Question

(1) Describe what you see, using terms that indicate the type of secondary structure shown. (2) What can you conclude about protein's cellular location from this view of the protei? (3) Why is this amino acid found predominantly on the side of the helices that face each other? (its Leucine) (4) The labels will include the l-letter designation of the amino acid, followed by a number and letter. What does the number indicate? What does the letter indicate? Is this structure a homodimer or heterodimer? (6) **What leucine atom is participating in the bond? What atom on which neighboring amino acid is at the other end of the bond? Are these backbone or side chain atoms? The residues involved in the H-bond are separated by how many residues? (7) What is the length of a typical hydrogen bond? What is the length of the hydrogen bond displayed? Why don't these values agree? (8) When would a researcher want to display the structure in the surface format? stick or wire format? ribbon format? What information is best delivered in each view?

Answer 1

1. There are two types of secondary structure alpha helix and beta sheet. In alpha helix first amino acid make bond with fifth amino acid that is if first amino acid is n then it will make bond with n+4 amino acid. Alpha helix show colied structure.

2. Since in this protein amino acids which is exposed is leucine given in question which is a non polar amino acid which do not interact with water and this is present in inside so there must be hydrophobic environment and thus outer environment will be hydrophilic. Thus cellular location of this protein is cytoplasm.

3. Leucine is hydrophobic amino acid it can't be present in hydrophilic environment so itbis present inside the core.

4. The number indicate the position of that particular amino acid and letter indicate the name of that amino acid. This is a homodimer since it appears like both the alpha helices are exactly same and have leucine at same position in both the polypeptides.

6.The residues involved in the H bonding are seperated by 3 residues. Since in alpha helix n amino acid make hydrogen bond with n+5th amino acid , so in between 3 amino acid comes. There is a difference in bonds, the amino acid make backbone or peptide chain by peptide bond and side chain interact with other side chain with hydrogen bonding.

(Due to time bound and HOMEWORKLIB RULES I am only able to solve 4 questions however I also solved one more question but due to time bound I am not able to solve next two questions, so can you please post the nest two questions again or specify to slove snly that two questions. And if you like these answers please upvote for it)