molecular biology

4 Articles

Binding of the Rab5(GTP) to EEA1 triggers a transition of the EEA1 molecule from a rigid, extended state to a more flexible, collapsed state. (Credit: Anupam Singh et al., 2023)

Not Just ATP: Two-Component Molecular Motor Using GTPase Cycle Demonstrates Mechanotransduction

May 17, 2023 by 15 Comments

For most of us who haven’t entirely slept through biology classes, it’s probably no secret that ATP (adenosine triphosphate) is the compound which provides the energy needed for us to move our muscles and for our body to maintain and repair itself, yet less know is guanosine triphosphate (GTP). Up till now GTP was thought to be not used for mechanical action like molecular motors, but recent research by Anupam Singh and colleagues in Nature Physics (press release) has shown that two GTPase hydrolase enzymes (Rab5 and EEA1) function effectively as a reversible molecular motor.

Although much of the heavy lifting in the body has shifted to use ATP with ATPases such as myosin and kinesin, GTPases have retained their functional roles in mostly signal transduction (acting as switches or timers), a tethered EEA1 enzyme performs mechanical force when a Rab5 enzyme (in its activated, GTP state) binds to it. Within e.g. a cell this can pull membranes and other structures together. Most importantly, the researchers found that no external influence was necessary for the inactive (GDP) Rab5 enzyme to separate and EEA1 to revert back to its original state, completing a full cycle.

This discovery not only gives us another intriguing glimpse into the inner workings of biological systems, but also increases our understanding of how these molecular motors work, opening intriguing possibilities for constructing our own synthetic structures such as protein engines, where mechanical movement is needed on scales which require such molecular motors.

(Heading image: Binding of the Rab5(GTP) to EEA1 triggers a transition of the EEA1 molecule from a rigid, extended state to a more flexible, collapsed state. (Credit: Anupam Singh et al., 2023) )

Retrotechtacular: Understanding Protein Synthesis Through Interpretive Dance

August 1, 2021 by 8 Comments

With the principles of molecular biology very much in the zeitgeist these days, we thought it would be handy to provide some sort of visual aid to help our readers understand the complex molecular machines at work deep within each cell of the body. And despite appearances, this film using interpretive dance to explain protein synthesis will teach you everything you need to know.

Now, there are those who go on and on about the weirdness of the 1960s, but as this 1971 film from Stanford shows, the 60s were just a warm-up act for the really weird stuff. The film is a study in contrasts, with the setup being provided by the decidedly un-groovy Paul Berg, a professor of biochemistry who would share the 1980 Nobel Prize in Medicine for his contributions to nucleic acid research. His short sleeves and skinny tie stand in stark contrast to the writhing mass of students capering about on a grassy field, acting out the various macromolecules involved in protein synthesis. Two groups form the subunits of the ribosome, a chain of ballon-headed students act as the messenger RNA (mRNA) that codes for a protein, and little groups standing in for the transfer RNA (tRNA) molecules that carry the amino acids float in and out of the process.

The level of detail, at least as it was understood in 1971, is impressively complete, with soloists representing things like T-factor and the energy-carrying molecule GTP. And while we especially like the puff of smoke representing GTP’s energy transfer, we strongly suspect a lot of other smoke went into this production.

Kitsch aside, and with apologies to Lewis Carroll and his Jabberwock, you’ll be hard-pressed to find a modern animation that captures the process better. True, a more traditional animation might make the mechanistic aspects of translation clearer, but the mimsy gyre and gimble of this dance really emphasize the role random Brownian motion plays in macromolecular processes. And you’ll never see the term “tRNA” and not be able to think of this film.

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Hacked Heating Instruments For The DIY Biology Lab

November 12, 2018 by 4 Comments

[Justin] from The Thought Emporium takes on a common molecular biology problem with these homebrew heating instruments for the DIY biology lab.

The action at the molecular biology bench boils down to a few simple tasks: suck stuff, spit stuff, cool stuff, and heat stuff. Pipettes take care of the sucking and spitting, while ice buckets and refrigerators do the cooling. The heating, however, can be problematic; vessels of various sizes need to be accommodated at different, carefully controlled temperatures. It’s not uncommon to see dozens of different incubators, heat blocks, heat plates, and even walk-in environmental chambers in the typical lab, all acquired and maintained at great cost. It’s enough to discourage any would-be biohacker from starting a lab.

[Justin] knew It doesn’t need to be that way, though. So he tackled two common devices:  the incubator and the heating block. The build used as many off-the-shelf components as possible, keeping costs down. The incubator is dead simple: an insulated plastic picnic cooler with a thermostatically controlled reptile heating pad. That proves to be more than serviceable up to 40°, at the high end of what most yeast and bacterial cultures require.

The heat block, used to heat small plastic reaction vessels called Eppendorf tubes, was a little more complicated to construct. Scrap heat sinks yielded aluminum stock, which despite going through a bit of a machinist’s nightmare on the drill press came out surprisingly nice. Heat for the block is provided by a commercial Peltier module and controller; it looks good up to 42°, a common temperature for heat-shocking yeast and tricking them into taking up foreign DNA.

We’re impressed with how cheaply [Justin] was able to throw together these instruments, and we’re looking forward to seeing how he utilizes them. He’s already biohacked himself, so seeing what happens to yeast and bacteria in his DIY lab should be interesting.

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Biohacking Lactose Intolerance

February 14, 2018 by 73 Comments

Would you pop a homemade pill containing genetically engineered virus particles just so that you can enjoy a pizza? Not many people would, but then again, if you’ve experienced the violent reaction to lactose that some people have, you just might consider it.

Such was the position that [The Thought Emporium] found himself in at age 16, suddenly violently lactose intolerant and in need of a complete diet overhaul. Tired of scanning food labels for telltale signs of milk products and paying the price for the inevitable mistakes, he embarked on a journey of DIY gene therapy to restore his ability to indulge in comfort foods. The longish video below details a lot of that journey; skip to 15:40 if you want to cut to the chase. But if you’re at all interested in the processes of modern molecular biology, make sure you watch the whole thing. The basic idea here is to create an innocuous virus that carries the lac gene, which encodes the enzyme β-galactosidase, or lactase, and use it to infect the cells of his small intestine. There the gene will hopefully be expressed, supplementing the supply of native enzyme, which in most adult humans is no longer expressed at the levels it was when breast milk was our primary food.

Did it work? We won’t ruin the surprise, but in any case, the video is a fascinating look at mammalian cell transfection and other techniques of genetic engineering that are accessible to the biohacker. Still, it takes some guts to modify your own guts, but bear in mind that this is someone who doesn’t mind inserting magnetic implants in his fingers.

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