Login

Join for Free!
117145 members


biochemistry for dummies (me, that is...)

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

Moderator: BioTeam

biochemistry for dummies (me, that is...)

Postby Goran » Sun Apr 27, 2008 8:04 am

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?
Goran
Garter
Garter
 
Posts: 2
Joined: Sat Apr 26, 2008 8:50 pm

Postby mith » Sun Apr 27, 2008 2:47 pm

Note that it contains both an alkaline group and an acidic group. The term you're looking for is probably zwitterion.
Living one day at a time;
Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
~Niebuhr
User avatar
mith
Inland Taipan
Inland Taipan
 
Posts: 5345
Joined: Thu Jan 20, 2005 8:14 pm
Location: Nashville, TN

Postby Goran » Mon Apr 28, 2008 9:53 am

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.
Goran
Garter
Garter
 
Posts: 2
Joined: Sat Apr 26, 2008 8:50 pm


Re: biochemistry for dummies (me, that is...)

Postby blcr11 » Mon Apr 28, 2008 2:39 pm

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.
blcr11
Viper
Viper
 
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am

Re: biochemistry for dummies (me, that is...)

Postby jsmcd1 » Sat Sep 06, 2008 9:32 pm

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.
jsmcd1
Garter
Garter
 
Posts: 2
Joined: Sat Sep 06, 2008 9:20 pm

Postby blcr11 » Sun Sep 07, 2008 11:27 am

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.
blcr11
Viper
Viper
 
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am

Re: biochemistry for dummies (me, that is...)

Postby jsmcd1 » Tue Sep 09, 2008 3:00 am

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....
jsmcd1
Garter
Garter
 
Posts: 2
Joined: Sat Sep 06, 2008 9:20 pm

Postby mith » Tue Sep 09, 2008 5:11 am

umm, I think the side chain can get charged.
Living one day at a time;
Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
~Niebuhr
User avatar
mith
Inland Taipan
Inland Taipan
 
Posts: 5345
Joined: Thu Jan 20, 2005 8:14 pm
Location: Nashville, TN

Re: biochemistry for dummies (me, that is...)

Postby blcr11 » Tue Sep 09, 2008 11:06 am

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.
blcr11
Viper
Viper
 
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am


Return to Molecular Biology

Who is online

Users browsing this forum: No registered users and 0 guests

cron