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In Practice

Practical consideration about using the Clark electrode to study oxidative phosphorylatoin are described in an article by Estabrook . Prior to the Clark electrode, the principal method had been the cumbersome and finicky mercury manometer.

Customs and traditions

African influences are found in every aspect of the Gullahs' traditional way of life:

• The Gullah word guber for peanut derives from the Kikongo and Kimbundu word N'guba.
• Gullah rice dishes called "red rice" and "okra soup" are similar to West African "jollof rice" and "okra soup". Jollof rice is a style of cooking brought by the Wolof people of West Africa.

  

  A gullah woman makes a sweetgrass basket in Charleston's City Market

• The Gullah version of "gumbo" has its roots in African cooking. "Gumbo" is derived from a word in the Umbundu language of Angola, meaning okra, one of the dish's main ingredients.
• Gullah rice farmers once made and used mortar and pestles and winnowing fanners similar in style to tools used by West African rice farmers.

  

  Wooden mortar and pestle from the rice loft of a S.C. low-country plantation

• Gullah beliefs about "hags" and "haunts" are similar to African beliefs about malevolent ancestors, witches, and "devils" (forest spirits).
• Gullah "root doctors" protect their clients against dangerous spiritual forces by using ritual objects similar to those employed by African traditional healers.
• Gullah herbal medicines are similar to traditional African remedies.
• The Gullah "seekin" ritual is similar to coming of age ceremonies in West African secret societies, such as the Poro and Sande.
• The Gullah ring shout is similar to ecstatic religious rituals performed in West and Central Africa.
• Gullah stories about "Bruh Rabbit" are similar to West and Central African trickster tales about the clever and conniving rabbit, spider, and tortoise.
• Gullah spirituals, shouts, and other musical forms employ the "call and response" method commonly used in African music.
• Gullah "sweetgrass baskets" are coil straw baskets made by the descendants of slaves in the South Carolina Lowcountry, and are almost identical to coil baskets made by the Wolof people in Senegal.
• Gullah "strip quilts" mimic the design of cloth woven with the traditional strip loom used throughout West Africa. The famous kente cloth from Ghana and Akwete cloth from Nigeria are woven on the strip loom.
• The folk song Michael Row the Boat Ashore (or Michael Row Your Boat Ashore) comes from the Gullah culture.

History

The island of Kiawah has a long and fascinating history, outlined here and with more details here.
Kiawah Island was included in land procured from the Kiawah Indians by the English. and granted to Captain George Raynor in 1699.

The island was put to agricultural use as early as 1837. The Vanderhorsts built a plantation which was destroyed by the British in the revolutionary war (>). During the civil war, a Yankee expedition marched the length of the island (from STONO sound to Seabrook island), stopping to rest at the VanderHorst plantation, to get behind Charleston and destroy the Savannah - Charleston railroad bridge. (link)

Evolution of ATP synthase

The evolution of ATP synthase is thought to be an example of modular evolution during which two functionally independent subunits became associated and gained new functionality. This association appears to have occurred early in evolutionary history, because essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life. The F-ATP synthase displays high functional and mechanistic similarity to the V-ATPase. However, whereas the F-ATP synthase generates ATP by utilising a proton gradient, the V-ATPase generates a proton gradient at the expense of ATP, generating pH values of as low as 1.

The F₁ region also shows significant similarity to hexameric DNA helicases, and the F_O region shows some similarity to H⁺
-powered flagellar motor complexes. The α₃β₃ hexamer of the F₁ region shows significant structural similarity to hexameric DNA helicases; both form a ring with 3-fold rotational symmetry with a central pore. Both have roles dependent on the relative rotation of a macromolecule within the pore; the DNA helicases use the helical shape of DNA to drive their motion along the DNA molecule and to detect supercoiling, whereas the α₃β₃ hexamer uses the conformational changes through the rotation of the γ subunit to drive an enzymatic reaction.

The H⁺
motor of the F_O particle shows great functional similarity to the H⁺
motors seen in flagellar motors. Both feature a ring of many small alpha-helical proteins that rotate relative to nearby stationary proteins, using a H⁺
potential gradient as an energy source. This link is tenuous, however, as the overall structure of flagellar motors is far more complex than that of the F_O particle and the ring with ca. 30 rotating proteins is far larger than the 10, 11, or 14 helical proteins in the F_O complex.

The modular evolution theory for the origin of ATP synthase suggests that two subunits with independent function, a DNA helicase with ATPase activity and a H⁺
motor, were able to bind, and the rotation of the motor drove the ATPase activity of the helicase in reverse. This complex then evolved greater efficiency and eventually developed into today's intricate ATP synthases. Alternatively, the DNA helicase/H⁺
motor complex may have had H⁺
pump activity with the ATPase activity of the helicase driving the H⁺
motor in reverse. This may have evolved to carry out the reverse reaction and act as an ATP synthase.

The characteristic color of a positive biuret test

How do I make a reference?

The structure of the bacterial reaction center was solved by Huber, Deisenhofer, and Michel. Later photosystem II of the cyanobacterium Genus name was solved by a number of groups. Most recently, the higher plant chloroplast Photosystem I was solved by N. Nelson's group .

Its gene product is a subunit of the respiratory chain protein Ubiquinol Cytochrome c Reductase (UQCR, Complex III or Cytochrome bc1 complex), which consists of the products of one mitochondrially encoded gene, MTCYTB (mitochondrial cytochrome b) and nine nuclear genes: UQCRC1, UQCRC2, Cytochrome c1, UQCRFS1 (Rieske protein), UQCRB, UQCRQ[1]("11kDa protein"), UQCRH (cyt c1 Hinge protein), UCRC("cyt. c1 associated protein"), and UQCR[2]("Rieske-associated protein"). After processing the cleaved leader sequence of the iron-sulfur protein is retained as subunit 9, giving 11 subunits from 10 genes.

SU #	name	#Residues	Description
1	UQCRC1	446	Core protein 1
2	UQCRC2	439	Core protein 2
3	MTCYTB	379	Cytochrome b

The concentration is given by c = A^corrected / ε.

For the general case, consider a mixture in solution containing m components, the concentration of the j'th component being c_j. The absorbance at any wavelength, λ is, for unit path length, given by

$A_{\lambda }=\sum _{j}c_{j}\ \varepsilon _{\lambda ,j}.$

In terms of vector or function space theory, the spectra of the m different pure components form a basis spanning the m-dimensional vector subspace which includes all spectra that could theoretically be obtained from solutions containing different combinations of the m components.

Now consider a series of absorbance measurements made at different wavelengths $\lambda _{i}$, i=1 to n, on this solution containing m absorbing species. These could be a few selected wavelengths, or could be all the points at which a digital spectrum is sampled. We take the notational shortcut of referring to the absorbance or extinction coefficient at the i'th wavelength, $A_{\lambda i}$ or $\varepsilon _{\lambda i,j}$ as $A_{i}$ and $\varepsilon _{i,j}$. In other words $\lambda _{i}$ is an actual wavelength (or energy) value, while i is an integer index to that wavelength and to the absorbance measured at that wavelength. Applyng the Beer Lambert law at all wavelengths simultaneously,

$A_{i}=\sum _{j}c_{j}\ \varepsilon _{i,j}.$

This has the form of matrix multiplication, in which the column vector of concentrations is multiplied on the left by the matrix E whose columns are the spectra of the pure components, to give the measured absorbance spectrum:

  (A) = [E](C)

If the number of wavelengths is the same as the number of species, the matrix [E] is square, and the solution is given by:

  (C) = [E]-1(A)

This can always be solved if the spectra are linearly independent (one is not a linear combination of the others), but if the solution actually contains an unexpected chromophore the result will be invalid, and unless one or more of the calculated concentrations is signficantly negative, there will be no warning. Multiwavelength analysis using a number of wavelengths equal to the number of components has been applied for measuring oxy- and deoxy-hemoglobin , Protein and Nucleic acid

(a modification of the Warburg-Christian method), Chlorophyll a and b

, and mitochondrial cytochromes .

 If the number of wavelengths is greater then the number of components, the problem is over-determined, and because the observed spectrum contains noise no set of concentrations will reproduce it exactly. In this case one can determine the set of concentrations giving the least-squares best fit, which can be argued to be the set of concentrations having the greatest probability of resulting in the observed spectrum. In this case the presence of unexpected absorbing components, i.e. ones not included in the set of fitting spectra, will result in a bad fit indicating that the results are not valid.

The best-fit set of concentrations can be obtained by multiplying the observed spectrum (A) by the "generalized inverse" of the matrix E of extintcion coefficients:

  (C) = [E]-1(A)

where for practical purposes [E]^-1(A) can be calculated as [E^tE]^-1[E]. . If the matrix E is nearly singular this method of calculating the generalized inverse becomes numerically unstable, but more robust methods exist. When used with full spectral data, i.e. a spectrum sampled at equal increments between some starting wavelength and ending wavelength, which avoids the necessity of choosing optimum wavelengths for the analysis and ensures the optimum wavelengths will be included, this method has been called the "spectrum reconstruction method" (SRCM). It has been used for analysis of mixtures of chlorophyll . It has also been used for analysis of mixtures of hemes .

.

Therefore, Beer-Lambert law in matrix form: Application of the Beer-Lambert law to the absorbance of a solution containing more than one chromophoric species measured at multiple wavelengths leads to a matrix equation relating the vector of Absorbance at each wavelength i to the matrix whose columns are the known standard spectra and the vector C of concentrations of each species j:

Ai = Sum{E_i,jC_j}

Perhaps the first report of TTFA as an inhibitor of respiration was by A. L. Tappel in 1960.. Tappel had the (erroneous) idea that inhibitors like antimycin and alkyl hydroxyquinoline-N-oxide might work by chelating iron in the hydrophobic mileau of respiraory membrane proteins, so he tested a series of hydrophobic chelating agents. TTFA was a potent inhibitor, but not because of its chelating ability. TTFA binds at the quinone reduction site in Complex II, preventing ubiquinone from binding. The first x-ray structure of Complex II showing how TTFA binds, 1ZP0, was published in 2005 .

The term "Wurster's blue" is often reserved for the radical cation, the diamine being called tetramethylphenylenediamine (TMPD). The midpoint potential for titration of the first electron is given as 0.276 V vs NHE, and this transition is useful in potentiometric titrations as both a redox mediator and an indicator. The two electron-oxidized form (di-iminium) is unstable in aqueous solutions , therfore highly oxidizing conditions should be avoided in titrations relying on TMPD, or reached only during the final stage of the titration. The second oxidation step is not well separated from the first on the redox scale, so some instability will be encountered on the oxidizing side of 0.276, and it is impossible to prepare pure aqueous solutions of Wurster's Blue due to its dismutation to the unstable diaminium and TMPD.

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Summary

File information

Description	NADH Dehydrogenase 2FUG Electron Carriers Labeled
Source	en:File:NADH Dehydrogenase Electron Carriers Unlabeled.png Own work
Date	2006
Author	Richard Wheeler (Zephyris)
Permission (Reusing this file)	See below.

The different structures of chlorophyll are summarized below:

	Chlorophyll a	Chlorophyll b	Chlorophyll c1	Chlorophyll c2	Chlorophyll d	Chlorophyll f
Molecular formula	C55H72O5N4Mg	C55H70O6N4Mg	C35H30O5N4Mg	C35H28O5N4Mg	C54H70O6N4Mg	C55H70O6N4Mg
Molar Mass	893.5	907.5	611.0	608.9	895.5	907.5
C2 group	-CH3	-CH3	-CH3	-CH3	-CH3	-CHO
C3 group	-CH=CH2	-CH=CH2	-CH=CH2	-CH=CH2	-CHO	-CH=CH2
C7 group	-CH3	-CHO	-CH3	-CH3	-CH3	-CH3
C8 group	-CH2CH3	-CH2CH3	-CH2CH3	-CH=CH2	-CH2CH3	-CH2CH3
C17 group	-CH2CH2COO-Phytyl	-CH2CH2COO-Phytyl	-CH=CHCOOH	-CH=CHCOOH	-CH2CH2COO-Phytyl	-CH2CH2COO-Phytyl
C17-C18 bond	Single (chlorin)	Single (chlorin)	Double (porphyrin)	Double (porphyrin)	Single (chlorin)	Single (chlorin)
Occurrence	Universal	Mostly plants	Various algae	Various algae	Cyanobacteria	Cyanobacteria