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Amino Acids, Peptides, Proteins


Amino acids, peptides and proteins. These topics are found in a few different sections of the MCAT list. The test makers see this as a big deal. And so if you're interested in this set of topics, concerned about it, you're on the right path, you should know a lot about amino acids. So here were looking at 1A, up here, a few of the topics that are gonna be covered in this lesson.

And then also in the chemical, physical section 5D, we see some of these same topics. But of course, when you're looking at it from the chemical side, the physical side, you're often going to be asked questions specifically about reactions. Whereas in the biological section, you're more likely to be asked questions about what are the results of every action.

And what are the causes of the reaction and how do these fit together in physiological processes. So as we know, amino acids are the building blocks of proteins. The basic structure of an amino acid is a central carbon atom and that's linked to a carboxylic acid group over here. Hydrogen atom, a distinct R group or side chain down here.

And then also an amino group. And these images up here are just giving you some examples of the structures, so you can see what the common pattern is, especially this center carbon. Amino acids are going to exist as either the L or the D-isomer. And isomers are mirror images, but only the L-amino acids are gonna be used to make proteins.

And almost all L-amino acids have an S absolute configuration. Amino acid exists mostly as dipolar ions at a neutral pH, and actually the official name for dipolar ions is zwitterion. Dipolar ions have a net neutral charge but at least two of the functional groups. We see two here of that ion have charges and the charges balance one another out. In neutral solutions, the carboxyl functional group is ionized.

You see over here, and the amino group is protonated. And that's what we're seeing here then on the right, the entire thing is a zwitterion. Ionization states then vary with changing pH levels. So at a very low pH level, we're actually going to see both of these functional groups being protonated.

At a medium pH, we get what we're seeing here, the zwitterion. And then at a high pH, both are gonna be deprotonated. The exact pH at which this occurs is gonna vary and that's according to what amino acid we're looking at. That actually is it starts to bring up some topics that I don't wanted to get in to this lesson.

It relates to isoelectric points, PKA levels. But since this is first lesson of the series, I'm not gonna get on that path. Right now, I just wanted you to know that the low pH levels lead to protonation and that it varies according to amino acids. And of course that the high pH has the opposite trend. I'm gonna introduce the amino acids by classifying them into four major groups.

And these classifications are based on the characteristics mostly of that unique R group, the side chain. There are many different ways that these amino acids can be grouped. And that's usually according to some combination of charged acidic properties. So these aren't like the four groupings set in stone. There is simply a useful way of thinking about these and starting to organize them by different patterns that we see among the amino acids.

That said, all though you don't need to memorize these exact groups, you should know whether a given amino acid is polar, acidic, hydrophobic, hydrophilic, positively charged, negatively charged. And of course, there's a lot more to learn about amino acids as well. But for this lesson, I just wanna start off with these groups of concepts. The first we're looking at here at the top of the screen is the hydrophobic group.

And the R group for this set is nonpolar. Beginning with the simplest amino acid, glycine, the R group is going to just have a single hydrogen. There are 9 amino acids that fit into this category, and that's alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, and valine.

Now in contrast to that, the second group contains the polar, uncharged amino acids. And these amino acids have a neutral R. And yet, at the level of the entire amino acid, they are polar, without a charge. These amino acids tend to be a little more hydrophilic, and six amino acids fit into this group, asparagine, cysteine, glutamine, serine, threonine, and tyrosine.

Taking a look at the final groups, we have the charged amino acids. Positively charged amino acids that contain the positive R group are going to be very hydrophilic. And that's going to be a major factor regarding how these types of amino acids are going to react. There are only three amino acids in this group and that's arginine, lysine and histidine.

The final group contains the negatively charged amino acids with a negatively charged R group. There are only two of them, and that's aspartate and glutamate, and they have acidic side chains. Each has a carboxylic acid on its side chain and that gives that it's acidic or proton-donating properties.

Next step when we have series of amino acids joined together, we get polypeptides. Change with a small number of amino acids, like fewer than 20, are called oligopeptides. But most are going to have 30 or more amino acids, and that's what we refer to as proteins.

So all of these are polypeptides but 30 are above our proteins. And the 20 to 30 range is kind of this grey zone. They usually just called peptides if they are in this middle region. Between the series of amino acids, peptide bonds are formed and they create a polypeptide. We have the alpha-carboxyl group of one amino acid, otherwise known as the C-terminus.

And that's going to link up with alpha-amino group of another, or the N-terminus. During this process, a water molecule is going to be lost. And so because of that, we are looking at a condensation process when peptide bonds are formed. So looking at the structure of the polypeptide, we can see that these two ends are not the same.

Meaning that the polypeptide chain is going to have directionality. And the naming convention is to write the amino acids starting with the N-terminus and then go down the chain ending with the C-terminus. We saw that peptide bond formation is a condensation reaction. The water molecule is lost. The two amino acids condensing into one.

So the reverse of that, the breaking up of peptide bonds is, as you would guess, achieved through hydrolysis. There's going to be the addition of water, and that's what helps break up the peptide bond. Now, the equilibrium for this does lie on the hydrolysis side. So it makes sense then why we need input of energy in order to synthesize those peptide bonds.

When we discuss protein structure, you're often gonna hear about the four different levels being discussed. The first is the primary structure. And in Biology I Section 1A that you've perhaps already listened to in this series, almost all of the references are at the primary and secondary structure. So the primary is just the naming of the amino acids and the chain sequentially.

And the order of this, the order of the sequence is defined by the DNA and the RNA that codes the proteins. The secondary structure refers to the spatial arrangement of amino acids that are near one another and is characterized by their hydrogen bonds, the backbone. Examples of this are the alpha helix and the beta sheet. These are regular, repeating structures of a particular folded polypeptide chain.

Some proteins have actually both an alpha helix pattern at one portion, and then at a different region have a beta pattern. The tertiary formation describes the three-dimensional structure of a protein. So what happens when its not flattened out but it actually folds into shapes? What we will see there is that the nonpolar portions of the polypeptide fold into the core of the protein.

And so that leaves the hydrophilic aspects on the outside. And there are so many things that go into both shaping and also affecting the tertiary structure of a protein. So it could be temperature, could be pH of a solution, ionic bonding. Some of these changes actually can denature the protein. And sometimes that's permanent, sometimes it's temporary.

And then the final level is the quaternary structure. And that refers to the spatial arrangement of the multiple polypeptide subunits. Sort of like multiple tertiary sections put together. And a lot of proteins don't even form this quaternary structure. There's a lot that proteins can do just at the tertiary structure and remain pretty stable.

Okay, so this is of course is a pretty basic overview. But I wanna just address the question, how might this be relevant to the MCAT? Would you actually be asked a question directly related to them or do you just need to know certain elements of them? I think you actually could be asked a question about the utility of one structure versus another.

In either describing or predicting some kind of a reaction or some kind of a physiological process. So you could get a question about a particular reaction and then be asked which of the four dimensions is going to demonstrate the biggest change as a result of the reaction. And if you get a question like that, you always kind of wanna look at the tertiary.

So many things contribute to the changes. Enzymes are often described at the tertiary level and so are genetic mutations with quaternary structures. They can be very useful biomedicine because they are used to describe things like globular proteins. And hemoglobin is the classic example of that.

And so if you see hemoglobin in relation to some question to ask something about structure or predictions. You wanna be primed to think about the quaternary structure. And what you need to know about that for hemoglobin, really, is just that there are four subunits.

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