Yggdrasil

It is probably sodium dodecyl sulfate (lauryl sulfate). It is a common surfactant used in biochemistry and molecular biology experiments.

Catalysis is a very complex subject. Usually, there is no formula to determine whether a substance can catalyze a certain reaction. To find a catalyst for a certain reaction you would usually search through the literature to see what catalysts are available for your reaction. If one wants to design a new catalyst for a reaction, it is generally a trial-and-error process although one can usually try to base the design off of existing catalysts (one such method is designing simplified analogues of enzyme active sites). Catalyst is also a very broad term. A catalyst could be something as simple as an inorganic acid to something as complicated as (R,R)-(-)-N,N'-bis(3,4-di-tert-butylsalicylidene)-1,2-cyclohexanediaminomanganese (III) chloride or even biological enzymes (which are much more complicated). The activity of a catalyst does not necessarily depend on its surface area. This is true only of heterogenous catalysts, or catalysts which are in a different phase than the reactants (for example, solid MnO2 in aqueous hydrogen peroxide or solid Pt with gaseous carbon monoxide and nitrogen oxides). However, the activity of homogenous catalysts will depend on their concentration (for example, in the case of biological enzymes see Michaelis-Menten Kinetics). A catalysts' mechanism of action is dependent on the catalyst itself. Not all catalysts work in the same way, so all you can only really say that catalysts lower the activation energy of a reaction. One must examine how the catalyst lowers the activation on a case-by-case basis.

Studying math at a university is actually pretty different from math in high school. What most people don't realize is that the farther up you go in math, the less numbers you use. For example, if I flip to a random page in my abstract algebra book, the only number's you'll generally see are 1 and 0 (and these don't necessarily represent numbers but rather the concept of the identity). A lot of higher-level math (at least theoretical math) is about learning definitions, concepts, and proofs, whereas lower-level math is about evaluating equations and solving problems. I'd say if you enjoy solving problems and working with number's you'd be more suited studying engineering, physics (or another science) or even applied mathematics. However, if you like deriving equations instead of memorizing them and if you would rather prove that a solution to a problem exists than solve the actual problem, you would be well suited to theoretical math. However, I'm only majoring in math and I've only taken the basic lower-division math courses (single-variable and multi-variable calculus, linear algebra, and differential equations) and a few upper-division courses (group theory and linear algebra). Perhaps someone who has taken a little more math can provide more insight.

The (delta)G for the hydrolysis of ATP is about -30.5 kJ/mol.

Bluenoise is correct. Decarboxylation makes many reaction step irreversible and more energetically favorable. For example, in fattly acid synthesis, decarboxylation (among other factors) helps drive the synthesis of fatty acids from malonyl CoA.

A computer program which could predict protein structure would aid researchers greatly in determining the function of all the proteins in the cell. However, the function defines just one aspect of that protein's role in the cell. A proteins full biological role also must take into account the various regulatory pathways which control the transcription of its mRNA, the translation/degredation of that mRNA, its localization within the cell, and any regulation of its activity (e.g. by allosteric regulators or covalent modification). It would take a much more sophisticated system to be able to predict the complex regulatory pathways altering the protein's function. Furthermore, many biologists believe that alternative splicing accounts for a large amount of the complexity in higher organisms like humans. Since a protein structure prediction program could not predict alternative splicing, it would not completely describe the entire function of the human proteome. So, just as the advent of high-throughput DNA sequencing technology spurred the Human Genome Project, the creation of a protein structure prediction program would spur a Human Proteome Project, where researchers could rapidly define the binding parters, substrates, and products of most of the expressed sequences in the genome. The next logical step would be to focus on functional genomics, which deals with determining the paterns of expression of our genome. Combining the information of protein function from proteomics with the information about its regulation from functional genomics would likely give enough information to model a reasonably simple organism.

Many textbooks will have good information about Western Blotting. Also, you can check reference books like Current Protocols in Molecular Biology or Methods in Enzymology.

The way I've heard it used, decarboxylation refers to a reaction in which a carboxylate group (R-COO[sup-[/sup]) or carboxylic acid (R-COOH) functions as a leaving group, forming carbon dioxide. Since carboylates and carboxylic acids are organic functional groups, the term decarboxylation suggests a removal of carbon dioxide from an organic compound, which is why I corrected budullewraagh's post. I have not heard the term used in the contect of an inorganic acid such as carbonic acid, so I'm not sure if it is accurate to call this reaction a decarboxylation.

There is an extra stability associated with having a half-filled shell or completely full shell. Since the 3d and 4s orbitals are comprable in energy, removing an electron from the 4s orbital to make the 3d subshell completely full or half full makes the atom more stable.

In the reaction between baking soda (sodium bicarbonate) and vinegar (acetic acid), the acetic acid is not being decarboxylated. Rather, it's just a result of the equilibrium between carbonic acid and carbon dioxide: HCO3- + H+ <--> H2CO3 <--> CO2 + H2O Since the acetic acid supplies extra protons and carbon dioxide gets removed from the system (since it is a gas), reactions are pushed to favor the right side of the equilibrium.

It may be worth trying to purify the protein under denaturing conditions (i.e. 6M urea) and refolding it (by dialyzing out the urea) once it has been purified from the DNA. When denatured, your protein shouldn't bind DNA so it should be fairly simple to remove the DNA (especially if you have an affinity tag on your protein). Since your protein is pretty small, you should recover good yields of folded protein when you dialyze out the urea.

Yes, the shotgun method is more of a method of assembling sequencs obtained from dideoxy sequencing into a full genome. An alternative to dideoxy sequencing is chemical sequencing which uses chemicals which degrade specific base pairs. First you label the 5' end of DNA with a 32P, then you would incubate the DNA with a low concentration of these chemicals for a specified time so that on average you have one clevage per DNA molecule. Electrophoresis of the fragments and visualization by autoradiography allows one to determne the sequence. Chemical sequencing methods are not widely used anymore because it's much easier to automate dideoxy sequencing. Also, using fluorescently tagged ddNTPs is preferable to using the radioisotopes and hazardous chemicals required in chemical methods.

Can't you just measure the optical rotation using a simple polarimeter? No need to involve some fancy (and expensive!) equipment like a CD spectrometer.

It really depends on how you want to use the vector. Most plasmids do come with a start codon in them upstream of the promoter elements on the plasmid. You can either clone your gene in upstream of the start codon, in which case your gene is translated using the ATG in pBABE and your protein is expressed with a leader sequence at the n-terminus, or you can clone your gene in downstream of the start codon, in which case the ATG of the gene acts as your site. If you choose the former option, you can be sure that your protein will be expressed (as long as you clone it into the correct reading frame). If you choose the latter option, you will have a better quality protein (since you will not have the N-terminal leader sequence which could potentially mess with the structure and function of your protein) but you cannot be sure that you protein will be well expressed. Try looking up the manual for pBABE from whatever company produces that plasmid. It should have more relevant information about that vector including the sequence around the start codon in the plasmid.

In the context of biochemistry and structural biology, crystallographers are generally growing protein crystals for use in X-ray diffraction studies.

One theory on why humans and other higher organisms lost the ability to produce various compounds essential to life, such as some amino acids, vitamins, and fatty acids, is so that our cells do not have to hold the intermediate metabolites from these reactions. Taking these metabolites out of the cell, may leave room for cells of higher-organisms to hold other compounds which allow us to perform more complex functions.

Based on the cloning technologies currently available, it is actually easier to clone females than males (since donor nuclei are generally taken from cumulus cells [cells which surround the egg], which are only found in females).

Sometimes when you run circular plasmid DNA, you will get two bands. The higher band corresponds to the "relaxed" plasmid and the lower band corresponds to the "supercoiled" plasmid. However, the simplest explanation is that your RE digestion is incomplete. Some of the plasmid DNA is being cut, while some remains uncut. Since circular and linear plasmid DNA run at different positions on the gel, you would expect two bands in an incomplete digestion. Ciruclar DNA runs lower than linear DNA, so if you excise the higher band and gel purify that, you may be able to use that for your cloning steps. Perhaps you should try increasing your incubation time or the amount of enzyme used. Alternatively, you can try using a new stock of enzyme as your old enzymes may have gone bad.

Energy is not the only factor affecting the favorability of natural processes; one must also consider the change in entropy. The solid state of any material, while more energetically stable than a solution, is much more ordered. Dissolution of the solid corresponds to a change in entropy large enough to counteract the minor decrease in energy when the crystal lattice of the solid is broken up. Interestingly, despite what people may tell you in high school or lower-division college courses, non-polar solutes don't disolve in polar solutions because of entropic factors, not energetic factors. Solvating non-polar solutes requires the solvent to become more ordered and thus decreasing its entropy.

Here's an article you may be interested in: Dwyer, et al. (2004). Computational Design of a Biologically Active Enzyme. Science 304: 1967-1971. Basically, they converted ribose binding protein into a triose phosphate isomerase (a glycolytic enzyme). The approach Dwyer, et al. used could possibly be extended to what you're thinking of since they first designed and obtained a protein which could bind their substrate, then designed the catalytic site afterward. Of course, designing a novel catalytic site from scratch is a daunting task. Modifying an existing catalytic site to work on a new substrate would be easier, but it's still a pretty difficult task.

Most transition metals act as the catalytic centers of many enzymes. Transition metal complexes are great for oxidation-reduction chemistry as transition metals can exist in a variety of oxidation states, allowing them to stabilize and coordinate various intermediates. In addition, it is relatively easy to oxidize and reduce these transition metal complexes, so they can easily oxidize one molecule then reduce another to regenerate the catalyst. Iron ions serve this role in electron transport; the iron-sulfur clusters can oxidize and reduce various substrates in order to pass electrons through the electron transport chain. Furthermore, many transition metals can act as lewis acids, which can facilitate many processes (for example, they can bond to a carbonyl oxygen and draw electron density away from the carbonyl carbon, increasing that carbon's electrophilicity). For example, the zinc ion in carbonic anhydrase hyperpolarizes the H-O bond in water, allowing water to perform a nucleophilic attack on carbon dioxide. Metal ions can also have electrostatic effects, either to stabilize charged groups generated as intermediates or to neutralize areas of high charge density. For example, magnesium ions (Mg2+) help stabilize the three negative phosphate groups in ATP, preventing the negative charge from causing a repulsion between ATP and its binding site on an enzyme. The reason many metal ions can be toxic is that even though these ions are integral components of our enzymes, they are needed in only very small (trace) amounts. Therefore, our bodies have limited capabilities for metabolizing these metals and too much of the metal will overload our ability to effectively handle them, causing toxicity.

This is true if you react with a non-chiral acid/base to form an enantiomeric salt. However, usually people will reach a racemic mixture with a chiral acid/base to form a diastereomeric salt. Since diastereomers exhibit different chemical and physical properties, it is possible to fractionally crystalize diastereomeric salts and recover one enantiomer from a racemic mixture. For example (R,R)-diaminocylclohexane can be isolated from a commerical mixture of 1,2-diaminocylcohexane by forming a relatively insoluble salt with L-(+)-tartaric acid (see Walsh, et al. J. Chem. Edu. 1998 75(11): 1459).

Here's an interesting fact. While the life expectancy of humans has increased significantly over the past 100 years, the maximum human life span has not increased at all. We still do not see people living past a maximum age around 120 (although more people are beginning to aproach this theoretical maximum). So, while we have been able to combat the causes of premature death with modern medicine, we have done little to combat the actual mechanism of aging.

The R represents the side chain of the amino acids which make up the anti-parallel beta sheet. Since a wide variety of side chains can exist on a beta -sheet, they generalize the structure by writing Rs instead of specific amino acid side chains. In general, an R is an abbreviation in a chemical structure showing that something else goes where the R is, but the authors are too lazy to show the rest of the molecule, or the R-group is variable.