Insulin has ____side chains
To calculate MW you need to multiply the # of amino acids by ____
Hemoglobin has ____side chains
Hexokinase has ____side chains
RNA polymerase has ____side chains
What do conjugated proteins contain
What does protein quantification rely on
Absorbance characteristics of aromatic amino acids
Free amino group where
At amino terminus
What is ion exchange chromotography
Separates on basis of electric charge
Anion exchange column has what?
Resin has fixed cationic groups and binds anionic substances
What does cation exchange column depend on
Resin has fixed anionic group and binds cations
What is affinity chromatography
Based on binding specificity.
a. Resin is cross linked with a specific ligand
b. Protein to be purified will bind tightly
c. all other protein is washed away
d. Purified protein is released by addition of excess ligand
What is molecular sieve chromatography
Based on SIZE
a. Resin is comprised of beads with tiny pores
b. Large proteins cant enter beads and fall through column quickly
c. Small proteins are trapped and move slowly, while BIG things come out quickly
What is gel electrophoresis
Separates on basis of size
a. SDS imparts overwhelming negative charge on proteins
b. Proteins will migrate towards (+ pole)
c. Largest move slowly, smallest moves faster
What does SDS-PAGE stand for
Sodium dodecyl sulfate polyacrylamide gel electrophoresis
What is Western blotting
Transfer to a membrane (paper filter) –>designed to bind proteins. Pushes protein out of gel and onto paper. Soak blot in specific antibody solution.
What is isolelectric focusing
Separates on basis of isolectric point
a. pH gradient is produced by allowing a mixture of ampholytes in PAGE to migrate to neutral positions in an electric field.
What is 2D gel electrophoresis
1st dimension: Isoelectric focusing
2nd dimension: SDS-PAGE
What is Proteomics
Uses 2D PAGE and Mass Spec to identify differences in protein profile of two cell populations
a. Shine light on cell; cells respond differently and start making different proteins based on light dosage
b. Label them with 2 diff dyes that will coalesce. Take two pops and mix them together and do 2D gel electrophoresis. When you expose them to infrared light you can see which ones are present in treatment group and not at all
What is Mass Spectrometry
a. Proteins are added to a light absorbing matrix, then pulsed with laser which ionizes the proteins
b. Proteins are desorbed from matrix and enter into vacuum.
c. Charged proteins introduced into magnetic fields
d. Path through field is a function of mass to charge ration
- Patterns are very specific!
What are antibody-antigen interactions
Identifies specific proteins using antibodies
What are the techniques that use antibody antigen interactions
- Immunoblots (Western Blots): Transfer of proteins from gel electrophoresis onto filter paper and soaking blot with antibody antigen solution
- ELISA: Plate is precoded with antibodies. Can put protein in solution. If protein your interested in is in solution it will bind to antibody and cause color change.
- Immunocytochemistry: Usually done with cells on culture. Using antibody to determine if a specific protein is present in tissue or cells that you’re working on.
What are antibodies
Proteins produced by B lymphocytes (immuglobulins) to destroy antigen containing foreign invaders.
What are antigens
Any kind of proteins that elecit an antibody response in your body.
What is Protein sequencing
Based on Edman Degradation:
a. Anything less than 50 aa can be directly sequenced
b. Peptide bonds are hard to break (covalent bonds)
c. if you have phenylisothiocyanate it gives nice ring structure to detect aa spectrophotometrically
d. Cyanide group makes next bond very vulnerable
d. Can use mild hyrolyssis condition to cleave off aa.
e. Keep repeating
What if you have more than 50 aa?
Must be fragmented prior to sequence analysis
- Divide it into multiple samples
- DO a.a. analysis to see how many sites there are for various digestive enzymes to cut it into 2/3 fragments.
- React with FDNB; labels the N terminus only; separates aa’s
- Reduce disulfide bonds and cleave with trypsin; separate fragements and sequences the fragments
- Cleave with CNBr to separate fragments
- Establish sequence
What are Protease fragmentation examples:
- Trypsin: cleaves on carbonyl side of basic amino acids (Lys or Arg)
- Chymotrypsin: Carbonyl side of aromatics (Phe or Tyr)
- S. aureus V8 protease: Carbonyl side of acidic a.a. (Glu or Asp)
- Cyanogen Bromide: Carbonyl side of methionine
Sequence proteins from ____terminus
amino; one at a time
Build proteins from ___terminus
C (carboxyl); opposite direction
What are the steps of protein synthesis
- Bring in each aa with amino group protected so that it doesnt bind on amino side and binds with carboxy side.
- Deprotect and bring in next aa that has been protected on amino terminus and activated on carboxy terminus