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MCAT
Course: MCAT > Unit 9
Lesson 9: Amino acids, peptides, proteins- Amino acids and proteins questions
- Central dogma of molecular biology
- Central dogma - revisited
- Amino acid structure
- Peptide bonds: Formation and cleavage
- Special cases: Histidine, proline, glycine, cysteine
- Isoelectric point and zwitterions
- Classification of amino acids
- Four levels of protein structure
- Conformational stability: Protein folding and denaturation
- The structure and function of globular proteins
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Isoelectric point and zwitterions
The isoelectric point of an amino acid is the pH at which the amino acid has a neutral charge. You will learn how to calculate the isoelectric point, and the effects of pH on the amino acid's overall charge. We will also discuss zwitterions, or the forms of amino acids that dominate at the isoelectric point. By Tracy Kovach. Created by Tracy Kim Kovach.
Want to join the conversation?
What are the consequences of an amino acid being charged electrically?(38 votes)
Because the sides chains of amino acids can be positive and negative, amino acids from different parts of the polypeptide chain will attract or repel each other so will determine how the protein folds and so the overall shape of the protein.
The charges will also determine how the protein interacts with other proteins and molecules. For example, a protein that interacts with DNA will need some positive charges on or near its surface so it can bind the negative charges of the phosphates on DNA.
Charges will affect how a protein binds small molecules and so are very often crucial in the reactions an enzyme catalyses.
Finally, the charges are useful for researchers because different proteins will have different combinations of amino acids and therefore different isoelectric points, which allows proteins to be separated from one another and thus purified.(80 votes)
can you please do a video showing how we would find the pi with an actual amino acid with a side chain, how we would go about figuring it out(60 votes)
Calculating pI for different side chains
(So I just learned this by getting an answer wrong on an MCAT practice exam...)
Neutral side chain: pI = 0.5[(pKa of main carboxyl group] + [pKa of main chain amino group])
Acidic side chain: pI = 0.5([pKa of main carboxyl group] + [pKa of side chain])
the pKa of the main chain amino group is NOT included in the equation
Basic side chain: pI = 0.5([pKa of main chain amino group] + [pKa of side chain])
the pKa of the main chain carboxyl group is NOT included in the equation(30 votes)
- what's the difference between a zwitterion and a molecule that is amphoteric?(18 votes)
A zwitterion is a molecule that possesses both a positive and negative charge on the same molecule. One stipluation is that these two opposing charges must exist on that one molecule at the same time. For example, at certain pH's, some amino acids will be zwitterionic. Note the diprotic amino acid, Alanine. Alanine has a non-protic side chain (a methyl) , and thus at pH = 7.4 (physiological pH), the carboxyl group has a negative charge (COO-), and the amino group has a positive charge (RNH3+). Therefore, at pH 7.4, L-Ala is zwitterionic. Amphoteric molcules are not necessarily zwitterionic. Take for example ammonia (NH3). Ammonia has a pKa of 38. Thus, any molecule with a pKa less than 38 will protonate ammonia, and if the pKa of the molecule is greater than ammonia, NH3 will deprotonate it. Ammonia will be protonated by acetic acid (pKa 4.76), but deprotonated by an alkane with a negative charge/lone pair (pKa 50). In this case ammonia can be acidic or basic, making it amphoteric (can act as an acid or a base). However, it can never have both a positive and negative charge at the same time, so ammonia cannot be zwitterionic. Really and truly, pretty much any molecule can be amphoteric, if put it in contact with molecules that have higher and lower pKa values then itself. This has limits, however, in the human body, as our pH homeostasis is tightly regulated. Hope that helps.(61 votes)
Does pH stand for "power hydrogen"?(11 votes)- Yes! Søren Peter Lauritz Sørensen, a Danish scientist coined the term pH in 1909 to mean "power of hydrogen".(26 votes)
- please elaborate the concept of pka(7 votes)
- You will need a separate video to understand it well. Take a generic dissociation of an acid
HA <-> H+ + A-
The Ka value (K being equilibrium constant and a being the denotation for acid) for this dissociation is equal to the concentration of products over reactants
[H+]*[A-]/[HA]. So if your Ka value is >1, you know more products formed than reactants remained. If it is <1, you know that the product didn't dissociate into completion very well. Just like pH is -log[H+], pKa is defined to be -log[Ka].(21 votes)
- You wrote NH3 in the video, isn't it suppose to be NH2(10 votes)
- -NH2 is the uncharged form, but at low pH (high concentration of H+), some of the H+ binds the nitrogen atom to form -NH3+.(9 votes)
What kind of general reaction would zwitterions undergo if dissolved into water instead of strong base or strong acid?(5 votes)
This is a great question! For most amino acids, zwitterions would be present at pH 7. Which is significant as, the physiological pH of the cells in our bodies is approximately 7.4. The amino acids in water would have the carboxy group unprotonated and the amino group protonated (zwitterion), and this is would be fluidly changing. However, it would reach equilibrium at the zwitterion state.(12 votes)
In a triprotic a.a. i learnt that the pI is the average of the pKas on either side of the region where the net charge is 0, not the average of all functional groups (as stated in the video). Which is correct?(8 votes)
What you refer to and what is shown is the same.
The Amino acid structures has a fixed <b>Nitrogen group-αCarbon-Carboxyl</b> backbone and the side chain is linked to α-carbon. so the only thing on the either side of the side chain region is Nitrogen group and Carboxyl group.(2 votes)
If NH3 was a H+ acceptor then why did it lose a H+ in the basic solution?(7 votes)- The way I like to think of it is that the basic solution was MORE basic than the basic NH3 group. Because both the solution and NH3 are basic, they both want to accept protons. However, the solutions was MORE basic than the NH3 groups, so it wants to accept protons more than the NH3 group. For that reason the NH3 lost it's proton. It didn't want the proton as much as the solution did.
Not necessarily an empirical way of thinking about it but makes sense to me and helps me wrap my mind around it! Hope it helps you too.(6 votes)
- how is NH3+ a H+ acceptor and O- an H+ donor? NH3+ already has an extra Hydrogen so how can it accept another H+?(6 votes)
- -NH2 group is a hydrogen acceptor and it becomes NH3+ by forming coordinate bond with a proton (by donating the lone pair that the Nitrogen has). and -COOH is a hydrogen donor, because the oxygen is bonded either side with an oxygen and with a hydrogen the EN difference between O and H is more hence the oxygen snatches the electron from the hydrogen making the hydrogen, a proton hence it donates proton.(1 vote)
Video transcript
Hey, so we're
going to be talking about the isoelectric point,
or pI as it's abbreviated. Now, the isoelectric point is
the point along the pH scale at which a molecule,
and in this case we're going to be talking
about an amino acid, exists in a neutral
form with zero charge. In other words, it is neither
positively or negatively charged overall. It is isoelectric,
and "iso" means equal. And it's nice to know
the isoelectric point for an amino acid, because then
we can predict whether or not it will be charged
at a certain pH. And who doesn't want
the power of prediction? So how do we figure out
the isoelectric point for an amino acid? Well, let's start with the
generic amino acid structure here. So now let's take a look at
the two functional groups on this amino acid. Ignoring the R group, or the
side chain, for the time being, we're going to be talking
about the amino group and the carboxylic acid group. So the amino group here,
it has this nitrogen, which is a very happy
proton acceptor. So we're going to
write that here. And because it's a
happy proton acceptor, it is considered to be basic. And we've drawn it out
in its protonated form here after it's accepted an
extra hydrogen, or proton. So now coming over to our
carboxylic acid group, this group is a very
willing proton donor. And because it is a proton
donor, we call this acidic. And so we've drawn it out
here after it's already donated its protons, so
it has a negative charge. And now looking at the overall
net charge of our amino acid, we can see that we have
a positive charge here and a negative charge here,
and so the overall charge is 0. And we have a
special name for when you have a molecule
that has both a positive and a
negative charge present. And that special word is
called a "zwitterion," which comes from the
German word for "hybrid." So now what would happen
if we take our amino acid and we put into a
solution that is a very low pH, say a pH of 1? In other words, an
acidic solution. Well, we can think
of acidic solutions as having a lot of
excess protons around. So anything that can be
protonated on our amino acid is going to be
protonated, and so it's going to look like this. And now if you
take a look at both of the groups on
our amino acid, you can see that our amino group
is still in its protonated form and carries a positive charge. But now our carboxylic acid
group has gained a proton and lost its negative charge. And now you can see that
the overall net charge on this molecule
is now positive 1. So now let's come over to the
other end of the spectrum. Let's put our amino acid in a
solution with a very high pH, say a pH of 12. And so this is going to
be really basic solution, and we can think of
really basic solutions as having a lot of excess
hydroxide anions around. And so now, everything
that can be deprotonated on our amino acid will be, so
it's going to look like this. And if we look at our overall
net charge of our amino acid now, our amino group
has been deprotonated so now it is neutral, and the
carboxylic acid group has been deprotonated and so it has
a negative charge again. And so it has an overall
net charge of negative 1. So now we know that we
have a range of forms that our amino acid can take. We have the positively
charged version at low pHs all the way up to
the negatively charged version at high pHs. Now back to our question
about the isoelectric point. So the isoelectric
point is the pH at which we go from the
positive to the negative form. In other words, it's where
we find the zwitterion. And to find out the
exact pH, we have to take the average of the pKa's
of our two functional groups. And recall that the pK
is just the negative log of the acid
dissociation constant. So on average, and
it varies between all the different amino acids, but
on average, the amino group has a pK of around 9. And then on average, the pK
for the carboxylic acid group is right around two. So now if we just give ourselves
a little bit more room here, we can calculate what the
pI, or isoelectric point, would be for our
generic amino acid. So taking the average
pK for the amino group and then the average pK for
the carboxylic acid group, then we divide by 2,
then you get 11 over 2. And we come to an
isoelectric point of 5.5. But say our amino
acid has a side chain or an R group that is
also a functional group? Then, we would also have to
take the pK for that group into account when we calculate
the isoelectric point. So what have we learned? Well, we've learned that
the isoelectric point is the pH at which a molecule's
found in neutral form, in this case, when an amino
acid is in its zwitterion form. And we also learned
how to calculate this isoelectric point
for an amino acid by taking the average of the
pKs of all the functional groups in that amino acid.