Problem Set 5 Spring 2018 Protein Structure Question Picture

Problem Set 5, Spring 2018; Protein Structure Question Pictured below are the structures of several proteins Answer the following questions about secondary and tertiary levels of organization. (a) What type of secondary structure dominates in the protein on the left What molecular forces dominate in this type of secondary structure? (be specific) (b) Same questions as (a) for the protein on the right- note that the top picture is a side view and the bottom is the same protein looking from the top (c) How are the forces different in protein (a) vs protein (by (d) For this one, describe the various secondary structures in the protein at the right, being as specific as possible. (e) Where is the \"hydrophobic core\" of the molecule on the right compared to the one of the top left (part-a-) (t1) In spite of its small size, the insulin protein is highly organized. This is probably because of the many disulfide bonds. How do these bonds help organize the structure of this protein? (g) How many chains is insulin made from? Are they the same or different? Describe the quaternary structure of insulin, using correct nomenclature (h) In solution, two molecules of insulin form a hydrogen bonded pair. What is the new quaternary structure? NOTE: this is an active, blood-soluble form of the molecule. (0) In the presence of divalent cations, such as Zn2, six molecules of insulin form a new, non-water-soluble mass. What is the quatermary structure of this new protein, which is much less clinically useful than the first one?

Solution

A. The structure is dominated by alpha helical structure as shown by the squiggly forms.This structure is formed by Hydrogen bonding (H-bonding) between the H of NH (amide) and the O in the -CO- (carbonyl group). In alpha helix formation, the H from NH forms a H-bond with the -CO- of the fifth amino acid in the same pepide chain.

B. The structure is dominated by beta sheet like structure as evident by the flat ribbon like things with arrowhead. Again H-bonding is the main force in giving the shape of beta sheets. The difference from alpha helix is that, in beta sheet, the H bonding is formed between two amino acid at such a distance so that the backbone can fold back and run in parallel to the former strech.

C. The main difference between \'a\' and \'b\' are in forming the tertiary structures.Tertiary structures are results of sulphur-sulphur di-sulfide linkage, hydrophobic and hydrophilic interaction with inself as well as surrroundings, and ionic bonds. As opposed to secondary structures, side chains of amino acids play key roles in forming tertiary structures.From the picture, it appears that the left figure describes a transmembrane protein where the alpha helical parts are hydrophobic in nature and thus buried in the lipid environment of the memberane. Whereas the right figure most iikely represents an ion channel. Thus it is expected that this beta sheets are composed of hydrophilic amino acids.

D. The structure has all three varieties of secondary structures. The squiggly spiral shapes are for alpha helices, the ribbons with arrow head represents the beta helices and the thread like parts are for random coils.

E. In the figure on the right side, the beta plated sheets are clustered together and folded inside the protein, shielding them from hydrophilic environment. Thus they represent the hydrophobic core, while in the figure at the top, the alpha helices are buried in the lipid bi-layers of the membrane forming the hydrophobic core.

F. Insulin has two peptide chains A and B (and a C peptide which is a part of pre-insuin). There are 6 cys residues in insulin chains which form three -S-S- bonds. One of the is intra chain (within the A-chain) and the rest two holds A and B together.