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Week 3 Notes

by: Natania Lipp

Week 3 Notes BSCI 105 - 5666

Natania Lipp


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These notes cover class material, videos posted, and textbook material from this week.
Principles of Biology I
Dr. Michael Keller
Class Notes
Bio, bsci105, Biology, transport, Proteins, Molecules, Energy, work, metabolism, cells
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This 6 page Class Notes was uploaded by Natania Lipp on Sunday February 21, 2016. The Class Notes belongs to BSCI 105 - 5666 at University of Maryland - College Park taught by Dr. Michael Keller in Winter 2016. Since its upload, it has received 13 views. For similar materials see Principles of Biology I in Biology at University of Maryland - College Park.

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Date Created: 02/21/16
BSCI105 Week 3 Notes Bulk transport, metabolism, energy & the membrane 02/15 Video Lecture 7 — Bulk Transport Bulk transport occurs because the cell has to transport larger molecules, and excrete many molecules at the same time - In bulk transport, the membrane itself is used - There are 2 types: - Endocytosis - Exocytosis Endocytosis: used to bring things into the cell - Phagocytosis: “cell eating” - Allows the cell to consume large things at once - Macrophage digests unwanted material - Amoeba surrounds other cells with arms from the cell membrane to connect and digest things - Pinocytosis: “cell drinking” - Brings in water (and solutes dissolved in water) without diluting cytoplasm, by using membrane vesicles - Receptor-Mediated Endocytosis - more specific - Brings in a particular molecule from the environment - Uses receptors to recognize specific molecules - Occurs in clathrin-coated pits; uses 2 types of protein: - 1. Receptor — recognizes something specific and bonds to it - 2. Clathrin (peripheral) — bends and creates a force bubble of membrane Exocytosis: reversed endocytosis; used for secretion - Cell makes a vesicle of membrane which goes to the plasma membrane protein - The plasma protein fuses them and the vesicle dumps its contents into the outside environment. - Membrane trasport: - Multiple membranes operate at the same time - Important because what happens with one mechanism could impact other mechanisms 02/19 In Class Lecture 8 — Intro to Energy and Metabolism Fundamentals of metabolism: - Metabolism (broad definition) = the sum of all biochemical reactions in every cell - All reactions in your body are connected. - Anabolic reactions (biosynthetic) = the body making things - Catabolic reactions (degradative) = the body breaking things down - Metabolic pathways: reactions that occur one after another, in a specific order - A system of molecules in which each step has a specific enzyme to reach the next step until the final product is reached. - Each enzyme has one specific job — one enzyme alone cannot be responsible for a whole reaction. - This method allows for a lot of complex, interconnected systems Energy: - Metabolism requires energy - Energy = the capacity to do work - Kinetic energy: goes from motion to something else - Potential energy: non-kinetic energy - Stored in bonds between atoms - 1st Law of Thermodynamics: Conservation of Energy - Energy cannot be created nor destroyed - 2nd Law of Thermodynamics: Entropy in the universe always increases. - Entropy = the drive for energy to spread out evenly throughout the universe; a measure of disorder - Energy is made available to work - Energy can be used to increase order in the system From the “SciShow: What is Energy” video - Energy is everywhere - Energy = ability to do work - Work = ability to do something by applying force - Every atom and every bond contains energy — even inanimate objects are made up of chemical energy - In a log, ripping apart the bonds between carbon and hydrogen and oxygen atoms creates a fire. - Energy - E = MC^2 - Energy can never be destroyed nor created, it can only be transferred from one object or form to another Textbook Notes: Chapter 7: Membrane Structure and Function The plasma membrane has selective permeability: it allows some substances to cross it more easily than others. - The ability to be selective about what enters is crucial to life, and the membrane is responsible for this function. 7.1 Cellular membranes are fluid mosaics of lipids and proteins. - The stable ingredients of membranes are lipids and proteins. - Phospholipids are the most important lipids. - Phospholipids are amphipathic: they have a hydrophilic region (attracts water) and hydrophobic region (repels water). - The amphipathic membrane is what creates the phospholipid bilayer: a two-layered membrane arranged with hydrophilic tails on the inside and hydrophobic heads on the outside. - Most membrane proteins are also amphipathic, and they can inhabit the phospholipid bilayer. - A fluid mosaic model is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids. - Membranes have fluidity. - Lipids and some proteins can shift laterally, and can even flop across the membrane. - Phospholipids are constantly switching positions. - Factors that affect fluidity: - Temperature: the hotter the temperature, the faster molecules move so the more fluid the membrane is. - Unsaturated carbon tails are more fluid than saturated, because they cannot pack together as closely. - Steroid cholesterol: when the temperature is higher, the membrane is more fluid. However, it also lowers the temperature and then makes it less fluid. - Viscous: the opposite of fluidity, when the lipid tails are packed tightly together. - The model is called a mosaic model because membranes within each cell have unique collections of proteins. - Phospholipids are the fabric of the membrane and the proteins determine most of the membrane’s functions. - There are 2 major populations of membrane proteins: - Integral proteins: penetrate the hydrophobic interior of the lipid bilayer. - Mostly made up of transmembrane proteins which span the entire membrane as opposed to only extending part way. - Peripheral proteins: not embedded in the lipid bilayer — loosely bound to the surface of the membrane - Some proteins are held in place by the cytoskeleton and some are attached to fibers of the extracellular matrix - Protein functions: a) Transport b) Enzymatic activity c) Signal transduction d) Cell-cell recognition: a cell’s ability to distinguish one type of neighboring cell from another - Important for defense and sorting cells into tissues and organs - Most membrane carbohydrates are covalently bonded to proteins, making glycoprotiens - Diversity of location on the cell’s surface allow them to function as markers to distinguish one cell from another. - Glycolipids: the membrane carbs that are covalently bonded to lipids. e) Intercellular joining f) Attachment o the cytoskeleton and extracellular matrix (ECM) 7.2 Membrane structure results in selective permeability. - Nonpolar molecules are hydrophobic, so they can dissolve easily in the lipid bilayer and can pass through without the help of membrane proteins. - Polar molecules are harder to pass through the lipid bilayer and require proteins to help transport them. - Transport proteins help move some ions and polar molecules through the membrane. There are 2 main types: 1. Channel proteins are a kind of transport protein that have a hydrophilic channel through which certain molecules or atomic ions can use as a tunnel to get through the membrane. - Aquaporins: a kind of channel protein that allow 3 billion water molecules to pass into the cell every second. 2. Carrier proteins: hold onto their passengers and change shape in a way that shuttles them across the membrane. 7.3 Passive transport is diffusion of a substance across a membrane with no energy investment. - Diffusion: the movement of particles of any substance so that they spread out into the available space. - How it works: the membrane’s pores allow molecules to pass through them. Molecules will move randomly through pores, and (in the absence of other forces) they move from where it is more concentrated to where it is less concentrated in order to achieve equilibrium. - Concentration gradient: the region along which the density of a chemical substance increases or decreases. Every substance diffuses down its concentration gradient. - Passive transport: the diffusion of a substance across a biological membrane that requires no energy from the cell. - Osmosis: the diffusion of water molecules across a membrane through the pores of the membrane. - Tonicity: the ability of surrounding solution to cause a cell to gain or lose water. - Depends on the solute concentration and membrane permeability - If there is higher concentration water will leave the cell, if there is lower, water will enter the cell. - Isotonic: when there is no net movement of water in or out of the cell because water diffuses in and out of the membrane at the same rate - Hypertonic: a solution that does not maintain enough water — the water leaves the cell faster than it enters. - Could cause the cell to shrivel and die. - Hypotonic: solution that has too much water — the water enters the cell faster than it leaves - Could cause the cell to swell and maybe burst. - In both hypertonic and hypotonic situations, the cells lack rigid cell walls - These cells need other adaptation to achieve osmoregulation: control of solute concentrations and water balance. - Cell wall — helps regulate the cell’s osmosis to achieve osmoregulation. - When the cell swells, the cell wall pushes back pressure called turgor pressure and make the cell turgid (very firm), which is a healthy state. - When the cell is isotonic, the cell becomes flaccid (limp). - When the cell is hypertonic the plant cell shrivels in and the cell undergoes plasmolysis which can be deathly. - Facilitated diffusion: when polar molecules and ions diffuse passively with the help of transport proteins on the membrane. - 2 types of transport proteins carry out facilitated diffusion: channel and carrier. - Ion channels: channel proteins that transport ions. - Many ion channels function as gated channels: open or close in response to stimulus (i.e. electrical stimulus). - Channel proteins slightly change their shape and move the solute across the membrane during their shape change. 7.4 Active transport uses energy to move solutes against their gradients. - Active transport: the pumping of a solute across a membrane that requires work. - Only carrier proteins do active transport. - Allows cells to maintain internal concentrations of small solutes that are different from the concentrations in the cell’s environment. - Examples: - Animal cells have higher concentrations of potassium ions and lower concentrations of sodium ions so the membrane helps by pumping sodium out of the cell and potassium into the cell. The sodium-potassium pump exchanges sodium for potassium across the membrane. - ATP supplies energy for active transport by transferring its terminal phosphate group to the transport protein which causes the protein to change shape and move the solution. - Voltage: electrical potential energy - All cells have voltage - Membrane potential: voltage across a membrane, which is negative on the cytoplasmic side and positive on the extracellular side because of an unequal distribution of anions and cations - Electrochemical gradient: the combination of two forces that drive the diffusion of ions across a membrane — a chemical force of the ions concentration gradient, and an electrical force, the effect of the membrane potential on the ion’s movement. - Electrogenic pump: the transport protein that generates voltage across a membrane. - Proton pump: the main electrogenic pump of plants, fungi, and bacteria - Helps store energy that can be tapped for cellular work. - Cotransport: when a transport protein couples the “downhill” diffusion of the solute to the “uphill” transport of a second substance against its own concentration gradient. - Helps drive the amino acids, sugars, and other nutrients into the cell. Chapter 8: An Introduction to Metabolism 8.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics. • Metabolism: the totality of an organism’s chemical reactions • Metabolic pathways: • Catabolic pathways: the degradative processes of releasing energy by breaking down complex molecules to simpler compounds • Cellular respiration: a major pathway of catabolism where sugar glucose and other organic molecules becomes available to do the work of the cell • Anabolic pathways: consume energy to build complicated molecules from simpler ones (aka biosynthetic pathways) • Bioenergetics: the study of how energy flows through living organisms. • Energy: the capacity to cause change • Used to do work — to move against opposing forces • Kinetic energy: energy that can be associated with relative motion of objects • Thermal energy: kinetic energy associated with the random movement of atoms or molecules • Heat: thermal energy transfer from one object to another • Potential energy: energy that is not kinetic • Chemical energy: potential energy available to be released in a chemical reaction • Thermodynamics: the study of energy transformations that occur in a collection of matter • Laws of thermodynamics: 1. The principle of conservation of energy can be transferred and transformed, but it cannot be created or destroyed. 2. Every energy transfer or transformation increase the entropy of the universe. - Entropy: the measure of disorder that occurs when energy transfer or transformation makes the world more disordered - Spontaneous process: the process that leads to an increase in entropy and can proceed without requiring and input of energy. - Energetically favorable - Non-spontaneous process: a process that can only occur if energy is supplied 8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously. • Universe = “the system” + “the surroundings” • Free energy: the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. • Represented in (delta)G • Can be calculated by: (delta)G = (delta)H - T(delta)S • H = the change in the system’s enthalpy: total energy • S = the change in the system’s entropy • T = the absolute temperature in Kelvin • Can use G to predict whether the process will be spontaneous — If G is negative then the process is spontaneous, if it is positive or zero it is non-spontaneous • The change in G equals G’s final state minus G’s initial state • Free energy is also a measure of stability — the more potential energy, the less stable • A process is spontaneous and can perform work only when it is moving toward equilibrium. • Chemical reactions can be classified as: • Exergonic reactions: is propelled forward by a net release of free energy • G is negative • Endergonic reaction: absorbs free energy from its surroundings • G is positive


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