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Interactions in biology: it’s binding all the way down


We use a several terms in IntroBio that all mean the same thing, but may mean little to students in the classroom–‘binding’, ‘specific interaction’, ‘interacts with’, ‘recognizes’. This is particularly dangerous with ‘recognizes’, because newcomers can envision a police line-up: targets appear and we visually choose one. Alternatively, we risk students imagining a somewhat mystical, or at least poorly-defined ‘way’ that molecules have that is beyond their ken. Nothing could be further from the truth; in some ways one of the easiest things to understand is why two molecules ‘stick to’ one another and overcome the force of Brownian motion, at least for a little while.

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Great experiments: Crick hypothesizes wobble pairing

Robotic hand with DNAToo often, biology is presented as gathering data and letting it lead us. While this is a valid and important component, there are also many glorious examples where the thinking came first and directed the experimentation. Many of the great experiments in biology came about this way–Meselson and Stahl (semi-conservative replication), Hershey-Chase (the Blender experiment, or ‘who is the genetic material)… and some that are more abstract–Pauling’s proposal of the alpha helix and beta sheet… and a number of Crick’s hypotheses. This post covers his prediction that efficiencies would be achieved in the tRNA pool through wobble pairing: relaxing orientation of the participants in a basepair to allow one base to partner with several others. Continue reading

What’s in tRNA structure: all alike; each unique

Too often we overlook the tough job that tRNAs do, seeing them only as the handmaidens of translation: matching up with mRNA; delivering a specific amino acid place on their heads by synthetases, arriving at the ribosome to first take the chain and then be stripped of it… These tiny (~100 nte.) elves  perform a series of amazing sleights-of-hand: sometimes they must all be the same (the ribosome must deal similarly with all of them); at other times, unique (codon matching) and still other times, as ‘family members’ (all those ‘serviced’ by a single tRNA synthetase. Just how much recognition-surface and information is stamped onto a tRNA?

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A machine to teach with: ATPase as a core cellular mechanism

Angry cartoon firecrackerBoth studies and common sense indicate that common threads running through our teaching provide students with reinforcement of both thread components and the things they connect. This approach also highlights conveying principles rather than fact collecting as our learning objective. The details of a basic ATP hydrolysis reaction illustrate both key principles (how enzymes actually implement their abstract aspects [speed up reaction; lower reaction barrier], roles for specific amino acids and protein folding), value of understanding chemistry in thinking about biology) as well as providing students with a tool that they’ll see over and over… and over again: the core mechanism is found in nucleotide addition, kinase and phosphatase reactions, pre-mRNA splicing, the timing mechanisms of GTPases [tubulin, EF-Tu, GPCRs], and… oh yeah: virtually every ATP-driven or -coupled reaction in the cell!

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Pull yourself together! Self-assembly in biology

Double stranded DNA moleculeLists of the ‘characteristics of life’ are a common element in introductory biology early lectures. Generally, these focus on movement, energy conversion, organization, etc.–all legitimate concepts. But the role of self-assembly in biology must not be underestimated; it’s a key feature of the flow of information in the Central Dogma (through the specific partnering of bases), folding of proteins from linear strings of amino acids (readily specified by linear structure of nucleic acids) gives rise to the functioning machines at the heart of almost all cellular work and action, and even membranes, while not members of the Central Dogma club, have function that relies critically on aspects of self-assembly. Without these properties, life would not only be impossible–they’re prerequisites for life to evolve from non-life.

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Molecule display in introductory biology

Molecule display of guanine as it 'feels'Teaching the world of molecules to relative newcomers is challenging because it’s an invisible world with ‘rules’ that don’t always have a 1-to-1 correspondence with the macroscopic world (looking at you, hydrophobicity). A second issue is that while the molecules themselves are concrete things, we discuss them using their labels–A or adenine or glucose or ‘protein’. Too often, students end up with vague notions (or none at all) about these entities. Given that everything in the cell is made of and run by molecules, student success in thinking and understanding is critically dependent on what they’re picturing as molecules. I think care in and improvements of molecule display can go a long way towards making their lives easier and their understandings richer.

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