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Biochemistry 2580 Final Exam Study Notes.docx

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Department
Biochemistry
Course
BIOC 2580
Professor
Peter Dawson
Semester
Fall

Description
Biochemistry 2580 Final Exam Study Notes Lecture 1: • Small molecules o Sugars, amino acids, nucleotides, carboxylic acid derivatives o Act as building blocks for macromolecules • Macromolecules o Proteins-chains of amino acids o Polysaacharides-chains of simple sugars o Nucleic acids-chains of nucleotides • Proteins o Linear chains of amino acids o Linked by peptide bonds o Each protein has a unique sequence of amino acids as well as defined size and structure o Catalyze reactions(enzymes) o Form complex subcellular structures o Combination of variable R groups give protein it’s properties • AminoAcids o Each amino acid has an amino group and a carboxylate group o Variable R group o The central backbone atom is an α carbon o The first atom of the side chain is β and the second is gamma • The C=O of an amide is the point of weakness *Study all amino acid cards and know polarity and structure* Lecture 2: • Amino acids always found in water • Polarity as follows: o O>N>S>C=H • Non-polar amino acids o Methionine o Isoleucine o Leucine o Phenylalanine o Valine o Alanine • Moderatly non-polar amino acids o Glycine o Cysteine o Proline-side chain is covalently bound back to amino acid group o Tyrosine-single polar group off sets the very non-polar benzene ring o Tryptophan • Polar uncharged side chain amino acids -These side chain groups do NOT gain o Serine Simple alcohols or lose H in aqueous solution, so they o Threonine are uncharged -all 4 side chains act as o Asparagine Polar amide group good hydrogen bond donors or acceptors o Glutamine • Polar positively charged side chain amino acids -Side chain gain H /become protonated at neutral pH o Histidine o Lysine -Basic o Arginine • Polar negatively charged side chain amino acids o Aspartate Acidic o Glutamate • Henderson-Hasselbalch equation pH=pK +alog (deprotonated) (protonated) o Acidic and basic amino acids are the only ones who can be protonated/deprotonated o Side chains are the only thing that can be protonated/deprotonated • How to assess the state of ionization of a functional group o If pH is one unit or more HIGHER than pK theagroup is fully deprotonated o pH is equal to pK tae group is 50/50 deprotonated/protonated o pH is one unit or more LOWER than pK the group is fully protonated a o pH less than 1 unit away a calculation may be needed to determine the exact state • The above relationships tells you whether a group is protonated/deprotonated NOT if it is positive or negative • To calculate the exact state of ionization: o Henderson-Hasselbalch equation to find ratio deprotonated/protonated o Find α-indicates fraction deprotonated Lecture 3: • Amino acid analysis: o Helps determine protein structure o 2 processes involved  Separation of mixture into components  Detection of the components of interest qualitative(what is present)vs quantitative(how much is present) • Partition Chromatography o Separates components of a mixture o Particles of a solid chosen with specific properties(ie silica gel hydrogen bonds to polar amino acids) o Liquid solvent or buffer flows past particles and is non polar o Polar amino acids hydrogen bond to silica gel and move slowly o Non-polar amino acids spend more time in solvent and move quickly • Thin Layer Chromatography o Silica gel is spread in a thin layer on a plastic sheet o Samples placed in lower edge and placed in solvent o At solvent is soaked up different components of the sample move with solvent at different rates o Each amino acid can be identified by its characteristic relative mobility  Low R vfry polar amino acid-don’t move far  High R fon-polar amino acid-travel far • Column Chromatography o Sample of amino acid mixture added to top of column o Buffer added, carries sample through tube, and drops them into different test tubes o Contents of collection tubes analysed results plotted • Ion Exchanged chromatography o Separates on the basis of charge o Uses charged resin as stationary phase o Cation exchanger resins contain negative groups which bind positive molecules(cations) o Anion exchanger resins contain positive groups, which bind negative molecules(anions) o Elution is done by:  Competiton with a high ion concentration, which displaces the amino acid from the resinexample Na , displaces weakly bound amino acids, as Na + is increased more tightly bound amino acids are progressively displaced  Changing the pH to alter the charge on the amino acid so it no longer binds to the resin • Seperation of amino acids by Ion Exchange o Based on charge differences among proteins o Amino acids detected and their concentration measured in buffer coming out of the column o The volume of buffer needed to move a give amino acid from the top to the bottom of the column is the elution volume o Elution volumes characteristic for each amino acid • Seperating proteins on basis of size o Gel filtration or molecular exclusion separate based on size o Gel filtration an be used to measure size of unknown protein and copare to proteins of known sizes  Beads of polymeric cell form a loose network of polymer with many water filled pores-protein molecules enter pore if they fit-larger proteins excluded from pores-small molecules enter pores and are retarted in movement down column • How amino acids are detected o Can be ditected by adding ninhydrin-reacts with primary and secondary amines  Gives purple colour or yellow for proline  Colour intensity proportional to quantity of amino acid and can be measured o Fluorescamine giving yellow fluorescence under UV light Lecture 4: • Ultracentrifugation o 10 000-500000 times the force of gravity o Molecules sediment at a rate based on size and shape • Electrophoresis o Separation based on movement of charged molecules in an electric field o Rate of movement depends on  Size-if protein is compact moves fatser  Shape  Charge o Separation carried out in porous gel-so solution doesn’t move • SDS-Polyacrylamide Gel Electrophoresis o Protein pre treated with sodium dodecyl sulfate(SDS) o SDS causes protein molecules to extend and gives a uniform charge per unit size o Negative charge used to move protein through gel o Separation based strictly on size o Smaller=faster movement • Isoelectric focussing o Separation based on charge o Isoelectric point-pH at which the net charge of a protein is zero o At high pH protein is deprotonated and moves towards + electrode o As pH decreases becomes more protonated and –ve charge decreases o When net charge = 0 protein stops moving o Each protein has different isoelectric point • Mass Spectrometry o Protein vaporized by a laser beam yielding charged protein particles o Particles travel towards detector o Velocity depends on mass larger= slower o Compare mass detected to data base to identify protein • Protein structure o Primary structure: linear sequence of amino acids o Secondary structure: regular repetitive structures, such as helical sections in myoglobin(α helix) o Tertiary structure: overall pattern of 3-D folding of whole polypeptide o Quaternary structure: ex hemoglobin is an assembly of 4 globin units • Peptide bonds of proteins are hydrolysed to release individual amino acids done by proteases o After hydrolysis amino acids can be analyzed by chromatography o Acidic hydrolysis destroys Trp o Basic hydrolysis destroys other amino acids by not Trp • Anucleophile is an atom with a lone pair of electrons available to share • An electrophile is electron deficient in case of C double bonded to an oxygen, the oxygen is more electronegative so the carbon is deficient Lecture 5: • Edman Degradation o Starts at the end of polypeptide and works it’s way to the front o Cycle can be repeated up to 50 times to give a 50 amino acid sequence o Coupling- requires base- reaction must be complete before the cyclization can occur o Cyclization-requires acid(ahydrous)-reaction must take place before next coupling o Requires phenylthiohydantoin o Step 1: nucleophilic attack o Step 2: turns acidic-protonation-internal nucleophile-general acid facilitates- get 5 member ring • DNAsequenceamino acid sequence • To study long polypeptide chains they are cut into shorter oligopepetides by selective hydrolysis o Selective hydrolysis: cuts at specific location o Trypsin-cuts Arg and Lys  If proline is found afterArg or Lys no hydrolysis will occur  All fragments will have anArg or Lys at the end EXCEPT c-terminus end o Chymotrypsin- cuts Phe, Trp and Tyr  Once again if proline follows will NOT cut o Cyanogen bromide-cuts polypeptide chains at methionine resiues  Attacks S atom of Met  Broken on carboxylate and Met is turned into Hse  Can cleave if Proline is present as it is smal l  All fragments have Hse at end EXCEPT C-terminus • The overlap method o Two samples of original pepetide are each cut seperatly by 2 different hydrolysis methods-each targeting different sites o Line the sequence of one oligopeptide over top of the other to get the amino acid sequence • Using Mass Spectrometry to sequence and identify proteins o Tandem mass spectrometry-2 mass specs work together o Stages:  Sample hydrolyzed by protease  First MS-1: separate peptides of different masses  Collision cell: fragment each peptide molecule once(usually peptide bond) in a random fashion  Second MS-2: measure fragment massesusing data can back calculate sequence o Peptides generated at low pH  Acidic residues have no charge on side chain  Basic residues have +1 charge on side chain o Peptides with charges produce the highest signal on MS-2 o When sequence is assembled it’s assembled backwards Lecture 6: • Determining the amino acid sequence Sanger o We can identify the first amino acid in a protein by tagging it with fluorodinitrobenzene(bright yellow)carbon on ring is an electrophile(as it’s bonded wit F which is very electronegative o Amino acid at the N-terminus of protein has a free α amino group o At high pH this group deprotonates to become NH -2 an nucleophile o Reacts with fluorodinitrobenzene HF is a good leaving group o Hydrolysis releases the N-terminal amino acid with yellow tag attachedcan identify by chromatography o Problems:  Hydrolysis destroys rest of chain  Can only find first amino acid • Determine the amino acid sequence Edman o N-terminal amino acid reacted, removed and identified WITHOUT hydrolysing the peptide bonds o Reaction can be repeated to identify all amino acids o Up to 50 amino acids can be identified • Single bonded structures are flexible due to bond rotation  BONDS DON’T BEND o How chain flexibility arises o Bond rotation allows the peptide chain to adopt a variety of shapes • Conformations: represent states of a molecule that can be interconverted by bond rotations without breaking covalent bonds o Ex different shapes of polypeptide chain o Usually concerned about these for macromolecules(ie proteins) • Configurations: can only be interchanged by breaking covalent bonds, not by bond rotation o Eg cis and trans forms of molecules with double bonds o Two chiral forms of amino acids (D and L) • X-ray Diffraction o Measures regular repeating patterns on the molecular scale o Atoms and molecules have similar dimensions to the wavelength of x-rays o If x-ray wavelength is known dimensions of the repeating pattern of molecules can be measured o Can measure regular patterns in fibrous proteins o Pauling found using this that single-bonded peptide chain seemed too flexible and no regular patterns would be stable • Peptide bond has 2 resonance forms- one with a double bond o Peptide bond is rigid o Fixed in trans-geometry o Behaves more like a double bond than a single bond • Restricted bond rotation and structure o Limits freedom of motion so that only a few regular structures can form o o Two possible regular repeating patterns-due to 109 direction change o In a helical shape every α carbon bond down the peptide chain turns in same direction o In an extended shape the α carbon bonds turn in alternate directions down the peptide chain o No regular repeating structureget random coil • Β-strand and Β-sheet o Occur when amino acids alternate in direction o Strands in same direction make a parallel β-sheet(H bonds connect strand to strand) o Strands in opposite direction make antiparallel β-sheet(H bonds align better here) • Amino acids that favour α helix o Ala,Arg, Gln, Glu, His, Leu, Lys, Met, (phe) • Amino acids that favour β sheet o Trp, Tyr,(Phe), Val, Ile, Thr, Cys o Need room for side chains • Local majority determines which secondary structure forms • Amino acids that act as breakers o Gly, Pro, Asn,Asp, Ser o Have side chains which interfere with secondary structure o 2 breakers in a group of 4 amino acids will for a turn or flexible loop in main chain Lecture 7: • Native state: most proteins are folded into a unique 3D tertiary structure which is required for their function • Denaturation: unfold proteins, unfolded form may be unstructured or aggregatedoften irreversible o Protein function typically lost o Proteins can be denatured by:  Heat  Disruptive solvents  Harsh detergents • Tertiary structure: o Overall pattern of folding o The simplest possible tertiary structure is continuous secondary structure • Secondary structures are rigid so these are fibrous proteins • Globular proteins o Requires polypeptide to fold back on itself o Folding requires breaks o Need breakers o Pro and Gly tend to be in turn • Hydrophobic effect o Major force driving protein folding o Polar amino acids form outer layer as they interact well with surrounding H 2(good H bonding) o Non-polar amino acids group together to minimize contact with water(hydrophobic effect) • Summary: o Amino acids elect secondary structure o Breakers allow for folding o Pattern of large and small side chains is arranged so that secondary structure components pair up with best possible fit • alpha Helix Bundle o Type of quaternary structure o AAthat prefer β sheet are scattered o Pattern that occurs allows one side to be polar and one side non polar • Β sheet o Majority β preferring o Anti-parallel more stable-hydrogen bonds line up better o Side chains project out o Sheet can be polar on one side and non-polar on another side  When this happen they can make an open fold  Forms anti-parallel β barrel • Alternate α β structure o Form parallel β sheets o Helical sections connect the strand o Helix lies above/below the plane of the sheet o Less stableneed to be sequestered away from H O 2 • alpha β barrel o Β sheet form the central barrel surrounded by the connecting helices o Happens when all helices lie on one side of sheet • alpha β sandwhich o Β sheet layered between two α helixes o Β sheet often twisted • Domains o Larger proteins fold up into small sections o Aprotein of 50kDa may have 3 or 4 domains o Each domain may adopt a different folding pattern • Protein stability and function o Native state essential for proper function o Covalent bonds link amino acids in a chain in a specific sequence o Non-covalent interactions dictate folding pattern and stability  Hydrophobic effect and van der waals most important • Van der Waal interactions o Interaction is a weak electrostatic attraction between atoms that are close but not bonded • Free energy of interaction o When atoms are too close they repel strongly o Atoms at ideal distance when “close” o Atoms further away are attracted o Frces fade when atoms are more then 2-3 diameters apart • Polar interactions and folding o H-bonds- may form between donors and acceptors that line up in folded protein o Ion-pairs-strong electrostatic interactions of negative side chains which pair up with positive side chains that are nearby in the folded protein-salt bridge • Urea weakens hydrophobic effect Lecture 8: • Function of most proteins involves ability to recognize and bind to other molecules • Protein-protein interactions fundamental in living processes o Proteins that form quaternary structure recognize and bind their partner proteins o Enzymes recognize and bind their specific target proteins and catalyze rxn of them o Anitbodies bind and identify foreign moleculestag for attack • Cymotrysin binds to polypeptide with aromatic chains o Groove binds to peptide chain by hydrogen bonding o Side chain bonding pocket is large and surrounded by non-polar amino acidsphe,tyr and trp fit best o If you have proline won’t bind • Trypsin side chain binding pocket is narrow, negative charge at end • Elastase(binds Ala and Gly best) smaller, non-polar pocket • All enzymes are proteins but not all proteins are enzymes • Substrate-target of enzyme • “ase” indicates enzyme • Chemical rxn must be able to occur spontaneously for an enzyme to help • Without catalysts reactions depend on: o Molecules must collide o They must be the right orientation(with respect to one another) o Require threshold energy • Arrhenius equation • D o Low E orahigh T make fraction bigger so reaction is favoured • Enzyme binds substrates in a special pocket known as an activation site-holds them together long enough for reaction to proceed o Proximity effect-increases z(collision frequency) • 2 molecules may collide by chance BUT reactive groups may not be properly lined up for reaction-enzymes bind substrates holding them together in the active site so reactive groups are aligned right o Orientation effect- increases P • Enzymes decrease activation entropy • Enzymes can use chemical catalysts to speed up reaction by lowering activation energy • Hydrolysis of a peptide is very slow because water is a weak nucleophile/weak acid • Enzymes must speed up reactions at neutral pH and normal temperature • Enzymes can speed up reactions by providing a better nucleophile • Electrophilic catalysis: o Electron seeking group o No good electrophile amino acid o Enzyme may contain a non-amino acid helper called a prosthetic group  Initiates reaction by withdrawing electrons from substrate • General acid/base catalysts o General acid- amino acid side chain donates H+ to reaction o General base-amino acid side chain removes H+ from reaction *H+ exchange takes place right @ site of rxn so pH is not affected* • Chemical catalysis o Nucleophilic catalysis o Electrophilic catalysis o General acid catalysis o General base catalysis • Reaction must pass through a transition state to proceed and key atoms may change shape or bond may stretch • Less activation energy if the enzyme active site is complementary to the transition site Lecture 9: • Chymotrypsin binds ahead of the target amino acid o Target amino acid fits into binding pocket so substrate can bind more tightly • Without catalystspeptide hydrolysis o Wat+r is nucleophile, oxygen not good nucleophile, makes O which is not favourable o Leads to oxyanion transition state o Transition state breaks  N is leaving group  Oxyanion return bond to C  If N takes back excess electrons bonds break *if electrons returned to O reactants are back to starting point* • Chymotrypsin does better because it simplifies it to 2 steps o Nucleophile in enzyme attack c=o  Splits c-terminal half off  Covalently binds to N-terminus  Forms acyl-enzyme intermediate o Brings in water to release N-terminal half an restores the enzyme group to original state • Chymotrypsin is a better nucleophile o *****look at diagram of the catalytic triad***** • Enzyme assay-process of measuring enzyme catalyzed reaction rate • Artificial substrate is a “molecular look-a-like of real substrate • Lactate dehydrogenase shows reaction by absorbance change o As NADH(340nm) is changed to NAD+(no absorbance) overall absorbance decreases • Aromatic rings absorb UV light • Larger chromophores absorb at longer wave lengths Lecture 10 • Rate of reaction=substrate used/time or concentration product formed/time • Enzyme activity=rate x volume(quantity of enzyme present) • Specific activity is a measure of enzyme efficiency o When pure and impure enzymes compare specific activity of enzyme purity • Molar activity= specific activity x molar mass of enzyme o Equal to turn over number o Turn over number-# of catalytic reaction cycles per molecule of enzyme per second o Turn over number is the fundamental property of an enzyme • Michaelis-menten equation “rules” Work at time=0 so o Total concentration of enzyme is constant [P]=0 and reverse o Define max velocity of reaction reaction can be ignored o Steady state assumption- rate of breakdown=rate formation • Initial rate • Michaelis-menten equation Lecture 11 and 12: • V maxatalytic rate when 100% of enzyme is occupied by substrate o Increase V ,maxster reaction= better catalysis • K mhow well substrate fist catalytic state o Low K =good recognitionbinds well m o High K =pmor recognitionbinds poorly o More than 1 substrate= more than 1 K vamue • Michaelis-menten equation is a hyperbolic curve when V is plotted vs [substrate]- o approaches V maxgradually • Linear transformations convert m-m equation to a straight line o Known as Lineweaver-Burk method o Slopes/intercepts of straight line give better Vmaxand K m • Lineweaver-burk plot o Take reciprocal of both sides of equation o X= -1/K  met K by mxtending graph onto the negative X-axis • Inactivators- irreversible reaction with enzyme-covalent chemical reactions –highly toxic-reaction destroys catalytic activity • Inhibitors- reversibly bind to enzyme-decrease enzyme activity without destroying catalytic function [ ] of inhibitor decreases, enzyme activity increases-non covalent bonds-binds to site on enzyme-inhibition governed by binding equilibrium o Competitive inhibition: affects ability to bind substrate  When inhibitor can only bind to unoccupied enzyme E  Formation of EI(enzyme + inhibitor) complex means less E to bind to substrate  High [S] can overcome competitive inhibitor  Inhibitor and substrate compete for available enzyme  S and I often share binding site and resemble eachother chemically  No effect on V maxwhen [S] increases and [I] held constant  Crosses at x-axis on Lineweaver-Burk plot  Slope increases as [I] increases o Non-competitive inhibition: when I can bind to E or ES(enzyme substrate intermediate)  affects catalytic rate  inhibitor NOT competing with substrate  I binding site different from substrate binding site  Inhibitor may disorganize catalytic component  Less ES to undergo catalasis so doesn’t effect Kmbecause substrate can still bind  V maxdecreases and [I] increases, slope increases as [I] increases  K=ihe [ ] of inhibitor that causes maxto half  Best to use lineweaver-burk to identify as lines do not cross at same point on y-axis  Same X-intercept because no effect on K m *for mixed inhibition lines meet above x-axis* Lecture 13: • Lipids are structurally diverse group of molecules that are NOT defined by chemical structure but by HYDROPHOBICITY • Use organic solvents(2:1 mix of chlorofor and methanol) to dissolve lipids can’t use “normal” solvents/buffers • Function of lipids o Energy storage-triacylglycerols(fats and oils)-most important form of stored energy o Structural elements of membranes-phospholipids and sterols o Signal transduction-steroid hormones, prostaglandins o Enzyme cofactors- coenzyme Q: mitochondrial electron transport chain o Vitamins-ADE and K o Light absorbing pigments-carotene • Lipids can occur covalently linked to other biomolecules o Glycolipids-made of lipids and carbs- important in cell membranes ex human blood type defined by glycolipids on outer surface o Lipoproteins-lipids and proteins associated with cardiovascular health/disease ex LDL, HDL and VLDL • Fatty acids o Carboxylic acids with hydrocarbon 4-36 chromosomes o When labeling them α carbon is the one next to –COO , # 1 is the carboxyl carbon o When naming: o Alternative naming is PUFAor the omega naming  Specify double bond related to last carbon(start at opposite end) o Features of commonly occurring fatty acids  Even number of carbons  Cis configuration  Unbranched  Double bonds in polyunsaturated in methylene bridge-separated by methylene carbon • Pattern-double-single-double-single o Common saturated fatty acids  Laurate-12 carbon-bay, laurel  Myristate-14 carbon-nutmeg  Palmitate- 16 carbon-palm  Stearate-18 carbon-tallow  Arachidate- 20 carbon-peanuts o Common unsaturated fatty acids  Oleate- 18:1  Linoleate:18:2  Linolenate: 18:3  Arachidonate: 20:4 o Saturated fatty acid: no double bonds  “saturated with hydrogens” o Unsaturated fatty acids: one or more double bonds o Due to strong vander waal forces saturated fatty acids pack closely together  As chain length increases • Melting point increases • Solubility decreases o Due to bonds(which cause a “kink-cis bond) unsaturated fats don’t pack closely  Melting point lowered  Less thermal energy needed to disrupt order  Effects membrane fluidity-IMPORTANT o Trans fatty acid  Partial hydrogenation causes a trans double bond allowing them to pack together more regularly-higher melting point  Negative effects on cardiovascular health o Derivatives of fatty acids  Carboxylic acids can combine with alcohols=ESTER  Carboxylic acids can combine with acid= acid anhydrides Lecture 14: • Triacylglycerols(TAG) o Acyl-acid derivative o Fats and oils-major constituent (even human fat) o Majority of fats found in this form o Each carbon contains a hydroxyl group o Highly hydrophobic o High melting pint associated with long chain(C16 and C18) fatty acids o Animal fat high melting point low unsaturation o Plant oil low melting point high unsaturation o Phosporylation add negative charges to molecules o Phosphoric acid reacts with alcohols and acids to form  Phosphate esters  Phosphoanhydrides • Glycerophospholipids (phosphoglycerides) o Biological membrane o Carbon 1 and 2 of glycerol esterfied to fatty acid “tail” o Phosphodiester linkage to C3 forms “head”  End up amphipathic-hydrophilic head and hydrophobic tail  This differentiates them from TAGsallows them to form lipid bylayers o Major classes: Name:  Choline phosphatidylcholine  Ethanolamine phosphatidylethanolamine  Serine phosphatidylserine  Glycerol phosphatidylyglycerol o Phosphatidylcholine(lecithin)  Class of lipid-not single molecule • Differences between TAGs and glycerophospholipids • Lipid complexes in water o Micelle- smallest/simplest o Bilayer- fundamental structure of membrane o Vesicle-when bilayers fold back on themselves • Analysis of lipids o 2 phase extraction  Tissue homogenized in chloroform/water/methanol  Separated into • Adsorption chromatography(produces following test tubes) • Thin layer chromo o Trans-esterfication  Take test tubes and NaOH/methanol(makes fatty acyl methy ester)  Separated into • Gas-liquid chromo • High performance liquid chromo • Carbohydrates o Variable, numerous possibilities o Most abundant molecule o Energy metabolism o Essential to nucleic acids o Sugars also known as saccharides  Monosaccharide(simple sugar) • Single sugar unit • Ex glucose  Oligosaccharides • Short chains of monosaccharide’s • Disaccharides-2 or more monosaccharide units  Polysaccharides • Polymers of 20 or more sugar units • Ex glycogen, cellulose • Monosaccharaides o Carbonyl group-aldehyde or ketone o At least 2 carbons bearing alcohols  Polyhydroxy-aldehyde(aldoses)  Polyhydroxy-ketones(ketoses) o Properties  Water soluble  Poorly soluble in organic solvents(ether or hexane)  Colorless  Sweet taste  (CH O2 n  Fisher projection formula  Perspective formula  Simplest monosaccharides contain 3 carbon atoms-trioses Lecture
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