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<\/a>I think we’re focusing on the wrong thing when we follow classical textbook approaches to ‘Biomolecules’ and their categories (DNA, RNA, protein, carbs, lipids). I don’t have much to say about the latter two, but there are some Big Ideas about the molecules of the central dogma\u00a0that I believe\u00a0get lost in the tedium of -OH groups and dehydration reactions…\u00a0I’ll discuss order of presentation and such later; now I want to talk about monomer structure.\u00a0To wit: How are (the group nucleic acid monomers) and (the group amino acids) all\u00a0similar<\/em>, and why<\/span> must this be so?<\/p>\n<\/p>\n
Short form:\u00a0the molecules of the Central Dogma (DNA, RNA, proteins)\u00a0are special; creating strings of these requires that a single<\/em> machine (DNA and RNA polymerases; the ribosome) join strings of any<\/em> sequence, whereas\u00a0most enzymes perform single, stereotypical reactions. What must we do to allow DNA Pol to put together ANY pair of nucleotides, and the ribosome to add ANY amino acid to another?<\/p>\n Note:\u00a0<\/span>This post focuses on the commonalities of the structures–how they are joined; how single machines put a diversity of pieces together. For an overview on the central dogma itself, try this pos<\/a>t; or\u00a0specifics on DNA<\/a> or amino acids<\/a> or translation<\/a>.<\/p>\n I’m a strong believer that sensible things can be taught to students “even though they’re freshmen”. If you think about it, the only reason they’re likely to be ‘smarter’ as upperclassmen is that we’ve contributed to making them that way. So shouldn’t we start early and be active about it?<\/p>\n In looking at the ‘parts’ of an amino acid, it’s easy to get caught up in the Naming of Parts\u00a0<\/a>–alpha carbon, amino group, carboxyl group… but\u00a0why?<\/em>\u00a0 I think the answer’s simple and obvious, in hindsight: if the ribosome had to have an active site for every combination of amino acids it might need to join together, that’d be 400 active sites!<\/p>\n What to do instead? Easy! Have each unit contain a stereotypical part on which the ‘sewing machine’ (polymerase\/ribosome) operates, and a ‘business end’ that confers its unique operational properties. Since all 20 amino acids have ye amino and carboxyl groups, identical recognition and chemistry events can be performed on all, regardless of order, regardless of properties.<\/p>\n The same core idea applies to nucleotides. No matter which is being joined to which, the\u00a0chemistry<\/em> is nucleophilic attack by 3’OH of a ribose (or deoxyribose–not directly relevant here) to the inner phosphorous atom of a triphosphate attached to the 5′ position of an incoming nucleotide.<\/p>\n I think halfway measures are the death of constructivism and introducing Big Ideas to introductory students. The differences between DNA and RNA are critical and readily understood…\u00a0if<\/em> we explain them in discussing the molecules of the central dogma. On the other hand, if they are rendered only as lists of compare-and-contrast, then we are adding meaningless terms as sub definitions of… other meaningless terms. If called upon, I could cheerfully defend the position that at the introductory level, there’s nothing\u00a0critically<\/em> different between DNA and RNA. Both…<\/p>\n Their differences generally don’t feature in any discussion of introductory biology (though both are fantastic evolutionary discoveries whereby a superior product [DNA] displaces its antecedent [RNA]; an explanation of thymine\u00a0vs. uracil here<\/a>, and its lecture materials here<\/a>). Condensed form:<\/p>\n On the other hand, my preferred approach is to attack these interesting (and\u00a0understandable<\/strong>) differences by devoting a couple class periods to investigating them. The uracil vs. thymine story offers deep insights into how evolution works, possibly into the origins of life, and challenges students to think ‘like a cell.’. The advantage of eliminating the 2′ -OH on RNA reinforces the structure of nucleic acid chains and ties in to the Sn2 reactions (this link<\/a> goes to a discussion of ATPase mechanism, of which such a reaction is part), which I have introduced in my own class by the time DNA\/RNA structure is covered.<\/p>\n I think the Big Idea we need to be communicating to students here is functional aspects of\u00a0structure <\/em>of the molecules of the central dogma. Teaching them that the ‘Genetic material’ uses ‘bases’ or ‘nucleotides’ which have ‘ribose’ and are synthesized “5′ to 3” while ‘proteins’ are made of ‘amino acids’ which have ‘carboxy termini’ and are synthesized “N-to-C” adds words upon words, with no clear requirement that any of them be anchored in concepts. The critical differences and the critical features all tie in to structure. Nucleic acids have the special ability of\u00a0partnering<\/em> specifically and unambiguously. Thus they can be copied and their sequences maintained. Amino acids represent a\u00a0toolkit<\/em>\u00a0filled with diverse ‘feels’ (interaction capabilities realized through neutrality, positive & negative charge, or H-bond donor and acceptor). Nucleic acids hold instructions; amino acids are building blocks for\u00a0machines<\/span>. These ideas are also discussed\u00a0here<\/a>.<\/p>\n thinkBio’s ‘Info Flow’ is an exercise designed to capture both the roles and the features-that-fit molecules to roles. As of January 2015 it’s still getting revised with new thinking and adaptation to lessons learned in offering it in classrooms, but versions can be explored here<\/a>.<\/p>\n More on the ‘matching’ of molecules to functions<\/a> in the Central Dogma<\/p>\n How amino acids<\/a> are well-fitted to the task of ‘building blocks of cellular machines’<\/p>\n<\/a>DNA vs. RNA: Go Big or Go Home<\/h3>\n\n
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Nucleic acid vs. protein: instructions vs. machinery<\/h3>\n
Making it an exploration: ‘Info Flow’<\/h3>\n
Further explorations<\/h2>\n