Marmara Üniversitesi Fen-Edebiyat Fakültesi Kimya Bölümü / Biyokimya Anabilim Dalı PURIFICATION AND CHARACTERIZATION OF PROTEINS

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1 EXPERIMENT VI PURIFICATION AND CHARACTERIZATION OF PROTEINS I- Protein isolation and dialysis In order to investigate its structure and properties a protein must be obtained in pure form. Since proteins are easily denaturated and found as a complex mixture in biological materials (such as body fluids and tissue extracts), their purification is quite difficult. Source for obtaining proteins are usually tissues and cells. First step in any purification process is destroying (or lysing) the cell and solubilize its protein content in lysis buffer. This solution is called as crude extract and it contains both targeted protein and all the other molecules in the cell that soluble in chosen lysis buffer. Later, crude protein extract fractioned according their different properties such as solubility, size, electrical charge, and polarity. Various separation techniques could be use in that purpose; differential centrifuge, salting out, precipitation with cold acetone or alcohol, ultrafiltration, and various chromatographic methods. A sample methodology for purification of an enzyme from crude extract is given below: a- Obtaining crude extract using a lysis buffer b- Salting out using ammonium sulfate (solubility in salt solutions) c- Ion exchange chromatography (electrical charge difference) d- Size exclusion (molecular sieve) chromatography e- Affinity chromatography (using a specifically binding ligand) Proteins become more and more pure in each purification step although they lost activity. When working with enzyme ph and temperature of the solutions should be controlled carefully. Process Step Fraction volume (ml) Total Protein (mg) Activity (Unit) Crude extract Salting out Spesific activity(unit/mg) Ion exchange Size exclusion Affinity Biyokimya Laboratuvarı I Güz 0

2 Ion Exchange Chormatography Marmara Üniversitesi Biyokimya Laboratuvarı I Güz 1

3 Size Exclusion (Molecular Sieve) Chromatography Biyokimya Laboratuvarı I Güz 2

4 Affinity Chromatography Marmara Üniversitesi Biyokimya Laboratuvarı I Güz 3

5 Salt ions that remains in the solution after the salting out interferes with the following experiments and therefore should be removed. Gel filtration, ultracentrifuge and dialysis could be used for that purpose. Dialysis is a separation technique that facilitates the removal of small, unwanted compounds from macromolecules in solution by selective and passive diffusion through a semi-permeable membrane. Membranes used in dialysis are made of cellulose and have definite pore size (usually Da). Salts at low concentration usually used as dialysis buffer. According to the rule of diffusion salts in the protein extract move to the outside of the membrane until concentration is equal both outside and inside of the dialysis tubing. However, since they are much bigger than salt molecules, proteins stay inside the dialysis sack. Equilibrium is reached approximately in 4-6 hours. At this point, dialysis buffer replaced with a fresh one. Dialysis usually complete in hours. CHEMICALS Potassium dihydrogen phosphate, disodium hydrogen phosphate, ammonium sulfate, urea, thiourea, trishydroxymethyl aminomethane (Tris), sodium dodecyl sulfate (SDS), dialysis tubings. METHOD In this experiments proteins extracted from 3 different sources; liver, egg yolk and egg whites. Biyokimya Laboratuvarı I Güz 4

6 Lysis Buffer: 9 M urea, 0.04 M Tris and 0.1 SDS% g Tris and g urea dissolved in a 100 ml volumetric flask using ph 7.4 Sørensen buffer. Homogenization Wash the liver, and get it into small pieces with lysis buffer in laboratory blender. Further homogenize it using a homogenizer. Add 1 ml 10% SDS to the homogenate and centrifuge. Supernatant decanted in to a beaker. Take egg yolk and egg white in a beaker and add lysis buffer and small amount of 10% SDS. Carefully mix it, centrifuge and collect supernatant into a beaker. Precipitation Salting out: Take 10 ml of supernatant into a plastic centrifuge tube and using saturation table add required amount of ammonium sulfate. Centrifuge and discard the supernatant. Precipitate will be used in further steps. Precipitation with acetone: Take 4 ml of supernatant into a plastic centrifuge tube and add 8 ml of cold acetone. Mix carefully, centrifuge and discard the supernatant. Precipitate will be used in further steps. Solubilization Add minumun amount of ph7.4 Sørensen phosphate buffer to the precipitate and carefully mix to solve proteins. Biyokimya Laboratuvarı I Güz 5

7 Dialysis After salting out step, solubilized proteins dialyzed against distilled water at cold for 2 days, distilled water refreshed every 4 hours. Protein solutions store at -80 C. Question 1- How proteins can be isolated from natural sources? Examine the scientific article and write down what kind of methods used in that experiment. Biyokimya Laboratuvarı I Güz 6

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