Question

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4. Secondary structure (a-helix): The image below is of a polypeptide in secondary (2) structure level of protein folding. Specifically it is of an a-helix. Use the image on the left to answer the questions a-e below. The image on the right is to help with question "f' only. a. Name the specific bond/interaction indicated by the dotted lines. b. Is this bond/interaction covalent or non-covalent? c. Is this bond/interaction permanent or transient? d. What parts of the amino acid (backbone or side chain) are involved in this bond/interaction? e. Find one amino acid involved in the bond/interaction. Determine how many residues away is the other amino acid involved in that interaction. f. In what direction are the side chains pointing? Into the helix? Or away from the helix? Both in and out of the helix? Explain why this conformation is the only option for this structure (max 1-2 sentences]. Use the ribbon diagram and top-view of a helix on the right to help you answer this question. Z H 450 pm 70= Q

Answer 1

A helix is formed by interaction between molecules of a protein. These interactions are caused by Hydrogen bonds, vander-vals forces, ionic interactions. All these interactions are non covalent.

a). Given figure has hydrogen bonds indicated by dotted lines. Hydrogen bonds are formed between hydrogen of one molecule and oxygen of another molecule.

b). Hydrogen bonds are non covalent bonds.

c). We already know that, non-covalent bonds are transient. They break easily.

d). Amino acids have a backbone molecule and a side chain. Backbone molecules consists of one amino group bonded with carboxylic group, and side chain consists of long chains denoted by R. It is clear in the figure that, hydrogen bonds are present between backbone molecules of amino acids and not between side chains.

e). As mentioned earlier, amino acid contains one carboxylic group bonded to amino group. Each amino acid has one alpha carbon to which both the groups are bonded, also side chains are bonded to this alpha carbon.

In the figure, the hydrogen bond is present between hydrogen of 1st amino acid and the fourth amino acid molecule.

This means, the interaction is 3 residues away.

f). The side chains are pointing away from the helix. This is the only conformation for thiis alpha helix beacuse, some side chains can be very long. This will create unwanted crowding of molecules if they point inside the helix, hindering the hydrogen bond formation, thus disrupting the formation of alpha helix structure.