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Select All matter anything takes up space and has mass compound substance consisting of two or more elements in a fixed ratio element any substance that cannot be broken down to any other substance trace elements an element indispensable for life but required in extremely minimum amounts atom smallest unit of matter that retains property of an element neutron an electrically neutral particle found in the nucleus of an atom proton a subatomic particle with single positive charge found in nucleus of an atom electron a subatomic particle with a single negative charge; one or more electrons move around the nucleus isotopes one of several atomic forms of an element each containing different number of neutrons and different in atomic mass valence electrons the electrons in the outermost electron shell chemical bonds an attraction between two atoms resulting from a sharing of outer shell electrons or the presence of opposite charges on the atom; the bonded atoms gain compounds outer electron shells covalent bonds a type of strong chemical bond in which two atoms share one pair of valence electrons polar covalent bonds a type of covalent bond between atoms that differ in electronegativity. the shared electrons are pulled closer to the more electronegative atom. making one slightly negative and the other slightly positive electronegativity the attraction of an atom for the electrons of a covalent bond anion a negatively charged ion cation an ion with a positive charge produced by the loss of one or more electrons hydrogen bond a type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecules is attracted to the slightly negative atom of a polar covalent in another bond cohesion the binding together of like molecules often by hydrogen bonds adhesion the attraction between different kinds of molecules surface tension a measure of how difficult it is to stretch or break the surface of a liquid heat total amount of kinetic energy due to molecular motion in a body of matter. It is energy in most random form temperature a measure of the intensity of heat in degrees reflecting molecules average kinetic energy specific heat the amount of heat that must be absorbed lost for one gram of a substance to change its temperature by one degree solution a homogeneous mixture of two or more substance (liquid) solvent dissolving agent of a solution solute a substance that is dissolved in a solution aqueous solution a solution in which water is the solvent acid a substance that increases the hydrogen ion concentration of a solution base a substance that reduces the hydrogen ion concentration of a solution hydrophilic having an affinity to water hydrophobic having aversion to water tend to coalesce and form droplets of water pH A measure of hydrogen ion concentration equal to -log [H+] and ranging in value from 0 to 14. buffers A substance that consists of acid and base forms in a solution and that minimizes changes in pH when extraneous acids or bases are added to the solution. acid precipitation Rain, snow, or fog that is more acidic than pH 5.6. organic chemistry The study of carbon compounds (organic compounds). hydrocarbons An organic molecule consisting only of carbon and hydrogen. isomers One of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types are structural , geometric and enantiomers. structural isomers Compounds that have the same molecular formula but differ in the covalent arrangements of their atoms. geometric isomers Compounds that have the same molecular formula but differ in the spatial arrangements of their atoms. enantiomers Molecules that are mirror images of each other. functional groups A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions. hydroxyl groups A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols. carbonyl groups A functional group present in aldehydes and ketones and consisting of a carbon atom double-bonded to an oxygen atom. aldehyde An organic molecule with a carbonyl group located at the end of the carbon skeleton. ketone An organic compound with a carbonyl group of which the carbon atom is bonded to two other carbons. carboxyl group A functional group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group. amino group A functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1. sulfhydryl group A functional group consisting of a sulfur atom bonded to a hydrogen atom (—SH). phosphate group A functional group important in energy transfer. macromolecule A giant molecule formed by the joining of smaller molecules, usually by a condensation reaction. Polysaccharides, proteins, and nucleic acids are macromolecules. polymer A long molecule consisting of many similar or identical monomers linked together. monomer The subunit that serves as the building block of a polymer. condensation reaction A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction. dehydration reaction A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule. hydrolysis A chemical process that lyses, or splits, molecules by the addition of water; an essential process in digestion. carbohydrates A sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides). monosaccharides The simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, the molecular formulas of are generally some multiple of CH2O. disaccharides A double sugar, consisting of two monosaccharides joined by dehydration synthesis. starch A storage polysaccharide in plants consisting entirely of glucose. glycogen An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch. cellulose A structural polysaccharide of cell walls, consisting of glucose monomers joined by b-1, 4-glycosidic linkages. fatty acid A long carbon chain carboxylic acid. vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat. saturated fatty acid A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton. unsaturated fatty acid A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton. phospholipids A molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail. cholesterol A steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids. steroids A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached. polysaccharides A polymer of up to over a thousand monosaccharides, formed by dehydration reactions. glycosidic linkage A covalent bond formed between two monosaccharides by a dehydration reaction. fat constructed from glycerol and fatty acids amino acid An organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of proteins. protein A three-dimensional biological polymer constructed from a set of 20 different monomers called amino acids. peptide bond The covalent bond between two amino acid units, formed by a dehydration reaction beta (B) pleated sheet One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds. denaturation For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. For DNA, the separation of the two strands of the double helix. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature. RNA A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses. DNA A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins. nucleic acid A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA. purines One of two families of nitrogenous bases found in nucleotides. Adenine (A) and guanine (G) are purines. pyrimidines One of two families of nitrogenous bases found in nucleotides. Cytosine (C), thymine (T), and uracil (U) are pyrimidines. organelles One of several formed bodies with specialized functions, suspended in the cytoplasm of eukaryotic cells. electron microscope A microscope that focuses an electron beam through a specimen, resulting in resolving power a thousandfold greater than that of a light microscope. A transmission electron microscope (TEM) is used to study the internal structure of thin sections of cells. A scanning electron microscope (SEM) is used to study the fine details of cell surfaces. cell fractionation The disruption of a cell and separation of its organelles by centrifugation. ultra centrifuges A machine that spins test tubes at the fastest speeds to separate liquids and particles of different densities. cytosol The semifluid portion of the cytoplasm. prokaryotic cell A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles; found only in the domains Bacteria and Archaea. nucleoid A dense region of DNA in a prokaryotic cell. cytoplasm The entire contents of the cell, exclusive of the nucleus, and bounded by the plasma membrane. plasma membrane The membrane at the boundary of every cell that acts as a selective barrier, thereby regulating the cell's chemical composition. nucleus (1) An atom's central core, containing protons and neutrons. (2) The chromosome-containing organelle of a eukaryotic cell. (3) A cluster of neurons. nuclear lamina A netlike array of protein filaments that maintains the shape of the nucleus. chromatin The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing,exists as a mass of very long, thin fibers that are not visible with a light microscope. food vacuoles A membranous sac formed by phagocytosis. contractile vacuoles A membranous sac that helps move excess water out of the cell. plastids One of a family of closely related plant organelles, including chloroplasts, chromoplasts, and amyloplasts (leucoplasts). central vacuole A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development. tonoplast A membrane that encloses the central vacuole in a plant cell, separating the cytosol from the cell sap mitochondria An organelle in eukaryotic cells that serves as the site of cellular respiration. chloroplasts An organelle found only in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water. cristae (plural, cristae) An infolding of the inner membrane of a mitochondrion that houses the electron transport chain and the enzyme catalyzing the synthesis of ATP. thylakoids A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy. grana A stacked portion of the thylakoid membrane in the chloroplast. Grana function in the light reactions of photosynthesis stroma The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water. peroxisome A microbody containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide. cytoskeleton A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical and transport functions. centrosome Material present in the cytoplasm of all eukaryotic cells, important during cell division; the microtubule-organizing center. flagella A long cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules, ensheathed in an extension of plasma membrane. cilia A short cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules ensheathed in an extension of plasma membrane. actin A globular protein that links into chains, two of which twist helically about each other, forming microfilaments in muscle and other contractile elements in cells. cell wall A protective layer external to the plasma membrane in plant cells, bacteria, fungi, and some protists. In plant cells, the wall is formed of cellulose fibers embedded in a polysaccharide-protein matrix. The primary cell wall is thin and flexible, whereas the secondary cell wall is stronger and more rigid and is the primary constituent of wood. extracellular matrix The substance in which animal tissue cells are embedded consisting of protein and polysaccharides. collagen A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom. chromosomes A threadlike, gene-carrying structure found in the nucleus. Each chromosome consists of one very long DNA molecule and associated proteins. nucleolus A specialized structure in the nucleus, formed from various chromosomes and active in the synthesis of ribosomes. ribosomes A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits smooth ER That portion of the endoplasmic reticulum that is free of ribosomes. Rough ER That portion of the endoplasmic reticulum studded with ribosomes. endoplasmic reticulum An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions. glycoproteins A protein covalently attached to a carbohydrate. golgi apparatus An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum. transport vesicles A tiny membranous sac in a cell's cytoplasm carrying molecules produced by the cell. lysosomes A membrane-enclosed bag of hydrolytic enzymes found in the cytoplasm of eukaryotic cells. phagocytosis A type of endocytosis involving large, particulate substances. selective permeability (the ability to allow some sub. to cross the plasma membrane more easily) A property of biological membranes that allows some substances to cross more easily than others. fluid mosaic model The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally in a fluid bilayer of phospholipids. integral proteins Typically transmembrane proteins with hydrophobic regions that completely span the hydrophobic interior of the membrane. peripheral proteins Protein appendages loosely bound to the surface of the membrane and not embedded in the lipid bilayer. diffusion The spontaneous tendency of a substance to move down its concentration gradient from a more concentrated to a less concentrated area. concentration gradient An increase or decrease in the density of a chemical substance in an area. Cells often maintain concentration gradients of ions across their membranes. When a gradient exists, the ions or other chemical substances involved tend to move from where they are more concentrated to where they are less concentrated passive transport The diffusion of a substance across a biological membrane hypertonic In comparing two solutions, referring to the one with a greater solute concentration. hypotonic In comparing two solutions, the one with a lower solute concentration. isotonic Having the same solute concentration as another solution. osmoregulation The control of water balance in organisms living in hypertonic, hypotonic, or terrestrial environments. osmosis The diffusion of water across a selectively permeable membrane. turgid Firm. Walled cells become turgid as a result of the entry of water from a hypotonic environment. flaccid Limp. Walled cells are limp in isotonic surroundings, where there is no tendency for water to enter. plasmolysis A phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment facilitated diffusion The spontaneous passage of molecules and ions, bound to specific carrier proteins, across a biological membrane down their concentration gradients aquaporins (water channel proteins that facilitate the amount of diffusion)A transport protein in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membrane (osmosis). gated channels A protein channel in a cell membrane that opens or closes in response to a particular stimulus. active transport The movement of a substance across a biological membrane against its concentration or electrochemical gradient with the help of energy input and specific transport proteins. sodium potassium pump A special transport protein in the plasma membrane of animal cells that transports sodium out of the cell and potassium into the cell against their concentration gradients. electrochemical gradient The diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration difference of the ion across a membrane and its tendency to move relative to the membrane potential. proton pump An active transport mechanism in cell membranes that consumes ATP to force hydrogen ions out of a cell and, in the process, generates a membrane potential cotransport The coupling of the "downhill" diffusion of one substance to the "uphill" transport of another against its own concentration gradient. exocytosis The cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane. endocytosis The cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch off to form an intracellular vesicle. phagocytosis A type of endocytosis involving large, particulate substances. pinocytosis A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes. ligands A molecule that binds specifically to a receptor site of another molecule. receptor mediated endocytosis The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances. electrogenic pump An ion transport protein generating voltage across the membrane. nucleus chromatin, nucleolus, nuclear envelope--> directs protein synthesis by synthesizing RNA (mRNA) and sending it to the cytoplasm via nuclear pores-->the mRNA is made according to instruction provided by DNA --> mRNA reaches cytoplasm ribosomes translate the genetic message into polypeptide chromatin organization of DNA and proteins into fibrous material nucleolus specialized structure in special type of RNA, ribosomal RNA, is synthesized + assembled w/ proteins imported from cytoplasm into main components of ribsomal subunits which pass nuclear portes to cytoplasm where they combine to form ribosomes nuclear envelope double membrane perforated by pores which regulate entry and exit of certain macromolecules and particles ribosomes use info, from the DNA to make proteins and carry out protein synthesis free ribosomes suspended in cytosol which will function in cytosol (ex:enzymes) bound ribosomes attached to outside of ER or nuclear envelope- proteins that are destined for insertion into membranes or packaging certain organelles (ex: lysosome) endoplasmic reticulum network of membrane sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes smooth ER synthesis of lipids, phospholipids and steroid sex hormones-help detoxify drugs and poisons (liver cells) involves adding hydroxyl groups to drugs to make soluble and easier to flush from body rough ER sythesis of secretory proteins (glycoproteins) specialized cells secrete proteins produced by rough ER ribosomes and membrane production golgi apparatus center of manufacturing, warehousing, sorting, and shipping products are usually modified during their transit from the cis pole to the trans pole cis face golgi appartus--> usually located near the ER a vesicle that buds from the ER will add its membrane and the contents of its lumen,cavity, to this face trans face golgi apparatus--> gives rise to vesicles which pinch off and travel to other sites lysosomes digestive compartments (macromolecules) carry out intracellular digestion . Use their hydrolytic enzymes to recycle the cell's own organic material (autophagy) mitochondria sites of cellular respiration the catbolic process that generates ATP by extracting energy from sugars, fats + other fuels w/ oxygens help chloroplast sites of photosynthesis. convert solar energy--> chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds from CO2 and H20 peroxisomes generate and degrade H2O2 in performing various metabolic functions transfer hydrogen from various substrates to oxygen and they produce H2O2. Use O to break fatty acids that can be sent to mitochondria cytoskeleton organizing the structures and activities of cells microtubules maintenance of cell shape (compression resisting girders) cell motility organelle and chromosome movement microfilaments actin (tension bearing elements ) muscle contraction intermediate filaments anchorage of nucleus and certain other organelles, formation of nuclear lamina centrosomes region where cells microtubules are initiated centrioles composed of nine sets of triplet microtubule arrange in a ring ECM function in support, adhesion, movement, and regulation (glycoproteins) collagen most abundant in animal cells tight junctions membranes of neighboring cells are actually fused forming continuous belts around cell to prevent leakage of extracellular fluid desmosome function like rivets fastening cells together into strong sheets Intermediate filaments reinforce this gap junctions provide cytoplasmic channels between adjacent animal cells amphipathic molecules Amphipathic molecules have both hydrophobic regions and hydrophilic regions <phospholipids>. fluid mosaic model The arrangement of phospholipids and proteins in biological membranes is described by the freeze-fracture splits a membrane along the middle of the phospholipid bilayer. When a freeze-fracture preparation is viewed with an electron microscope, protein particles are interspersed in a smooth matrix, supporting the fluid mosaic model. Peripheral proteins are not embedded in the lipid bilayer at all. Instead, the are loosely bound to the surface of the protein, often connected to integral proteins Integral proteins penetrate the hydrophobic core of the lipid bilayer, often completely spanning the membrane (as transmembrane proteins). functions of the proteins 1. Transport of specific solutes into or out of cells. 2. Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway 3. Signal transduction, relaying hormonal messages to the cell. 4. Cell-cell recognition, allowing other proteins to attach two adjacent cells together 5. Intercellular joining of adjacent cells with gap or tight junctions 6. Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape and stabilizing the location of certain membrane proteins. Cell-cell recognition the ability of a cell to distinguish one type of neighboring cell from another is crucial to the functioning of an organism carbohydrates are important for this transport proteins span the membrane 1. channel proteins which have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane (aquaporins facilitate the passage of water through the membrane) 2. carrier proteins bind to molecules and change shape to shuttle them across the membrane diffusion the tendency of molecules of any substance to spread out in the available space it is driven by intrinsic kinetic energy (thermal motion or heat) of molecules passive transport the diffusion of a substance across a biological membrane because it require no energy from the cell to make it happen - the concentration gradient represents potential energy and drives fusion concentration gradient an increase or decrease in the density of a chemical substance in an area -->substances tend to move form where there are more concentrated to where they are less concentrated osmosis the passive transport of water; diffusion of water across a selectively permeable membrane; the direction of osmosis is determined only by a difference in total solute concentration ; the kind of solutes in the solution do not matter facilitated diffusion the passive movement of molecules down their concentration gradient via transport proteins gated channels many ion channels function as gated channels these channels open or close depending on the presence or absence of a chemical or physical stimulus active transport uses energy to move solutes against their gradients; requires the cell to expend metabolic energy; enables a cell to maintain its internal concentrations of small molecules that would otherwise diffuse across he membrane ; ATP supplies the energy for active transport ATP ATP can power active transport by transferring a phosphate group from ATP to the transport protein. This may induce a conformation change in the transport proteins translocating the solute across the membrane sodium potassium pump actively maintains the gradient of sodium ions (Na+) and potassium ions (K+) across the plasma membrane of animal cells . K+ concentration is low outside animal cell and high inside the cell. Na+ concentration is high outside an animal cell and low inside the cell. the sodium potassium pump maintains these concentration gradients using the energy of one ATP to pump three Na+ out and two K+ in voltage electrical potential energy due to the separation of opposite charges membrane potential voltage across a membrane. ranges from -50 to -200 millivolts. inside of cell negative compared to the outside electrochemical gradient drive the diffusion of ions across a membrane 1. chemical force based on an ions concentration gradient. 2. the other is an electrical force based on the effect of the membrane potential on the ion's movement ion diffuses down its electrochemical gradient electrogenic pumps special transport proteins that generate the voltage gradient across a membrane an example is the Na+-K+ pump restores the electrochemical gradient not only by the active transport of Na+ and K+ setting up a concentration gradien but because it pumps 2 K+ for every 3 Na+ setting up a voltage across membrane proton pump in plants bacteria and fungi it is the major electrogenic pump actively transporting H+ out of the cell cotransport a single ATP powered pump that transports one solute can indirectly drive the active transport of several other solutes in this mechanism as the solute that has been actively transported diffuses back passively through a transport protein its movement can be coupled with the active transport of another substance against its concentration gradient phagocytosis the cell engulfs a particle by extending psedopodia around it and packaging it in a large vacuole pinocytosis a cell creates a vesicle around a droplet of extracellular fluid thermodynamics (1) The study of energy transformations that occur in a collection of matter. See first law of thermodynamics and second law of thermodynamics. (2) A phenomenon in which external DNA is taken up by a cell and functions there. 1st law of thermodynamics The principle of conservation of energy. Energy can be transferred and transformed, but it cannot be created or destroyed. 2nd law of thermodynamics The principle whereby every energy transfer or transformation increases the entropy of the universe. Ordered forms of energy are at least partly converted to heat, and in spontaneous reactions, the free energy of the system also decreases. entropy A quantitative measure of disorder or randomness, symbolized by S. free energy The portion of a system's energy that can perform work when temperature is uniform throughout the system. exergonic reaction A spontaneous chemical reaction in which there is a net release of free energy endergonic reaction A nonspontaneous chemical reaction in which free energy is absorbed from the surroundings ATP An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells. energy coupling In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction. phospholipid A molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail. catalyst A chemical agent that changes the rate of a reaction without being consumed by the reaction. activation energy The amount of energy that reactants must absorb before a chemical reaction will start. substrate The reactant on which an enzyme works competitive inhibitor A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics. noncompetitive inhibitor A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate. active site The specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds. induced fit The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate. cofactor Any nonprotein molecule or ion that is required for the proper functioning of an enzyme can be permanently bound to the active site or may bind loosely with the substrate during catalysis. coenzyme An organic molecule serving as a cofactor. Most vitamins function in important metabolic reactions. allosteric site A specific receptor site on some part of an enzyme molecule remote from the active site. feedback inhibition A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway. fermentation A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid. cellular respiration The most prevalent and efficient catabolic pathway for the production of ATP, in which oxygen is consumed as a reactant along with the organic fuel. redox reactions A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction oxidation The loss of electrons from a substance involved in a redox reaction. reduction The addition of electrons to a substance involved in a redox reaction. reducing agent The electron donor in a redox reaction. oxidizing agent The electron acceptor in a redox reaction. NaD+ a coenzyme present in all cells that helps enzymes transfer electrons during the redox reactions of metabolism electron transport chain A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP. glycolysis The splitting of glucose into pyruvate. Glycolysis is the one metabolic pathway that occurs in all living cells, serving as the starting point for fermentation or aerobic respiration krebs Cycle A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion; the second major stage in cellular respiration. Oxidative Phosphorylation The production of ATP using energy derived from the redox reactions of an electron transport chain. Substrate-Level Phosphorylation The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism. Acetyl CoA The entry compound for the Krebs cycle in cellular respiration; formed from a fragment of pyruvate attached to a coenzyme. Cytochrome An iron-containing protein, a component of electron transport chains in mitochondria and chloroplasts ATP synthase A cluster of several membrane proteins found in the mitochondrial crista (and bacterial plasma membrane) that function in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion concentration gradient to make ATP. Provide a port through which hydrogen ions diffuse into the matrix of a mitrochondrion. proton motive force The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across biological membranes during chemiosmosis. aerobic Containing oxygen; referring to an organism, environment, or cellular process that requires oxygen. anaerobic Lacking oxygen; referring to an organism, environment, or cellular process that lacks oxygen and may be poisoned by it. alcohol fermentation The conversion of pyruvate to carbon dioxide and ethyl alcohol. lactid acid fermentation The conversion of pyruvate to lactate with no release of carbon dioxide. faculative anaerobes An organism that makes ATP by aerobic respiration if oxygen is present but that switches to fermentation under anaerobic conditions. beta oxidation A metabolic sequence that breaks fatty acids down to two-carbon fragments which enter the Krebs cycle as acetyl CoA. autotrophs An organism that obtains organic food molecules without eating other organisms or substances derived from other organisms. Autotrophs use energy from the sun or from the oxidation of inorganic substances to make organic molecules from inorganic ones. heterotrophs An organism that obtains organic food molecules by eating other organisms or their by-products. chlorophyll A green pigment located within the chloroplasts of plants. Chlorophyll a can participate directly in the light reactions, which convert solar energy to chemical energy. stroma The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water. light reactions The steps in photosynthesis that occur on the thylakoid membranes of the chloroplast and that convert solar energy to the chemical energy of ATP and NADPH, evolving oxygen in the process. calvin cycle The second of two major stages in photosynthesis (following the light reactions), involving atmospheric CO2 fixation and reduction of the fixed carbon into carbohydrate. NADP+ An acceptor that temporarily stores energized electrons produced during the light reactions. photophosphorylation The process of generating ATP from ADP and phosphate by means of a proton-motive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosynthesis. wavelength The distance between crests of waves, such as those of the electromagnetic spectrum. electromagnetic spectrum The entire spectrum of radiation ranging in wavelength from less than a nanometer to more than a kilometer. visible light That portion of the electromagnetic spectrum detected as various colors by the human eye, ranging in wavelength from about 380 nm to about 750 nm. protons A quantum, or discrete amount, of light energy. spectrophotometer An instrument that measures the proportions of light of different wavelengths absorbed and transmitted by a pigment solution. absorption spectrum The range of a pigment's ability to absorb various wavelengths of light. chlorophyll A A type of blue-green photosynthetic pigment that participates directly in the light reactions. chlorophyll B A type of yellow-green accessory photosynthetic pigment that transfers energy to chlorophyll a. action spectrum A profile of the relative performance of different wavelengths of light. carotenoids An accessory pigment, either yellow or orange, in the chloroplasts of plants. By absorbing wavelengths of light that chlorophyll cannot, carotenoids broaden the spectrum of colors that can drive photosynthesis. reaction center The chlorophyll a molecule and the primary electron acceptor in a photosystem; they trigger the light reactions of photosynthesis. The chlorophyll donates an electron, excited by light energy, to the primary electron acceptor, which passes an electron to an electron transport chain. primary electron acceptor A specialized molecule sharing the reaction center with the chlorophyll a molecule; it accepts an electron from the chlorophyll a molecule. photosystem I One of two light-harvesting units of a chloroplast's thylakoid membrane; it uses the P700 reaction-center chlorophyll. photosystem II One of two light-harvesting units of a chloroplast's thylakoid membrane; it uses the P680 reaction-center chlorophyll. noncyclic electron flow A route of electron flow during the light reactions of photosynthesis that involves both photosystems and produces ATP, NADPH, and oxygen. The net electron flow is from water to NADP+. bundle sheath cell A type of photosynthetic cell arranged into tightly packed sheaths around the veins of a leaf. mesophyll cell A loosely arranged photosynthetic cell located between the bundle sheath and the leaf surface. CAM A plant that uses crassulacean acid metabolism, an adaptation for photosynthesis in arid conditions, first discovered in the family Crassulaceae. Carbon dioxide entering open stomata during the night is converted into organic acids, which release CO2 for the Calvin cycle during the day, when stomata are closed. noncyclic phosphorylation The production of ATP by noncyclic electron flow. cyclic electron flow A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or oxygen cyclic photophosphorylation The generation of ATP by cyclic electron flow. rubisco Ribulose carboxylase, the enzyme that catalyzes the first step of the Calvin cycle (the addition of CO2 to RuBP, or ribulose bisphosphate). C3 plants A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material, forming a three-carbon compound as the first stable intermediate. photorespiration A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata close and the oxygen concentration in the leaf exceeds that of carbon dioxide. C4 plants A plant that prefaces the Calvin cycle with reactions that incorporate CO2 into four-carbon compounds, the end product of which supplies CO2 for the Calvin cycle. cell division reproduction of cells cell cycle sequence of events in the life of a cell, from its origin in the division of a parent cell until its own division into two composed of M, G1, S, and G2 phases genome complete complement of organisms genes; genetic material chromosomes gene carrying structure found in nucleus- consists of 1 very long DNA molecules and associated proteins somatic cells any cell in multicellular organism except an egg or sperm gametes sex cells (haploid cells; egg or sperm) unite to form a diploid zygote chromatin complex of DNA and proteins that makes up a eukaryotic chromosome sister chromatids replicated forms of chromosomes joined together by the centromere and separated during mitosis and meiosis II centromere centralized region that joins the two sister chromatids mitosis nuclear division process; prophase, prometaphase, metaphase, anaphase, and telophse cytokenisis the division of the cytoplasm to form two seperate daughter cells after mitosis meiosis a two stage type of cell division in sexually reproducing organims that results in cells with half the chromosomes number of the original cells mitotoic phase phase of cell cycle that includes mitosis and cytokenisis interphase period when cell cycle when cell is not dividing- cell metabolic activity is high, chromsomes and organelles are duplicated and cell size may increase. 90% of cell cycle G1 phase first growth phase of the cell cycle, consisting of the portion of interphase, after DNA synthesis occurs G2 phase the second growth face of the cell cycle consisting of the portion of interphase after DNA synthesis occurs S phase synthesis phase of cell cycle; portion of interphase which DNA is replicated prophase the first subphase of mitosis in which the chromatin is condensing and the mitotic spindle begins to form but the nucleolus and nucleus are still in intact cell plate a double membrane across the midline of a dividing plant cell between which the new cell wall forms during cytokenisis prometaphase The second subphase of mitosis, in which discrete chromosomes consisting of identical sister chromatids appear, the nuclear envelope fragments, and the spindle microtubules attach to the kinetochores of the chromosomes. metaphase 3rd subphase in mitosis; spindle is complete and the chromosomes attached to microtubules at their kinetochores are aligned at he metaphase plate anaphase fourth subphase of mitosis in which the chromatids of each chromosome have separated and the daughter chromosomes are moving to the poles of the cell telophase the fifth and final subphase of mitosis in which daughter nuclei are forming and cytokenisis actually begins mitotic spindle an assemblage of microtubules and associated proteins that is involved in the movements of chromosomes during mitosis kinetochore a specialized region on the centromere that links each sister chromatid to the mitotic spindle binary fission prokaryotes cell division . Each daughter cell receives a copy of the single parental chromosome cleavage cytokenisis process; pinching of the plasma membrane; the succession of rapid cell division without growth during early embryonic development that converts the zygote into a ball of cell cell cycle control system a cyclically operating set of molecultes in the cell that triggers and coordinates key events in the cell cycle G0 phase a non dividing face of the cell cycle consisting of the portion of interphase before DNA synthesis begins cyclin a regularity protein whose concentration fluctuates cyclically growth factor a protein that must be present in the extracellular environment for the growth and normal development of certain types of cells density dependent inhibitor any factor that has a greater impact on a population as the population increases transformation the conversion of a normal animal cell to a cancerous cell. tumor a mass of abnormal cells within otherwise normal tissue, caused by the uncontrolled growth of a transformed cell benign tumor a mass of abnormal cells that remains at the site of origin malignant tumor cancerous tumor that is invasive enough to impair function of one or more organs metastasis the spread of cancer to locations distant form original site genes A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses). heredity The transmission of traits from one generation to the next. variation Differences between members of the same species. genetics The scientific study of heredity and hereditary variation. asexual reproduction A type of reproduction involving only one parent that produces genetically identical offspring by budding or by the division of a single cell or the entire organism into two or more parts. sexual reproduction A type of reproduction in which two parents give rise to offspring that have unique combinations of genes inherited from the gametes of the two parents. clone (1) A lineage of genetically identical individuals or cells. (2) In popular usage, a single individual organism that is genetically identical to another individual. (3) As a verb, to make one or more genetic replicas of an individual or cell. See also gene cloning. life cycle The generation-to-generation sequence of stages in the reproductive history of an organism. somatic cell Any cell in a multicellular organism except a sperm or egg cell. karyotype A method of organizing the chromosomes of a cell in relation to number, size, and type. homologous chromosomes Chromosome pairs of the same length, centromere position, and staining pattern that possess genes for the same characters at corresponding loci. One homologous chromosome is inherited from the organism's father, the other from the mother. crossing over The reciprocal exchange of genetic material between nonsister chromatids during synapsis of meiosis I. sex chromosomes One of the pair of chromosomes responsible for determining the sex of an individual gametes A haploid cell such as an egg or sperm. Gametes unite during sexual reproduction to produce a diploid zygote. haploid cells A cell containing only one set of chromosomes (n). fertilization The union of haploid gametes to produce a diploid zygote. diploid cells A cell containing two sets of chromosomes (2n), one set inherited from each parent. meiosis A two-stage type of cell division in sexually reproducing organisms that results in cells with half the chromosome number of the original cell. alternation of generations A life cycle in which there is both a multicellular diploid form, the sporophyte, and a multicellular haploid form, the gametophyte; characteristic of plants. sporophyte The multicellular diploid form in organisms undergoing alternation of generations that results from a union of gametes and that meiotically produces haploid spores that grow into the gametophyte generation. gametophyte The multicellular haploid form in organisms undergoing alternation of generations that mitotically produces haploid gametes that unite and grow into the sporophyte generation. synapsis The pairing of replicated homologous chromosomes during prophase I of meiosis. tetrad A paired set of homologous chromosomes, each composed of two sister chromatids. Tetrads form during prophase I of meiosis. chiasmata The X-shaped, microscopically visible region representing homologous chromatids that have exchanged genetic material through crossing over during meiosis. character A heritable feature. trait A characteristic true breeding Plants that produce offspring of the same variety when they self-pollinate. hybridization The mating, or crossing, of two varieties. P. generation The parent individuals from which offspring are derived in studies of inheritance; P stands for parental. F1 generation The first filial, or hybrid, offspring in a genetic cross-fertilization. F2 generation Offspring resulting from interbreeding of the hybrid F1 generation. dominant allele In a heterozygote, the allele that is fully expressed in the phenotype. recessive allele In a heterozygote, the allele that is completely masked in the phenotype. codominance A phenotypic situation in which the two alleles affect the phenotype in separate, distinguishable ways complete dominance A type of inheritance in which the phenotypes of the heterozygote and dominant homozygote are indistinguishable. law of segregration Mendel's first law, stating that allele pairs separate during gamete formation, and then randomly re-form as pairs during the fusion of gametes at fertilization. punnett square A diagram used in the study of inheritance to show the results of random fertilization. homozygous Having two identical alleles for a given trait. heterozygous Having two different alleles for a given genetic character phenotype The physical and physiological traits of an organism. genotype The genetic makeup of an organism monohybrids An organism that is heterozygous with respect to a single gene of interest. A monohybrid results from a cross between parents homozygous for different alleles. For example, parents of genotypes AA and aa produce a monohybrid genotype of Aa. law of independent assortment Mendel's second law, stating that each allele pair segregates independently during gamete formation; applies when genes for two characteristics are located on different pairs of homologous chromosomes. incomplete dominance A type of inheritance in which F1 hybrids have an appearance that is intermediate between the phenotypes of the parental varieties pleiotropy The ability of a single gene to have multiple effects. epistasis A phenomenon in which one gene alters the expression of another gene that is independently inherited quantitive characters A heritable feature in a population that varies continuously as a result of environmental influences and the additive effect of two or more genes (polygenic inheritance). polygenic inheritance An additive effect of two or more gene loci on a single phenotypic character. pedigree A family tree describing the occurrence of heritable characters in parents and offspring across as many generations as possible. cystic fibrosis A genetic disorder that occurs in people with two copies of a certain recessive allele; characterized by an excessive secretion of mucus and consequent vulnerability to infection; fatal if untreated. sickle cell anemia A human genetic disease of red blood cells caused by the substitution of a single amino acid in the hemoglobin protein; it is the most common inherited disease among African Americans. amniocentesis A technique for determining genetic abnormalities in a fetus by the presence of certain chemicals or defective fetal cells in the amniotic fluid, obtained by aspiration from a needle inserted into the uterus. chromosome theory of inheritance A basic principle in biology stating that genes are located on chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns. wild type An individual with the normal phenotype. sex linked genes A gene located on a sex chromosome. duchenne muscular dystropy A human genetic disease caused by a sex-linked recessive allele; characterized by progressive weakening and a loss of muscle tissue. linked genes Genes that are located on the same chromosome. genetic recombination The general term for the production of offspring with new combinations of traits inherited from the two parents. parental types Offspring with a phenotype that matches one of the parental phenotypes. linkage map A genetic map based on the frequencies of recombination between markers during crossing over of homologous chromosomes. The greater the frequency of recombination between two genetic markers, the farther apart they are assumed to be. See also genetic map. cytological maps Charts of chromosomes that locate genes with respect to chromosomal features. hemophilia A human genetic disease caused by a sex-linked recessive allele, characterized by excessive bleeding following injury. nondisjunction An accident of meiosis or mitosis, in which the members of a pair of homologous chromosomes or sister chromatids fail to move apart properly. trisomic A chromosomal condition in which a particular cell has an extra copy of one chromosome, instead of the normal two; the cell is said to be trisomic for that chromosome. monosomic A chromosomal condition in which a particular cell has only one copy of a chromosome, instead of the normal two; the cell is said to be monosomic for that chromosome. polyploidy A chromosomal alteration in which the organism possesses more than two complete chromosome sets. duplication An aberration in chromosome structure resulting from an error in meiosis or mutagens; duplication of a portion of a chromosome resulting from fusion with a fragment from a homologous chromosome. inversion An aberration in chromosome structure resulting from an error in meiosis or from mutagens; specifically, reattachment of a chromosomal fragment to the chromosome from which the fragment originated, but in a reverse orientation. barr body A dense object lying along the inside of the nuclear envelope in female mammalian cells, representing an inactivated X chromosome. transformation (1) The conversion of a normal animal cell to a cancerous cell. (2) A change in genotype and phenotype due to the assimilation of external DNA by a cell. bacteriophage A virus that infects bacteria; also called a phage. See phage. double helix The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape. origins replication Sites where the replication of a DNA molecule begins. RNA polymerase An enzyme that links together the growing chain of ribonucleotides during transcription. leading strand The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' 3' direction. lagging strand A discontinuously synthesized DNA strand that elongates in a direction away from the replication fork. DNA ligase A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 39 end of a new DNA fragment to the 59 end of a growing chain. primer An already existing RNA chain bound to template DNA to which DNA nucleotides are added during DNA synthesis. helicase An enzyme that untwists the double helix of DNA at the replication forks. nuclease A team of enzymes that hydrolyze DNA and RNA into their component nucleotides mismatch repair The cellular process that uses special enzymes to fix incorrectly paired nucleotides. replication fork A Y-shaped region on a replicating DNA molecule where new strands are growing. telomeres The protective structure at each end of a eukaryotic chromosome. Specifically, the tandemly repetitive DNA at the end of the chromosome's DNA molecule. See also repetitive DNA. transcription The synthesis of RNA on a DNA template. mRNA A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. translation The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids RNA processing Modification of RNA before it leaves the nucleus, a process unique to eukaryotes. primary transcript An initial RNA transcript; also called pre-mRNA. triplet code A set of three-nucleotide-long words that specify the amino acids for polypeptide chains. template strand The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript. codons A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. promoter A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA. terminator A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene transcription unit unit, a region of a DNA molecule that is transcribed into an RNA molecule RNA splicing The removal of noncoding portions (introns) of the RNA molecule after initial synthesis. introns A noncoding, intervening sequence within a eukaryotic gene. exons A coding region of a eukaryotic gene. Exons, which are expressed, are separated from each other by introns. spliceosome A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron, and joining the two adjacent exons. ribosomes A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits. domains A taxonomic category above the kingdom level. The three domains are Archaea, Bacteria, and Eukarya. transfer RNA An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA. anticodon A specialized base triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule. ribosomal RNA The most abundant type of RNA, which together with proteins, forms the structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons. polyribosomes An aggregation of several ribosomes attached to one messenger RNA molecule. point mutation A change in a gene at a single nucleotide pair base pair substitution A point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides. missense mutations The most common type of mutation, a base-pair substitution in which the new codon makes sense in that it still codes for an amino acid. frameshift mutation A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons. insertion A mutation involving the addition of one or more nucleotide pairs to a gene. deletion (1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene. mutagens A chemical or physical agent that interacts with DNA and causes a mutation. capsid The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complete in shape. viral envelope A membrane that cloaks the capsid that in turn encloses a viral genome.