The new Clayden pp. 1134 – 1168

1135 — Mnemonic for nucleoTide vs. nucleoSide.  A nucleoTide has Three things — base + sugar + phosphate.  A nucleoside has only 2 — base + sugar.

1136 — Interesting idea of ATPylating a metabolic intermediate to make it more reactive — just like Tosylating an alcohol.  For lots more on ATP — see

Even though the post is over 2 years old it gets hits every day.  One fact to whet you interest — we make (and consume) half our body weight of ATP every day [ Nature vol. 417 p. 25 ’02 ] 

1136 — What is supercritical CO2 using to extract caffeine from coffee.

1136 — Excellent explanation of why S-adenosyl methionine (SAM) forms so easily — S being a soft nucleophile attacking at a primary carbon attached to a good leaving group (triphosphate).  A similiarly good explanation of why the methyl group of SAM is also attacked by many nucleophile metabolic intermediates to methylate them. 

1137 — It’s worth noting the way the sequence of bases on a single strand of DNA or RNA is read (by us).  The example shows two adenosine and a thymine linked together.  The sequence given is read as AAT, where the first letter has the phosphate on the 5′ and the last has it on the 3′.  Always read 5′ to 3′.    When DNA is copied, the coding strand is read this way which probably gave rise to the convention. 

1138 — There are other ways to G, A, T, C to pair with each other.  Look up Hoogsteen base pairing, and G quartet. 

1138 — Although DNA is more chemically stable than RNA, the current thinking is that life arose in an ‘RNA world’ with RNA acting to both store information, and to act as enzymes (RNAase P is the first known example of an enzyme whose active site is made entirely of RNA). 

1139 — No question that cyclic AMP is an important biological messenger (an undefined term which should have been), but so is cyclic guanosine monophosphate (cGMP). 

1138  The ribosome as the most elaborate structure in the universe.  Here’s some elaboration.  The hydrogen atom has a molecular mass of 1 Dalton.  The ribosome contains  about 4500 nucleotides (base + sugar + phosphate) and 50 proteins with a molecular mass of 2.5 megaDaltons.  The average mammalian cell contains 10,000,000 ribosomes. 

1141 I can’t believe a British textbook didn’t mention of James Lind when discussing scurvy.  He kneweth not vitamin C but by supplying limes to sailors, brought scurvy to an end in the British fleet.  It’s where the term Limey comes from.  

1143 — Sad that that a huge opportunity was missed to explain why glucose rather than most of the other 2^4 possible stereoisomers is used in cellular biochemistry.  It’s right there at the top of the page.  See if you can figure out why — answer at the bottom of the post. 

1145 — Med students love mnemonics.  The one for alpha and beta orientation at the 1 carbon of glucose is very good.  Alpha should stand for above, beta for below, but just the opposite occurs. 

1145 — While sulforaphane may reduce the risk of prostate cancer, it probably does so by decreasing androgen levels.  This may explain why vegetarian men are such wimps.  For details see —

1148 — The kink in oleic acid produced by the cis double bond is crucial for membrane function.  It essentially prevents the hydrocarbon tails of the saturated fatty acids found there, from perfectly aligning with each other and forming a liquid crystal.  This would cause all sorts of permeability and ridigity problems for the cell (since it is bounded by a lipid membrane). 

1153 Nice discussion of why thiol esters are so labile and why the body uses them. Ditto for why histidine is so often found at catalytic sites. 

1154 Be careful with pyruvate kinase.  The nomenclature is tricky.  There is a huge amount of organic chemical work being done to develop inhibitors of protein kinases, as they have been successfully used to treat cancer (Gleevec, imatinib).  Our genome codes for some 518 protein kinases (out of about 20,000 protein coding genes).  Protein kinases are enzymes which put phosphate on other proteins.  Pyruvate kinase is just the reverse, it takes phosphate from phosphoenolpyruvate and puts it on adenosine monophosphate form adenosine diphosphate. 

1161 — Again note that all the double bonds in the unsaturated fatty acids and polyunsaturated fatty acids (PUFAs) found in the body and shown here, are cis, for the same reason as given earlier (p. 1148)

p. 1162 — The acylation of acetyl coenzyme A with carbon dioxide is a rather remarkable reaction as CO2 is pretty inert.  More should be made of this fact. 

p. 1167 — Nice to see where the 4 membered ring in pinene (and other terpenes) comes from. 

At the end of the chapter several books are cited for more in the way of biochemistry.  I’d like to put in a plug for Voet’s biochemistry (full disclosure:  Don and I were good friends in grad school).  It’s a book for chemists and the pictures are great.  I don’t know that the others are inferior. I will say that I found Lehninger horribly dull.  If you want to see how dull Biochemistry was in the 50’s and 60’s, go to the library and look at Fruton and Simmonds. 

Answer — all substituents coming off the 6 membered ring are equatorial (except from #1 which can vary)
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  • MJ  On November 16, 2012 at 1:49 am

    “What is supercritical CO2 using to extract caffeine from coffee.”

    At fairly modest temperature and reasonably attainable pressure, carbon dioxide becomes a supercritical fluid. It dissolves nonpolar compounds fairly well as is, but some amount of polar solvent (I recall hearing of a preference for alcohols) can adjust its solubility properties and can begin to extract more polar compounds. I don’t know what they do for caffeine in particular, though. I believe the one thing that is enjoyed by this method is that the solvent is very easy to remove – just adjust the conditions until it wafts away as a gas.

    “The ribosome as the most elaborate structure in the universe.”

    Nuclear pore complexes tend to be larger (~120 MDa in mammals), but fewer unique proteins are present – there’s just a lot more of them…….

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