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Gen-bio reviewer Module 1 — cell theory, structure and function Cell Theory 1839 by Schleiden & Schwann foundation of modern biology. The CELL THEORY, or cell doctrine, states that all organisms are composed of similar units of organization, called cells. 1. All living thing...

Gen-bio reviewer Module 1 — cell theory, structure and function Cell Theory 1839 by Schleiden & Schwann foundation of modern biology. The CELL THEORY, or cell doctrine, states that all organisms are composed of similar units of organization, called cells. 1. All living things are composed of cells 2. Cells are the basic units of structure and function in living things 3. All cells are produced from other cells Modern Tenets of the Cell Theory all known living things are made up of cells. the cell is structural & functional unit of all living things all cells come from pre-existing cells by division cells contains hereditary information which is passed from cell to cell during cell division All cells are basically the same in chemical composition. all energy flow (metabolism & biochemistry) of life occurs within cells. Prokaryotes vs Eukaryotes Prokaryotes Eukaryotes do not have membrane bound nucleus membrane bound nucleus DNA- bundled together in the nucleoid nucleus- where eukaryotes stores their region genetic information Not stored within a membrane bound nucleus Parts of the Cell 1. Cell membrane 2. Nucleus 3. Cytoplasm The Cell Membrane – Also known as the Cell membrane/cytoplasmic membrane – A biological membrane that separates the interior of a cell from its outside environment  – To protect cell from its surroundings – composed of phospholipid bilayer ( with embedded proteins) plasma membrane 1. regulates the movement of substances in and out of the cell 2. must be very flexible to allow certain cells ( red and white blood cells) to change shape as they pass through narrow capillaries The Organelles – Carries out unique functions inside the cell Membranous Non-membranous Mitochondria Ribosomes Plastids Cytoskeleton Golgi apparatus Nucleolus Endoplasmic reticulum Centrosome The compartmentalization of the cell into membrane-bound organelles – allows conflicting functions (i.e., synthesis vs. breakdown) and several cellular activities to occur simultaneously without interference from each other – separates the DNA material of the nucleus, mitochondria, and chloroplast – increases the surface area-volume ratio of the cell Plans cell vs Animal cell Plant Animal Have plastids ( chloroplast ) Do not have plastids Have a cell wall ( made of cellulose ) Do not have cell wall Have a large central vacuole Have a small temporary vacuole ( in any) May have plasmodesmata Do not have plasmodesmata Do not have centrioles Have paired centrioles with centrosome Do not have cholesterol in a cell Have cholesterol in the cell membrane membrane Store excess glucose as starch Store excess glucose as glycogen Generally have fixed, regular shape Generally have an amorphous shape Endomembrane System, Mitochondria, Chloroplasts, Cytoskeleton, and Extracellular Components – The endomembrane system (endo- = “within”) – a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. – It includes a variety of organelles Parts of the endomembrane syatemy. Endoplasmic reticulum – rough er – smooth er. Golgi apparatus. Lysosomes. vacuoles. Peroxisomes endoplasmic reticulum – modification of proteins and the synthesis of lipids. rough ER – gets its name from the bumpy ribosomes attached to its cytoplasmic surface smooth ER – continuous with the rough er but has few or more ribosomes on its cytoplasmic surface golgi appratarus – sorting, tagging, packaging, and distribution of lipids and proteins occur lysosomes – acts as the organelle-recycling facility of an animal cell. – It breaks down old and unnecessary structures so their molecules can be reused. vacuoles – stores water and wastes, isolates hazardous materials, and has enzymes that can break down macromolecules and cellular components, like those of a lysosome. – Plant vacuoles also function in water balance and may be used to store compounds such as toxins and pigments (colored particles). peroxisomes – houses enzymes involved in oxidation reactions, which produce hydrogen peroxide as a by- product. – The enzymes break down fatty acids and amino acids, and they also detoxify some substances that enter the body. Module 2 Plant Cells - are multicellular eukaryotic cells that make up a plant - (a group of eukaryotes belonging to the Plantae kingdom, with the ability to synthesis their own food using water, Sunlight and CO2). Types of plant cell PARENCHYMA CELLS - are live thin-walled cells with permeable walls that are undifferentiated - do not have a specialized structure - hence they easily adapt and differentiate into a variety of cells performing different function TWO TYPES of PARENCHYMA CELLS: Palisade parenchyma: columnar elongated structured cells found in a variety of leaves, lying below the epidermal tissue. Ray parenchyma: has both radial and horizontal arrangement majorly found within the stem wood of the plant. Functions of Parenchyma Cells light penetration and absorption and regulating gas exchange transportation of small molecules between the cells and the cell cytoplasm. assists in light absorption used in photosynthesis. transport materials along the plant stem transportation of water and food materials in the plant. COLLENCHYMA CELLS - are elongated cells found below the epidermis and/or in young plants on the outer layers of their stems and leaves. - found in the vascular and/or on the plant stem corner - occur in the peripheral region of the plant and they are not found in the plant roots. TYPES OF COLLENCHYMA CELLS (based on thickness of wall and cell arrangement) Angular collenchyma - most common type of collenchyma cells. - are found below the epidermis as hypodermis. Annnular collenchyma  - are uniformly thickened. The cells appear to be circular in shape Lamellar collenchyma - cells are thickened on the periphery making them appear tangentially arranged in rows. - are closely packed together and therefore they don’t have intracellular spaces. - are commonly formed and found in the leaf's petioles. Lacunar collenchyma - are cells are formed spaciously leaving intracellular spaces between each other. - cell wall thickens around the intracellular spaces. - appear spherically shaped. - are formed and found in the walls of fruits. FUNCTION OF THE COLLENCHYMA CELLS: Being the living cells in plant tissues, they give support to the plant areas that are growing and maturing in length. They offer flexibility and tensile strength to plant tissues, allowing the plants to bend. They also allow the plant parts to grow and elongate. Collenchyma can combine with the chloroplast and perform the process of photosynthesis. 3.SCLERENCHYMA CELLS - are collenchyma cells that have an agent of the cell wall that plays a major role in hardening its cell wall. - are found in all plant roots and they are important in anchoring and giving support to the plants Types of sclerenchyma cells Fiber sclerenchyma cells Sclereid sclerenchyma cells Functions of the sclerenchyma cells Due to their thickened cell wall, they offer protection and support to other plants’ tissues especially the tree trunks and fibers of large herbal trees. The hardened cell wall discourages herbivory. Ingestion of the hard cell wall causes damage to the digestive tract of larval stage insects, especially in peach fruits. Sclerenchyma found fibers are used in making fabric, thread, and yarns. 4.Xylem Cells - cells are complex cells found in the vascular tissues of plants, mostly in woody plants. - primary function of the xylem cells is to transport water and soluble nutrients, minerals and inorganic ions upwardly from the roots of the plants and its parts. - elements flow freely through the xylem tracheids and vessel elements with the aid of the xylem sap. 5.Phloem Cells - cells are located outside the xylem layer of cells. - become alive at maturity because they need the energy to move materials. - function to transport food from the plant leaves to other parts of the plant. - also have a flaccid cell wall 6.MERISTEMATIC CELLS - are also known as the meristems. - are the cells in a plant that divide continuously throughout the life of a plant. - have a self-renewal ability and high metabolisms to control the cell. Types of meristematic cells Apical meristems – they are found at the tips of roots and stems that have started growing and they contribute to the length of the plant Lateral meristems – They are found in the radial part of the stem and roots and they contribute to the plant thickness Intercalary meristems – they are found at the base of the leaves and the contribution to the size variance of the leaves Functions of the meristematic cells They play a major role in the length and width sizes of the plants they also give variance in the sizes of the plant leaves.  They differentiate and mature into permanent tissues of the plants. 7.Epidermal Cells - are the external cells of the plants offering protection from water loss, pathogenic invaders such as fungi. - are placed closely together with no intracellular spaces. - covered with a waxy cuticle layer to reduce water loss. - cover the plant stems, leaves, roots and plant seeds. Types of epidermal cells Pavement cells: maintain the plants’ internal temperature Stomatal guard cells: There are two types of guard cells defined by the structure those that control water availability by opening and closing the stomata by maintaining turgor pressure and those that regulate the exchange of gases into and out of the leaves’ stomata. Trichomes: These are also known as epidermal hairs found on the epidermal tissue. They play a major role in protecting the plants from predators and pathogens, by acting as trappers and poisoners to animal predators ANIMAL CELLS - are generally smaller than plant cells. - defining characteristic is its irregular shape. This is due to the absence of a cell wall. Epithelial Tissue - cells are the cellular components of the epithelium (pleural: epithelia). -are layers of contiguous cells that line the surfaces of organs and tissues. Location Covering the whole external surface of the body, as part of the skin. Lining interior tracts which open to the exterior, such as the respiratory, gastrointestinal and genitourinary tracts. Lining interior enclosed spaces, such as blood vessels, the peritoneum, the pleura and the pericardial sac.  Types of Epithelial Cells According to Layers Simple: epithelia which are one cell layer thick Stratified: consist of multiple layers of cells, with one layer anchored to the basement membrane, known as the basal layer. Types of Epithelial Cells According to Shape cuboidal—for secretion simple columnar—brick-shaped cells; for secretion and active absorption simple squamous—plate-like cells; for exchange of material through diffusion stratified squamous—multilayered and regenerates quickly; for protection pseudo-stratified columnar—single layer of cells; may just look stacked because of varying height; for lining of respiratory tract; usually lined with cilia Connective Tissue Cells BLOOD — made up of plasma (i.e., liquid extracellular matrix); contains water, salts, and dissolved proteins; erythrocytes that carry oxygen (RBC), leukocytes for defense (WBC), and platelets for blood clotting. CONNECTIVE TISSUE PROPER (CTP)— made up of loose connective tissue that is found in the skin and fibrous connective tissue that is made up of collagenous fibers found in tendons and ligaments. Adipose tissues are also examples of loose connective tissues that store fats which functions to insulate the body and store energy Connective Tissue Cells CARTILAGE —characterized by collagenous fibers embedded in chondroitin sulfate. Chondrocytes are the cells that secrete collagen and chondroitin sulfate. Cartilage functions as cushion between bones. BONE —mineralized connective tissue made by bone-forming cells called osteoblasts which deposit collagen. The matrix of collagen is combined with calcium, magnesium, and phosphate ions to make the bone hard. Blood vessels and nerves are found at a central canal surrounded by concentric circles of osteons Nervous Tissue— are composed of nerve cells called neurons and glial cells that function as support cells. These neurons sense stimuli and transmit electrical signals throughout the animal body. Neurons connect to other neurons to send signals. The dendrite is the part of the neuron that receives impulses from other neurons while the axon is the part where the impulse is transmitted to other neurons. Cell specialization (or modification or differentiation) is actually a process that occurs after cell division where the newly formed cells are structurally modified so that they can perform their function efficiently and effectively. MODULE 3 “Cell Cycle and Cell Division” life cycle of plants, animals, and humans, the sequence begins with an adult organism. this adults produces gametes—sperm and eggs—through a process called meiosis. When a sperm and an egg combine in fertilization, they form a new cell called a zygote The zygote then develops into a young organism, which eventually grows into an adult between two types of cells: diploid cells-which have two sets of chromosomes haploid cells-which have just one set. The cycle moves from diploid to haploid and then returns to diploid as it repeats. Cell Cycle The cell cycle is an ordered series of events involving cell growth and cell division that produce two new daughter cells. cycle has different stages called G1, S, G2, and M. G1 where the cell is preparing to divide Interphase cell undergoes normal growth processes while also preparing for cell division STAGES OF INTERPHASE: G1 phase-Metabolic changes prepare the cell for division. S phase-DNA synthesis replicates the genetic material. -Each chromosome now consists of two sister chromatids. G2 phase-Metabolic changes assemble the cytoplasmic materials necessary for mitosis and cytokinesis. Cell Division/Mitotic Phase Cell Division the distribution of identical genetic material or DNA to two daughter cells. most remarkable is the fidelity with which the DNA is passed along, without dilution or error, from one generation to the next. functions in reproduction, growth, and repair. Types of Cell Division Mitosis- the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. Meiosis- cell division that produces haploid sex cells or gametes (contain a single copy of each chromosome) from diploid cells (contain two copies of each chromosome). Prophase first phase of mitosis process that separates the duplicated genetic material carried in the nucleus of a parent cell into two identical daughter cells. Prometaphase second phase of mitosis process that separates the duplicated genetic material carried in the nucleus of a parent cell into two identical daughter cells. Metaphase stage during the process of cell division (mitosis or meiosis). individual chromosomes are spread out in the cell nucleus. Anaphase shortest stage of mitosis the sister chromatids break apart, and the chromosomes begin moving to opposite ends of the cell. Telophase fifth and final phase of mitosis separates the duplicated genetic material carried in the nucleus of a parent cell into two identical daughter cells. Meiosis 1 Prophase 1 chromosomes condense and attach to the nuclear envelope and begin migrating toward the metaphase plate. stage where genetic recombination may occur. Metaphase 1 chromosomes align at the metaphase plate. homologous chromosomes-the centromeres are positioned toward opposite poles of the cell. Anaphase 1 homologous chromosomes separate and move toward opposite cell poles. The sister chromatids remain attached after this move to opposite poles. Telophase 1 cytoplasm divides producing two cells with a haploid number of chromosomes. Sister chromatids remain together. Meiosis 2 Prophase 2 chromosomes begin migrating to the metaphase II plate.  These chromosomes do not replicate again. Metaphase 2 chromosomes align at the metaphase II plate kinetochore fibers of the chromatids are oriented toward opposite poles. Anaphase 2 sister chromatids separate and begin moving to opposite ends of the cell. The two cell poles also grow further apart in preparation for telophase 2. Telophase 2 new nuclei form around daughter chromosomes. cytoplasm divides and forms two cells in a process known as cytokinesis. Cytokinesis final cellular division to form two new cells. In plants a cell plate forms along the line of the metaphase plate in animals there is a constriction of the cytoplasm. The cell then enters interphase - the interval between mitotic divisions. Comparison between Mitosis and Meiosis Meiosis Mitosis 1. Requires two nuclear divisions 1. Requires one nuclear division 2. Chromosomes synapse and cross over 2. Chromosomes do not synapse nor cross 3. Centromeres survive Anaphase || 3. Centromeres dissolve in mitotic anaphase 4. Halves chromosome number 4. Preserves chromosome number 5. Produces four daughter nuclei 5. Produces two daughter nuclei 6. Produces daughter cells genetically diferent from parent and each other 6. Produces daughter cells genetically identical to parent and to each other 7. Used only for sexual reproduction 7. Used for asexual reproduction and growth Cell Cycle Checkpoint 1. Cell Growth checkpoint Occurs toward the end of growth phase 1 (G1). Checks whether the cell is big enough and has made the proper proteins for the synthesis phase. If not, the cell goes through a resting period (GO) until it is ready to divide. 2. DNA Synthesis Checkpoint Occurs during the synthesis phase (S). Checks whether DNA has been replicated correctly. If so, the cell continues on to mitosis (M). 3. Mitosis Checkpoint Occurs during the mitosis phase (M). Checks whether mitosis is complete. If so, the cell divides, and the cycle repeats. Errors in Cell Division 1.Incorrect DNA Copy Incorrectly paired nucleotides cause deformities in the secondary structure of the final DNA molecule enzymes recognize and fix these deformities by removing the incorrectly paired nucleotide and replacing it with the correct nucleotide. 2.Chromosomes are attached to string-like spindles and begin to move to the middle of the cell Down Syndrome, Alzheimer’s, and Leukemia 3. Aneuploidy presence of chromosome number that is different from simple multiple of the basic chromosome number. an organism contains one or more incomplete chromosome sets is known as aneuploid due to loss of one or more chromosomes (hypo-ploidy) due to addition of one or more chromosomes to complete chromosome complement (hyper-ploidy). Module 4 — Transport mechanism membrane transport refers to the collection of mechanisms that regulate the passage of solutes such as ions and small molecules through biological membranes, which are lipid bilayers that contain proteins embedded in them. Plasma Membrane The plasma membrane, also called the cell membrane  is the membrane found in all cells that separates the interior of the cell from the outside environment. According to the fluid mosaic model, the plasma membrane is a mosaic of components— primarily, phospholipids, cholesterol, and proteins—that move freely and fluidly in the plane of the membrane. Phospholipid Bilayer: – A phospholipid is a lipid made of glycerol, two fatty acid tails, and a phosphate-linked head group. Biological membranes usually involve two layers of phospholipids with their tails pointing inward, an arrangement called a phospholipid bilayer. Cell Transport Mechanisms 2 Types of Transport Mechanism Passive transport: – occurs when substances cross the plasma membrane without any input of energy from the cell. – No energy is needed because the substances are moving from an area where they have a higher concentration to an area where they have a lower concentration. Active transport – require energy to cross a plasma membrane often because they are moving from an area of lower concentration to an area of higher concentration. Passive Transport Simple Diffusion: – molecules move down their gradients through the membrane. – Molecules that practice simple diffusion must be small and nonpolar*, in order to pass through the membrane. Osmosis: – a specific type of diffusion; – it is the passage of water from a region of high water concentration through a semi- permeable membrane to a region of low water concentration. – Water moves in or out of a cell until its concentration is the same on both sides of the  – plasma membrane Facilitated Diffusion: – diffusion that is helped along (facilitated by) a membrane transport channel – These channels are glycoproteins (proteins with carbohydrates attached) that allow molecules to pass through the membrane. – they are tightly linked to certain physiologic functions. MODULE 5 “Structure and Function of Biological Molecules” Carbon and Carbon Bonding * bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. * contains four electrons in its outer shell. * can form four covalent bonds with other atoms or molecules. * This diversity of its molecular forms accounts for the diversity of functions(biological macromolecules) * large degree on the ability of carbon to form multiple bonds with itself and other atoms Carbohydrates * examples of macromolecules. * chainlike molecules called polymers made from repeating units like monomers. * Polymers can be formed from covalently-bonded monomers * structure can be made out of repeated building blocks linked to each other. Lipids * class of large biomolecules that are not formed through polymerization. * diverse structures but are all non-polar and mix poorly, if at all, with water. * They may have some oxygen atoms in their structure but the bulk is composed of abundant nonpolar C-H bonds * function for energy storage, providing nine food calories or 37 kJ of energy per gram, also for the cushioning of vital organs and for insulation * play important roles in plasma membrane structure, precursors for important reproductive hormones. PROTEINS * large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. * most abundant organic molecules in living systems * way more diverse in structure and function than other classes of macromolecules. AMINO ACIDS * monomers that make up proteins. * protein is made up of one or more linear chains of amino acids, each is called polypeptide * share a basic structure, consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group, a carboxyl group, and a hydrogen atom PEPTIDE BONDS * amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bond * bond forms in a dehydration synthesis (condensation) reaction. * protein in your cells consists of one or more polypeptide chains. * made up of amino acids, linked together in a specific order. Nucleic Acids * key macromolecules in the continuity of life * carry the genetic blueprint of a cell * carry instructions for the functioning of the cell * molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. * nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. Enzymes * organic or biological catalysts * castalysts-substances that speed up a reaction without being used up, destroyed, or incorporated into the end product. * vital to the regulation of the metabolic processes of the cell * many enzymes are protiens. Module 6 — ATP-ADP cycle ATP (adenosine triphosphate) – the energy currency for cellular processes.  – ATP provides the energy for both energy-consuming endergonic reactions and energy- releasing exergonic reactions, which require a small input of activation energy. – When the chemical bonds within ATP are broken, energy is released and can be harnessed for cellular work. – The more bonds in a molecule, the more potential energy it contains. – Because the bond in ATP is so easily broken and reformed, ATP is like a rechargeable battery that powers cellular process ranging from DNA replication to protein synthesis. Molecular Structure – Adenosine triphosphate (ATP) is comprised of the molecule adenosine bound to three phosphate groups. – Adenosine is a nucleoside consisting of the nitrogenous base adenine and the five-carbon sugar ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Glucose and ATP – Glucose, a sugar that is delivered via the bloodstream, is the product of the food you eat, and this is the molecule that is used to create ATP. – Sweet foods provide a rich source of readily available glucose while other foods provide the materials needed to create glucose. – This glucose is broken down in a series of enzyme controlled steps that allow the release of energy to be used by the organism. – This process is called respiration. Creation of ATP – ATP is created via respiration in both animals and plants. – The difference with plants is the fact they attain their food from elsewhere. – Two processes convert ADP into ATP: – 1) substrate-level phosphorylation; and – 2) chemiosmosis. – Substrate-level phosphorylation occurs in the cytoplasm when an enzyme attaches a third phosphate to the ADP – (both ADP and the phosphates are the substrates on which the enzyme acts). ATP Hydrolysis and Synthesis – Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction combines ADP + Pi to regenerate ATP from ADP. – Since ATP hydrolysis releases energy, ATP synthesis must require an input of free energy. – ADP is combined with a phosphate to form ATP in the following reaction: ADP + Pi + free energy → ATP + H2O ATP and Energy Coupling – The calculated ΔG for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). – However, this is only true under standard conditions, and the ΔG for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol  – (−57 kJ/mol). – ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. – To harness the energy within the bonds of ATP, cells use a strategy called energy coupling Module 7 — Photosynthesis – Light is actually energy, electromagnetic energy to be exact. – When that energy gets to a green plant, all sorts of reactions can take place to store energy in the form of sugar molecules. – Even when light gets to a plant, the plant doesn't use all of it. – It actually uses only certain colors to make photosynthesis happen. Plants mostly absorb red and blue wavelengths. Chloroplast Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water and carbon dioxide gas to produce food for the plant. Chloroplasts capture light energy from the sun to produce the free energy stored in ATP and NADPH through a process called photosynthesis. ATP and NADPH through a process called photosynthesis.  Chloroplasts are one of the many unique organelles in the body, and are generally considered to have originated as endosymbiotic cyanobacteria. Plastids Plastids are a group of phylogenetically and physiologically-related organelles found in all types of plants and algae. In the cells, plastids are primarily involved in the manufacture and storage of food. They are therefore involved in such processes as photosynthesis, synthesis of amino acids and lipids as well as storage of various materials among a few other functions. In their roles, the different types of plastids contribute to plant metabolism thus promoting plant growth and development. One of the main characteristics of these organelles is the fact that they have a double membrane. Chlorophyll Chlorophyll is a green photosynthetic pigment found in plants, algae, and cyanobacteria. Chlorophyll absorbs mostly in the blue and to a lesser extent red portions of the electromagnetic spectrum, hence its intense green color. Green substance in producers that traps light energy from the sun, which is then used to combine carbon dioxide and water into sugars in the process of photosynthesis Chlorophyll is vital for photosynthesis, which helps plants get energy from light. Photosynthesis Photosynthesis, the process by which green plants and certain other organisms transform light energy into chemical energy. During photosynthesis in green plants, light energy is captured and used to convert water, carbon dioxide, and minerals into oxygen and energy-rich organic compounds. Photosynthetic process. Light dependent reaction ( light reaction) Light-dependent reaction requires sunlight. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and converted into stored chemical energy, in the form of the electron carrier molecule NADPH (nicotinamide adenine dinucleotide phosphate) and the energy currency molecule ATP (adenosine triphosphate). The light-dependent reactions take place in the thylakoid membranes in the granum (stack  of thylakoids), within the chloroplast.. Light-Independent Reaction (Calvin Cycle) In the light-independent reactions or Calvin cycle, the energized electrons from the light- dependent reactions provide the energy to form carbohydrates from carbon dioxide molecules. The light-independent reactions are sometimes called the Calvin cycle because of the cyclical nature of the process. Although the light-independent reactions do not use light as a reactant (and as a result can take place at day or night), they require the products of the light-dependent reactions to function. The light-independent molecules depend on the energy carrier molecules, ATP and NADPH, to drive the construction of new carbohydrate molecules. After the energy is transferred, the energy carrier molecules return to the light-dependent reactions to obtain more energized electrons. MODULE 8: PIGMENTS - are chemical compounds which reflect only certain wavelengths of visible light. This makes them appear "colorful". Flowers, corals, and even animal skin contain pigments which give them their colors. - In plants, algae, and cyanobacteria, pigments are the means by which the energy of sunlight is captured for photosynthesis. CLASSES OF PIGMENTS: Chlorophylls - are greenish pigments which contain a porphyrin ring. - a stable ring-shaped molecule around which electrons are free to migrate. Because the electrons move freely, the ring has the potential to gain or lose electrons easily, and thus the potential to provide energized electrons to other molecules. This is the fundamental process by which chlorophyll "captures" the energy of sunlight. Carotenoids - are usually red, orange, or yellow pigments, and include the familiar compound carotene, which gives carrots their color. - are composed of two small six-carbon rings connected by a "chain" of carbon atoms. As a result, they do not dissolve in water, and must be attached to membranes within the cell. Carotenoids cannot transfer sunlight energy directly to the photosynthetic pathway, but must pass their absorbed energy to chlorophyll. For this reason, they are called accessory pigments. One very visible accessory pigment is fucoxanthin the brown pigment which colors kelps and other brown algae as well as diatoms Phycobilins - are water-soluble pigments, and are therefore found in the cytoplasm, or in the stroma of the chloroplast. They occur only in Cyanobacteria and Rhodophyta. Phycobilins are not only useful to the organisms which use them for soaking up light energy; they have also found use as research tools.