Dilettante Fascination
SCIENTIFIC ILLUSTRATION: Nucleosome
The Mediterranean Institute for Life Sciences
Split, CroatiaHigh resolution ray-traced model of a nucleosome, isolated on black.
A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around four histone protein cores. This structure is often compared to thread wrapped around a spool.
Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it. In mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter.
Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression.
When it comes to replication, cells must produce more histones in order to compact the newly synthesized DNA.
When it comes to transcription, however, they’re a bit of a pain because they need to be removed or displaced in order to expose transcriptional factor binding sites. How does a cell do this? Well, transcription factors can recruit things like histone acetyltransferases to acetylate certain basic residues of the nucleosome; this weakens the interaction between the negatively charged DNA and the relatively positive nucleosome.
Cancerous cells like to recruit “activators” such as histone acetyltransferases in order to upregulate their transcription and, subsequently, protein production.
(via molecularlifesciences)
10^23 is an astonishingly large number. The number of grains of sand in all the beaches in the world is around 10^18. The number of stars in our galaxy is about 10^11. The number of stars in the entire visible Universe is probably around 10^22. And yet the
number of water molecules in a cup of tea is more than 10^23.
(via centralscience)
Barns Are Painted Red Because of the Physics of Dying Stars
Have you ever noticed that almost every barn you have ever seen is red? There’s a reason for that, and it has to do with the chemistry of dying stars. Seriously.
Yonatan Zunger is a Google employee who decided to explain this phenomenon on Google+ recently. The simple answer to why barns are painted red is because red paint is cheap. The cheapest paint there is, in fact. But the reason it’s so cheap? Well, that’s the interesting part.
Red ochre—Fe2O3—is a simple compound of iron and oxygen that absorbs yellow, green and blue light and appears red. It’s what makes red paint red. It’s really cheap because it’s really plentiful. And it’s really plentiful because of nuclear fusion in dying stars. Zunger explains:
The only thing holding the star up was the energy of the fusion reactions, so as power levels go down, the star starts to shrink. And as it shrinks, the pressure goes up, and the temperature goes up, until suddenly it hits a temperature where a new reaction can get started. These new reactions give it a big burst of energy, but start to form heavier elements still, and so the cycle gradually repeats, with the star reacting further and further up the periodic table, producing more and more heavy elements as it goes. Until it hits 56. At that point, the reactions simply stop producing energy at all; the star shuts down and collapses without stopping.
As soon as the star hits the 56 nucleon (total number of protons and neutrons in the nucleus) cutoff, it falls apart. It doesn’t make anything heavier than 56. What does this have to do with red paint? Because the star stops at 56, it winds up making a ton of things with 56 neucleons. It makes more 56 nucleon containing things than anything else (aside from the super light stuff in the star that is too light to fuse).
The element that has 56 protons and neutrons in its nucleus in its stable state? Iron. The stuff that makes red paint.
And that, Zunger explains, is how the death of a star determines what color barns are painted.
Oh, and one more treat to celebrate the end of the Cmdr. Hadfield era on the ISS as he readies for his return tomorrow.
Here he is singing David Bowie’s “Space Oddity”, in space.
Your head now has permission to explode.
This guy. Such an awesome space dude.
The Alkaline Metals simply added to water. (last gif features Cesium, and unfortunately i could not find any with Francium which is the most explosive)
In light of the previous post, this is an example of the stuff (this is from relatively early in the semester, so this particular example looks simple) that goes on in Biochem II, which is really more of the nitty gritty of molecular biology. It focuses more on the mechanisms of replication, transcription and translation. I’m one of the few people that’s actually enjoying this class, probably much more than Biochem I. It may be because I have a proper studying method down or the professors are better or whatnot, but the stuff clicks much better in my head than the stuff from last semester.
The biggest difference between this and Biochem I is that this focuses more on structure and function. It doesn’t look like an organic chemistry roadmap; rather, it’s more along the lines of studying how mechanical structures (DNA/RNA polymerase, spliceosomes, ribosomes) function, and under what circumstances. How does binding of a hormone regulate transcription? How does a cell manage when it has a mutated mRNA which lacks a stop codon, arresting any ribosomes transcribing it? How does DNA polymerase maintain such high accuracy in replicating DNA strands?
The context of these questions just appeal to me much more. I really don’t know why.
My method of studying for this class? Take notes in class, then during the week, look over the powerpoint slides and transcribe notes again, but in the back of the notebook (the above example is taken from this little “glossary” section of my notebook). It’s a reinforcement of information, and again, while time-consuming, really helps.
Yesterday: carbohydrate metabolism
Today: citric acid cycle, electron transport/oxidative phosphorylation, beta oxidation, and ketone bodies
Tomorrow: fatty acid biosynthesis, amino acid synthesis and degradation, and nucleic acids
This, and enzyme kinetics almost killed me when I had to take Biochem I. Memorizing mechanisms for this course is one thing—it’s not like professors would ask for simple spitback. The curveballs I got used to seeing were along the lines of inhibiting a certain step in the pathway and asking what would happen. More relevant, probably, in the Electron Transport Chain. For example, you could toss in something like Antimycin A and inhibit Complex III. How much ATP would be produced? What could you put in the cell to bypass this roadblock? (I’m a bit rusty, but I still remember being asked that)
Of course, the mileage of professors may vary. For me, I not only had to memorize mechanisms, but names of activators and inhibitors which could affect various steps of the pathway as well. One could argue that, despite the information overload, it’s more integrative that way. Despite nearly ending my social life for that semester (I can’t say it killed me because I came out of it relatively unscathed), I can’t really complain against it. I think Biochem was (and still is) one of the more enlightening science courses I’ve taken in college.
If you’re taking Biochem (or at least Biochem I, which deals with mechanisms of the Citric Acid Cycle, ETC, Beta oxidation, etc), the best strategy is to just draw out the mechanisms, by yourself, with reactants and products and any possible inhibitors, repeatedly. Just draw them over, and over, and over. Staring at a slide or a page in the textbook won’t do much. Drawing the mechanisms out yourself, while time consuming, forces you to look at what you’re doing and see exactly what happens at a step. From there, you could probably imagine why a certain reaction has to occur, or why inhibiting a certain step could lead to a particular output.
Scientific American via science-junkie:
A Toxic Cascade: When the Brain Consumes Itself
In recent years neuroscientists have come upon an astonishing revelation: Alzheimer’s, Parkinson’s, Lou Gehrig’s and other major brain diseases may have a similar underlying cause. They may all result from the mis-folding of proteins in a process similar to the one linked to mad cow and other prion-based diseases.
The growing number of research findings that point to this conclusion are set out in “Seeds of Dementia,” by Lary C. Walker and Mathias Jucker in the May issue. The accompanying slide show illustrates this cascading process of one protein corrupting another, leading to the build up of toxic aggregations, which underlie diseases that cause brain cell degeneration.
Source: sciam.com
Ah, prion-based diseases; Prion proteins propagate themselves by changing the structure of other “normal” proteins into the infectious form. The nature of their lethality isn’t encoded by DNA, or even RNA, but by the very presence of just one misfolded protein.
(Although technically these proteins were encoded by DNA, and the sequence of proteins isn’t changed so this technically doesn’t break the Central Dogma of Molecular Biology)
(via thecraftychemist)
