Chem 153A – Homework 1   

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Chem 153A – Homework 1                                                                                                         

  1. [Exploratory] The Van der Waals radius of a carbon atom is 170 pm. How much larger are the following? (Notes: Estimate end-to-end; feel free to use google for this question)
  1. The length of the average amino acid residue (from amine to amine)
  2. The average alpha helix (length)
  3. Eukaryotic ribosome (radius)
  4. E. Coli cell size
  5. The average human skin cell
  6. The length of the tip of your thumb (measured from first knuckle to the edge of your nail)
  • Consider two molecules, X and Y.
  • X is able to dissolve in water. What does this imply about the favorability of interactions between molecules of X?
  • Y is unable to dissolve in water. What does this imply about the favorability of interactions between molecules of Y? Draw what happens to Y in water.
  • [Exploratory] Vitamins are an interesting class of organic molecule because they aren’t, in any way, distinguished by specific functional groups; their only common denominator is that they’re essential nutrients. Make an educated guess as to whether the following vitamins are water or fat soluble.
  • Given two acids, HA and HB, with pKas of 4 and 6 respectively, answer the following.
  • Which has the higher proton affinity?

Weak acids have a higher proton affinity. In this case, HB with pKas of 6 will have a higher proton affinity.

  • When deprotonated, which has a less stable negative charge?
  • Which will dissociate more when added to water?
  • For each, what is the major (predominant) protonation state at pH 3, pH 4, and pH 7?
  • For each, at what pH is the ratio of protonated to deprotonated 3:1?
  • Consider the intermolecular interactions occurring within a group of methanol molecules. List the types of interactions that can occur, then draw these interactions individually, labeling any partial charges.
  • You are handed a solution containing 0.125 M acetic acid and 0.25 M sodium acetate. The pKa of acetic acid is 4.75. Using this information, answer the following.
  • What is the Ka of acetic acid?
  • b. Is this a buffer system? How do you know?
  • c. Using the Henderson-Hasselbach equation, determine the pH of this system.
  • You are given a solution of alanine at pH 4.5:
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  • Is alanine a good buffer at pH 4.5? Briefly explain why or why not. If you answered no, include the pH range(s) at which alanine would be a good buffer.
  • You dissolve 0.01 moles of glycine in 1 liter of water and begin to titrate the resulting solution using concentrated NaOH (insignificant volume added).
  • Draw the titration curve in terms of pH vs equivalents of base. Locate and label any buffering regions that may be present.
  • You adjust the pH to 7.0. After that you add 0.005 moles of NaOH. Draw the structure(s) of the species of glycine present in the solution and indicate the proportion of each species.
  • What is the approximate pH of the solution in part b?
  • Would this solution be a good buffer? Explain your answer.
  • Consider the tripeptide Y – E – S.
  • Draw the structure of Y – E – S at physiological pH.
  • Calculate the pI of the tripeptide (apply pKas from the chart for AA residues).
  1. Consider the peptide Cys-His-Ile-Glu-Phe.
  2. Draw the structure of Cys-His-Ile-Glu-Phe at physiological pH.
  • Name the functional groups in each amino acid side chain in part a.

Cys: thiol, His: imidazole, Ile: sec-butyl, Glu: carboxylic acid, and Phe: benzyl

  • [Exploratory] Given that there are 20 amino acids in humans, how many pentapeptides are possible?
  • Calculate the pI of this peptide (apply pKas from the chart for AA residues).