The polyacrylamide gel is used to separate proteins as they are small as compared to DNA. Let's understand this in detail:

1. Introduction:
Polyacrylamide gel electrophoresis (PAGE) is a widely used technique in biochemistry and molecular biology to separate and analyze proteins based on their size. It is particularly useful for separating proteins that have similar molecular weights but differ in other properties such as charge or conformation.

2. Principle of PAGE:
The principle of PAGE is based on the fact that proteins have different mobilities in an electric field depending on their size and charge. The gel matrix provides a medium through which proteins can migrate, and the electric field applied during electrophoresis drives their movement.

3. Polyacrylamide Gel:
Polyacrylamide is a synthetic polymer that forms a gel-like substance when cross-linked. The gel can be prepared with different concentrations of acrylamide and bisacrylamide, which determines the pore size and hence the separation range of the gel.

4. Protein Separation:
In PAGE, proteins are loaded into wells created in the polyacrylamide gel. When an electric field is applied, the proteins migrate through the gel matrix. The smaller proteins move more quickly and travel further through the gel, while larger proteins move more slowly and remain closer to the loading wells.

5. Comparison with Agarose Gel:
Agarose gel electrophoresis is another commonly used technique for separating biomolecules, such as DNA. However, agarose gel is not suitable for protein separation due to several reasons:
- Agarose gel has larger pore sizes compared to polyacrylamide gel, which allows for the separation of larger molecules like DNA. Proteins, being smaller in size, would not be efficiently separated in agarose gel.
- Agarose gel may react with proteins, leading to unwanted interactions and distortion of the separation pattern.
- Agarose gel is commonly used for separating DNA fragments based on their size, while polyacrylamide gel is specifically designed for protein separation.

6. Conclusion:
In conclusion, the polyacrylamide gel is used to separate proteins as they are smaller in size compared to DNA. The gel matrix allows for the efficient separation of proteins based on their size and other properties. Agarose gel is not suitable for protein separation due to its larger pore size and potential interactions with proteins.