chapter 4.docx - Chapter 4 Protein structure 1 What is...

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Chapter 4: Protein structure 1. What is protein function based on? a. Structure 2. What is the structure depend on? a. The sequence of the weak, noncovalent forces 3. How many protein folding atoms are their? a. A large amount but finite 4. Are the structures of globular proteins stable? a. Yes they are marginally stable 5. What does marginal stability facilitate? a. Motion 6. What does motion enable? a. Function 7. What is a proteins conformation? a. It is the spatial arrangement of its atoms 8. Can conformations change? a. Yes if there is a single bond rotation and no breaking of covalent bonds 9. What are native proteins? a. Proteins in there functional, folded conformations 10. How can you define stability? a. It is defined as the tendency to maintain a native conformation 11. What does an unfolded cahin have with water? a. Hydrogen-bonding interactions 12. Why are the non-covalent interactions the stabilizing force in the structure, if covalent disulfide bonds are stronger? a. Because the non-covalent interactions are more numerus 13. What is the driving force with proteins that have hydrophobic groups? a. Folding is favored to reduce the exposure to water, and to prevent water from forming too many solvation layers 14. What is the driving force for folding with proteins that have polar groups a. The presence of water will cause a net decrease in hydrogen bonding pure unit mass of water, since water-water has more H-bonds than water-polar group. This mean that a solvation shell will also form to some extent around polar groups 15. How is entropy affected while folding is occurring? a. There will be increased entropy of the surrounding aqueous solution, which outweighs the loss of conformation entropy when a protein is forced to fold. 16. What is a clathrate? a. A solvation layer 17. What are the weak forces and whata are the strengths? a. Van der waals- .4 -4 b. Hydrogen bonds 5-30 c. Ionic bonds 20 d. Hydrophobic interaction- <40
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18. How is the secondary, tertialry and he quadrianry structure of protiens stabilized? a. Weak forces 19. Where will a ionic bond usually occur? a. Usually occurs on the protein surface 20. How many covalent bonds are acid residues separated by? a. 3 21. what allows the partial sharing of electrons between the carbonyl oxygen and the amide nitrogen? a. It is because all the atoms associated with the peptide bond are coplanar 22. What are the 6 coplaner atoms called? a. The peptide group 23. Why is the hydrogen and the carbonyl group trans to each other in the peptide group? a. It is because of the partial double bond charicteristics of the C-N bond partial double bond characteristics 24. How is the rotation of the N-C-alpha? a. Phi 25. How is the AlphaC-C bond labeled? a. Psi 26. At what angel is the polypeptide in its fully extended conformation and all will have all the peptide groups co planer?
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