Homework

For in-person students please answer atleast 2-3 questions in Part A and 1 question in Part C. Questions marked with * are for extra credit

Part A: Using the PDB

<aside> ⚠️ Mandatory for MIT/Harvard Students and Committed Listeners Due at the start of class March 5

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• 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?

  Some interesting ideas I learnt from this research: Because I did not know where to begin with this question. I asked chatgpt how are proteins processed by the human body? what would happen if we ate an alien? what would happen if the alien had synthetic nucleotides and the human body did not have the required enzymes? are foods poisonous because we do not possess the enzymes to break them down or are there other mechanisms. and finally could you eat a mirrored cow?

  Because of these questions I could get to the answer from these sources

  Protein digestion and absorption: When you eat food, the body’s digestive system breaks down dietary protein into individual amino acids, which are absorbed and used by cells to build other proteins and a few other macromolecules, such as DNA. Let’s follow the path that proteins take down the gastrointestinal tract and into the circulatory system.

  Protein Metabolism: The digestion of proteins begins in the stomach. When protein-rich foods enter the stomach, they are greeted by a mixture of the enzyme pepsin and hydrochloric acid (HCl; 0.5 percent). The latter produces an environmental pH of 1.5–3.5 that denatures proteins within food. Pepsin cuts proteins into smaller polypeptides and their constituent amino acids. When the food-gastric juice mixture (chyme) enters the small intestine, the pancreas releases sodium bicarbonate to neutralize the HCl. This helps to protect the lining of the intestine. The small intestine also releases digestive hormones, including secretin and CCK, which stimulate digestive processes to break down the proteins further. Secretin also stimulates the pancreas to release sodium bicarbonate. The pancreas releases most of the digestive enzymes, including the proteases trypsin, chymotrypsin, and elastase, which aid protein digestion. Together, all of these enzymes break complex proteins into smaller individual amino acids, which are then transported across the intestinal mucosa to be used to create new proteins, or to be converted into fats or acetyl CoA and used in the Krebs cycle.

  • If you make an alpha-helix using D-amino acids, what handedness (right or left) would you expect?

  left handed https://wou.edu/chemistry/files/2020/03/Review-of-Chirality-and-Amino-Acids.pdf

Part B: Protein Analysis & 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.

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

   I picked the bioluminescent protein 3FGC

   

   • Identify the amino acid sequence of your protein.

     • 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

     D and L are the most frequent

     

     • 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.

       

   

   • Does your protein belong to any protein family?

   • Identify the structure page of your protein in RCSB

   • When was the structure solved? Is it a good quality structure?

   5th Dec 2008 - YEs

   • Are there any other molecules in the solved structure apart from protein?

   • Does your protein belong to any structure classification family?

   • Open the structure of your protein in any 3D molecule visualization software:

   • Examine and analyze your protein, visually:

     • Visualize the protein as "cartoon", "ribbon" and "ball and stick".

     Pymol

     

     

     

     

     • Color the protein by secondary structure. Does it have more helices or sheets?

     

     • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?

     

     • Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?