BIOORGANIC CHEMISTRY - Vsmu.by

An example of the variant:TEST 11. Define the sign (negative or positive) of inductive and resonance (mesomeric)effects of functional groups and heteroatoms in the structure of benzocain (ethyl 4–aminobenzoate). Show these effects with arrows. Indicate electrono-donating (ED)or electrono-accepting (EA) effects of functional groups.2. Draw the standard Fischer projection formulas of stereoisomers that correspondto the structure of 2,3,4-trihydroxybutanal. Indicate diastereoisomers and enantiomers.3. Carboxylic acids: acidic properties of mono- and dicarboxylic, saturated, unsaturated and aromatic carboxylic acids.4. Show the reaction centers of butanamine-1, butanethiol-1 and butanol-1. Writethe scheme and outline mechanism of the SN reaction with HCl for the most activecompound.5. Write the schemes of reactions, represent and name reaction centers, takingpart in each reaction, indicate the mechanism of the following reactions:tONaHCO3C2H5OH / H2SO4(conc.)4-hydroxypentanoic acidCH3COClHCl(conc.), tOPRACTICAL SKILLS.Qualitative functional analysis of organic compounds.THE STUDENT EDUCATIONAL-INVESTIGATIVE WORK 1The student educational-investigative work is experimental investigation of the given organic compound to choose from two proposed compoundson base qualitative tests for discovery of functional groups and specific qualitative reactions for certain compounds. The student must know the structuralformulas, aggregative state, colour and solubility in the water of the compounds proposed for qualitative functional analysis. For theoretical explanation and experimental carrying out of the practical skills task the student mustknow the schemes of qualitative reactions for discovery of functional groupsin the structure of proposed compounds and specific qualitative reactions forcertain compounds.10

LIST OF COMPOUNDSFOR QUALITATIVE FUNCTIONAL ANALYSIS(student educational-investigative work 1)The nameThe structural formula1Аcetone2OH3CAcetylsalicylicacidCCH 3OOHCAggregative state,colour3colorless liquid,specific smellsolid,white powderSolubility inthe water4partiallywater solublewaterinsolublecolorless liquid,specific smellwaterinsolubleliquid,specific smellirritative colorlessliquidviscous colorlessliquidwatersolublewatersolublewater soluble slowlyyellow-brown liquid,cold smellsolid, white insolublesolid, white powderwatersolubleO C CH3OCyclohexeneEthanolCH3 CH2 OHFormaldehydeOH-C HGlycerolCH2-OHCH-OHCH2-OHLactic acidH3CCH COOHOHOxalic acidOOCCHOOHPhenolOH( )-tartaric acidOOHOHHOCOHCHHO11

AN EXAMPLE OF THE PRACTICAL SKILLSVARIANT PAPER:TEST 1“Theoretical bases of the main organic compound families structure andreactivity”PRACTICAL SKILLS.Qualitative functional analysis of organic compounds.Student educational-investigative work 1Define, which of the following compounds is present in task 30:lactic acid or acetone.REQUIREMENTS FOR WRITING ANSWER1) To write the structural formulas of the investigated organic compounds, toclassify them according to the functional groups and principles of classification as bioorganic compounds.2) To write the schemes of qualitative reactions for discovery of functionalgroups in investigated compounds and to show the specific reactions forsome groups of compounds, to indicate its conditions and results.3) To make the qualitative tests according to the sequence of operations, tocheck the practical results.4) To analyse and to explain the experiment results, to write the final conclusion as answer of experimental task.SPECIFIC EXAMPLE OF PRACTICAL TASK SOLUTION.THE TASK: Define, which of the following compounds is present in task 30: lactic acid or acetone.I. To write:1. The structural formulas of the investigated organic compounds and theirclassification according to the families of functional groups and principles of classification as bioorganic compounds.H3C2HCO 1COOHOH21H3CCAcetonelactic acid12CH3

1. A carboxyl group, a carboxilic acid, 1. A carbonyl group, a ketone,2. A hydroxyl group, a secondary al- 2. An -methylketone.cohol.1,2. An -hydroxyacid.2. Proposed physical properties: aggregative state (solid or liquid), colour,smell, solubility in the water.Lactic acid - colourless liquid, cold Acetone - colourless liquid, specificsmell, water soluble.smell, water soluble.3. The schemes of the qualitative reactions for discovery of functionalgroups in investigated compounds and the specific reactions for somegroups of compounds, their results.Lactic acid The qualitative tests for discovery of carboxyl group in the structureof lactic acid as water soluble carboxylic acid.H3CHCCOOHH2OHCH3COHCOOOHH3OpH 7The practical result: indicator paper becomes red.H3CHCCOOHNaHCO 3H3COHHCCOONaCO2H2OOHThe practical result: bubbles of gas. The qualitative test for discovery of secondary alcohol hydroxylgroup in the structure of lactic acid.HH3C C COOHOHoK2Cr2O7 H2SO4tH3C C COOH K2SO4 Cr2(SO4)3 H2OOThe practical result: orange solution of K2Cr2O7 becomes blue-green solutionof Cr2(SO4)3.13

The specific qualitative test for discovery of lactic acid as hydroxycarboxylic acid.O to (H2SO4(concd)) H-C O CH -C OCH3-CH-C3HOHOHOHmethanoic ethanallactic acidacidoOtH-CCO H2OOHmethanoicacidThe practical result: the blue flame.I2 2NaOICH3-CNaI NaOI H2OOO 3NaOII3C-CHH-3NaOH NaOHCHI3 H-COO-Na iodoformethanalThe practical result: white-yellow precipitate in the test-tube 2.Acetone. The qualitative test for discovery of carbonyl group in the structure ofacetone.NO2NO2OH3C C CH3 H2N-NHN NHNO2-H2OH3C ophenylhydrazoneThe practical result: yellow precipitate. The qualitative test for discovery of -methylketo group in the structure of acetone as -methylketone (iodoform test).I2 2NaOHNaI NaOI H2OCH3-C-CH3 3NaOICH3-C-CI3 NaOH-3NaOHOOOCH3-C ONa CHI3The practical result: white-yellow precipitate.14

The specific qualitative test for discovery of acetone with sodium nitroprussiate.acetonesodium nitroprussiateH3C C CH3Na 2[Fe(CN)5NO]NaOHOthe result: CH3COOH the result:blood-redcherry-redsolutionsolutionII. To write in a separate paper:The plan of investigation:InvestigatedcompoundsReagents, conditionsLactic acid1) H2O, indicator paper, pH 72) NaHCO33) K2Cr2O7/H2SO4(2n)/to4) a) H2SO4(conc.)/tob)I2/NaOH5) 2,4-Dinitrophenylhydrazine6) I2/NaOH (immediately)7) a)Na2[Fe(CN)5NO]/NaOHb)CH3COOHAcetone. - III. To make the qualitative tests experimentally according to sequenceof operations.IV. To write the report about the experiment and conclusions accordingto results about discovering functional groups and families, the finalconclusion about the discovering compound.1) Task 30 contains a colourless liquid water soluble compound withcold smell.2) The water solution of investigated compound 30 is a weak acid(pH 7) because an indicator paper becomes red. It means task 30 containsa carboxyl group of a water soluble carboxylic acid.3) Addition of the NaHCO3 saturated solution to the water solution of investigated compound 30 gives bubbles of gas. It means task 30 contains a carboxyl group of a carboxylic acid.4) Heating of investigated compound 30 with the water solution ofK2Cr2O7 and diluted H2SO4 leads to change of colour from orange to bluegreen. It means task 30 contains a hydroxyl group of a primary or a secondary alcohol.15

5) Heating of investigated compound 30 with concentrated H2SO4 givesthe blue flame. Heating of the investigated compound 30 with concentrated H2SO4 and the following iodoform test of the gaseous product leads toform the white-yellow precipitate in test-tube 2. This gaseous productcontains a -methylcarbonyl group of a -methylcarbonyl compound resulted decomposition of a -hydroxyacid. That’s why the gaseous product isidentical with acetaldehyde. It means task 30 is identical with lactic acid.6) Addition of 2,4-Dinitrophenylhydrazine to investigated compound 30 doesn’t give the yellow precipitate. It means task 30 doesn’t containa carbonyl group of an aldehyde or a ketone.7) Addition of investigated compound 30 to I2/NaOH doesn’t give thewhite-yellow precipitate immediately. It means task 30 doesn’t contain a -methylketo group of a -methylketone.8) Addition of investigated compound 30 to the mixture of the sodiumnitroprussiate and the NaOH solutions doesn’t give blood-red colour. Itmeans task 30 doesn’t contain acetone.Final conclusion: the compound of task 30 is identical with lactic acid.CONTROL-TEST 2.«Biopolimers and their structural units»Theoretical part.Question 1. Program questions of the following topics:Monosaccharides. Classification of monosaccharides. Stereoisomerism. D- and L-families. The structures of the most important pentoses andhexoses. Amino sugars and their properties. Open-chain structures and cyclicforms. Furanoses and pyranoses; α- and β-anomers. Fischer projection formulas and Haworth formulas. A cyclo-oxo tautomerization. Mutarotation. Theconformations of pyranose forms of monosaccharides. Chemical propertiesof monosaccharides. Nucleophilic substitution at an anomeric atom in cyclicforms of monosaccharides. O- and N-glycosides. Hydrolysis of glycosides.Phosphates of monosaccharides. Oxidation of monosaccharides. Reducingproperties of aldoses. Aldonic, aldaric, uronic acids. Reduction of monosaccharides to alditols. Epimerization reaction of monosaccharides, the reversible transformation of aldoses to ketoses.16

Oligosaccharides and polysaccharides. Classification of polysaccharides. Oligosaccharides. The disaccharides: maltose, cellobiose, lactose, sucrose. The conformational structure. The cyclo-oxo tautomerization. The reducing properties. Hydrolysis. Polysaccharides. Homo- and heteropolysaccharides. Homopolysaccharides: starch (amylose, amylopectine), glycogen,dextran, cellulose. Primary structure, hydrolysis. Notion about secondarystructure (amylose, cellulose). Pectins. Heteropolysaccharides: hyaluronic acid, chondroitin sulfates. Primary structure.Natural amino acids. Amino acids that can be obtained from proteins.Classification of naturally occurring amino acids taking into account differentsigns: acid and base properties, chemical nature of a side chain and its substituents. Structure, nomenclature. Stereoisomerism. Acid and base properties, dipolar ions. Essential amino acids. The formation of α-amino acids: hydrolysis of proteins, synthesis from α-halo acids. Reducing amination reactions and transamination reactions. Chemical properties of α-amino acids asheterofunctional compounds. Formation of intracomplex salts. Esterification,acylation, alkylation, deamination reactions, formation of imines. Biologically important reactions of α-amino acids.Peptides and proteins. Electronic and steric structure of a peptidebond. Hydrolysis of polypeptides. The establishment of primary structure ofpolypeptides. The strategy of peptide synthesis. Secondary, tertiary (domains) and quaternary structures.Nucleosides. Nucleotides. Nucleic acids. Nucleic (heterocyclic) basethat can be obtained from nucleic acids. A lactim–lactam tautomerization.Deamination reactions. Structure of nucleosides and mononucleotides thatcan be obtained from nucleic acids. Nomenclature. Hydrolysis. Primarystructure of nucleic acids. Ribonucleic and deoxyribonucleic acids. The nucleotides found in RNA, the nucleotides found in DNA. Hydrolysis of nucleic acids. Secondary structure of DNA. The role of hydrogen bonds in formation of the DNA secondary structure. Complementarity of heterocyclic bases. The hydrogen bonds in the complementary pairs of heterocyclic bases.Nucleoside mono- and polyphosphates. AMP, ADP, ATP. The role of ATPas the accumulator and the carrier of free energy in cell. Coenzymes. Structures of NAD and its phosphate (NADPh ). NAD -NADH system; hydridetransfer as one of the stages of the biological oxidation–reduction reactionswith participation of this system.Question 2. Write the formulas of: Oxo- and cyclic forms of biologically important monosaccharides;17

Disaccharides;Ionic forms of natural α-amino acids at given pH;Dipeptides;Nucleosides, nucleotides and dinucleotides.Question 3. Write the schemes of reactions, represent and name reaction centers, taking part in each reaction, indicate the mechanisms ofthe following reactions:H3C COCl 2 NaOHHC OH NaNO2 / CH3COOH HCllysineasparticacid NaOH C2H5OH / H2SO4 (conc.), toOOH3C C OH3C CphenylalanineOOH3C C O NaOHtotyrosine HCl HNO3 / H2SO4, to NaOH H2O / H asparagine 2 C2H5OH / H2SO4 (conc.), toOH3C CClH3C C HCl NaOH Br2 / FeBr3HC OHto NaNO2 / CH3COOHto H2O / OHHC OH C2H5OH /H2SO4(conc.),totryptophan NaOHH3C C HCl18OCl

HCl NaNO 2 / CH3COOH NaNO2 / CH3COOHhistidine C2H5OH / H2SO4(conc.),tOH3C CClHC OH HClo H2O / H glutamine H2O / OHOH3C CCl H2O / H -lactose (CH3O)2SO2 / NaOH CH3OH / HCl(gas) [Ag(NH3)2]OH, to CH3I / NaOH Br2 / H2OH3C CH3C C Br2 / H2O -maltose Cu(OH)2OOH3C CO Cu(OH)2sucrose (CH3O)2SO2 / NaOHOH3C COH3C CO H2O / HCl, to? H2O / NaOH, to? CH3OH / HCl(gas) -cellobiose Cu(OH)2? CH3I / NaOHH3C C -maltoseOCl [Ag(NH3)2]OH, to (CH3O)2SO2 / NaOH?to H2O / HCl, to H2O / NaOH, to H2O / HCl, to19OCl

H3C COCl NaNO2 / CH3COOHguanosine5'-phosphate H2O H2O / H H2O / OH-OOH3C C O H2OH3C C5'-adenylicacid H2O NaNO2 / CH3COOH5'-cytidilycacid H2O / H H2O / OH- H2O / H H2O / OH CH3I NaNO2 / CH3COOHpKa values for the 20 common amino acidsα-Amino Acidp(Ka)1(α-COOHGroup)p(Ka)2(α-NH3 Croup)pKaR(Side .8Asparagine2.18.8-5.4Aspartic acid2.09.93.93.0Cysteine1.910.88.35.0Glutamic 2.39.7-6.0Lysine2.29.210.89.820

6.0PRACTICAL SKILLS:THE STUDENT EDUCATIONAL-INVESTIGATIVE WORK 2The student educational-investigative work is experimental investigation of the given bio-organic compound to choose from two proposed compounds on base qualitative tests for discovery of functional groups and specific qualitative reactions for certain compounds. The student must know thestructural formulas, tautumerism, aggregative state, colour and solubility inthe water of the compounds proposed for qualitative functional analysis. Fortheoretical explanation and experimental carrying out of the practical skillstask the student must know the schemes of qualitative reactions for discoveryof functional groups in the structure of proposed compounds and specificqualitative reactions for certain compounds.LIST OF COMPOUNDSFOR QUALITATIVE FUNCTIONAL ANALYSISThe nameThe structural formulaAggregativestate, colour123OD-( )-glucosesolid,CHCH2OHwhite powderHOHHOHHHOHOHCH2OHGlycineHThe solubilityin the water4water solubleOHOHHHOHOHOHOH2N-CH2-C OH21solid,white powderwater soluble

CH2OHOLactoseHOCH2OHOOOHCH2OHOHOCH2OHOOHwater solubleOHOHsolid,white powderpartially water solublesolid,white powderwater solublesolid,white powderinsoluble incold water, inheating withwater formsgelOOHOHOHCH2OHOHCH2OHOHOOHSalicylic acidOCOHOHOHsolid,white powderOHCH2OHOMaltoseHCOOHOHCH 2COOHHwater solubleOCOHOH( )-Malic acidsolid,white powderOHCH2OHOOHwater solubleOHOHOHHOsolid,white HOStarchOOHCH2OHOOOHCH2OHOOHOOHAmylose22OHOH

CH2OHOOHCH2OHOOHOOCH2OHOOHOOHHO solid,white powderwater solublesolid,white powderwater solubleHOHOH2CHO OOHOOH( )-tartaricacidCH2OHOOHOHHOCOHCHHOAN EXAMPLE OF THE PRACTICAL SKILLSVARIANT PAPER:PRACTICAL SKILLS.Qualitative functional analysis of organic compounds.Student educational-investigative work 2.Define, which of the following compounds is present in task 55:D-( )-glucose or glycine.REQUIREMENTS FOR WRITING ANSWER AND SPECIFICEXAMPLE OF PRACTICAL TASK SOLUTION.I. To write in the exercise book:1) The structural formulas of investigated organic and bioorganic compoundsand their classification according to the families of functional groups andprinciples of classification as bioorganic compounds. In the water solutionD-( )-glucose exist as the mixture of five tautomeric forms: the openchain structure and four cyclic forms. Everyone provides one of qualita-23

tive tests. It is necessary to write equilibrium between the open-chainstructure and at least one of cyclic forms of D-( )-glucoseOC3H4HOHH2HOH 4HOH 4OH 4CH 2OH5CH2OHOH4OHHOH4H 4 OHH1OHH2N-CH2-COOH123D-( )-glucose:I. Classification according to the functional groups:1. A hemiacetal;2. A carbonyl group, an aldehyde;3,4,5. Hydroxyl groups:3. A polyhydric vicinal alcohol;4. A secondary alcohol;5. A primary alcohol.II. Classification as bioorganic compound:1. A monosaccharide;2. An aldohexose.Glycine:I.Classificationaccording to the functional groups:1. An amino group, aprimaryaliphaticamine.2. A carboxyl group,carboxylic acid.II.Classification asbioorganic compound:A neutral -amino acid.2) Proposed physical properties: aggregative state (solid or liquid), colour,smell, solubility in the water.D-( )-glucose – solid, white powder, Glycine - solid, white powder, waterwater soluble.soluble.3) The schemes of qualitative reactions for discovery of functional groups inthe investigated compounds and specific reactions for some groups ofcompounds, practical results.D-( )-glucose The qualitative test for discovery of polyhydric vicinal alcohol in thestructure of D-( )-glucose as a monosaccharide.24

CuSO4 2NaOHCu(OH)2 Na2SO4light-blue precipitateCH 2OHO2OH Cu(OH)2OHOHCH 2OHOOHOH-2H2OOHOHOCu 2 D-glucose2The practical result: the dark-blue solution. Qualitative tests for proof of an aldehyde functional group presencein the structure of D-( )-glucose as an aldose.a) The copper mirror reaction with Cu(OH)2:CuSO4 2NaOHCu(OH) 2 Na2SO4light-blue precipitateCH2OHCH2OHOCH2OHOOH Cu(OH)22 OH-2H2OOHOHOHOHOHOHOHD-glucoseCHOHOCu2 Cu2O 2H2OcuprousoxidetoO2OCu2 2D-glucose oxidation productsThe final practical result: brick-red precipitate of cuprous oxide.b) The silver mirror reaction with Tollen’s reagent.AgNO3 NaOHAg2O NaNO3 H2OAg2O NH4OHAg(NH3)2 OHTollen’s reagent25

OCHHOHHOHHOHHOHto 2[Ag(NH3)2] 3OH2Ag 4NH3 2H2OD-glucose oxidation productsCH2OHPractical result: silver coating on walls inside of a test tube (silver mirror).Glycine. The qualitative test for proof that glycine is a neutral -amino acid

The acylating reagents: carboxylic acid anhydride, acid chlorides, carboxylic acids, esters, thioesters. Classification of poly- and heterofunctional compounds. Polyalcohols, dihydric phenols, dicarboxylic acids, amino alcohols, amino phenols, hy-droxy-acids, oxo-acids (aldehyde and keto acids). Examples. Acid-base prop-erties.