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Ahfad University for women Biology 121: Part one: Plant morphology Lecture one: A View of Life How to Define Life: Biology is the scientific study of life. There is great diversity among living thin gs. Living things are comp...

Ahfad University for women Biology 121: Part one: Plant morphology Lecture one: A View of Life How to Define Life: Biology is the scientific study of life. There is great diversity among living thin gs. Living things are composed of the same chemical elements as nonliving thin gsobey the same physical and chemical laws that govern everything in the unive rse. Because life is so diverse, it seems reasonable that it cannot be defined in a straightforward manner. Instead, life is best defined by several basic characteris tics shared by all organisms. Characteristics of life : 1- Living things are organized: The levels of biological organization range from atoms to the biosphere. The cell is the basic unit of structure and function of all living things they can be unicellular or multicellular. Each level of organization is more complex than the level preceding it as biological complexity increases. 2. Living things acquire materials and energy: Energy is the ability to do work. Energy is required to maintain organization and conduct life-sustaining processes such as chemical reactions. Metabolism is all the chemical reactions that occur in a cell. The sun is the ultimate source of energy for nearly all life on Earth. Plants, algae, and some other organisms capture solar energy and perform photosynthesis. Photosynthesis is a process that converts solar energy into the chemical energy of carbohydrates. 3. Living things maintain homeostasis: Homeostasis is the maintenance of internal conditions within certain boundaries. Ability to maintain a state of biological balance. Feedback systems monitor internal conditions and make adjustments. 4. Living things respond to stimuli: Living things interact with the environment and respond to changes in the en vironment.The ability to respond often produces movement 5. Living things reproduce and develop: All living organisms must reproduce to maintain a population. The manner of reproduction varies among different organisms. When organisms reproduce, they pass on copies of their genetic information (genes) to the next generation. Genes determine the characteristics of an organism. Genes are composed of DNA (deoxyribonucleic acid). 6. Living things have adaptations: An adaptation is any modification that makes an organism better able to function in a particular environment. The diversity of life exists because over long periods of time, organisms respond to changing environments by developing new adaptations. Organizing Diversity Taxonomy: is the branch of biology that identifies, names, and classifies organ isms. Systematics: is the study of evolutionary relationships between organisms. Classification categories:  From least inclusive category (species) to most inclusive category (domain): Sp ecies, genus, family, order, class, phylum, kingdom, and domain. Each successive c ategory above species includes more types of organisms than the preceding one. All living organisms are classified into three domains: 1- Archaea Domain ◦ Contains unicellular prokaryotes that live in extreme environments  Prokaryotes lack a membrane-bound nucleus. 2- Bacteria Domain ◦ Contains unicellular prokaryotes that live in all environments 3- Eukarya Domain ◦ Contains unicellular and multicellular eukaryotes ◦ Eukaryotes contain a membrane-bound nucleus.  Lecture 2: External Features of flowering plants Flowering plants have bodies consisting of two parts which live under differ ent conditions. One part is aerial exposed to sunlight, and called shoot system; t he other part is embedded in the soil and known as root system. The root syste m grows vertically downwards in the opposite direction to that taken by the sho ot system. This main root may bears side branches which further produce lateral roots spreading out in all directions. The shoot system has a main axis, the stem, carr ying branches. The lateral branches arise in the axils of leaves. Branches carry l eaves, buds and flowers. The part of the stem from which a leaf arises is called a node, while the portion between two successive nodes is called internode.  The stem and its branches carry food materials up and down and elevate th e green parts (leaves) to the sunlight to carry out photosynthesis and expose flo wers to pollinating agents. The leaves usually called foliage leaves and are arranged on the stem or branches. The typical leaf consists of three parts, the leaf base, petiole and flattened green lea f-blade or lamina. The leaf has a main vein extending from the base to the tip of th e lamina known as midrib. From this midrib arise a number of lateral veins which branch further to form a reticulate venation (in dicot plants). The size of the plant varies considerably. 1) Herbs: Those plants whose stems develop a small amount of wood and remain soft. 2) Shrubs: they develop short and much branched, with erect woody stems. 3) Trees: develop tall, woody. erect stems growing to a large size. Regarding the length of life plants are divided into: 1) Annuals: Plants that complete their whole life from seed to fruit in one year or less. 2) Biennials: completing their life cycle in two years. 3) perennials: extend for more than two years. According to environmental conditions plants are classified into: 1) Xerophytes: live in scarcity of water e.g., desert plants. 2) Mesophytes: live in medium conditions e.g., wheat. 3) Hydrophytes: live in abundance of water e.g., Eichornia spp Flowering plants are classified into two main groups: 1) Dicotyledonous (Dicot). -Have two cotyledons in the seed embryo. -Reticulate leaf venation. -Tap root system. 2) Monocotyledonous (Monocot). -Have one cotyledon in the seed embryo. -Parallel leaf venation. -Fibrous root system (adventitious)  Lecture 3: Seeds and Seed Germination The seed is a mature fertilized ovule. Characteristics of the Seed: The seed has one point of attachment. Structure of the seed: The mature seed consists of: 1)The Seed coat (Testa): It is the protective wall surrounding the embryo and storage tissue. In most seeds a scar is present on the testa marking the point of attachment of the seed to the funiculus, the scar is known as the hilum. A minute pore is mostly present in the testa of many seeds it represents the micropyle of the ovule. 2)The embryo: In many seeds, the embryo is formed of a plumule, radicle and one or two cotyledons (one cotyledon-monocotyledonous plant: two cotyledons- dicotyledonous plant). 3) The Storage tissue: Some seeds possess a special storage tissue called endosperm (endospermic seeds). Those lack endosperm are called non-endospermic seeds  Embryo parts: a-Plumule: It is the terminal upper portion of the embryo which give rise to shoot system. b-Radicle: It is the terminal lower portion of the embryo, from which the primary root arises. c- Cotyledons: They are mainly concerned with storage of food which is used d uring germination because the plant is not capable of producing its own food. Seed germination is the emergence or protrusion of the embryo parts. Conditions necessary for seed germination: 1) State of the seed: These are internal conditions necessary fo seed germination include: a-Viability: The capacity of the seed to grow under favorable conditions. (Can be tested by TTC solution). b-Dormancy of the seed: A rest period needed by the seed 2) Presence of water 3) Presence of oxygen. 4) Suitable temperature. Epicotyl: It is the portion between the cotyledons and the first leaf. Hypocotyl: It is the portion between the cotyledons and the first lateral root Types of seed germination: 1) Hypogeal germination: The cotyledons remain inside the soil. a) Broad Bean (Vicia faba) Stage I: In this stage the testa is ruptured and the radicle comes out. Stage II: The radicle elongates and the plumule comes out.  Stage III: The radicle and the plumule elongate to considerable size. The root system complete and also shoot system, this stage called seedling. eal b) Hypogeal germination of Zea mays It is a fruit (grain), the testa of the seed fused with the pericarp (fruit wall). Stage I: In this stage the pericarp is ruptured and the radicle comes out through its sheath. Stage II: The radicle elongates and the plumule comes out enclosed by coleoptile. Stage III: Is characterized by emergence of the foliage leaves. Radicle is replaced by developing adventitious roots  2) Epigeal germination: The cotyledons come above the soil. Lupinus termis Stage I: In this stage the testa is ruptured and the radicle elongates rapidly downwards. Stage II: The hypocotyl elongates and the cotyledons are pushed above the soil surface. Stage III: The independent seedling possesses a differentiated roots system and shoot system.  Lecture 4: THE ROOT The root is the descending organ of the plant, and originally is the direct prolongation of the radicle. Functions of the roots:- 1-Fix the plant to the ground. 2-Absorb water and salts from the soil. 3-Synthesize hormones necessary for plant growth. Characteristics of root: Does not has buds, leaves, flowers, nodes or internodes. Regions of root: 1) Root cap: Cover the root apex which protects the tender apex. 2) Region of cell division: The growing apex of the root, the cells of this region undergo repeated divisions (meristematic region). 3) Region of elongation. Lies above the meristematic, responsible for growth in length in the root. 4) Region of maturation: Externally at the basal portion produces root-hairs and lateral roots. Types of the root: 1) Tap roots: Develop from the radicle, consist of primary root and lateral roots 2) Adventitious roots: Do not develop from the radicle Both tap and adventitious roots when performing some special functions they get modified in various ways ( normal functions of roots are fixation and absorption of water and minerals and production of some hormones). Modified tap roots: a) Modified primary roots for storage of food: i- Conical root: When the root is broad at the base and gradually tapers towards the apex like a cone, e.g. carrot. ii- Fusiform Root: When the root is swollen at the middle and gradually tapering towards the apex and the base. e.g., Radish. iii- Napiform Root: When the root is considerably swollen at the upper part becoming almost spherical and sharply tapering towards the lower part. e.g., Beet. b) Modified Lateral tap Roots ( respiratory roots): Many plants growing in marshy places and salt lakes develop special kind of roots, called respiratory roots for respiration as in Mangroves plant (Avicennia sp.) Such roots grow from the underground roots of the plant but rise vertically upwards. )  Lecture 5:The Stem The Stem is the ascending organ of the plant, and is the direct prolongation of the plumule. Characteristics of the stem: 1- It bears buds, leaves, branches and flowers. 2- provided by nodes and internodes. Functions of the stem: 1) Bearing leaves and flowers. 2) Conduction of water and mineral salts from root to the leaf, and prepared food material from the leaf to the different parts. 3) Support branches. The bud: - A bud is a young undeveloped shoot consisting of a short stem and a number of tender leaves arching over the growing apex. In the bud the internodes not developed and the leaves remain closely crowded together forming a. Types of buds: 1)Normal: a) Apical or Terminal bud: -Grows at the apex of a stem or branch. -Leads the growth. b) Axillary bud: -Grows in the axil of a leaf.  -Gives branches. 2) Accessory buds: An extra buds develop by the side of the axillary bud. 3) Adventitious buds: Arises in any other part of the plant body. Forms of stems (habits): 1) Erect stems: Grow upright to the soil level. This may be: a) Herbaceous b) Woody 2) Weak stems: Cannot stand upright on their own and may either be: a)Twining stems: The stem twines its body around a support. e.g., Leptadenia sp. b) Climbing stems: Use special device to attach to the support. e.g., tendrils as in Antigonon sp. c) Creeping stems: Growing horizontally above the ground, have one tap root, lack adventitious roots at the nodes. e.g., Tribulus sp.  Modification of the stem: Stem or branches of certain plants are modified into various shapes to perform special functions. Types of stem modifications; 1) Underground modifications (subterranean). 2) Sub-aerial modifications. 3) Aerial modifications. Underground modifications: For the purpose of perennation stems of certain plants develop underground and lodge there permanently, lying in a dormant leafless condition for some period and then giving off aerial shoots annually under favourable conditions. They can be distinguished from roots by presence of: i. Nodes and internodes. ii. Scale leaves. iii. Buds (axillary and terminal). The main functions of underground stems are: i. Perennation. ii. Storage of food materials.  iii. Vegetative propagation. Types of modified underground stems: a) Rhizome. b) Tuber. c) Corm. d) Bulb. e) Bulbil b) Tuber: It is a swollen end of a special underground branch.The underground branch arises from the axil of a lower leaf, grows horizontally outwards and swells up at the apex due to the accumulation of food. e.g., Potato.. 2-Subaerial modifications: For the purpose of vegetative propagation some of the lower buds of the stem in certain plants grow out into long or short, lateral branches. Types of sub-aerial modifications: a) Runner. b) Offset. A) Runner: This is a slender branch with long internodes, growing horizontally on the ground surface and rooting at the nodes. The runner arises as an axillary bud and grows some distance away from the mother plant, then strikes roots and grow into a new plant. e.g., (Cynodon sp. and Strawberry). B) Offset: Like the runner, it originates in the axil of a leaf as a short branch, it elongates to some extent only The apex turns up and produces leaves aba cluster of roots below. e.g., Eichhornia sp. Aerial modifications; Vegetative and floral buds which would normally develop into branches and flowers, often undergo extreme degree of modification in certain plants for definite purposes. Typesof aerial modifications: a) Thorns for protection. b) Cladode for photosynthesis. c) Phylloclade for photosynthesis. 1) 2) 3) b) Cladode:-These are green branches of limite d growth (usually one internode long) which have taken up the functions of leaves. True leaves are reduced to scales or spines. e.g., Asparagus sp. c)Phylloclade: It is green, flattened, cylindrical stem or branch of unlimited growth, with distinct nodes and internodes.  It is thick, fleshy and succulent, as in Opuntia sp.  In xerophytes, leaves get modified into spines or get reduced in size to check the loss of water due to transpiration and thus stem takes up the function of leaf (photosynthesis)    Lecture 6:The Leaf The leaf is the flattened, lateral outgrowth of the stem or the branch. Developing from a node and having a bud in its axil. Characteristics of leaf: An axillary bud is often present in the axil of each leaf. Functions of leaf: 1) Photosynthesis (Manufacture of food). 2) Exchange of gases through stomata. 3) Evaporating of water (Transpiration). 4) Storage of food. Parts of leaf: 1) Leaf base: It’s the part attached to the stem. 2) Petiole: It’s the stalk of the leaf. When the petiole is absent the leaf is said to be sessile; and when present it is said to be petiolate. 3) Leaf- blade or lamina: It is the green, expanded portion containing a strong vein, known as the mid-rib; this produces thinner lateral veins and veinlets. The lamina is the most important part of the leaf since this is the seat of food- manufacture for the entire plant. Kinds of leaves: 1) Foliage leaves: These are the normal green leaves and very common in all plants. 2) Cotyledonary leaves: In epigeal germination he cotyledons are puhd above the soil and turn green in colour to carry out photosynthesis till the ordinary leaves are formed. 3) Prophylls: the first formed leaves of some developing seedling as in Vicia faba seedling and differ from the succeeding leaves. 4) Scale leaves: they are protective structures. They have no chlorophyll brown, red or white they are found in underground stems. 5) Bracts (attractive leaves) Changes colour to attract insects as in Bougainvellia sp. 6) Floral leaves: Like sepals and petals.  Duration of leaves: 1) Caducous: fall soon after it appears. 2) Deciduous: lasts one season (e.g., falling off in winter) 3) Ever green (Persistent). The mode of arrangement of veins in leaves. Types of venation: 1) Reticulate (Dicot plants) the main vein divides into various branches and form a net-like structure in the lamina. 2) Parallel (Monocot plants) Here all veins run parallel to each other Types of leaves: 1) Simple leaf: A leaf is said to be simple when it consists of a single blade. 2) Compound leaf: When the incision of the leaf-blade goes down to the mid-rib (rachis) or to the petiole so that the leaf is broken up into a number of segments called leaflets these being free from one another. Types of compound leaf: 1) Pinnate: Leaflets arrange laterally on the rachis. 2) Palmate: Leaflets radiate from a common point like fingers from the palm. Comperison between a compound leaf and abranch: Phyllotaxy: The mode in which the leaves are arranged on the stem or the branch. Types of phyllotaxy: 1)Alternate (spiral): A single leaf arises at each node. 2) Opposite: Two leaves arise at each node standing opposite each other. i) Superposed ii) Decussate 3) Whorled: There are more than two leaves at each node and these are arranged in a circle or whorl. Modifications of leaf: 1) Leaf-tendril. 2) Leaf spines (for defensive purpose). 3) Phyllode. 4) Bladder: In aquatic plants helps in floating. 5) Pitcher: Capture insect and digest them.  Lecture 7: The Flower The flower is a modified shoot for the reproduction of the plant. It is a collection of four different kinds of floral members arranged in four separate whorls. Parts of flower: 1- Pedicel: the stalk of the flower. 2- Thalamus: the swollen end of the axis which the floral leaves inserted on. 3-The four whorls: arranged in a definite order, one just above the other. a- Calyx: consists of a number of green leafy sepals. b- Corolla: consists of a number of usually coloured petals. c- Androecium: the male whorl, consists of a number of stamens, each stamen is made of: i-Anther (composed of four champers or pollen sacs), filled with pollen grains (male gametes). ii-Filament. d- Gynoecium (pistil): the female whorl, it’s component parts are called carpels. The gynoecium is made of three parts: i-Stigma. ii-Style. iii-Ovary containing ovules (female gametes). Androecium and gynoecium are reproductive whorls, while calyx and corolla are accessory whorls.  Some descriptive terms: Complete flower: When all the four whorls are present. Incomplete flower: When any of the four whorls is absent. Hermaphrodite flower: When male parts and female parts are present in same flower. Monoecious plants: Having separate male and female flowers on the same plant. e.g., family Cucurbitaceae. Dioecious plants: Male flowers are on one plant and female flowers are on another plant. e.g., Date-Palm. Pollination: Is the transference of pollen grains from the anther to the stigma. Types of pollination: 1) Self-pollination: Here pollination taking place within a single flower or between two flowers in the same plant. 2) Cross pollination: Pollination taking place by two separate plants. Fertilization: Is the fusion of male gametes (pollen grains) and female gametes (ovules).  Lecture 8; The Fruits The fruit is a mature fertilized ovary. Characteristics of fruits: Fruits have two points of attachments (scars). One at the apex marking remains of the style, and the other at the base where the ovary had been attached to the thalamous.. Parts of fruits: 1) Pericarp and 2) Seeds The pericarp may be thin or thick. The thick pericarps are differentiated into three regions: 1) Epicarp: It is the outermost thin layer 2) Mesocarp: The middle thick and fleshy layer which forms the pulp 3) Endocarp: The innermost layer which may be membranous or hard Functions of fruits: 1) Store food materials 2) Protect the seed 3) Help in seed dispersal Types of fruits; 1) True fruits: develop from the ovary. 2) False fruits (Pseudocarp): other floral parts, particularly the thalamus or even the calyx may form apart of the fruit e.g., Apple. Classification of fruits: There are three types of fruits based on their origin, texture and dehiscence: 1) Simple fruits 2) Aggregate fruits 3) Multiple or composite fruits  Simple fruits: It is a single fruit develops from the ovary (either of one carpel or many united carpels) of a flower with or without accessory parts. simple fruits may be: a- Dry or b- Fleshy (Succulent). The dry simple fruits may be i- Dehiscent ii- Indehiscent iii- Schizocarpic   Fleshy (succulent ) fruits: The fruits usually remain fleshy and juicy even at maturity. The pericarp is differentiated into epicarp, mesocarp and endocarp.  The Cell Structure and functions All organisms are composed of cells, which arise from pre-existing cells. There are two types of cells: 1) Prokaryotic: e.g., Bacteria, Archea. 2) Eukaryotic: e.g., Protists, Plants, Fungi and Animals Prokaryotic cells do not have a membrane bounded nucleus, nor the various membranous organelles of eukaryotic cells. Structure of Eukaryotic cells: Cell wall: Surround plant cells, shapes, supports, and protects cell Cell membrane: Immediately inside the cell wall, surrounds cytoplasm, and regulates entrance and exit of molecules Nucleus: command centre of cell and contains the genetic material. Nucleolus: produces subunits of ribosomes Cytoplasm: semifluid matrix outside nucleus that contains organelles Endoplasmic reticulum: location of protein and lipid metabolism. Ribosomes: makes protein. Mitochondria: carries out cellular respiration, producing ATP molecules for energy. Golgi apparatus: vesicle that is involved in fatty acid metabolism Vacuole: large, fluid-filled sac that stores metabolites and helps maintain turgor pressure. Chloroplasts: are only found in green plants. They are green-colored bodies that carry out photosynthesis to make sugar for the plant  Diffusion Diffusion is the movement of particles from higher concentration to lower concentration according to concentration gradient. Laws of Diffusion: 1-It is a physical process. 2-It is spontaneous and no energy in required. 3-Atoms and molecules move from higher concentration to lower concentration. 4-The rate of diffusion is inversely proportional to the size of the diffusing particles. 5-The rate of diffusion is inversely proportional to the atomic weight and molecular weight of the diffusing compound (KMnO4 & CuSO4). 6-The previous laws apply to both solvent and solute. Osmosis Osmosis is the diffusion of water across a differentially (selectively) permeable membrane due to concentration differences. The U-tube contains pure water on the right and water plus a solute on the left, separated by a selectively permeable membrane. Water molecules cross the membrane in both directions. Solute molecules cannot cross. The fluid level would normally rise on the left and fall on the right because net movement of water would be to  the left. However, the piston prevents the water from rising. The force that must be exerted by the piston to prevent the rise in fluid level is equal to the osmotic pressure of the solution. Turgor pressure One of the differences between plant and animal cells that the pant cell has a cell wall but the animal cell has no wall.The cell-wall of plant cells has some unelastic properties. which allows it to live and survive in different environment concentrations. Equally, the animal cell which has no cell-wall lives in concentrations similar to its osmotic concentrations i.e it lives in isotonic solutions. It is noted that when a plant cell is immersed in pure water, water will definitely go inside it because the cell sap contains water + salts + sugars + carbohydrates + proteins + fats +…etc. The plant cell will be swollen and can be called a turgid cell the pressure arising from the plasmalemma of the cell acts against the pressure arising from the cell wall (see Fig). The pressure formed then is called turgor pressure which is equal to the pressure formed in the cell-wall and celled the wall-pressure. This wall-pressure forbids full plant cells with water to explode.  Tonicity Cells can be placed in solutions that are: 1) Isotonic. 2) Hypotonic. 3) Hypertonic.  Conduction Conduction in plants is in same way as blood circulation in animals. Plants have specialized conduction tissue consisting, in the main of xylem and phloem. The woody tissues have also a skeletal function. Some conduction is also affected by the circulation of protoplasm or cytoplasm (as you have seen in Elodea leaf) Transpiration Transpiration is the loss of water as water vapour mainly through the stomata in the leaves to the outside atmosphere. The rate of evaporation of water from plants depends upon environmental factors such as humidity, temperature, wind, light and pressure. Also evaporation rates depend upon internal factors such as the degree of opening of the stomata and the water content of the leaf cells surrounding the stomatal space.  HORMONES 1- The word hormone came from the Latin word “hormaein” means to activate. 2- Hormones are organic substances produced in very small quantities to control growth and development of living organisms e.g. growth hormones and sex hormones. 3- hormones are consumed in their reactions. 4- Hormones are usually produced in one organ and transported to another organ of the animal or plant where they have their effects. For example insulin is produced in the pancreas of man and control the glucose level in blood and stimulates the liver, fat and muscle cells to take up and metabolize glucose, also it stimulates the conversion of glucose into glycogen in muscle and liver cells. Likewise the hormone floragien is secreted by the plant leaves and responsible for the initiation of flowers in plants. Enzymes 1- Enzymes are proteins which in very small quantities catalyze and controls all cellular reactions of metabolism. 2- Enzymes are NOT consumed in their reactions i:e they carry multiples of reactions in the cells. 3- An enzyme forms a complex with its substrate (reactant) but do not changed or consumed in the reaction. The substrate and enzyme fit together like a key fits a lock 4- Enzymes lower the energy of activation. Generally molecules do not react with one another unless they are activated in some way. In the laboratory activation is very often achieved by heating the reaction flask or beaker to increase the number of effective collisions between molecules to react with one another is called the Energy of Activation. Energy of Activation is the energy needed to speed up the reaction. The following Fig. illustrates that an enzyme lowers the energy of activation. Therefore an enzyme lowers the energy of activation by forming an enzyme-substrate-complex. 5- Factors affecting enzyme activity: The enzyme activity is affected by: Temperature pH Enzyme and substrate concentrations Enzyme inhibitors.  Vitamins Many enzymes require a non-protein co-factor to assist them in carrying out their function. ++ + ++ Some co-factors are inorganic ions for example Mg , K , Ca are often involved in enzymatic reaction. Other co-factors called co-enzymes or vitamins they are small organic molecules that bind to enzymes and serve as electrons carriers. Vitamins are required in trace amounts in our diet, vitamins must be in an organism's diet, because it cannot be synthesized by our bodiesA deficiency of any of these vitamins results in the lack of certain enzymatic reaction this eventually results in vitamin deficiency symptoms. For example niacin (NAD) deficiency results in a skin disease called pellagra and riboflavin (FAD OR B2) deficiency results in cracks in the corners of the mouth. NAD= Nicotine Amide Dinucleotide. FAD= Flavine adenine dinucleotide. Both NAD and FAD are co-enzymes that carry electrons and works with enzymes called dehydrogenases.  Photosynthesis Photosynthesis converts solar energy into the chemical energy of a carbohydrate. Photosynthetic organisms are plants, algae, and cyanobacteria, are called autotrophs because they produce their own food. Heterotrophs organisms take in preformed organic molecules. Both autotrophs and heterotrophs use organic molecules produced by photosynthesis for building their bodies and as a source of energy.. Oxygen is a by-product of photosynthesis. Oxygen is used by animals for cellular respiration and forms an ozone shield in the atmosphere. Raw materials for photosynthesis are carbon dioxide and water. Roots absorb water that moves up vascular tissue in the stem until it reaches the leaf veins. Carbon dioxide enters a leaf through small openings called stomata. Chloroplasts are the organelles that carry on photosynthesis. Carbon dioxide and water diffuse into the chloroplasts. The chloroplast has a double membrane enclosing a fluid-filled space called the stroma. Thylakoids are flat sacs in the stroma, which are organized into stacks to form grana. Spaces within the thylakoids are connected to form the thylakoid space. Chlorophyll and other pigments are located in thylakoid membranes; these pigments absorb solar energy and energize electrons to reduce CO to carbohydrate 2. Photosynthesis involves oxidation-reduction, where the carbon dioxide has been reduced by hydrogen atoms and energy, and the water has been oxidized. In 1930, van Niel showed that O2 given off by photosynthesis comes from water and not from CO2 in the air by using the radioactive isotope 18O. Solar energy is not used directly, but rather converted to ATP molecules. Electrons and H+ required to reduce carbon dioxide are carried by coenzyme NADPH which is the redox coenzyme because NADPH is oxidized, so it gives up the two e- and one H+ and become NADP+. Then  oxidized NADP+ accepts two electrons and one Hydrogen ion (H+) to form NADPH again. So, the energized electrons are taken up by NADP+, converting it to NADPH. When these energized electrons move down an electron transport chain, energy is captured and used for ATP production. The electromagnetic radiations The electromagnetic radiations from the sun are of different wavelength and different energy contents. Higher energy wavelengths are screened out by the ozone layer in the upper atmosphere. Lower energy wavelengths are screened out by water vapor and CO2. Visible light is the dominant radiation in the environment. Living bodies and certain processes (e.g., vision, photosynthesis) are adapted to visible light. Photosynthetic pigments The major Photosynthetic pigments are chlorophyll a and chlorophyll b and carotenoids. Photosynthetic pigments use the visible light portion of the electromagnetic radiation; this is called their absorption spectrum.  Chlorophyll reflect most of the green light (this is why leaves appear green). Carotenoids reflect the yellow-orange light, When chlorophyll breaks down in the fall, the yellow-orange pigments in leaves show through.. In photosynthesis there are two sets of reactions: 1) Light reactions: (light dependent reactions), occurs during day time, only in the presence of light, they are the energy capturing reactions. 2) Calvin cycle reactions: (light independent), occurs during day or night. 1) Light reactions: photosystem I (PS I) and photosystem II (PS II) are complexes that contain pigments located in thylakoid membranes absorbing solar energy and energizes electrons. Steps of the light reactions: a) The PS II pigment complex absorbs solar energy; high-energy electrons leave the reaction-center of chlorophyll a, PS II takes replacement + electrons from H O, which splits, releasing Oxygen as gas (O ), H ions 2 2 + - and electrons: H O = 2 H + 2 e + ½ O. 2 2 + b) The H ions temporarily stay within the thylakoid space and contribute to + + a H ion gradient. As H flow down electrochemical gradient through ATP synthase enzyme, chemiosmosis occurs producing ATP molecules. c) Low-energy electrons leaving the electron transport chain enter PS I. PS I pigment complex absorbs solar energy, high-energy electrons leave reaction-center chlorophyll and are captured by an electron acceptor. The electron acceptor passes them on to NADP+. NADP+ takes an H+ to become NADPH: NADP+ + 2 e- + H+ = NADPH.  NADPH and ATP (produced by noncyclic-flow electrons in the thylakoid membrane) are used by enzymes in the stroma during the light-independent reactions. Facts about light reactions: 1- Photosystms absorbs sun light. 2-Electrons move down the electron transport chain providing energy to pump protons into thylakoid space. 3-Photophosphrylation (production of ATP). 4-Water photolysis and production of oxygen. 5-Production of NADPH. Conclusion: The light reactions collect energy from the sun and break water molecule to produce oxygen, ATP and NADPH. ATP and NADPH are two energy storing molecules are then used in the light independent reactions. 2) Calvin cycle reactions: The cycle is named for Melvin Calvin who used a radioactive isotope of carbon to trace the reactions. Calvin cycle reactions take place in the stroma; the reactions can occur in the presence or absence of light, these reactions  follow the light reactions. These are reactions use NADPH and ATP ( as products of the light reactions)to reduce CO producing carbohydrates. 2 The Calvin cycle includes three steps: 1- CO fixation is the attachment of CO to RuBP (ribulose bisphosphate) 2 2 which is a five-carbon molecule. The enzyme RuBP carboxylase (rubisco) speeds this reaction. 2- Reduction of Carbon Dioxide The resulting 6-carbon molecule then splits into two 3-carbon molecules, a 3PG (3-phosphoglycerate). 3PG molecules undergoes reduction to G3P (glyceraldehyde-3-phosphate). Light-dependent reactions provide NADPH (electrons and H) and ATP (energy) to reduce 3PG to G3P. 3- regeneration of ribulose 1,5-bisphosphate (RuBP): For every three turns of the Calvin cycle, five molecules of G3P are used to re-form three molecules of RuBP.  The Importance of the Calvin Cycle: Glyceraldehyde-3-phosphate (G3P) which is the product of the Calvin Cycle can be converted into many other molecules e.g. glucose phosphate it is a common energy molecule. Glucose phosphate can bond with fructose to form sucrose. Glucose phosphate is the starting point for synthesis of starch and cellulose. The G3P is used to form fatty acids and glycerol; the addition of nitrogen forms various amino acids. Cellular Respiration Cellular respiration is the break down carbohydrates and other metabolites and buildup Adenosine Triphosphate (ATP). Cellular respiration consumes oxygen and produces CO ; because oxygen is required, cellular respiration is an aerobic 2 process. ATP is a nucleotide, used to supply energy for synthetic reactions and for transport and mechanical work. A nucleotide is a complex of 3 molecules: 1- Phosphate. 2- pentose sugar. 3- nitrogen containing base. A Nucleoside consist of nitrogenous base covalently attached to a pentose sugar.  Glucose is a high-energy molecule; CO and H O are low-energy molecules; 2 2 cellular respiration is thus exergonic because it releases energy. Glucose is broken down in steps to insure the maximum transfer of its energy to ATP molecules. In contrast, if glucose was broken down rapidly in one step, most of its energy would be lost as non-usable heat. The breakdown of glucose yields synthesis of 36 or 38 ATP (depending on certain conditions); this preserves about 39% of the energy available in glucose. This is relatively efficient compared to, for example, the 25% efficiency of a car burning gasoline. NAD & FAD Each metabolic reaction in cellular respiration is catalyzed by a specific enzyme. + NAD (nicotinamide adenine dinucleotide). FAD (Flavin adenine dinucleotide) Both are coenzymes of oxidation-reduction, accepting and giving up + electrons; thus, called redox coenzymes. -As a metabolite is oxidized, NAD + accepts two electrons and a hydrogen ion (H ); this results in NADH. FAD accepts two electrons and two hydrogen ions to become FADH. Only a small amount of 2 + NAD and FAD is needed in small amount because each molecule is used + repeatedly. Electrons received by NAD and FAD are high-energy electrons and + are usually carried to the electron transport chain. FAD can replace NAD. The structure of mitochondrion The mitochondrion is a cellular organelle with a double membrane and intermembrane space (between the outer and inner membrane). The inner membrane folds forming projections known as Cristae. The matrix is a gel-like fluid filling the innermost compartment of a mitochondrion. Most of the ATP produced in cellular respiration is produced in the mitochondria; therefore, called the “powerhouses” of the cell Phases of Cellular Respiration Cellular respiration includes four phases: 1- Glycolysis: occurs in the cytoplasm outside the Mitochondria To continue cellular respiration there are three sets of reactions occur inside the Mitochondria 2- The preparatory (prep) reaction occurs in the in the matrix 3- The citric acid cycle occurs in the in the matrix. 4- The electron transport chain occurs in the cristae. 1- Glycolysis is universally found in organisms and does not utilize oxygen; it is therefore an anaerobic process. In glycolysis, glucose is broken down into two molecules of pyruvate. Pyruvate enters the mitochondrion (if oxygen is available) and cellular respiration ensues. If oxygen is not available, fermentation occurs. i) The Energy-Investment Step where two ATP molecules are used to start glycolysis by breaking of glucose to two glyceraldehyde-3-phosphate (G3P) resulting in 4 ATP molecules. (ii) The Energy-harvesting Step Two of the four ATP molecules produced replace the two ATP molecules used in starting glycolysis; therefore there is a net gain of two ATP from glycolysis.  3- The citric acid cycle OR Krebs cycle: Named for Sir Hans Krebs, who described the steps of the reactions in the 1930s. CoenzymeA carries the acetyl group to the citric acid cycle. The cycle turns twice because two acetyl-CoA molecules enter the cycle per one glucose molecule. The citric acid cycle Is a series of reactions begins by the addition of a two- carbon acetyl group to a four-carbon molecule, forming a six-carbon citrate (citric acid) molecule. Two ATP are formed one by substrate-level ATP synthesis and the other is by converting ADP to ATP. That produces of citric acid cycle (per glucose molecule) are 4 CO , 2 ATP, 6 2 NADH, and 2 FADH. 2 Production of CO 2. The six carbon atoms in the glucose molecule have become the carbon atoms of six CO molecules, two from the prep reaction and four from the citric 2 acid cycle. 4- The electron transport chain (ETC) is located in the cristae. The ETC is a series of electron carriers, where electrons are passed from carrier to carrier until received by oxygen. Movement of electrons from higher to lower energy states, allowing energy to be released and stored for ATP production. Members of the Chain. NADH and FADH carry the electrons ETC, NADH gives up its electrons and 2 + becomes NAD ; FADH becomes FAD the next carrier then gains electrons and is 2 thereby reduced. At each redox reaction, energy is released to form ATP molecules. Other carriers are proteins, cytochrome molecules, complex carbon rings with a heme (iron) group in the center. Oxygen serves as the final electron acceptor and combines with hydrogen ions to form water. Most of the ATP is produced in the electron transport chain by chemiosmosis. Under certain conditions FAD replace NAD in glycolysis reducing the production of ATP to 36 ATP molecules per glucose molecule instead of 38ATP. Outside the mitochondria Fermentation is an anaerobic process (i.e., occurs in the absence of oxygen) which consists of glycolysis plus reduction of pyruvate. In human, muscle cells when oxygen is not enough e.g. during exercises, carry lactic acid fermentation to produce two ATP molecules per glucose molecule. Advantages of Fermentation; Fermentation provides a quick burst of ATP energy for muscular activity. Disadvantages of Fermentation; Fermentation products are toxic to cells. lactic acid changes pH of the body and causes muscles to fatigue. When blood cannot remove all lactate from muscles, the individual is in oxygen debt because oxygen is needed to restore ATP levels and rid the body of lactate. Recovery occurs after lactate is sent to the liver where it is converted into pyruvate; some pyruvate is then respired or converted back into glucose. EFFICIENCY OF FERMENTAION: Fermentation produces two ATP per glucose molecule equivalent to 14.6 kcal. Cellular respiration produces 38 ATP molecules per glucose equivalent 686 kcal. Efficiency of fermentation is 14.6/686 or about 2.1%, far less efficient than complete breakdown of glucose in cellular respiration. The products of fermentation by different organisms depend on the organism:- 1- Animal cells including human fermentation results in lactate. 2- Yeast Fermentation: Yeasts produce alcohol and CO. Baker’s yeast, 2 Saccharomyces cerevisiae, is added to bread. The bread rises when yeasts give off CO. Yeasts ferment the carbohydrates of fruit and grains to produce ethyl alcohol 2 3- Bacterial Fermentation: Bacteria can produce an organic acids , alcohol and CO. Bacterial fermentation produces yogurt, cheese and pickled vegetables (e.g. 2 cucumber). Flow of energy Energy flows through organisms. Autotrophic organisms (plants, algae and cyanobacteria ) use the sun the energy to produce carbohydrates in chloroplasts. In the mitochondria of all living organisms the carbohydrate energy is converted into ATP molecules during cellular respiration. Mitochondria use carbohydrates and oxygen produced in chloroplasts, and chloroplasts use carbon dioxide and water produced in the mitochondria. PLANT ANATOMY The Tissues  A tissue is defined as a collection of cells of same origin and same methods of development performing a particular function. CLASSIFICATION OF PLANT TISSUES 1) Meristematic Tissues: These are composed of cells that are in a state of division or retain the power of dividing. 2) Permanent Tissues: These are composed of cells that have lost the power of dividing. MERISTEMATIC TISSUES According to the position meristematic tissues are grouped into: 1) Apical Meristem: lies at the apex of the stem and the root and gives rise to primary permanent tissues. 2) Lateral Meristem: lies among masses of permanent tissues and gives rise to secondary permanent tissues e.g. cambium 3) Intercalary L.S through a shoot apex L.S through a root apex Apical Meristem  Cambium Lateral Meristem PERMANENT TISSUES  They are formed by differentiation of the cells of the meristems (apical and lateral), and may be primary and secondary.  The primary permanent tissues may be classified as simple (it’s made up of one type of cells) and complex (it’s made up of more than one type of cells working together as a unit). SIMPLE TISSUES 1) Parenchyma Are oval, spherical or polygonal in shape, their walls are thin and made of cellulose, they are usually living. They play a role in metabolic processes, such as photosynthesis, cellular respiration, and food storage and they also transport food and water. COLLENCHYMA CELLS The cells are more or less elongated with a deposit of cellulose and pectin at corners or intercellular spaces. The thick walls of collenchyma cells provide strength to the plant, containing chloroplast it also manufacture sugar and starch. Collenchyma cells are a live at maturity. SCLERENCHYMA CELLS  Consists of very long narrow thick walled and lignified cells (lignin).  Sclerenchyma cells are commonly dead at maturity.  It gives strength to the plant. COMPLEX TISSUES 1) Xylem It is complex system which is formed from different types of cells. a) Xylem vessels b) Tracheids c) Wood fibers d) Wood parenchyma Xylem vessels PHLOEM The phloem is the principal food- conducting tissue of the vascular plants. The main elements of phloem are: a) Sieve tubes. b) Companion cells. c) Phloem parenchyma d) Bast fibers  Plant Tissues Meristematic Tissues Permanent Tissues Apical Primary Secondary Lateral Simple Complex Intercalary Parenchyma Xylem Collenchyma Phloem Sclerenchyma  TISSUE SYSTEMS  The plant tissues of varied nature and functions are aggregated to form tissue systems.  There are three tissue systems in plant body: 1) Epidermal tissue system. 2) Fundamental tissue system. 3) Vascular tissue system. 1) EPIDERMAL TISSUE SYSTEM  It consists mainly of a single outermost layer called epidermis which protects the plant body.  In the root the outer most layer is called epiblema which extends outward and form root- hairs to increase the absorption surface.  In the leaves the outer walls of the epidermis are often thickened and cutinized (cuticle) protect plant of desiccation also epidermis possesses numerous minute openings called stomata (for interchange of gases between the plant and the atmosphere).  Cuticle Stoma Epidermis T.S through a monocot leaf Stomata (surface view) 2) FUNDAMENTAL TISSUE SYSTEM  This system forms the main bulk of the plant body, and extends from below the epidermis to the centre excluding the vascular bundles.  This system consists of various kinds of tissues, of which parenchyma is the most abundant.  It is differentiated into i- Cortex ii- Pericycle iii- Pith Fundamental tissue system 3) VASCULAR TISSUE SYSTEM  The vascular tissue system consists of a number of vascular bundles. Each bundle made up of both xylem and phloem tissues with or without cambium.  The function of this system is to conduct water from the roots to the leaves, and prepared food materials from the leaves to the roots. ELEMENTS OF VASCULAR BUNDLE  A vascular bundle consists of: 1- Xylem 2- Phloem 3- Cambium (may be absent) TYPES OF VASCULAR BUNDLES  According to the arrangement of xylem and phloem , the vascular bundles are of the following types: 1) Radial : When xylem and phloem form separate bundles and these lie on different radii alternating with each other, as in roots. 2) Conjoint: When xylem and phloem combine into one bundle. TYPES OF CONJOINT VASCULAR BUNDLES a) Collateral: When xylem and phloem lie together on the same radius, xylem being internal and phloem external. i) Open: When the cambium is present. ii) Closed: When the cambium is absent. b) Bicollateral When in a collateral bundle both phloem and cambium occur twice-once on the outer side of xylem and then again on the its inner side. Phloem Types of Vascular bundles ANATOMY OF ROOTS DICOTYLEDONOUS ROOTS  The transverse section of the dicot root shows the following plan of arrangement of tissues from the periphery to the centre.  Epiblema -The outermost layer is a single row of thin walled cells. -Unicellular root hairs are present. -This layer has no cuticle.  Cortex -It consists of many layers of parenchyma cells. -Numerous intercellular spaces are present. -Contain leucoplasts and store starch grains. Endodermis -It is the inner layer of the cortex. -Surrounds the stele as a cylinder. -Consist of a single ring-like layer of barrel-shaped cells. - Compact without intercellular spaces. -The radial and the inner tangential walls of endodermal cells are thickened with suberin. These thickenings are known as casparian strips  Pericycle -It follows the endodermis. -The cells are thin walled and compactly arranged.  Vascular bundles: Arranged in ring, xylem and phloem form an equal number of separate bundles, their arrangement is radial. Their number varies from two to six, the cambium is absent.  Phloem bundle: consists of sieve tubes, companion cells and phloem parenchyma.  Xylem bundle: consists of protoxylem and metaxylem. Pith: small area in the center of the root or absent in some plants.  epiblema pericycle T.S through Dicot root  Endodermis Pericycle Phloem Protoxylem Metaxylem T.S through Dicot root T.S through Dicot root MONOCOTYLEDONUS ROOTS  Epiblema: The single outermost layer with a number of unicellular root-hairs.  Cortex: This is multi-layered zone of rounded or oval cells, it differentiates into lignified parenchyma cells called hypodermis, and non- lignified cells called general cortex.  Endodermis: The innermost layer of the cortex forms a definite ring around the stele. Each endodermal cell has a band-like suberized thickening, the casparian strip that goes around the cell.  Pericycle: The ring-like layer lying internal to the endodermis. Its cells are very small and thin walled.  Vascular bundles: xylem and phloem form an equal number of separate bundle arranged in ring. Bundles are numerous. -Phloem bundle: consists of sieve tubes, companion cells. - Xylem bundle: consists of protoxylem and metaxylem.  Pith: Large area of parenchymatous cells in the centre.  epiblema hypodermis general cortex T.S through monocot root  Epiblema Hypodermis General cortex Endodermis T.S through monocot root  General cortex Protoxylem Casparian strip Endodermis Metaxylem Pericycle Phloem Pith T.S through monocot root  Differences between roots and stems Root Stem 1 Hairs Unicellular Multicellular 2 Protoxylem Outside Inside  Differences between Dicot roots and Monocot roots Dicot root Monocot root 1 Xylem bundles 2-6 Numerous 2 Pith Small or absent Large Anatomy of Stems DICOTYLEDONOUS STEM  Epidermis: - It is the outermost single layer of parenchyma cells without intercellular spaces. - The outer walls of the epidermal cells have a layer called cuticle and multicellular hairs  Cortex Below the epidermis and differentiated into three layers: 1) Hypodermis Consists of 4 to 5 layers of collenchymatous cells. 2) General cortex Consists of a few layers of parenchymatous cells. 3) Endodermis - The cells of this layer are barrel shaped arranged compactly without intercellular spaces. -Due to abundant starch grains in these cells, this layer is also known as starch sheath.  Pericycle: Occurs between the endodermis and vascular bundles in the form of a few layers of sclerenchyma cells patches outside the phloem in each vascular bundle.  Vascular Bundles: - In dicot stem, vascular bundles are arranged in a ring around the pith. - Each vascular bundle is conjoint, collateral and open. - Composed of Phloem, Cambium and Xylem.  Pith: - Occupies the major portion of the stem. - Composed of parenchyma cells with intercellular spaces. - The extension of pith between vascular bundles are called as pith ray or medullary rays. T.S Through Dicot Stem  Cuticle Pericycle Epidermis Hypodermis Cortex Vascular Bundle Phloem General Cortex Cambium Endodermis Metaxylem Protoxylem Medullary ray Pith T.S Through Dicot Stem  General cortex T.S Through Dicot Stem MONOCOTYLEDONOUS STEM  Epidermis It is the outermost layer made up of single layer of tightly packed parenchyma cells with thick cuticle.  Hypodermis A few layers of sclerenchyma cells lying below the epidermis.  Ground Tissue - This is a continuous mass of thin-walled parenchyma. - It is not differentiated into cortex, endodermis, pericycle and pith.  Vascular Bundles -They are scattered in the ground tissue. -Each vascular bundle is surrounded by a sheath of sclerenchyma called bundle sheath. -The vascular bundles are conjoint, collateral and closed  Phloem - Consists of sieve tubes and companion cells (phloem parenchyma is absent).  Xylem - The two metaxylem vessels are located at the upper two arms and one protoxylem vessels at the base. (Y shaped). - The lowest protoxylem disintegrates and forms a cavity known as water containing cavity. T.S Through Monocot Stem  Hypodermis Cuticle Epidermis Ground Tissue Vascular Bundle T.S Through Monocot Stem Vascular Bundle of Monocot Stem  BUNDLE SHEATH PHLOEM METAXYLEM PROTOXYLEM BUNDLE SHEATH Vascular Bundle of Monocot Stem  Differences between Dicot stem and Monocot stem Dicot stem Monocot stem 1 Arrangement of Arranged in a circle Scattered vascular bundles 2 Type of vascular Open Closed budndle 3 Phloem Present Absent Parenchyma ANATOMY OF LEAVES DICOTYLEDONOUS LEAF  Epidermis 1- Upper epidermis: This is a single layer of cells with a thick cuticle to reduce the evaporating of water from the surface. 2-Lower epidermis: This is a single layer but with a thin cuticle, it contains numerous stomata. The lower epidermis is meant for the exchange of gases between the atmosphere and plant body, also excess water evaporates from the plant body mainly through the lower epidermis.  Mesophyll (ground tissue): - The ground tissue lying between the upper and lower epidermis is known as mesophyll. -It differentiates into palisade tissue and spongy tissue.  Palisade tissue: Consists of 2 or 3 layers of elongated, more or less cylindrical in shape, the cell contain numerous chloroplasts and manufacture starch in the presence of sun light.  Spongy tissue: Consist of oval, rounded or commonly irregular in shape, loosely arranged towards the lower epidermis, enclosing numerous, large, intercellular spaces and air- cavities. Spongy cells help diffusion of gases through the empty spaces, also they manufacture sugar and starch to some extent only as they contain a few chloroplasts. Vascular bundle Each vascular bundle consists of xylem towards the upper epidermis and phloem towards the lower epidermis. 1- Xylem: It consists of protoxylem, metaxylem and wood parenchyma. 2- Phloem: It consists of sieve tubes, companion cell and phloem parenchyma. 3- Cambium: Lies between xylem and phloem tissues.  Surrounding each vascular bundle a layer of thin walled cells known as boarder parenchyma.  Connected to the vascular bundle layers of parenchyma cells followed by layers of collenchyma cells on both sides (upper and lower).  Palisade tissue Xylem Upper epidermis Cuticle mesophyll Spongy tissue Cuticle Lower epidermis Stoma Phloem T.S through Dicot leaf T.S through Dicot leaf MONOCOTYLEDONOUS LEAF  Epidermis - This is a single layer of cells on both; upper and lower epidermis. - The epidermis on either side bears more or less an equal number of stomata, and is also somewhat uniformly thickened with cuticle.  Mesophyll (ground tissue): - Is often not differentiated into palisade and spongy tissues, but consists of parenchyma cells only (parenchyma of ground tissue), in which chloroplast are evenly distributed  Vascular bundles Each vascular bundle consists of xylem and phloem and surrounded by sheath of sclerenchyma which is closed to the mesophyll tissue. 1. Xylem: It consists of protoxylem and metaxylem. 2. Phloem: It consists of sieve tubes and companion cell.  Monocotyledonous leaves develop relatively large amount of Sclerenchyma cells in association with the vascular bundles (bundle sheath) or in separate strands. T.S Monocot leaf