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BBMB404Chapter3 - Chapter 3 Exploring Proteins and...

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Chapter 3: Exploring Proteins and Proteomes
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Protein function Lots of Functions
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How many proteins are there? A lot. Currently data from the Human Genome project estimates that humans have 20,000-25,000 genes, but due to alternate splicing, and post- translational modifications including cleavage and chemical modification, it is now estimated that there may be as many as 1,000,000 different protein products….in humans alone. A group studying human blood plasma estimates that there are probably some 100,000 plasma proteins, but as of 2004 only about 1000 have been detected and studied.
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How do we learn the functions of all these proteins? After all, that’s what biochemistry is all about….
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Studying protein structure and function A typical experimental format: 1. Develop an assay to identify and quantify the protein (or its activity) 2. Select a biological source of the protein and prepare the cell homogenate 3. Separate the cell homogenate into fractions by fractional centrifugation 4. Chromatography [ion exchange, gel filtration, affinity] 5. Determine protein’s purity and molecular size 6. Carry out further investigation
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1. Break open cells 2. Gross fractionation, usually based on size Differential centrifugation 3. Subfractionation based on size, charge (hydrophobicity), and affinity. Protein purification: how do you do it?
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Protein purification: size exclusion by dialysis
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Liquid Chromatography Collect fractions Different Proteins migrate at different rates Stationary phase Solid packed in column Migration through solid differs according to properties Ion exchange Gel filtration Affinity Mobile phase Liquid medium that transports sample through column
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Protein purification: size exclusion column chromatography (or “gel-filtration” ) Sephadex, Sepharose, Bio-gel: ~ 100μM beads of insoluble carbohydrate matrix like agarose, dextran, or polyacrylamide.
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ein purification: hydrophobic interaction chromatography (“ HIC”) ed on hydrophobicity At high salt concentrations, water is even more in demand for polar interactions This effectively increases hydrophobic interactions.
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“Ion exchange” chromatography based on charge This time the beads have charged groups, either positive or negative. By varying pH and salt, proteins can be separated by exploiting their differing charges and charge densities. “Anion exchange” pH ≤ 7 to ensure charge “Cation exchange” pH ≥ 4.4 to ensure charge At pH 7, which is retained most: KKKKK or DDDDD? At pH 7, which is retained most: KKKKK or DDDDD? Protein charge varies with pH and sequence, and the strength of interaction with the column depends on the ionic strength of the solvent.
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“Affinity” chromatography based on unique binding behavior Antibodies, metal-chelation/ “tagging” (e.g. “His-tag”)… H 2 N CH C CH 2 OH O N N Ni NH 2 CH C H 2 C HO O N N H 2 N CH C H 2 C OH O N N NH 2 CH C CH 2 HO O N N His “tags” (6xHis at N- or C-terminus) are very common these days
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HPLC: High Pressure (or Performance) Liquid Chromatography es pressure to take advantage of smaller bead size (and thus greater surface of interaction also speeds up separation because it moves more solvent through (due to pressure).
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