biochemistry for dummies (me, that is…)

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    • #9537
      Goran
      Participant

      I guess, since it says "answers all your questions", I can post even a stupid biochemistry 101 question.

      So, how can I define amino acids in termsof ionization? Of course I can talk about pH, pK etc., but they are never unionized, even as solids; if I start with "dipolar ions"; they aren’t always that, and bringing in the definition of "intramolecular neutralization"… So, can I say that they are alway"molecular ions" (although that term isn’t quite propriate)… any suggestions?

    • #83713
      mith
      Participant

      Note that it contains both an alkaline group and an acidic group. The term you’re looking for is probably zwitterion.

    • #83733
      Goran
      Participant

      Thanx…

      I guess I’ll start with zwitter ions in neutral water solutions… and then, I’ll add that aa. can be precipitated nad crystalized and explain the whole intramolecular neutralization, the difference: pKa1 << pKa2 (so, the predominant form is always ionized..) and also add something abouth "ionic character" of aa.

      Thing that bothers me a bit, is the correct definition of zwitter ions…
      Different books give different definitions…
      Is it when alpha-COO- and alpha-NH3+ are in that form (ionized) so the whole molecule is electrically neutral? What about ionizable side chains? Are they unionzed in zwitter ions… and finally, one definition is that "zwiter ion is form when pH=pI" – taking into consideration ionazble side chains, that could give zwitter ions with unionized alpha groups…

      g. sh.

    • #83736
      blcr11
      Participant

      The charge on an amino acid in solution depends on the pH of the solution. At its pI, the amino acid is neutral, below its pI it should be positively charged and above its pI it should be negatively charged. Same thing for peptides and proteins. The side chains ionize independently of the beta-amino and alpha-carboxy groups, when the side chains are ionizable, that is, which will include amino acids like Glu, Asp (and to a lesser extent their amides Gln and Asn), His, Tyr, Trp, Lys, and Arg, typically. You can argue about Pro, Cys, Ser, and Thr, which under certain circumstances may ionize, but not typically. The rest have strictly non-ionizable side chains.

      The nature of the side chain will influence where the pI of the amino acid is. If the side chain is acidic, the pI of the entire free amino acid will be towards the acidic side of things. Contraiwise for basic side chains. For example the pI of Aspartic acid (an acidic side chain) is 2.97, and for Glycine (whose side chain is a hydrogen atom) is 5.97 and for the basic amino acid Lysine is 9.59.

    • #85779
      jsmcd1
      Participant

      Greetings all. After a 20 yr hiatus for general chemistry I thought it would be a good idea to jump right into Biochemistry…. I need help with the following question. "the pKa of the acid group in aspirin is 3.5. What percent of the aspirin is in the neutral form in the stomach (pH 2.0)? What percent is in the acid form in the intestines (pH 6.5)? I have no problem determining the ratio using the Henderson-Hasselbalch equation, but not sure where to go from there.

      Thanks for tolerating my question.

    • #85790
      blcr11
      Participant

      The Henderson-Hasselbach Equation relates the pH of a solution to the pKa of the acid and the ratio of the concentrations of conjugate base to its acid. Here, ionized aspirin is the conjugate base of the unionized, acidic form of aspirin.

      pH = pKa + log([ionized aspirin]/[unionized aspirin])

      or

      log([ionized]/[unionized]) = pH – pKa

      If you plug in the values for the pKa at the two pH’s and take the antilog, you calculate the ratio of the concentrations of ionized to unionized aspirin. At pH 2.0 this works out to a ratio of 0.024 while at pH 6.5 the ratio is about 1995. In other words:

      at pH 2, [ionized aspirin] = 0.024 x [unionized aspirin]—about 2% of aspirin is ionized at this pH;

      at pH 6.5, [ionized aspirin] = 1995 x [unionized aspirin]—virtually 100% of aspirin is ionized at this pH.

    • #85808
      jsmcd1
      Participant

      Last one for a bit I hope. I need to find the two main ionization states of histidine at pH of 5.0, and the percent of ea present. My approach is this: pKa of COOH is 1.82, pKa of H3N+ is 9.17.

      Ph= pKa + log [coo-]/[cooh], 5.0 = 1.82 log [A-]/[HA], 3.18 = log [A-]/[HA], 3.18 antilog = [A-]/[HA] = 151/1

      Doing the same for H3N+ the ratio is 6.76E-5/1.

      Is the path I’m traveling down the correct path, and if so how do I derive the percent present from this information.

      Regards….

    • #85810
      mith
      Participant

      umm, I think the side chain can get charged.

    • #85814
      blcr11
      Participant

      Like mith said, the side chain of histidine has an active nitrogen with a pKa of 6.5 or so–I would check that value. I’m not certain I remember it exactly, but any biochemistry textbook should list the amino acids and their pKas somewhere. You have shown that not much of the primary amino group is ionized, though.

      There are a number of ways to turn the ratio into a percent. Perhaps the simplest is to play a little mind game with your ratio. For your 151/1 ratio, for instance, for every 152 molecules of histidine, 151 will be COO- and 1 will be COOH.

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