Experiment V: Protein Concentration via BCA and Bradford Assays; Beer-Lambert Law and UV-VIS Spectroscopy

Transcription

1 Experiment V: Protein oncentration via BA and Bradford Assays; Beer-Lambert Law and UV-VIS Spectroscopy I. ITRDUTI Although 50 to 90% of the mass of a cell is due to water, 50% of its dry mass is due to proteins. Proteins are organic compounds with a wide variety of cellular functions such as biochemical catalysts, energy sources, molecular messengers, structural components, transport vehicles, etc. The proteins found in all living organisms are synthesized from 20 common amino acids which are linked in a linear sequence to form an unbranched polymer (a polypeptide) ranging from 50 to several thousand amino acids in length. All of the amino acids in a polypeptide are structurally identical except for unique structural moieties on each called an R-group. These R-groups differ in polarity, size, solubility, and electrical charge. In the polypeptide, the linkage between adjacent amino acids is called a peptide bond and is formed by the condensation of a carboxylic acid moiety in one amino acid with an amino moiety of another. The figure below illustrates the linear sequence of a short peptide formed from the condensation of 5 amino acids. The pentapeptide is seen to contain four peptide bonds (circled) and five residues of amino acids. Proteins play such a variety of important roles in the living cell that it should be no surprise that an enormous amount of time and effort has been spent in elucidating the structure and function of these versatile macromolecules. An absolute prerequisite to meaningful progress in the study of any protein is an amply supply of highly purified material. Unfortunately, few if any proteins exist in nature at the desired concentration or at the degree of purity required for such detailed analysis. onsequently, it has been necessary that lab procedures be developed for the extraction, concentration, and purification of cellular proteins. The development of these procedures, which has taken a considerable period of time, has been hampered by the fact that the concentration of any given protein in a cell is usually extremely low (less that 0.01 % of the total cell mass) and further complicated by the presence of many other macromolecules (nucleic acids, carbohydrates, etc) which must be eliminated. The task of a biochemist that chooses to develop an isolation technique for large amounts of purified protein is a difficult one and would typically include the following considerations: The development or selection of a simple assay that specifically demonstrates the presence and concentration of the protein in question. The choice of material from which the protein can be isolated. The overriding factors in this choice typically are the absolute concentration of the protein in a given natural source and the cost and availability of the material. The selection of cell-disruption technique appropriate to the cell or tissue type being used. Some materials, such as plant cells, for example, require harsher techniques for cell disruption. The selection of a series of precipitation and centrifugation procedures that maximize the concentration of the chosen protein and minimize that of the other contaminating molecules. Biochemists have, through a process of trial and error, addressed these considerations and have developed an impressive array of techniques for the extraction and purification of proteins. This experiment will deal with an effective way for measuring the concentration of a given protein. Biochemists measure protein amounts in the microgram ( g) range. There are several methods of 2 R 1 R 2 R 3 R 4 R 5 1

2 2 3 protein determination currently used. The most common ones are the Bradford, BA, Lowry, Biuret, and A 280 methods. In most all cases protein standard curves are plotted as absorbance (or another measured parameter) vs total protein amount, not concentration. This method of analysis conveniently makes use of the equivalence of different units of mass/volume, such as: 1.0 g/ L = 1.0 mg/ml = 1.0 g/l. Thus if a 10 ul volume of standard protein solutions from g/ L (or, given in more standard units, the equivalent mg/ml) are added to a standard assay (typically 300 L total volume), then the total protein range is 1.0 to 10.0 g. If 10 L of an unknown is added to the same assay, and the total protein is determined as 7.8 g from unknown absorbance and the standard curve, then the dilute concentration is 7.8 g/10 L = 0.78 mg/ml. The Bradford assay utilizes the dye oomassie blue G-250. This dye, when dissolved in acid at a p below 1, turns a red-brown color. owever, when it binds to protein the blue color is restored due to a shift in the pka of the bound dye. The procedure is simply to add a sample of protein to the reagent and measure the blue color at 595 nm. While fast (15 min), sensitive (~1 g) and accurate, this assay is subject to interference by a number of agents such as detergents and organic solvents. The structure of oomassie blue is given below S 3 a S 3 The BA (bicinchoninic acid) assay is a recently developed assay, which is similar in principle to the old technique known as the Lowry assay. opper, in the form of copper sulfate is added to an alkaline solution of BA. This gives an apple green colored complex. When this solution is added to a protein solution, the u ++ ions are converted to u + by interaction with the peptide bonds of the protein. This changes the color of the complex from apple green to purple with an absorbance maximum of 562 nm. Unlike the Bradford assay, the BA is time dependent and will continue to develop color for at least 24 hours. The aromatic amino acids (especially tryptophan) absorb strongly around 280 nm. Because of this all proteins, which contain aromatic residues (or UV absorbing cofactors), have a unique extinction coefficient at 280 nm. For example, a 1% (10 mg/ml) solution of pure BSA has an absorbance of 6.6. Your 1 mg/ml stock, therefore, should have an absorbance of 0.66 if measured undiluted. In fact, the molar extinction coefficient at 280 nm of a protein can be approximated from the number of tryptophan and tyrosine residues using the following formula: protein = (# trp)(5690) + (# tyr)(1280) Spectrophotometric analysis. The trend in biochemistry has been toward very low concentrations. Therefore, biochemists require very sensitive analytical procedures for quantitating the concentration of compounds in biological tissues or extracts from them. Spectrophotometric procedures are generally more sensitive than gravimetric and volumetric procedures and are the most widely used and versatile of all bioanalytical tools. The difficulty encountered with spectrophotometry is that you are limited to molecules that either absorb light or that form derivatives with molecules that absorb light. The advantages are that in many cases, it is a Step 1: Step 2: - - Protein + u +2 u BA u

3 nondestructive method and each chemical has its characteristic spectrum. ften, a particular compound in a mixture can be singled out for observation. Since absorption occurs in a short time period (10-14 sec), it is possible to follow fast reactions. Most importantly, the measurements are of high accuracy and can be made in a short time. Beer-Lambert Equation. The Lambert law of absorption states that: a) the fraction of light absorbed is proportional to the thickness of the absorbing solution and b) is independent of the light intensity. Mathematically that says that: if I o=intensity of the light entering a colored solution; I = intensity of light leaving the solution; and l = length of the light path through the solution; then log (I o/i) is proportional to 1. The term log (I o/i) is called the absorbance, A of the solution. Beer's law states that the light absorbed by a solution is also proportional to the number of absorbing molecules through which the light passes. Thus, if the absorbing substance is dissolved in transparent solvent, the absorption of the solution is proportional to its molar concentration,. log (I o/i) is proportional to. ombining the two equations gives the Beer-Lambert equation: A = log (I o/i) = l where is the molar extinction coefficient (sometimes written as cm ). Extinction coefficients. As you can see, the extinction coefficient is a proportionality constant that relates absorbance to the concentration and pathlength. = A/cl Because absorbance is dimensionless, the units of the extinction coefficient are the reciprocal of the denominator of the right side of the equation. For example, the pathlength is nearly always 1 cm but you do have to pay attention to the units of concentration. When the concentration is molar, the extinction coefficient,, is expressed in terms of M -1 cm -1. This is equivalent to the absorbance of a 1 M solution of the substance with a light path of 1 cm. The Beer Lambert equation can be used to quantify the amount of a substance in solution as long as the absorptivity and pathlength are known. When it is not known, then biochemists normally generate a standard curve using standard solutions. The data is plotted as Absorbance (y-axis) vs amount (molarity, mole, or mass). For linear responses, the equation obtained is linear of the form y = mx+b where y is abs, m is l, and b is the y intercept (absorbance in the absence of the substance). The standard curve can then be used to calculate the amount x of a sample given its response y under identical conditions. For protein assays using the BA and the Bradford methods, the standard curve is generally plotted as Abs vs amount of protein in ug. Using mass is important for two reasons. First, the BSA protein used for the standard curve has a specific molar mass that is most often different from the protein of interest, so molarity is T appropriate. Second, the unknown amount in g calculated using the linear equation can be converted directly to mg/ml by dividing by the volume added in L (notice the g/ L = mg/ml = g/l) and then divided by the dilution factor (volume ratio). Absorption Spectrum Many biochemicals absorb light. A plot of the amount of light absorbed at given wavelengths ( ) is called the absorption spectrum. The absorption spectrum is characteristic for each compound at any given set of conditions. Thus, initial characterization of an unknown compound frequently includes measurement of its absorption spectrum to provide qualitative identification. Solution conditions can greatly influence the character of an absorption spectrum. This is especially true if the compound contains a titratable group (important examples would be adenosine, cytosine, guanosine, uracil, tyrosine, p indicators, etc.). For this reason, all spectra should include the solution conditions such as p and buffer concentration in which they were obtained. In spectrophotometric determinations, the absorbance is usually measured at the wavelength of maximum absorbance, max. This wavelength gives the greatest sensitivity to the method. 3

4 After choosing the wavelength, you should obtain a Standard urve for the compound to be measured. This is a plot of absorbance versus known concentration and will be a straight line if Beer's law holds. The standard curve can then be used to determine the concentration of an unknown sample if you know its absorbance. The standard curve should be obtained at the same time that the unknown's absorbance is taken and the same buffer conditions should be used in both. II. EXPERIMETAL Pre-Lab: In addition to the procedure, prepare a dilution table for the BSA with total protein added to the assay, and calculate the total dilution needed for the unknown milk sample. Also, calculate the EXPETED absorbance of a 1/5 dilution (300 L total volume) of the 1.00 mg/ml BSA standard solution. The BA reagent will be provided by the Instructor Part A. BA assay The BA assay first requires dilutions of 1.0 mg/ml BSA from 0:100 to 100:0 in 10 L increments in water. These dilutions can be prepared in the microplate, say row A or B, and shake by gently tapping the plate against the edge of the bench. The unknown is a sample of non-fat milk which has a reported protein concentration of 34.0 mg/ml. This sample needs to be diluted such that the amount in 10 L added to the BA assay is within the range of the BSA amounts used for the standard curve ( g). The final dilution of the milk sample should be 10/250 L in BA. Be sure that the milk BA assays are set up at the same time as the BSA assays since results are time dependent. The dilute solutions of BSA (10 L of the dilutions) can then be assayed with 290 L of BA reagent (tree green colored solution) in a VIS microplate. A protocol is set up it reads 1-11 for the standard curve, D1-D3 for the unknown sample, and displays the standard curve named 485_BA_Protein_Assay. therwise, you ll need to set up your own protocol. The BA assay needs to be covered and incubated for at least 30 min in the incubator above 45 o. The absorbance is then read at 562 nm on the plate reader. Part B. Bradford assay of BSA The Bradford assay requires the same dilutions of BSA, and the assay is prepared with 10 L of dilute BSA and milk dilutions with 290 L Bradford reagent in a VIS-BRADFRD plate. The plate is incubated at room temperature for at least 10 minutes and the absorbencies taken at 595 nm using the UV/VIS micro plate reader. A protocol is already setup, and reads the standard curve in cells 1-11, the unknowns in D1- D3, and gives a standard curve, named 485_Bradford. 4

5 Part. UV calibration of 1.0 mg/ml BSA stock The concentration of the BSA stock should be determined accurately by measuring the absorbance at 280 nm. This must be done in UV plates to be most accurate. The 1.00 mg/ml BSA stock is diluted 1/5 (300 L total volume) in cell A1 of your UV microplate. Add 300 L 2 to cell A2 as a blank. Read the plate in the micro plate reader at 280 nm (a protocol named 485_BSA_A280 can be used). The A280 is for the dilute solution, so the dilute absorbance is multiplied by 5 to give the absorbance of the BSA stock. ow that you know the absorbance of the stock BSA solution, you can use the info about BSA absorbance in the introductory material to calculate the exact concentration of the standard protein solution by setting up a simple mathematical ratio. III. Lab Report Use the A280 of the stock BSA, the extinction coefficient for a 1.00 mg/ml BSA given in the introduction, and assuming a pathlength of 1 cm, calculate the [BSA] in the stock solution. Given a molecular weight of 68,000 g/mole for BSA, calculate the molar extinction coefficient from the A280 data. Also, given that BSA contains 2 tryptophans and 19 tyrosines, calculate a theoretical molar extinction coefficient for BSA. ow do these compare? ow did your experimental and theoretical molar extinction coefficients compare? What might be the sources of error? If you did not get a slope/intercept from the plate reader, use the absorbance data to generate standard curves for both the BA and the Bradford assays as absorbance vs total protein. Report the slopes and intercepts. ext, calculate the amount of protein in the milk stock from both standard curves. Please put you re data and results in Table columns. ompare the results of the Bradford and BA assays with respect to ease, accuracy, and sensitivity. Which assay is likely to be the most accurate in this case? ow does the most reliable concentration compare with that reported by the manufacturer? Watch out for dilution factors!! 5