Second-Quarter GenBio Notes PDF

Source 1: \"2-chlorophyll and other pigments.pdf\" **Accessory Pigments:** Energy-capturing pigment molecules other than chlorophyll a. Chlorophyll b and carotenoids are accessory pigments in plants. They transfer the absorbed light to chlorophyll a since only chlorophyll a can perform photosynthes...

Source 1: \"2-chlorophyll and other pigments.pdf\" **Accessory Pigments:** Energy-capturing pigment molecules other than chlorophyll a. Chlorophyll b and carotenoids are accessory pigments in plants. They transfer the absorbed light to chlorophyll a since only chlorophyll a can perform photosynthesis.1 **Carotenoids:** Pigments in plants, algae, and photosynthetic bacteria that produce the bright yellow, red, and orange colors in plants, vegetables, and fruits. They reflect longer wavelengths of light.12 **Chlorophyll:** A green photosynthetic pigment in plants, algae, and cyanobacteria that allows plants (including algae) to photosynthesize. Chlorophyll a and b absorb red and blue wavelengths and appear green because they reflect green light.134 **Electromagnetic Radiation:** A type of energy that is all around us and takes many forms, such as radio waves, microwaves, X-rays and gamma-rays. Sunlight is also a form of electromagnetic energy.56 **Electromagnetic Spectrum:** The range of all possible frequencies of electromagnetic radiation.6 **Infrared Radiation:** A type of electromagnetic radiation with longer wavelengths than visible light. Infrared radiation contains too little energy per photon to be useful to organisms, and most of its energy is converted immediately to heat.3 **Light Energy:** Energy from the sun that travels to Earth in the form of light. Sunlight is actually a mixture of different wavelengths of light.5 **Photosynthesis:** The process by which plants (including algae) use sunlight to convert simple molecules into organic compounds.4 **Photons:** Discrete packets of kinetic energy that make up all electromagnetic radiation, including light. The length of a photon\'s wavelength is the distance it moves during a complete vibration. The shorter the photon's wavelength, the more energy it contains.67 **Pigment:** Any colored material found in a plant or animal cell. Pigments absorb and reflect different wavelengths of light, making things appear to be certain colors. Photosynthetic pigments have distinct colors because they absorb only some wavelengths of visible light, while transmitting or reflecting others.4 **Ultraviolet Radiation:** The shortest wavelength of the three main components of sunlight. Ultraviolet radiation\'s high-energy photons can damage DNA, causing sunburn and skin cancer.8 **Visible Light:** The portion of the electromagnetic spectrum that is visible to the human eye. Visible light provides the energy that powers photosynthesis. Different wavelengths of visible light are perceived as distinct colors. The visible colors from shortest to longest wavelength are: violet, blue, green, yellow, orange, and red.569 **Wavelength:** The distance between peaks (high points) of a wave. Each wave has a certain shape and length.7 Source 2: \"2.5-Transport Mechanisms in Cells part 1.pdf.pdf\" **Active Transport:** A process that requires energy for substances to cross a plasma membrane. This often occurs when substances are moving from an area of lower concentration to an area of higher concentration.10 **Concentration Gradient:** The unequal distribution of molecules.11 **Diffusion:** The net movement of particles from an area of greater concentration to an area of lesser concentration.12 **Dynamic Equilibrium:** A state where molecules continue to move, but there is no net change in concentration over time.11 **Facilitated Diffusion:** Diffusion with the help of transport proteins.13 **Hypertonic Solution:** A solution where the concentration of solute is greater than the concentration of solute in the cells, causing a net flow of water out of the cell.14 **Hypotonic Solution:** A solution where the concentration of solute is less than the concentration of solute in the cells, causing a net flow of water into the cell.15 **Isotonic Solution:** A solution where the concentration of solute is equal to the concentration of solute in the cells, resulting in no net flow of water in or out of the cell.14 **Osmosis:** A specific type of diffusion where water passes 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.16 **Passive Transport:** A process that does not require energy for substances to cross a plasma membrane. 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.10 **Plasma Membrane (Cell Membrane):** The membrane found in all cells that separates the interior of the cell from the outside environment. It controls everything that enters and leaves the cell.17 **Semi-permeable Membrane:** A thin layer of material that allows some things to pass through but prevents other things from passing through. Cell membranes are an example of semi-permeable membranes.1618 **Solute:** The substance that is dissolved in a solvent to form a solution.10 **Solution:** A mixture formed when a solute is dissolved in a solvent. Water solutions are very important in biology.10 **Solvent:** A substance, typically a liquid, that dissolves a solute to form a solution. Water is the solvent in many biological solutions.10 **Transport Proteins:** Special proteins in the membrane that help hydrophilic molecules, charged ions, and relatively large molecules such as glucose diffuse across the membrane. There are several types of transport proteins, including channel proteins and carrier proteins.1315 Source 3: \"2.5-Transport Mechanisms in Cells part 2 TO GIVE.pdf\" **Active Transport:** A process that requires energy for substances to cross a plasma membrane. This often occurs because they are moving from an area of lower concentration to an area of higher concentration. The energy for active transport comes from the energy-carrying molecule ATP.19 **Anion:** An ion with a negative charge.20 **ATP (adenosine triphosphate):** The energy-carrying molecule that provides energy for active transport.19 **Carrier Proteins:** Proteins that bind with specific ions or molecules, and in doing so, they change shape. As carrier proteins change shape, they carry the ions or molecules across the membrane.20 **Cation:** An ion with a positive charge.20 **Electrochemical Gradient:** The electrical gradient across the cell membrane, called the membrane potential.21 **Electrolytes:** Substances that dissociate into ions in solution, which allows them to conduct electricity.22 **Endocytosis:** A type of vesicle transport that moves a substance into the cell. It is used by all cells of the body because most substances important to them are polar and consist of big molecules, and thus cannot pass through the hydrophobic plasma membrane.2324 ○ **Phagocytosis:** When an entire cell or other solid particle is engulfed during endocytosis.24 ○ **Pinocytosis:** When fluid is engulfed during endocytosis.24 ○ **Receptor-Mediated Endocytosis:** When the content is taken in specifically with the help of receptors on the plasma membrane.24 **Exocytosis:** A type of vesicle transport that moves a substance out of the cell.25 **Ion:** An atom or group of atoms that has an electric charge. Many normal substances exist in the body as ions.20 **Membrane Potential:** The difference in charge across the cell membrane created by differences in ion concentrations.21 **Plasma Membrane (Cell Membrane):** The membrane found in all cells that separates the interior of the cell from the outside environment. It controls everything that enters and leaves the cell.26 **Primary Active Transport:** Moves ions across a membrane and creates a difference in charge across that membrane. This process uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance out of the cell.2728 **Pump:** A type of active transport mechanism for the transport of small-molecular weight material and macromolecules. There are two types of pumps: primary and secondary active transport.27 **Secondary Active Transport:** A type of active transport that describes the movement of material using the energy of the electrochemical gradient established by the primary active transport.21 **Sodium-Potassium Pump:** A mechanism of active transport that moves sodium ions out of the cell and potassium ions into the cell. This process requires energy because both ions are moved from areas of lower to higher concentration. The energy is provided by ATP.28 **Vesicle Transport:** Requires energy to move large molecules, such as proteins, across the plasma membrane. There are two types of vesicle transport: endocytosis (moving substances into the cell) and exocytosis (moving substances out of the cell).23 Source 4: \"3-Light dependent reactions.pdf\" **ATP (adenosine triphosphate):** A small, energy-carrying molecule generated through processes like cellular respiration and fermentation. ATP provides cells with immediate energy.29 **Carbon Fixation:** The process of incorporating carbon from carbon dioxide (inorganic carbon) into organic molecules.30 **Cellular Respiration:** A process that harvests the chemical energy of glucose molecules to generate ATP.29 **Chemiosmosis:** The process of ATP production driven by the flow of H+ ions down their gradient and into the stroma through ATP synthase.31 **Chlorophyll:** A pigment found in chloroplasts that absorbs different colors of the light spectrum to create energy.32 **Chloroplasts:** Organelles in plant cells where photosynthesis takes place. Chloroplasts contain chlorophyll.32 **Electron:** A negatively charged subatomic particle found in all atoms.3334 **Electron Transport Chain:** A series of protein complexes that transfer electrons, releasing energy as they go. This energy is used to pump H+ ions, creating a gradient that drives ATP production.3536 **Enzymes:** Proteins that act as biological catalysts by accelerating chemical reactions.35 **Excited State:** A state of an electron when it absorbs energy from light, increasing its energy level.34 **Fermentation:** A process that harvests the chemical energy of glucose molecules to generate ATP, typically in the absence of oxygen.29 **Fixed Carbon:** Carbon that has been incorporated into organic molecules from inorganic sources, such as carbon dioxide. The carbon fixed during photosynthesis can be used to build other types of organic molecules needed by cells.30 **Glucose:** A simple sugar that provides organisms with energy and fixed carbon. It is a product of photosynthesis and serves as fuel for cells.37 **Light-Dependent Reactions:** A set of reactions in photosynthesis that use light energy to make two molecules needed for the next stage of photosynthesis: ATP and NADPH. These reactions take place in photosystems I and II, which are large complexes of proteins and pigments optimized to harvest light.3032 **Light-Independent Reactions (Calvin Cycle):** A set of reactions in photosynthesis that do not require light. The Calvin Cycle uses ATP and NADPH from the light-dependent reactions to produce high-energy sugars.30 **Mesophyll:** The tissue in the interior of leaves where chloroplasts are located.32 **NADPH:** A molecule that carries electrons and is a product of the light-dependent reactions. NADPH helps to fuel the reactions that occur in the light-independent reactions.36 **Photon:** A particle of light that carries energy. When a photon is absorbed, there is a positive energy change; when a photon is emitted, there is a negative energy change.34 **Photosynthesis:** The process in which light energy is converted to chemical energy in the form of sugars.37 **Photosystems:** Large complexes of proteins and pigments that are optimized to harvest light. Photosystems play a key role in the light-dependent reactions. There are two types of photosystems: photosystem I (PSI) and photosystem II (PSII).33 **Pigments:** Light-absorbing molecules found in photosystems.33 **Reaction Center:** The location in a photosystem where energy is transferred to a special pair of chlorophyll molecules, boosting an electron to a high energy level.38 **Stroma:** The fluid-filled space within a chloroplast, surrounding the thylakoid membranes.35 **Thylakoids:** Membrane-bound compartments within chloroplasts where the light-dependent reactions of photosynthesis occur. Thylakoids contain chlorophyll.32 Source 5: \"4-light independent reactions.pdf\" **ATP (adenosine triphosphate):** A molecule that provides energy for the Calvin cycle. ATP and NADPH from the light-dependent reactions are not stable enough to store energy for more than a few minutes, so the Calvin Cycle uses them to build high-energy compounds that can be stored for longer periods.39 **Calvin Cycle:** A set of reactions in photosynthesis also called light-independent reactions because they do not require light. The Calvin Cycle uses ATP and NADPH from the light-dependent reactions to produce high-energy sugars. It occurs in the stroma of the chloroplast.3940 **Carbon Fixation:** The first stage of the Calvin Cycle, where three CO2 molecules combine with three five-carbon acceptor molecules called ribulose-1,5-bisphosphate (RuBP), resulting in three six-carbon compounds. These unstable compounds split to form six molecules of 3-phosphoglyceric acid (3-PGA). This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, or rubisco.3941 **G3P (Glyceraldehyde-3-phosphate):** A three-carbon sugar produced during the reduction stage of the Calvin cycle. Some G3P molecules are used to make glucose, while others are recycled to regenerate RuBP.4243 **Light-Dependent Reactions:** Reactions that produce ATP and NADPH, providing energy and electrons for the Calvin Cycle.40 **Light-Independent Reactions (Calvin Cycle):** Reactions that use ATP and NADPH from the light-dependent reactions to convert 3-PGA into G3P.40 **NADPH:** A molecule that provides electrons for the Calvin cycle.39 **Reduction:** The second stage of the Calvin Cycle, where ATP and NADPH are used to convert the 3-PGA molecules into G3P molecules. This stage is named \"reduction\" because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P.42 **Regeneration:** The third stage of the Calvin Cycle, where some G3P molecules are used to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP.43 **Rubisco (RuBP carboxylase/oxygenase):** The enzyme that catalyzes the reaction in carbon fixation.41 **RuBP (Ribulose-1,5-bisphosphate):** The five-carbon acceptor molecule that combines with CO2 in the carbon fixation stage.39 **Stroma:** The fluid-filled space within a chloroplast where the Calvin Cycle takes place.40