BCHEM 5180 Study Guide

Three energy barriers Form ES convert substrate to product release product Rate limiting step step with highest activation barrier enzyme substrate binding models lock and key enzyme complimentary induced fit hy ...

Three energy barriers Form ES convert substrate to product release product Rate limiting step step with highest activation barrier enzyme substrate binding models lock and key enzyme complimentary induced fit hypothesis lock and key favors ES complex barrier between ES and EP enzyme complimentary substrate changes to fit enzyme induced fit hypothesis enzyme and substrate change after initial fit preferred model types of enzyme catalyzed reactions general acid base catalysis covalent catalysis metal ion catalysis electrostatic catalysis catalysis through transition state binding covalent catalysis forming covalent intermediate with enzyme Covalent CatalysisAdvertisement  Side chains of AAs provide nucleophilic centers for attack on electrophilic centers of substrates.  Form covalent intermediate which can be changed by water or a second substrate for desired product  Ping-pong kinetic mechanisms transition state binding catalysis enhanced by enzyme making optimal conacts to the transition state irreversible inhibitors modifies by: chemical that reacts directly with amino acid or suicide inhibitor suicide inhibitor resembles substrate goes through steps of catalysis metal ion catalysis stabilize s binding stabilize reaction intermediate redox interactions (donate electron) electrostatic catalysis stabilize s binding stabilize reaction intermediates storage polysaccharides starch glycogen starch found in plants amylose amylopectin d-glucose Starch Carbohydrate storage in plantsamylose long unbranched 1- 4 amylopectin branched 1-6 glycogen animal liver Glycogen Carbohydrate storage in animal liver structural polysaccharides cellulose chitin cellulose plant cells Cellulose Structural component of plant cell walls Glycine Gly,G Alanine Ala,A Proline Pro,P Valine Val,V Leucine Leu,L Isoleucine Ile,I Methionine Met,M PhenylalaninePhe,F Tyrosine Tyr,Y pKa: 10.07 Tryptophan Trp,W Aspartate Asp,D pKa: 3.63 Glutamate Glu,E pKa: 4.25 Serine Ser,S Threonine Thr,T Cysteine Cys,C pKa:8.18Selenocysteine Sec,U pKa: 5.7 Asparagine Asn,N Glutamine Gln,Q Pyrrolysine Pyl,O Lysine Lys,K pKa: 10.53 Arginine Arg,R pKa: 12.48 Histidine His,H pKa: 6.0 Trehalose Transport/storage in insects Chitin Exoskeleton of insects Hyaluronate Viscosity, lubrication of extracellular secretions Proteoglycan Extracellular matrix of animal tissues HexokinaseGlucose-6-phosphatase Phospho-fructokinase Fructose - 1,6 - bisphosophatase Pyruvate Kinase Pyruvate carboxylase = Oxaloacetate = PEP Carboxykinase Three steps for dissolving water 1. Break water hydrogen bonds 2. Break solute reactions 3. Make new water-solute interactions Important interactions involving water (4) 1. Polar compounds 2. Hydration of salts 3. Non-polar substances 4. Amphipathic compounds How do polar compounds interact with water? They dissolve in water and form hydrogen bonds with solutes capable How is water involved in the hydration of salts? Water interacts with charged solutes (ion-dipole interaction) When crystalline substances dissolve in water their is an _ in entropy. increase How is water involved in reaction with non-polar substances? Hydrophobic substances such as carbohydrate (C-H weakly polar) tend to aggregate in order to minimize the amount of surface exposition to water. The water in the vicinity of the solute are constrained to their possible orientations and form cage-like shells around them.How does water interact with amphipathic compounds? The compounds form micelles in which their hydrophobic areas are arranged as to expose the least amount to water. The forces that hold these non-polar regions together are called hydrophobic interactions. Why are hydrophobic interactions favored? Thermodynamic stability, it minimizes the number of water molecules required to surround the hydrophobic portions of the solute molecules. Buffers Aqueous systems that tend to resist changes in pH when small amounts of acid (H+) or base (OH-) are added. A buffer system consists of a weak acid (proton donor) and its conjugate base (proton acceptor) Two examples of water as a reactant 1. Formation/breakdown of ATP (phosphoanhydride bond) 2. Synthesis/breakdown of polypeptides (peptide bond) Water's important interactions among biomolecules 1. hydrogen bonds 2. ionic interactions 3. van der waals (London-dispersion, dipole-dipole) 4. hydrophobic interactions Effective Concentration In polypeptides many interactions occur in close proximity, and are therefore, not totally independent (AB)Ceff=Kintra/Kinter Common amino acids 22 different amino acids found in proteins and peptides. Coded for by 3-nucleotide codons in DNA and RNA and have their own tRNA that is used during peptide synthesis on ribosomes. Uncommon amino acids (3) 1. modifications 2. different side groups 3. D-amino acids Uncommon AA due to modificationPost-translational modifications of common residues already part of polypeptide. Typical modifications: hydroxylations, phosphorylations, and methylations Uncommon AA due to different side group Can be intermediates in metabolic pathways or found in small peptides made by bacteria D-amino acids Found in small peptides made by bacteria that can have antibiotic properties To find the pI of a peptide Use the pKa values directly above and below the pH where the overall charge is neutral NMR Spectroscopy purified protein placed in a strong magnetic field and bombarded with radio waves, useful for proteins not incorporated into crystals crystal structure:ribbon model of protein protein is purified and crystallized, then subjected to an intense beam of X-rays. protein model that shows how the single polypeptide chain folds and coils to form the functional protein, can provide very detailed atomic information, showing every atom in a protein along with atomic details of ligands, inhibitors, ions, and other molecules that are incorporated into the crystal Basis for the ribbon model? Peptide Bond Resonance Structures-each peptide bond has some double-bond character and cannot rotate a helix is stabilized by _. hydrogen bonds What does the ribbon model represent? The C-N bond in the peptide bond has a partial double bond, prohibiting rotation around it. As a result, the C,N, and four atoms attached are in the same plane. The peptide chain is therefore thought of rectangles in the same plane attached by Ca atoms on opposite corners of these rectangles. It represents the flow of the amino acid chain. What does the ribbon model represent?The presence of alpha helices and beta sheets Worm Model The amino acid backbone is indicated by a tube like structure. Sheets are indicated by flat ribbon arrows. The helices are indicated by solid tubes or cylinders. This is to emphasize that these structures are not hollow. Surface Contour These structures show what surfaces are available to interact with other proteins and molecules. The ribbon and worm model might give the impression that their is a lot of empty space which is not true. A separate amino acid chain of a protein, several identical or different chains can make up a protein. Subunit Part of a subunit that if separated from the rest of a subunit, still forms a structurally stable unit Domain Monomer Individual subunits Combination of certain secondary structures like a helices and B sheets that can be found in several proteins, forming a protein family. Protein fold Examples of protein folds a/B-barrels,a/B sandwiches, B propellers Dimer Protein consisting of two monomers/subunits. Superfamily large group of proteins/enzymes that all show a very similar folding pattern Active site Place in protein structure where substrate can bind.protomer repeating structural unit in a multimeric protein, can be a single subunit or group of subunits How does ammonium sulfate precipitation work? The solubility of proteins varies according to salt concentration. At low salt concentrations, the solubility of proteins increases with increased salt concentration. As the salt concentration is increased further the solubility of the protein decreases. At sufficiently high ionic strength the protein will almost all be precipitated out from the solution, called salting out. Describe how salting out works Salt ions attract water molecules away from protein. As more salt ions are added they bind to water molecules and the proteins are forced to interact with each other. The proteins aggregate and precipitate. Ion-exchange -separates molecules on the basis of charge, not mass -beads of the resin are modified so that they contain cationic or anionic functional groups -a solution that contains the protein of interest is applied to the column containing the resin, and the sample either binds to resin or passes through the column -a gradient (e.g., salt or pH) can then be used to elute the desired compound if the compound adhered to the resin Size-Exclusion Chromatography  separates proteins on the basis of size  column contains beads with many tiny pores  very small molecules can enter the beads, which slows down their progress, while large molecules move around/between the beads and thus travel through the column faster Define hydrophobic chromotography. the columns are packed with beads that contain hydrophobic side chains which the proteins interact with affinity chromatography: specific interactionsbeads in the column have a covalently attached ligand that is designed specifically to attract specific proteins with an affinity for the ligand separation based on complimentary biochemical interactions stationary phase is covalently bound w/ ligands What does the purification table describe? How many purification steps are needed. If the protein is pure. The ratio of enzyme activity relative to total protein is called . specific activity absorbance spectroscopy measures the concentration of a substance in solution uses Beer-Lambert law What does absorbance spectroscopy identify? Aromatic side chains SDS-PAGE SDS is a detergent. It will denature the proteins, and bind to them. Since the SDS molecules are charged it ends up giving all proteins a reproducible ratio of size to charge. The upshot of all this is that the position of a protein on the final gel is related solely to its size. Smalley proteins go faster/farther than large proteins. Isoelectric focusing Electrophoresing a mixture of proteins through a pH gradient until each protein stops at the pH that matches its isoelectric point (pI); because the proteins have no net charge at their isoelectric points, they can no longer move toward the anode from the cathode. Four steps of protein sequencing 1. Obtain amino acid composition 2. Determine which amino acid is present at the N-terminus 3. Break disulfide bonds if present 4. React with first fragmenting agent and sequencing of fragments 5. React with different fragmenting agent and sequencing those fragment6. Try to fit all pieces together 7. Repeat (5) with another fragmenting agent if necessary Trypsin Cuts the peptide bond at a C-terminal side of the side chain Asp-N-protease Cuts the peptide bond at the N-terminal side of the side chain What can amino acid sequencing tell us?  Can tell us what type of protein the sequenced protein is.  Function of protein  Whether it contains one functional domain or many domains  Within a gene family its shows which amino acids are conserved  Can indicated whether a specific cofactor is bound due to specific order and spacing What proteins are associated with the membrane through electrostatic interactions and H bonding with the hydrophilic domainsof integral proteins and the polar head groups of membrane lipids ? Membrane proteins How can peripheral proteins be removed from the membrane? By altering the pH or salt concentration (ionic strength), removal of a Ca+ group by a chelating agent, or addition of urea or carbonate What are firmly associated with the membrane, removed only by agents that interfere with hydrophobic interactions, such as detergents, organic solvents, or denaturants. Integral proteins Covalently attached proteins can be removed from the membrane how? Phospholipase that releases it from the membrane lipid it is attached to. Hydropathy Plot computer analysis of AA sequence -nonpolar regions --> predited membrane spanning-sequence of >20 AA hydrophobic residues indicative of membrane spanning Globular Proteins -Hydrophobic effect dominates formation -Non-polar inside, polar (charged) outside -Commonly enzymes and transport proteins fibrous proteins -form extended sheets or strands joined by disulfide cross bridges which makes them strong -made up of repeating a-helices OR B-sheets -tough and durable -insoluble structural roles -common ex. are collagen & a-keratin membrane proteins -Transmembrane a-helices and B-sheets -Tyr and Trp residues found predominantly at water-lipid surface, with other residues in hydrophobic area Sequence alignment Compares two amino acid sequences from homologous proteins to different organisms in order to identify regions of similarity from a common ancestor Scoring matrices  Gives an idea about the similarities of AA sequences  Table of all pairwise scores for every combination of AAs BLOSUM scoring matrices BLOSUM = Blocks substitution matrices – Based on BLOCKS database (Henikoff & Henikoff, 1992) of over 2000 conserved amino acid patterns in over 500 proteins – Based on short conserved sequences (blocks) How does BLOSUM scoring matrices work?-Replacement of an amino acid penalized with -sign and conservation rewarded with + sign -If the mutation does not result in a change of function of protein then the score remains close or the same -Replacing a charge (pos-->neg or opp.) can change local structure or function, but if not then score of 0 What amino acids/sequences are most likely to be conserved?  regulatory sites of enzymes  catalytic sites  amino acids important for structure (cysteine)  hydrophobic/hydrophilic regions Conserved amino acids important in the function of enzyme/protein Evolutionary relationships  Protein sequencing finds a degree of identity between the sequences that can used to make a distance matrix, which indicates how closely related they are  Based on this a phylogenetic tree can be made Protein/gene family  Group of evolutionarily related proteins, synonymous with gene family  Common ancestor and typically have similar: 3-D structure, functions, and significant sequence similarity Protein Superfamily Proteins with similar 3-D structure, but generally differ in function and sequence Proteolytic Cleavage Modification of the polypeptide chain in which parts of the chain are cleaved off by proteolytic enzymes and the chain is consequently shortened Changes at N-terminus  Removal of Met  Acetylation  Addition of fatty acyl groupsChanges at C-terminus  Amidation  Prenylation Removal of Met  Met is initiating AA in all proteins, which is formulated in prokaryotes  Formyl group is removed  In many residues the Met residue is cleaved off Acetylation N-terminus is acetylated Addition of fatty acyl groups  Fatty acid-associated proteins can be attached to the lipid bilayer of the membrane and are usually membrane proteins  Can become soluble proteins after fatty acid chain is cleaved Amidation  Common in peptides/peptide hormones  Enabling full activity  Protects against breakdown Prenylation  Attachment of isoprenoid:frankly diphosphate or geranylgeranyl diphosphate  Anchor for membrane proteins Changes in individual AAs  glycosylation  phosphorylation  hydroxylation  sulfation  attachment of lipids  attachment of prosthetic groups glycosylation the addition of glucose to blood and tissue proteins; typically impairs protein structure and function Phosphorylation added to Ser,The,Tyr,His,Arg,Lys  protein kinase tacks a phosphate group onto the switch protein, in the other direction a protein phosphatase plucks the phosphate off again.  causes conformational changes, which changes the hydrophobic/hydrophilic profileof the phosphorylated protein Hydroxylation  Hydroxyl group added to Pro and Lys  Example collagen Sulfation  Addition of sulfate group to Tyr  In membrane and secreted proteins  Strengthens protein-protein interaction by the introduction of negatively charged,highly polar group (more water soluble) Attachment of lipids to individual AAs  To Cys  G-proteins, seven transmembrane receptors Prosthetic groups  Cofactors that are permanently bound to the enzyme  FAD,FMN,biotin,metal-contatining cofactors Denaturation is a loss of _ and _ structure. The _ structure stays intact. tertiary,secondary,primary What four things denature proteins?  urea  high temperature  low pH  detergent How does urea denature a protein? It disrupts hydrophobic interactions How does low pH denature a protein? Causes protonation of side chains Asp,His,and Glu, preventing electrostatic interactionsHow do high temperatures denature a protein? Provide thermal energy greater than the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and Van Der Waals) involved, causing them to break. How do detergents denature proteins? The detergents interact with the hydrophobic regions of the protein and therefore the protein cannot interact with other molecules Tm Melting point where [folded]=[unfolded] Circular dichroism spectroscopy Measurement of the differences in the absorption of left-handed versus right-handed planepolarized light which are given rise to by structural asymmetry in a molecule. Measures the amount of helical structure in protein. How is circular dichroism spectroscopy used? Equal amounts of left and right-handed circularly polarized light at radiated into a chiral (circular) solution. One of the 2 types is absorbed more than the other, and this wavelengthdependent difference in absorption is measured, yielding the CD spectrum DNAK and DNAJ are chaperone proteins that bind to newly synthesized proteins to slow down folding process (ATP dependent) How do chaperons DnaJ and DnaK function in protein folding?  DnaJ binds to regions of unfolded residues on the target polypeptide chain rich in hydrophobic residues, preventing aggregation.  Polypeptide becomes low-affinity ATP-DnaK complex (DnaJ released)  This stimulates ATPase activity of DnaK,causing a conformational change into highaffinity ADP-DnaK-substrate complex  GrpE binding to DnaK results in disassociation of ADP and binding of ATP  This destabalizes the interaction of DnaK and substrate protein, causing release of substrate from chaperone Isomerase function in protein folding  Protein disulfide isomerase- catalyzes the interchange or shuffling of disulfide bonds Peptide prolyl cis-trans isomerase- catalyses the interconversion of the cis and trans isomers of Pro peptide bonds Prevent folding of parts of the chain until the whole chain has been synthesized Chaperones Provide a protected environment for the protein to fold properly Chaperonins Steps of Gro-EL-GroES chaperoning function in order 4,3,1,2,5 Role of ubiquitin in breakdown of cellular proteins  Chain of ubiquitin molecules covalently attached to Lys residue of target protein  3 separate enzymes, E1,E2,and E3 involved in process  A polyubiquintylated protein is first recognized by the 19s regulatory particle andthe ubiquitin is cleaved off  The protein is then fed through the base complex, is unfolded and digested into short peptides that are released into the cytosol where they are cleaved into ind. AAs by peptidases What methods are available to detect the folding/unfolding of a protein/enzyme?  loss of activity  absorption spectroscopy  circular dichroism proteasome function ◦ degrades unneeded,damaged, or faulty proteins by cutting them into small peptides ◦ reulates protein activity by removing it from the cell when ubiquitin moleculesbecome attached (by destroying it) The binding of a ligand is often coupled to a conformational change in the protein that makes the binding site more complementary to the ligand Induced FitA model of protein function that pictures the binding site of protein and the ligand fitting together like a _. lock-and-key model Ka=1/Kd what is this relationship? The larger the Ka (and hence the smaller the Kd),the higher the affinity of the protein for the ligand Why do we need proteins to transport oxygen? oxygen is poorly soluble in aqueous solutions and cannot be carried to tissues in sufficient quantities if it is simply dissolved in blood serum diffusion of O2 through tissue is insufficient for long distances Amino acids are not capable of binding to oxygen, so this capability is provided by _. hemoglobin Why does oxygen bind to heme C and not a single Fe ion? The electron donating character of the N-ligands prevent the Fe2+ from being oxidized when O2 binds, the binding of oxygen to a single Fe2+ ion would result in the formation of reactive oxygen species that can damage biological structures. A _ residue is able to form a hydrogen bond with the bound oxygen, increasing the affinity for oxygen relative to that of free heme C, histidine In a multi-subunit protein, a conformational change in one subunit often affects the conformation of other subunits Allosteric Effect What is the change in hemoglobin affinity for molecular oxygen? Bohr Effect The hemoglobin tetramer shifts between the _ affinity T-state and high affinity _-state. What is this shift due to? low,R,result of a structural change in the tetramer structureHow do different pHs affect hemoglobin?  Low pH- several AAs get protonated and get a positive charge and can now form salt bridges with other negative AAs. These bridge are only formed in the T-state and trap the enzyme in this state. The R/T equilibrium is shifted towards the T-state.  High pH-opposite Why are enzymes such good catalysts?  Accelerates chemical reaction rates  Function in aqueous solutions under very mild conditions of temperature and pH  Highly specific for its substrate and the reaction it will catalyze  To provide for and balance the needs of the cell, enzyme activity is regulated Transition State vs. Intermediate Transition states have partially formed bonds and have partially charged atoms. Intermediates have fully formed bonds. Michaelis-Menten Equation (equation) V0= (Vmax * [S]) / ([Km+ [S] ) V0= rate of reaction at a given substrate concentration Vmax = maximum reaction rate [S] = substrate concentration Km = Michaelis constant, represents the [S] at which 1/2 Vmax is achieved What are the benefits of measuring the initial rate of a reaction V0? Changes in [S] are negligible, so [S] can be treated as a constant What does the steady state assumption, as applied to enzyme kinetics, imply? It assumes the formation of an enzyme-substrate complex that is formed and broken down at equivalent rates Catalytic Efficiency -If [S] << KM, then V0 = kcat/KM[E]T[S]-The rate law resembles a second-order reaction, with kcat/KM being the second-order rate constant -In this situation, the substrate binding enzyme becomes the rate-limiting step; kcat/KMcannot be faster than the frequency which the enzyme and substrate collide competitive inhibitor  competes with a substrate for the enzyme-substrate binding site  inhibitor can be overcome with high enough substrate concentrations Inhibitors that bind covalently with or destroy a functional group that is essential for the enzymes activity Irreversible Inhibitor Reversible Inhibitor competitive and non-competivie inhibitors Mixed Noncompetitive Inhibitor  Binds at a site distinct from substrate active site, but it binds to either E or ES  Influences the binding of S at active site Acid-Base Catalysis Catalysis in which a proton is transferred in the transition state Catalysis involves H+ or OH- diffusion into catalytic center Specific acid-base catalysis Involves acids and bases other than H+ and OH-. These other acids and bases facilitate transfer of H+ in transition state. general acid-base catalysis Catalysis Mechanisms: Metal Ion Catalysis Multiple possible functions: 1. Serves as electrophilic catalyst by stabilizing -charge intermediate or increased electron density 2. Generate nucleophile by increasing the acidity of a nearby molecule (i.e. H20) 3. Bind to the substrate, increasing the number of interactions with the enzyme andthus the binding energy noncompetitive inhibitorinhibitor binds to another site of enzyme, either E or ES when there is no substrate uncompetitive inhibitor binds to enzyme ONLY after substrate binds, only binds to ES complex Sequential/Single Displacement Reaction leads to the formation of a _. ternary complex Double displacement reactions proceed via the formation of _. a covalently modified enzyme intermediate What is the turn over number?  number of substrate molecules converted to products per sec by a single enzyme under optimal conditions and when enzyme is saturated with substrate  Calculated as the initial velocity of the catalyzed reaction (Kcat) at [S]>>Kmdivided by the enzyme concentration Three steps of glycolytic pathway that differ from gluconeogenesis  Conversion of glucose into glucose-6-phosphate  Conversion of fructose 6-phosphate into fructose 1,6-bisphosphate  Conversion of phosphoenolpyruvate into pyruvate Why is gluconeogenesis catalyzed by different enzymes?  Glycolysis is exergonic with ΔG°'=-74 kJ/mol mainly due to the 3 steps that differ, the other steps are reversible under cellular conditions  For gluconeogenesis to be thermodynamically favorable enzymes must catalyze reactions Steps of glycolysis/gluconeogenesis that differ  In glycolysis an ATP used in step 1 and 2, to make the reverse process favorable the reaction is uncoupled from ATP synthesis and a single Pi is released instead.  In step 3 in glycolysis ATP is produced, to make the reverse step possible an ATP and GTP are hydrolyzed to put in additional energy to make the step thermodynamically favorable in the opposite direction. Main reactive oxygen species superoxide, hydrogen peroxide, and hydroxyl radicalsWhat role does the pentose phosphate pathway play in removal of reactive oxygen species? Production of NADPH in the glucose-6-phosphate dehydrogenase reaction regenerates GSH from its oxidized form GSSG. Reduced GSH protects the cell by destroying free hydroxyl radicals. Also the co-substrate for glutathione peroxidase that removes hydrogen peroxide. In both cases, GSH is oxidized to GSSG. Structural role of sugar Sugars are the framework of DNA & RNA: The basic building blocks contain a phosphate group, a ribose (or deoxyribose), and a base. These form the repeating units in RNA and DNA chains. Linear chains of glucose or derivates form the structural elements in the cell walls of bacteria and plants. What about sugars makes it them good structural features of fibers? The B linkages that form straight chains between sugar molecules is optimal for fibers with high tensile strength. Bacterial Cell Wall Additional peptides are added to further crosslink the carbohydrate chains Sugar Code Select proteins and all tissues and cell types have unique carbohydrate units that can be used in their identification Last 2 steps of enzyme hydrolase  Residue is recognized by special receptor (or lectin)  When a section of the Golgi complex containing this receptor buds off to form a transport vesicle, proteins containing manner phosphate residues are dragged intothe forming bud by integration of the receptor and man. phos.; the vesicle then moves to and fuses with a lysosome, depositing its contents within 1st 3 steps of enzyme hydrolase  Hydrolase protein contains a signal sequence recognized by SRP particle and as a result the enzyme is guided to ER during synthesis  In ER lysozyme is glycosylated  Lysosomal enzymes contain a single patch that is recognized by an enzyme that phosphorylates a mans residue at the terminus end of an oligosaccharide chainHydrolysis of ATP: Charge separation Charge separation due to hydrolysis relieves electrostatic repulsion among the four negative charges on ATP. The phosphorous atoms are electron withdrawing groups (partial positive) and destabilize the molecule with respect to hydrolysis products Hydrolysis of ATP:Resonance The product inorganic phosphate (Pi) is stabilized by formation of a resonance hybrid, in which each of the 4 phosphorous-oxygen bonds has the same degree of double-bond character and the hydrogen is not permanently associated with any one oxygen. Hydrolysis of ATP:Ionization Product ADP2-immediately ionizes, releasing a proton into a medium of very low [H+] (pH7). The entropy of the solution increases because the more particles, the more disordered the system. Hydrolysis of ATP:Standard Conditions The ΔG' value is highly dependent on ATP,ADP,Pi,H+ (pH) and Mg2+. Deviation from the standard condition causes the value of ΔG' to be more negative. Hydrolysis of ATP: Solvation A greater degree of solvation (hydration) of the products Pi and ADP relative to ATP, which further stabilizes the products relative to the reactants What does the pentose phosphate pathway create? Ribose and NADPH How does the pentose phosphate only create NADPH or ribose?  When both r5p and NADPH are needed by the cell, the first 4 reactions of the pathway (oxidative steps) predominate. NADPH is produced and r5p is the principal product of carbon metabolism.  When more r5p is needed than NADPH, the oxidative reactions of the pathway are bypassed, Withdraw of fructose-6-phosphate and glyceraldehyde-3-phosphate (not glucose- 6-phosphate) from glycolysis and conversion into r5p via a reversal of the transketolase and transaldolase reactions How does bifunctional enzyme phosphofructokinase-2/fructose- 2,6-bisphosphatase and product fructose-2,6-bisphosphate regulate glycolysis and gluconeogenesis Fructose-6-phosphate activates PFK-2 and inhibits F-2,6-BPase  Production of F-2,6-BP stimulates glycolysis by allosteric activation of PFK-1 and inhibits gluconeogenesis by allosteric inhibition of F-1,6-BPase  Phosphorylation by cAMP-dependent protein kinase inhibits PFK-2 activity and stimulates F-2,6-BPase What happens if a muscle preparation containing glycogen phosphorylase is treated with: phosphorylase kinase and ATP Conversion of glycogen phosphorylase to the more active, phosphorylated form, phosphorylase a, glycogen breakdown accelerates. What happens if a muscle preparation containing glycogen phosphorylase is treated with: PP1 Converts the active phosphorylase a to the less active phosphorylase b; glycogen break down slows What happens if a muscle preparation containing glycogen phosphorylase is treated with: epinephrine epinephrine causes the synthesis of cyclic AMP, which activates phosphorylase kinase. The kinase converts phosphorylase b to a; glycogen breakdown accelerates How is glycolysis regulated by levels of ATP/AMP When the cell has ample ATP (low AMP) glycolysis will be inhibited How is gluconeogenesis regulated by levels of ATP/AMP? Ample ATP and it is stimulated What activates or inhibits phosphofructokinase? activates: AMP (reverse inhibition of ATP), F-2,6-BP inhibit: ATP, Citrate, decreased pH (lactic acid buildup) Glycogen synthesis Activation of UDP-glucose, a reaction catalyzed by UDP-glucose phosphorylase. Glycogen synthase uses UDP-glucose as a substrate and add the glucose units to growing glycogen chain. Branches introduced by a branching enzyme. It transfers 6 or 7 residue segments of a growing glycogen chain to the C-6 hydroxyl group of a glucose residues on the same or nearby chainGlycogen breakdown Enzyme glycogen phosphorylase cleaves glucose from the nonreducing ends of glycogen molecules and forms glucose-1-phosphate. It can only do so to long chains and limit dextran are broken down by a debranching enzyme. In the first step a trisaccharide group from a limit dextran branch is transferred to the end of a nearby branch. The remaining glucose unit from the branch is cut off. The glucose-1-phosphate is converted into glucose-6-phosphate by phosphoglucomutase. anabolic pathway •Anabolic pathways consume energy to build complex molecules from simpler ones •The synthesis of protein from amino acids is an example of anabolism catabolic pathway pathway that releases energy by breaking down complex molecules to simples compounds (polymers to monomers) ex: cellular respiration How is NADH recycled under anaerobic conditions? NADH reduces pyruvate to lactate and is thereby recycled to NAD+ How is NADh recycled in aerobic conditions? NADH passes electrons to O2