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- 1.Here is an oligomeric protein, which has two binding sites:1)Write the formulas of side chains of amino acids which are located in binding sites and suggest two ligands,which can be bound with this protein. 2) Name the types of bonds which will be formed between the ligands and amino acids of binding sites.3)Give the definition of quaternary structure. What do you know about the properties of proteins with the quaternary structure?1. The following protein crystal structure is the Human Serum Albumin complexed with octadecanoic acid (PDB ID: 1E7I). According to the protein data bank, Human Serum Albumin is composed of 72% helical structure. Among the following options (a-c), select the possible Ramachandran plot for the above Human Serum Albumin. (a) (b) (c) Phi Phi Phi1.Describe in detail how to determine the primary structure of protein. 2.You have been given a mixture of lysine, histidine and cysteine.The isoelectric point of the amino acids are as follows; histidine 7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.
- 1.Describe in detail how to detect the primary structure of protein. 2.Given a mixture of lysine,histidine and cysteine.The isoelectronic point of the amino acids are as follows: histidine:7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to the free energy. A) If A is the native fold structure, which state is a molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the folding funnel, only the entropy of the protein alone is considered). E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.5. Indicate whether the following amino acid residues would be more likely to be found on the surface or in the interior of a folded protein: Leu, Arg, Phe, Asn, and Glu. Give your reasoning for each case (diagrams not required).
- 24. What is the quaternary structure of a protein? Do all proteins have quaternary structure?2. a. In the following diagram of a portion of a protein, label the types of interactions that are shown. b. What level of protein structure are these interactions producing? b. CH CH3 CH3 Polypeptide backbone CH2 H3C H3Ç 10 CH С—ОН - CH,-S-S-CH,- а. CH2 с. -CH,-CH,-CH2-CH2-NH 0-C-CH2- d.2. A functional protein that is approximately 110 kDa in size has all its cysteine residues joined with disulfide bonds. It has one cysteine residue per 100 amino acids. When heated at 85°C it lost activity, but when it was allowed to cool, the activity was restored? Please answer the following questions: a) How many disulfide bonds the protein has? Show how you came up with the answer. b) What is the molecular basis for the protein behavior in restoring activity?
- 7. Identify the primary structure of a hexapeptide containing five different amino acids if the following smaller peptides are among the partial hydrolysis products: Gly-Cys, Ala-Ser, Ala-Gly, and Cys-Val-Ala1. An intrinsically disordered protein (IDP) is a protein that lacks a fixed three- dimensional structure. Estimate the size of an IDP of 100 amino acids by calculating the most probable end-to-end length of the protein. Assume the protein is a freely-joined chain with the length of each segment (amino acid) b = 3Å.1)Explain 3 benefits of proteins forming higher oligomeric states. 2) Why are peptide bonds planar?