SATHYABAMA UNIVERISY DEPT.OF BIOINFORMATICS SBIX4001 - Biochemistry Lab Manual List of Experiments 1. Estimation of Glycine. 2. Estimation of Ascorbic Acid. 3. Estimation of Protein by Biuret Method. 4. Estimation of Protein by Lowry’s Method. 5. Estimation of DNA by Diphenylamine Method. 6. Colorimetric Assay for Salivary Amylase Activity. 7. Colorimetric Assay for Catalase Activity. 8. Estimation of Glucose by Anthrone Method. 9. Qualitative Analysis of Sugars. 10. Qualitative Analysis of Amino Acids. Experiment 1 Estimation of glycine by Sorenson’s Formol Titration AIM: To estimate the amount of amino acid present in the given solution. PRINCIPLE: The acid group present in the glycine can be titrated with NaOH. It is not easy in this case because the amino group present will interfere at the end point. To prevent i t e x c e s s o f f o r m a l d e h y d e i s u s e d b y w h i c h t h e a m i n o g r o u p i s b l o c k e d b y t h e formation of methylene glycine. Then it is titrated with NaOH using phenolphthaleinindicator. REAGENTS REQUIRED: (i) (ii) (iii) (iv) (v) Standard oxalic acid 0.1 N Link solution NaoH Formaldehyde Phenophthalein indicator Amino acid solution PROCEDURE: Standardisation of NaOH Rinse a clean burette first with distilled water and then with the link solution of Na O H. R i n s e a c l e a n 2 0 ml pipette first with distilled water and then with the givenstandard oxalic acid. Pipette out 20ml of oxalic acid into a clean conical flask. Add a few drops of phenolphthalein indicator and titrate against NaOH taken in the burette. Thee n d p o i n t i s th e a p p e a r a n c e o f p e r ma n e n t p a l e p i n k c o l o u r . R e p e a t t h e t i t r a t i o n f o r concordant values. Estimation of Amino acid Make up the given amino acid solution with distilled w a t e r t o 1 0 0 m l i n a volumetric flask, observing the usual precautions. Shake the solution well for uniformconcentration. Pipette out 20ml of amino acid solution into a clean conical flask. Add5 ml of HCHO and keep it for 2 minutes. Then titrate it against the NaOH solution takenin the burette. Phenolphthalein is used as the indicator. The end point is the appearanceof permanent pale pink colour. Repeat the titration for concordant values Blank titration Pipette out 20ml of distilled water in a clean conical flask. Add 5ml of HCHOand keep it aside for a few minutes. Add 1-2 drops of phenolphthalein indicator. Titrateit against the NaOH solution taken in the burette. The end point is the appearance of permanent pale pink colour. Repeat the titration for concordant values. Result: The amount of amino acid present in the whole of the given solution = _______ g EXPERIMENT 2 Estimation of Ascorbic acid AIM: To estimate the amount of Ascorbic acid present in the given solution. PRINCIPLE: Ascorbic acid (Vitamin C) is a strong reducing agent. Ascorbic acid can readily lose two of its hydrogen atoms from the hydroxyl groups on the double bonded enediolcarbons.The titration method for estimation of ascorbic acid is based on an oxidation reduction reaction,in which it reduces the dye 2,6-dichlorophenol indophenols and In turn ,It gets oxidized to dehydro ascorbic acid by 2,6 dichlorophenol indophenol dye. The dye originally blue in colour, gets reduced to a colourless form,and at the end of the titration ,when no more of ascorbic acid is available for the reduction of the dye, the excess oxidized dye in the acidic solution imparts a faint pink colour to the titration mixture. REAGENTS REQUIRED: Standard Indophenol solution 42mg of sodium bicarbonate and 52mg of 2, 6 dichlorophenol indophenol were dissolved in 50ml of water and diluted to 200ml. The solution was filtered and stored. Standard Ascorbic acid o 50mg ascorbic acid was dissolved and made up to 250ml using 0.6% oxalic acid. Preparation of test solution o Given solution was made up to 100ml with 0.6% oxalic acid. o PROCEDURE: Titration I: Standardisation of dye The burette was rinsed and filled up to the convenient mark with dye solution. 10ml of std ascorbic acid solution was pipetted out into a clean conical flask. It was titrated against the dye taken in the burette. The end point was the appearance of permanent pale pink colour which remains for 10 minutes. The titrations were repeated for concordant value. The dye equivalent of std ascorbic acid was calculated. Titration II: Estimation of Ascorbic acid 10ml of made up solution was pipetted out into a clean conical flask. It was titrated against the dye taken in the burette, till the permanent pale pink colour was obtained. The titrations were repeated for concordant value. Using the dye equivalent of ascorbic acid, the amount of ascorbic acid in the given solution was calculated. RESULT: - The amount of ascorbic acid present in 100ml of given solution=_______mg EXPERIMENT 3 Estimation of Protein by Biuret method Aim: To estimate the protein using Biuret method. Principle: The –CO-NH- bond (peptide) in polypeptide chain reacts with copper sulphate in an alkaline medium to give a purple which can be measured at 540 nm. Reagents Required: 1. Biuret Reagent: Dissolve 3 g of copper sulphate (CuSO4.5H2O) and 9g of sodium potassium tartarate in 500 ml of 0.2 mol/lttre sodium hydroxide; add 5 g of potassium iodide and make up to 1 litre with 0.2 mol/litre sodium hydroxide. ProteinStandard:5 mg BSA/ml. Apparatus and Glass wares required:Test tubes, Pipettes, Colorimeter, etc., Procedure: Pipette out 0.2, 0.4, 0.6, 0.8 and 1 ml of working standard in to the series of labeled test tubes. Pipette out 1 ml of the given sample in another test tube. Make up the volume to 1 ml in all the test tubes. Atube with 1 ml of distilled water serves as the blank. Now add 3 ml of Biuret reagent to all the test tubes including the test tubes labeled 'blank' and unknown'. Mix the contents of the tubes by vortexing / shaking the tubes and warm at 37 ºC for 10 min. Now cool the contents and record the absorbance at 540 nm against blank. Then plot the standard curve by taking concentration of protein along X-axis and absorbance at 540 nm along Y-axis. Then from this standard curve calculate the concentration of protein in the given sample. Result: The given unknown sample contains ----μ g protein/ml S.No Contents Blank S1 Volume of Working Standard 1 Solution (ml) ----Concentration of working standard 2 (µg) ----3 Volume of Unknown Solution (ml) 4 Volume of Distilled Water (ml) 3 Volume of Biuret solution 5 (ml) 7 Optical density at 540nm 0.2 Standards S2 S3 S4 0.4 0.6 0.8 Test Solution T1 T2 S5 1 ----- ----- 50 100 150 200 250 1 0.8 3 0.6 3 0.4 3 0.2 ---3 3 0.5 1 0.5 ---3 3 EXPERIMENT 4 ESTIMATION OF PROTEIN BY LOWRY’S METHOD. AIM: To estimate the amount of protein present in the given unknown solution by Lowry‟s method. PRINCIPLE: The aromatic amino acids tyrosine and tryptophan present in the protein sample reacts with folin‟s phenol reagent to give a blue color complex. The color intensity was measured colorimetrically at 620nm. REAGENTS REQIRED: 1. Stock solution: 100mg of BSA (Bovine Serum Albumin) is made up to 100ml with distilled water in SMF. 2. Working standard solution: 10ml of stock standard is made up to 100ml with distilled water in SMF. 3. Alkaline copper reagent: Solution A: 2% Sodium carbonate in 0.1N Sodium hydroxide Solution B: 0.1% Copper sulphate in 1% Sodium potassium tatrate 4. Mix 50ml of solution A with 1ml of solution B prior to use. 5. Folin‟s phenol reagent: Dilute the reagent with water in 1:2 ratio. PROCEDURE: 0.5, 1.0, 1.5, 2.0 and 2.5ml of the working standard solution of protein is pipetted out into a clean dry test tube marked as S1 to S5 respectively. The given unknown solution is diluted to 100ml using distilled water, from that take 0.5 and 1.0ml into the test tube marked as T1 and T2. The final volume is made up to 2.5ml with distilled water. 2.5ml of distilled water serves as blank. Add 4.5ml of Alkaline copper reagent and 0.5ml of folin‟s reagent to all the tubes. The contents are mixed well and kept it in a room temperature for 30min‟.The intensity of color developed is read colorimetrically at 620nm. A standard graph is drawn from the obtained values. From the graph the amount of protein present in the given unknown solution is calculated. S.No Contents Blank S1 Standards S2 S3 S4 S5 Test Solution T1 T2 Volume of Working Standard 1 Solution (ml) ----0.5 1 1.5 2 2.5 ----- ----Concentration of working standard (µg) 2 ----50 100 150 200 250 3 Volume of Unknown Solution (ml) 0.5 1 4 Volume of Distilled Water (ml) 2.5 2 1.5 1 0.5 2 1.5 Volume of Alkaline Copper Solution 5 (ml) 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 6 Volume of Folin's Reagent (ml) 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 Keep all the tubes in room temperature for 30 Minutes 7 Optical density at 620nm RESULT: Amount of protein present in the given unknown sample is _________mg/100ml EXPERIMENT 5 ESTIMATION OF DNA BY DIPHENYLAMINE METHOD. Aim: To estimate the DNA content of the given unknown solution by diphenylamine method. Principle: The Reaction is specific for deoxyribose .Deoxypentose on acid hydrolysis forms dihydroxy linoleic acidwhich is ablue coloured complex compound. Inthisreaction,thedeoxyribose of the purine nucleotide alone react.The value obtained therefore represents only one halfofthe value ofthedeoxyribose present. Reagents Required: 1. Phosphoric acid 2. Diphenylamine 3. Standard DNA Solution: 20mg of DNA was dissolved in 100ml of Trichloroacetic acid and was heated in a boiling waterbath for 10minutes l Procedure: 0.4 to 2ml of working DNA solution of concentration range of 40 ug to 200ug was pippetted out in a 5 different test tubes and marked as S1 to S5.1.0 and 2ml of unknown DNA solution were taken in another 2 test tubes worked as T1 and T2.The volumes of all test tubes were made up to 2.0 ml using distilled water.Then 4ml of the diphenylamine reagent was added to all the test tubes . A blank was simultaneously prepared using 2.0 ml of distilled water and 4mlof diphenylamine reagent.The test tubes were treated in a boiling waterbath for 10minutes and then cooled. The blue colur developed was read using colorimeter at 620nm. A standard graph was drawn with optical density on the y axis and concentration on X axiss.Fromthisgraph,the amount of DNA graph present in unknown solution can be determined. Result: The amount of DNA present in the given unknown solution is __________mg/dl S.No Contents Blank Standards S2 S3 S4 S1 Volume of Working Standard 1 Solution (ml) ----0.4 0.8 1.2 1.6 2 Concentration of standard (µg) ----3 Volume of Unknown Solution (ml) 4 Volume of Distilled Water (ml) 2.0 1.6 1.2 0.8 0.4 Volume of diphenyl amine reagent 4.0 4.0 4.0 4.0 5 (ml) 4.0 Keep all the tubes in boiling water bath for 10 Minutes 6 Optical density at 620nm S5 Test Solution T1 T2 2.0 ----- ----- 4.0 1.0 1.0 4.0 2.0 4.0 EXPERIMENT 6 EFFECT OF PH ON THE ACTIVITY OF SALIVARY AMYLASE Aim To determine the optimum PH for salivary amylase. Principle Amylase present in salivary secretion hydrolysis α1,4-linked D-Glucose units and produce maltose as a final product. Materials required 1. Substrate 2. Activator 3. Inhibitor 4. Buffer Solution A water. Solution B water. :1% Starch solution :1% Sodium chloride :2N Sodium hydroxide :Phosphate buffer : 0.2m Disodium hydrogen phosphate-28.392g/1000ml distilled : 0.2m Sodium dihydrogen phosphate-31.202g/1000ml distilled S.No Solution A(ml) Solution B(ml) PH 1. 6.5 93.5 5.7 2. 18.5 81.5 6.2 3. 49.0 51.0 6.8 4. 84.0 16.0 7.5 5. 94.7 5.3 8.0 5. Dinitro salicylate:30g of sodium potassium tatrate, 1g of 3,5- Dinitro salicylate and 1.6g of sodium hydroxide is weighed and made upto 100ml 6. Enzyme source :1ml of saliva is diluted to 20ml. Procedure A set of testtubes marked as ET and EB are taken. Add 2.5ml of buffer (prepared at various PH ), 2.5ml of substrate followed by 1ml of activator to all the tubes, the tubes are then preincubated at 37’ C for 10min. Add 0.5ml of enzyme to tubes marked as ET and incubated at 37’ C for 15min, then the reaction is arrested by adding 0.5ml of sodium hydroxide, then add 0.5ml of enzyme to the test tube marked as EB, then 0.5ml of DNS is added to all the test tubes. The colour developed is read at 540nm RESULT The optimum PH for salivary amylase is _____________ S.No Contents B 5.7 1. 6.8 7.5 8.6 Volume of buffer 2.5 2.5 (ml) 2. Volume of 2.5 2.5 substrate(ml) 3. Volume of 1.0 1.0 Activator(ml) Preincubate all the tubes at 37’ C for 10min 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 4. Volume of 0.5 Dis.water(ml) 5. Volume of Enzyme (ml) Incubate all the tubes at 37’ C for 15min - - - - - - - 0.5 - 0.5 - 0.5 - 0.5 6. 7. 8. Volume of NaoH (ml) Volume of Enzyme (ml) Volume of DNS (ml) 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 - 0.5 - 0.5 - 0.5 - 0.5 - 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 Keep all the tubes in boiling water bath for 5min 9. 10. Optical density at 540nm Difference in OD EXPERIMENT 7 Estimation of catalase activity (CAT) (EC 1.11.1.6) Catalase (CAT) scavenges highly toxic H2O2 produced in several reactions in the cell, thus preventing injury to metabolic machinery of the tissue. It detoxifies H2O2 without consuming cellular reducing equivalents and provides cell with energy efficient mechanism to remove H2O2. It is found abundantly in plant tissues and its activity is associated with peroxisomes where, it removes H2O2 produced during photorespiration. Reagents 1. Assay buffer: 0.1 M potassium phosphate buffer (pH 7.0) 2. 0.2 M H2O2 3. Dichromate reagent: Prepare 5% potassium dichromate. Mix it with glacial acetic acid in the ratio of 1:3 Procedure 1. To 0.55 ml of 0.1 M potassium phosphate buffer (pH 7.0), add 0.4 ml of 0.2 M H2O2 and 50 μl of enzyme extract. Mix thoroughly and incubate for one minute.3. Add 3.0 ml of 5% potassium dichromate: acetic acid (1:3) solution to it. . Run a control containing 0.6 ml assay buffer and 0.4 ml of 0.2 M H2O2 without enzyme extract along with the samples. Keep the tubes in boiling water bath for 10 min, cool and record the absorbance at 570 nm using dichromate: acetate solution as blank. 2. Subtract the absorbance of samples from that of control and calculate the amount of H2O2 from the standard curve. One CAT unit is defined as amount of enzyme required to consume one μmol of H2O2 min-1 or mg-1 protein. EXPERIMENT 8 Determination of Total Carbohydrate by Anthrone Method PRINCIPLE Carbohydrates are first hydrolysed into simple sugars using dilute hydrochloric acid. In hot acidic medium glucose is dehydrated to hydroxymethyl furfural. This compound forms with anthrone a green coloured product with an absorption maximum at 630 nm. MATERIALS 2.5 N HCl Anthrone reagent: Dissolve 200 mg anthrone in 100 mL of ice-cold 95% H2SO4. Prepare fresh before use. Standard glucose: Stock—Dissolve 100 mg in 100 mL water. Working standard—10 mLof stock diluted to 100 mL with distilled water. Store refrigerated after adding a fewdrops of toluene. PROCEDURE 2. Weigh 100 mg of the sample into a boiling tube.Hydrolyse by keeping it in a boiling water bath for three hours with 5 mL of 2.5 N HCl and cool to roomtemperature.Neutralise it with solid sodium carbonate until the effervescence ceases.Make up the volume to 100 mL and centrifuge.Collect the supernatant and take 0.5 and 1 mL aliquots for analysis.Prepare the standards by taking 0, 0.2, 0.4, 0.6, 0.8 and 1 mL of the working standard.'0' serves as blank.Make up the volume to 1 mL in all the tubes including the sample tubes by adding distilled water.Then add 4 mL of anthronereagent.Heat for eight minutes in a boiling water bath.Cool rapidly and read the green to dark green colour at 630 nm. Draw a standard graph by plotting concentration of the standard on the Xaxis versus absorbance on the Y-axis.From the graph calculate the amount of carbohydrate present in the sample tube. S.No 1 2 3 4 5 7 Contents Blank B S1 Standards S2 S3 S4 Volume of Working Standard Solution (ml) ----0.2 0.4 0.6 0.8 Concentration (µg) ----20 40 60 80 Volume of Unknown Solution (ml) --------- ---- ----- ----Volume of Distilled Water (ml) 1.0 0.8 0.6 0.4 0.2 Volume of Anthrone Reagent (ml) 4.0 4.0 4.0 4.0 4.0 Keep all the tubes in boiling water bath for 10 Minutes Optical density at 620nm S5 Test Solution T1 T2 1.0 100 --------4.0 --------0.2 0.8 4.0 CALCULATION Amount of carbohydrate present in 100 mg of the sample = (mg of glucose / volume of test sample) X 100 NOTE: Cool the contents of all the tubes on ice before adding ice-cold anthrone reagent. EXPERIMENT 9 Qualitative Analysis of Carbohydrates No. 1 Test Molisch’s Test 2-3 drops of betanaphthol solution are added to 2ml of the test Observation Inference A deep violet coloration is produced Presence of at the junction of two carbohydrates. layers. --------0.4 0.6 4.0 solution. Very gently add 1ml of Conc. H2SO4 along the side of the test tube.. Iodine test Presence of polysaccharide. 4-5 drops of iodine Blue colour is observed. solution are added to 1ml 2 of the test solution Absence of No Blue colour is polysaccharide andcontents are mixed observed. gently. Fehling's test About 2 ml of sugar A red precipitate is solution is added to about formed 2 ml of Fehling’s solution taken in a test-tube. It is No red precipitate is then boiled for 10 min formed Presence of reducing sugar Absence of reducing sugar Benedict’s test 4 To 5 ml of Benedict's solution, add 1ml of the test solution and shake each tube. Place the tube in a boiling water bath and heat for 3 minutes. Remove the tubes from the heat and allow them to cool. Formation of a green, red, or yellow precipitate Presence of reducing sugars No formation of a green, red, or yellow precipitate Absence of reducing sugars Barfoed’s test 5 To 2 ml of the solution to be tested added 2 ml of freshly prepared Barfoed's reagent. Place test tubes into a boiling water bath and heat for 3 minutes. Allow to cool. A deep blue colour is formed with a red ppt. settling down at the bottom or sides of the test tube. Presence of reducing sugars. Appearance of a red ppt as a thin film at the bottom of the test tube within 3-5 min. is indicative of reducing monosaccharide. If the ppt formation takes more time, then it is a reducing disaccharide. Seliwanoff test To 3ml of ofSeliwanoff’s reagent, add 1ml of the test solution. Boil in A cherry red colored water bath for 2 minutes precipitate within 5 minutes is obtained. Presence of ketoses [Sucrose gives a positive ketohexose test ] 6 No cherry red colored solution formed Absence of ketoses . 7 Bial's test Add 3ml of Bial’s reagent A blue-green product to 0.2ml of the test solution. Heat the solution in a boiling water bath for A muddy brown to gray 2 minutes. product Presence of pentoses. Presence of hexoses. 8 Osazone Test Two two ml of the test solution, add 3ml of phenyl hydrazine hydrochloride solution and mix. Keep in a boiling water bath for 30mts. Cool the solution and observe the crystals under microscope. Formation of beautiful yellow crystals of osazone Needle shaped crystals Hedgehog crystals Sunflower shaped crystals Glucose/fructose Presence of lactose Presence of maltose EXPERIMENT 10 Qualitative Analysis of Amino Acid S.NO Experiment 1 Ninhydrin Test: To 1ml of amino acid solution taken in a test tube, add few drops of ninhydrin reagent and vortex the contents. Place the test tube in a boiling water bath for 5 minutes and cool to room temperature. 2 Inference Indicates the presence of alpha amino acids The colourof the solutionchanges to orange Indicates the presence of aromatic amino acids The appearance of Indicates the Indicates the presences of imino acids Xanthoproteic acid Test: To 1ml of the amino acid solution taken in a test tube, add few drops of nitric acid and vortex the contents. Boil the contents over a Bunsen flame, using a test tube holder, for few minutes. Cool the test tube under running tap water and add few drops of alkali. 3 Observation Observe the colour of the solution. If the colour of thesolution is blue, And if the colour ofsolution is yellow, Pauly'sdiazo Test: Take 1ml of sulphanilic acid reagent in a test tube and chill the contents in a small ice bucket. Add few drops of prechilled sodium nitrite solution and vortex. Add immediately few drops of pre chilled amino acid solution and vortex. This is followed by dropwise addition of sodium carbonate solution until the color appears. 4 The colour of the solution in the test tube changes to blue This indicates the presence of Histidine purple-violet ring appears in the test tube Indicates the presence of tryptophan . Sakaguchi Test: To 1 ml of prechilled amino acid solution and few drops of NaOH is mixed and 2 drops of alpha naphthol is added. Mix thoroughly and add 4-5 drops of hypobromite reagent and observe. 8 Indicates the presence of tyrosine Hopkins-Cole Test: Mix 1 ml of the amino acid solution with 1 ml acetic acid – glyoxilic acid reagent, in a test tube, vortex. Then carefully, add conc. Sulphuric acid along the side of the test tube, keeping the tube in an inclined position (do not shake the test tube , while adding acid) 7 The colour of the solution in the test tube changes to red Histidine Test: To 1ml of amino acid solution, add 5% bromine in 33% acetic acid until an yellow color was formed. After 10 minutes, add 2ml of 5% ammonium carbonate solution and placed in a boiling water bath for 10 minutes. 6 presence of histidine and tyrosine Millon's Test: To 1ml of the amino acid solution in a test tube, add few drops of millon’s reagent and vortex. Boil the contents over a Bunsen flame for 3 – 5 minutes. Cool the contents under running tap water and add few drops of sodium nitrite solution. 5 red colour during the addition of sodumcarbonate solution Lead sulphide Test: The color of the solution in the test tube changes to red Indicates the presence of arginine A black precipitate appears in the test tube Indicates the presence of Cysteine To 1ml of the amino acid solution taken in The content of the a test tube, add few drops of sodium test tube changes to hydroxide (5N), followed by addition of few red colour drops of glycine (1%) and 10% sodium nitroprusside solution and vortex. Place the test tube in a hot water bath, maintained at 40°C, for 15 minutes. Cool the test tube in ice cold water for 5 minutes and add 0.5ml of 6N HCl. Vortex the contents and allow to stand for 15 minutes at room temperature. Indicates the presence of Methionine To 1ml of the amino acid solution taken in a test tube, add few drops of sodium hydroxide (40%) and boil the contents for 5 – 10min over a bunsen burner. Cool the contents and add few drops of 10% Lead acetate solution and observe. 9 Folin's McCarthy Sullivan Test: