Lab Techniques
How can you find the molecular weight of a protein using Gel Electrophoresis (Hint... Friday’s Quiz)
Plot the log of the molecular weight vs the distance each band travelled
Which amino acids contain sulfur?
Methionine and Cysteine
The primary structure of a protein determines the overall ____ Structure
3D or Tertiary
Which Protein Sequencing method involves finding m/z?
Mass Spectrometry
What is the name of the plot that visualizes the phi and psi angles?
Ramachandran Plot
What is the highest number of residues per peptide chain that the Edman Degradation can be used for?
50 Residues
Which Amino Acid cannot be present in alpha helices?
Prolin
Why is rotation restricted about a peptide bond
It has partial double bond character
The Edman Degradation Cleaves Amino Acids from which terminus?
The N-Terminus
What level of protein structure is visualized based on the phi and psi angles plotted?
Protein Secondary Structure
What stain is used in SDS PAGE to help view the protein bands?
Coomassie Blue
Cyanogen Bromide is a Protease that cleaves peptides at which amino acid?
Methionine
The sequence of amino acids can freely rotate about the nitrogen-alpha carbon bond for all the amino acids except:
Proline
Once protein fragments have been identified and arranged, what must be done to finish the complete sequence?
The location of the S-S Bonds bust be determined
Which amino acid has the greatest number of potential psi and phi angle conformations?
Glycine
What is used to deprotect the final amino acid and remove the completed chain from the column in the Merrifield Synthesis?
Hydrofluoric Acid (HF)
Proline structure can differ from other amino acids in beta turns (in terms of its configuration.) Which configuration is more common in proline than the other amino acids? (Not talking about it being a secondary amine)
The cis configuration
What is the driving force for the assumed conformations of a protein under biological conditions?
Thermodynamics / Free Energy / Delta G
How much protein is needed for MALDI MS?
Less than one microgram
What protein structure can be seen around +60 psi and +60 phi angles
Left Handed Alpha Helices
What two amino acids show ambiguous results in Tandem Mass Spectroscopy and Why?
Leucine and Isoleucine, due to their mass being the same
What are the two most prevalent amino acids in silk and spider webs?
Glycine and Alanine
Describe the conformational entropy of unfolded proteins
Unfolded proteins have high conformational entropy.
What chemical prevents spontaneous oxidation of disulfide bonds during sequencing?
Iodoacetate
There are multiple protein structures associated with the upper right quadrant of the phi and psi plot (Psi 0 to 180, Phi -60 to -180). List three of them
Antiparallel Beta Sheets, Parallel Beta Sheets, Collagen Triple Helix, Right-Twisted Beta Sheets, Some Beta turns/loops