References

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

A

B

C

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D

F

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G

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H

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L

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M

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N

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O

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P

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R

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S

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T

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Z

Notes

[1] Where the term 'morphological' characters appears in single quotes, it is used in a broader sense than usual—not just morphological characters per se, but any character that might arguably be used in a phylogenetic analysis the same way as a true morphological character. So synthesis or not of certain proteins, or gene-structural characters such as indels, might also count as 'morphological' characters.

[2] Here's the remedial thermodynamics for those who need it. The magic equation is ΔG = ΔH - TΔS. The free energy (ΔG) needed to get something done at constant temperature is equal to the change in potential energy (enthalpy) between the initial and final states (ΔH) less the absolute temperature multiplied by the change in entropy (TΔS). Entropy is an elegant philosophical and and physical concept which can variously be conceptualized as "disorder" or "randomness," but also "freedom" or "potential number of future states." We pause briefly to allow the philosophical implications to sink in... Ready? Now, consider a simple model of a protein as a chain of paperclips. We know that the final, properly folded state of the protein has low enthalpy because the final state is quite stable. It has to be or the protein could never maintain its useful shape. So ΔH is negative, and the reaction is favored. So far so good. However, if we have to fasten together distant parts of the chain, this drastically reduces the number of states which the chain can assume. This reduces entropy, and the -TΔS term becomes strongly positive, especially under heat stress (higher T), and the conformation change becomes prohibitively expensive in terms of free energy. When the chain is suckered into a small volume, taking due advantage of random fluctuations in shape to accomplish the task, the number of possible conformations is strongly reduced because there is no room to assume extended shapes. Thus the change in entropy needed to make distant parts of the chain interact is no longer so great a problem, and the final state is reached without much grief. (This sounds as if we're getting something for nothing, and reducing total entropy, neither of which happen in thermodynamics. The key is that the GroEL molecule and ATP have to be considered as part of the system.)

[3] c'est-à-dire un alcool avec une longue chaîne composées de plusieurs (une dizaine) unités de 3-mèthyl-2-butene (isoprène). Ça c'est un motif chimique très courrant, par exemple en l'omniprésent co-facteur métabolique ubiquinone. Image: Faculté de la Pitié Salpêtrière.

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