Chemistry 471 - Elementary Physical Chemistry

1) Do proteins fold against entropy?

As we will see, the 2nd law of thermodynamics states that the entropy of the universe is always increasing (why?). Basically, randomness is more likely than order. If an unfolded protein is a large collection of a large number of random states, why do proteins fold into a single unique structure? Do proteins have a special exemption from the second law?

2) In vivo genetic selection vs. in vitro measurements

Plasmid diagram The enzyme studied in the Martin lab, T7 RNA polymerase, binds to a unique target sequence in the DNA (a promoter) and then begins synthesizing RNA from that spot. The entire T7 viral genome (40 kB) was sequenced in the early 1980's and was found to contain seventeen promoters. Alignment of these promoters reveals a 17 bp consensus sequence, with many DNA sequence positions completely conserved. Presumably these highly conserved positions are important for function.

In the early 90's, a research group designed an experiment to let nature tell us which bases in the promoter sequence are truly important. T7 RNA polymerase was expressed inside bacteria (no virus here). In a separate plasmid, a randomized 17 base pair sequence was placed immediately ahead of an antibiotic resistance gene and the plasmids were introduced into bacteria. Presumably a few of the 417 possible sequences will represent a good promoter (assume that each bacterium gets only one plasmid). If the cells are treated with the antibiotic, all will die, except those containing a good promoter sequence. Thus as the surviving cells multiply, the DNA within them will contain good promoters.

Sequencing of the resulting DNA revealed that there were some positions, which were indeed uniquely defined (eg., position -10 was always an A). Other positions had all four possible DNA bases (25% each of A, C, G, and T). Some of these unselected positions were nevertheless completely conserved in the viral genome (ie., a G in all 17 viral promoters).

The authors concluded that since their selection said that the RNA polymerase didn't care about these positions, that part of the DNA must have some other, as yet unknown function in the virus (resulting in their being conserved in the viral genome).

Subsequent in vitro measurements showed that although their experiment was valid, their conclusion was wrong. Why?

3) Binding of a factor reverses catalysis?

At a scientific conference on gene regulation some time back, a colleague was describing a system which he studied. It seems that there is a signaling molecule in the cell which undergoes phosphorylation as a part of a particular signaling pathway. My colleague told me that the enzyme he studies catalyzes the phosphorylation of this signaling molecule, and that when a special cofactor binds to his enzyme, the enzyme-cofactor complex now catalyzes the reverse reaction. A very cute signaling mechanism, but as stated, wrong. Why?

4) Fine tuning light absorption

In the latter half of the course, we will see how it is that nature builds molecules which absorb in the visible spectrum (benzene and other small molecules absorb in the UV). Porphyrins are big, naturally occurring molecules with absorbances in the visible spectrum. Recently some chemists took a cue from nature and, using porphyrins as building blocks, built molecules which absorb in the infrared. How do you think they achieved this?

Their real goal was not making an absorber, but creating a good conductor of electricity. Explain why they did what they did.