Chapter 5: Methods in Protein Biochemistry Flashcards
What is the Proteome?
The entire collection of proteins found in an organism
How is Cell Fracturation prepared?
- Cells are broken which produces cell extracts (homogenates)
- Cell suspension prepared by mincing via 1/3 ways
a. Sonication - disrupts cell membranes through vibrational ultrasonic waves
b. Shearing - forcing cells through small opening
c. Incubation with mild detergents - disrupts cell membrane
Once the Cell Fracture has been prepared how is centrifugation carried out?
- Once target protein is isolated it undergoes preparative centrefugation
- Four fractions containing Nuclei, mitochondria, plasma membrane, and cytosol
- An estimate for the total amount of protein can be made by measuring sample absorbance at 280 nm
Why is absorbance measured at 280 nm?
Because it is the wavelength where tryptophan most absorb light
What is salting out?
A process to separate proteins
- Add increasing amounts of saturated salt solution to form ionic interactions with water
- Results in insoluble aggregates of proteins
- Often use (NH4)2SO4
What is dialysis?
- A process of removing a salt (ammonium sulfate) from the protein sample
- small pores in tubing which allow salt to diffuse out but protein stays trapped
What is Column Chromatography?
A process which separates proteins based on chemical or physical interactions
- A column with a matrix in combination witha continuous flow of buffer causes separation of protein
- Measure protein by 280 nm
- Fractions are then collected in small containers
What is Gel Filtration Chromatography?
- Also called size exclusive chrom.
- separates proteins by size
- Beads have pores which means there is selectivity for which proteins travel
- large proteins travel through while small proteins get stuck(delayed) in carbohydrate beads
How does protein size factor into elution profile?
The larger the protein the faster it elutes
What is HPLC?
- High Performance Liquid Chromatography
- Column contains very small beads leading to better separation
- High pressure needed to force buffer and protein through column
- Expensive
What is Ion-Exchange chromatography?
- Uses difference in charges of proteins
- Can have anion or cation charged matrix
- Charged beads will allow same charged proteins to travel freely while oppositely charged proteins are bound until elution buffer is run.
What is Affinity Chromatography?
- ## Uses the binding properties of a target protein to separate it from proteins that lack the same properties
What is Ni-Affinity Chromatography?
- Protein starts or ends with 6 His
- Binds to Ni
- Elute with Imidazole buffer
Rank the efficiency of purification of Chemical methods
- Preparation of a crude cell extract
- Subcellular fraction using centrifugation
- Ammonium sulfate precipitate
- Gel-filtrate Chromatography
- Ion-Exchange Chromatography
- Affinity Chromatography
What is Gel Electrophoresis?
- Cheap
- Apparatus is used to determine protein purity
- provides an approximate mass of proteins (subunit composition)
- PAGE (Polyacrylamide gel electrophoresis)
- PAGE = separates proteins based on charge
Describe the setup of a PAGE electrophoresis and what it does.
- Electric field pulls proteins according to charge
- Gel matrix hinders proteins based on size and shape
- Velocity = (E*z)/f (f = 6pi)
What is SDS-Page
- SDS is a detergent that adds net negative charge to each protein to aid in the migration toward the anode
- Provides uniform charge
- Denatures shape so only size is accounted for
- Small molecules move the fastest
What process is done to make the protein bands visible?
- Staining with coomassie Brilliant Blue G-250
- Binds to Arg and Lys sidechains
What is Isoelectric Focusing?
- No SDS needed
- Gel matrix has pH gradient
- Protein migrates until they are uncharged when pH = pI
What is 2D Gel Electrophoresis?
Separation of proteins by pI then SDS page (sorts by molecular mass)
What is Edman Degredation?
- Improved Sanger’s protein sequencing technique
- Polypeptide is cleaved between first and second amino acid
- Takes ~50 min per amino acid
- Does not work on proteins that have blocked (acetylated) N-terminus
How does Edman Degradation work?
- PITC treated with trifluoroacetic acid
- This cleaved b/t first and second peptide
- Thiazolinone derivative is made and the amino acid chain loses an amino acid
- Proton is added to N
- Process repeats ( Treat next aa with PITC and base and repeat)
- Only works for up to 50 aa
What is Mass Spectrometry?
- Measures mass to charge ratio (m/z) of molecules
- Can determine molecular mass of proteins
- Can be used for aa sequencing
- Ionizes proteins and leaves them intact
- Two types ESI and MALDI
What are the differences between Matrix-assisted laser ionization and Electrospray ionization?
Matrix-assisted laser desorption ionization (MALDI)
- Laser pulse ionizes sample in absorbing matrix
- Collision with protein and transfer change occurs
- Detector in mass spectrometer measures acceleration of ions determining their mass
Electrospray Ionization (ESI)
- Polypeptide fragments (usually tryiptic fragments which is fragments of a trypsin cleaved protein) are released via high voltage metalic capillary
- Conditions cause solvent containing peptides to evaporate
- This makes highly charged gas molecules