratory enzymes. The energy stored within the glucose molecules are released gradually. This is far more useful to the organism than a sudden release of energy. Only a small portion of energy is lost in maintaining the body temperature. A larger portion of the energy is used to synthesise ATP from ADP and inorganic phosphate. ATP which is an instant source of energy is the main supply for all living cells. Each ATP molecule consists of three phosphate groups and the phosphate bonds can be easily broken down to release energy.

Anaerobic Respiration During vigorous exercise such as running a race, the muscles initially respire aerobically. However, the muscles soon used up all the available oxygen. In spite of the increased breathing rate and heartbeat rate, the blood cannot supply oxygen fast enough to meet their requirements. The rate at which oxygen is used by the muscles exceeds the amount of oxygen supplied by the blood. The muscles are in a state of oxygen deficiency, and an oxygen debt is incurred. As such, the muscles obtain extra energy from anaerobic respiration because oxygen is not available. During anaerobic respiration, the glucose molecules break down partially into an immediate substance called lactic acid instead of carbon dioxide and water. Because glucose is not completely broken down, the energy released during anaerobic respiration is much less than the energy released during aerobic respiration. In fact, for every molecule of glucose, anaerobic respiration releases only two molecules of ATP or 150kJ of energy per mole of glucose. In contrast, aerobic respiration generates 38 molecules of ATP or 2898kJ of energy per mole of glucose. Thus, in terms of energy yield, anaerobic respiration is less efficient than aerobic respiration. 2| Page

Yvonne Choo Shuen Lann November 28, 2009 Much of the energy is still trapped within the molecules of lactic acid. The accumulation of lactic acid can reach a high level of concentration which can cause muscle cramps and fatigue. This contributes to the exhaustion a person feels during and after a period of intense exercise. The person needs to breathe more deeply and rapidly in order to inhale more oxygen. The excess oxygen is used by the body to oxidise the accumulated lactic acid to carbon dioxide and water. Oxidation of lactic acid occurs mainly in the liver where a portion of it is oxidised to produce energy while the remaining ones is converted into glycogen for storage in the muscle cells. The oxygen debt is paid off when all the lactic acid is removed. This happens through the increased breathing rate after vigorous exercise. Therefore, an oxygen debt is the amount of oxygen needed to remove lactic acid from the muscle cells.

Digestion Ruminant When a cow feeds on grass, it partially chews the grass. This partially chewed food is swallowed into the rumen, the largest compartment of the stomach. Here, cellulose is broken down by the cellulose produced by symbiotic microorganisms such as bacteria and protozoa. Part of the breakdown products are absorbed by the bacteria and protozoa, the rest by the cow. As the food enters the reticulum, the cellulose undergoes further hydrolysis. The content of the reticulum, called the cud, is then regurgitated bit by bit into the mouth to be thoroughly chewed again. This process helps soften and break down cellulose, making it more accessible to further microbial action in other parts of the stomach. The cud is then re-swallowed and moves into the omasum. Here, large particles of food are broken down into smaller pieces by peristalsis. Water is removed from the cud. The food particles finally move into the abomasums, the true stomach of the cow. Here, gastric juices containing digestive enzymes complete the digestion of proteins and other food substances. The food then passes through the small intestine to be digested and absorbed in the normal way.

Rodents In rodents like squirrels, the caecum and appendix are enlarged to store the cellulose-producing bacteria. The breakdown products pass through the alimentary canal twice. The faeces in the first batch are usually produced at night and are soft and watery. Those are eaten again to enable the animals to absorb the products of bacterial breakdown as they pass through the alimentary canal for the second time. The second batch of faeces becomes drier and harder. 3| Page

Yvonne Choo Shuen Lann November 28, 2009 This adaptation allows squirrels to recover the nutrients initially loss with the faeces.

Colonisation and Succession Definition *Colonisation: is the process whereby living organisms move into a newly formed area which is devoid of life. *Succession: is the gradual process by which one community changed its environment so that it is replaced by another community. Mangrove Swamp The pioneer species of a mangrove swamp are the Sonneratia sp and Avicennia sp. The presence of these species gradually changes the physical environment of the habitat. The extensive root systems of these plants trap and collect sediments, including organic matters from decaying plant parts. As time passes, the soil becomes more compact and firm. This condition favours the growth of the Rhizophora sp. Gradually, the Rhizophora sp replaces the pioneer species. The seeds of the Rhizophora sp show distinct viviparity. The prop root system of the Rhizophora sp traps silt and mud, creating a firmer soil structure overtime. The ground becomes higher. As a result, the soil is drier because it is less submerged by sea water. The condition now becomes more suitable for another mangrove species, the Bruguiera sp, which replaces the Rhizophora sp. The buttress root system of the Bruguiera sp forms loops which extend from the soil to trap more silt and mud. As more sediment is deposited, the shore extends further to the sea. The old shore is now further away from the sea and is like terrestrial ground. Over time, terrestrial plants like the nipah palm and Pandanus sp begin to replace the Bruguiera sp. The gradual transition and succession from a mangrove swamp to a terrestrial forest and eventually to a tropical rainforest, which is a climax community, takes a long time. That is why we need to conserve and preserve our mangrove forest.

Pond Succession in a disused pond begins with the growth of pioneer species such as phytoplankton, algae and submerged plants like the Hydrilla sp, Cabomba sp and Elodea sp. These plants have special adaptive features which enable them to colonise the pond. Their fibrous roots penetrate deep into the soil to absorb nutrients and bind sand particles together. Plenty of sunlight penetrates through the clear water to allow photosynthesis to take place. When the pioneer species die and decompose, more organic nutrients are released into 4| Page

Yvonne Choo Shuen Lann November 28, 2009 the pond. The organic matter is converted into humus at the pond base. The humus and soil which erode from the sides of the pond are deposited on the base of the pond, making the pond shallower. The condition becomes more unfavourable for submerged plants but more suitable for floating plants such as duckweeds (Lemna sp), water hyacinths (Eichornia sp) and lotus plants (Nelumbium sp). These plants float freely on the surface of the water. Since these plants receive sunlight directly and can reproduce rapidly by vegetative propagation, they spread to cover a large area of the water surface and prevent sunlight from reaching the submerged plants. As a result, the submerged plants die because they cannot photosynthesise. The decomposed remains of the submerged plants add more organic matter on the base of the pond. At the same time, more erosion occurs at the edge which results in more sediments being deposited on the base of the pond. As a result, the pond becomes more and more shallow which makes it unsuitable for the floating plants. The floating plants are subsequently replaced by emergent (amphibious) plants which can live in water as well as on land, for example, sedges and cattails. The rhizomes of these plants grow horizontally across the habitat. Their extensive roots bind the soil particles together and penetrate deeply to absorb more mineral salts. These plants spread rapidly and colonise the habitat, changing it. The emergent plants grow from the edge of the pond towards the middle of the pond as the pond becomes shallower. When these plants die, their decomposed remains add to the sediments on the base of the pond. This further reduces the depth of the pond. The condition of the pond now becomes more favourable for land plants like small herbaceous weeds, for example, Ageratum conyzoides, Euphorbia hirta and Oldentandia dichotoma. As time passes, the land becomes drier and the pond dries up. Land plants such as shrubs, bushes and woody plants become more numerous. A primary forest emerges and eventually turns into a tropical rainforest which is also known as a climax community.

Cell Division Mitosis The two major phases mainly interphase and mitotic cell division also known as the M phase which consists of mitosis and cytokinesis begins and ends according to the cell cycle. Mitosis begins with interphase. Interphase is divided into three shorter stages, G1, S and G2. In G1 phase, the cell synthesises protein and new cytoplasmic organelles such as mitochondria and chloroplast. The chromosomes are not condensed and appear as thread-like structures called chromatin. In S phase, however, synthesis of DNA occurs. This means that the DNA in the nucleus undergoes replication. Each duplicated chromosome now consists of two identical sister chromatid which contain identical copies of the chromosomes DNA molecule. The cell continues to grow and remain metabolically active during G2 stage as a preparation for cell division. Interphase 5| Page

Yvonne Choo Shuen Lann November 28, 2009 is followed by the M phase which contains mitosis and cytokinesis. Mitosis can further subdivided into four phases mainly prophase, metaphase, anaphase and telophase. The mitosis in an animal cell begins with prophase. During prophase, the chromosomes in the nucleus condense and become more tightly coiled. The chromosomes appear shorter and thicker. Each chromosome now consists of a pair of sister chromatids joined together at the centromere. In the cytoplasm, spindle fibres begin to form and extend between the centrioles. Each pair of centrioles then migrates to lie at the opposite poles of the cell. The chromatids are attached to the fibres of the spindle by their centromeres. In most plant cell, the spindle fibre forms without the presence of centrioles. At the end of prophase, the nucleolus disappears and the nuclear membrane disintegrates. Metaphase begins when the centromeres of all the chromosomes are lined up on the metaphase plate, an imaginary plane across the middle of the cell. The mitotic spindles is now fully formed. The two sister chromatids are still attached to one another at the centromere. Metaphase ends when the centromeres divide. During anaphase, two sister chromatids of each chromosome separate at the centromere. The sister chromatids are pulled apart to the opposite poles by the shortening of the spindle fibres that connect the centromeres to the poles. Once separated, the chromatids are referred to as daughter chromosomes. By the end of anaphase, the two poles of the cell have completed and have equivalent sets of chromosomes. Telophase begins when the two sets of chromosomes reach the opposite poles of the cell. The chromosomes start to uncoil and revert to their extended state (chromatin). The chromosomes become less visible. The spindle fibres disappear and a new nuclear membrane forms around each set of chromosomes. The nucleolus also reforms in each nucleus; the process of mitosis is now completed. Cytokinesis, the division of the cytoplasm occurs towards the end of telophase. In animal cell, the actin filaments in cytoplasm contracts to pull a cleavage furrow. The cleavage furrow pinches at the equator of the cell and deepens progressively until the cell is separated into two daughter cells. Although plant cells undergo the same stages of mitosis as in animal cells, cytokinesis in plant cells us markedly different. A cleavage furrow does not form. Instead, membrane enclosed vesicles fuse to form a cell plate. The cell plate grows outwards until its edges fuse with the plasma membrane of the parent cell. New cell walls and plasma membranes are formed from the contents of the cell plate, which eventually divide the cell into two daughter cells. At the end of cytokineses, cellulose fibres are produces by the cell to strengthen the new cell walls. After cytokinesis, the new cells enter the G1 stage of interphase, thus completing the cell cycle. Each daughter cell contains diploid number of chromosomes.

Meiosis

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Yvonne Choo Shuen Lann November 28, 2009 Meiosis only occurs in gametes which are reproductive cells. This is because meiosis is a reduction division of diploid cells to produce haploid sex gametes. Meiosis begins with a single duplication of chromosomes in the parent cells, followed by two cycles of nuclear and cell division mainly meiosis I and meiosis II. In meiosis I, basically, the chromosomes begin to condense. They become shorter, thicker and clearly visible. Unlike mitosis, the homologous chromosomes come together to form bivalents through a process called synapse. Each bivalent is visible under the microscope as a four-part structure called a tetrad. A tetrad consists of two homologous chromosomes, each made up of two sister chromatids. Non sister chromatids exchange segments of DNA in a process known as crossing over. Crossing over results in a new combination of genes on a chromosome. The points at which segments of chromatids cross over are called chiasmata. At the end of prophase I, the nucleolus and the nuclear membrane disappear. The two pairs of centrioles migrate to the opposite poles of the cells. Each pair of centrioles acts as a central point from which the spindle fibres radiate. In metaphase I, the chromosomes are lined up side by side as tetrads on the metaphase plate. The chromosomes are still in homologous pairs. The chromosome of each pair is attached to the spindle fibres from one pole while its homologue is attached to the fibre from the opposite pole. The centromere does not divide. During anaphase I, the spindle fibres pull the homologous chromosomes away from one another and move them to the opposite poles of the cell. Each chromosome still consists of two sister chromatids which move as a single unit. Although the cell started with four chromosomes, only two chromosomes move towards each pole. Next will be telophase I. The chromosomes arrive at the poles. Each pole now has haploid daughter nucleus because it contains only one set of chromosomes. The spindle fibres disappear. The nuclear membrane reappears to surround each set of chromosomes. The nucleolus then reappears in each nucleus. Cytokinesis usually occurs simultaneously with telophase I, resulting in two haploid daughter cells, and each receiving one chromosome from the homologous pair. Hence, another cell division is required as the chromosomes are still duplicated. Meiosis II follows immediately after cytokinesis, no interphase between them. DNA replication does not occur again and the chromosomes remained in a condensed state. In prophase II, the nuclear membrane of the daughter cells disintegrates again. The spindle fibres reform in each daughter cell. During metaphase II, the chromosomes each still make up of sister chromatids, are positioned randomly on the metaphase plate with the sister chromatids of each centromere pointing towards the opposite poles. Each sister chromatid is attached to the spindle fibres at the centromere. In anaphase II, however, the centromeres of the sister chromatids finally separated and the sister chromatids of each chromosome are now individual chromosomes. The chromosomes move towards the opposite poles of the cell. Lastly in telophase II, the nucleoli and the nuclear membrane reform. The spindle fibres break down. Cytokinesis follows 7| Page

Yvonne Choo Shuen Lann November 28, 2009 and four haploid daughter cells are formed, each containing half the number of chromosomes and is genetically different from the parent diploid cell. These haploid cells will develop into gametes.

Tissue Culture Technique A small piece of a plant’s leaf, shoot, bud, stem or root tissues are cut out. These cut out plants tissues are called explants. Alternatively, enzymes are used to digest the cell walls of tissues, for example, the mesophyll tissue from a leaf. This result in naked cells without cell walls called protoplasts. The explants or protoplasts are sterilised and then placed in a glass container which contains a nutrient solution with a fixed chemical composition. A culture medium or growth medium normally consists of a complex mixture of glucose, amino acids, minerals, and other substances required for the growth of the tissues. The culture medium and the apparatus used must be in a sterile condition and free from microorganisms which can contaminate the tissue culture. The pH and the temperature of the culture medium also need to be maintained at optimum levels. The explants or protoplasts begin to divide by mitosis. Cell division produces aggregates of cells. The aggregates of cells develop into a callus, an undifferentiated mass of tissue. The callus develops into a somatic embryo. The embryo dev...