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Study Guide for Test 2

by: Rebecca Sharp

Study Guide for Test 2 BSC 114

Rebecca Sharp

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These notes cover the things we've been over in class that will be on Thursday's exam
Principles Of Biology I
Stevan Marcus
Study Guide
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This 7 page Study Guide was uploaded by Rebecca Sharp on Sunday February 28, 2016. The Study Guide belongs to BSC 114 at University of Alabama - Tuscaloosa taught by Stevan Marcus in Winter 2016. Since its upload, it has received 242 views. For similar materials see Principles Of Biology I in Biological Sciences at University of Alabama - Tuscaloosa.

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Date Created: 02/28/16
Cell Theory  All living things consist of at least one cell  Cells are the smallest collections of matter capable of performing all activities of life o Meaning not viruses, because they need to invade another cell to reproduce  All cells come from the division of early cells The Endomembrane System  Nuclear Envelope o Also known as the nuclear membrane. Not all cells have cell walls, but all cells have at least a nuclear envelope.  Rough Endoplasmic Reticulum  o Rough ER has ribosomes and does protein synthesis  Smooth Endoplasmic Reticulum o Smooth ER stores calcium and does lipid synthesis  Golgi Apparatus o Has flattened membrane sacks called cisternae. Each side has its own name, the receiving side is called the cis side (always near the ER) and the side that sends away the completed proteins is called the trans side. The Golgi Apparatus folds proteins.  Lysosomes o Sac of hydrolytic enzymes, they break down other stuff. Think of these as the piranhas of the cell. Lysosome Lumen (space inside the lysosome) has a higher acidity level than the rest of the cell. The lysosomes eat primarily old and malfunctioning organelles.  Autophagy: when the cell eats little bits of itself (like lysosomes)  Phagocytosis: when the cell eats other cells (like white blood cells)  Vesicles o Formed when the cell wraps itself around something, or when the cell needs to kick some substance out of the cell. They’re the taxi service of the cell. Other organelles  Mitochondria o The Power House of the Cell. If you know nothing else, know this. Produces Adenosine TriPhosphate (ATP), the energy used by a cell. Creates lots of free oxygen radicals which are very very bad  Peroxisomes o Clean up mitochondria’s mess and break free oxygen radicals down to hydrogen peroxide which is still bad but less so, as it can be broken down into water and hydrogen  Chloroplasts o Site of photosynthesis in plant cells, where plant cells fuse carbohydrates with the power of sunshine. Exclusively specific to plant cells. Vacuoles (a cell may have more than one type of vacuole)  Contractile Vacuoles pump out excess water from the cell to prevent it from bursting from the Great Forces of Osmosis. Food Vacuoles are formed by phagocytosis, they hold onto emergency food for the cell, think of them as the cell’s Doomsday Preppers.  Central Vacuoles are like the cell’s attic, it’s where the cell stores things that are largely irrelevant to the cell.  Fungal Vacuoles break down and store macromolecules, for most intents and purposes, consider it the lovechild of the lysosome and the central vacuole. Cytoskeleton Organization  First off, what the cytoskeleton does is organize cell structure and activities, it can move the organelles anywhere they need to go, it keeps the cell supported, and enables cellular motion. It can be fused together very quickly as well as torn apart. It’s made of 3 types of fibers;  Microtubules; 13 columns of hollow tubes made of alpha and beta tubulins. These are 25 nanometers across with a hole in the middle (lumen) 15 nanometers across. They’re responsible for chromosome movements in cell division, and most organelle movement  Microfilaments (Actin filaments); made of two intertwined actin filaments. They’re 7 nanometers in diameter. They’re responsible for cell movement also, they hold cellular tension, and help form the break off points in cell division, and helps direct the flow of cytoplasmic fluid (called cytoplasmic streaming)  Intermediate filaments; made of strings of various proteins, including keratin, that are wrapped together into thick cables. 8-12 nanometers across, also responsible for maintaining cell shape, for anchoring the nucleus and the ER within the cell, and for the formation of nuclear lamina o Nuclear lamina; structure that regulates the most important processes of the cell. It’s the president, congress, and supreme court all at once. It deals with DNA replication, RNA transcription, chromatin organization, and cell replication  The Microtubule Organizing Center grows out of the centrosome. Experimentation has found that cell replication can happen without it. The MTOC has a pericentriolar matrix (cloud of amorphous material)  Motor Proteins; powered by ATP, they transport other proteins and organelles along the vesicles. This is possible because they contain the protein myosin, which is able to lock up (interdigitate) with the actin proteins, allowing the motor proteins to “walk” down vesicles Extra Cellular Structures  The cell wall (varies from plants, prokaryotes, and fungi) protects the cell and helps maintain shape  Extra cellular matrix is found only in animal cells, it segregates tissues and helps regulate inter cellular communication. o Made of glycoproteins, mostly collagen. Makes up 25% of whole body protein count. They’re the thick fibers outside of the cell.  Fibronectins bind to transmembrane proteins, they connect cells to EXM  Extra Cellular Junctions allow for passage into and out of the cell o Plasmodentia; thin channels between adjacent plant cells o Tight Junctions; where two cells are pressed up against each other, prevents fluid leakage o Desmosomes; in one little spot, anchor cells together into sheets of cells o Gap junctions; for communication between cells through cytoplasmic channels The Phospholipid Bi Layer  Made out of a hydrophilic head and a hydrophobic carbon/fatty acid tail, linked by a phosphate group. Called “amphipathic molecules”  They line up with the tails facing each other, making a hydrophobic layer sandwiched by a hydrophilic layer. This is a membrane.  When mixed vigorously with water, phospholipids naturally assemble into bilayers, which was helpful in the origination of life on earth  Hydrophilic heads flip laterally about 10^7 times a second  Head/Tail pairs rotate about the fatty acid tail joint about once a month Proteins involved with the Phospholipid Bi Layer  Transmembrane Proteins go all the way through the phospholipid bi layer. They have an N terminus and a C terminus. (C faces the cytoplasm, N faces the outside) They contain an alpha helix.  Peripheral Proteins are connected to the phospholipid bilayer or the transmembrane proteins.  Aquaporin channel proteins that facilitate the passage of H2O into a cell Major Functions of Membrane Proteins  Transport Membrane Proteins work like a pump moving materials into and out of the cell  Signal Transduction proteins read signals in the cell to coordinate complex cellular activities  Cell-Cell Recognition proteins allow cells to connect to the correct cells by shape recognition, the proteins embedded in the bi layer change the shape of the cell.  Intercellular Joining works the same way as cell-cell recognition  Attachment to Extra Cellular Matrix and the Cytoskeleton  Enzymic Activity is facilitated by proteins Movement Across Membranes  Diffusion is defined as the tendency of molecules to spread out evenly into the available space. Diffusion with the concentration gradient is called passive transport o Facilitated diffusion is when transport proteins speed passive diffusion o Active diffusion is when molecules are moved against the concentration gradient with an expenditure of energy  Osmosis is defined as the diffusion of a solvent (like water) across a selectively permeable membrane  Osmoregulation is the control of solute concentration/water balance. o Hypertonic is a high water balance o Hydrotonic is a low water balance o Isotonic is a balanced water balance  Nonpolar molecules (hydrophobic) can easily cross, or diffuse, across cell membranes. EX; O2, N2, CO2  Small polar molecules can cross cell membranes with some difficulty, like H2O, Glycerol Urea, and Ethanol  Large polar molecules cannot cross cell membranes, like Glucose, or Sucrose  Ions cannot cross cell membranes, like H, Na, K, Ca, Cl Electricity as it Relates to Cells  Membrane Potential; voltage difference across a membrane. Maintaining voltage potential is very important to cellular respiration. Is generated primarily by o The Sodium Potassium Pump in animal cells o The Proton Pump in all the other cells  Electrochemical Gradient; chemical force (ion concentration gradient) combined with electrical force (effect of membrane potential on ion movement) Transport  Cotransport; when the active transport of one solute indirectly causes the transport of another solute  Bulk Transport is used for bigger molecules and requires energy, it uses vesicles o Vesicle Use in Bulk Transport; Endocytosis; a cell takes in a macro molecule by forming a bubble around it called a vesicle.  Phagocytosis; the cell eats a large molecule or possibly another cell by forming a food vacuole. That food bubble meets up with a lysosome, and then they digest the contents of the food bubble.  Pinocytosis; stuff that dissolves outside the cell is pulled in to the cell by a vesicle.  Receptor-Mediated Endocytosis; ligands and receptors bind together and trigger vesicle formation. Ligands are any molecule that binds specifically with another molecule’s receptor site. o Vesicle Use in Bulk Transport; Exocytosis; how stuff is exported from the cell. Transport/Secretory vesicles merge with the cell membrane and proceed to empty their contents in to the outsides of the cell Cell Metabolism  Cell Metabolism is defined as the totality of chemical reactions in a living organism  A starting molecule begins the process, and it ends with a product  Each step is catalyzed by an enzyme, like the hydrolyzation of sucrase o A catalyst is something that helps the reaction to happen easier, ie using less energy, without being used up in the actual reaction itself  Metabolic Pathways can be either Catabolic (release energy) or Anabolic (sonsume energy) o Catabolic breaks down more complex molecules into simple ones o Anabolic builds up complex molecules from simple ones Energy And Its Various Incarnations as it Relates to the Cell  Energy is defined as the ability to do work  Kinetic Energy is the energy of speed, this is the kind of energy a roller coaster has just after screaming down the first hill.  Thermal Energy is the energy of heat, for biological purposes it’s caught up with and concerned with the random movement of atoms and assorted molecules  Potential Energy is officially defined as energy an object has by virtue of its location or structure. This is the kind of energy the roller coaster has at the top of that first hill looking down.  Chemical Energy is the Potential Energy that’s available for release in the chemical reaction Entropy  All living things are ‘open systems’ which means energy and matter can be transferred between us and our surroundings  This means we lose a LOT of heat energy, life as a biological process is really incredibly inefficient  Entropy is the name for the tendency of things to disproportionately lean towards chaos. This trend has been gradually increasing since the beginning of the universe. It’s represented by an ‘S’  Heat increases entropy. So the existence of life is just hastening the end of the universe because the thing about heat energy is that it just dissipates. Lots of other energies are translated into other forms of energy as they’re used up, for example potential energy can become kinetic, or chemical energy can become electric, but heat energy just vanished off into the universe and cools. So what’s coming is eventually all the energy in the universe will become heat energy and dissipate into nothing. Free Energy  Free Energy is the amount of energy available for use when temperature and pressure are uniform in a cell. Represented by ‘G’. It’s a measure of the instability of the system.  Energy used in a cell can be expressed as “Delta G = G final-G initial”  When free energy decreases in a system, the system is more stable  Max stability happens at equilibrium. The only time a cell can do work is when it’s moving towards that equilibrium. So, since work has to be done, nothing is at equilibrium ever.  Processes with a negative change in free energy release energy that can be used for work  The change in energy (Delta G) can be found by the formula; “Delta G=Delta H – T Delta S”, which, in words, means ‘the change in free energy equals the change in heat energy minus the combined amount of the temperature in kelvins times the change in entropy’  When the change in G is positive, the reaction is called Endergonic, and the reaction absorbs free energy  When the change in G is negative, the reaction is called Exergonic, and the reaction releases free energy How Work Works  There’s 3 major types of work  Chemical, like the synthesis of macromolecules  Mechanical, like moving chromosomes around during cell division  Transport, like motor proteins moving vesicles alone the cytoskeleton  ATP powers most of the thing done in a cell, it balences reactions between endergonic and exergonic to help the cell get the energy balance it needs to get things done.  ATP can be broken down into ADP, a much more stable molecule, in an exergonic reaction. Water breaks off a phosphate group in hydrolysis.  This exergonic reaction triggers an endergonic reaction. They work in pairs that way, like yin and yang.  This is reversible, you can stick that phosphate right back on ADP to make ATP again, which allows the ATP to work both ways, to trigger both kinds of reactions. Anatomy of an Enzyme  The enzyme’s reactant that it acts on is called its substrate  When the enzyme binds to its substrate, it’s called an enzyme- substrate complex  The place the substrate binds is called the active site o Things other than substrates can bind to active sites, for example competitive inhibiters which prevent the enzyme from actually getting any work done. Competitive enzymes are the Netflix tab; the enemy of productivity. o Noncompetitive inhibiters also bind to enzymes, but don’t directly interfere with an enzyme’s ability to bind substrates, but do lower the enzyme’s ability to catalyze reactions  When an enzyme changes its shape to accommodate its substrate, it’s called an induced fit  One enzyme can influence thousands of substrate molecules per second o I.e. catalase can convert millions of hydrogen peroxides to water molecules per second. Things that Effect Enzymes  Temperature; each enzyme has a specific temperature it functions best at, human enzymes function best around 35-40 degrees Celcius, while more heat resistant bacteria have enzymes that function best around 75-80 degrees Celcuis.  PH; each enzyme has a specific PH it functions best at. They’re all over the map, some function best on the basic side of the scale (trypsin, 8) and some function best at the acidic end of the scale (pepsin, 2)  Chemicals that specifically affect the enzymes in question


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