Biochem discussion

Post ID: 3008996

Overview

Please do the following:

1. Navigate to the PepDraw website: https://pepdraw.com
  - Take some time to explore this site! Create different polypeptides and look at their structures (and net charges) at different pHs.
2. Create a peptide that is 5-7 amino acids in length. Your peptide should contain the following AAs (in any order):
  - At least one nonpolar amino acid
  - At least one polar amino acid
  - At least one acidic amino acid
  - At least one basic amino acid
  - One phosphorylated amino acid (under "Special Amino Acids" - pSer, pThr, or pTyr)
3. Generate TWO versions of your peptide - one at a LOW pH (pH = 2)and one at a HIGH pH (pH = 11).
  - Note the difference in the charges on the functional groups of your peptide (and total net charge)!
4. Copy/transfer these TWO peptide structures (low & high pH) to a blank page or Word document. You can do this by saving the image (right-clicking on the image and selecting "Save Image") and then pasting the two images into a new document, OR hand-draw/copy the two structures on a blank sheet of paper Be sure to leave enough space in between your two peptide structures for annotations!
5. On your LOW pH peptide structure, annotate the following (you can do this by hand or via computer:
  1. Label the N- & C- termini
  2. Label ALL alpha-carbons (with an alpha)
  3. Label ALL peptide bonds(highlight or draw an X through these)
  4. Circle all AA residues - label which ones are nonpolar, polar, acidic, & basic
  5. For each side chain, label/identify what types of R-group interactions it can participate in (H-bond, disulfide bond, ionic/electrostatic interactions, or hydrophobic interactions.)
6. On your HIGH pH peptide structure, identify/label the following:
  1. Label ALL alpha-carbons (with an alpha)
  2. Label ALL peptide bonds(highlight or draw an X through these)
  3. Draw in ALL the amide planessurrounding EACH peptide bond (i.e., draw a box around the coplanar atoms)
  4. Label the bonds rotated for the phi and psi angles (with a phi or a psi).
  5. Circle ALL functional groups that have changed with high pH (e.g., deprotonated)