Chromatin is one of those things that I never really paid any attention until I suddenly realized how important and interesting it is. How is it that so much information (DNA) can be stored in such a small space (the nucleus)? How is it that this information is used when it is so tightly packaged? It may sound nerdy, but I’m still in awe at how important chromatin really is. This next set of posts will explore the basics of chromatin and begin to touch on the effects it has on genes and cells. I’ve already mentioned how it affects DNA repair, but the process has even more far-reaching effects.
Wednesday, March 31, 2010
Tuesday, March 30, 2010
This will be the final post about thermodynamics, but related posts (namely on some biophysics-type topics) will be posted down the line. The equations presented are summarized at the bottom of this post.
As mentioned, entropy is a measure of disorder, in a way. Entropy can be calculated as
Monday, March 29, 2010
Today’s post will be a slight departure from cell biology and genetics and will focus, instead, of some of the basics of biochemistry. It is true that I disliked biochemistry, and that’s putting it lightly, but it’s still something that is important (how important is another question) to understand. I took a few days off from updating but I return with more review fun. This set of posts will include a number of equations that I will summarize after all of the thermodynamics notes have been posted. Also, the illustrations for these posts will be simplistic, but if you have some better ideas of how to illustrate thermodynamics, I'd like to know because I'm coming up with nothing...
ΔH = ΣHproducts - ΣHreactants
Endothermic reactions are those that absorb heat (ΔH > 0); exothermic reactions release heat energy (ΔH < 0). Adding heat will affect the equilibrium of the reaction (whether it favors products or reactants). Because endothermic reactions require energy for the reaction to occur, raising the temperature favors the reactants forming products. Conversely, adding heat to an exothermic reaction will favor the formation of reactants from products because, in fact, heat is a product of the reaction.
ΔS = ΣSproducts - ΣSreactants
Friday, March 26, 2010
Today is the final part of the cell cycle that I will be writing, though more information about cell division will be posted eventually in the meiosis study notes. I find that the pathways involved in mitosis are rather easy to understand, as everything fits together - it just takes some effort to realize how everything works with everything else.
Phase of the Cell Cycle
The cell is preparing to duplicate; centrosomes appear outside the nucleus
Spindle poles form and sister chromatids condense
Sister chromatids are condensed and begin to be attached by kinetochore MTs
Sister chromatids align at the metaphase plate
The cell begins to divide the sister chromatids by releasing them to each pole
The nuclear envelope reforms and the cells begin to structurally split
Thursday, March 25, 2010
I'm going to try to make this blog post a little different with a short introduction before jumping right into my writings and ramblings about the cell cycle. This post is the second of three concerning the cell cycle, though more information will be eventually posted that is somewhat related to this topic (notably the meiosis notes). I haven't drawn a diagram for this particular post, but there are not many mechanisms involved. Tomorrow's post will include a cool drawing of separase, securin, and a bunch of other cool stuff.
When I was in college and learning the cell cycle, my professors weren't interesting or very organized. Therefore, I've tried to organize this in a way that makes sense to me. Since this organization might not make sense to everyone else, I'll be including a list of links to review articles and other websites that concern the cell cycle when all of the sections have been posted.
Wednesday, March 24, 2010
| || |
G1 – S
G2 – M
Monday, March 22, 2010
- The MRN complex recognizes and binds the free ends of the DNA
- ATM is recruited to the foci
- ATM phosphorylates H2AX, Chk2 and p53
- Chk2 phosphorylates CDC25
- Cell cycle is arrested and chromatin opens for DNA repair
Several diseases are associated with defects in the DSB response pathway. Among them are ataxia-telangiectasia, resulting from mutations in ATM. Several mutations in ATM will result in the A-T phenotype, and approximately 1% of the population carries one mutated allele. Those that suffer from this syndrome show immunodeficiency and increased cancer rates, and they have a life expectancy of 17-23 years. In addition to A-T, Nijimegen breakage syndrome results from mutations in Nbs1, and A-T like disorder (ATLD) results from Mre11 mutations. Breast cancer may also have connections to DSB repair, as BRCA1 is associated with the BASC complex, which is involved in this and many other pathways for DNA repair. BRCA1 acts as an ATM substrate and localizes to IRIFs, possibly acting as a scaffold.
Friday, March 19, 2010
Thursday, March 18, 2010
- Detection of lesion by XPC and HR23
- XPB, XPD, and TFIIH bind and act as helicases
- XPC and ERCC1-XPF act as endonucleases to remove 24-32 nucleotides
- Replacement and ligation of DNA by DNA pol and ligase
- Uracil DNA glycosylase (UDG) recognizes uracil and flips the base
- AP endonuclease (APE) nicks the site of the uracil
- Lyase removes the sugar phosphate
- Replacement of base by DNA polymerase β
- Ligation of DNA by ligase
Wednesday, March 17, 2010
Tuesday, March 16, 2010
Some of the most common mutations in DNA occur via hydrolysis a nucleotide base. Due to the high concentration of water within the cell, the DNA is constantly exposed to the harmful effects of water. Depurination results in a nucleotide without its guanine or adenine base. Deamination is a base conversion event in which a methylated cytosine residue to converted to thymine. Such an event can be especially dangerous to the cell because it can induce base changes if the mutation is not fixed immediately.
The Ames Test Simplified:
- Expose mouse to potential mutagen
- Inject mouse with arochlor to induce hepatic function
- Isolate and homogenize liver
- Combine homogenized liver with Salmonella typhimurium (His-)
- Plate Salmonella on agar lacking histidine
- Count number of colonies that have grown on the plate as a measure of mutagenicity.