Effect of Puromycin on the Rate of an Enzymatic Reaction
Sarah Wigodsky
Introduction
An experiment was conducted by Treloar in 1974 in which an enzyme was added to a susbtrate. The enzyme binds to the substrate to enable a reaction to occur. The concentration of substrate was varied and the reaction rate was measured. The experiment was conducted 23 times. The enzyme was treated with Puromycin in the first 12 trials. In the last 11 trials, the enzyme was not treated with Puromycin. The data is stored in the R data frame called Puromycin. I am interested in determining the effect of adding Puromycin on the rate of the reaction.
The data collected is shown below.
## conc rate state
## 1 0.02 76 treated
## 2 0.02 47 treated
## 3 0.06 97 treated
## 4 0.06 107 treated
## 5 0.11 123 treated
## 6 0.11 139 treated
## 7 0.22 159 treated
## 8 0.22 152 treated
## 9 0.56 191 treated
## 10 0.56 201 treated
## 11 1.10 207 treated
## 12 1.10 200 treated
## 13 0.02 67 untreated
## 14 0.02 51 untreated
## 15 0.06 84 untreated
## 16 0.06 86 untreated
## 17 0.11 98 untreated
## 18 0.11 115 untreated
## 19 0.22 131 untreated
## 20 0.22 124 untreated
## 21 0.56 144 untreated
## 22 0.56 158 untreated
## 23 1.10 160 untreated
This data shows the substrate concentration in parts per million, the rate of the reaction in counts/min/min, and whether the enzyme was treated with puromycin, which is a protein synthesis inhibitor.
Summary
## conc rate state
## Min. :0.0200 Min. : 47.0 treated :12
## 1st Qu.:0.0600 1st Qu.: 91.5 untreated:11
## Median :0.1100 Median :124.0
## Mean :0.3122 Mean :126.8
## 3rd Qu.:0.5600 3rd Qu.:158.5
## Max. :1.1000 Max. :207.0
The following scatter plot shows the relationship between the reaction rate and the substrate concentration.
## `geom_smooth()` using method = 'loess'
With the exception of the lowest reaction rate for the treated and untreated samples, the samples treated with Puromycin had greater reaction rates than samples at the same concentration that were not treated with Puromycin.
At low concentrations of substrate, the reaction rate increases linearly with increases in substrate concentration. However at larger concentrations of substrate, the reaction rate increases slowly with increases in substrate concentration.
The histogram above shows the number of counts of the reaction rates per concentration of susbstrate. It distinguishes the data based on whether the sample was treated with Puromycin. Most of the data has lower reaction rates per concentration. It is challenging to glean meaningful conclusions based on this histogram, as changing the number of bins showed different trends. The samples that were not treated with Puromycin tend to have lower reaction rates per concentration of substrate than the treated samples.
A quantitative summary of the untreated and treated samples are below.
Untreated Samples - Summary
## Concentration Rate of Reaction State
## Min. :0.0200 Min. : 51.0 treated : 0
## 1st Qu.:0.0600 1st Qu.: 85.0 untreated:11
## Median :0.1100 Median :115.0
## Mean :0.2764 Mean :110.7
## 3rd Qu.:0.3900 3rd Qu.:137.5
## Max. :1.1000 Max. :160.0
Treated With Puromycin - Summary
## Concentration Rate of Reaction State
## Min. :0.020 Min. : 47.0 treated :12
## 1st Qu.:0.060 1st Qu.:104.5 untreated: 0
## Median :0.165 Median :145.5
## Mean :0.345 Mean :141.6
## 3rd Qu.:0.560 3rd Qu.:193.2
## Max. :1.100 Max. :207.0
Conclusion
Treating the enzyme with Puromycin increased the reaction rate. This is evident from looking at the scatter plot. For the same concentration of substrate, the reaction rate was higher when the sample was treated with Puromycin. There was the greatest variation in reaction rates for the same concentration of substate for both the treated and untreated samples at the lowest concentration of substrate. Perhaps this is due to the fact that the likelihood of the enzyme binding to the subtrate may have to do with how the enzyme is distributed in the sample since there is not a lot of substrate present. For the lower concentration of substrate, the rate of the reaction increases linearly as the concentration of substrate is increased. At a substrate concentration of about .15 ppm, the rate that the reaction rate increases slows down as substrate concentration increases. However the effect of Puromycin on reaction rate is greater at higher concentrations, where the reaction rate for the samples treated with Puromycin is much greater than that for the untreated samples. At higher concentrations of substrate, the reaction rate slows down because adding enzyme does not have an appreciable affect on the reaction rate. When the concentration of substrate is high, it is likely that the locations on the substrate that bind to the enzyme are full. So adding more substrate without adding more enzyme does not change the reaction rate.
