Question

in the plasmid isolation procedure, phenol is the main denaturant that removes proteins from the lysed cells. how does phenol denature proteins? why doesn't it denature DNA?

clue in the picture .

08. DNA and phenol are acids. Proteins are folded with many hydrogen and ionic surface bonds that phenol can attack.

Answer 1

Phenol is a less polar molecue than water.water has an electronegative oxygen atom which pulls the electrons towards it. Due to this hydrogen atoms aquire a slight positive charge and oxygen a slight negative charge. Phenol also has an oxygen atom but its electronegativity is countered by the phenyl ring o charge is not polarised in phenol.

In proteins the side chains of amino acids can be positively charged or negatively charged or uncharged( due to their side chains). The proteins fold into three dimensional structure according to the polarity of the solvant ( in cytoplasmic contaxt the sovant is water). Their hydrophobic residues are buried inside while the hydrophillic residues are exposed towards the solvant.

During plasmid isolation proteins are exposed to a nonpolar solvant phenol which forces the hydrophobic residues to flip outside and hydrophillic residues inside. Due to this their structure is denatured and they become more soluble in phenol. While DNA is a negative molecule( due to the negative charge on the phosphate backbone) so it is more solube in water.