MCAT Biology Notes from Princeton Review
MCAT Biology Notes from Princeton Review
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MCAT: Biology and Biochemistry Review Notes Chapter 3: Biologically Important Molecules All four of biological macromolecules are polymers 3.1 Protein Building Blocks protiens act as enzymes, hormones, receptors, channels, transporters, antibodies, and support structures inside and outside cells amino acids building blocks of proteins; 20 different known composition of amino acid: tetrahedral alpha carbon connected to a hydrogen, an alpha-carboxyl group (COOH); alpha amino group (NH ); and a variable R group (side chain) 2 side chain (R group) the unique feature of the amino acid which gives it the physical and chemical properties that distinguish it from the other nineteen important properties of side chains: shape, charge, ability to hydrogen bond, and ability to act as acids or bases hydrophobic (nonpolar) amino acids tend to associate with each other rather than water, and are found on the interior folded globular proteins, away from water o the larger the hydrophobic group, the greater the hydrophobic force repelling it from water o glycine, alanine, valine, leucine, isoleucine, phylalanine, tryptophan, methionine, prline polar amino acids characterized by an R-group polar enough to form hydrogen bonds with water, but not polar enough to act as an acid or base o kinase regulatory enzyme that adds a phosphate group (in this case to the hydroxyl group of an amino acid; phosphate group is extremely hydrophilic) o serine, cysteine, tyrosine, threonine, asparagine, glutamine acidic amino acids those with carboxylic acid function groups (pKa=4) in their sides chains, have three acidic/basic functional groups (amino group, carboxyl group and R group) (glutamic acid and aspartic acid) o aspartic acid, glutamic acid basic amino acids pKa’s of R group is in the basic range at physicological pH (7.4) o histidine only side chain with a pKa (6.5) in the basic and acidic range at physiological pH o lysine, arginine, histidine sulfur-containing amino acids two amino acids with sulfur in their R group o cysteine contains a thiol (SH) and is polar o methionine contains a thioether (RSR) and is nonpolar proline a unique amino acids in that its amino group is bound covalently to a part of the side chain, creating a secondary alpha- amino group and a distinctive ring structure 8 essential amino acids that cannot be synthesized by adult humans and must be obtained from the diet: valine, leucine, isoleucine, phylalanine, tryptophan, methionine, threonine, lysine 3.2 Protein Structure two common covalent bonds of proteins: peptide bonds and disulfide bridges peptide bonds link amino acids together; formed between the carboxyl group of one amino acids and the alpha-amino group of another amino acid with the loss of water backbone of the polypeptide the N-C-C-N-C-C pattern formed from the amino acids residue an individual amino acid when it is part of a polypeptide chain amino terminus (amino-terminal residue always written first) the first end made during polypeptide synthesis carboxy terminus the last end made during polypeptide synthesis dipeptides are less energetically favorable than individual amino acids stored energy is used to force peptide bonds to form and hydrolysis of the bond is thermodynamically favorable but kinetically slow, due to high activation energy and does not occur proteolysis/proteolytic cleavage hydrolysis of a protein by another protein o proteolytic enzyme/ protease the protein that does the cutting in the hydrolysis of one protein by another disulfide bridges a covalent sulfur-sulfur bond that forms between cysteine R groups; plays an important role in stabilizing tertiary protein structures cysteine a cysteine residue that is disulfide-bonded to another cysteine residue denatured a protein that is folded improperly and therefore not functional denaturation the disruption of a protien’s shape without breaking peptides bonds o protines are denatured by urea (disrupts hydrogen bonding interactions); extremes of pH; extremes of temperature; and changes in salt concentration (tonicity) primary structure (amino acid sequence) the simplest level of protein structure; the linear order of amino acids bonded to each other in the polypeptide chain o peptide bond bond that determines primary structure, links one amino acid to the next secondary structure the initial folding of a polypeptide chian into shapes stabilized by hydrogen bonds between backbone NH and Co groups o main bond: hydrogen bonds o alpha helix always right handed; 5 angstroms in width; with each subsequent amino acid rising 1.5 angstroms; 3.6 amino acid residues per turn with alpha-carboxyl oxygen of one amino acid residue hydrogen bonded to the alpha-amino proton of an amino acid three residues away (don’t memorize numbers understand meaning) proline never appears in alpha-helix because its unique structure forces it to kink the polypeptide chain favorable structure for a hydrophobic transmembrane region because all polar NH and CO groups in the backbone are hydrogen bonded to each other on the inside of the helix (hormone receptors and ion channels); would have hydrophobic R groups that radiate out from the helix and interact with hydrophobic interior of membrane o B-pleated sheet hydrogen bonding occurs between residues distant from each other in the chain or even on separate chains; side groups occur aboe or below the plane; parallel B-pleated sheet a Beta-sheet with adjacent polypeptide strands running in the same direction antiparallel a Beta-pleated sheet with adjacent polypeptide strands running in the opposite direction if a single polypeptide folds once and forms a B- pleated sheet with itself, would this be parallel or antiparallel B-pleated sheet? (antiparallel because one would be C-N while the other was N-C) o a protein that disrupts H-bonding (urea) would leave primary structure in tact but would cause secondary structure to be disrupted, unfolding a-helixes and b-sheets o Tertiary Structure concerns interactions between amino acid residues located more distantly form each other on the polypeptide chain; driven by interactions of R-groups with each other and with the solvent (water) type of bond: hydrophobic/hydrophilic interactions (with the exception of disulfide bonds being included) hydrophobic R groups tend to fold into the interior of the protein hydrophilic R groups tend to be exposed to water on the surface of the protein Would a protein end up folded normally if you (1) first put it in a reducing environment, (2) then denatured it by adding urea, (3) next removed the reducing agent, allowing disulfide bridges to reform, and (4) finally removed the denaturing agent? (No because disulfide bridges forming before the secondary structure (hydrogen bonds) would cause it to be locked into an abnormal shape) o Quaternary Structure describes interactions between polypeptide subunits in a multisubunit complex; the arrangement of subunits in a multisubunit complex subunit a single polypeptide chain that is part of a large complex containing many subunits forces stabilizing are generally non-covalent interactions of secondary and tertiary structure (hydrogen bonds, and van der Waals interactions) but can include disulfide bonds (covalent) peptide bond may not be involved in quaternary structure 3.3 Carbohydrates carbohydrates broken down to CO in a process called oxidation, 2 burning, or combustion carbohydrates serve as the principle energy source for cellular metabolism due to the large amounts of energy released in their oxidation monosaccharide (simple sugar) a single carbohydrate molecule; has the general chemical formula C H On 2n n glycosidic linkage bond between two sugar molecules (monosaccharides); covalent bond formed in a dehydration reaction that requires enzymatic catalysis glycogen serves as an energy storage carbohydrate in animals and is composed of thousands of glucose units joined in a alpha-1,4 linkage (alpha-1,6 branches are also present) starch same as glycogen (branches are slightly different) and serves the same purpose in plants (energy storage) cellulose a polymer of cellobiose (doesn’t exist freely in nature) with Beta-glycosidic bonds that allow the polymer to assume a long, straight, fibrous shape hydrolysis of polysacchardies into monosaccharies favored thermodynamically and essential in order for these sugars to enter the metabolic pathway and be used for energy by the cell; but doesn’t occur at a significant rate without an enzyme catalyst o each enzyme is highly specific for the linkage is hydrolyzes, and is named for that specific linkage lactose malabsorbers people without lactase, any lactose they eat ends up in the colon; if this causes symptoms such as gas or diarrhea they are said to be lactose intolerant o all babies product lactase but most adults stop producing it explain of stereochemistry mammals cannot breakdown B-glycosidic linkages found in cellulose and lactose even though they are sugars 3.4 Lipids lipids oily or fatty substances that play three physiological roles: 1. store energy as triglycerides (fats) in adipose cells 2. phospholipids constitute a barrier between intracellular and extracellular environments in cellular membranes 3. cholesterol is a special lipid that serves as the building block for the hydrophobic steroid hormones hydrophobicity the cardinal characteristic of lipids; water-fearing lipophilic lipid loving; synonym for hydrophobic lipophobic lipid fearing; synonym for hydrophilic fatty acids composed of long unsubstituted alkanes that end in a carboxylic acid; typically 14-18 carbons long; and synthesized 2 carbons at a time from acetate (only even numbered fatty acids are made in human cells) saturated a fatty acid with no carbon-carbon double bond; every carbon in the chain is covalently bound to the maximum number of hydrogens unsaturated0 fatty acids that have one or more double bonds in the tail; double bonds are almost always Z (or cis) two fatty acids in water: will interact with each other and expose the charged carboxyl group to the aqueous environment hydrophobic interaction the force that drives the fatty acid tails into the center of the micelle solvation shell water molecules must form an orderly ___ around each hydrophobic substance allowing for more water-water interactions (H 2 can share its charge with other polar molecules) and fewer lipid- water interactions o formation of a solvation shell is an increase in order and thus a decrease in entropy, thermodynamically unfavorable michelle a circle of fatty acids with hydrophilic heads on the exterior interacting with the solvation sphere (water) and hydrophobic fatty acid tails on the interior interacting with one another triacylglycerol/triglyceride the storage form of the fatty acid; composed of three fatty acids esterified to a glycerol molecule; stored in fat cells (adipose cells) as an energy source o undergo reactions similar to esters such as base-catalyzed hydrolysis o amphipathic have both hydrophilic and hydrophobic regions o saponification production of soap (sodium salts of fatty acids: RCOO-Na+) by base-catalyzed hydrolysis of triglyceride from animal fat into fatty acid salts lipases enzymes that hydrolyze fats fats are better for energy storage than carbohydrates: o packinage: hydrophobicity allows fats to pack together more closely (carbohydrates carry a great amount of water-of- solvation) causing their carbohydrate per unit area/weight to be greater (cannot store sugar in dry powder for in our body) water-of-solvation water molecules hydrogen bonded to their hydroxyl group o Energy content fat molecules store much more energy than carbohydrates because they are more reduced, oxidizing them (energy metabolism requires oxidation of food to release energy) releases more energy animals store most of their energy as fats but plants store a large percentage as carbohydrates (starch) membrane lipids phospholipids derived from diacylglycerol phosphate or DG-P phospholipids are detergents o detergents substances that efficiently solubilize oils while remaining highly water-soluble o lipid bilayer an orderly structure formed by phospholipids to minimize their interactions with water (similar to the micelle formed by fatty acids) hydrophobic interactions drive the formation of the bilayer once formed, stabilized by van der Waals forces unsaturated fatty acids bent form causes it to not fit as well and not interact as strongly with neighboring phospholipids as saturated (which make the membrane more solid) membrane fluidity: double bonds increases membrane fluidity decreasing the length of fatty acid tails also increase fluidity steroid cholesterol (membrane antifreeze) increases fluidity at low temperatures in the same way as kinks in fatty acid tails; reduces membrane fluidity at high temperatures cholesterol keeps membrane fluidity at an optimum temperature separates the interior of the cell from the exterior ion channels and integral proteins are necessary for membrane to allow entrance of ions and/or their signals second messenger cascade signal transmitted into the cell by protein receptors in the cell membrane that bind to hormones (charged ions) terpene a member of a broad class of compounds built from isoprene units (C 5 8 with a general formula (C H 5 8 nay be linear or cyclic and are classified by the number of isoprene units they contain; a simple hydrocarbon squalene a triterpene (made of six isoprene units) that is biosynthetically utilized in the manufacture of steroids; a component of earwax terpenoids-> built from an isoprene C H )5s8eleton and functionalized with other elements (O, N, S, etc); an example is vitamin A steroids similar to fats because of their hydrophobicity; have basic tetracyclic ring system based on the structure of cholesterol (a polycyclic amphipath) atherosclerotic vascular disease the build-up of cholesterol “plaques” on the inside of blood vessels; caused by one type of lipoprotein cholesterol obtained from the diet and synthesized in the liver; carried in the blood and packaged with fats and proteins into lipoproteins lipoproteins cholesterol packaged with fats and proteins steroid hormones made from cholesterol; due to highly hodrophobic nature, they can diffuse right through the lipid bilayer membrane into cytoplasm, so therefore the receptors are located within cells o testosterone an androgen (male sex hormone) o estradiol an estrogen (female sex hormone) IMPORTANT: difference between peptide hormones and steroid hormones o peptide hormones (ie insulin) exert their effects by binding to receptors at the cell-surface o steroid hormones (estrogen) diffuse into cells to find receptors 3.5 Phosphorus-Containing Compounds phosphoric acid an inorganic acid (does not contain carbon) with the potential to donate three protons (Ka’s of 2.1, 7.2, and 12.4 at equilibria) o at physioligcal pH, phosphoric acid is significantly dissociated, existing mostly in anionic form phosphate is also known as orthophosphate pyrophosphate two orthophosphates bound together via an anhydride linkage high energy phosphate bond the P-O-P bound in pyrophosphate (an example); hydrolysis of pyrophosphate is thermodynamically extremely favorable why phosphate anhydride bonds store so much energy: o when phosphate are linked together, their negative charges repel each other stronger o Orthophosphate has more resonance forms and thus a lower free energy than linked phosphates o orthophosphate has a more favorable interaction with the biological solvent (water) than linked phosphates nucleotides the building blocks of nucleic acids (RNA and DNA); composed of 1. ribose (or deoxyribose) sugar group; 2. purine or pyrimidine base joined to a carbon number one of the ribose ring; and 3. one, two, or three phosphate units joined to a carbon five of the ribose ring Adenosine triphosphate (ATP) a nucleotide that plays a central role in cellular metabolism in addition to being an RNA precursor; the universal short-term energy storage molecule o energy extracted from oxidation of food is immediately stored in the phosphonanhydride bonds of ATP and can be later used for cellular processes or synthesis of glucose or fats for longer-term energy storage; applies to all living organisms and some viruses Chapter 4: Biochemistry Life depends on chemical reactions, to avoid proceeding to complete disorder within a cell, biological reactions have high activation energies that can be overcome only in the presence of enzymes, the availability of enzymes is controlled by the body so that reactions occur in the right place at the right time 4.1 Thermodynamics thermodynamics the study of the energetics of chemical reactions heat energy movement of molecules potential energy energy stored in chemical bonds (most important is the ester bonds between phosphate groups in ATP) First law of thermodynamics/law of conservation of energy states theat the energy of the universe is constant; when the energy of a system decreases, the energy of the rest of the universe (the surroundings) must increase second law of thermodynamics disorder, or entropy, of the universe tends to increase Gibbs free energy equation: ΔG=ΔH-TΔS o ΔG increases with increasing ΔH and decreases with increasing entropy o determines whether a reaction is spontaneous or not o exergonic energy exits the cell; negative ΔG o endergonic positive ΔG; can only occur if energy is added; in the lab heat is added; in the body, they are coupled to exergonic reactions o value of ΔG depends on the centrations of reactants and products, which can be variable in the body o ΔG°’ (standard free energy change) reacts and products present at 1 M concentration and a pH of 7 ΔG°’= -RT ln K’ eq where K’ eqis the ratio of products to reactants at ❑ [C]eqD] eq equilibrium: K 'eq [A] [B] eq eq ΔG= ΔG°’ + RT ln Q where K’ eqis the ratio of products to reactants: C ]D ] Q= [ ][ ] o ΔG does not depend on the pathway a reaction takes, only a measurement in the difference of free energy between reactants and products Enthalpy equation: ΔH=ΔE-PΔV o where E represents the bond energy of products or reactants in the system, P is pressure and V is volume o in cells , where reactions take place in the liquid phase, H is approximately equal to E since change in volume is negligible o exothermic negative ΔH, liberate heat more metabolic reactions are exothermic, which is how homoeothermic organisms maintain a constant body temperature o endothermic positive ΔH, require the input of heat signs of thermodynamic quantities are assigned from the point of view of the system, not the surroundings or the universe equilibrium the point where the rate of reaction in one direction equal the rate of reaction in the other Le Chatelier’s principle when we add or remove a reactant or product, there will be a change in Q but not K eqand the reaction will proceed in the direction necessary to reestablish equilibrium o a reaction which favors reacts at equilibrium can be driven to generate additional products (such strategies are employed frequently in cellular respiration) two factors that determine spontaneity of reaction in cells: the intrinsic properties of the reactants and products (ΔG°’) and the concentration of reactants and products (RT ln Q) spontaneous means that a reaction may proceed without additional energy input, but it says nothing about the rate of reaction 4.2 Kinetics and Activation Energy (E )A chemical kinetics the study of reaction rates activation energy the energy required to produce the transient intermediate; the barrier that prevents many reactions from proceeding even though the ΔG is negative transient intermediate all reactions proceed through a ____ that is unstable and takes a great deal of energy to produce the activation barrier determines the kinetic of a reaction transition state exists or a very short time, either moving forward to form product or back down into reactants catalyst lowers activation energy of a reaction by stabilizing the transition state (making its existence less thermodynamically unfavorable) without changing the ΔG o not consumed by a reaction, regenerated with the reaction cycle o have a kinetic role not a thermodynamic role o enzymes biological catalysts o cannot control the direction in which a reaction proceeds, so an enzyme may have a reverse function o hydrolase hydrolyzes chemical bonds (includes ATPase, proteases, etc.) o isomerase rearranges bonds within a molecule to form an isomer o ligase forms a chemical bond (e.g. DNA ligase) o lyase breaks chemical bonds by means other than oxidation or hydrolysis (ie. pyruvate decarboxylase) o kinase transfers a phosphate group to a molecule from a high energy carrier, such as ATP (ie. phosphofructokinase [PFK]) o oxidoreductase runs redox reactions (include oxidases, reductases, dehydrogenases, and others) o polymerase polymerization (ie. addition of nulceotides to the leading strand of DNA by DNA polymerase III) o phosphatase removes a phosphate group from a molecule o phosphorylase transfers a phosphate group to a molecule from inorganic phosphate (ie, glycogen phosphorylase) o protease hydrolyzes peptide bonds (ie. trypsin, chymotrypsin, pepsin, etc.) many have an active site with a sreine residue whose OH group can act as a nucleophile, attacking the carbonyl of an amino acid residue in a polypeptide chain usually have recognition pockets near the active site, enzyme always cuts polypeptides at the same site, one side of the recognition residue o many “real life” reactions in the cell: enzyme controls outcomes by selectively promoting unfavorable reactions via reaction coupling reaction coordinate graph: x-axis: physical progress of the reaction system or reaction coordinate; y-axis plots free energy reaction coupling thermodynamically unfavorable reactions (positive ΔG, biosynthesis of macromolecules) in the cell can be drive forward by ___; one very favorable reaction is used to drive an unfavorable one o free energy changes are additive o ATP hydrolysis is ΔG°’ is -7.3 kcal/mol and in the cell ΔG is about -12 kcal/mol can cause a conformational change in a protein transmembrane transport transfer of phosphate group from ATP to a substrate 4.3 Enzyme Structure and Function most enzymes are proteins and must fold into specific three- dimensional structures to act as catalysts (can exist as a single polypeptide chain); folding of enzyme is important to the proper formation of the active site o enzymes are likely to be globular/spherical and have a cleft that acts as the active site some enzymes are RNA or contain RNA sequences with catalytic activity, most catalyze their own splicing and the rRNA in ribosomes helps in peptide-bond formation active site the region in an enzyme’s three-dimensinoal structure that is directly involved in catalysis o highly specific, including stereospecificity (in humans: L amino acids are found and D sugars) substrates—reactants in an enzyme-catalyzed reaction active site model (lock and key hypothesis) states that the substrate and active site are perfectly complimentary induced fit model asserts that the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme recognition pock a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides enzymes that act on hydrophobic substrates have hydrophobic amino acids in their active sites, while hydrophilic/polar amino acids will comprise the active site of enzymes with hydrophilic substrates denatures when temperatures rises sufficiently, the protein __ and loses its orderly structure o as temperature increases, the thermal motion of the peptide and surrounding solution destabilizes the enzymes structure pH of surrounding medium also impacts protein stability, because several amino acids possess ionizable R groups that change charge depending on pH can decrease affinity of a substrate for active site and extreme changes in pH can denature protein cofactors metal ions or small molecules (not themselves proteins) are required for activity in many enzymes; various organic and inorganic substances necessary to the function of an enzyme but which never actually interact with the enzyme o majority of vitamins in our diet are precurosors for ccoefactors o coenzyme (ex. CoA is coenzyme A) a cofactor that is an organic molecule; often bind to the substrate during the catalyzed reaction 4.4 Regulation of Enzyme Activity metabolic pathways in the cell must be tightly regulated to maintain health regulate activity of enzymes to accomplish this covalent modification proteins can have several different groups covalently attached to them, and this can regulate their activity, lifespan in the cell, and/or cellular location o phosphorylation by a protein kinase (transferring a phosphoryl group from a molecule of ATP) of an enzyme can either active or inactivate the enzyme o protein phosphorylases also phosphorylate proteins using free- floating inorganic phosphate in the cell instead of ATP, can be reversed by protein phosphatases proteolytic cleavage many enzymes (and other proteins) are synthesized in active forms (zymogens) that are activated by a protease (hydrolyzes peptide bond) association with other polypeptides some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit o constitutive activy enzymes that demonstrate continuous rapid catalysis if their regulatory subunit is removed o some require association with another peptide in order to function o protiens can bind many regulatory subunits allosteric regulation modification of active-site activity through interactions of molecules with other specific sites on the enzyme (allosteric sites) o binding of small molecules to particular sites on an enzyme that are distinct from the active site (allosteric site) o binding of the allosteric regulator to the allosteric site is generally noncovalent and reversible o when bound, allosteric regulator can alter the conformation of the enzyme to increase or decrease catalysis o possible for more than one small molecule to be capable of binding to an allosteric site enzymes usually act as part of pathways, not alone; therefore, every enzyme in a pathway does not have to be regulated, usually just one or two key enzymes are negative feedback/feedback inhibition when excess of an end-product shut off an enzyme early in the pathway feedforward stimulation the stimulation of an enzyme by its substrate, or by a molecule used in the synthesis of the substrate o when the first reactant in a pathway stimulates a reaction further down the line in addition to acting as switches, enzymes act as valves because they regulate the flow of substrates into products 4.5 Basic Enzyme Kinetics enzyme kinetics the study of the rate of formation of products from substrates in the presence of an enzyme reaction rate the amount of product formed per unit time, in moles per second o depends on the concentration of substrate and enzyme usually enzyme is held constant, since substrate concentration is more variable in cells o if there is only a little substrate, then the rate is directly proportional to the amount of substrate added o eventually, there is so much substrate that the active site of the enzyme becomes saturated and adding more substrate doesn’t increase the reaction rate as much, slope of the V vs S curve decreases saturated when there is much substrate that every active site is continuously occupied, and adding more substrate doesn’t increase the reaction rate at all, the enzyme is ___ V the reaction rate when the enzyme is saturated; a property of max each enzyme at a particular concentration of enzyme Michaelis constant (K m the substrate concentration at which the reaction velocity is half its maximum; unique for each enzyme- substrate pair and give information on the affinity of the enzyme for its substrate o low K imdicates high substrate-enzyme affinity cooperative enzymes name given to multi-subunit enzymes wherethe binding of substrate to one subunit allosterically increases the affinity of other subunits for substrate; must have more than one active site o tense the conformation of a multi-subunit enzyme prior to substrate binding, with low substrate affinity o relaxed the conformation of a multi-subunit enzyme after substrate binding, with increased substrate affinity sigmoidal curve results from cooperative binding cooperatively does not apply just to catalytic enzymes: hemoglobin (carries oxygen, not a catalyst), a protein complex made of four polypeptide subunits, each of which contains a heme prosthetic group with a single O 2inding site, exhibits cooperative binding of O 2 competitive inhibitors molecules that compete with substrate for binding at the active site o must resemble the substrate, but most effective ones resemble transition state which the active site normally stabilizes o inhibition can be overcome by adding more substrate o V maxis not affected but Kmis noncompetitive inhibitors bind at an allosteric site, not at the active site o cannot be overcome by increase in substrate o V maxis lowered but K ms not typically altered (substrate can still bind to active site but inhibitor prevents catalytic activity) uncompetitive inhibitor an inhibitor that can only bind to the enzyme- substrate complex (cannot bind before substrate is bound) o decreases V maxby limiting the amount of available enzyme- substrate complex which can be converted to product o decreases K bymsequestering the enzyme bound to substrate, increasing the apparent affinity of the enzyme for the substrate since it cannot dissociate mixed-type inhibition occurs when an inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex o if the enzyme has greater affinity for the inhibitor when it is unbound to substrate, the interaction will resemble competitive inhibition (lower affinity for substrate) o if the enzyme substrate complex has greater affinity for the inhibitor it will resemble uncompetivie inhibition (higher affinity for substrate) o if affinity is equivalent for both the bound and unbound enzyme, it acts as a noncompetitive inhibitor o in each situation, the inhibitor binds to an allosteric site and additional substrate cannot overcome inhibition (V max decreases) See Table 2 for summary (89) 4.6 Cellular Respiration photosynthesis the process by which plants store energy from the sun in the bond energy of carbohydrates photoautotrophs (plants) use energy from light to make their own food chemoheterotrophs (animals) use the energy of chemicals produced by other living things reduced molecules (carbohydrates and fats) plants and animals store chemical energy in ___ oxidized reduced molecules are ___ to produce CO and 2Tp ATP the energy of ___ is used in turn to drive the energetically unfavorable reactions of the cell oxidize bind to oxygen o attach oxygen (or increase the number of bonds to oxygen) o remove hydrogen o remove electrons reduce remove oxygen o remove oxygen (or decrease the number of bonds to oxygen o add hydrogen o add electrons when you reduce something, you store potential energy redox pair when one atom gets reduced, another one must be oxidized catabolism the process of breaking down molecules anabolism building up metabolism (or molecules) oxidative catabolism break down of molecules by oxidizing them (how we extract energy from glucose) Four steps in the oxidation of glucose: glycolysis, the pyruvate dehydrogenase complex (PDC), the Krebs cycle, and electron transport/oxidative phosphorylation o C H6O12 6 + 6O 2 6 CO +26H O 2 o carbon is oxidized and oxygen is reduced cellular respiration is a big coupled reaction (oxidize glucose to power ATP synthesis and use ATP to power cellular produces) oxidation of glucose is accompanied by the reduction of high-energy electron carriers: NAD and FAD to NADH and FADH whic2 are later oxidized when they deliver the electrons to the electron transport chain, which generates the proton gradient that is used to generate ATP + NAD and FAD can serve as enzymatic cofactors and fulfill diverse roles in biological processes o NAD is required for activation of adenylate cyclase by cholera toxin o FAD can associate with a protein to become a flavoprotein, many of which are commonly involved in redox reactiosn (ie amino acid metabolism) o electron carrier molecule that is responsible for shuttling energy in the form of reducing power (reduction potential) o FADH ul2imately results in the production of less ATP glycolysis (glucose splitting): occurs in the cytoplasm and does not require oxygen o universal first step in glucose metabolism, the extraction of energy from carbohydrates o glucose is partially oxidized while it is split in half, into two identical pyruvic acid molecules o produces a net surplus of 2 ATP (from ADP + P) and i NADH (from NAD + H ) + o envolves several reactions, each catalyzed by a different enzyme o steps: phosphate taken from ATP and used to phosphorylate glucose, producing glucose 6-phosphate (G6P) Hexokinase catalyzes the first step in glycolysis G6P feedback inhibits hexokinase G6P is isomerized to fructose 6-phosphate (F6P) F6P is phosphorylated on carbon #1 with a phosphate from ATP to produce fructose-1,6-biophosphate (F1,6bP) committed step phosphofructokinase (PFK) catalyzes the transfer of a phosphate group from ATP to F6P o key biochemical valve controlling the flow of substrate to product in glycolysis o allosterically regulated by ATP (high concentration of ATP in the cell slows glycolysis) thermodynamically very favorable, so it’s practically irreversible o irreversible reactions like this tend to be subjected to allosteric regulation G6P can be sent to different pathways, but F1,6P can only react in glycolysis F1,6bP is split into two 3-carbon units that are oxidized to pyruvate, producing 2 ATP and 1 NADH per pyruvate (4 ATP and 2 NADH per glucose) NADH is produced in only one step: when an aldehyde (-de) is oxidized to a COOH (-ate) pyruvate dehydrogenase complex pyruvate produced in glycolysis is decarboxylated to form an acetyl group which is then attached to coenzyme A; a small amount of NADH is produced o pyruvate produced in glycolysis in the cytoplasm is transported into the mitochondrial matrix o oxidative decarboxylation a reaction in which a molecule is oxidized to release CO 2nd produce NADH o pyruvate is changed from a 3-carbon molecule to a 2 carbon molecule, activated acetyl unit while CO i2 given off and NADH is produced activated indicates that acetyl is not floating around freely but rather attached to a carrier, namely coenzyme A o coenzyme A a carrier that can transfer the acetyl group into the Krebs cycle basically a long angle with a sulfur at the end, abbreviated CoA-Sh when loaded with an acetyl group abbreviated acetyl-CoA bond between sulfur and the acetyl group is high energy, making it easy for acetyl CoA to transfer the acetyl fragment into the Krebs cycle for further oxidation o PCD is composed of three different enzymes more efficient that 3 individual enzymes since intermediates can be passed directly from active site to active site o prosthetic group a nonprotein molecule covalenty bound to an enzyme as part of the enzyme’s active site PDC contains a thiamine pyrophosphate (TPP) prosthetic group at one of its active sites thiamine is vitamin B 1 vitamins often serve as prosthetic groups Krebs cycle (tricarboxylic acid TCA cycle/citric acid cycle a group of reactions which take the 2-carbon acetyl unit from acetyl-CoA, combine it with oxaloacetate, and release two CO mo2ecules o citrate the first intermediate produced in the cycle, as soon as the acetyl unit is supplied; possess three carboxylic acid function groups (tricarboxylate) a molecule with three carboxylic acids is ready to be oxidatively decarboxylated o the acetyl group from the PDC is added to oxaloacetate to form citric acid which is then decarboxylated and isomerized to regenerate the original oxaloacetate o 2 GTP (converts to 2 ATP), 6 NADH, and 2 FADH are pro2uced o alpha-ketoglutarate dehydrogenase complex, which catalyzes the third step in the Krebs cycle, has a TPP prosthetic group and catalyzes an oxidative decarboxylation o Stage 1: two carbons in the acetate fragment of acetyl-CoA are condensed with the 4-carbon compound oxaloacetate (OAA) producing citrate QUESTION: If pyruvate is radiolabeled on its number one (most oxidized) carbon, where will the labeled carbon end up in Krebs cycle? In CO ,2Pryuvate’s most oxidized carbon is a carboxylic acid which is removed by the PDC o Stage 2: Citrate is further oxidized to release CO and2to produce NADH from NAD with each oxidative decarboxylation the two carbons that leave as CO are2not the same ones that entered the cycle as acetate, two original acetyl carbons remain within the Krebs cycle o Stage 3: OAA is regenerated so that the cycle can continue reducing power is stored in 1 NADH and 1 FADH , and2a high-energy phosphate bond is produced directly as GTP (plays the role of ATP but eventually transfers its high- energy phosphate bond to ADP to make ATP) PDC and Krebs cycle can only occur when oxygen is present, but neither used oxygen directly both occur in the innermost compartment of the mitochondria, the matrix oxygen is necessary for electron transport system electron transport/oxidative phosphorylation the high energy electrons carried by NADH and FADH are o2idized by the electron transport chain in the inner mitochondrial membrane; reduced electron carriers dump their electrons at the beginning of the chain and oxygen is reduced to H 2 at the end o electron energy liberated by the electron transport chain (oxidation of NADH and FADH ) i2 used to pump protons out of the mitochondrial matrix o electron-transport chain a group of 5 electron carriers, each of which reduces the next down the line, all five are named for their redox roles three are large protein complexes found embedded in the inner mitochondrial membrane cytochromes, due to presence of heme group heme group a porphyrin ring containing a tightly- bound iron atom pump protons out of the matrix across the inner mitochondrial membrane into the intermembrane space every time electrons flow past other two are small mobile electron carriers NADH dehydrogenease (cytochrome; also known as coenzyme Q reductase) receives electrons (reducing power) from NADH (which is oxidized to NAD+), it passes its electrons to ubiquinone (coenzyme Q, a small carrier) which passes its electrons to cytochrome C reductase which passes them to cytochrome C which passes them to cytochrome C oxidase which oxidizes O into H O, the final 2 2 electron acceptor cytochrome C a small hydrophilic protein bound loosely to the inner mitochondrial membrane FADH gives its electrons to ubiquinone (bypassing 2 the first proton pump) o inner mitochondrialmembrane is highly impermeable to protons, the ETC creates a large proton gradient, with the pH being much lower higher inside the matrix (less protons) than the rest of the cell o proton gradient is the source of energy used to drive the phosphorylation of ADP to ATP, protons are allowed to flow back into the mitochondrion and the energy of this proton flow is used to produce the high-energy triphosphate group ATP o ATP synthase important protein embedded in the inner mitochondrial membrane that contains a proton channel that spans the inner membrane, the passage of protons from the intermembrane space through the ATP synthase channel causes it to synthesize ATP from ADP + P i o GOALS: reoxidize all the electron carriers reduced in glycolysis, PDC, and the Krebs cycle store energy in the form of ATP in the process o NADH from glycolysis must be transported into the mitochondria but the rest are in the right place o prokaryotes: all reduced electron carrier are located in cytoplasm because they do not have membrane-bound organelles a proton gradient must be created and then used to power ATP synthesis by the membrane-bound ATP synthase bacteria use their cell membrane difference: when eukaryotes perform aerobic respiration, they have to shuttle the electrons from cytosolic NADH into the mitochondrial matrix (at the cost of energy) but bacteria do not prokaryotes get two more high-energy phosphate bonds from aerobic respiration o oxidative phosphorylation the oxidation of high-energy electron carriers NADH and FADH cou2led to the phosphorylation of ADP to produce ATP o the overall process of electron transport and ATP production is said to be coupled by the proton gradient +2 Mg it’s necessary for all reactions involving ATP in anerobic conditions (without oxygen) electron transport cannot function, and the limited supply of NAD becomes entirely converted to NADH + ferementation regenerates NAD in anaerobic condtions, therby allowing glycolysis to continue in the absence of oxygen o uses pyruvate as the acceptor of high energy electrons from NADH o reduction of pyruvate to ethanol o the reduction of pyruvate to lactate in human muscle cells lactate is thought to contribute to the “burn” that athletes encounter during anaerobic exertion, such as sprinting, when the cardiovascular system fails to deliver enough oxygen to keep the electron transport chain running in muscle cells o limit to anaerobic glycolysis as an energy source: ethanol or lactate build up, have no other use in the cell and act as poison at high concentrations lactate in human muscle cells is transported to the liver where it is converted back to pyruvate(while making NADH and NAD ) when oxygen is available in the Cori Cycle mitochondrion contains two membranes, each composed of a lipid bilayer o outer membrane is smooth and contains large pores formed by porin proteins o inner membrane is impermeable, even to very small items like + H , and is densely folded into cristae enzymes of the electron transport chain and ATP synthase involved in oxidative phosphorylation are bound here o cristae extend into the matrix o matrix the innermost space of mitochondrion where the enzymes of Krebs cycle and the pyruvate dehydrogenase complex are located o intermembrane space space between the two membranes which is continuous with the cytoplasm due to the large pores in the outer membrane quinone a particular type of aromatic molecule ubi prefix indicating that this molecule is ubiquitous, present in all cells + for every NADH that is oxidized to NAD , three large electron transport proteins pump about 10 protons across the inner mitochondrial membrane into the intermembrane space ATP synthase requires three protons to generate a molecule of ATP from ADP and P andian additional proton to bring Pito the matrix o each NADH provides the energy to produce approximately 2.5 ATP molecules o each FADH pr2duces approximately 1.5 ATP molecules (bypasses first large electron transport protein and only pumps 6 protons) glycerol phosphate shuttle pathway that transports electrons from the NADH (2) generated in glycolysis to the mitochondria, directly to ubiquinone (just like FADH 2 o results in production of 1.5 ATP molecules/NADH from glycolysis o since bacteria do not have to shuttle NADH across any membranes, they produce 2 more ATP per glucose Summary Chart Process Moelcules ATP Equivalents Formed/Used Glycolysis -2 ATP -2 ATP 4 ATP 4 ATp 2 NADH 3 ATP (euk)/5 (pro) Pryuvate Dehydrogenase 2 NADH 5 ATP Complex Krebs Cycle 6 NADH 15 ATP 2 FADH 2 3 ATP 2 GTP 2 ATP Total 30 ATP (euk)/32 (pro) glycogenolysis glycogen breakdown; occurs in response to the hormone glucagon , when blood sugar levels are low; results in glucose being released into the blood (can be taken up by cells and used for glycolysis) o glycogen a polymer of glucose that is found in muscle and liver cells, main form of carbohydrate storage in animals o synthesis of glycogen (glycogenesis) and glycogenolysis are opposing processes controlled by hormones that regulate blood sugar levels and energy o smilar proess occurs in higher plants where polymerized glucose, in the form of starch, can be broken down for various cellular processes including glycolysis o glycogen and starch are glucose polymers with alpha-1,4 and alpha- 1,6 glycosidic bonds glucogenesis occurs when dietary sources of glucose are unavailable, and when the liver has depleted its stores of glycogen and glucose; occurs primarily in the liver (and to a lesser extent the kidneys) and involves converting non-carbohydrate precursor molecules (lactate, pyruvate, Krebs cycle intermediates, and carbon skeletons of most amino acids) into intermediates of the above pathways where they ultimately become glucose o basically reverse glycolysis in an 11 step pathways that uses many of the same enzymes as glycolysis (those that catalyze irreversible reaction have been replaced) pyruvate carbonxylase catalyzes the conversion of pyruvate to oxaloacetate, which can be further converted into phosphoenolpyruvate, the second-to-last product in glycolysis acetyl-CoA cannot take part in gluconeogenesis why fatty acids cannot be converted to glucose during periods of starvation, while glycerol backbone can amino acid catabolism o proteins in cells are constantly being made, kept for a certain period of time and then degraded back into amino acids o humans absorb amino acids from dietary proteins which can be catabolized via several pathways o amino group is removed and converted into urea for excretion and the remaining carbon skeleton (also called an alpha-keto acid) can either be broken down into water and CO or 2an be converted to glucose or acetyl-CoA Pentose hosphate pathway (PPP) diverts glucose-6-phosphate from glycolysis in order to form ribose-5-phosphate (and other products) which can be used to synthesize nucleotides o sometimes referred to as a shunt o composed of an oxidative phase (that also generate NADPH) followed by a non-oxidative phase producing additional sugar precursors o NADPH shares much of its structure with NADH, but has a different cellular role and serves as an important reducing agent in many anabolic processes and aids in the neutralization of reactive oxygen species o glucose-6-phosphate dehydrogenase (G6PDH) the first enzyme in PPP; the primary point of regulation and generates NADPH deficiency limits the ability of red blood cells to eliminate reactive oxygen species, can lead to cell death and potential renal and hepatic complications (common heritable disease) 4.7 Metabolic Regulation futile cycling when two metabolic pathways with opposing rules (ie glycolysis and gluconeogenesis) are simultaneously activated resulting in the net loss of energy reciprocal control preventing two metabolic pathways with opposing rules to be active at the same time o compartmentalization, regulation of enzyme quantity and regulation of enzymatic activity for glycolysis & gluconeogenesis o phosphofructokinase (PFK, in glycolysis) and fructose-1,6- biphosphophatase (F-1,6-BPase, in gluconeogenesis) are allosterically regulated by glycolytic intermediates that activate one enzyme while inhibiting the other (they catalyze opposing reactions in glycolysis and gluconeogenesis) fructose-2,6-biophosphate (F-2,6-BPase)’s intracellular concentration is set by a single large protein that functions as two separate enzymes: phosphofructokinase- 2 (PFK-2), which synthesizes F-2,6-BP, and fructose-2,6- biphosphate (F-2,6-BPase) which breaks it down insulin (is released in response to elevated blood glucose, activates glycolysis while inhibiting gluconeogenesis) and glucagon (released from alpha cells in the pancrease when blood glucose levels fall, beindng to cells in the liver causing the production of cAMP and the activation of protein kinase A, leading to deactivation of PFK-2 and activation of F-2,6-BPase by phosphorylation) help control concentration of F-2,6-BP by regulating the activity of PFK- 2 and F-2,6-BPase F-2,6-BPase consumes F-2,6-BP, which enhances the activity of F-1,6-BPase (the enzyme involved in glucogenesis) an ddecreases the activity of PFK if pyruvate is converted to acetyl-CoA it can no longer be utilized by gluconeogenesis isocitrate dehydrogenase an enzyme in krebs cycle that changes with energy needs of the cell (elevated levels of ATP inhibit the enzyme) glycogen serves ats the principle storage site for glucose in the liver and muscles, must be synthesized and broken down in response to changes in blood glucose and metabolic demand o glycogen synthase and glycogen phosphorylase are reciprocally controlled glycogen synthase the principle enzyme responsible for glycogen generation from glucose-1-phosphate o activated by elevated levels of insulin o suppressed by glucagon glycogen phosphorylase catabolize glycogen o inhibited by elevated levels of insulin o stimulated (in the liver but no the muscle) by glucagon o elevated levels of epinephrine, triggered by a “flight or fight” response, trigger glycogenolysis in both the liver and muscle in order to provide the rapid surge of energy necessary to respond to the stimuli principles for predictions of the activity of a given pathway in response to cellular conditions: o those enzymes which catalyze irreversible (exergonic) reactions are frequently sites of regulation o increased concentrations of intermediates in a pathway generally serve to decrease the activity of the pathway (citrate decreases the activity of PFK in glycolysis) o each pathways responds to the energy state of cell. cellular respiration is stimulated by energy deficits (ie high ADP:ATP or NAD :NADH rations) or inhibited by energy surpluses Pathway Enzyme Positive Negative Regulators Regulators Glycolysis PFK F2,6-bP ATP AMP Gluconeogene F1,6bP F2,6bP sis AMP Krebs Cycle Isocitrate ADP ATP dehydrogenase NADH 4.8 Fatty Acid Metabolism chylomicrons composed of fat and lipoproteins are transported, following the initial step of digestion, via the lymphatic system and blood stream to the liver, heart, lungs and other organs; where the dietary fat, triglycerol, is hydrolyzed to liberate free fatty acids which can undergo beta-oxidation beta-oxidation process that begins at the outer mitochondrial membrane with the activation of the fatty acid; reaction is catalyzed by acel-CoA synthetase, and requires the investment of two ATP equivlanets to generate a fatty acyl-CoA fatty acyl-CoA is transported in the mitochondrion, and once in the matrix, undergoes a repeated series of four reactions which cleave the bond between the alpha and beta carbons to liberate an acetyl-CoA and generate one FADH an2 one NADH each round of beta-oxidaiton cleaves two carbon acetyl-CoA from the molecule, but the final round cleaves one of the four-carbon fatty acyl- CoA to generate two acetyl-CoA which can enter Krebs Cycle oxidation of unsaturated fatty acids requires addition steps o an isomerase moves the double bond and allows the fatty acid to continue oxidation o if more than one double bond is present, both the isomerase and a reductase are required ketongenesis a process in the mitochondrial matrix that allows the liver to generate ketone bodies to supply the central nervous system with energy when glucose supply is short ketone bodies acetone, acetoacetate, and beta-hydroxyburyate (can be converted back to acetyl-CoA when adequate glucose is present in the blood but cannot enter the cell) o acetone present in blood can cause fatigue, confusion and fruity- scented breath without insulin, glucose cannot enter the cell de novo synthesis of fatty acid o anabolism takes place in the cytoplasm, allowing for easier regulation since catabolism occurs in mitochondrion o involves the repeated addition of two-carbon subunits o acetyl-CoA is first activated in a carboxylation reaction the committed step; requires investment of ATp and is facilitated by acetyl-CoA carboxylase to generate malyonyl-CoA o Fatty acid synthase a single peptide with multiple catalytic domains, catalyzes a decarboxylation reaction where malonyl- CoA provides two carbons to the growing fatty acid requires reducing power of NADPH, generating NADH, obtained from the PPP (pentose phosphate pathway) o once a 16-Carbon long fatty acid is generate, additional enzymes aid in further rmodification of the fatty acid o no template is required (polypeptides use mRNA as a template and DNA uses itself) o lack of a specific enzyme (due to genetic mutation) can result in a certain fatty acid or amino acid being required in the diety (an essential fatty/amino acid) Chapter 5: Molecular Biology All life is derived from other life DNA and protein two substances found in cells which seemed appropriate vehicles for transmission of inherited information; eventually the structure of DNA by Watson and Crick and the proof from experiments by Avery, Herriott, Hershey, Chase and their coworkers confirmed DNA as the fundamental unit of genetic inheritance 5.1 DNA Stru