SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. ___/___/2005 ________________________ (Student Name) Assignment sheet: Organic molecules 1. Benedict’s Test for Reducing Sugars One of the most common reagents for testing for the presence of mono-sugars, such as glucose or maltose, is Benedict’s reagent. Monosaccharides and some disaccharides are able to add (donate) electrons to reduce other molecules. These sugars are called reducing sugars. These sugars have a free aldehyde group or a free ketone group in close proximity to one or more hydroxyl groups (-OH). The hydroxyl groups serve as the source of electrons. A reagent which becomes easily reduced in the presence of “reducing sugars” is Benedict’s reagent. When a Benedict's solution is heated in the presence of a reducing sugar, the copper ions are reduced to metallic copper. As a consequence of this chemical reaction, the color of the product changes from blue to green to yellow to reddish-orange, depending on the amount of reactive sugar present. An orange and red color change indicate the highest concentration of these sugars. The Benedict’s test will only show a positive reaction for starch if the starch polymer has been broken down into maltose or glucose units by excessive heating. Test the following solutions and substances below for the presence of reactive sugars with the help of Benedict’s reagent following the Procedure A as outlined on the “Biomolecules” website. Formulate a hypothesis to predict your expected experimental findings, perform the experiment and record your findings in the Results Table below. Results Table I: Benedict’s Test Tested Solution or Substances Hypothesis Experimental Finding [ Color before boiling ] Experimental Finding [ Color after boiling ] Water Starch Glucose Maltose Sucrose Diluted Honey Onion Juice 1 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Potato Slice Paper (slurry or pulp) Milk Other 2. Lugol’s Test for Starch Lugol’s reagent (I2KI solution) changes its color from yellowish-brownish color to intense blue-black in the presence of the polysaccharide starch, but there is no color change in the presence of mono- or disaccharides. This test does NOT require a heating of the samples under investigation. Test the following solutions and substances below for the presence of starch with the help of Lugol’s reagent following the Procedure B as outlined on the “Biomolecules” website. Formulate a hypothesis to predict your expected experimental findings, perform the experiment and record your findings in the Results Table below. Results Table II: Lugol’s Test for Starch Tested Solution or Substances Hypothesis Experimental Finding [ Color before boiling ] Experimental Finding [ Color after boiling ] Water Starch Glucose Maltose Sucrose Diluted Honey Onion Juice Potato Slice Paper (slurry or pulp) Milk 2 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. 3. Testing for Lipids Lipids are members of a rather heterogeneous group of organic molecules that share the characteristic that they all are very hydrophobic and all are only soluble in organic solvents, such as chloroform or hexane. Although lipids include fats (triglycerides), steroids, and phospholipids, this lab’s exercise will focus primarily on tests proofing the presence of fats in a sample. Triglycerides (TGs), a popular topic in discussions about diets, nutritional ingrediences, overweight and obesity, are the most common biological form of fats in biological organisms, especially animals. Due to the heavily saturated character of their fatty acids, fat molecules form solid structures, e.g. lard, at room temperature. Triglycerides are primarily found in form of intracellular droplets in fat cells (= adipocytes) of adipose tissue. TGs store more energy per gram than any other types of biomoleules. Lipids, which contain unsaturated fatty acids in varying degree (especially the ones found in plants) appear as viscous liquids, often referred to as oils, at room temperature. Vegetable oils is a mixture of triglycerides containing a high proportion of unsaturated fatty acids. In this lab you will test different samples for the presence of lipids and fats applying the simple “grease spot test” and using the more specific reagent Sudan IV, a nonpolar dye with a high affinity for the nonpolar fats and lipids. Sudan IV, in the presence of lipids and fats, forms small intensively red colored precipitates in the samples under test. Test the following solutions and substances below for the presence of lipids and fats using a piece of unglazed brown paper (“Grease Spot Test”) and with the help of the Sudan IV reagent following the Procedure C as outlined on the “Biomolecules” website. Formulate a hypothesis to predict your expected experimental findings, perform the experiment and record your findings in the Results Table below. Results Table III: Testing for Lipids & Fats Tested Solution or Substances Hypothesis Experimental Finding [ Grease Spot Test ] Experimental Finding [ Sudan IV Test ] Water Onion Juice Diluted Honey Potato Juice Hamburger Juice or Lard Vegetable Oil Egg Yolk 3 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. just write “positive reaction” or “negative reaction” into the Results Columns 4. Testing for Proteins & Amino acids Proteins are biological components that are made up of one or more highly folded and coiled polypeptides. Polypeptides are linear polymers made up from serial linkage of smaller molecules called amino acids. Polypeptide chains are formed when amino acids are joined together by peptide bonds between the amino group of one amino acid and the carboxyl group of a second amino acid (see the Introductory part of the “Biomolecules” Bio210A lab section on my website). 4.1. - Testing for Proteins with Biuret Reagent or Coomassie Blue Stain Scientists discovered many molecules and dyes, such as Coomassie Blue stain or Biuret Reagent (see Figure below), which specifically interact or chemically react with proteins to confer a color change O C H2N O N C N2H H Biuret Reagent (= Carbamoylurea) Expected result (after SDS-PAGE & Protein staining) H3C – CH2 N CH2 _ SO3 Na+ Protein Binding H3C _ SO3 C H3C – CH2O N H H3C + N CH2 H3C – CH2 Coomassie Brilliant Blue G-250 sensitive protein staining dye detects > 5ng protein in PA gels Stained proteins Names of separated proteins 4 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. - - - The Biuret Reagent you will be working with in this lab part reacts with peptide bonds – and therefore with proteins such as ovalbumin or actin, but not with free amino acids Biuret reagent is light blue, but in the presence of proteins (long-chain polypeptides) it will turn violet after about 2-5 minutes incubation at room temperature; in the presence of short-chain polypeptides it will turn pink Test the following solutions and substances below for the presence of proteins and polypeptides with the help of the Biuret Reagent following the Procedure D as outlined on the “Biomolecules” website. Formulate a hypothesis to predict your expected experimental findings, perform the experiment and record your findings in the Results Table below. Results Table IV: Testing for Proteins Tested Solution or Substances Distilled water Hypothesis Color with Biuret Reagent [ after 2 min ] Conclusion Protein present (+) Protein absent (-) Ovalbumin Diluted Honey Potato Starch Bovine Serum Albumin (BSA) Glucose Solution Egg Yolk Amino Acid Solution 5 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. 4.2. - Testing for Amino Acids with Ninhydrin Reagent A very popular and specific chemical reagent which is commonly used, e.g. in forensic science and clinical research, to detect free amino acids is Ninhydrin (see Figure below) Ninhydrin Amino acid (1,2,3-indanetrione monohydrate) Heat Purple/Violet-colored Reaction product (conjugated ring system) - - The Ninhydrin reagent reacts with the free amino group (-NH2) of amino acids, after which it forms a purple/violet-colored reaction product; it does not lead to a color reaction in the presence of polypeptide chains and proteins Due to the unique ring-structure of the amino acid proline (see Figure below), Ninhydrin reacts differently and forms a cobalt-yellow reaction product COOH H2C CH N H H2C CH2 Proline COOH H2N C H COOH H2N C CH2 CH2 OH CH Serine H3C H CH3 Leucine 6 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. - Test the following solutions labeled A, B, C and D on your work bench and for the presence of free amino acids with the help of the Ninhydrin reagent following the Procedure E as outlined on the “Biomolecules” website. Formulate a hypothesis to predict your expected experimental findings, perform the experiment and record your findings in the Results Table below. Results Table V: Ninhydrin Test for Free Amino Acids Tested Solution Final Color with Ninhydrin Amino Acid Present (+) or Absent (-) (Type of molecule in Solution) Distilled water A B C D 4.3. Identification of Amino Acids using Paper Chromatography While Ninhydrin in the previous experimental part was only able to tell the presence or absence of an amino acid in a given sample, the following method, called paper chromatography (from Greek: chromos = color & grapheion = drawing), you will be using in the last part of this “Biomolecules” lab, will allow you to identify a specific amino acid in a sample (Make sure that you have read the paper chromatography introduction and procedure section of the “Biomolecules” page on my website before you start with the experiment!) The 20+ amino acids found in living organisms can be classified in three major types based on the chemical properties of their R-groups (see Figure below): 1. Non-polar - amino acids with an R-group composed of an unsubstituted hydrocarbon chain 2. Polar uncharged - amino acids with R-groups composed of a substituted group , usually non-ionized (no positive or negative net charge) 3. Polar acidic - amino acids which R-groups contain an acidic (- COO- H+) group which confers a net negative charge in an aqueous milieu 4. Polar basic - amino acids which R-groups contain a basic (- NH3+) group which confers a net positive charge in an aqueous milieu 7 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Different R-groups and polarity of selected amino acids COOH H2N C COOH COOH H H2N CH2 C H H2N CH2 CH H3C C H OH (nonpolar) Tyrosine (nonpolar) CH2 CH2 Glutamate (polar, charged) acidic COOH H2C H2C CH N H CH2 C CH2 _ Leucine H2N CH2 COO CH3 COOH H CH2 + CH2 – NH3 Lysine (polar, charged) basic COOH H2N C H CH2 OH Proline (nonpolar) Serine (polar, uncharged) Depending on the chemical nature of the R-group of an amino acid, different amino acids will be more or less soluble in non-polar (or hydrophobic) solvents, such as chloroform, acetone, hexane or esters, whereas polar (= amino acids with net electrical charges) will be more soluble in polar solvents, such as water. Paper chromatography exploits these subtle differences in solubility of amino acids in different solvents and allows separation of mixtures of amino acids according to chemical nature and size. Sort the 20 known amino acids according to the chemical nature of their R-groups (polar, unpolar, etc.) and their expected solubility in a non-polar solvent into the Table VI below (Use your Biology text book and the info above to complete the Table below) 8 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Table VI: Chemical properties of amino acids Chemical property Amino acid Solubility Non-polar Polar uncharged Polar acidic Polar basic Based on your understanding of the ascending paper chromatography method and your knowledge of the chemical properties of the 20 amino acids, which amino acid(s) would be found rather at the top of the chromatogram (= would have run with the non-polar solvent to the top)? ______________________________________________________________________ ______________________________________________________________________ After separation of the amino acids in your mixture with the help of the paper chromatography method and spraying of your (dried) chromatography paper with the Ninhydrin solution (following the lab procedure), you will identify the separated amino acids by calculating the Rf values for the individual amino acid spots observed with your sample and compare these Rf values with the calculated Rf values of the simultaneously applied and separated 4 “known” amino acid (= internal) standards. Write down the names of your amino acid standards (your “knowns”) below. Regarding their chemical properties to which type of amino acid to they belong? Amino acid standard 1: ___________________________________ Amino acid standard 2: ___________________________________ Amino acid standard 3: ___________________________________ Amino acid standard 4: ___________________________________ 9 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Based on the chemical structures of your amino acid standards, formulate a hypothesis about the expected differences in their migration behavior as measured by ascending paper chromatography using a non-polar solvent. Hypothesis: ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ After you developed your chromatogram with the help of the Ninhydrin Reagent, (1) observe the color of each of your spots and (2) calculate the individual Rf values for each of the spots you observe on your paper. Write your observations and the numbers of the Rf values into the Result Table VII below and do you final result analysis. Remember: The Rf value is the ratio of the distance traveled by a compound in a given solvent to the distance traveled by the solvent in the same time. Use following formula below to calculate your individual Rf values of your spots. Rf = distance of spot from origin of application distance of solvent (solvent front) from origin of application Calculations: 10 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Result Table VII: Paper chromatography & Amino acid identification Spot No. Color Rf value Amino Acid (from bottom) Standard Amino acid 1 Amino acid 2 Amino acid 3 Amino acid 4 Sample #1 Spot 1 Spot 2 Spot 3 Spot 4 Sample #2 Spot 1 Spot 2 Spot 3 Spot 4 Compare the Rf values for your internal standards (= amino acid 1 – 4) and of your unknowns mixture. Identify and record the names of the identified amino acids into the Results Table VII above. Do you have (an) amino acid(s) in your samples which Rf values did not correspond with the Rf values of your internal standards? If yes, speculate about the identity and chemical properties of this(these) amino acid(s) based on (1) color and (2) the running behavior during paper chromatography and the calculated Rf value. Which amino acid(s) could it be? How could you proof your case? 11 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. 5. Testing for Components of an Unknown Solution In this last section of this “Biomolecules” lab you will apply your now gained knowledge about molecules and the different tests to proof their presence to identify the presence of biomolecules in unknown solutions. We brought in a couple of commercial products and food samples into this lab today, all of which contain a variety of compounds available for testing with the methods and dyes you learned to use in the previous lab sections. Procedure: 1. Use the reagents, methods and procedures from the previous exercises and identify the kinds of molecules contained in these unknown solutions. 2. Formulate a hypothesis and predict what you might expect to find for each test (positive or negative result) based on your knowledge of the commercial product and/or food source and the tests performed during this lab section. (Your instructor will tell you which samples you will be testing) - if your food sample has a food label you may use this piece of information to form an adequate hypothesis 3. Conduct all tests according to the directions and procedures in Exercises 1 – 4, record your experimental outcomes (findings) into the Results Table VIII below. - make sure that all tests have a suitable negative control to be able to clearly discriminate between a positive reaction - avoid cross-contaminations between different bottles and solutions by using separate and clean pipettes for each individual test - never insert any of the pipettes you use during the test set-ups into the stock solution containing your “Unknowns”! 12 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Results Table VIII. Sample # 1 2 3 Hypothesis Applied Test Benedict’s Lugol’s Biuret Ninhydrin Sudan IV Sample Identification 13 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. 6. Lab Summary Questions & Exercises ________________________ (Student Name) (Completion of the summary questions below are a mandatory part of your weekly lab report; answer the questions below and turn the stapled sheets back to your instructor at the beginning of the next lab session) Q. 1: Which part of the sugar actually reacts with Benedict’s reagent? Make a drawing to show the actual chemical reaction of the Benedict’s reagent with the critical functional group of the reactive sugar. Q. 2: Why does starch (under testing conditions) not react with Benedict’s reagent and show a color change? Q. 3: Under which circumstances or experimental conditions (if at all) would you expect a reaction of Benedict’s reagent with starch? Describe an experimental set-up which would lead to a positive reaction of starch with Benedict’s Reagent. Q. 4: Would you expect a reaction of acid (HCl)-treated paper (cellulose) with Benedict’s reagent? Why or why not! 14 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 5: You examine an acid-hydrolyzed protein solution with the Benedict’s reagent and – after performing the test – and find a positive reaction (= color change) with this sample. What happened? How would you interpret this surprising experimental finding? (Hint: Think of post-translational modification of proteins) Q. 6: Describe in your own words the chemical reaction of Lugol’s Reagent with starch and discuss the specificity of this reagent regarding polysaccharides. Q. 7: What is the major ingredient of Lugol’s reagent? A) potassium B) iodoacetamide C) iodine D) indophenol E) phenolred Q. 8: You observe with a sample withdrawn from a starch solution that Lugol’s Reagent surprisingly does not lead to a color change even though the same amount of a sample withdrawn two hours earlier (and tested at the same temperature and conditions) showed a strong reaction with the starch-reactive reagent. Explain this finding. The presence of which of the following enzymes (as a contaminant in the starch solution) or conditions may explain the experimental finding described under 8.) A) cellulase contamination B) amylase contamination C) beta-glucosidase contamination D) the starch solution was heated at high temperature after withdrawal of the first sample E) hemicellulase contamination F) any of the above 15 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 9: List the substances which did not react the with Sudan IV dye and explain your findings. Why and how does Sudan IV work as an indicator dye for fats? Q. 10: Look at the chemical structures below and answer the following questions: H3C 1 COOH H3C 2 COOH b H2C OH HC OH H2C OH 4 H3C 3 COOH a O H3C C O H3C CH2OH OH O 5 a. Which of the following molecules show(s) (a) fatty acid(s)? Name it/them. ___________________________________________________________ b. Which molecules above show (a) lipid(s)? ___________________________________________________________ c. Which of the following molecules depict an unsaturated fatty acid? ___________________________________________________________ d. Which ones is/are unsaturated fatty acids? ___________________________________________________________ 16 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. e. Which of the molecules above are used by cells to build up a fat molecule? Draw the end result of the chemical reaction leading to a fat molecule. Circle or high-light the functional groups involved in the chemical reaction. f. What is the name of the molecule shown above depicted by number 5? Mark the lipophilic and hydrophilic sections of this molecule using two different colored high-lighting markers. ____________________________________________________________________ g. Is molecule 5 a lipophilic molecule. Argue your answer. Would molecule 5 react with Sudan IV dye? _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Q. 11: You are involved in a clinical study which investigates the effect of an investigative antiobesity drug on humans. You want to see whether the drug lead to a reduction of fat deposits in the test persons over the investigative time period. Which of the following tissue samples, cell types and test dye would you use and examine to answer your question. A) muscle tissue – myocyte – Lugol’s reagent B) fat tissue – adipocyte – Biuret Reagent C) fat tissue – adipocyte – Sudan Red or Sudan IV D) nervous tissue – neurons – Sudan Red or Sudan IV E) blood – erythrocyte – Benedict’s Reagent Q. 12: What did you learn about the specificity of the Biuret reagent? 17 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 13: You examine a freshly extracted solution from a newly discovered tropical fruit for the presence of proteins and observe a strong purple color change in the presence of Biuret reagent. You leave the solution on the bench and repeat the experiment the next day again to confirm your earlier finding. To your surprise you only get a very weak pinkish color reaction after addition of Biuret reagent to your solution. What happened? Explain this finding and come up with (a) solution(s) to avoid an experimental outcome like this in future experiments. Q. 14: Would the use of Coomassie Blue stain instead of Biuret reagent have avoided the problem encountered under Q. 13? Argue your answer. Q. 15: With which part (functional group) of an amino acid does Ninhydrin react during the heating step of the procedure? A) the carboxyl group B) the amino group C) the hydroxyl group D) the R-group Q. 16: Is Ninhydrin able to react with any part of a polypeptide chain? If yes, with which part? If yes, why can Ninhydrin reagent NOT be used as a protein staining dye? Argue. Q. 17: Ninhydrin reacts with a solution of an amino acid mixture and turns the liquid purple. Could proline be one of the amino acids in the mixture? Yes _______ , because ___________________________________________ No 18 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 18: How could you find out whether the amino acid mixture in Q. 17: contained proline? Q. 19: Several individual unknowns are tested to determine the type of molecules present in the samples. Given the completed results table below, indicate whether unknowns 1 through 5 contain protein, reducing sugars, starch, lipid or free amino acid (+ = positive result = molecule present) Results Table Sample Benedict’s Reagent Lugol’s Reagent Biuret Test Ninhydrin Test Sudan IV Test + - + - + + + + - 1 2 3 4 5 Answer (Molecules present) Q. 20: An FDA lab examines the claimed fat-free and low calorie product of a food company and receives following test results (see Table below). (+ = positive result = molecule present) Results Table Sample Benedict’s Reagent Lugol’s Reagent Biuret Test Ninhydrin Test Sudan IV Test 1 + + - - - Is the food product free of fat? Argue your answer. Do you think the food product is a low calorie food source? Argue your answer. 19 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 21: You are member of a nutritional analysis lab team which examines the product of two different company (A and B) which both claim to have pure high protein-made products (product A and Product B) they plan to sell to fitness stores to support fast muscle build-up in athletes. The lab investigations using the indicated reagents and tests below obtain following results for both products. Results Table Product Benedict’s Reagent Lugol’s Reagent Biuret Test Ninhydrin Test Sudan IV Test A Blue Black-blue Violet Clear B Orange yellow Violet Light Purple No precipitate No precipitate Do both products as claimed contain protein? Why or why not. Do the examined product contain other molecule types other than protein? If yes, which one(s)? Product A: __________________________________________________ Product B: __________________________________________________ Does any of the products under investigation contain amino acids? If yes, which one? If they haven’t intentionally been added by the company, what might be the reason(s) that this (or these) product(s) contain amino acids? Argue. Q. 22: Some amino acids are called essential amino acids. What does this mean and which ones are these? 20 SAN DIEGO MESA COLLEGE Intro to Molecular & Cellular Biology Laboratory (Bio210a) Instructor: Elmar Schmid, Ph.D. Q. 23: Which foods are rich in essential amino acids? Which ones not? Q. 24: Fatty acids that have one or more double bonds in their hydrocarbon chain are referred to as (Circle the correct answer!) A) saturated fatty acids B) unsaturated fatty acids C) trans fatty acids D) complex fatty acids E) phospholipids Q. 25: Animals (and humans) cannot make fatty acids with more than one double bond or socalled poly-unsaturated fatty acids (PUFAs), despite the fact that PUFAs are crucial components of important animal and human structures and hormones, e.g. prostanoids. What are good sources for the essential PUFAs in the human diet? 21 SOUTHWESTERN COLLEGE School of Mathematics, Science & Engineering Intro Molecular & Cellular Biology Lab (BIO 211): Instructor: Elmar Schmid, Ph.D. 22