User:Eaberry/sandbox

Sub- and Super-scripts
Use the HTML tags "sub" and "sup": I22

What is the pKa?
The text gives the pKa as 8.00 in one place, and 7.7 in another. Sigma-Aldrich reports 7.92. I suspect the iargest value is the thermodynamic pKa extrapolated to infinite dilution, and the other two are at more reasonable ionic strengths. Because the dianionic red form is stabilized by high ionic strength more than the mono-anionic yellow form, ioonic strength will favor dissociation, making it a stronger acid. Does anyone have a reference to the determination of the pKa, preferably with ionic strength dependence? I purchased the sodium salt from sigma. When dissolved in the standard pH 7.02 phosphate buffer using for calibrating pH electrodes, the molar ratio of the dibasic 559 cpd to monobasic 432 nm compound was 0.187, consistent with a pKa of 7.75 at this ionic strength (which I suspect is rather high).

Dependence of pH on ionic strength and temperature
The Henderson-Hasselbach equation gives the pH of a solution relative to the pKa of the acid-base pair. However the pKa is dependent on ionic strength and temperature, and as it shifts so will the pH of a solution based on that acid-base pair. Because the doubly charged HPO4-2 is stabilized more by high ionic strength than is the singly-charged H2PO4-, their pKa is somewhat dependent on ionic strength. The thermodynamic pKa of ~7.2 is the value extrapolated to zero ionic strength, and is not applicable at physiological ionic strength. Phillips et al. measured the pKa at 10, 25, and 37°C at various ionic strength. For the latter two temperatures they report pKa in Debye-Hückel equations (plotted in the accompanying figure for µ up to 0.5 M): at 25C: pKa2 = 	7.18 - 1.52 sqrt(µ) + 1.96 µ at 37C: pKa2 = 	7.15 - 1.56 sqrt(µ) + 1.22 µ

The pKa0 is weakly dependent on temperature. Phillips et al. reported ∆H0 at 25C of 760 cal/mol (3180 J/mol) and a linear dependence of pKa0 on 1/T (Van 't Hoff equation). The positive ∆H0 results in an increase in Ka, and thus a decrease in pKa0 with rising temperature, the change in pKa0 being 166 × the change in (1/T), which around 25C results in a change in pKa0 of -0.00187 per degree. This applies strictly to the extrapolated thermodynamic pKa0 at infinite dilution, and as the Figure shows, the temperature effect can be much larger at higher ionic strength.

Latex
LaTeX (formatted as La Te X, pronounced , , , or ), is a document markup language and document preparation system for the TeX typesetting program. The term LaTeX refers only to the language in which documents are written, not to the editor application used to write those documents. In order to create a document in LaTeX, a .tex file must be created using some form of text editor. While most text editors can be used to create a LaTeX document, a number of editors have been created specifically for working with LaTeX.

LaTeX is widely used in academia. It is also used as the primary method of displaying formulas on Wikipedia. As a primary or intermediate format, e.g., translating DocBook and other XML-based formats to PDF, LaTeX is used because of the high quality of typesetting achievable by TeX. The typesetting system offers programmable desktop publishing features and extensive facilities for automating most aspects of typesetting and desktop publishing, including numbering and cross-referencing, tables and figures, page layout and bibliographies.

LaTeX is intended to provide a high-level language that accesses the power of TeX. LaTeX essentially comprises a collection of TeX macros and a program to process LaTeX documents. Because the TeX formatting commands are very low-level, it is usually much simpler for end-users to use LaTeX.

LaTeX was originally written in the early 1980s by Leslie Lamport at SRI International. The current version is LaTeX2e (styled as La Te X 2 &epsilon; ). LaTeX is free software and is distributed under the LaTeX Project Public License (LPPL).

Typesetting system
LaTeX is based on the philosophy that authors should be able to focus on the content of what they are writing without being distracted by its visual presentation. In preparing a LaTeX document, the author specifies the logical structure using familiar concepts such as chapter, section, table, figure, etc., and lets the LaTeX system worry about the presentation of these structures. It therefore encourages the separation of layout from content while still allowing manual typesetting adjustments where needed. This is similar to the mechanism by which many word processors allow styles to be defined globally for an entire document or the use of Cascading Style Sheets to style HTML.

Structure and Mechanism
The X-ray structures of yeast MPP, and a cleavage-deficient MPP with substrate bound, are available. The sequence around the scissile bond binds as a beta strand in such a way that the scissile bond aligns with the zinc binding site to allow nucleophilic attack by a zinc--coordinated water molecule on the carbonyl carbon of the residue before the scissile bond (last residue of the signal peptide).

How to use a template
You transclude it just as was done in Thames, by using and then including whichever parameters you wish to use. You might find it easier to copy the blank from the "Usage" section from Template:Infobox river/doc and then fill in the values for each parameter you wish to use (and you might want to tidy up by deleting the parameters which you aren't using). - David Biddulph (talk) 12:13, 5


 * Here

Wiki-Math
When each receptor has a single ligand binding site, the system is described by

[R] + [L] \underset{k_{\text{off}}}{\overset{k_{\text{on}}}{\rightleftharpoons}} [RL] $$

[R] + [L] \underset{K_{\text{D}}}{\rightleftharpoons} [RL] $$ with an on-rate (kon) and off-rate (koff) related to the dissociation constant through Kd=koff/kon. When the system equilibrates,

k_{\text{on}} [R] [L] = k_{\text{off}} [RL] $$ so that the average number of ligands bound to each receptor is given by

\bar{n} = \frac{[RL]}{[R] + [RL]} = \frac{[L]}{K_d + [L]} = (1 - \bar{n}) \frac{[L]}{K_d} $$ which is the Scatchard equation for n=1.

n = [RL] + [R]; [R] = n - [RL] 			(2) From (1): $$	Kd = [R]\frac{[L]}{[RL]}		(3)$$ $$	Kd\frac{[RL]}{[L]} = [R]       $$ Substituting for [R] from (2) $$Kd\frac{[RL]}{[L]} = n - [RL]$$ $$[RL] = n - Kd\frac{[RL]}{[L]}	(4)$$ plotting [RL] vs [RL]/[L] (bound vs bound/free) give n as the Y intercept, -Kd as the slope.

Molecular target
Buparvaquone resistance appears to be associated with parasite mutations in the Qo quinone-binding site of mitochondrial cytochrome b. Its mode of action is thus likely to be similar to that of the antimalarial drug atovaquone, a similar 2-hydroxy-1,4-napthoquinone that binds to the Qo site of cytochrome b thus inhibiting Coenzyme Q – cytochrome c reductase.

Dinoseb
Dinoseb is also a weak inhibitor of Complex III and Complex II of the repiratory chain.

Mitochondrial vs Cytoplasmic Protein Synthesis
Mitochondrial protein synthesis is resistant to inhibition by cycloheximide. On the other hand chloramphenicol inhibits mitochondrial (and bacterial) protein synthesis, but synthesis on mitochondrial ribosomes is resistant. Before genomes were available, this dichotomy was used to determine which mitochondrial proteins were synthesized in the cytoplasm from nuclear genes.

At higher concentrations, stigmatellin also inhibits Complex I, as a "Class B" inhibitor of that enzyme Crystal structures for stigmatellin-inhibited bc1 complex from bovine, avian, yeast (Saccharomyces cerevisiae) and bacterial (Rhodobacter capsulatus, Cereibacter sphaeroides, and Paracoccus denitrificans) sources are available.

The chromone inhibitor stigmatellin--binding to the ubiquinol oxidation center at the C-side of the mitochondrial membrane. von Jagow G, Ohnishi T. FEBS Lett. 1985 Jun 17;185(2):311-5. doi: 10.1016/0014-5793(85)80929-7. PMID: 2987042 In 1979 Trumpower's lab isolated the "oxidation factor" from bovine mitochondria and showed it was a reconstitutively-active form of the Rieske Iron-sulfur protein

Chicken ovomucoid is synthesized as a pre-protein consisting of 208 or 210 amino acids. A 24-residue presequence is removed to give the mature 20 kDa protein of 185 residues. Ovomucoid has serine protease inhibitor activity. The structure of turkey ovomucoid complexed with the serine protease subtilisin has been determined by X-ray crystallography.

Template Furthermore, the "intensity statistics" of centric reflections ($$ P(|E|) = 2 |E| e^{-|E|^2} $$ ) set xrange [0:5] plot 2*x*exp(-x*x) are different from those of acentric reflections ($$ P(|E|) = \sqrt{\frac{2}{\pi}} e^{-|E|^2/2} $$ ) set xrange [0:5] plot sqrt(2/3.14)*exp(-x*x/2)

ATPase
Further updates: These figures may still require further tweaking as new structural details become available. The above value of 3 H+/ATP for the synthase assumes the synthase translocates 9 protons, and produces 3 ATP, per rotation. The number of protons depends on the number of c subunits in the Fo c-ring, and it is now known that this is 10 in yeast Fo and 8 for vertebrates. Including one H+ for the transport reactions, this means that synthesis of one ATP requires 1+10/3=4.33 protons in yeast and 1+8/3 = 3.67 in vertebrates. This would imply that in human mitochondria the 10 protons from oxidizing NADH would produce 2.72 ATP (instead of 2.5) and the 6 protons from oxidizing succinate or ubiquinol would produce 1.64 ATP (instead of 1.5). This is well within the margin of experimental error described in a recent review.

blah blah blah. .

Use of capital letters to designate the type of heme
Note Palmer's IUPAC article on nomencllature of electron transfer proteins makes no mention. Started by Caughey?) who named his preparation of heme "heme A" to distinguish it from heme a, heme a', heme a* etc which were various modified forms of heme. In a later paper he used capital letters for hemesA, B, and C. The practice was formalized by Wikstrom who explained the usage: --- lower case when it is really a cytochrome, i.e. in a particular environment in a protein as opposed to the substance. For example cytochome oxidase (complex III) contains heme a and a3, for a total of 2 mol heme A/mol protein. Complex III contains cytochrome b with heme bH and bL, and cytochrome c1, for a total of 2 mol heme B and 1 mol heme C per mole of the complex. Papers by halestrap, berry and Rich follow this practice

Although not sanctioned/proscribed by official convention (e.g. Palmer)International Union of Biochemistry (1979) Enzyme Nomenclature(Academic, New York), pp. 593-601., the practice of designating hemes with upper case letters has been used by a number of authors (caughey, Halestrap, Wikstrom, rich, berry).

The practice of designating hemes with upper case letters was formalized in a footnote in a paper by Puustinen & Wikstrom which explains under which conditions a capital letter should be used: "we prefer the use of capital letters to describe the heme structure as isolated. Lowercase letters may then be freely used for cytochromes and enzymes, as well as to describe individual protein-bound heme groups (for example, cytochrome bc, and aa3 complexes, cytochrome b5, heme c1 of the bc1 complex, heme a3 of the aa3 complex, etc)." In other words the chemical compound would be designated with a capital letter, but specific instances in structures with lowercase. Thus cytochrome oxidase, which has two A hemes (heme a and heme a31) in its structure, contains two moles of heme A per mole protein. Cytochrome bc1, with hemes bH, bL, and c1; contains heme B and heme C in a 2:1 ratio. The practice seems to have originated in a paper by Caughey and York in which the product of a new isolation procedure for the heme of cytochrome aa3 was designated heme A to differentiate it from previous preparations: "Our product is not identical in all respects with the heme a obtained in solution by other workers by the reduction of the hemin a as isolated previously (2). For this reason, we shall designate our product heme A until the apparent differences can be rationalized." . In a later paper, Caughey's group uses capital letters for isolated heme B and C as well as A.

Biochemical process of fermentation of sucrose


The chemical equations below summarize the fermentation of sucrose (C12H22O11) into ethanol (C2H5OH). Alcoholic fermentation converts one mole of glucose into two moles of ethanol and two moles of carbon dioxide, producing two moles of ATP in the process.

The overall chemical formula for alcoholic fermentation is:


 * C6H12O6 → 2 C2H5OH + 2 CO2

Sucrose is a dimer of glucose and fructose molecules. In the first step of alcoholic fermentation, the enzyme invertase cleaves the glycosidic linkage between the glucose and fructose molecules.


 * C12H22O11 + H2O + invertase → 2 C6H12O6

Next, each glucose molecule is broken down into two pyruvate molecules in a process known as glycolysis. Glycolysis is summarized by the equation:


 * C6H12O6 + 2 ADP + 2 Pi + 2 NAD+ → 2 CH3COCOO− + 2 ATP + 2 NADH + 2 H2O + 2 H+

The chemical formula of pyruvate is CH3COCOO−. Pi stands for the inorganic phosphate.

The enzyme in step 3 is pyruvate decarboxylase.

Finally, pyruvate is converted to ethanol and CO2 in two steps, regenerating oxidized NAD+ needed for glycolysis:
 * 1. CH3COCOO− + H+ → CH3CHO + CO2

catalyzed by pyruvate decarboxylase
 * 2. CH3CHO + NADH+H+ → C2H5OH + NAD+

This reaction is catalyzed by alcohol dehydrogenase (ADH1 in baker's yeast)

As shown by the reaction equation, glycolysis causes the reduction of two molecules of NAD+ to NADH. Two ADP molecules are also converted to two ATP and two water molecules via substrate-level phosphorylation.

Related processes
Fermentation of sugar to ethanol and CO2 can also be done by Zymomonas mobilis, however the path is slightly different since formation of pyruvate does not happen by glycolysis but instead by the Entner–Doudoroff pathway. Other microorganisms can produce ethanol from sugars by fermentation but often only as a side product. Examples are
 * Heterolactic acid fermentation in which Leuconostoc bacterias produce Lactate + Ethanol + CO2
 * Mixed acid fermentation where Escherichia produce Ethanol mixed with Lactate, Acetate, Succinate, Formate, CO2 and H2
 * 2,3-butanediol fermentation by Enterobacter producing Ethanol, Butanediol, Lactate, Formate, CO2 and H2

PMID reference
The term Fo stands for ologomycin sensitivity conferring factor (or fraction) .or or maybe use this: or Use this. It seems that Title is the only thing that is required (as long as PMID is provided?). Another template:this.

and later this

Complex II
Succinate dehydrogenase was first isolated as a two subunit enzyme (EC 1.3.99.1) lacking the two membrane subunits, called succinic dehydrogenase .

The 4-subunit succinate:ubiquinone oxidorectase (EC 1.3.5.1) was first isolated by Hatefi and co-workers in 1962 and named "Complex II" to differentiate it from the other three respiratory complexes described in that paper. Unrelated reference. Which was further shown in a later paper, and a follow-up work.