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BioChem Handout
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Paul D. Adams • University of Arkansas
Mary K. CampbellShawn O. Farrellinternational.cengage.com/
Chapter FiveProtein Purification and
Characterization Techniques
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Isolation of Proteins from Cells
Many different proteins exists within one cell
• Many steps needed to extract protein of interest, and separate from many contaminants
• Before purification begins, protein must be released from cell by homogenization
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How We Get Proteins Out of Cells
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Salting Out
• After Proteins solubilized, they can be purified based on solubility (usually dependent on overall charge, ionic strength, polarity
• Ammonium sulfate (NH4SO4) commonly used to “salt out”
• Takes away water by interacting with it, makes protein less soluble because hydrophobic interactions among proteins increases
• Different aliquots taken as function of salt concentration to get closer to desired protein sample of interest (30, 40, 50, 75% increments)
• One fraction has protein of interest
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Differential Centrifugation
• Sample is spun, after lysis, to separate unbroken cells, nuclei, other organelles and particles not soluble in buffer used
• Different speeds of spin allow for particle separation
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Column Chromatography
• Basis of Chromatography
• Different compounds distribute themselves to a varying extent between different phases
• Interact/distribute themselves
• In different phases
• 2 phases:
• Stationary: samples interacts with this phase
• Mobile: Flows over the stationary phase and carries along with it the sample to be separated
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Column Chromatography
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Size-Exclusion/Gel-Filtration
• Separates molecules based on size.
• Stationary phase composed of cross-linked gel particles.
• Extent of cross-linking can be controlled to determine pore size
• Smaller molecules enter the pores and are delayed in elution time. Larger molecules do not enter and elute from column before smaller ones.
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Size Exclusion/Gel-filtration (Cont’d)
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Affinity Chromatography
•Uses specific binding properties of molecules/proteins
•Stationary phase has a polymer that can be covalently linked to a compound called a ligand that specifically binds to protein
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Group Specific Affinity Resins
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Ion Exchange
• Interaction based on overall charge (less specific than affinity)
• Cation exchange
• Anion exchange
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Electrophoresis
• Electrophoresis- charged particles migrate in electric field toward opposite charge
• Proteins have different mobility:• Charge
• Size
• Shape
• Agarose used as matrix for nucleic acids
• Polyacrylamide used mostly for proteins
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Electrophoresis (Cont’d)
• Polyacrylamide has more resistance towards larger molecules than smaller
• Protein is treated with detergent (SDS) sodium dodecyl sulfate
• Smaller proteins move through faster (charge and shape usually similar)
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Isoelectric Focusing
• Isolectric focusing- based on differing isoelectric pts. (pI) of proteins
• Gel is prepared with pH gradient that parallels electric-field. What does this do?
• Charge on the protein changes as it migrates.
• When it gets to pI, has no charge and stops
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Primary Structure Determination
How is 1˚ structure determined?
1) Determine which amino acids are present (amino acid analysis)
2) Determine the N- and C- termini of the sequence (a.a sequencing)
3) Determine the sequence of smaller peptide fragments (most proteins > 100 a.a)
4) Some type of cleavage into smaller units necessary
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Primary Structure Determination
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Protein Cleavage
Protein cleaved at specific sites by:
1) Enzymes- Trypsin, Chymotrypsin
2) Chemical reagents- Cyanogen bromide
Enzymes:
Trypsin- Cleaves @ C-terminal of (+) charged side chains
Chymotrypsin- Cleaves @ C-terminal of aromatics
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Peptide Digestion
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Cleavage by CnBr
Cleaves @ C-terminal of INTERNAL methionines
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Determining Protein Sequence
After cleavage, mixture of peptide fragments produced.
• Can be separated by HPLC or other chromatographic techniques
• Use different cleavage reagents to help in 1˚ determination
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Peptide Sequencing
• Can be accomplished by Edman Degradation
• Relatively short sequences (30-40 amino acids) can be determined quickly
• So efficient, today N-/C-terminal residues usually not done by enzymatic/chemical cleavage
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Peptide Sequencing
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