User:Nicole Bonan/Notebook/Chem 571 Lab Notebook/2015/11/04

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Objective

Today's objective is to measure the absorbance of AuNP and peptides that result from degradation by 1nM alpha-chymotrypsin for varying lengths of time.

Protocol

  1. We made a stock solution of our protease, alpha-chymotrypsin, using 50mM Tris/10mM CaCl2 buffer (pH=8) and one of the stock masses of alpha-chymotrypsin that we measured out earlier in the semester. The concentration of this solution was 41.016µM.
  2. We prepared 4 samples of AuNP fibers that Dr. Hartings prepared before class:
    1. We spun the samples down at 300 RPM for 10 minutes
    2. We pipetted the water off of the samples, being careful not to break andy fibers
    3. We labeled the samples based on the time that they would be incubated in the 37 degree Celsius water bath:
      1. 30 min
      2. 60min
      3. 90 min
      4. 120 min
      5. 1380 min (23 hours)
    4. Next, we determined how much of our protease stock we should add to each of the sample tubes in order to make the final concentration of alpha-chymotrypsin 1nM and the final volume of the sample 1mL.
      1. Because the concentration of chymotrypsin was so low, we did a serial dilution or our chymotrypsin stock:
        1. First, we made a 1:200 dilution of our stock protease in Tris buffer. We pipetted 5µL of our stock solution into 995µL of Tris buffer. This brought the concentration of alpha-chymotrypsin to 0.20506µM.
        2. Next, we did the following calculation to determine how much of this solution we would need to add to each sample and blank to bring the final concentration of chymotrypsin to 1nM in each:
          Let
          M1=concentration of original protease stock = 0.20506µM
          V1=volume of protease stock needed
          M2=concentration of alpha-chymotrypsin in the sample tube = 1nM = 0.001µM
          V2=volume of the solution in the sample tube = 1mL
          M1V1=M2V2
          V1=(M2V2)/(M1)
          V1=((0.001µM)(1mL))/(0.20506µM)
          V1=0.00488mL=4.88µL
    5. After that, we determined and how much Tris/CaCl2 buffer to add to the sample to bring the volume up to 1mL by subtracting the volume of the protease we added from the final volume of the sample:
      1000µL-4.88µL=995.12µL
    6. We then added the volume of buffer and alpha-chymotrypsin stock calculated in steps 2.4.1.2 and 2.5, respectively, to each of the sample tubes.
  3. Next, we prepared 10 blanks:
    1. We labeled each blank with an incubation time, as we did for the samples
    2. We put the same volume of buffer and alpha-chymotrypsin stockin each blank as we did in each of the samples
  4. We placed all the samples and blanks in the 37 degree Celsius water bath for their respective incubation times. We did not vortex the samples because we did not want to break the fibers.
  5. While each sample and blank was incubating, we pipetted 600µL of pre-mixed Bradford dilution into the cuvette for the samples and blanks with which we would take the UV-Vis measurements. (The Bradford dilution was 1 part Bradford reagent:3 parts Tris buffer). We also pipetted 1650µL of buffer into each of the cuvettes that would be used for the samples and blanks.
  6. When the samples and blanks were finished incubating, we prepared them for measurement:
    1. We removed them from the water bath and spun the samples and blanks down at 12000 RPM for 1 minute
    2. We pipetted 750µL of each of the samples or blanks into their respective cuvettes
  7. We recorded the UV-Vis spectrum for the samples and blanks in the cuvettes from 400-800nm.

Data

Figure 1: Absorbance of alpha-Chymotrypsin Blanks as a Function of the Wavelength of Incident Light (nm)
20151104 bradford 1nm achymo blanks bonan.png

The above figure shows the absorbance of the alpha-chymotrypsin blanks as a function of the wavelength of incident light. The absorbance was corrected by first subtracting the absorbance of a Bradford blank* from the absorbance each data point at their respective wavelengths. The absorbance was then corrected by subtracting the absorbance at the isosbestic point of each sample and blank from all of the absorbance values for the respective sample and blank.

  • NOTE: The blank was just Bradford reagent and Tris buffer.


Figure 2: Absorbance of AuNP Fiber Samples as a Function of the Wavelength of Incident Light (nm)
20151104 bradford 1nm aunp samples bonan.png

The above figure shows the absorbance of the AuNP fiber samples as a function of the wavelength of incident light. The absorbance was corrected in the same way that the absorbance for the alpha-chymotrypsin blanks was corrected.


Figure 3: Absorbance of alpha-Chymotrypsin Blanks and AuNP Fiber Samples at 600nm as a Function of Incubation Time (min)
20151104 bradford 1nm samples blanks 600nm bonan.png

The above figure shows the absorbance of the alpha-chymotrypsin blanks and the AuNP fiber samples at 600nm as a function of the amount of time that they were incubated. The absorbance values are taken directly from the absorbances in Figures 1 and 2.


Figure 4: Absorbance of AuNP Fiber Samples-alpha-Chymotrypsin Blanks at 600nm as a Function of Incubation Time (min)
20151104 bradford 1nm peptides 600nm bonan.png

The above figure shows the absorbance of the AuNP fiber samples (after subtracting out the absorbance of the alpha-chymotrypsin blanks) at 600nm as a function of incubation time. It effectively shows the absorbance of the peptides and AuNP that had gone into solution as a result of degradation by alpha-chymotrypsin.