Proteins

  1. Where do protein sequences come from?

 

 

 

 

  1. How can proteins be tethered so Edman degradation can occur? Where are they often tethered?

 

 

 

 

  1. What are three problems that sequencing by Edman degradation might face?

 

 

 

 

  1. What’s a good rule of thumb for sequence alignments? Should they be immediately trusted?

 

 

 

 

  1. Where could someone make a multiple protein sequence alignment? What is this even useful for?

 

 

 

 

  1. Why doesn’t everyone just use mass spectrometry to sequence proteins?

 

 

 

 

  1. Where might one find many, many useful online tools for protein investigation?

 

 

 

 

  1. How is it possible that sequences can be incredibly different yet the overall 3D structure is conserved?

 

 

 

 

  1. Why is most of the space in a Ramachandran unoccupied?

 

 

 

 

  1. Draw a crude peptide backbone and indicate the psi and phi angles

 

 

 

  1. What is a stronger, more stable secondary structure: alpha helix or beta sheet?

 

 

 

 

  1. Remind me why we only concern ourselves with two bond angles in the polypeptide backbone when there are three bonds: y, f, w

 

 

 

 

  1. Draw a crude alpha helix and a beta sheet. Indicate where the hydrogen bonds are and where the side chains are.  What purpose does amphipathicity serve?

 

 

 

 

 

 

 

 

 

  1. On page 370 of the Creighton book, there is a Ramachandran plot for a real protein that has been examined crystallographically. There are a number of residues outside the “normal” regions.  Give two reasons for this.

 

 

 

 

  1. Why are predictions of secondary structure with Chou-Fasman not more than 50% successful? Why are such predictions in general not particularly reliable?

 

 

 

 

  1. A protein was found in a person’s blood during an autopsy. Only a partial sequence fragment could be recovered. The fragment was subjected to trypsin digestion and GluC digestion and yielded the following pieces, as determined by Edman degradation:

 

 

Trypsin digest:

GDQMVVLEESGEWWK

VDSLETEEWFFK

EGYIPSNYVAR

SLATR

 

GluC digest

WWKARSLATRKE

GYIPSNYVARVD

WFFKGISRKD

QMVVLEE

FQKGD

 

 

 

Assemble the sequence of the fragment in the correct order:

 

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