Ch. 5 Flashcards
What is protein purification?
Multi-step fractionation process to isolate a single protein from a mixture
What are the steps of cell fractionation?
- Prep cells
- Lyse cells
- Protein activity is retained - Centrifuge to get different fractions
- Separation of organelles - Salting out
- Dialysis
What is salting out?
- Used to exploit differences in solubility of target protein relative to other proteins in the fraction
- Adding increasing amounts of saturated salt solution to protein sample
- Causes formation of insoluble protein aggregates that are functional when resolubilized
- Often use (NH4)2SO4
What is dialysis? (in terms of protein purification)
- Used to remove ammonium sulfate from protein sample
- Uses diffusion to leave protein in buffer of proper ionic strength and pH
- Pores have to be small enough that salt can exit but protein can’t
How should total protein and specific activity change as you purify?
Total protein should decrease as activity increases
What are the different column chromatography techniques?
- Size exclusion/gel filtration
- Ion exchange
- Affinity
What is column chromatography?
Used to separate proteins based on different physical/chemical interactions between the proteins and column matrix
What is size exclusion/gel filtration chromatography?
Separates proteins based on size
What is ion-exchange chromatography?
Exploits charge differences between proteins
What is affinity chromatography?
Exploits specific binding properties of the target protein to separate it from other cellular proteins that lack this binding function
What is gel electrophoresis?
Separates proteins on the basis of charge and size
What is SDS-PAGE?
Separates denatured proteins by size (final step in protein purification)
- Used to approximate molecular mass of protein or determine whether purified protein includes more than 1 polypeptide chain
What do SDS and β-mercaptoethanol do in SDS-PAGE?
- SDS adds a negative charge to all the proteins
- β-mercaptoethanol breaks disulfide bonds
What is isoelectric focusing?
Separates proteins on the basis of charge as a function of pH
What is 2D gel electrophoresis?
Isoelectric focusing combined with SDS-PAGE
- Based on pI and molecular mass
What are polyclonal antibodies?
Heterogeneous mixture of Ig proteins that recognize 1 or more epitopes on antigenic protein
What are monoclonal antibodies?
Homogeneous Ig species that recognizes 1 epitope on antigenic protein
What research methods use antibodies?
- Western blot
- Affinity chromatography
- Immunofluorescence
- Immunoprecipitation and CoIP
- ELISA
What is a Western blot?
Used to detect proteins separated by gel electrophoresis
- Uses primary (protein-specific) and secondary (detection) antibodies
What is immunofluorescence?
- Used to identify proteins in cells that have been chemically treated in a way that preserves the cell’s architecture
- After washing, cells can be visualized through fluorescence microscopy
What is ELISA?
- Identifies low level antigenic proteins
- Direct and indirect ELISA
What is the Edman degradation?
Protein sequencing method based on labeling and cleaving the N-terminal residue without disrupting the rest of the polypeptide chain
How is protein cleavage carried out?
- Trypsin: cleaves on C side of lys and arg
- Chymotrypsin: cleaves on C side of tyr, trp, and phe
- Cyanogen bromide: cleaves on C side of met
- S. aureus: cleaves on C side of asp and glu
What kind of enzymes are trypsin and chymotrypsin?
Proteases
What is mass spectrometry?
Method of measuring the mass-to-charge ratio of molecules, which is then used to deduce the molecular mass
What is X-ray crystallography?
Diffraction of X-rays from crystals of biomolecules is used to determine the locations of atoms in the structure
What are the pros and cons of X-ray crystallography?
- Pro: protein can be big
- Con: protein is dead
What is NMR spectroscopy?
Detects nuclear spin properties of certain atoms (1H, 13C, 15N) to deduce their relative locations
What are the pros and cons of NMR spectroscopy?
- Pro: protein is dynamic (not dead yay)
- Con: protein has to be small
