Problem 1
Matters of stability. Proteins are quite stable. The lifetime of a peptide bond in aqueous solution is nearly 1000 years. However, the free energy of hydrolysis of proteins is negative and quite large. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases considerable energy?
Problem 4
First abbreviate, then charge. Examine the following peptide, and answer parts \(a\) through \(c .\) Thr-Glu-Pro-Ile-Val-Ala-Pro-Met-Glu-Tyr-Gly-Lys (a) Write the sequence using one-letter abbreviations. (b) Estimate the net charge at \(\mathrm{pH}\) 7. (c) Estimate the net charge at \(\mathrm{pH} 12 .\)
Problem 5
Neighborhood peer pressure? Table 3.1 gives the typical \(\mathrm{p} K_{\mathrm{a}}\) values for ionizable groups in proteins. However, more than \(500 \mathrm{pK}_{\mathrm{a}}\) values have been determined for individual groups in folded proteins. Account for this discrepancy.
Problem 6
Prohibitions. Why is rotation about the peptide bond prohibited, and what are the consequences of the lack of rotation? (EQUATION CANNOT COPY)
Problem 7
Don't they make a lovely pair? Match the terms with the descriptions. (EQUATION CANNOT COPY) (a) Primary structure (b) Peptide (amide) bond (c) Disulfide bond (d) phi ( \(\phi\) ) angle (e) psi \((\psi)\) angle (f) Ramachandran plot\( (g) \quad \alpha\) helix (h) \(\beta\) pleated sheet (i) \(\beta\) strand (j) Secondary structure 1\. Forms between two cysteine amino acids 2\. A rodlike structure with a tightly coiled backone 3\. Angle of rotation about the bond between the \(\mathrm{N}\) atom and the \(\alpha\) -carbon atom 4\. Fully extended polypeptide chain 5\. Formed by hydrogen bonds between parallel or antiparallel chains 6\. Regular repeating three-dimensional structures 7\. The bond responsible for primary structure 8\. Sequence of amino acids in a protein 9\. Angle of rotation between the \(\alpha\) -carbon atom and the carbonyl carbon atom 10\. A plot of phi and psi angles
Problem 9
Alphabet soup. How many different polypeptides of 50 amino acids in length can be made from the 20 common amino acids? (EQUATION CANNOT COPY)
Problem 11
Vertebrate proteins? What is meant by the term polypeptide backbone?
Problem 12
Not a sidecar. Define the term side chain in the context of amino acid or protein structure.
Problem 13
One from many. Differentiate between amino acid composition and amino acid sequence.
Problem 14
Knowledge is good. List some of the benefits of knowing the primary structure of a protein.
