Biochemistry

Biochemistry Practice Problems I

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Question 1

Which of the following statements is true about water? Select all answers that apply.

  • it is non-polar
  • it fully ionizes at neutral pH
  • liquid-phase water is more dense than solid-phase water
  • it is a weak acid
  • it is a weak base

Question 2

The Ka for a weak acid (HA) is known to be 1.9 x 10-5. What is the ratio of [A-] to [HA] at a pH of 6?

Question 3

For questions 3-6, consider the titration curve below. The chemical species being titrated by a strong base must be a __________ , since it is capable of donating ______ proton(s).

1

  • weak base; no
  • strong base; three
  • monoprotic acid; one
  • diprotic acid; two
  • triprotic acid; three

 

Question 4

The chemical group being titrated around the point labeled (C) in the graph is most likely a(n) ________________ (basic or acidic) group.

Question 5

The titration curve shown in Question #3 is that of a free amino acid in aqueous solution. Based on the graph, which particular amino acid is most likely represented? Simply name the amino acid.

Question 6

Assume that the equilibrium represented around point (A) in the titration can generically be described as:
H3A + OH- —> H2A- + HOH
What is the pH at which the ratio of [HA2-] to [H2A] is 25:1?  Show all work & clearly explain your answer.

Question 7

For Questions #7-13, consider the following peptide: His-Met-Asp-Tyr-Phe-Ser

The code for this peptide, using one-letter symbols, is _________

Question 8

How many distinct “ionizable” groups exist within this peptide?

A. 2
B. 3
C. 4
D. 5
E. 6

Question 9

At a pH of 6, which of the following best approximates the net charge on the peptide?

  • -1
  • -0.5
  • 0
  • +0.5
  • +1

 Question 10

Within this peptide, which amino acid residue is the most hydrophobic? Explain your answer.

 Question 11

Calculate an approximate pI (isoelectric point) for this peptide.

Question 12

Based on your answer for Question #11, would you categorize this peptide as “acidic” or “basic”?  Explain.

Question 13

At a pH of 10, would you expect this peptide to be retained for a longer time within an anion exchange column or a cation exchange column?

Question 14

The amino acid residues commonly found within a β turn are:

  • Ala & Gly.
  • two Cys.
  • hydrophobic.
  • Pro & Gly.
  • those with ionized R groups.

Question 15

Cellular proteins are oftentimes post-translationally modified.  Choose one of the following PTMs:  N-linked glycosylation, phosphorylation, ubiquitination, or GPI-anchor.  Clearly indicate your choice, then address the following:

(a) How is the PTM attached to the protein of interest?  At which amino acid residue(s)?  What enzyme(s) is involved, if any?
(b) Is the PTM relatively stable or highly dynamic?  Explain.  How does the PTM become detached from the protein of interest?  What enzyme(s) is involved, if any?
(c) What is the function of the PTM?  Provide one specific example.

 Question 16

Disulfide linkages:

  • are covalent bonds.
  • are a type of electrostatic interaction.
  • occur between methionine residues.
  • can be disrupted by SDS.
  • can only occur within the same polypeptide chain.

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Categories: Biochemistry, Biology