BIOC 223

Now that we’ve finished with our introductory (beginning) course to biochemistry, and are off to enjoy the summer, I’ve been feeling a bit nostalgic. So, I figured I’d share something that I found way back in the summer after my freshman year of high school, when I first started thinking I might be interested in scientific research.

http://www.mcsweeneys.net/articles/my-first-graduate-school-rotation-written-as-a-buddy-cop-movie

Its a bit silly, but I thought some of you might enjoy it!

Enjoy the summer!
Houda

We talked briefly about money and science. How one could have great ideas and brilliant skills but without money be unable to do much. With recent declines in dispensable government funds, other sources of funding, namely really rich people, have been tapped into by scientists. An interesting Times article about this is below.

This emphasizes the need for we upcoming scientists to be able to communicate science and its significance to non science literate people. You wouldn’t want your potential donor to not be able to understand anything you were saying!

http://www.nytimes.com/2014/03/16/science/billionaires-with-big-ideas-are-privatizing-american-science.html?_r=0

How is it that winter always feels so long and yet in a matter of a few sunny days, all of the dreary, grey colors of winter are happily forgotten, and the landscape returns to its collage of beautiful greens?

The answer is a wonderful molecule called chlorophyll! There are several photosystems in the chloroplasts of plant cells which serve to translate light energy into chemical energy. No matter how familiar one is with this chemistry of this biological process, it is really a wonder of nature I think that plants have this ability to generate their own energy, and of course it is an evolution-based necessity-we are here because of chlorophyll I guess is another way of putting it. We are also hear because of nucleic acids, and amino acids, lipids and carbohydrates. For me, this is why biochemistry is amazing- we study what allows for life to exist on the molecular level. And as a class of musicians and artists, we also know what it means to appreciate what life is like beyond our biological make-ups, and yet I think as many past posts have illustrated (more so in the intersection of psyc. and biochem than other areas) that these two the biological, and our creations/our extensions of who we are, are intertwined.

Ok will get back on the track. So Chlorophyll helps in the early stage of the energy conversion process by absorbing energy from light. As you can see in the below image, it most strongly absorbs UV light in the blue and red electromagnetic ranges, and is a poor absorber of light in the green range. Hence why tissues with chlorophyll appear GREEN! Chlorophyll is hard for the plant to make and therefore plants will only make it, when it is profitable, meaning when there is enough light energy to be harvested, which is not the case in the short days of the winter. Cheers to it almost being summer, full of beautiful nature to be in awe of and exhilarating hikes and outdoors activity. We’re almost there, we can do this!

I really like the theme that has developed in our blog-pertaining to how to bring science to the public or how to get the public excited about science. So I went to the TED talk website to get some ideas, because they seem to be a front runner in this regard.

I typed in biochemistry in the search bar, and one of the selections to come up was a talk by James Watson from 2005. The movie we watched dispelled the notion I had that anyone who could make such a discovery or be awarded such an award must be a serious scholar and elegant in how they describe science. Thats not to say that James Watson isn’t a serious scholar. But the way in which he described the DNA discovery was a bit off-putting, at least for me. The audience was laughing the entire time though, and I’m sure he has told the story many, many times, so maybe he’s a bit tired of doing so.

He began his speech talking about Darwin, and the significance of spending time bird-watching with his father, which prompted him to major in Biology. He then mentioned Erwin Schrodinger’s paper “What is life,” in which Schrodinger explains that the essence of life is present in info on a molecule, in digital form. Watson said he thought about going into Biochem, and then discovered it was “boring!”

He said the impetus for the DNA work came when Wilkins showed the DNA crystal photograph, which proved DNA had a structure and that there was something universal about it, which countered the initial belief that the genetic info was on proteins.

He then mentioned that Pauling got the “alpha helix” but thought it was held together by H bonds between phosphates. But they knew that H-bonds between phosphates couldn’t exist at biological pH because the oxygen on the phosphate would have already been de-protenated. He was somewhat dismissive of Rosalind, saying that she was primarily a crystallographer and did not know organic chemistry.

He then spoke briefly about the confirmation of the structure, which he said took place over 2 hours. He summarized: I was told the H atoms were in the wrong place and so I changed them, and thereby found the base pairs. Crick immediately knew that the chains went in opposite directions.  This seems to be an awfully condensed version of what happened.

He ended by talking about what clicks for him now- genetics research looking at how diseases can be screened for via genome analysis, when contrasting to normal genomes. But his take on it I thought was peculiarly simplified. He basically said that the cause of such diseases as cancer, autism, and bipolar disorder is just a huge gap of DNA missing. He wrapped up the speech by saying that if I had enough money, I would find all the genes for these diseases this year. I think one issue when science is presented to the public is that it is over-simplified and under-estimated how much the public, with relatively less understanding of more specific science can understand, if explained well. Many pop science articles try to translate science articles for the public and leave out important details. It begs the question: is it the science authors that aren’t including enough supporting info as to how they got their results or the pop. science writers. I think it might be more the latter.

We’ve been having lovely sunny weather, and among other dreams of summer days and happiness, being outside has made me wonder about textures, and, specifically, why the warm summer light makes our stone campus look so soft. It’s curious to me that our brain biochemistry is so complex that we can take stimulus from one sensory organ and translate that stimulus to another sense. What? That’s crazy. But what’s even more crazy is that different light wavelengths can make objects seem soft, even when our brains “know” they’re rough (i.e., we have the tactile memory of the stones). I couldn’t find any articles on the biological mechanism of this translation, but I did find a psychological study that found some people are naturally adept at visually perceiving the texture of objects correctly. If any of you know what is going on on a biochemical level, please comment!

Article on visual tactile judgement (click here).

Interestingly, chemical binding on a plate in lab (think: LAL assay for endotoxins) is not the only way to determine substance concentration by fluorescence. A new assay has been developed using the largest plate well (and dilution!) in the world–the ocean. Scientists have been using bioluminescent marine bacteria to quantify aquatic toxicity. Under normal conditions, these bacteria fluoresce, making pretty lights when you paddle in the ocean at night (shameless plug: join Outing Club!). However, at high toxin concentration, the bacteria’s health of metabolic processes shut down so that the (usually dead) bacteria no longer emit light. The dangerousness of each toxin is recorded by their EC50 value, or the concentration at which the bacterial fluorescence level decreases to half the initial output.

I thought this mechanism was a kind of neat application of biochemistry found in nature as well as in the lab!

See here for more information (though it’s not really an article, per se): http://www.ineos.com/Global/Oligomers/SHE/Durasyn%20Environmental%20Summary%20202009.pdf

I found this cool picture of a different chromophores and the various colors where they fluoresce! As we talked about in class, aromatic residues play a big part in fluorescence, and the different aromatic residues that form these chromophores are evident.

I’m not sure how many of you went to the concert on Friday night, but something happened there that made me think of biochemistry! Ok, it was actually AFTER the concert, which is a little better. I’m not sure how many of you noticed all the men wandering around campus that day, but my roommate and I noticed a trend when we were in the lulu later–all the men clustered together to about two tables, even if they didn’t appear to know each other. After seeing some really great descriptions of the hydrophobic effect over the course of last week, I couldn’t help thinking of it when I saw the little clusters of guys amid all the women.