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What is protein purification?

Multi-step fractionation process to isolate a single protein from a crude mixture


What is the most challenging job as a biochemist?

Protein purification


What was the first enzymes purified and crystalized?

Urease and Pepsin


What are the steps for protein purification?

1. Cell lysis
2. Differential centrifugation
3. Salt fractionation
4. Dialysis
5. Ion-exchange
6. Gel filtration
7. Affinity
8. Concentration
9. Purified protein which will go through structural and functional analysis


What is cell lysis?

Disruption of cells

Physical methods - mechanical shearing

Chemical methods - solubilizing plasma membranes

Enzymatic methods - cell wall digestion


What is cell fractionation?

Using centrifugation (applying centrifugal field), will isolate high density proteins into a pellet and low density protein as the supernatant

Size and density of particle, duration of centrifugation

Bacteria has less organelles so fractionation is simple but eukaryotic have many organelles.


What is differential centrifugation (subcellular fractionation)?

RPM between small and large will stay constant which is bad but RCF will change.

RCF important factors:
- angular velocity (speed)
- average radius


What is zonal centrifugation?

Fractionate into bands

- the large particles rapidly sediment
- the more spherical particles rapidly sediment
- influenced by the density of particles and the medium

vacuoles never reach bottom because equal density


What is salt fractionation?

1. Protein dissolved in water
- proteins are soluble because it is polar and makes hydrogen bonds

2. Salt (precipitate and concentrate protein)

3. Protein in ammonium sulfate
- water divided from protein to ions
- need to aggregate with each other to bind


Less soluble proteins require how much % of salt saturation?

Less soluble proteins require less % of salt saturation.


What is the ammonium sulfate precipitation equation?

Weight of salt (g) = Gsat (S2-S1) / 1-(PS2)


What is dialysis?

A separation technique of removal of small molecules from a protein mixture using semipermeable membrane


What are the uses of dialysis?

- removal of salt and many other small molecules from a protein mixture

Removal of small peptides and proteins
- anything under molecular cut-off (MWCO) such as 10 kDA will leave the bag
- anything above will stay inside the bag

Change to fresh buffer to remove more salt due to osmosis


Is changing the buffer multiple times better for dialysis?



What are the positively charged amino acids?

Lysine (Lys, K)

Arginine (Arg, R)

Histidine (His, H)


What are the negatively charged amino acids?

Aspartic acid (Asp, D)

Glutamic acid (Glu, E)


When a protein is coated with positive charges, which ion exchange to use?

Use a carboxymethyl (CM) sepharose which is a cation exchanger with negatively charged beads


When a protein is coated with negative charges, which ion exchange to use?

Use a diethyl amino ethyl (DEAE) sepharose which is a anion-exchanger with positively charged beads


What are the three properties that affect ion-exchange chromatography?

Charge state of peptide of protein

pH of buffer

pI value, need to be 2.5 pH higher or lower than pI


What is cation exchange chromatography?

Negative charged beads in the column

Negative charged proteins are collected in the flow through

Positive charged proteins will bind to the beads

Elution buffer is used to elute the bounded proteins


How does separation of proteins depend upon net charge?

With an anion-exchange chromatography (DEAE, + beads), the most positive charge will elute first as it won't bind and the most negative will tightly bind and elute last


What is required to elute proteins?


Protein binds at low ionic strength and elutes differentially by increasing salt concentration


What is gel filtration?

Separation based on size (molecular weight)

Largest molcules are excluded from the beads and elute first

Smallest molecules are included in the beads and elute last


What is elution volume (Ve)?

the volume of a buffer required to elute a compound from the time of its injection to its exit from a column

Measures how well a compound interacts with a stationary phase


What is the retention factor (K')?

K' = Elution volume of a compound (Ve) / Elution volume for a solute which does not interact with stationary phase (void Vo)


What can the retention factor (K') determine?

Determine the molecular weights of unknown proteins


What is resolution?

Ability of a column to separate two components (proteins) wide apart

Peaks elute at different volume and do not overlap

Resolution equal or higher than 2 is considered significant

Higher resolution means better separation


What does resolution depend on?

Particle size

Flow rate

Column length and diameter

Sample volume