Part A. Conceptual Questions

• Answer any of the following questions by Shuguang Zhang:
  • How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)
  • Why humans eat beef but do not become a cow, eat fish but do not become fish?
    • When you eat, your body breaks food down into their lower level molecules like amino acids and carbohydrates, etc. Your DNA / RNA then informs what proteins must be assembled with the available amino acids
  • Why there are only 20 natural amino acids?
    • It seems this is a byproduct of many millions of years of evolutionary pressure to find a stable set of amino acids that also give life a sufficient amount of functionality. It is not strictly a technical constraint that limited life to 20 natural amino acids; it’s more of a path dependency.
  • Can you make other non-natural amino acids? Design some new amino acids.
    • Yes, but I am still reasoning through how to design them in my own words.
  • Where did amino acids come from before enzymes that make them, and before life started?
    • Amino acids could spontaneously form because of their chemical makeup. They likely existed before enzymes and may have formed in space
  • If you make an alpha-helix using D-amino acids, what handedness (right or left) would you expect?
  • Can you discover additional helices in proteins?
  • Why most molecular helices are right-handed?
  • Why do beta-sheets tend to aggregate?
    • What is the driving force for b-sheet aggregation?
  • Why many amyloid diseases form b-sheet?
    • Can you use amyloid b-sheets as materials?
  • Design a b-sheet motif that forms a well-ordered structure.

Part B: Protein Analysis and Visualization

In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins.

1. Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions.

Lysozyme C from Gallus Gallus (chicken)

• Briefly describe the protein you selected and why you selected it.

I picked lysozyme because it is a relatively simple protein that I have a better chance of understanding, given my newness in this field.

• Identify the amino acid sequence of your protein.

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

• How long is it? What is the most frequent amino acid? You can use this notebook to count most frequent amino acid - https://colab.research.google.com/drive/1vlAU_Y84lb04e4Nnaf1axU8nQA6_QBP1?usp=sharing

Length: 129 amino acids

Most frequent: N is the most frequent, with 14

• How many protein sequence homologs are there for your protein?Hint: Use the pBLAST tool to search for homologs and ClustalOmega to align and visualize them. Tutorial Here

• Does your protein belong to any protein family?

https://www.uniprot.org/uniprotkb/P00698/entry

According to uniprot, it is part of the Allergome family