The compound Allin naturally occurs in Garlic. When the garlic clove is chopped, Allin converts into Allicin with the action of an enzyme. allicin shows the antibacterial & antifungal effects . But when cooked, as allicin decomposes, diallile sufide is made, which has much lower antibacterial & antifungal effects.
After chopping the garlic clove, when it is dissolved in a solvent like eddible oil, an unsaturated disulfide is made by binding three Allicin molecules together. This compound is known as Ajoene. Ajoene also can be found naturally in Garlic bulbs.
Ajoene has anticlotting properties. So it prevents platelets in the blood from forming blood clotts. This reduces the potential of forming heart disease & strokes. Another very important thing is that it is effective in inhibiting the growth of tumor cells. This is done by targetting the microtubule cytoskeleton of such cells. Also it shows antioxidant effects by inhibiting the release of superoxidents. And as it has antimicrobial activities, Ajoene is used in Yeast infections.
Thursday, July 31, 2008
Tuesday, July 29, 2008
Amino acid sequencing in proteins from the N terminal
The determination of amino acid sequence in proteins is known as protein sequencing. First of all, the protein should be extracted from the tissue & should separate the protein. before analyzing the amino acid sequence, should determine whether the protein contains more than one polypeptide chain. As the number of polypeptide chains is equal to the number of N terminal a.a. residues, we determine the no. of N terminal a.a. residues per molecule of protein. If the polypeptide chains have no covalent cross linkages, they can be separated by altering PH, 8M Urea/6M Guanidium HCl, high salt concentration. But if the chains are covalently cross linked by disulfide bonds, commonly they are cleaved by reducing the disulfide bond to sulfhydryl groups with mercaptoethanol. Then check the purity by using a method like polyacrylamide gel electrophoresis.
Now complete hydrolysis is done either by acid hydrolysis or by alkaline hydrolysis. In the acid hydrolysis, excess 6N HCl is added in a sealed evacuated tube at 110-120 C for 24-72h. In the alkaline hydrolysis, add 5N Ba(OH)2 under reflux for 18-24h.
Identification of N terminal amino acids -
The first useful method for this was described by Sanger. He used Fluorodinitrobenzene for this. Free unprotonated alpha amino group of peptides react with this & forms a yellow coloured derivative. Now subject to acid hydrolysis with 6N HCl. Then all the peptide bonds hydrolyses, but the bond between DNFB & alpha amino group of N terminal amino acid is stable. Then this labelled residue is separated from other amino acids by chromatography.
Another common method is Edman's method. Here, Phenyl isothiocyanate is used to cleave N terminal a.a. from peptide without disrupting other amino acids. It binds with the free amino group of a peptide to yeild the corresponding phenylthiocarbamoyl peptide. Then treat with anhydrous acid. Then the N terminal a.a. splits off as a phenylthiocarbamoyl a.a. Then it is crystallized separated & identified usually by gas liquid chromatography. The great advantage of this method is that it does not disturb the rest of the peptide chain after the removal of the N terminal a.a.
Now complete hydrolysis is done either by acid hydrolysis or by alkaline hydrolysis. In the acid hydrolysis, excess 6N HCl is added in a sealed evacuated tube at 110-120 C for 24-72h. In the alkaline hydrolysis, add 5N Ba(OH)2 under reflux for 18-24h.
Identification of N terminal amino acids -
The first useful method for this was described by Sanger. He used Fluorodinitrobenzene for this. Free unprotonated alpha amino group of peptides react with this & forms a yellow coloured derivative. Now subject to acid hydrolysis with 6N HCl. Then all the peptide bonds hydrolyses, but the bond between DNFB & alpha amino group of N terminal amino acid is stable. Then this labelled residue is separated from other amino acids by chromatography.
Another common method is Edman's method. Here, Phenyl isothiocyanate is used to cleave N terminal a.a. from peptide without disrupting other amino acids. It binds with the free amino group of a peptide to yeild the corresponding phenylthiocarbamoyl peptide. Then treat with anhydrous acid. Then the N terminal a.a. splits off as a phenylthiocarbamoyl a.a. Then it is crystallized separated & identified usually by gas liquid chromatography. The great advantage of this method is that it does not disturb the rest of the peptide chain after the removal of the N terminal a.a.
Lippincott's Illustrated Reviews : Biochemistry
Today I bought the Lippincott's Biochemistry book (4th edition), as I am reading for a Biochemistry M.Sc. It covers all the sections in Metabolism. It contains very clear coloured figures in Lipid metabolism, Nitrogen metabolism & also in Intermediary metabolism. And also the book gives a very good idea about the genetic information. The main thing is that, the book has been written in a simple way that anyone can understand. Because of that, I recomend this book for those who are interested in Biochemistry, specially in Metabolism.
Friday, July 25, 2008
Rational drug design
Most of the drugs are discovered by chance observations. With the development of Science, large scale screening experiments were done for drug targets (receptors) using a large number of different compounds.
To be effective, a drug must be bound with its targeted receptor. Unlike the traditional way, in the rational drug design, a drug is designed considering its receptor structure or one of its natural ligands. RDD involves the use of three-dimensional information about biomolecules obtained from such techniques as x-ray crystallography and NMR spectroscopy. This is also known as structure based drug design.
There are databases containing the structures of many different chemical compounds. Using the developed software, computer can identify what are the molecules that show higher affinities with the discovered structure of the receptor. If such a molecule was not discovered, there are programmes that can build molecules having the ability to interact with the receptor. If not, there are some other programmes that can identify molecules having similar properties to the ligands that interact with the receptor. When those are identified, they are tested in the laboratory. As this method reduces the large scale screening, it decreases the expense.
To be effective, a drug must be bound with its targeted receptor. Unlike the traditional way, in the rational drug design, a drug is designed considering its receptor structure or one of its natural ligands. RDD involves the use of three-dimensional information about biomolecules obtained from such techniques as x-ray crystallography and NMR spectroscopy. This is also known as structure based drug design.
There are databases containing the structures of many different chemical compounds. Using the developed software, computer can identify what are the molecules that show higher affinities with the discovered structure of the receptor. If such a molecule was not discovered, there are programmes that can build molecules having the ability to interact with the receptor. If not, there are some other programmes that can identify molecules having similar properties to the ligands that interact with the receptor. When those are identified, they are tested in the laboratory. As this method reduces the large scale screening, it decreases the expense.
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