‍

I. PROTEIN ANALYSIS

1 Answer any of the following questions

• 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)

               1 Dalton = 1.66e-24 gram; 100 Daltons = 1.66e-22 gram

                500 g/1.66e-22 = 3e24 mol

• Why are there only 20 natural amino acids?

               There is a believe that the proteinogenic amino acids are chosen initially from the RNA world. It is also related to their abilities to do catalysis directly. Although the accurate reason remains arbitrary, there is a possibility that all amino acids are developed non-randomly . It is also possible that these adaptations are related to increases in molecular oxygen levels on earth. (chemistryworld)

• Why most molecular helices are right handed?

               It is proved in experiments that the left-handed spinning electrons in cosmic rays could have preferentially destroyed left-handed precursors of molecules, leaving only right-handed molecules. (phys.org)

• Where did amino acids come from before enzymes that make them, and before life started?

               From the subsequent Archean eon (approximately 3,500 million years ago), the age of bacteria and archaea. (https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445)

• What do digital databases and nucleosomes have in common?

               Both of them are formed with single units, like digital databases has "0" and "1", the nucleosome is constructional unit for eukaryotic chromosome. They both stored information and can transfer data by coping and pasting itself.

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

‍

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

This is the MoaC, from the molybdenum co factor, an essential component of a large family of enzymes involved in important transformations in carbon, nitrogen and sulfur metabolism. The MoaC together with MoaA is involved in Moco biosynthesis. This enzyme is involved in carbon, nitrogen and sulfur metabolism. I selected this one because of its triangular form and symmetrical shape is quite identifiable. The form seems a loop of several repeated structure. I am curious about how nature create such mathematical behavior.

(https://www.masterfile.com/image/en/679-07150626)

2.2 Identity the amino acid sequence of your protein.

Length: 161 . The most frequent amino acid is A. The protein is quite identical , it does not belong to any protein family.

2.3 Identify the structure page of your protein in RCSB

The structure is solved in 2000-03-09. It is quite a stable structure. There is no structure alignment results are available for 1EKR.A explicitly.

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

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

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

It has more sheets.

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

The distribution of hydrophobic vs hydrophilic residues are balanced and repeated from its three wings. It seems there are more hydrophilic residues.

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

‍

Looks like yes.

‍