Question

4. What characteristic would indicate that a topoisomerase inhibitor could be used as an antibiotic or chemotherapeutic agent? Can you name some common topoisomerase inhibitors and explain how these inhibitors lead to cell or bacterial death?

5. How is a chromosome different from chromatin? What can be confusing about this terminology?

6. What noncovalent interaction is responsible for DNA binding to histones? Explain how DNA binds to a histone.

7. Name the subunits of a histone. What is the oligomeric designation for a histone (α, β, etc.)?

8. List the noncovalent interactions that may occur to stabilize a protein binding to DNA. What is the difference between direct and indirect H-bonding?

9. What are the major protein structural motifs that play a role in a protein binding to DNA? • What structural motif does not bind to DNA but is commonly found in DNA binding proteins? What is the function of the preceding motif?

10. What are the structural characteristics of the motifs that you mentioned in the previous question? Which of these motifs provides the greatest recognition of a specific sequence of nucleotides in DNA by the protein? Why?

11. What are the typical physical-chemical characteristics of a molecule that can intercalate DNA?

Answer 1

4. Topoisomerase inhibitors are the chemicals which inhibits the action of enzyme topoisomerase which control the change in DNA structure by catalyzing the breaking and rejoining of phosphodiester bonds of DNA strands during normal cell cycle.

This propert of these chemicals are used as antibiotics and chemotherapeutic agents.

For example- nalidixic acid ,ciprofloxacin,doxorubicin ,daunorubicin etc

These act by either encouraging the forward cleavage reactions or by inhibiting the religation reactions.

5. In the nucleus, the DNA double helix is packaged by special proteins (histones) to form a complex called chromatin. The chromatin undergoes further condensation to form the chromosome. So while the chromatin is a lower order of DNA organization, chromosomes are the higher order of DNA organization.

6.

Histones are proteins which have a arginine (R) and lysine (K) residues on their surface. These amino acids are positively charged at physiological pH and hence can form ionic interactions with negatively charged phosphate groups in DNA.

Histones are of following types - H1, H2A, H2B, H3, H4. H1 serves as guide for incoming DNA. The other residues form a tetramer around which the DNA is coiled. The R and K residues are arranged such that the DNA is coiled in a spiral staircase like structure.

7. The subunit of histone is called nucleosome.