1. Explain How Nonspecific Interactions Between Individual Macromolecules

Short answers – (only concise, coherent, and to-the-point answers can earn full credit!)

1. Explain how nonspecific interactions between individual macromolecules and their immediate surroundings (‘background interactions’) within a medium as heterogeneous and highly volume occupied as the interior of a living cell can greatly influence the equilibria and rates of reactions in which they participate. Discuss a specific example and draw sketches.

2. Enzymes are able to perform a number of remarkable synthetic transformations at neutral pH and ambient temperatures through elegant control of coordination geometry, substrate orientation and base- and acid-assisted reaction. Choose an enzyme that employs metal ions and illustrate how an

enzymatic reaction is often achieved with enormous rate enhancements, sometimes to such an extent that the process is effectively diffusion controlled, compared to its unanalyzed analogues.

3.

An electron transport in a photosynthetic system can take place over large distances without a direct contact between the electron donor and acceptor. The tunneling mechanism provides an efficient electron transport between donor and acceptor groups as well. Suggest a structural arrangement of light-harvesting complexes that you think could provide a probable pathway. (Draw sketches to explain your example).

4. We have discussed various cell-wall associated biopolymers. Select one irregular biopolymer and describe its structural arrangements in the context of molecular and supramolecular level -- draw sketches. Indicate an experimental technique that could show how the biopolymer may respond to abiotic/environmental stresses

5. Give an example -- how the secondary structure of proteins can be determined by CD spectroscopy. Suggest a single-molecule technique that may rely on the information about the secondary structure in order to determine the mechanical properties of a protein.

6. NMR experiments can provide useful structural information and probe different aspects of the molecule’s nuclear environment. Suggest two NMR experiments that may illustrate how a globular protein could respond to the changes of pH, temperature, and

viscosity.

7. Describe some common structural attributes when we compare antifreeze proteins with irregular biopolymers? Suggest an experimental technique that could elucidate their supramolecular structures and energetic contributions.

8. Give an example to depict consequences of cooperativity in a supramolecular system. Describe a “thought experiment” in order to describe changes in its spatial patterns that may relate to its functional properties.

9. You are studying an ion channel for which you want to know the opening pore dimension. Fortunately, there are two and only two sites at the mouth of the pore to each of which a fluorescent label may be attached. You decide to study the dimension with Forster analysis, the efficiency of Forster transfer is given by: