05b-protein_characterizaton

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Georgia Institute Of Technology *

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4581

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Chemistry

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Feb 20, 2024

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Lab #5b | CHEM 4581 1 Purification and Characterization of Green Fluorescent Protein Updated on January 5 th , 2023 | Hui Zhu, Ph.D. Experiment 2 of 2 Overview In Part 2 of the two-week study, students will characterize the fractions obtained from the purification of GFP from E. coli . The fractions will be analyzed quantitatively to deduce the recovery of protein using the Bradford Protein Assay as well as measuring the fluorescence, and to deduce the MW of purified protein using SDS-PAGE. The data will be qualitatively analyzed for purity based on SDS-PAGE results. In the interest of time, only an aliquot of some samples will be tested. Students are expected to use logical reasoning to scale up when quantifying amounts of protein recovered from the purification. Teaching and Learning Goals Upon completing this laboratory session, students should be able to: Pour, load, run, stain, destain and photograph SDS-PAGE gels Interpret SDS-PAGE gels for MW determination of specific protein bands Interpret SDS-PAGE gels for purity based on visual inspection Perform a Bradford Protein Concentration Assay Compute dilution factors Estimate protein concentrations using Bradford Protein Concentration Assay data Compute % Recovery of protein from the purification experiment Gain more experience with handling samples of biomolecules Practice biochemical and instrument safety MATERIALS AND REAGENTS Bradford Assay q Bradford Protein Assay Reagent (ThermoScientific or Bio-Rad; record source) q Bovine Serum Albumin (BSA; ThermoScientific) q Disposable cuvettes with 2 optical windows q Spectrophotometer: o Shimadzu UV1601 o Vernier SpectroVis instrument with LoggerPro software SDS-PAGE Equipment q Mini-Protean (or Mini-Proten Tetra) Vertical Gel Electrophoresis System (Bio-Rad) q Power Supply q Rocking Platform Buffers q Resolving Gel Buffer: 1.5 M Tris-HCl, pH 8.8 q Stacking Gel Buffer: 0.5 M Tris-HCl, pH 6.8 q 10% SDS
Lab #5b | CHEM 4581 2 q 30% or 40% Acrylamide:Bisacrylamide Solution (37.5:1 molar ratio) o Record SOURCE and CONCENTRATION in laboratory notebook q Catalysts: o 10% (w/v) Ammonium Persulfate – TA prepares 1 mL daily (0.1g in 1 mL dI H 2 O.) § Record source in laboratory notebook o N,N,N’,N’ -Tetramethylethylenediamine (TEMED) – smells like fish eggs! § Record source in laboratory notebook q 2x Laemmli Sample Buffer o 4%(w/v) SDS, 20% glycerol, 0.004% bromophenol blue, 120 mM Tris-HCl, pH 6.8 o Before use, add 50 μL of 2-mercaptoethanol to 950 μL of 2x Laemmli Sample Buffer . q 10x Electrophoresis Buffer (a.k.a. Running or TGS Buffer)- Dilute to 1X before use. q Coomassie Stain Solution: 0.25% Brilliant Blue R250, 40% methanol, 10% acetic acid q Destain Solution: “Slow” Destain Solution (for overnight) “Fast” Destain Solution (for in-lab) 10% methanol, 10% acetic acid 40% methanol, 10% acetic acid Disposables q Gel Loading Tips q Locking microcentrifuge Tubes q N-Butanol (saturated with water) q Filter Paper wedges (to remove butanol) q Disposable transfer pipettes Samples/Standards q Bio-Rad Precision Plus Protein Unstained Standards EXPERIMENTAL PROCEDURES Please refer to the electronic lab notebook on LabArchives
Lab # 5b | CHEM 4581 3 LABORATORY REPORT GUIDANCE – LONG REPORT Total = 200 points General Reminders § Do not exceed 10 pages excluding the cover page (Only print on one side of the paper.) § Double-space the text and indent the first line of every paragraph, even for subheadings. § Detailed calculations may be shown in an Appendix (optional: not graded, but clarity report) § Use 12-point font and Use 1-inch margins § Number your pages, except over page. (Avoid putting your name on each page) COVER PAGE 10 points § Experiment Title § Student name § Due Date § Honor Code Statement § Signature of compliance with the Georgia Tech Honor Code INTRODUCTION 10 points § Background on the significance of studying proteins broadly in biochemistry § Background on green fluorescent protein and its significance specifically § Explicitly state the goal and support the goal statement EXPERIMENTAL PROCEDURES 50 points Please use subheadings! § Materials – state the key materials used and their sources in sentence format § Affinity Chromatography and Buffer Exchange § SDS-PAGE § Bradford Protein Assay RESULTS ( P lease use subheadings!) Gel Electrophoresis Results § Describe the SDS-PAGE data for all pre-elution lanes, referring to the figure. 10 points o What did you expect to see vs. what did you observe? o Describe the overall MW’s of bands in the pre-elution lanes o Any other noteworthy observations? § Describe the SDS-PAGE data for all elution lanes, referring to the figure. 10 points Do you observe a protein band in any of the elution lanes that would indicate the presence of GFP? § Qualitatively by visual inspection § Quantitatively based on MW § Describe the overall qualitative analysis of purity (based on elution lanes only). 10 points Do you observe any additional bands in lanes from your elution fractions indicating residual impurities? If so, then what are their molecular weight values? § Figure: SDS-PAGE gel image 10 points § Figure: MW marker analysis 10 points
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Lab # 5b | CHEM 4581 4
Lab # 5b | CHEM 4581 5 Protein Concentration Assay Results § Describe the results of the protein concentration assay. 20 points o Describe the linearity of the BSA standard curve in words o Describe the overall relative concentrations of samples (refer to table) o Contrast the volumes of samples collected vs. the volumes of samples precipitated with ammonium sulfate o Identify fractions containing purified protein (refer to gel) o Total amount of pure GFP § Figure: Bradford Protein Assay Standard Curve 10 points Measurement of GFP Recovery by Fluorescence Measurement § Describe the results of fluorescence measurement 10 points o Describe how GFP recovery% was calculated in words and show the equation § Table of fluorescence measurement 10 points o Sample Name o Relative Fluorescence o Total Volume of Protein Solution o Scale Factor o Total Fluorescence DISCUSSION 20 points Each bullet below should be a full paragraph! Please use subheadings! § Explain whether or not you purified GFP and your basis for assessment. § Overall effectiveness of the chromatography REFERENCES 10 points Include at least 3 sound references. Use formatting guidelines for the journal Nucleic Acids Research. Do not reference web sites (especially Wikipedia) or other non-published/non-copyrighted materials. APPENDIX (optional) Include any pertinent calculations made. This section will NOT be included in the 10-page limit and can be neatly and legibly handwritten instead of typeset in Equation Editor. Please start the Appendix on a new page and attach it to the end of your report.