p. 298 — I always have trouble keeping enantiomer and diastereomer straight. The mnemonic I use is that mirrorEnantiomer is easier to pronounce than mirrorDiastereomer.
p. 300 — Nice distinction between chiral and optically active — hadn’t thought of it before.
p. 304 — Ah, the Cahn Ingold Prelog system, a classic example of cognitive dissonance. For those who don’t know about this, Google the Stroop test, where you are to read aloud words for colors, themselves colored with the wrong color (example — RED written in green etc. etc.). It’s harder than you think. Try it.
So in the Cahn Ingold Prelog system you assign the various groups ‘high’ priorities, and give the highest priority the LOWEST integer value (e.g. 1), causing simlar mental flipflops.
p. 304 — Another mnemonic — Zus (short for zusammen) sounds like cis.
p. 304 — “Thus, it is commonly stated that all natural amino acids are L, while natural sugars are D”. It’s ‘commonly stated’ because it’s true !
p. 305 — Helical descriptors — I thought I’d find out what left and right handed DNA helices were all about. The section gives no clue about how this could be applied to DNA. This isn’t trivial as Z-DNA is unwound and forms a left handed helix (A and B DNA have right handed helices). All 3 forms are crucial physiologically. — p. 336 neither does this discussion of DNA helices.
p. 307 — Nice to see what the naturally occurring amino acids (the L-amino acids) turn out to be in the Cahn Ingold Prelog system, and to have a clear explanation of just what allo-isoleucine and allo-threonine really are.
p. 308 — The chiral shift reagent is poorly described. I assume Eu is Europium — something we never used 50 years ago. Does the 2 D 2 Phe EtOH bump off one of the 3 ligands, or occupy a fourth coordination position?
p. 315 – 317 — A blizzard of terminology. Hopefully it will turn out to be useful. My old chief used to say that there was never any progress in neurology, but every ten years they renamed the diseases.
p. 325 — The proteins known to contain cystine knots ( basically a disulfide bridge formed by cystine forms a ring through which another portion of the amino acid chain passes ! ! ) are a very important bunch. Nerve growth factor, Vascular endothelial growth factors, and human chorionic gonadotropin (the latter responsible for placental formation).
[ Proc. Natl. Acad. Sci. vol. 107 pp. 8189 – 8194 ’10 ] Proteins with knots in them defy popular concepts of protein folding which say that cooperativity, an increasing degree of nativeness and smooth energy landscapes (whatever they are — perhaps chapter 7 will explain this) are needed for rapid and efficient protein folding. All this implies that proteins should be knot-free.
However, trefoil, figure of eight and penta knots with 3, 4 and 5 projected crossings of the polypeptide backbone (respectively) have been found in proteins from all 3 domains of life.
p. 325 What’s the fun of commenting on a text if you can’t be petty? Euclidian isomerism should be Euclidean isomerism.
p. 326 — I never thought I’d learn some math reading A&&D, but there it is — only two types of nonplanar graphs ! ! !
pp. 327 – 330 — Great fun
pp. 331 — “Going Deeper” I did exactly the same calculation a few years ago, but this time for proteins. Before looking at the link see if you can figure out the following: Assume the earth is made of C, H, O, N and S in whatever proportions you need. Then find the value of n for which 20^n (20 to the nth power) times the average mass of an amino acid (100 Daltons) times n gets you to a mass larger than the earth. Just make one copy of each of the 20^n possibilities. Here’s the link — https://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/
If you haven’t had enough, try your hand at the number of possible RNA molecules you can make (now you need to assume that the earth is made of C, H, O, N, S and P in the proportions you need). Here’s the link — https://luysii.wordpress.com/2009/12/28/how-many-distinct-rna-polymers-can-be-made-using-the-mass-of-the-earth-to-do-so/
We live in a very small corner of a very large protein and RNA space.
p. 332 — A pleasure to read about the Zn metallocene catalysts and the cleverness involved in figuring them out. I’m still far from convinced that statements using the jargon of “chirotopic but non stereogenic” helps you understand what’s going on.
p. 334 — The discussion of s-cis and s-trans is quite good, particularly as it applies to proline. I don’t think most people dealing with proteins know this, although it is well recognized that proline causes unusual protein structures (type I and type II polyProline helices). Just a 4 kCal difference between s-cis and s-trans and the low (19 kCal) activation energy means most proteins (except proline) have a largely (over 1000 times the s-cis) s-trans conformation.
p. 335 — Good to remember the glycogen (animal starch) and plain old starch (from plants) both have alpha 1 –> 4 glycosidic links between the glucoses. Glycogen has a lot more branching (via 1 –> 6 glycosidic links) than plant starch.
p. 339 — The problem origin of enantiomeric excess is similar to the problem of the excess of matter over antimatter in our neck of the universe. People make noises about how it could happen, but no one has a convincing explanation.
pp. 340 – 344 — What a blizzard of terms. Nice to have them all in one place, but I’m not sure how helpful they are. Remember, at least half your cerebral cortex is involved in analyzing visual input, and each optic nerve has about 1,000,000 fibers which can fire ‘up to’ once a milliSecond, so visual information can be flowing into your brain at 2 gigaBits/second.
The terms remind me of the Lilliputians trying to tie down Gulliver by tiny threads. Our perception of space is so complex, that such reductionism has a very long way to go.