Use the following terms to create a concept map: atoms, valence electrons, ions, cations, anions, and ionic compounds.
BIO III Exam #1 Review Limitations of cell size: three factors, how they are influenced, and ways cells have developed to regulate these factors 3 factors that limit cell size: 1. Rate of Diffusion of molecules Diffusion: the free, unassisted movement of a substance from a region of high concentration to a region of low concentration (overcome this with enzymes and cytoplasmic streaming-swirl the cytoplasm to make things diffuse faster) Factors that influence the rate of diffusion: 1. Steepness of the concentration gradient - the greater the difference, the higher rate of diffusion 2. Temperature - greater the temp, higher the rate of diffusion 3. Mass of the diffusing substance - larger the mass, slower the diffusion rate 4. Surface area - larger the area of the membrane, the faster the diffusion 5. Distance - the greater the distance to diffuse, the longer it takes 2. The requirement for adequate surface area/volume ratio (overcome by compartmentalization of organelles) Cell surface: exchange between the cell and environment Cell volume: determines the number of nutrients imported and waste excreted 3. The need to maintain adequate local concentrations of specific molecules involved in cellular processes. (overcome by enzymes) Cell membrane: composition, membrane fluidity & permeability Phospholipid bilayer, integral proteins, cell membrane functions as a bilayer fluidity-ability to bud off and make vacuoles and have secretion and lateral movement of cellular compartments, permeability Saturated - single covalent bonds - each carbon of the hydrocarbon chain is “saturated” with hydrogen atoms Unsaturated - one or more double covalent bonds in the hydrocarbon chain - monounsaturated: one double bond; polyunsaturated: two or more double bonds selectively permeable-cell attempts to regulate which molecules can enter the cell and some molecules will not be allowed in fluid mosaic- uneven distribution Cytoplasmic streaming: process that involves active movement and mixing of cytoplasmic contents Specialized proteins that actively transport molecules in the cell – transport proteins and microtubules Vesicle - small spherical sac that transport substances within the cell - import from or export materials to the extracellular fluid endocytosis and exocytosis Cellular Functional groups: determines functional properties; recognize common functional groups organelles: structure and function Reference organelle work sheet (matching) Carbon: unique properties Amine, Phosphate, Carboxyl, etc. Isomers- Molecules with the same molecular formula but different structures Monomers: what is the purpose Water soluble, they do not need a carrier in the blood, small enough to be imported across the cell membrane by receptors so they can be assembled inside of the macromolecule, they are building blocks Proteins: monomer; how they are joined; purpose of side chains; nonessential vs. essential amino acids; structure (primary, secondary, tertiary, quaternary); types of bonds; how proteins can be denatured Monomer of Proteins- Amino acids, joined by peptide bonds, side chains play a role in binding proteins and the side chains or R-groups give the function such as hydrophobic or hydrophilic -Non-essential- means made in the body, do not need to ingest -Essential-needs to be consumed, not made in the body -primary-hydrogen bonding polypeptide chain -secondary-hydrogen bonds, alpha helices and beta sheet -tertiary-complex, cannot predict, types of bonds -quaternary- Proteins can be denatured by heat Self-assembly principal-all information to fold proteins properly is in the genetic material, should be in the amino acid chain, in a biological system, this happens over time and not at an appreciable rate, (need assistance by chaperone) molecular chaperones try and fold the protein properly Energy: types of change that require energy & an example; phototrophs & chemotrophs; oxidation vs. reduction; cyclic flow of matter Laws of thermodynamics Negative delta G means Spontaneous What is ∆E, ∆S, ∆G, ∆H, and Keq If positive or negative, or if >1 or <1, what does this mean Different types of work Phototrophs-producers Chemotrophs-consumers Flow of Matter Light energy comes in as photons that animals cannot use, it is fixed/utilized with CO2, generates … Only two thirds of the energy generated in the reaction is used, rest is given off as heat, always increasing enthalphy in the biosphere Laws of Thermodynamics 1. energy cannot be created or destroyed 2. universe tends to go to disorder/chaos/increased entropy Enzymes: what are they; what do they do; why are they important; Enzyme catalysis: virtually all cellular processes or reactions are mediated by protein (sometimes RNA) catalysts called enzymes • The presence of the appropriate enzyme makes the difference between whether a reaction can take place and whether it will take place EA: the minimum amount of energy required before collisions between the reactants will give rise to products • Reactants need to reach an intermediate chemical stage called the transition state • The transition state has a higher free energy than that of the initial reactants The rate of a reaction is always proportional to the fraction of molecules with an energy equal to or greater than EA • The only molecules that are able to react at a given time are those with enough energy to exceed the activation energy barrier, EA • For most reactions at normal cell temperature, the activation energy is so high that few molecules can exceed the EA barrier • Reactants that are thermodynamically unstable, but lack sufficient EA, are said to be in a metastable state • Life depends on high EAs that prevent most reactions in the absence of catalysts EA; transition state; active site; cofactors; specificity; sequence of events during catalysis; inhibitors – irreversible/reversible/competitive/noncompetitive; feedback inhibition; allosteric regulation and covalent modification; proteolytic cleavage • The EA barrier must be overcome in order for needed reactions to occur • This can be achieved by either increasing the energy content of molecules or by lowering the EA requirement • Input of heat can increase the kinetic energy of the average molecule, ensuring that more molecules will be able to take part in a reaction • However, cells, are isothermal • Isothermal: constant in temperature • Lowering activation energy can speed up the reaction A catalyst enhances the rate of a reaction by providing such a surface and effectively lowering EA • Catalysts do not change the position of a reaction (endergonic to exergonic) • Catalysts themselves proceed through the reaction unaltered • Every enzyme contains a characteristic cluster of amino acids that forms the active site •Most enzymes function at body temperature at 30 degrees Celcius •cys, his, ser, asp, glu, and lys are involved in the active site (don’t have to memorize these), These can participate in binding the substrate and several serve as donors or acceptors of protons Some enzymes contain nonprotein cofactors needed for catalytic activity, often because they function as electron acceptors • These are called prosthetic groups and are usually metal ions or small organic molecules called coenzymes • Coenzymes are derivatives of vitamins • Prosthetic groups are located at the active site and are indispensable for enzyme activity • The requirement for certain prosthetic groups on some enzymes explains our requirements for trace amounts of vitamins and minerals •enzymes have a very high substrate specificity •Enzymes of cryophilic (cold-loving) organisms such as Listeria bacteria can function at low temperatures, even under refrigeration ￼￼Most enzymes are active within a pH range of about 3–4 units • pH dependence is usually due to the presence of charged amino acids at the active site or on the substrate • pH changes affect the charge of such residues, and can disrupt ionic and hydrogen bonds The Catalytic sequence of events: – 1. The random collision of a substrate molecule with the active site results in it binding there – 2. Substrate binding induces a conformational change that tightens the fit (induced-fit), facilitating the conversion of substrate into products – 3. The products are then released from the active site – 4. The enzyme molecule returns to the original confirmation with the active site available for another molecule of substrate Enzyme Inhibition • Enzymes are influenced (mostly inhibited) by products, alternative substrates, substrate analogs, drugs, toxins, and allosteric effectors • The inhibition of enzyme activity plays a vital role as a control mechanism in cells • Irreversible inhibitors, which bind the enzyme covalently, cause permanent loss of catalytic activity and are generally toxic to cells – For example, heavy metal ions, nerve gas poisons, some insecticides • Reversible inhibitors bind enzymes noncovalently and can dissociate from the enzyme Competitive and Noncompetitive inhibitors • The fraction of enzyme available for use in a cell depends on the concentration of the inhibitor and how easily the enzyme and inhibitor can dissociate • The two forms of reversible inhibitors are competitive inhibitors and noncompetitive inhibitors • Competitive inhibitors bind the active site of an enzyme and so compete with substrate for the active site • Enzyme activity is inhibited directly because active sites are bound to inhibitors, preventing the substrate from binding • Noncompetitive inhibitors bind the enzyme molecule outside of the active site (to the allosteric site) negative allosteric regulation • They inhibit activity indirectly by causing a conformation change in the enzyme that – Inhibits substrate binding at the active site, or – Reduces catalytic activity at the active site Enzyme Regulation • Enzyme rates must be continuously adjusted to keep them tuned to the needs of the cell • Regulation that depends on interactions of substrates and products with an enzyme is called substrate-level regulation • Increases in substrate levels result increased reaction rates, whereas increased product levels lead tolower rates • Cells can turn enzymes on and off as needed by two mechanisms: allosteric regulation and covalent modification • Usually enzymes regulated this way catalyze the first step of a multi- step sequence • By regulating the first step of a process, cells are able to regulate the entire process Allosteric Regulation • Allosteric regulation is the single most important control mechanism whereby the rates of enzymatic reactions are adjusted to meet the cell’s needs • In feedback (or end-product) inhibition, the final product of an enzyme pathway negatively regulates an earlier step in the pathway • Allosteric enzymes have two conformations, one in which it has affinity for the substrate(s) and one in which it does not • Allosteric regulation makes use of this property by regulating the conformation of the enzyme • An allosteric effector regulates enzyme activity by binding and stabilizing one of the conformations • An allosteric effector binds a site called an allosteric (or regulatory) site, distinct from the active site • The allosteric effector may be an activator or inhibitor, depending on its effect on the enzyme • Inhibitors shift the equilibrium between the two enzyme states to the low affinity form; activators favor the high affinity form • Most allosteric enzymes are large, multisubunit proteins with an active or allosteric site on each subunit • Active and allosteric sites are on different subunits, the catalytic and regulatory • Binding of allosteric effectors alters the shape of both catalytic and regulatory subunits • Many allosteric enzymes exhibit cooperativity • As multiple catalytic sites bind substrate molecules, the enzyme changes conformation, which alters affinity for the substrate • In positive cooperativity the conformation change increases affinity for substrate; in negative cooperativity, affinity for substrate is decreased Enzymes Can Also Be Regulated by the Addition or Removal of Chemical Groups • Many enzymes are subject to covalent modification • Activity is regulated by addition or removal of groups, such as phosphate, methyl, acetyl groups, etc. • Covalent modification can change its function Phosphorylation • The reversible addition of phosphate groups is a common covalent modification • Phosphorylation occurs most commonly by transfer of a phosphate group from ATP to the hydroxyl group of Ser, Thr, or Tyr residues in a protein • Protein kinases catalyze the phosphorylation of other proteins Dephosphorylation • Dephosphorylation, the removal of phosphate groups from proteins, is catalyzed by protein phosphatases • Depending on the enzyme, phosphorylation may be associated with activation or inhibition of the enzyme Regulation of glycogen phosphorylase • Glycogen phosphorylase exists as two inter- convertible forms – An active, phosphorylated form (glycogen phosphorylase-a) – An inactive, non-phosphorylated form (glycogen phosphorylase-b) • The enzymes responsible – Phosphorylase kinase phosphorylates the enzyme – Phosphorylase phosphatase removes the phosphate Proteolytic Cleavage • The activation of a protein by a one-time, irreversible removal of part of the polypeptide chain is called proteolytic cleavage (cutting the peptide bond and letting go of part of the polypeptide chain) Polysaccharides: monomers; bond; types; starch and glycogen; structure depends on the type of glycosidic bond; anabolic vs. catabolic pathways ATP: composition; why it is important that ATP occupies an intermediate position in the overall spectrum of energy rich compounds Polysaccharides • Polysaccharides are long chain polymers of sugars and sugar derivatives that are not informational molecules • They usually consist of a single kind of repeating unit, or sometimes an alternating pattern of two kinds • Short polymers, oligosaccharides, are sometimes attached to cell surface proteins -monomer is monosaacharide The Monomers Are Monosaccharides • Repeatng units of polysaccharides are monosaccharides • Sugars within these groups are named generically based on how many carbon atoms they contain • The single most common monosaccharide is the aldohexose D- glucose (C H O ) 6 12 6 • The formula C HnO2nsncommon for sugars and led to the general term carbohydrate • For every molecule of CO i2corporated into a sugar, one water molecule is consumed • D-glucose is often depicted as a linear molecule, as in the Fischer projection • The Haworth projection shows the ring form of the molecule • These forms are designated α (hydroxyl group downward) and β (hydroxyl group upward) • Glucose exists as disaccharides, in which two monosaccharide units are covalently linked • The linkage of disaccharides is a glycosidic bond, formed between two monosaccharides by the elimination of water Glycogen • The most familiar storage polysaccharides are starch in plant cells and glycogen in animal cells and bacteria • Glycogen is stored mainly in the liver (as a source of glucose) and muscle tissues (as a fuel source for muscle contraction) of animals • Bacteria also store glycogen as a glucose reserve Starch • Starch is the glucose reserve commonly found in plant tissue • It occurs both as unbranched amylose (10-30%) and branched amylopectin (70-90%) • Starch is stored as starch grains within the plastids (major organelles in plants & algae) – Chloroplasts, the sites of carbon fixation and sugar synthesis in photosynthesis – Amyloplasts, which are specialized for starch storage Structural polysaccharides • The best-known structural polysaccharide is the cellulose found in plant cell walls • Mammals cannot digest cellulose (some have microorganisms in their digestive systems that can) • Cellulose - fungal cell walls (differs from that of plants) • Chitin - insect exoskeletons, crustacean shells, and fungal cell walls Polysaccharide Structure Depends on the Type of Glycosidic Bonds Involved • α-andβ-glycosidic bonds are associated with marked structural differences • Starch and glycogen(αpolysaccharides)form loose helices that are not highly ordered due to the side chains • Cellulose(that formsβlinkages)exist as rigid linear rods that aggregate into micro fibrils, about 5-20 nm in diameter • Plant and fungal cell walls contain these rigid micro fibrils in a non- cellulose matrix containing other polymers (hemicellulose, pectin) and a protein called extensin Chemotrophic Energy Metabolism: Glycolysis and Fermentation • Cells cannot survive without a source of energy or a source of chemical building blocks • In many organisms these requirements are related • Chemotrophs obtain energy from the food they engulf or ingest Metabolic Pathways • To accomplish any task, a cell requires a series of reactions occurring in an ordered sequence • This requires many different enzymes to catalyze each individual reaction • All the chemical reactions in a cell are referred to as its metabolism, which consists of many specific metabolic pathways Anabolic Pathways • Anabolic pathways synthesize cellular components, often polymers, such as starch and glycogen • They usually involve an increase in order and a decrease in entropy • So, they are endergonic (energy-requiring) Cathobolic pathways • Catabolic pathways are involved in the breakdown of cellular constituents, such as the hydrolysis of glucose • These degradative pathways typically involve a decrease in order and increase in entropy • So, they are exergonic, energy-liberating reactions • Catabolic pathways involve the production of metabolites, small organic building blocks • Catabolism can be carried out in the presence (aerobic) or absence (anaerobic) of oxygen ATP • The efficient linking (coupling) of energy- yielding and energy- requiring processes is crucial to cell function • The most common energy intermediate is adenosine triphosphate (ATP) -composed of an adenine, ribose, three phosphates -role is to transfer phosphate bond Other high-energy molecules • High-energy molecules such as GTP and creatine phosphate store chemical energy that can be converted to ATP • Chemical energy is also stored as reduced coenzymes such as NADH Phosphoanhydride bonds • Phosphoanhydride bonds are referred to as energy-rich bonds • This term is a shorthand way of saying that free energy is released when the bond is hydrolyzed TP Hydrolysis Is Highly Exergonic Because of Charge Repulsion and Resonance Stabilization • Hydrolysis of ATP to ADP and Pi is exergonic because: - Charge repulsion between the adjacent negatively charged phosphate groups - Resonance stabilization of both products of hydrolysis - Increased entropy and solubility of the products of hydrolysis ***ATP and ADP are higher-energy than AMP o’ o’ ΔG is an underestimate • Because ΔG from this equation is based on equal concentrations of ADP and ATP (1M each), it is an underestimate • This is because under most biological conditions, the concentration of ATP is much larger (makes it more of an exergonic reaction) • In most cells ATP/ADP is in the range of about 5:1 • TheΔGʹ′is thus in the range of–10to– 14 kcal/mol in cells ATP Is an Important Intermediate in Cellular Energy Metabolism • ATP occupies an intermediate position in the overall spectrum of energy-rich phosphorylated compounds in the cell • Under standard conditions, a compound can phosphorylate a less energy-rich compound, but not a more energy-rich compound ATP is intermediate among the energy-rich phosphorylated compounds in the cell • ATP can be formed from ADP by the transfer of a phosphate group from PEP, but not from glucose-6-phosphate • The reverse is also true; ATP can phosphorylate glucose but not pyruvate ΔGoʹ′transfer • ΔGoʹ′transfer refers to the standard free energy change that accompanies the transfer of a phosphate from a donor to an acceptor Group transfer reactions • Reactions that involve the movement of a chemical group from one molecule to another are called group transfer reactions • The phosphate group is one of the most frequently transferred, especially in energy metabolism • It is important that ATP/ADP occupy an intermediate position in terms of bond energy ATP/ADP: intermediate in terms of bond energy • ATP can serve as a phosphate donor in some reactions • Its dephosphorylated form, ADP, can serve as an acceptor in other reactions • That is because there are compounds both above and below the pair in energy ATP/ADP • The ATP/ADP pair represent a reversible means of conserving, transferring, and releasing energy within the cell • As catabolic processes occur in the cell, the energy liberated is used to produce ATP from ADP • Then energy released from hydrolysis of ATPis used for essential processes of life that use energy Chemotrophic Energy Metabolism • Chemotrophic energy metabolism describes the reactions and pathways by which cells catabolize nutrients and conserve the released energy in the form of ATP • Much of chemotrophic energy metabolism involves energy-yielding oxidative reactions (oxidation) Biological Oxidations Usually Involve the Removal of Both Electrons and Protons and Are Highly Exergonic • Substances that are energy sources for cells are oxidizable compounds, the oxidation of which is highly exergonic • Oxidation is the removal of electrons Oxidation in biological chemistry • In biological systems oxidation involves removal of hydrogen ions (protons) in addition to electrons = DEHYDROGENATION Transfer of electrons • Because oxidation reactions involve the removal (in effect) of two hydrogen atoms, many of the enzymes involved are called dehydrogenases • The electrons must be transferred to another molecule, which is reduced • Reduction, the addition of electrons, is an endergonic process Hydrogenation • In reduction, the electrons that are transferred are frequently accompanied by protons • Therefore, the overall reaction is a hydrogenation Oxidation and reduction • Equations describing reductions or oxidations are half reactions • In real situations, reduction and oxidation always take place simultaneously • Any time an oxidation occurs, the electrons (and protons) must be added to another molecule in a reduction Coenzymes Such as NAD+ Serve as Electron Acceptors in Biological Oxidations • Usually electrons and hydrogens removed during biological oxidation are transferred to one of several coenzymes • Coenzymes are small molecules that function along with enzymes by serving as carriers of electrons or small functional groups • They are in low concentrations in the cell as they are recycled NAD+ • The most common coenzyme involved in energy metabolism is nicotinamide adenine dinucleotide, NAD+ • It serves as an electron acceptor, adding two electrons and a proton to its aromatic ring, generating NADH plus a proton Most Chemotrophs Meet Their Energy Needs by Oxidizing Organic Food Molecules • Most chemotrophs depend on organic food molecules as oxidizable substrates • Oxidation of these organic compounds— carbohydrates, fats, and proteins—produces energy for the cell in the form of ATP and reduced coenzymes