11. What do y and o represent in terms of protein structure? Physically, why do these have limitations?
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- 4. In the following diagram of a portion of a protein, label the types of interactions that are shown. CH H;Ć `CH, | H;C _CH3 ! CH - Polypeptide backbone c=OH CH2 -CH5–S}-CH,-- -CH;-CH-CH;-CH, NH," 0-C-CH, d. What level of protein structure are these interactions producing?24. What is the quaternary structure of a protein? Do all proteins have quaternary structure?8. The following proteins represent a wide range of molecular weights and isoelectric points. Mr is the molecular weight of a single protein chain. • Protein 1: Mr 68,544; pl 6.11 (monomer) • Protein 2: Mr 29,041; pl 5.32 (dimer) • Protein 3: Mr 15,805; pl 5.7 (dimer) • Protein 4: Mr 12,165; pl 4.74 a. Which protein is the most acidic? Explain your answer. b. Which protein will migrate the slowest in an SDS-PAGE? Explain your answer. c. In what order will these proteins elute from a cation exchanger at pH 8? Explain your answer. d. In what order will these proteins salt out from a pH 7 solution by the dropwise addition of saturated ammonium sulfate? Explain your answer. 83°F 立
- 9. A) Please write down the names of the following protein folds. A B C B) Which one(s) is made of more than one polypeptide? D E 000 C) Give an example of a protein containing the motif in C and explain how the structure of this motif facilitates function. 10. What is Levinthal's paradox? Describe the paradox and explain the conclusion to which it led.5.) If a mutation in an organism's DNA causes the resulting protein to possess a glutamine instead of a glycine in the 13th position, what level(s) of the resulting protein's structure would potentially be affected? Why?17. Protein folding results in a large decrease in entropy since a polypeptide is now constrained and more ordered. However, what counterbalances the loss of entropy associated with protein folding?
- 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.1.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.8. List 4 tertiary interactions that exist in protein molecules and include what type of R groups (side chains) that must be present to undergo that specific interation.
- 5. In the early days of protein biochemistry, these proteins were described using "operational definitions." What is an "operational definition?"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.1. Explain the significance φ, ψ contour diagram in proteins and explore how is it interpreted?