Lecture 22 - Purification, detection and characterization of proteins Flashcards
4 characteristics of proteins that can be used for protein purification
Mass/size/shape
Density
Charge
Binding affinity
3 broad methods of protein separation
Centrifugation
Electrophoresis
Chromatography
Centrifugation : Where is it done and what is required
In a centrifuge tube. Need liquid medium (aqueous) and protein of interest
What force acts on particles during centrifugation and how it is measured
Centrifugal force -> measured in earth’s gravity (1 earth gravity = 1g)
What happens in centrifuge tube if particles are denser than suspending medium ? And if less dense
Go to bottom of the tube.
Less dense = go to the top of the tube
What happens in centrifuge tube if particles have same density as medium
Stay where they are
Name of medium and product in bottom after centrifugation where protein is denser
Supernatant = medium. Pellet = particles accumulation in the bottom
For a given centrifugal force and proteins of similar shapes, what influences the rate at which the supernatant is cleared of the particles ?
Size/mass ratio of particles.
What unit is used to calculate ‘‘size’’ unit of particles during centrifugation/rate of supernatant being cleared from particle
The Svedberg
How Svederg units work
The greater the number, the faster the particle goes down the tube
Possible utility of centrifugation method
Differential centrifugation to separate cell constituants : Exemple : Nucleus denser than mitochondria so take off pellets of nuclei first and mitochrondrias left in supernatant
Electrophoresis IN FREE SOLUTION : What determines the direction of migration
Net charge
Electrophoresis IN FREE SOLUTION : What determines the speed of migration
Net charge/Mass ratio
What happens during gel electrophoresis
Migrating molecules are impeded by the gel (and larger ones more than smaller ones) so molecules that have a same net charge/mass ratio but diff. size migrate to diff. places
What is SDS and how it is used in electrophoresis
sodium dodecylsulfate : Used to denature sample of proteins so that their shape doesn’t influence their migration rate
2 characteristics of SDS (charge and binds what)
Negatively charged and binds hydrophobic residues
Something particular about proteins denatured with SDS
All have same charge:mass ratio
Proteins denatured with SDS : Migration in free solution
All would have the same eletrophoretic mobility
Proteins denatured with SDS : Migration in polyacrylamide gel (SDS PAGE = SDS Polyacrylamide gel)
Gel impedes larger molecules so migration rate is inverely related to protein size (polypeptide length)
What is the isoelectric point of a substance/protein
the pH at which it carries no charge (sum of all particles’ charges = 0)
How protein charge evolves with pH and why
Lower pH = more positive ( NH2 -> NH3 +)
Higher pH = more negative (COOH -> COO-)
What influences isolectric point of a protein
its amino acid composition
Principle of isoelectric focusing + separates protein based on what **
pH gradient created using special buffers (ampholytes) immobilized in polyacrylamide gel. Separation based on CHARGE
How ampholytes work when subjected to electric field
When subjected to electrical field, create pH gradient, lower pH towards cathode (+) and higher pH towards anode (-)
How are proteins incorporated in the medium during isoelectric focusing and where do they migrate
incorporated (mixture of proteins) into gel during formation (of gel). Positively charged proteins go towards anode and negatively charged ones go towards cathode
Where proteins stop migrating during isoelectric focusing and why
At the point in the medium where the pH is equal to their isoelectric point. Have charge of 0 so electric field doesn’t do anything
Two-dimensional gel electrophoresis on mixture of proteins 2 steps and how you pass from 1st to 2nd
1) Isoelectric focusing - separate by charge
2) SDS PAGE separate by size
From first to 2nd step, just have to apply first gel on top of second one
Antibodies principle + why useful for protein separation
Can recognize 1 specific chemical including 1 specific epitope of a protein so can be used to isolate 1 protein in a complex mixture
Other name for Western blot and principle
Immunoblot. Recognize individual protein species in a mixture of proteins separated by SDS PAGE
First step of immunobloting
Use horizontal electric field to transfer proteins from PAGE on a membrane
Second step of immunobloting
Incubate membrane with an antibody and wash excess. If needed (but not necessary) incubate w/ 2nd antibody specific to 1st one and wash again.
Western blot : Why use a second antibody specific to the first one
To detect the first one better
Third step of immunobloting (how visualization is done)
Chromogenic detection : Check where antibody is/which protein
How Western blot (immunoblot) could be used to see where in the body certain proteins are expressed more
SDS PAGE on protein mixtures from different cell types / cells from diff. tissues. Probe a western blot of this PAG with antibodies of proteins of interest to see in which cells they (the proteins) occur more
Mass spectrometry goal and what is done ultimately (and what is not done)
High-precision determination of the charge/mass ratio of ionized molecules. Used to analyze but not purify
Concept of mass spectrometry 3 steps
1) Produce gas-phased ions in a vacuum
2) Measure acceleration of ions in electric field
3) Acceleration depends on mass/charge (m/z) ratio
Produce gas-phased ions in a vacuum : Most common method used and principle
Electrospray : Molecules of interest (peptides) chopped with proteases and put in a needle with a strong voltage across it
What spectrometer detects about an ion (2)
Mass/charge ratio and abundance -> Can put these in a graph
How mass over charge ratio is measured (what units)
Daltons per electron (or proton) charge unit
Principle of MS/MS (Tandem MS) spectroscopy
Take a peptide from a first mass spectroscopy experiment, fragment it with high energy collision in an inert gas chamber and do mass spectroscopy on the fragments
What second graph of a Tandem MS can show (3)
1) Mass/charge ratio and 2) abundance of different fragments from original peptide + 3) NUMBER OF FRAGMENTS = NUMEBR OF A.A IN ORIGINAL PEPTIDE
Possible use of all mass/charge ratios of fragments from a peptide
All have 5 or 6 figures so computer can try to identify which sequence in genome could give a peptide with fragments having these m/z ratio -> 1 possiblity = peptide is identified !
How can original peptide mass be estimated
Given that we estimated the number of a.a in the original peptide and each a.a is approx 100 Da, we multiply estimated number of a.a * 100
What are proteomics
Analysis of subcellular organelles using MS and computer to find the proteins in them
