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Coverage Cycle 1 - Introduction to Botany Main Topics: 1. Plant Cell Types 2. Meristems 3. Plant Tissues Cycle 2 - The Root, Stem, and Leaves Main Topics: 1. Roots 2. Stems 3. Leaves Cycle 3 - Flowers, Fruits, and Seeds Main Topics: 1. Flowers 2. Fruits 3. Seeds Cycle...

Coverage Cycle 1 - Introduction to Botany Main Topics: 1. Plant Cell Types 2. Meristems 3. Plant Tissues Cycle 2 - The Root, Stem, and Leaves Main Topics: 1. Roots 2. Stems 3. Leaves Cycle 3 - Flowers, Fruits, and Seeds Main Topics: 1. Flowers 2. Fruits 3. Seeds Cycle 4 - Cell Parts & Functions + Cell Cycle Main Topics: 1. Cell Types 2. Cell Parts 3. Cell Functions 4. Cell Cycle 5. Meiosis Cycle 5 - Cell Membrane and Cell Transport + Biomolecules Main Topics: 1. Meiosis (Continuation)  2. The Cell Membrane 3. Transport Mechanism 4. Biomolecules Cycle 6 - Photosynthesis Main Topic: 1. Photosynthesis 2. Light Dependant Reaction 3. Light Independent Reaction CYCLE 1 Plant Cell Types: Ground Tissue - Makes up the majority of a plant - Consists of: Parenchyma, Collenchyma, Sclerenchyma Parenchyma: - Alive at maturity - Most abundant - Functions: photosynthesis, respiration, gas exchange, storage of starch and other materials Collenchyma: - Elongated living cells - Unevenly thickened primary cell walls - Function: Elastic support Sclerenchyma: - Dead at maturity - Inelastic support to non-growing plant parts - Thick, rigid, secondary cell walls - Contain lignin: a tough, complex molecule wall that adds strength to cell walls Conducting Cells in Xylem and Phloem Vascular Tissues: - Transport water, minerals, carbohydrates, and other dissolved compounds throughout the plant Xylem: - Tracheids - Long, narrow cells that overlap at tapered ends - Water moves from tracheid to tracheid through pits (thin areas of the cell wall - Vessel Elements - Short, wide, barrel shaped - Side walls have pits; end walls are perforated or absent - Water movement is faster than tracheids Phloem: - Sieve Tube Elements - Main conducting cells of phloem - Align end to end to form sieve tube - Alive, but no nucleus and little cytoplasm - Companion Cells - Adjacent to sieve tube elements - Specialized parenchyma cell - Transfer carbohydrates in and out of the sieve tube elements - Provides energy and proteins to the conducting cells Determinate vs. Indeterminate Growth Determinate: - Plants that stop growing after reaching their mature size - Ex. bush types Indeterminate: - Plants that continue to grow as long as environmental conditions allow it - Ex. majority of tomato varieties Meristems: - Regions that undergo active mitotic cell division - Has patches of “immortality” – grow, replace damaged parts and respond to environmental changes - Apical - small patches of actively dividing cells near the tip of roots and shoots - Lateral - produce cells that thicken the stem or root Shoot Apical Meristem: - Primary growth - Lengthens shoot or root by adding cells, which originate at the apical meristems - Daughter cells give rise to: ground, epidermis, vascular tissue - Remnants remain in the axillary buds that form at stem nodes Root Apical Meristem: - (In order, going down) Area of Maturation, Area of Elongation, Area of Cell Division – MEC(D) shortcut lol - Some of the cells produced differentiate into the root cap - Other cells elongate by absorbing water - Zone of Maturation: cells complete their differentiation and mature into the functional ground, dermal, and vascular tissues Lateral Meristems: - Secondary Growth - Increases the girth of stems and roots in woody plants - Vascular Cambium: Internal cylinder of meristem tissue; produces thin layer (cork cambium) between primary xylem and phloem. Cork Cambium: - Gives rise to parenchyma to the inside and cork to the outside - Cork: densely packed, waxy cells on the surface of mature stem and roots; waterproof, insulating; dead at maturity and form layers Heartwood: - Innermost, darker - Gradually loses ability to conduct water - Dark-colored chemicals accumulate Sapwood: - Outer portion, lighter - Transports water and dissolved minerals Plant Tissues: Ground, Dermal, and Vascular Ground Tissue: - Fills the spaces between specialized cell types inside roots, stems, leaves, fruits, and seeds - Photosynthesis, respiration, and storage Dermal Tissue: - Herbaceous, covers the plant - Epidermis: single layer of packed, flat, transparent parenchyma cells - Woody plant; tough bark  - Cuticle: a waxy layer that coats the epidermis of the leaves and stem; conserves water and protects the plant; impermeable not only to water but CO2 and O2 - Stomata are pores through which leaves and stems exchange gasses with the atmosphere. - Guard cells surround the stomata and control its opening and closing. - Vascular Tissue: - Xylem: transports water and dissolved minerals - Phloem: transports dissolved organic compounds, mainly sugar - Vascular bundle: strand of tissue containing xylem and phloem, often having collenchyma tissue or sclerenchyma fibers Cycle 2 - The Root, Stem, and Leaves Cycle 2 Main Topic 1: Roots What are roots? - a plant organ that; - anchors a vascular plant in the soil - absorbs minerals and water - stores carbohydrates and other reserves Functions of Roots anchorage storage of food and materials absorption (uptake) and conduction (movement) of water and material nutrients to the other parts of the plant growth symbiotic relationship with nitrogen-fixing bacteria production of gibberellins (hormones that stimulate stem growth) Types of Roots Taproot Fibrous Root - Has a large primary root and - Primary root dies and many small smaller lateral roots. secondary roots arise from the - Grows straight downward and base of the stem becomes the dominant root of - the sizes of the roots are similar the plant - plants under this group are called - Some are fleshy and store food monocot plants - Plants under this group are called dicot plants  Monocot vs Dicot root under the microscope THINGS TO NOTE Monocot Dicot the Phloem are scattered around the the Phloem are in organized compact vascular cylinder groups the Xylem form a ring-like formation in the Xylem in the vascular cylinder form the center a cross or an X shape formation contains Pith in the center Root Anatomy Epidermis - outer layer of thin-walled, rectangular cells that act as protective coating Cortex - thin walled parenchyma cells that function in food storage Endodermis - boundary between cortex and the vascular cylinder Pericycle - first layer of cells within the endodermis - starting point of lateral roots Vascular tissue - both monocots and dicots have vascular cylinders that contain xylem and phloem Growth Zones of a Root Zone of Maturation (Cell Differentiation) - mature and fully differentiated cells - easily recognized due to the presence of root hairs Zone of Elongation - cells become longer as they become more specialized Zone of Cell Division - contains meristematic cells - newly formed cells are added to root cap below and on the zone of elongation above Root Cap - Covers and protects root tip - Releases CO2 that combines with water forming carbonic acid to corrode rocks and other coarse particles Root Modifications Buttress Roots - architectural support to the tree trunk - exposed - root systems are shallow Prop Roots - examples of adventitious roots, which arise from any plant part other than the root - extra mechanical support - increases absorption capacity Aerial Roots - epiphytes have aerial roots for a variety of reasons  - Green roots for photosynthesis - Tinospora cordifolia - Roots for climbing - English Ivy - Roots for capturing moisture - Orchids Pneumatophores - specialized root of some trees that grows into the air, allowing oxygen to diffuse in Root Symbiotic Relationships - symbiotic interactions with soil bacteria or fungi that increase a plant’s ability to absorb water and minerals Storage Roots - some roots are enlarged to store large amounts of starch. Parasitic Roots - some roots absorb nourishment from the host plant How can roots help economically? source of income food source medicinal source soil preservation Cycle 2 Main Topic 2: Stems What is a stem? - the organ bearing leaves and buds - elongates and orients the shoot in a way that maximizes photosynthesis by the leaves - lateral branches grow from lateral buds located at the angle where a leaf joins a stem - a node is the location where leaves, or the buds for branches, are attached to the stem - an internode is the region between nodes Functions of a stem - attachments for leaves, flowers, and fruits - conduction of water and minerals from the roots to all parts of the plant - storage of nutrients, organic molecules, water, and by products - contains meristematic tissue for cell production Parts of a stem Terminal Bud contains the shoot tip protected by modified leaves called bud scales Node points of attachments for leaves Internode space in between nodes Axillary Bud embryonic shoot that lies at the junction of the stem and petiole that gives rise to a branch Lenticels small raised areas where gas exchange in woody stems occurs Anatomy of Non-Woody Stem Epidermis covered by a waxy cuticle to prevent water loss Cortex fills the area between the epidermis and vascular tissue  Vascular Bundles scattered in monocots, single ring in dicots Pits occupies the center in dicots, lacking in the arrangement in monocots Anatomy of Wood Stem Bark contains cork, cork cambium, cortext, and phloem Cork Cambium lateral meristem that produce cork cells and replace the epidermis Cork Cells consists of densely packed dead cells with waxy walls called suberin protects, insulates, and waterproofs the surface of the stem Vascular cambium lateral meristem that produce most of the diameter of stem Secondary Xylem cells that matures outside the vascular cambium Wood secondary xylem that builds up year after year Springwood secondary xylem that contains wide vessels with thin walls produced by vascular cambium during spring Summerwood secondary xylem that produce cells within lower proportion of vessels Anatomy of Tree Trunk Heartwood older layers of secondary xylem that no longer transport water and minerals (xylem sap) closer to the center of the stem darker in color due to resin Sapwood newest, outer layers of secondary xylem that still transport xylem sap This growth will produce what we see as annual rings. Annual Rings - helps us recognize the age of a tree Stem Modification Stolons - horizontal stems that sprout from an existing stem and grow above ground, forming roots and new shoots at their own nodes Rhizomes - thickened, underground horizontal stems that produce shoots and roots - survive winter and contribute to asexual reproduction Tubers - swollen regions of rhizomes or stolons that store starch - potatoes are tubers and the potato “eyes” are the buds that mark the nodes Corms - bulbous underground stems that lie dormant during winter - solid and has no fleshy scales Succulents - specialized photosynthetic stem for water storage Thorns - modified branches appearing as hard, woody, sharp outgrowths that protect the plant Tendrils - allow the plant to climb from the forest floor to the canopy, maximizing exposure to sunlight. Economic Importance of Stem Food Shelter Clothing Source of Income Medicine Cycle 2 Main Topic 3: Leaves What are Leaves? - main photosynthetic organ that exchanges gasses with the atmosphere, dissipates heat, and defends itself from herbivores and pathogens - main site of transpiration Primary Functions Manufacture food through photosynthesis Site for gas exchange Evaporation of water through transpiration Protection of buds Conduction of water and dissolved solutes Prevent water loss through stomata  Leaf Parts Blade: large, flat part of the leaf where photosynthesis occurs Apex: tip of the leaf Margin: edge of the leaf Vein: carry food/water throughout the leaf, also acts as structural support Midrib: thick, large, single vein along the midline of the leaf Base: bottom of the leaf Petiole: the stalk that joins a leaf to the stem Stipule: the small, leaf-like appendage to a leaf, usually found at the base of the petiole Leaf Shape Simple Leaf - single undivided blade - some can be deeply lobed Compound Leaf - leaf blade consists of multiple leaflets - each leaflet has no axillary bud at its base - in some plants, leaflets are divided further into smaller leaflets Leaf Arrangement Alternate - attached singly (attached on alternating sides along the twig). Opposite - attached to the twig in opposing pairs Whorled - attached in clusters of three or more Leaf Venation Reticulate - if veins branch and re-branch into an elaborate network - DICOT Parallel - if all visible veins run side by side for the length of the leaf - MONOCOT Leaf Anatomy Epidermis Cuticle - helps keep it from drying out Stomata - opening where gas exchange occurs Guard Cells - regulate the opening and closing of the stomata Vascular Tissue Vein - vascular bundles that provide support for the leaf and transport to substances Xylem - transports water and minerals from roots to leaves Phloem - transports sugar from one part of the plant to another Ground Tissue Mesophyll - parenchyma cells that is sandwiched between upper and lower epidermis for photosynthesis Comparing Monocot and Dicot leaves: Mesophyll Cells Palisade Mesophyll - consists of one or more layers of elongated parenchyma cells on the upper part of the leaf Spongy Mesophyll - found below the palisade mesophyll with parenchyma cells that are more loosely arranged Comparing Monocot and Dicot leaves: Arrangement of Stomata Monocot: stomata are often present on both surfaces Dicot: typically most abundant on the lower surface Leaf Modifications Leaf Tendrils and Hooks - leaves that are modified to attach the plant to a support. Spines - leaves that protect the fleshy stem from herbivores Bulb - a short flattened stem encased in overlapping layers of thickened modified leaves called scales - Used to store food Bracts - leaves that look like petals, attracts pollinators Plantlets - some plants produce tiny, identical plantlets, each of which may fall to the ground and take root. - in this case, plants reproduce asexually. There are also a few carnivorous plant species with leaves that capture, digest prey, and absorb nutrients. Economic Important of Leaves Food Medicine Industry Dyes Fibers Cycle 3 - Flowers, Fruits, and Seeds Flowers Pollination helps with reproduction for flowers. Methods of Pollination: - Abiotic Pollination: 98% rely on wind, and 2% on water. Since their reproductive success doesn’t depend on attracting pollinators, there has been no selective pressure flavoring colorful or scented flowers. - Biotic Pollination: Most angiosperm species depend on insects, birds, or other animal pollinators to transfer pollen directly from 1 flower to another. Coevolution: The joint evolution of 2 interacting species, each in response to selection imposed by the other, is called coevolution. For example, some species have fused flower petals that form long, tubelike structures bearing nectaries tucked deep inside. Parts of a Flower: - Petals: Attract pollinators. - Sepals: Protect the bud as the flower develops. - Carpels: The female portion of a flower. - Stamens: The male portion of a flower.\ Stamens: The male portion of the flower. This has 2 parts namely Anther and Filament. The anther houses the pollen grains, while filament supports the anther. Carpel: This has 4 parts namely Stima, Style, Ovary, and Ovule. Stigma receives the pollen and is sticky. Style is the pathway for pollen. Ovary’s structure will become a fruit. Ovule’s structure will become the seed. Monocot vs. Dicot Flowers - Monocotyledon: 1 seed leaf. Have petals in multiples of 3. - Dicotyledon: 2 seed leaves. Have 4 or 5 petals. Complete flowers: Has sepals, petals, stamens, and carpels. If a flower lacks one or more, it’s an incomplete flower. Perfect flowers: Possess both stamens and carpels, if a flower only possesses one then it is an imperfect flower. 2 forms of pollination: - Self Pollination: Can reproduce by itself. - Cross Pollination: Needs another flower to reproduce. Alternation of Generations: Describes the life cycle of a plant as it alternates between a sexual phase and asexual phase. The sporophyte produces flowers.  - Pollination - Fertilization - Sporophyte Generation: The non-sexual stage of plant, plant grows and develops to form flowers. The flower produces reproductive cells called spores: Microspore and megaspore. Diploid stage. - Gametophyte Generation: The sexual stage of plants. Development of sperm cells and egg cells. Haploid stage. C3D2 Angiosperm: Sexual Reproduction Flowers (Sexual Reproduction) In this life cycle, a diploid (2n) sporophyte alternates with a haploid (n) gametophyte. The sporophyte (2n) produces haploid spores by meiosis. The spores develop into gametophytes. The gametophytes (n) produce gametes. Diploid (2n): A cell or organism that has paired chromosomes, one from each parent. Haploid (n): A cell or organism that contains a single set of chromosomes. Mitosis: Produces 2 diploid somatic cells that are genetically identical to each other. The chromosomes are still the same. This happens in body cells. Meiosis: Produces 4 haploid gametes that are genetically unique from each other. The chromosomes divide to half. This happens in sex cells. Microspore develops into sperm - Four microspores are produced via meiosis. Each one becomes a pollen grain. - A pollen grain first consists of 2 cells. - The larger the cell will eventually produce a pollen tube. - The smaller cell divides, either right way or later, to become 2 sperms. Megaspore develops into Embryo Sac: - 4 megaspores are produced via meiosis but only 1 survives. - The remaining cell divides 3 times through mitosis. - Embryo sac is developed containing seven celled structures containing a single egg cell. Eight-Nucleate, Seven-Cell Female Gametophyte From the eight generated haploid cells: - Two haploid cells move in the middle and join, forming a diploid cell. - Three cells move at the end of the embryo sac and later disintegrate. - Three cells move in the entry of the embryo sac. - One of the sperm will fertilize the egg cell which will be a diploid which will become the embryo, and the other one in fused polar nuclei which will be a triploid which will become the fruit. Endosperm will enclose the embryo, the embryo is either a monocot or a dicot, and it's covered by a seed coat. The seed is the ovule and the fruit is the ovary. Fruits: Protection of the seed and promotes seed dispersal. General Overview: - Inside the anther's pollen sacs, diploid cells divide by meiosis to produce four haploid microspores. - Meanwhile, meiosis also occurs in the female flower parts. The diploid cell in megaspores initially produces four haploid cells. Three of these cells disintegrate leaving one large megaspore. - In the anther of the flower, each of the four haploid microscopes develops and forms pollen grains. Each of these pollen grains contain one large and one small cell. The large cell becomes the pollen tube, and the small cell eventually forms two-sperm nuclei. - In the embryo sac of the flower, the large haploid megaspore undergoes three mitotic divisions forming eight cells. Eventually, two cells fuse together thus becoming one cell with two nuclei. Thus the result is a seven-celled structure. - After a pollen grain lands on the stigma, a pollen tube emerges. When the pollen tube reaches an ovule, it discharges its two sperm nuclei into the embryo sac. - One sperm nucleus fertilizes the egg cell and forms a diploid zygote which will later develop into an embryo. - The other sperm nucleus fuses with the embryo sac central cell's two nuclei. The result is a triploid cell that will become a tissue called endosperm. - Immediately after fertilization, the ovule contains an embryo sac with a diploid zygote and a triploid endosperm. - The ovule eventually develops into a seed: a plant embryo together with its stored food, surrounded by a seed coat. - The ovary grows rapidly to form the fruit. FRUITS Seeds develop from ovules, and fruits develop ovaries. Fruit Structure: - A fruit is the mature ovary of a flower. - The fruit protects the enclosed seeds and, when mature, aids in their dispersal by wind or animals. There are 3 layers of the ovary and all of it is called the Pericarp. During fruit development, the ovary wall becomes the pericarp, the thickened wall of the fruit. Regions of pericarp: - Outer Exocarp - Middle Mesocarp - Inner Endocarp Types of Fruits Simple Fruit: Derived from a single carpel or several fused scalpels. A simple fruit is either fleshy or dry. Examples of simple fleshy fruits: - Berry: Has a thin exocarp, fleshy mesocarp, and an endocarp enclosing one to many seeds. - Hesperidium: A berry that has a tough & leathery rind, such as oranges, lemons, and other citrus fruits. - Pepo: A specialized berry has a tough outer rind while the mesocarp and endocarp are fleshy. All members of the squash family, including pumpkins, melons, and cucumbers, form pepos. - Drupe: Has a thin exocarp, a fleshy mesocarp, and a hard, stony endocarp that encases the seed. Cherries, peaches, and plums are examples. Cherries, peaches, and plums are examples. - Pome: Fruits that develop from flower parts other than just the ovary. Apples and pears are pomes.  - Accessory Fruits: In apple flowers, the ovary is embedded in the receptacle to which the fleshy part is derived. It is only the apple core that develops from the ovary, the rest comes from the “Receptacle.” Simple Dry Fruits Dehiscent Fruits crack along two seams and shed their seeds into the environment when the fruit is ripe. Example of Simple Dehiscent Dry Fruits: - Legume: Derived from a single ovary with 2 rows of ovules. It split along 2 lines of dehiscence following maturation and drying. - Capsule: Composed of more than 1 carpel. The lily splits lengthwise into sections corresponding to the number of carpels. The sweet gum fruit, being a cluster of capsules, releases winged seeds as each ovary cracks open at maturity. - Follicle: Develops from a single ripened ovary and split once to release their seeds. The split is open along one seam and is always lengthwise. Indehiscent fruits on the other hand retain their seeds and do not crack open after ripening. Examples of Simple Indehiscent Dry Fruits: - Achene: Consists of a single seed that is attached to the wall of the ovary at only 1 point. Examples of achenes include sunflowers, dandelions, and buckwheat. - Grain: If the wall of the dry indehiscent fruit is thin, transparent and firmly attached to all points of the seed coat, the fruit is a grain. - Samara: A wind-borne fruit containing a single seed. Winged samara fruits are characteristic of elms, maples, and ashes.  - Nuts: One-seeded fruits with hard, stony pericarps. Examples are hazelnuts, chestnuts, and acorns. Compound fruits: Develops from several ovaries in either a single flower or multiple flowers. - Aggregate Fruit: More than one separate carpel. Results from the joining together several ovaries of the same flower. It’s either true or an accessory fruit.  - Multiple Fruit: Develops from an inflorescence, a group of flowers tightly clustered together. When the ovaries mature and thicken, they fuse together and become incorporated into one fruit. - Accessory fruit: Doesn’t develop from ovary walls but rather from the receptacle of flowers. SEEDS - Develops from the fertilized ovule and includes the embryo and endosperm within a seed coat. Double fertilization yields a diploid zygote (embryo) and a triploid central nuclei (endosperm). Endosperm Development: Usually develops first before the embryo. The central nuclei divides to form a multinucleate “supercell” with a milky consistency. Coconut “milk” and “meat” are examples of liquid and solid endosperm, respectively.  - Monocot Endosperms: The endosperm of grains such as corn, wheat and rice occupies the bulk of the kernel and is the main energy reserve for the development of the young seedling. A monocot stores the bulk of its energy in the endosperm. - Dicot Endosperms: Most dicot seeds lack endosperms upon maturity. Food reserves of the endosperm are completely transferred to the embryo. A dicot stores its food in the two cotyledons. Seed Structure: - Embryo: Young plant. - Endosperm: Stored food for the embryo. - Seed Coat: Encase the seed. - Radicle: Embryonic root.  - Epicotyl: Embryonic shoot. - Hypocotyl: Junction between roots and shoots. - Cotyledon: Seed leaf. Embryo Development: - Zygote undergoes mitotic division and gives rise to terminal and basal cells. - Basal cell gives rise to a suspensor which attaches to the parent plant. - Suspensor helps in transferring nutrients to the embryo. - Terminal Cell gives rise to most of the embryo. - Terminal Cell divides several times and forms into proembryo. - Here, cotyledons begin to form. - As the embryo elongates, shoot and root apex appear. Seed Dormancy: A survival mechanism by which seeds can delay germination until the right environmental conditions for seeding growth and development. Adaptation for Tough Times: Seeds of desert plants germinate after a heavy rainfall. Some seeds require fire to break dormancy. Seeds germinate after the harsh winters. Lettuce varieties break dormancy in shallow soil and ample sunlight. Seed Germination: Young roots grow downward in response to gravity. The shoot produces leaves as it grows upward and toward the light. First leaves begin photosynthesis. Seeds that are buried too deep in the soil will NOT emerge. - Germination in Dicots: The first organ to emerge is the radicle. Hook forms in the hypocotyl, and growth pushes the hook above ground. Hypocotyl straightens, the cotyledons separate, and the epicotyl spreads its first true leaves. - - Germination in Monocots: Shoot tip grows through the coleoptile (sheath) once it has pushed through the surface of the soil. The cotyledon remains belowground. - Does seed size matter? Larger seeds are better able to support themselves initially, while smaller seeds have a better chance for dispersal over a wide area, helping at least some seedlings survive. Cycle 4 - Cell Parts & Functions + Cell Cycle CELL TYPES - Prokaryotic Cells: No definite nucleus, much smaller than eukaryotic cells, less complex internal structures, no nuclear membrane, no membrane-bound organelles in their cytoplasm. Bacteria is an example. - - Eukaryotic Cells: Nucleus surrounded by a nuclear membrane, bigger in size, more complex structure. Eukaryotic cells are compartmentalized, which allows specialization for the organelles. - - 4 main basic features: Cytoplasm, DNA, Ribosomes, and Cell Membrane. Cal Woese’s 3 Domains of Life: - Bacteria: Simple unicellular organisms. - Archaea: Simple unicellular organisms that often live in extreme environments. - Eukarya: - Protista: Unicellular and are more complex than bacteria/archaea. - Fungi: Unicellular or multicellular and absorb food. - Plantae: Multicellular and make their own food. - Animalia: Multicellular and take in their food. Endosymbiotic Theory: Some eukaryotic cell organelles, such as mitochondria and chloroplast, evolved from free-living prokaryotes. Explanation of how eukaryotes evolved from prokaryotic cells. Some of the large cells engulfed, and the small bacteria became intact and lived with the large cells. “Endo”= inside, “Symbiosis”= living together. Mitochondria and chloroplasts are similar to bacteria in size and in structure. Both organelles are surrounded by a double membrane. Both organelles contain a limited amount of genetic material and divide by splitting. Both organelles have their own ribosomes and they produce some proteins. Ribosomes resemble those of prokaryotes. Cell Structure and Function Plasma Membrane: Phospholipid bilayer embedded with proteins and steroid molecules. Encloses the Cytoplasm. Regulates interactions with the external environment. The proteins allow the entrance and exit. - Phospholipids: Amphipathic. It’s composed of Hydrophilic region which is polar and allows water in, and a hydrophobic region which is non-polar which doesn’t let water in. The polar head is hydrophilic and the nonpolar tails are hydrophobic. - Fluid Mosaic Model: The membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids.  - Phospholipid: Responsible for the selective permeability of cells. - Sterols (fml): Fats that maintain the membrane’s fluidity as the temperature fluctuates. - Glycoproteins: Sugar attached to proteins for cell identification. Tour of the Cell Nucleus (Information Central): Houses of the cell’s genetic material (DNA). Controls the passage of molecules across its membrane. Components of Nucleus: - Chromatin: DNA and associated proteins. - Nucleoplasm: Semifluid Interior - Nuclear Envelope: Double membrane with nuclear pores that control which substances enter and exit the nucleus. - Nucleolus: Region where ribosomal subunits are being produced. Ribosomes (Protein Factories): Cellular components that carry out protein synthesis. May be suspended in the cytoplasm or bound to membranes. Cytoplasm: Composed of a semifluid substance made of water, salts and organic compounds called “Cytosol.” Where organelles are suspended. Cytoskeleton: Network of fibers extending throughout the cytoplasm. Give mechanical support to the cell and maintain its shape. For support: - Actin: Consists primarily of subunits of the protein actin. Form scaffolding for proteins that function in cellular movement, contraction, shape changes, and migration. - - Intermediate Filaments: Made from a variety of proteins. Form a stable framework that lends structure and resilience to cells and tissues. - - Microtubules: Consist of subunits of the protein tubulin and can rapidly assemble when they are needed, and disassemble when they are not. - Cell Division: - Centrosome: Microtubule organizing center located near the nucleus. - Centrioles: Barrel shaped microtubules that assist in animal cell division. Endoplasmic Reticulum (ER): Consists of a network of membranous tubules and sacs called “Cisternae.” ER consists of rough ER and smooth ER which have different structures and functions. - Rough ER: Ribosomes attached in rough ER produce proteins. Add carbohydrate (sugar) chains to proteins, forming glycoproteins. Form transport vesicles. Adds membrane proteins and phospholipids to its own membrane. Manufacturing. - - Smooth ER: Synthesize lipids, including oils, steroids, and new membrane phospholipids. Detoxify drugs and poisons, especially in liver cells. Store calcium ions for muscle contraction. Form vesicles for transport. - Golgi Apparatus: Shipping and receiving center. Flat, membrane bound sacs. Sorts, modifies, packages, distributes molecules to their destination. Produces Vesicles. Lysosomes: Digestive Compartments. Vesicles produced by golgi bodies. Contain enzymes that dismantle and recycle food particles, captured bacteria, worn-out organelles, and debris. Mitochondria: Chemical energy conversion. Power generation. Changes the energy stored in food to ATP (Adenosine Triphosphate). Chloroplasts: Capture of light energy. Contains the green pigment called “Chlorophyll,” along with enzymes and other molecules that function in the photosynthetic production of sugar. Cristae is not part of chloroplasts, more for mitochondria. Peroxisome: Oxidation; membrane-bound vesicles that contain enzymes break down fatty acids and dispose of toxic substances. Vacuoles: Diverse maintenance compartments; large vesicles derived from the ER and Golgi apparatus that vary in function. Plant vs Animal Cell: Plant cells have cell walls composed of cellulose and a cell membrane. Animals have small vacuoles, while plants have large central vacuoles. Plants cells contain plastids such as chloroplasts, while animals do not. Cell Modifications and Adaptations: - Cilia and Flagella: Whiplike projections of cells. Cilia are short and move stiffly, and flagella are longer and move in an undulating, snakelike fashion. - - Villi and Microvilli: Villi is a finger-like projections that arise from epithelium of some organs. Microvilli are small projections that arise from the cell’s surface; both increase the surface area. - Cell Wall (Plants): Extracellular structure of plant cells that provides support to the cell. - Primary Wall - Middle Lamella - Secondary Wall - Extracellular Matrix (Animals): - Collagen: Forms strong fibers outside the cell. - Proteoglycan: Protein core with carbohydrate chains. - Fibronectin: Attaches the ECM to integrins. - Integrins: Bind to the ECM on the outside. - Cell Junctions (Plants): Plasmodesmata: Allow substances to move between plant cells. Cell Junctions (Animals): Desmosomes: Connect adjacent animal cell membranes in one spot; connect cells to the extracellular matrix. Tight Junction: Close the spaces between animal cells by fusing cell membranes.  Gap Junction: Form channels between animal cells, allowing exchange/communication of substances. Summary Cell Cycle Basic of Cellular Reproduction: - Children grow - Tissue repair - Amoebas reproduce - Zygotes develop Chromatin to Chromosome: - Chromatin: Collective term for all of the cell’s DNA and its associated proteins. Organized into nucleosomes so that it will be equal once it divides, each consisting of a stretch of DNA wrapped around eight proteins (histones). Loosely packed compared to chromosomes. Structure of DNA in a non-dividing cell. - Chromosomes: Condensed form of chromatin. Duplicates before cell division. Composed of two identical halves, called “Sister chromatids,” held together at a constricted region called a “Centromere.” A single chromatid should duplicate to be able to be a chromosome. Replicated structure of the DNA before dividing. Cell Cycle: Orderly sequence of stages that involve cell growth and cell division. Interphase - G1 Phase: The cell doubles its organelles and accumulates material that will be used for DNA replication. The cell grows in size, and it performs normal daily functions. - - G0 Phase: Resting phase; cells in G1 may temporarily or permanently exit the cell cycle by entering a reversible, non-dividing state. In the G0 phase, a cell continues to function, but it does NOT replicate its DNA or divide. Most cells in the human body are in G0 (e.g. nerve cells). - S Phase: The cell replicates its DNA. DNA replication occurs here. At the beginning of the S phase, each chromosome has one chromatid consisting of a single DNA double helix. At the end of this stage (M Phase), each chromosome is composed of two sister chromatids, each having one double helix. Duplication of centrosomes in animal cells. Centrosomes are structures that organize the mitotic spindle, a set of microtubule proteins that coordinates the movement of chromosomes during mitosis. - - G2 Phase: The cell synthesizes the proteins that will be needed for cell division. The cell synthesizes proteins that will assist cell division (microtubules). The DNA winds more tightly, and this starts chromosome condensation signals.  - M Phase & Cytokinesis - Mitosis: Nucleus and its contents divide and are evenly distributed, forming two daughter nuclei. - Cytokinesis: Cytoplasm along with all the organelles is divided in two. - G2 Late Interphase: A nuclear envelope encloses the nucleus. Nucleolus is visible. Chromosomes, duplicated, can’t be seen yet because they have not yet condensed. - - Prophase: Chromosomes are condensed and become visible, while nucleolus disappears. Spindle forms as centrosomes move to opposite poles. - - Prometaphase: Nuclear envelope breaks up. The microtubules extending from each centrosome can now invade the nuclear area. Spindle fibers attach to kinetochores on chromosomes. - - Metaphase: Chromosomes line up along the equator of the cell called metaphase plate. The centrosomes are now at opposite poles of the cell. - - Anaphase: Centromeres split as sister chromatids separate and move to opposite poles of the cell. By the end, the two ends of the cell have equivalent and complete collections of chromosomes.  - - Telophase: Nuclear envelope and nucleolus form at each pole. Chromosomes decondense. Nucleoli reappear, spindle disappears. - - Cytokinesis: Division of the cytoplasm into two cells. - Animal Cytokinesis: For animal cells, contractile rings form. The cytokinesis process is known as cleavage. - - Plant Cytokinesis: Vesicles fuse at the middle forming a membranous disc called the cell plate, which grows outward until it reaches the cell wall.  - Checkpoints: Several internal “checkpoints” ensure that a cell doesn’t enter one stage of the cell cycle until the previous stage is completed - G1 Checkpoint: The cell can enter G0 or undergo apoptosis if DNA is damaged beyond repair. If the cell cycle passes this checkpoint, the cell is committed to complete the cycle. - G2 Checkpoint: The cells check to make sure DNA has been replicated properly. Allows damaged DNA to be repaired before it is passed on daughter cells. - Mitotic Checkpoint: The cell makes sure the chromosomes are properly aligned and ready to be partitioned to the daughter cells. Apoptosis (Programmed Cell Death): Apoptosis shapes structures and kills cells that could become cancerous. It eliminates excess cells, and weeds out aging or defective cells. - Benign: Not cancerous, and usually does not grow larger. - Malignant: Cancerous and possesses the ability to spread.  - Development of Cancer Cells: Cell (red) acquires a mutation for repeated cell division. New mutations arise, and one cell (teal) has the ability to start a tumor. One cell (purple) mutates further. It invades the other parts, spreading if it’s malignant. Many cancer cells are essentially immortal as the telomore doesn’t become short like normal cells does. Cancer cells have uncontrolled division as well, as if proto-oncogene or tumor suppressor gene become mutated, it would become a cancer cell. Characteristics of Cancer Cells: Cancer cells lack anchorage dependence. Cancer cells lack contact inhibition. Tumor cells keep on dividing even if the layer is already filled. Summary  Sexual Reproduction and Meiosis (1) The Human Life Cycle - Mitosis: Makes sure that every body cell has 23 pairs of chromosomes. It occurs during growth and repair. - Meiosis: Involved in the formation of sex cells. Ensures that the gametes are haploid and have 23 chromosomes, 1 from each of the pair of chromosomes. - Meiosis is important as it reduces the chromosome number, and shuffles the chromosomes and genes to produce genetically different gametes, called sperm and eggs. Homologous Chromosomes: The same size with the same centromere position, and they contain the same genes. Diploid cells in humans have 22 homologous pairs of autosomes (body chromosome) and 1 pair sex chromosomes, for a total of 46 chromosomes. And sex chromosomes of males are XY, and females are XX. Y is smaller, and X is bigger. Human Karyotype.  - Homologous Chromosomes (Not Identical): Two homologs differ in the combination of alleles, or versions, of the genes they carry. Each allele of a gene encodes a different version of the same protein. - Overview of Meiosis: During meiosis 1, homologous chromosomes pair and separate. During meiosis 2, the sister chromatids of each duplicated chromosome separate. At the completion of meiosis, there are four haploid and daughter cells. Synapsis and Crossing Over: During meiosis 1, the homologous chromosomes of each pair come together and line up side by side in an event called synapsis. Synapsis results in a tetrad, and association of four chromatids (two homologous chromosomes consisting of two chromatids each.) For crossing over, they change in the alleles only. Genetic Recombination: Chiasma indicates where crossing over has occurred. The exchange of color represents the exchange of genetic material. Independent Assortment of Homologous Chromosomes: Homologous chromosome pairs separate independently, or randomly. When homologues align at the metaphase plate, the maternal or paternal homologue may be oriented toward either pole. Phases of Meiosis 1: - Prophase 1: Tetrads form, synapsis and crossing-over occurs as chromosomes condense; the nuclear envelope fragments. Homologous chromosomes pair during synapsis. - Metaphase 1: Homologous chromosome pairs align at the metaphase plate. Either homologue can face either pole. - Anaphase 1: Homologous chromosomes separate, pulled to opposite poles by centromeric spindle fibers. - Telophase 1: Daughter nuclei are haploid, having received one duplicated chromosome. - Interkinesis: A short rest period prior to the beginning of the second nuclear division, meiosis 2; replication does not occur anymore. Similar to interphase, except that DNA replication does not occur. Meiosis 2: - Prophase 2: Chromosomes condense, and the nuclear envelope fragments so that the chromosomes inside attach to spindle fibers - Metaphase 2: The dyads align at the spindle equator. - Anaphase 2: Sister chromatids start to separate. - Telophase 2: Four haploid daughter cells are genetically different from each other and from the parent cell. - - Meiosis I vs Mitosis Meiosis II vs Mitosis Part #2 Changes in Chromosome Number Nondisjunction: Accounts for the inheritance of an abnormal number of chromosomes. For example, a homologous pair of chromosomes fails to separate during meiosis I. Another example is when the sister chromatids fail to separate during meiosis II. - Down Syndrome: An example of autosomal syndrome, the individual inherits three copies of chromosome 21. - Extra or missing sex chromosomes: - Triplo-X (XXX): Female has three x chromosomes. Many girls don’t experience symptoms or have only mild symptoms. Increased learning disabilities. Delayed speech. Weak muscle tone. - - Klinefelter (XXY): A condition that occurs in men who have an extra X chromosome. The syndrome can affect different stages of physical, language, and social development. The most common symptom is infertility. Boys may be taller than other boys their age, with more fat around their belly. - - Jacobs Syndrome (XYY): Characterized by an extra copy of the Y chromosome in each of a male’s cells. Although many male’s with this condition are taller than average, the chromosomal change sometimes causes no unusual physical features. - - Turner Syndrome (XO): The cause is a missing or incomplete X chromosome. Turner syndrome is a genetic disorder that affects a girl’s development. Girls who have it are short, and their ovaries don’t work properly. - Changes in chromosome structure may be harmful: It can delete or duplicate genes. An inversion flips gene order; in a translocation, two non-homologs exchange parts. Cycle 5 - Cell Membrane and Cell Transport + Biomolecules Cycle 5 Main Topic 1: Meiosis (Continuation) Stuff not already mentioned: Importance of Meiosis 1. Reduces the chromosome number 2. Shuffles the chromosomes and genes to produce genetically different gametes, called sperm (males) and eggs (females) Meiosis I vs Meiosis II Prophase I Prophase II Pairing of homologous chromosomes, No pairing of chromosomes crossing over Metaphase I Metaphase II Tetrads at spindle equator Haploid number of dyads at spindle equator Anaphase I Anaphase II Homologues of each tetrad separate, Sister chromatids separate, becoming dyads move to poles daughter chromosomes that go to poles Telophase I Telophase II Two haploid daughter cells, not Four haploid daughter cells, not identical to the parent cell identical to each other and parent cell Cycle 5 Main Topic 2: The Cell Membrane (Biochem) Prominence of Membranes - a membrane is an essential feature of every cell - it is the boundary of the cell and its internal compartments Functions of Membranes - transport - signaling - adhesion The Plasma Membrane - the plasma membrane contains a phospholipid bilayer with numerous proteins embedded in it. - cholesterol provide support Phospholipids are Amphipathic Composed of: - Hydrophilic layer (polar) - Hydrophobic layer (non-polar) Lipids and small, nonpolar molecules pass freely across the membrane Saturated and Unsaturated Fat Saturated Unsaturated - at room temp, solid - at room temp, liquid - molecules are packed closely - cannot pack together closely together enough to be solid - structural formula of a saturated - structural formula of an fat molecule: unsaturated fat molecule: Due to the presence of double bonds in the hydrophobic tail of phospholipids, a kink (bend) is formed. This causes the membrane to be “fluid”. Fluid-Mosaic Model - in this model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids Membrane Lipids - Fluid Part in Fluid-Mosaic Phospholipid - responsible for the selective permeability of cell - basically, responsible for the ability of the cell to choose what goes through the membrane Sterols - maintain the membrane’s fluidity as the temperature fluctuates Functions of Membrane Proteins Channel Proteins - allows only one or a few types of specific molecules to move across Carrier Proteins - moves substances across the membrane with an input of energy Enzymatic Activity - enzymatic proteins directly participate in metabolic reactions Adhesion Proteins - The junctions assist cell-to-cell adhesion and communication Glycoproteins - Enable our bodies to distinguish between our own cells and others Receptor Proteins - has a shape that allows a specific molecule, called a signal molecule, to bind to it Membrane Proteins - Mosaic Part in Fluid-Mosaic Integral Proteins proteins embedded within the membrane types: ○ Integral monotopic protein  ○ Singlepass protein ○ Multipass protein ○ Multi-subunit protein Peripheral Proteins proteins bound to the surface of the membrane a.k.a. peripheral membrane proteins Lipid-anchored Proteins proteins located on the surface of the cell membrane that are attached to the lipids within the cell membrane types: ○ fatty acid or isoprenyl anchor ○ GPI anchor Cell to Cell Recognition Glycolipids - carbohydrate groups attached to lipids Glycoproteins - carbohydrate groups attached to proteins for cell recognition Attachment to the cytoskeleton and extracellular matrix (ECM) - microfilaments of the cytoskeleton may be bound to membrane proteins to maintain cell shape and stabilize the location of certain membrane proteins. Fluidity of Membrane - membranes are not static sheets of molecules locked rigidly in place Factors affecting membrane fluidity Double Bonds - Because of the kinks in the fatty acid chains where double bonds are located, unsaturated hydrocarbon tails cannot pack closely together, thus making the membrane more fluid. Steroids - the steroid cholesterol has different effects on membrane fluidity at different temperatures Cycle 5 Main Topic 3: Transport Mechanism Mechanisms for regulating the passage of material 1. Passive Transport - does not require energy input - ex. Diffusion, Facilitated Diffusion, and Osmosis 2. Active Transport - does require energy input - ex. Sodium-Potassium Pump 3. Bulk Transport - use vesicles to transport substances - Endocytosis and Exocytosis Passive transport - substance moves across a membrane without the direct expenditure of energy Simple diffusion - spontaneous movement of a substance from a region where it is more concentrated to where it is less concentrated - also occurs across membranes - substances may enter or leave cells by simple diffusion only if they can pass freely through the membrane Facilitated diffusion - some substances cannot cross a membrane on their own (too large) so they are assisted by transport proteins Effects of Osmosis on Water Balance - water diffuses across the membrane from the region of high free water concentration to that of lower free water concentration until the solute concentration on both sides of the membrane are nearly equal Diffusion vs Osmosis Diffusion Osmosis - solute molecules move from high - solvent molecules move from low to low concentration to high solute concentration Effects of Osmosis on Cells - Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water - Hypo (less than) - Iso (same as) - Hyper (more than) - Isotonic: cell is normal - Hypotonic: cells swell and burst, turgid - Hypertonic: cells shrivel up, cytoplasm shrinks from cell wall If an ANIMAL cell is placed in an environment that is: Isotonic to the Cell Hypertonic to the Cell Hypotonic to the Cell There will be no net The water inside the cell Water enters inside the movement of water goes out. cell faster than it leaves. across the membrane. The cell is stable. The cell shrinks. The cell bursts. If a PLANT cell is placed in an environment that is: Isotonic to the Cell Hypertonic to the Cell Hypotonic to the Cell the solution inside the cell the solution outside the the solution outside the is similar or equal to the cell has greater solute cell has less solute than solution outside the cell than the one inside cell the one inside the cell The cell is flaccid. Water inside goes out. The cell is turgid. Active transport - a cell uses a transport protein to move a substance against its concentration gradient (from less concentrated to more concentrated) Sodium-Potassium Pump - cells must contain high concentrations of potassium (K+) and low concentrations of sodium (Na+) to perform many functions Bulk Transport - macromolecules are often too large to be moved by just transport proteins, so vesicles are formed - vesicles are like bubbles that carry stuff - ex. transport vesicles that buds from and to the golgi apparatus Phagocytosis - also known as cellular-eating - cells engulf a particle by extending pseudopodia around it and packaging it within a membranous sac called a food vacuole. Pinocytosis - also known as cell drinking - this occurs when vesicles form around a liquid or around very small particles Receptor-Mediated Endocytosis - a form of endocytosis in which receptor proteins on the cell surface are used to capture a specific target molecule - human cells use this to take in cholesterol - cholesterol travels in the blood in particles called low-density lipoproteins Cycle 5 Main Topic 4: Biomolecules (Biochem) just the biochem lessons cycle 1-3 Cycle 6 - Photosynthesis Cycle 6 Main Topic 1: Photosynthesis What is Photosynthesis? - Metabolic pathway by which most autotrophs use the energy of light to make sugars from carbon dioxide and water. - it is a Redox Reaction, the reduction of carbon dioxide using energy from the sun produces carbohydrate. in cellular respiration, the oxidation of carbohydrates produces energy and carbon dioxide. Redox Reactions - the transfer of electrons from one molecule to another is an oxidation-reduction reaction - the loss of electrons from one substance is called oxidation - the addition of electrons to another substance is called reduction Life Depends on Photosynthesis Autotrophs - organism that makes its own food using energy from the environment and carbon from inorganic molecules such as CO2. Heterotrophs - organism that obtains carbon from organic compounds assembled by other organisms Sunlight is the Energy Source - the sunlight that reaches Earth’s surface consists of three main components: UV radiation, visible light, and infrared radiation - the segment most important to life is visible light (380 nm-750 nm) Photosynthetic Pigments - chlorophylls a and b absorb red and blue wavelengths; they appear green because they reflect green light - carotenoids absorb light in the violet-blue-green range, but not the yellow-orange range Chloroplasts are the Site of Photosynthesis - the raw materials for photosynthesis are carbon dioxide and water - mesophyll cells contain chloroplasts that carry out photosynthesis - inside the chloroplasts are thylakoids which contain pigments like chlorophyll - the stroma is a fluid-filled space where Calvin cycle occurs Cycle 6 Main Topic 2: Light Dependent Reactions Light Reactions - pigment molecules capture sunlight energy and transfer it to molecules of ATP and NADPH ATP Molecule: Energy for Cells - is a nucleotide composed of the nitrogen-containing base adenine and the 5-carbon sugar ribose (together called adenosine), and three phosphate groups - stores energy in its high-energy phosphate bonds ATP-ADP Cycle - when ATP is used as an energy source, a phosphate group is removed by hydrolysis - phosphorylation is the process of adding a phosphate group to a molecule - the reverse reaction, dehydration synthesis, releases water and regenerates ATP from ADP and P. this requires energy. - ATP is primary regenerated in the mitochondria by cellular respiration NADPH - is a mobile electron carrier - in photosynthesis, its function is to transport two electrons and a proton from the light dependent reactions to the calvin cycle Photosystems - in the thylakoid membrane, chlorophyll molecules are organized into clusters called photosystems - a reaction-center complex contains a pair of special chlorophyll a molecules and a molecule called the primary electron acceptor. - a light-harvesting complex consists of various pigment molecules bound to proteins The Light Reactions Use Two Photosystems Photosystem II and Photosystem I are named for the order in which they were discovered, so basically 2 comes first Overview of Light Dependent Reactions - the following occurs in the thylakoid membrane during light reactions: Both photosystems II and I receive photons - chlorophyll within the thylakoid membrane absorbs solar energy and energizes electrons PS II splits water - water is oxidized, releasing electrons, hydrogen ions, and oxygen The electron transport chain establishes an energy gradient - ATP is produced from ADP + P with the help of an electron transport chain PS I produces NADPH - NADP+ accepts electrons (is reduced) and becomes NADPH Steps 1. A special pair in photosystem II absorbs energy and emits electrons (e-) 2. the photosystem pulls replacement electrons from water molecules, which then break apart into hydrogen ions and oxygen atoms. the oxygen leaves the cell in O2 gas. 3. the electrons enter an electron transfer chain in the thylakoid membrane 4. energy released by the electrons as they move through the chain is used to actively transport hydrogen ions from the stroma into the thylakoid compartment. this forms a hydrogen ion gradient across the thylakoid compartment. 5. photosystem I absorbs energy and its special pair emits electrons. replacement electrons come from photosystem II via electron transfer chain. 6. electrons from photosystem I enter an electron transfer chain, then combine with NADP+ and H+ to form NADPH 7. hydrogen ions in the thylakoid compartment follow their gradient across the thylakoid membrane by flowing through ATP synthases 8. hydrogen ion flow causes ATP synthases to phosphorylate ADP, so ATP forms in the stroma. Electron transfer chain - each photoexcited electron passes from the primary electron acceptor of PS II to PS I via an electron carrier (plastoquinone (Pq), cytochrome complex, and plastocyanin (Pc)) - the fall of electrons to lower the energy level provides energy for the synthesis of ATP - photoexcited electrons are passed down from the primary electron of PS I through a protein called ferredoxin (Fd) - the enzyme NADP+ reductase catalyzes the transfer of electrons from Fd to NADP+, two electrons required ATP Production - during light dependent reactions, the thylakoid space acts as a reservoir for hydrogen ions - each time water is split, two hydrogen ions remain in the thylakoid space - hydrogen ions are pumped from the stroma into the thylakoid space due to ETC - this hydrogen ion gradient contains a large amount of potential energy ATP Synthase - a channel in ATP synthase allows the hydrogen ions trapped inside the thylakoid space to return to the chloroplast’s stroma - as the gradient dissipates, energy is released - the ATP synthase enzyme uses this energy to add phosphate to ADP, generating ATP Cycle 6 Main Topic 3: Light Independent Reactions Calvin Cycle uses the energy made from the light dependent reactions to build sugar molecules out of carbon dioxide the following events occur in the stroma during calvin cycle: ○ CO2 is taken up by one of the molecules in the cycle carbon dioxide (CO2) from the atmosphere is utilized in 3 steps: (1) Carbon Dioxide Fixation (2) Carbon Dioxide Reduction (3) Regeneration of RuBP ○ ATP and NADPH from the light reactions reduce CO2 to a carbohydrate (G3P) reactions produce molecules of G3P, which plants use to make glucose and other types of organic molecules Inputs and Outputs Inputs ATP - from light reactions NADPH - from light reactions CO2 - from the air, via stomata Outputs G3P - from calvin cycle, can be used for cellular respiration, cellulose, and food storage  Carbon Fixation - 3 CO2 enters the cycle one at a time - CO2 attaches to a 5-carbon sugar called ribulose bisphosphate (RuBP) through the enzyme called rubisco - the product of this reaction is an unstable 6-carbon intermediate that immediately splits in half, forming 2 molecules of 3-phosphoglycerate (PGA) for each CO2 fixed. - since there will be 3 CO2 that will enter the cycle, there will be 3 unstable 6-carbon molecules which will split in half, forming a total of six 3-PGA Simplified: 3 RuBP ---(interacts with)> Rubisco & 3 CO2 ---(turns into)> 3 Unstable 6-Carbon ---(instantly splits into)> 6 3-PGA Carbon Reduction - each 3-PGA receives an extra phosphate group from ATP, becoming 1,3-bisphosphoglycerate - a pair of electrons donated from NADPH reduces 1,3-bisphosphoglycerate to become glyceraldehyde 3-phosphate (G3P). - a phosphate group is lost in the process - of the 6 G3Ps, 5 will be recycled into RuBP and the other 1 exits the cycle Simplified: 6 3-PGA ---(interacts with)> 6 ATP ---(to form)> 6 1,3-bisphosphoglycerate ---(receives electrons from)> 6 NADPH ---(to form)> 6 G3P, 1 leaves cycle, 5 to be recycled  Regeneration of RuBP - the remaining 5 G3P molecules are rearranged into 3 molecules of RuBP - to do this, the cycle uses 3 more molecules of ATP Simplified: 5 G3P ---(interacts with)> 3 ATP ---(to form)> 3 RuBP Fate of G3P G3P is the product of the Calvin cycle that can be converted into other molecules a plant needs such as: ○ carbohydrates; sucrose, starch, and cellulose ○ fatty acid synthesis leads to triglycerides making up plant oils ○ production of amino acids allows the plant to make proteins credit to creators: @justin.ctby @gelopanganiban @hayiladana