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I need help interpreting the result of an experiment. My class performed an experiment measuring protein concentration between heart, liver, and kidney tissue samples. The results were:

  1. Heart: 4.714 mg/ml
  2. Liver: 10.586 mg/ml
  3. Kidney: 9.140 mg/ml

The DNA concentration was given to us and they were:

  1. Heart: 8.6 ug/ml
  2. Liver: 57.6 ug/ml
  3. Kidney: 28 ug/ml

Computing the Protein:DNA ratio:

  1. Heart: 0.548
  2. Liver: 0.184
  3. Kidney: 0.326

Doesn't this mean that the protein-to-DNA ratio has an inverse relationship with cell size as the results show that the liver tissue has the highest protein concentration and DNA concentration, yet has the lowest protein:DNA ratio. Also, why does DNA concentration differ so significantly between each tissue sample? My understanding is that genome remains the same between different cell types. So why does DNA size change?

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  • $\begingroup$ Is this DNA concentration nuclear DNA only or does it also contain mitochondrial DNA? The amount of mitochindrial DNA will scale with cell size but also energy consumption rates, so it could influence an experiment like this. The nuclear-DNA/protein ratio for sure depends on cell size (and surface area) but also a lot of other factors like general protein expression levels and potentially multiple nuclei (this shouldn't apply to these organs though). $\endgroup$ – Nicolai Mar 6 at 13:47
  • $\begingroup$ @Nicolai - there can be multiple nuclei in liver. It is quite known for its paritial polyploidy: "Cell and nuclear size varied between hepatocytes, as well as the number of nuclei per cell." $\endgroup$ – BagiM Mar 6 at 15:51
  • $\begingroup$ Regarding your last question: ignoring polyploidy, if a cell has the same genome packed into a smaller volume, it will have a higher DNA concebtration. $\endgroup$ – canadianer Mar 6 at 16:07
  • $\begingroup$ @bleubambooglu I am not sure from your question what are your thoughts on number of cells per sample (ml of sample). Your first question appears as if you think: more DNA in 1ml -> implies -> more cells in 1ml -> implies -> cells are smaller. However, your second question appears as if you think: there is equal number of cells in 1 ml -> implies -> there should be equal amount of DNA. $\endgroup$ – BagiM Mar 6 at 16:17
  • $\begingroup$ @BagiM I had overlooked that simple aspect of the data, thank you! $\endgroup$ – bleubambooglu Mar 7 at 12:15
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So after discussing my concerns with my professor, I have found out that I overlooked the simple fact that the DNA concentration is not measured based on a single cell of tissue type.

Protein-to-DNA ratio is directly proportional to cell size and the reason why liver cells has the highest DNA concentration at 57.6 ug/ml is because they have a smaller cellular size compared to the other two. So a single ml of liver homogenate is going to present with a significantly higher cell count and thus, a higher DNA concentration. This is also why a single ml of heart muscle DNA concentration is only 8.6 ug/ml due to there much larger cellular size.

This finding can be confirmed from calculating the Protein:DNA ratio as the liver homogenate with its smaller cellular size is only 0.184 and the heart homogenate with its larger cellular size is the highest at 0.548.

Thank you everyone for trying to help me with this problem!

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