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?

1. What is the isoelectric point (pI) of lysine which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group and 10.5 for the side chain amino group? 2. Which of the following is most likely to be found on the exterior of a protein? A) Pro B) Trp C) Ser D) Glu 3. The type of reaction that forms a peptide bond is A) Elimination B) Hydrolysis C) Nucleophilic substitution D) Condensation

Non covalent bonds are very important in cell biology, could you explain why and provide an example that illustrates their importance ( do not chose protein folding as an example) What are the different levels of protein structure and what are the different parameters (sequence, type of bonds, etc...) that influence protein folding at these different levels?

Which of the following, if any, is correct about protein folding? a)2° structure formation is primarily entropic, 3° structure formation is primarily entropic b)2° structure formation is primarily entropic, 3° structure formation is primarily enthalpic c)2° structure formation is primarily enthalpic, 3° structure formation is primarily entropic d)2° structure formation is primarily enthalpic, 3° structure formation is primarily enthalpic e)None of the above

19. Draw all 20 of the genetically encoded amino acids at (a) pH = 1; (b) pH = 1; (c) pH = 12. Include the charges on all functional groups that have titrated.

1. Hen Egg Lysozyme (HEL) is a commonly studied protein. One study reported that HEL unfolded at a "melting" temperature (TM) of 77.8 °C and calorimetric measurements determined the enthalpy for melting to be 500 kJ/mole. At the melting temperature, what are AG and AS°?

2. Consider the following quaternary cartoon structure below, where each colored shape represents a different subunit. i. ii. iii. How many N-termini are there in this complex? Suppose the blue square and orange triangle subunit are held together by a disulfide bond, sketch below what you would expect to see after the addition of BME. What kind of interactions may be responsible for holding the orange triangle and green circle subunits together? List at least three.

in determining the structure of a fully folded protein? involving the amino acid side chains of the polypeptide. Which has the largest effect 5. hydrogen bonding ionic interactions a) b) c) d) hydrophobic interactions van der Waals interactions none of the above The misfolded, insoluble, and aggregated proteins characteristic of Alzheimer's disease and Parkinson's disease are known as: zymogens b) c) d) e) open quaternary structure proteins protein domains amyloid deposits molecular chaperones 6.

. Theoretical and experimental measurements show that in many cases, the contributions of ionic and hydrogen-bonding interactions to AH for protein folding are close to zero. Provide an explanation for this result.,

7. Consider the role of energetic and entropic factors for protein folding. a. Draw a PEC diagram that represents the relative potential energy and number of configurations for the unfolded and folded protein.