BIOL 202 Notes PDF - Concordia University

lOMoARcPSD|47875752 BIOL 202 notes - Concordia University - Madoka Gray-Mistumune General Biology (Concordia University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Download...

lOMoARcPSD|47875752 BIOL 202 notes - Concordia University - Madoka Gray-Mistumune General Biology (Concordia University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 BIOL 202 NOTES CHAPTER 1: SCIENTIFIC THINKING - Science is not simply a body of knowledge or a list of facts to be remembered. It is an intellectual activity, encompassing observation, description, experimentation, and explanation of natural phenomena. Put another way, science is a pathway by which we can come to discover and better understand our world. - Scientific literacy, a general, fact-based understanding of the basics of biology and other sciences, is increasingly important in our lives, and literacy in matters of biology is especially essential. - biological literacy: the ability to (1) use the process of scientific inquiry to think creatively about real-world issues that have a biological component, (2) communicate these thoughts to others, and (3) integrate these ideas into your decision making. - Empirical knowledge is based on experience and observations that are rational, testable, and repeatable. The empirical nature of the scientific approach makes it self-correcting: in the process of analyzing a topic, event, or phenomenon with the scientific method, incorrect ideas are discarded in favor of more accurate explanations. - Scientific method: 1. make observations 2. formulate a hypothesis 3. Devise a testable prediction 4. Conduct a critical experiment 5. Draw conclusions and make revisions. - A hypothesis must: (1) establish an alternative explanation for a phenomenon. That is, it must be clear that if the proposed explanation is not supported by evidence or further observations, a different hypothesis is a more likely explanation. (2) generate testable predictions. - A hypothesis that states a lack of relationship between two factors is called a null hypothesis. - Alternative hypothesis: there is a relationship. - A hypothesis is a proposed explanation for a phenomenon. - A theory is an explanatory hypothesis for natural phenomena that is exceptionally well supported by the empirical data. A theory can be thought of as a hypothesis that has withstood the test of time and is unlikely to be altered by any new evidence. - Elements common to most experiments. 1. Treatment: any experimental condition applied to the research subjects. It might be the shaving of one of an individual’s eyebrows, or the pattern used to show “suspects” (all at once or one at a time) to the witness of a staged crime, or a dosage of Echinacea given to an individual. 2. Experimental group: a group of subjects who are exposed to a particular treatment—for example, the individuals given Echinacea rather than Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 placebo in the experiment described above. It is sometimes referred to as the “treatment group.” 3. Control group: a group of subjects who are treated identically to the experimental group, with one exception—they are not exposed to the treatment. An example would be the individuals given placebo rather than Echinacea. 4. Variables: the characteristics of an experimental system that are subject to change. They might be, for example, the amount of Echinacea a person is given, or a measure of the coarseness of an individual’s hair. When we speak of “controlling” variables—the most important feature of a good experiment—we are describing the attempt to minimize any differences (which are also called “variables”) between a control group and an experimental group other than the treatment itself. That way, any differences between the groups in the outcomes we observe are most likely due to the treatment. - Placebo effect: the frequently observed, poorly understood phenomenon in which people respond favorably to any treatment. The placebo effect highlights the need for an appropriate control group. - Pseudoscience: individuals make scientific-sounding claims that are not supported by trustworthy, methodical scientific studies. - Anecdotal observations: based on just one or a few observations, people conclude that there is or is not a link between two things. - Biology is, literally, the study of life. But what is life? And how is it distinguished from non-life? Spend a few moments trying to define exactly what life is and you’ll realize that it is not easily described with a simple definition. A useful approach is to consider the characteristics shared by all living organisms and living systems:  A complex, ordered organization consisting of one or more cells. Cells carry out the functions necessary for life.  The use and transformation of energy to perform work. Organisms can perform many reactions and activities, by acquiring, using, and transforming energy.  Sensitivity and responsiveness to the external environment. Living organisms are able to respond to stimuli—such as light, moisture, or another organism.  Regulation and homeostasis. Organisms are able to maintain relatively constant internal conditions that may differ from the external environment.  Growth, development, and reproduction. Organisms can grow and develop, and they carry information relating to these and other processes that they can pass on to offspring.  Evolutionary adaptation leading to descent with modification over time. Populations have the capacity to change over time. As a consequence of Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 organisms’ ability to reproduce and of evolutionary change, populations may become better adapted to their environments. In this guide to biology, as we explore the many facets of biology and its relevance to life in the modern world, you will find two central and unifying themes recurring throughout. Hierarchical organization. Life is organized on many levels within individual organisms, including atoms, cells, tissues, and organs. And in the larger world, organisms themselves are organized into many levels: populations, communities, and ecosystems within the biosphere. The power of evolution. Evolution, the change in genetic characteristics of a population over time, accounts for the diversity of organisms and the unity among them. CHAPTER 2: CHEMISTRY - An element is a substance that cannot be broken down chemically into any other substances. - An atom is a bit of matter that cannot be subdivided any further without losing its essential properties. A charged atom is called an ion. - Groups of atoms held together by bonds are called molecules. - When two atoms share electrons, a strong covalent bond is formed. - The sharing of two pairs of electrons between two atoms is called a double bond. - An ionic bond occurs when the two oppositely charged ions attract each other. Unlike covalent bonds, in ionic bonds each electron circles around a single nucleus. Ions of two or more elements linked by ionic bonds form an ionic compound. - Hydrogen bonds: attraction between a polar (electrically charged) atom or molecule and a hydrogen atom. - Water is held together by polar covalent bonds, with an oxygen atom having a partial negative charge and hydrogen atoms having partial positive charges. A hydrogen bond is an attractive force between the oxygen atom of one water molecule and a hydrogen atom of another water molecule. Because each water molecule can participate in multiple hydrogen bonds, this makes water molecules stick together and resist being separated. - Properties of water that make it essential to life (ability to form hydrogen bonds results from these properties): 1. cohesion: it can travel up tree trunks to provide trees with water. 2. Large heat capacity: water resists warming. It takes a lot of energy to change the temperature of water even a small amount. 3. Low density as a solid. 4. Good solvent. - Buffer: chemicals that act to resist changes in pH. They can quickly absorb excess H+ ions to keep a solution from becoming too acidic, and they can quickly release H+ ions to counteract any increases in OH− concentration. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Macromolecule: a large molecule made up from smaller building blocks or subunits - Four types of macromolecule are essential to the building and functioning of living organisms: carbohydrates, lipids, proteins, and nucleic acids. - Carbohydrates are molecules that contain carbon, hydrogen, and oxygen: they are the primary fuel for running all of the cellular machinery and also form much of the structure of cells in all life forms. Sometimes they contain atoms of other elements, but they must have carbon, hydrogen, and oxygen to be considered a carbohydrate. - The simplest carbohydrates are the monosaccharides, or simple sugars. Two common: glucose and fructose. - What happens to sugar in your blood? 1. Fuel for cellular activity. Once it arrives at and enters a cell, glucose can be used as an energy source. Through a series of chemical reactions, the relatively high-energy bonds in the glucose molecule are converted into lower-energy bonds of other molecules (a process explained in detail in Chapter 4). The change from higher-energy to lower-energy bonds releases energy, and organisms use the released energy to fuel cellular activity, including the muscle contractions that enable you to move and the nerve activities that enable you to think. 2. Stored temporarily as glycogen. If there is more glucose circulating in your bloodstream than is necessary to meet your body’s current energy needs, the excess glucose can be temporarily stored in various tissues, primarily your muscles and liver. The stored glucose molecules are linked together to form a large web of molecules called glycogen. When you need energy later, the glycogen can easily be broken down to release glucose molecules back into your bloodstream. Glycogen is the primary form of short-term energy storage in animals. 3. Converted to fat. Finally, glucose circulating in your bloodstream can be converted into fat, a form of long-term energy storage. - “Carbo-loading” is a method by which athletes can, for a short time, double or triple the usual amount of glycogen stored in their muscles and liver, increasing the store of fuel available for extended exertion and delaying the onset of fatigue during an endurance event - When two simple sugars are bonded together they form a disaccharide. - Much larger numbers of simple sugars may be joined together—sometimes as many as 10,000. In this case, the resulting carbohydrate is called a polysaccharide, or a complex carbohydrate. - In plants, the primary form of energy storage is a complex carbohydrate called starch, found in roots and other tissues (see Figure 2-24). Starch consists of a hundred or more glucose molecules joined together in a line. Grains such as Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 barley, wheat, and rye are high in starch content, and corn and rice are more than 70% starch. - Two different complex carbohydrates—both indigestible by humans—serve as structural materials for invertebrate animals and plants: chitin (pronounced kite- in) and cellulose (complex carbs). - Chitin forms the rigid outer skeleton of most insects and crustaceans (such as lobsters and crabs) - We find cellulose in trees and the wooden structures we build from them, in cotton and the clothes we make from it, in leaves and in grasses. In fact, it is the single most abundant compound on earth. - Cellulose (indigestible) in our diet is known as “fiber”. It is also appropriately called “roughage” because, as the cellulose of celery stalks and lettuce leaves passes through our digestive system, it scrapes the wall of the digestive tract. Its bulk and the scraping stimulate the more rapid passage of food and the unwanted, possibly harmful products of digestion through our intestines. That is why fiber reduces the risk of colon cancer and other diseases (but it is also why too much fiber can lead to diarrhea). - LIPIDS (non-polar molecules that don’t dissolve in water, greasy to the touch, can be a significant source of energy storage): fats, sterols and phospholipids. - Fats: long-term energy storage and insulation. - Sterols: regulate growth and development. - Components of fats (triglycerides: fats having three fatty acids linked to the glycerol molecule.): head (glycerol) and tails (fatty acids). - The fat molecule carries the maximum number of hydrogen atoms and is said to be a saturated fat. - An unsaturated fat is one in which some of the carbon atoms are bound to only a single hydrogen (and are connected to each other by a double bond). - Hydrogenation of unsaturated fats is doubly problematic from a health perspective because it also creates trans fats, the “trans” referring to the unusual orientation of some or all of the double bonds that remain following the addition of hydrogen atoms. This orientation differs from that in other unsaturated dietary fats—which have their double bonds in an orientation called “cis.” Trans fats in your diet cause your body to produce more cholesterol, further raising the risk of heart disease, and they also reduce your body’s production of a type of cholesterol that protects against heart disease. - A triglyceride consists of a single glycerol molecule covalently linked to three fatty acids. Triglycerides that are solid at room temperature are called fats, and triglycerides that are liquid at room temperature are called oils. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Sterols are lipids with a basic structure formed from four interlinked rings of carbon atoms. - The steroid hormones estrogen and testosterone are built through slight chemical modifications to cholesterol. These hormones are among the primary molecules that direct and regulate sexual development, maturation, and sperm and egg production. In both males and females, estrogen influences memory and mood, among other traits. Testosterone has numerous effects, one of which is to stimulate muscle growth. - Phospholipid: A type of lipid that is the major component of the plasma membrane. Phospholipids are structurally similar to fats, but contain a hydrophilic phosphorus atom (phosphate group) and have two, not three, fatty acid chains (hydrophobic). - Phospholipids: form cellular membranes. - proteins are the chief building blocks of all life. They make up skin and feathers and horns. They make up muscles and are a significant component of bone. In your bloodstream, proteins fight invading microorganisms and stop you from bleeding to death from a shaving cut. Proteins control the levels of sugar and other chemicals in your bloodstream and carry oxygen from one place in your body to another. And in just about every cell in every living organism, proteins called enzymes initiate and assist every chemical reaction that occurs. - Proteins are constructed from 20 molecules known as amino acids. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - - The essential amino acids are the ones that human cannot manufacture, so it is essential that they are supplied in our diet. - Proteins are formed by linking individual amino acids together with a peptide bond, in which the amino group of one amino acid is bonded to the carboxyl group of another. Two amino acids joined together form a dipeptide, and several amino acids joined together form a polypeptide. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Denaturation: The disruption of protein folding, in which secondary and tertiary structures are lost, caused by exposure to extreme conditions in the environment such as heat or extreme pH. - Enzyme: A protein that initiates and accelerates a chemical reaction in a living organism. Enzymes are found throughout the cell; enzymatic proteins take part in chemical reactions on the inside and outside surfaces of the plasma membrane. - active site: the part of an enzyme to which reactants (or substrates) bind and undergo a chemical reaction. - Substrate: The molecule on which an enzyme acts. The active site on the enzyme binds to the substrate, initiating a chemical reaction; for example, the active site on the enzyme lactase binds to the substrate lactose, breaking it down into the two simple sugars glucose and galactose - activation energy: The minimum energy needed to initiate a chemical reaction (regardless of whether the reaction releases or consumes energy). - The rate at which an enzyme catalyzes a reaction is influenced by several chemical and physical factors (FIGURE 2-43). These include: 1. Enzyme and substrate concentration. For a given amount of substrate, an increase in the amount of enzyme increases the rate at which the reaction occurs. Similarly, for a given amount of enzyme, an increase in the substrate concentration increases the reaction rate. In both cases, once all of the enzyme molecules are bound to substrate, or vice versa, additional enzyme or substrate no longer increases the reaction rate. 2. Temperature. Because increasing the temperature increases the speed of movement of molecules, reaction rates generally increase at higher temperatures. Reaction rates continue to increase only up to the optimum temperature for an enzyme. At temperatures above the optimum, reaction rates decrease as enzymes lose their shape or even denature. Enzymes from different species can have widely differing optimum temperatures. 3. pH. As with temperature, enzymes have an optimum pH. Above or below this pH, excess hydrogen or hydroxide ions interact with amino acid side Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 chains in the active site. These interactions disrupt enzyme function (and sometimes structure) and decrease reaction rates. 4. Presence of inhibitors or activators. One of the most common ways that cells can speed up or slow down their metabolic pathways is through the binding of other chemicals to enzymes. This binding can alter enzyme shape in a way that increases or decreases the enzyme’s activity. Inhibitors reduce enzyme activity and come in two types. Competitive inhibitors bind to the active site, blocking substrate molecules from the site and thus from taking part in the reaction. Noncompetitive inhibitors do not compete for the active site but, rather, bind to another part of the enzyme, altering its shape in a way that changes the structure of the active site, thus reducing or blocking its ability to bind with substrate. Often, it is the very product of a metabolic pathway that acts as an inhibitor of enzymes early in the pathway, effectively shutting off the pathway when enough of its end product has been produced. - Activator: A chemical within a cell that binds to an enzyme, altering the enzyme’s shape or structure in a way that causes the enzyme to catalyze a reaction. - Nucleic acid: One of the four types of biological macromolecules, involved in information storage and transfer. The nucleic acids DNA and RNA store genetic information in unique sequences of nucleotides. - There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). - Nucleic acids and are made up of individual units called nucleotides. All nucleotides have three components: a molecule of sugar, a phosphate group (containing a phosphorus atom bound to four oxygen atoms), and a nitrogen- containing molecule. - Nucleic acids store information that is used to code proteins. - When the cell needs to synthesize a protein, a short strip of RNA is produced using a segment of a DNA strand as a model. The RNA nucleotides are therefore complementary to the DNA nucleotides, so the RNA molecule contains all the information present in the order of nucleotides of that DNA segment. The RNA moves to another part of the cell and then directs the linking together of amino acids to form a polypeptide chain that folds into a three-dimensional protein. CHAPTER 3 - Cell: The smallest unit of life that can function independently; a three- dimensional structure, surrounded by a membrane and, in prokaryotes and most plants, by a cell wall, in which many of the essential chemical reactions of the life of an organism take place. - Cell theory: A unifying and universally accepted theory in biology that holds that all living organisms are made up of one or more cells and that all cells arise from other, preexisting cells. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Eggs are cells. - Eukaryotic cell: A cell with a membrane-surrounded nucleus containing DNA, membrane-surrounded organelles, and internal structures organized into compartments. - Prokaryotic cell: A cell bound by a plasma membrane enclosing the cell contents (cytoplasm, DNA, and ribosomes); there is no nucleus or other organelles. - endosymbiosis theory: Theory of the origin of eukaryotes. For photosynthetic eukaryotes, the theory holds that, in the past, two different types of prokaryotes engaged in a close partnership and eventually one, capable of performing photosynthesis, was subsumed into the other, larger prokaryote. The smaller Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 prokaryote made some of its photosynthetic energy available to the host and, over time, the two became symbiotic and eventually became a single, more complex organism in which the smaller prokaryote had evolved into the chloroplast of the new organism. A similar scenario can be developed for the evolution of mitochondria. - Invagination: The folding in of a membrane or layer of tissue so that an outer surface becomes an inner surface. - Eventually, the photosynthetic prokaryote evolved into a chloroplast, the organelle in plant and eukaryotic algae cells in which photosynthesis occurs. A similar scenario might explain how another large host prokaryote engulfed a smaller prokaryote unusually efficient at converting food and oxygen into easily usable energy and this smaller prokaryote evolved into a mitochondrion, the organelle in plant and animal cells that converts the energy stored in food into a form usable by the cell. - The idea of the role of endosymbiosis in the evolution of eukaryotes is supported by several observations. 1. Chloroplasts and mitochondria are similar in size to prokaryotic cells and divide by splitting (fission), just like prokaryotes. 2. Chloroplasts and mitochondria have ribosomes, similar to those found in bacteria, that allow them to synthesize some of their own proteins; this ability is Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 not found in other organelles, which rely on proteins made by cytoplasmic ribosomes. 3. Chloroplasts and mitochondria have small amounts of circular DNA, similar to the circular DNA in prokaryotes and in contrast to the linear DNA strands found in a eukaryote’s nucleus. 4. Analysis of chloroplast and mitochondrial DNA has revealed that it is highly related to bacterial DNA, much more closely than it is related to eukaryotic DNA. - nucleus (cell biology): A membrane-enclosed structure in eukaryotic cells that contains the organism’s genetic information as linear strands of DNA in the form of chromosomes. - Organelles: Specialized structures in the cytoplasm of eukaryotic cells, with specific functions; include, among others, the rough and smooth endoplasmic reticulum, Golgi apparatus, and mitochondria. - Functions of plasma membrane: holds contents of cell in place, takes in food and nutrients, aids in building and exporting molecules, allows interactions with the environment and neighbouring cells. - Plasma membrane made of phospholipids packed together (head: glycerol and phosphate group, two long tails: carbon-hydrogen chains.) - Transmembrane protein: A protein that penetrates the phospholipid bilayer of a cell’s plasma membrane. - Surface protein: A protein that resides primarily on the inner or outer surface of the phospholipid bilayer that constitutes the cell’s plasma membrane. - Cystic fibrosis: malfunctioning transmembrane protein that allows chloride ions to move freely inside and out of the cells in lungs and digestive tract. Individuals with the genetic disorder cystic fibrosis do not produce a functional chloride ion transport protein that is important in the lungs and digestive tract. As a result, chloride ions accumulate within cells, and overly thick and sticky mucus collects in the lungs, impairing lung function and increasing the risk of bacterial infections. - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Diffusion: solutes spread from the area of high concentration to the area of low concentration until all gradient is eliminated. - Passive transport: Molecular movement that occurs spontaneously, without the input of energy; the two types of passive transport are diffusion and osmosis. - Diffusion: Passive transport in which a particle (the solute) is dissolved in a gas or liquid (the solvent) and moves from an area of higher solute concentration to an area of lower solute concentration. - Simple diffusion: Diffusion of molecules directly through the phospholipid bilayer of the plasma membrane, without the assistance of other molecules; oxygen and carbon dioxide, because they are small and carry no charge that would cause them to be repelled by the middle layer of the membrane, can pass through the membrane in this way. - Facilitated diffusion: Diffusion of molecules through the phospholipid bilayer of the plasma membrane that takes place through a transport protein (a “carrier molecule”) embedded in the membrane. Molecules that require the assistance of a carrier molecule are those that are too big to cross the membrane directly or are electrically charged and would be repelled by the middle layer of the membrane. - Osmosis: A type of passive transport in which water molecules move across a membrane, such as the plasma membrane of a cell; the direction of osmosis is determined by the relative concentrations of all solutes on either side of the membrane. - Tonicity: For a cell in solution, a measure of the concentration of solutes outside the cell relative to that inside the cell. - Isotonic: Refers to solutions with equal concentrations of solutes. - Hypotonic: concentration outside of cell is lower therefore water will move into the cell and it will swell. - Hypertonic: concentration inside the cell is lower therefore water will move out of the cell and it will shrivel. - Active transport: Molecular movement that depends on the input of energy, which is necessary when the molecules to be moved are large or are being moved against their concentration gradient. - Primary active transport: uses energy released directly from the ATP. - Secondary active transport: Active transport in which there is no direct involvement of ATP (adenosine triphosphate); the transport protein simultaneously moves one molecule against its concentration gradient while letting another flow down its concentration gradient. - Endocytosis: A cellular process in which large particles, solid or dissolved, outside the cell are surrounded by a fold of the plasma membrane, which pinches off, forming a vesicle, and the enclosed particle moves into the cell. The three types of endocytosis are phagocytosis, pinocytosis, and receptor-mediated endocytosis. - Exocytosis: A cellular process in which particles within the cell, solid or dissolved, are enclosed in a vesicle and transported to the plasma membrane, where the membrane of the vesicle merges with the plasma membrane and the material in the vesicle is expelled to the extracellular fluid for use throughout the body. - Phagocytosis: large solid particles are engulfed by the plasma membrane, a vesicle is formed, and the particle is moved into the cell. - Pinocytosis: dissolved particles and liquids are engulfed by the plasma membrane, a vesicle is formed, and the material is moved into the cell. The vesicles formed in pinocytosis are generally much smaller than those formed in phagocytosis. - Receptor-mediated endocytosis: receptors on the surface of a cell bind to specific molecules; the plasma membrane then engulfs both molecule and receptor and draws them into the cell. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Nucleus: genetic control center by directing most cellular activities by controlling which molecules are produced, and in what quantity and holds hereditary information (holds most of the DNA). - Nuclear membrane: A membrane enclosing the nucleus of a cell, separating it from the cytoplasm; consists of two bilayers and is perforated by pores, enclosed in embedded proteins, that allow the passage of large molecules between the nucleus and the cytoplasm; also called the nuclear envelope. - Nuclear pore proteins: regulate transport of molecules across the nucleus. Two important types of transport are 1) the movement from the cytosol into the nucleus of proteins that interact with DNA and catalyze nuclear activities, and 2) the movement from the nucleus to the surrounding cytosol of RNA and RNA-protein complexes. - Chromatin: A mass of long, thin fibers consisting of DNA and proteins in the nucleus of the cell. - Nucleolus: An area near the center of the nucleus where subunits of the ribosomes are assembled - Ribosomes: create proteins. - Cytoskeleton: A network of protein structures in the cytoplasm of eukaryotes (and, to a lesser extent, prokaryotes) that serves as scaffolding, adding support and, in some cases, giving animal cells of different types their characteristic shapes. The cytoskeleton serves as a system of tracks guiding the intracellular traffic flow and, because it is flexible and can generate force, gives cells some ability to control their movement. - Microtubules: One of three types of protein fibers (the others are intermediate filaments and microfilaments) that make up the eukaryotic cytoskeleton, providing it with structure and shape. These are the thickest elements in the cytoskeleton; they resemble rigid, hollow tubes, functioning as tracks to which molecules and organelles within the cell may attach and be moved along; also help pull chromosomes apart during cell division. - intermediate filaments: One of three types of protein fibers (the others are microtubules and microfilaments) that make up the eukaryotic cytoskeleton, providing it with structure and shape; a durable, rope-like system of numerous different overlapping proteins. - Microfilaments: One of three types of protein fibers (the others are intermediate filaments and microtubules) that make up the eukaryotic cytoskeleton, providing it with structure and shape. These are the thinnest elements in the cytoskeleton; long, solid, rod-like fibers that help generate forces, including those important in cell contraction and cell division. - cilia (sing. cilium); Short projections from the cell surface, often occurring in large numbers on a single cell, that beat against the extracellular fluid to move the fluid past the cell. - Flagella: Long, thin, whip-like projection from the cell body of a prokaryote that aids in cell movement through the medium in which the organism lives; in animals, the only cell with a flagellum is the sperm cell. - Mitochondria: The organelle in eukaryotic cells that converts the energy stored in food, in the chemical bonds of carbohydrate, fat, and protein molecules, into a form usable by the cell for all its functions and activities. - intermembrane space: In a mitochondrion, the region between the inner and outer membranes. - mitochondrial matrix: The space enclosed by the inner mitochondrial membrane, where the carriers NADH and FADH2 begin the electron transport chain by carrying high-energy electrons to molecules embedded in the inner membrane. - mitochondria are similar to bacteria in size and shape. Mitochondria have their own DNA that is highly related to bacterial DNA. Mitochondria divide by fission. Also, mitochondria have ribosomes, similar to those found in bacteria, allowing them to synthesize some of their own proteins. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Lysosome: A round, membrane-enclosed, enzyme-and acid-filled vesicle in the cell that digests and recycles cellular waste products and consumed material. - Endomembrane system: A system of organelles (the rough endoplasmic reticulum, the smooth endoplasmic reticulum, and the Golgi apparatus) that surrounds the nucleus; it produces and modifies necessary molecules, breaks down toxic chemicals and cellular by- products, and is thus responsible for many of the fundamental functions of the cell. - Rough endoplasmic reticulum: An organelle, part of the endomembrane system, structurally like a series of interconnected, flattened sacs connected to the nuclear envelope; called “rough” because its surface is studded with ribosomes which make protein. - - Smooth endoplasmic reticulum: An organelle, part of the endomembrane system, structurally like a series of branched tubes; called “smooth” because its surface has no ribosomes. Smooth ER synthesizes lipids such as fatty acids, phospholipids, and steroids. Lipids produced by the smooth ER are packaged in transport vesicles and then sent to other parts of the cell or to the plasma membrane for export. - - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Golgi apparatus: An organelle, part of the endomembrane system, structurally like a flattened stack of unconnected membranes, each known as a Golgi body. The Golgi apparatus processes molecules synthesized in the cell (primarily proteins and lipids) and packages those molecules that are destined for use elsewhere in the body. - The molecules pass through about four successive Golgi body chambers. In each Golgi body, enzymes make slight modifications to the molecules (such as the addition or removal of phosphate groups or sugars). The processing that occurs in the Golgi apparatus often involves tagging molecules (much like adding a postal address or tracking number) to direct them to some other part of the organism. After they are processed, the molecules bud off from the Golgi apparatus in a vesicle, which then moves into the cytosol. If the molecules are destined for delivery and use elsewhere in the body, the transport vesicle eventually fuses with the cell’s plasma membrane and dumps the molecules into the bloodstream via exocytosis. - In plants, cell wall = cellulose. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - - plasmodesma (pl. desmata) In plants, microscopic tube-like channels connecting the cells and enabling communication and transport between them. - A plant’s cell wall provides structural strength to the cell, makes the cell more water resistant, and provides some protection from insects and other animals. - vacuole (central): A membrane-enclosed, fluid-filled, multipurpose organelle prominent in most plant cells (but also present in some protists, fungi, and animals); its functions vary but Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 can include storing nutrients, retaining and degrading waste products, accumulating poisonous materials, containing pigments, and providing physical support. - The vacuole: multipurpose storage.  1. Nutrient storage. The vacuole stores hundreds of dissolved substances, including amino acids, sugars, and ions.  2. Waste management. The vacuole retains waste products and degrades them with digestive enzymes, much like the lysosome in animal cells.  3. Predator deterrence. The poisonous, nasty-tasting materials that accumulate inside the vacuoles of some plants make a powerful deterrent to animals that might try to eat parts of the plant.  4. Sexual reproduction. The vacuole may contain pigments that give some flowers their red, blue, purple, or other colors, enabling them to attract birds and insects that help the plant reproduce by transferring pollen.  5. Physical support. High concentrations of dissolved substances in the vacuole can cause water to rush into the cells through the process of osmosis. The increased fluid pressure inside the vacuole can cause the cell to enlarge a bit and push out the cell wall. This process is responsible for the pressure (called turgor pressure) that allows stems, flowers, and other plant parts to stand upright. The ability of non-woody plants to stand upright is due primarily to turgor pressure. Wilting is the result of a loss of turgor pressure. - Stroma: In the leaf of a green plant, the fluid in the inner compartment of a chloroplast, which contains DNA and protein-making machinery. - Thylakoids: Interconnected membranous structures in the stroma of a chloroplast, where light energy is collected and converted to chemical energy in photosynthesis. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 CHAPTER 5: ENERGY - Photosynthesis: The process by which some organisms, including plants and some protists and bacteria, are able to capture energy from the sun and store it in the chemical bonds of sugars and other molecules. - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - - chlorophyll: A light-absorbing pigment molecule in chloroplasts. - Light energy: A type of kinetic energy made up of energy packets called photons, which are organized into waves. - Photons: The elementary particle that carries the energy of electromagnetic radiation of all wavelengths. - cellular respiration: The process by which all living organisms extract energy stored in the chemical bonds of molecules and use it for fuel for their life processes. - Energy: The capacity to do work, which is the moving of matter against an opposing force. - Kinetic energy of an object is the energy that it has due to its motion. - potential energy: Stored energy; the capacity to do work that results from an object’s location or position, as in the case of water held behind a dam. - chemical energy: A type of potential energy in which energy is stored in chemical bonds between atoms or molecules. - Thermodynamics: The study of the transformation of energy from one type to another, such as from potential energy to kinetic energy. - first law of thermodynamics: A physical law that states that energy cannot be created or destroyed; it can only change from one form to another. - second law of thermodynamics: A physical law that states that every conversion of energy is not perfectly efficient and invariably includes the transformation of some energy into heat. - adenosine triphosphate (ATP): A molecule that temporarily stores energy for cellular activity in all living organisms. ATP is composed of an adenine, a sugar molecule, and a chain of three negatively charged phosphate groups. - electromagnetic spectrum: The range of wavelengths that produce electromagnetic radiation, extending (in order of decreasing energy) from high-energy, short-wave, gamma Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 rays and X rays, through ultraviolet light, visible light, and infrared light, to very long, low- energy, radio waves. - Pigment: In photosynthesis, molecules that are able to absorb the energy of light of specific wavelengths, raising electrons to an excited state in the process. - chlorophyll a The primary photosynthetic pigment. Chlorophyll a absorbs blue-violet and red light; because it cannot absorb green light and instead reflects those wavelengths, we perceive the reflected light as the color green. - chlorophyll b A photosynthetic pigment similar in structure to chlorophyll a. Chlorophyll b absorbs blue and red-orange wavelengths and reflects yellow-green wavelengths. - carotenoids Pigments that absorb blue-violet and blue-green wavelengths of light and reflect yellow, orange, and red wavelengths of light. - The primary photosynthetic pigment is chlorophyll a, but the pigments chlorophyll b and carotenoids also help absorb a wider range of wavelengths of light. The pigments capture packets of light energy called photons. - photosystems Two arrangements of light-absorbing pigments, including chlorophyll, within the chloroplast that capture energy from the sun and transform it first into the energy of excited electrons and ultimately into ATP and high-energy electron carriers such as NADPH. - primary electron acceptor In photosynthesis, a molecule that accepts excited, high-energy electrons from chlorophyll a, beginning the series of electron handoffs known as an electron transport chain. - electron transport chain The path of high-energy electrons moving from one molecule within a membrane to another, coupled to the pumping of protons across the membrane, creating a concentration gradient that is used to make ATP; occurs in mitochondria and chloroplasts. - The energy in sunlight is captured and stored in ATP and NADPH molecules. When water molecules are split to provide electrons for this process, oxygen molecules also are formed. - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Calvin cycle In photosynthesis, a series of chemical reactions in the stroma of chloroplasts in which sugar molecules are assembled. - rubisco An enzyme (ribulose 1,5-bisphosphate carboxylase/ oxygenase) involved in photosynthesis; it fixes carbon atoms from in the air, attaching them to an organic molecule in the stroma CO2 of the chloroplast. This fixation is the first step in the Calvin cycle, in which molecules of sugar are assembled. Rubisco is the most abundant protein on earth. - fixation In genetics, the point at which the frequency of an allele in a population is 100%, and thus there is no more variation in the population for this gene. - - 1. Sugar creation. The newly built molecule is chemically modified: a phosphate from ATP is added, and the molecule receives some high-energy electrons from NADPH and is split in two. For every three carbon dioxide molecules added to the Calvin cycle, one sugar product is produced. This product, a three-carbon sugar, is called glyceraldehyde 3-phosphate (G3P). Some of the G3P molecules are combined to make the six-carbon sugars glucose and fructose. These sugars can be used as fuel by the plant, enabling it to grow. They can also be used as fuel by animals that eat the plant. 2. Regeneration. Not all of the G3P molecules are used to produce sugars. In the third and final phase of the Calvin cycle, some G3P molecules are rearranged to regenerate the original five-carbon molecule in the chloroplast to which the carbon from CO 2 is attached. Rearranging G3P to regenerate the starting molecule requires energy from ATP produced in the “photo” reactions of photosynthesis. With this regeneration, the Calvin cycle can continue to fix carbon and produce molecules of G3P. Ultimately, to synthesize one molecule of G3P, the Calvin cycle requires three “turns” of the Calvin cycle and fixation of three atoms of carbon from carbon dioxide to the initial organic Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 molecule; this process consumes nine molecules of ATP and six molecules of NADPH generated in the “photo” reactions of photosynthesis. - The first step of the Calvin cycle is carbon fixation, in which carbon dioxide molecules are attached to organic molecules. The next step is sugar creation, in which these organic molecules are modified into sugars. The third and final step is regeneration, where some of these sugars are used to regenerate the original organic molecules. - glycolysis In all organisms, the first step in cellular respiration, in which one molecule of glucose is broken into two molecules of pyruvate. For some organisms, glycolysis is the only means of extracting energy from food; for others, including most plants and animals, it is followed by the Krebs cycle and the electron transport chain. - pyruvate The end product of glycolysis. - - During glycolysis, glucose is broken down into two pyruvate molecules. Energy is captured and stored in the high-energy molecules ATP and NADH. - Krebs cycle The second step of cellular respiration, in which energy is extracted from sugar molecules as additional molecules of ATP and NADH are formed. - During the Krebs cycle, in which the two pyruvate molecules formed during glycolysis are broken down into carbon dioxide, energy is captured and stored in the high-energy molecules ATP, NADH, and FADH2. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - glycolisis takes place in cytosol, krebs cycle and electron transfer chain take place in mitochondrion. - - Energy is released from electrons while they travel through the electron transport chain, which ultimately leads to the formation of most of the ATP needed by the cell. These low- energy electrons are ultimately combined with oxygen and hydrogen ions to form water. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - ethanol The end product of fermentation of yeast (when oxygen isn’t present); the alcohol in beer, wine, and spirits. - fermentation The process by which glycolysis occurs in the absence of oxygen; the electron acceptor is pyruvate (in animals) or acetaldehyde (in yeast) rather than oxygen. - Fermentation involves the partial breakdown of glucose in the absence of oxygen. Both processes produce energy in the form of ATP without oxygen. This results in the production of lactic acid in animals and the production of ethanol and carbon dioxide in yeast. - - Lipids. Dietary lipids are broken down into their two constituent parts: a glycerol molecule and fatty acids. The glycerol is chemically modified into one of the molecules produced during glycolysis. It enters the glycolysis pathway at that step and is broken down to yield energy. The fatty acids, meanwhile, are chemically modified into acetyl-CoA, at which point they enter the Krebs cycle. Proteins. Proteins are chains of amino acids. After consumption, the chains are broken down chemically, then each amino acid is broken down into (1) an amino group that may be used in the production of tissue or excreted in the urine, and (2) a carbon compound that is Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 converted to one of the intermediate compounds in glycolysis or the Krebs cycle, allowing the energy stored in its chemical bonds to be harnessed. - Metabolic machinery can extract energy from (besides glucose): Other carbohydrates, proteins, and fats also can be broken down to yield energy. This breakdown is accomplished by either converting these molecules into glucose or converting them into some intermediate molecule in glycolysis or the Krebs cycle. CHAPTER 5 - DNA (deoxyribonucleic acid) is a nucleic acid, a macromolecule that stores information. It consists of individual units called nucleotides, which have three components: a molecule of sugar, a phosphate group (containing four oxygen atoms bound to a phosphorus atom), and a nitrogen-containing molecule called a base. - nucleotide A molecule containing a phosphate group, a sugar molecule, and a nitrogen-containing molecule. Nucleotides are the individual units that together, in a unique sequence, constitute a nucleic acid. - base (of DNA) One of the nitrogen-containing side-chain molecules attached to a sugar molecule in the sugar-phosphate backbone of DNA and RNA. The four bases in DNA are adenine (A), thymine (T), guanine (G), and cytosine (C); the four bases in RNA are adenine (A), uracil (U), guanine (G), and cytosine (C). The information in a molecule of DNA and RNA is determined by its sequence of bases. - code In genetics, the base sequence of a gene; information encoded within the genetic information can be translated into proteins. - genome The full set of DNA present in an individual organism; also can refer to the full set of DNA present in a species. - chromosome A linear or circular strand of DNA with specific sequences of base pairs. The human genome consists of two copies of each of 23 unique chromosomes, one from the mother and one from the father. - locus (pl. loci) The location or position of a gene on a chromosome. - gene The basic unit of heredity; a sequence of DNA nucleotides on a chromosome that carries the information necessary for making a functional product, usually a protein or an RNA molecule. - alternative versions of a gene that code for the same feature are called alleles. - Any single characteristic or feature of an organism is referred to as a trait. - intron A non-coding region of DNA. - genotype The genes that an organism carries for a particular trait; also, collectively, an organism’s genetic composition. - phenotype The manifested structure, function, and behaviors of an individual; the expression of the genotype of an organism. - transcription The process by which a gene’s base sequence is copied to mRNA. - translation The process by which mRNA, which encodes a gene’s base sequence, directs the production of a protein. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - messenger RNA (mRNA) The ribonucleic acid that “reads” the sequence for a gene in DNA and then carries the information from the nucleus to the cytoplasm, where the next stage of protein synthesis will take place. - promoter site Part of a DNA molecule that indicates where the sequence of base pairs that makes up a gene begins. - ribosomal subunits The two structural parts of a ribosome, which function together to translate mRNA to build a chain of amino acids that will make up a protein. - transfer RNA (tRNA) The type of RNA molecules in the cytoplasm that link specific triplet base sequences on mRNA to specific amino acids. - codons Three-base sequences in mRNA that link with complementary tRNA molecules, which are attached to amino acids that are specified by that codon; a codon with yet another sequence ends the process of assembling a protein from amino acids. - protein synthesis The construction of a protein from its constituent amino acids, by the processes of transcription and translation. - A nucleotide consists of a sugar, a phosphate group, and a nitrogen-containing base. The nitrogen-containing bases of one strand of DNA interact through hydrogen bonds with the bases on the opposite strand. - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - gene expression The process by which information in a gene’s sequence is used to synthesize a gene product (commonly a protein, but also RNA). - gene regulation The processes by which cells “turn on” or “turn off” genes, influencing the amount of gene products formed. - operon A group of several genes, along with the elements that control their expression as a unit, all within one section of DNA. Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - - The first step is to recognize and initiate protein building. This involves the subunits of a ribosome recognizing and assembling around a codon on the mRNA transcript called the start sequence (the AUG codon). The second step, elongation, involves an amino acid- carrying tRNA recognizing the next three-base sequence on the mRNA, attaching to the mRNA at that point, and the ribosome facilitating the connection of this amino acid to the previous one. Once attached, the tRNA detaches, floats away, and a new amino-acid carrying tRNA moves in. This process (called protein synthesis) continues, elongating the amino acid chain. The third step, termination, occurs when the ribosome arrives at a codon on the mRNA that signals the end of translation. At this stop sequence, the amino acid chain and the mRNA molecule are released from the ribosome. - In the absence of lactose, the lac operon is turned off because the repressor protein binds to the operator, preventing RNA polymerase from binding and transcribing the genes for lactose metabolism. In the presence of lactose, the lac operon is turned on because lactose binds to the repressor protein, preventing it from binding to the operator. RNA polymerase then binds to the promoter and transcribes the genes necessary for metabolism. - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 - Downloaded by Chhaya Patel ([email protected])  lOMoARcPSD|47875752 Downloaded by Chhaya Patel ([email protected])