Biocurious is a weblog about biology, quantified.

Molecule of the Month: 70S Ribosomes

by PhilipJ on 7 January 2010

Ribosomes are one of the wonders of the cellular world, and one of the many wonders you can explore yourself at the RCSB PDB. In 2000, structural biologists Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath made the first structures of ribosomal subunits available in the PDB, and in 2009, they each received a Nobel Prize for this work. Structures are also available for many of the other players in protein synthesis, including transfer RNA and elongation factors. Building on these structures, there are now hundreds of structures of entire ribosomes in the PDB, revealing the atomic details of many important steps in protein synthesis.

After solving the structures of the individual small and large subunits, the next step in ribosome structure research was to determine the structure of the whole ribosome. This work is the culmination of decades of research, which started with blurry pictures of the ribosome from electron microscopy, continued with more detailed cryoelectron micrographic reconstructions, and now includes many atomic structures. By using small pieces of mRNA, various forms of shortened or chemically-modified tRNA, purified protein factors, and modified ribosomes, researchers have solved the structures of ribosomes in the act of building proteins. These structures are so large that they don’t fit into a single PDB file—for instance, the structure shown here was split into PDB entries 2wdk and 2wdl.

Looking at all the different forms of life on the Earth, we find that all living organisms have ribosomes and that they come in two basic sizes. Bacteria and archaebacteria have smaller ribosomes, termed 70S ribosomes, which are composed of a small 30S subunit and large 50S subunit. The “S” stands for svedbergs, a unit used to measure how fast molecules move in a centrifuge (note that the values for the individual subunits don’t add up to the value for the whole ribosome, since the rate of sedimentation is related in a complex way to the mass and shape of the molecule). The ribosomes in our cells, and in other animals, plants and fungi, are larger, termed 80S ribosomes, composed of a 40S small subunit and a 60S large subunit. Strangely, our mitochondria have small 70S ribosomes that are made separately from the larger ones in the cytoplasm. This observation has lead to the hypothesis that mitochondria (and chloroplasts in plant cells) are actually bacteria that were caught inside cells early in the evolution of eukaryotic cells. Now, they live and reproduce happily inside cells, focusing on energy production and relying on the surrounding cell for most of their other needs.

Read more from David Goodsell at the RCSB PDB, here.

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Science resolutions for 2010

by PhilipJ on 2 January 2010

The past year hasn’t been a bad one, scientifically: I’ve published my first paper on a key piece of infrastructure for my experiments (I’ll write a bit more about this paper in a few days), and made some contributions to other experiments going on in the laboratory which should bear some fruit later in the year. That doesn’t mean there aren’t a few things I want to improve upon. Key science resolutions for 2010 are:

  • Get back into blogging.
  • Get the bulk of my experiments finished, which should result in at least a couple of first author papers for calendar year 2010.

I have gotten away from doing much writing, and that can and should be remedied. Writing about your research helps keep your accomplishments and goals clear in your own mind, and keeps the focus on the important aspects of lab work. It is easy to get distracted, but blogging about your work is a great way of staying on track (who’d have thought, blogging to try and stop wasting time!).

By following through with my first resolution, I should be able to make a good push towards finishing my PhD in a reasonable amount of time. Keeping lab goals in better focus should result in a more efficient and productive 2010, particularly since my lab infrastructure projects are just about finished. This is my third year in Toronto, and after a couple of years of building equipment and learning some new biochemistry skills, everything seems to be coming together at once.


Analyze this

by PhilipJ on 22 December 2009

I was surprised the read, over at Incoherently Scattered Ponderings, about the difference The Ponderer sees in hiring a graduate student or a postdoc. Of particular interest were the anecdotes regarding a postdoc who didn’t care to do any of the ‘grunt’ work (soldering), or another postdoc who didn’t want to do any data analysis, favouring undergraduates to do both tasks:

A postdoc in my group wanted to “outsource” most data analysis to an undergrad – which we did (I was lucky to have several talented undergrads) – mostly because postdoc did not want to get heavy into MATLAB. In retrospect, this was a mistake, because now every time we/I had a new idea for data analysis, postdoc had to go looking for undergrad, who was busy with classes, etc. When I was a postdoc I did all of my data analysis – no matter how mind-numbing it was (even though I was often grumpy about it too).

We all like and dislike different aspects of our research. In my field, lots of people hate having to realign lasers, or construct flow cells, or from my old life, pull micropipettes. But I have yet to find someone (other than The Ponderer and his postdoc) who doesn’t love playing around with their data, data that is usually only collected after a significant struggle in the lab. Compound this with the importance of being able to trust and repeat the manipulations you do to tease our important parameters from your data, and I can’t understand why anyone would want to hand off the analysis to someone else. I would prefer to analyze data in lieu of basically any other lab task I can think of.

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