Chapter 1 of Nelson's book to me felt a bit like revision. It went over a few important concepts for us to know, focusing on thermodynamics, which is very important for a biological system. I think that there was a lot of focus on making sure we realise how physics, and physical methods can apply to biological systems.
I think a lot of the main concepts in the chapter have already been discussed by Ross, but an important concept for me was the concept of minimisation of free energy, which can spontaneously drive processes in a system. Whilst the book doesn't give many direct biological examples, I still think that this is important. Free energy minimisation can be an important tool in structure prediction of proteins, where it is used to try and determine how a protein will fold, based on its amino acid sequence. A likely structure is found when there is a free energy minimum, found using computational methods and taking into account forces between the atoms. Unfortunately, though, this free energy minimum may be only a local minimum, so several likely protein structures can be found. I am yet to find a good reference on the internet that explains this further - so if anyone has one, feel free to comment.
Molecular motors were described as "free energy transducers" by Nelson. This is a youtube video of the molecular motor kinesin. This molecule transports other molecules, and sometimes organelles such as mitochondria around the cell by converting ATP into energy, and using that energy to "walk" along.
For me, this chapter didn't bring much that was new to the table, but I think laid the foundation for future chapters. It will be interesting to see how Nelson further develops the main ideas in Chapter 1 as the book progresses.
- Kristen
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http://www.youtube.com/watch?v=686qX5yzksU&NR=1
ReplyDeletehas a good explanation/description of the kinesin molecular motor
That was a really great clip. I particularly enjoyed the "whoosh"-ing sounds followed by the "pop"!
ReplyDeleteYou might (or might not..) find this correspondence interesting. It's about the rotation of the flagellar motor of Eschericia coli. (Like many bacteria, E. coli have tails on the back called flagelli. A powered flagellar motor causes a flagellum to spin, propelling its bacterium.) There is a good yet brief introduction on the topic at the start of the letter, and a video of Fig 2a (30x slower than real time).
ReplyDeleteI like this as an example of molecular motors, as bacterial motility is something you can see for yourself with a microscope.. If you've never had a chance yourself, head here for links to a couple of movies.
Tomas,
ReplyDeleteI downloaded the video of Figure 2a and all I could really see was different coloured pixels moving around the screen. I couldn't actually see anything rotating. Is that what it looks like to you? Perhaps my computer went funny when it downloaded the file, or I don't realise what I'm actually looking at.
I started the reading for this week and read that "individual cells take in chemical or solar energy" on page 39 of Nelson. Whilst it isn't the main focus of the chapter, all I could think of was the euglena, a single celled organism (and a eukaryote) that is not only able to consume particles of "food" (in the form of small bacteria), but also has chloroplasts and can produce sugars by photosynthesis. Chloroplasts are the green organelles also found in plants that actually conduct photosynthesis. In case anyone is interested, I have found a youtube video(http://www.youtube.com/watch?v=hiZ85y0g3UI) so you can see it. As Tomas pointed out, some micro-organisms are able to get around using flagella - if you look closely at the video, you can actually see the flagellum on the euglena in that clip. This clip (http://www.youtube.com/watch?v=Macyj2ruVuA) is much prettier looking, and you can see the bright red spot which is used to detect the sunlight and so that euglena can adjust its orientation so that the photosensitive areas are able to better absorb the sunlight.
ReplyDeleteHey Kristen,
ReplyDeleteI also saw a bunch of pixels moving around the screen what I downloaded the video of Figure 2a but I'm pretty sure that's what the video was meant to look like. I have been shown similar videos by slightly over excited lecturers =P. If you watch the yellow area as a whole, it slowly moves in an overall circular shape a couple times. If this video is similar to some of those shown in my lectures it may be pixelated as its real footage at a ridiculously high magnification of a molecular pump/motor with some sort of fluorescent label attached to the end of a moving arm.
The language is a bit journalist-esque but while we're on the topic of videos, I found this site about entropy and DNA elasticity really interesting: http://focus.aps.org/story/v9/st15
ReplyDelete