- 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
Amino acids can be classified according to their side chain's chemical properties (the R-group). This video will show you how! By Tracy Kovach. Created by Tracy Kim Kovach.
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- Would you recommend memorizing all 20 amino acids, their structures and their classifications for the MCAT?(29 votes)
- You should be able to classify all the amino acids by polarity, charge, aliphatic vs aromatic, and probably learn the structures and functional groups of the special amino acids (for example: two cysteines close in space may form disulfide bridges under oxidizing conditions, prolines tend to introduce kinks in polypeptides and are often found at the beginning of alpha helices).(78 votes)
- Why are non-polar molecules hydrophobic? I mean, they do not have any partial charge in their structure, thus neither attraction nor repulsion will occur.
Then why is it hydrophobic?(13 votes)
- Well you're right that non-polar things will not have any attraction or repulsion with water. It's not that water doesn't like oil, it's that water doesn't like oil as much as it likes other water (or other polar molecules that act like water).
Each water molecule will try to lower its energy state by maximizing its number of hydrogen bonds with other polar molecules. This is seen at the macroscopic level as oil getting pushed away so that water can maximize the amount of polar-polar bonds.(13 votes)
- I was taught that tryptophan is a polar molecule due to NH bond next to the aromatic making it slightly polar. Your video seems to say otherwise. So is tryptophan polar or non polar?(6 votes)
- You're right, it would be slightly polar. However, since it is not strongly polar, tryptophan is still generally classified as having a nonpolar R group.(15 votes)
- At5:51, she says that she remembers that the amino acids are basic because they have N atoms. So why aren't Proline and Tryptophan also polar/basic?(6 votes)
- The three amino acids are Lysine, Arginine, and Histidine, and how I remember these three is using the abbreviation for the strong base LAH (lithium aluminum hydride). They are basic because their side chain is basic and are positively charged at pH values below their pKa’s. Only the guanidine group (HNC(NH2)2) in Arg (pKa = 12.5) and amine group in Lys (pKa = 10.5) will accept a proton and exist with an overall charge of +1 at physiological pH. The imidazole group (ring structure with two N’s) in His (pKa = 6.0) would exist predominantly in neutral form.
Proline is not polar and basic because the N is not from the side chain. Proline originates from glutamic acid, the carboxy reduced to an aldehyde, amino group attacking to form the Schiff base, and further reduction. Basically, the N is from the original alpha-amino group. Proline qualifies as nonpolar and cyclic. As for tryptophan, it has an indole substituent on the beta-carbon. The N in the indole group (2 ring structure with one N) has no free lone pair to act as a base because it is already participating in the resonance. Tryptophan qualifies as nonpolar and aromatic.(14 votes)
- At4:36she says she remembers polar amino acids by the presence of an oxygen or a sulfur atom in their side chains, but at2:26, she says methionine is a nonpolar amino acid, even though there is a sulfur atom in its side chain. How are we supposed to recognize the difference between those? Is there another way to identify which are polar and which are nonpolar?(5 votes)
- Methionine contains a sulfur atom in its side chain, but it is surrounded by three carbon atoms. Cysteine, however, is only bonded to one carbon atom and one hydrogen atom. In methionine, then, there is certainly polarity in the molecule, but overall, the three carbons (and their hydrogen atoms) are more significant. When a molecule of some substance mixes with water, it disrupts the hydrogen bonding between water molecules. For very polar molecules, this isn't a problem, because they can interact strongly with water. For only weakly polar molecules, the energy "payoff" of bonding with water isn't enough to compensate for the disruption in water hydrogen bonding. You can see this effect with alcohols of different sizes; small alcohols like methanol and ethanol are miscible with water because they are strongly polar (-OH group attached to only one or two carbon atoms). Larger alcohols (propanol or hexanol) are not miscible with water because even though they are technically polar, they have such large hydrocarbon chains that they can't interact favorably with water, despite the hydroxyl group.(11 votes)
- 4:38I'm confused. In the books I'm reading, Basic Medical Biochemistry by Lieberman et al, and Lippincott's Biochemistry, Tyrosine is classified under aromatic amino acids, making it nonpolar like Tryptophan and Phenylalanine. They also say that Tyr and Try are more polar than Phe, but they still are relatively nonpolar. Can anyone help me understand?(7 votes)
- Tyrosine's phenol group can indeed hydrogen bond with water, but it can also energetically-favorably pi stack with surrounding aromatic amino acids (similar to DNA nitrogenous base stacking), typically within a protein's hydrophobic core. In fact, tyrosine pi stacking is commonly observed in known protein structures, and possibly more often than exposed tyrosines hydrogen bonding with water at the protein surface.(5 votes)
- Do amino acids in a low pH solution always have a positive charge?(4 votes)
- The word "always" is very difficult in biological science. But in most cases of extremely low pH (1-2) then yes all of the amino acids would carry a positive charge.(9 votes)
- Oil is an example of Hydrophobic, isnt it?(3 votes)
- Yes, oil is a non-polar molecule and so it will not mix with water, which is a polar molecule. This makes oil hydrophobic ("water fearing") and is why oil floats on top of water.(7 votes)
- At4:38, Tyrosine is included as a Polar aa (also the side box says that it can be included as an aromatic acid. My question then is, is Tyrosine considered both non polar and polar amino acid then? My Kaplan textbook only shows tyrosine as an aromatic.(3 votes)
- I am not sure what is the right answer because I have been finding conflicting answers. This source says tyrosine is polar: http://www.thinkpeptides.com/aminoacidproperties.html. While this source says tyrosine is non-polar: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/Tyrosine.html(3 votes)
All right. So let's go through the classification of amino acids. And I've highlighted the word class within classification for you, because I'm going to paint for you a picture of a classroom that is full of 20 different amino acids. And just picture this as the most diverse classroom you've ever seen, because each amino acid has their own unique side chain, and this makes them distinctly different from the amino acid next to them. And just like a real classroom full of kids, even though each amino acid is unique and special in their own way, you can start to see that some of these amino acids are more alike than they are different. And we can start to see these similarities in the chemical properties of the side chains, and this allows us to group them together into various categories. And those chemical properties include the charge of the side chain, the ability of the side chain to undergo hydrogen bonding, and also whether or not we can classify that side chain as being either acidic or basic. So the 20 amino acids can be split broadly into kind of two main groups. The first group includes the nonpolar amino acids, and then the second group includes the polar ones. And the nonpolar amino acids can also be thought of as the hydrophobic, or water-fearing, amino acids. And conversely, you have the polar ones. Those can be considered hydrophilic, meaning water-loving. And yet another way that I like to kind of think about these two main groups are the hydrophobic amino acids-- they're kind of like the water-haters. They don't really want to interact with water at all. They'd rather just interact with themselves. Whereas the hydrophilic amino acids are very open and welcoming to interacting with water, and so they're water-lovers. And then within the two groups of nonpolar hydrophobic and polar hydrophilic amino acids, you then have a further breakdown into subgroups. And those subgroups include those amino acids that have alkyl side chains, aromatic side chains, neutral ones, acidic ones, or basic ones. So let's take a closer look at those amino acids that have alkyl groups as side chains. And as you can see here, we have seven different amino acids, and I've just drawn out the side chain for you. I've left the rest of the molecule out just to fit everything in here. And we have glycine, alanine, valine, methionine, leucine, isoleucine, and proline. And proline is the exception. I've drawn out the entire amino acid there, because as you can see, its side chain forms this interesting ringed structure with the amino group in the backbone of the molecule. So I just included it there for completeness. So all these side chains are made up of alkyl groups, with the one exception being glycine, because its side chain has only a hydrogen atom in it. But because it behaves similarly to an alkyl chain side group, it gets slumped into this category of amino acids. And whenever you see an amino acid with an alkyl group as its side group, you should be thinking that this amino acid is nonpolar. And so they're also going to be hydrophobic. Now, let's take a closer look at those amino acids that have aromatic groups as part of their side chain, and remember, we're still under the umbrella of nonpolar hydrophobic amino acids here. And so I've drawn out for you here two amino acids, phenylalanine and tryptophan. And what should you be thinking when you're looking at these amino acids? So besides thinking, oh, those amino acids must smell really good, because they're called aromatic amino acids-- well, that might be true, but you should also be thinking the same thing that you think when you see amino acids with alkyl groups as their side chains. These amino acids that you see here are also nonpolar and hydrophobic. And that kind of makes sense, because aromatic chains are also just made up of carbons and hydrogens. And you weren't wrong if you thought that aromatic compounds might smell really good, because many of our most aromatic herbs and spices that we're all familiar with, like basil or cinnamon and vanilla, are composed of the same sorts of ring structures that we see here. All right. So now that we've tackled the nonpolar hydrophobic amino acids, let's dive on into the polar and hydrophilic amino acids. The first group that we will look at is the neutral group. Here we have serine, threonine, asparagine, glutamine, cystine, and tyrosine. The way that I remember that these are the polar amino acids is that these amino acids have a side chain that contain an oxygen or a sulfur atom, which tends to hog all the electrons around them to create a localized negative charge over that atom and then a positive charge over the rest of the side chain. So you can kind of see why these amino acids like to hang out with water now, since water is also polar in the same way. And these amino acids are considered neutral, because although they are polar enough to interact with water, they're not strongly polar enough to qualify as an acid or a base. So which of the polar hydrophilic amino acids do qualify as acidic? Well, that would be these two amino acids here, aspartic acid and glutamic acid. As you can see, these amino acids have a carboxylic acid as part of their side chain, which is a very willing, strong hydrogen donor which qualifies these amino acids as acidic. When these side chains do donate their hydrogen and they're left in anion form, then in that case, we refer to them as aspartate and glutamate, respectively. So you might see them referred to in that way. Last but not least, we have the basic amino acids, and they're histidine, lysine, and arginine. And the way I remember that these amino acids are basic is that if you take a closer look at their side chains, you see a few nitrogen atoms. And remember that nitrogen is a very willing proton accepter, and this is why they qualify as basic.