Letters from Terra - Biochemistry section

Welcome to the long awaited, much delayed Letters from Terra biochemistry section. Oddly, after the terrors of the metamorphosis of the original PascalGames.co.uk programming site into the shiny new Letters from Terra programming section, I thought the construction of the new material would have be a little lighter on my time constraints. Sadly, I was (more than slightly) mistaken, and it's taken the best part of six months before I have enough material to justify including a whole section of my now monsterously proporetioned devoted to biochemistry. However, because of the labour (and even passion) involved, what I have to offer you is not only completely original and entirely my own work, not to be found anywhere else on the net, but also I hope will be (unlike the cryptic source in the programming section) of real and tangible use for anybody studying biochemistry at degree level, or just anyone that likes to take a helathy interest in the way living things work. My passion, as always, is metabolism, the mechanisms of enzymatic catalysis, and enzyme kinetics itself, and it is these topics which are most heavily represented in the biochemistry section to date; although there is a nice computer simulation of darwinian evolution, as well as an attempt to write a program that can describe the evolution of intelligent behaviour strategies for the geneticists out there. Both of the latter two programs are inspired by the wonderful books of Richard Dawkins, a man who is unafraid to be fiercly orthodox, and whos clarity of argument are testement to this fact. I recommend his books without reservation. Also included is a marvel of programming, well, tenacity, the automatic rate equation generator. This is a tool pitched at those (very) interested in enzyme kinetics, and makes use of the King-Altman method for the automatic derivation of rate equations for complex enzymatic processes. Although it's somewhat clumsy to use, as far as I can tell it works perfectly, accurately generating rate equation from the simple reversible michaelis-menton type to more complex two-substrate models. It also includes some very elegant delphi code, and is well worth taking a look at. Another small offering is for anyone interested in the metabolism; microbial biosynthesis and mammillain catabolsim; of the twenty standard amino acids. This is a large poster depicting the complete metabolic pathways for each amino acid, complete with chemical structures, enzyme names, cofactors, alternative pathways, and statistics on each amino acid. The poster is around 1Mx1M when viewed at the correct size, and is in adobe PDF format, making it very quick to download (less than a minute on a modem). It's a must for any biochem student, and looks great when displayed on a wall, as I have done. Another project (that has almost sunk into obscurity in comparison with the new material) is the ramachandran diagram generator, a wonderful piece of programming (and indeed molecular modelling), and a miracle in that it actually generates an accurate ramachandran diagram. The biggest, most important, and generally most impressive section of this site is, however, the LFT metabolte database. This ASP based web resource resides on another (ASP supporting) server, and will eventually be a catalogue of all the common metabolites used across the spectrum of life, and the metabolic pathways that connect them. Extremely useful for any student of metabolism, this allows simple or complex searches to be conducted on metabolites, a detailed description, the immediate precursors and products, and statistics such as ATP equivalent and biosynthetic matierals to be viewed for each metabolite, and biochemical pathways to be browsed in single clicks. All metabolites are graphically presented, and the site is clear and easy to use, as well as expanding continuously as I increase the size of the database. Important metabolites such as pyruvate have long, detailed descriptions (up to 3,500 words in some cases), and contain all the enzymatic basics as well as wider musing on the chemical and functional relevance of each metabolite. Be sure to take a look at it. I hope you enjoy the various projects as much as I've enjoyed putting them together. Have fun,

Jon - February 2004

Amino acid metabolism | Ramachandran diagram | Rate equation generator