- 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
Certain amino acids stand out for their unique properties. In this video, you'll learn more about what makes histidine, proline, glycine, and cysteine unique. By Tracy Kovach. Created by Tracy Kim Kovach.
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- Why are glycine and proline called alpha helix "breakers" if they are responsible for forming alpha helix?(12 votes)
- Glycine and Proline start secondary structures called beta turns. A beta turn is a turn in the primary structure, stabilized by hydrogen bonding. Because Proline has an odd, cyclic structure, when it forms peptide bonds, it induces a bend into the amino acid chain. I challenge you to draw the peptide chain with proline; you will see it. Glycine can cause a bend in the chain, because it has extreme conformation mobility, due to its small size. Thus, steric hindrance about a bend is minimized. Think about it. The next largest side chain is of alanine. Alanine's R-group has a mass of 15 amu. Glycine's in only 1 amu! Thus, there is a significantly higher steric hindrance of rotation for alanine than glycine. There is no such hindrance in Glycine. Thus, if the protein needs a bend, as in globular proteins, Pro or Gly will often be found. Thus, the alpha-helix is broken to bend, because Pro and Gly are thermodynamically destabilizing to alpha-helices.(39 votes)
- I don't understand why a reducing environment keeps the sulfur protonated, while an oxidizing environment deprotonates the sulfur. I thought oxidation/reduction has to do with electrons, not protons. Can someone explain for me? Thanks!(13 votes)
- When a compound is oxidized, it loses an electron, but that is not the only definition of oxidation. These redox reactions (oxidation/reduction) are also characterized by the loss or gain of oxygen and hydrogen. In summary, if something is oxidized, it either loses electrons, loses hydrogen, or gains oxygen. If something is reduced, it either gains electrons, gains hydrogen, or loses oxygen.
Sources and further explanation:
- Why is methionine not considered a special case for amino acids?(10 votes)
- Its sulfur atom is nonreactive, since it is bound to two carbon atoms, rather than a hydrogen that can be lost in an oxidation reaction.(2 votes)
- At1:44, it says that histidine exists in both protenated and deprotenated forms because its pKa is so close to the human body's regular pH. How come it wouldn't be in a neutral form? Also, what class of amino acids is histidine in?(6 votes)
- You shall tihnk of it as "can exist" in both a protonated and a deprotonated form. Actually what she doesn't tell you is that the pKa can be altered hugely depending on the actual local environment the chemical group is present in. Proteins are very good at altering the environment of different amino acids by folding into an ordered state.
Histidine has a pKa around 6-7ish dependent on who you ask. This is close to physiological pH (i.e. the pH most proteins would encounter). As the pKa is very close to the pH, only small changes in the local environment can change the protonation state of the amino acid.(5 votes)
- Chemistry Question here: In the discussion of Cysteine, the author refers to the reducing environment as the one where the Sulfur is protonated with the Hydrogen atom, making a thiol group. Is it true that reducing environments will be ones where molecule are protonated or exist in their protonated states? Is this even the correct way of phrasing the question?
Thank you.(4 votes)
- A reducing environment is one that is rich in electrons, but this is relative to the electronegativity of the atom in the molecule. Oxygen is very electronegative and tends to take electrons from nearby atoms which is why it is usually an oxidizing agent (Oxidize=take electrons). Hydrogen usually has a lower electronegativity than biological molecules and usually donates its electrons to nearby atoms ( Reduce=Gain electrons)
Just keep a general idea of electronegativites
LEO goes GER
Lose Electrons, Oxidation
Gain Electrons, Reduction(3 votes)
- Are there any tests quizzes available on these topics on the site? I wanted to see how much I actually retained.(3 votes)
- Is the classification of amino acids into acidic, basic and neural based on natural PH in the body (7.4)? If the answer to my question is Yes, then why Histidine is listed as basic amino acids then? Histidine will be deprotenated at 7.4 PH ( since 7.4> 6.5) and it will be acidic, it will rain negative charge and will be acidic; is that reasoning wrong?(5 votes)
- You are an amazing instructor... the lectures are so well paced and you speak so clearly...
On a separate note, I'm not really sure why this particular lecture is relevant. In what context would it be applicable? How might a question on the MCAT ask us to recall this information? Thanks.
- There is a practice question in my Kaplan MCAT biochem book that says "Collagen consists of three helices with carbon backbones that are tightly wrapped around one another in a "triple helix." Which of these amino acids is most likely to be found in the highest concentration in collagen?"
Answering this question should help you see the relevance of this video. It's one of the one's discussed by the way.(5 votes)
- At6:25, do cystine amino acids form disulphide bonds only when they are exactly next to each other in a polypeptide chain or is there a way for them to form these bonds even if there are other amino acids between them in a polypeptide chain?(3 votes)
- May i know why is the extracellular space an oxidizing environment?(1 vote)
Hey. So welcome to the Amino Acids Show. And this show is going to be featuring just 4 of the 20 amino acids. And those amino acids are histidine, proline, glycine, and cysteine. And these four amino acids deserve sort of an extra time in the spotlight because they each have a side chain that sort of sets it apart from the rest. And so let's go through one-by-one and see what exactly these side chains are all about. So first up we have histidine, and I've drawn the structure of histidine for you here. And here is the backbone of the amino acid. So this is the same for all the amino acids. And then, you see here is the side chain of histidine. So what is so special about histidine, then, with this side chain? Well, as it turns out, this side chain has a pKa of around 6.5. And this turns out to be really close to physiological pH, which is right around 7.4. So what does this really mean-- to have a pKa that's close to physiological pH? Well, recall that, at a pH below an amino acid's pKa, the amino acid will exist in a protonated-- or positively charged-- form. And at a pH above an amino acid's pKa, it will exist in deprotonated form. Now, since the physiological pH-- which is the pH of the fluid within our own bodies-- is roughly equal to the pKa of histidine, then histidine's going to exist in both protonated and deprotonated forms. So this makes it a particularly useful amino acid to have at the active site of a protein where it can both stabilize or destabilize a substrate. So next step we have proline and glycine. If we go ahead and take a closer look at proline, we have the backbone structure here-- just like all the other amino acids. But then, you can see that the side chain is this alkyl group that wraps around and forms a second covalent bond with the nitrogen atom of the backbone. And so we say that proline has a secondary alpha amino group. And so this is just referring to the fact that the side chain forms a second bond with the alpha nitrogen-- the nitrogen in the backbone-- of this amino acid. Now, let's come over here and take a look at glycine. Here we have the backbone of the glycine molecule. And then, here we have the side chain. And the side chain for glycine is the simplest of all side chains. It is just 1 hydrogen atom. And I've drawn it out in wedge-and-dash form here to help emphasize how-- because the side chain of glycine is a hydrogen atom-- you have a duplication of atoms coming off of this carbon here-- the alpha carbon. And so now this carbon is no longer a chiral carbon. So we'll write that here. No chiral alpha carbon. And this kind of sets it apart from the rest of the amino acids because the rest of the amino acids do have a chiral carbon-- meaning optical activity under plane-polarized light. And glycine is also considered to be very flexible because it just has this little hydrogen atom as its side chain. And so there's a lot of free rotation around this alpha carbon. So we also consider it to be very flexible. So why are these two amino acids groups together? Well, they both play a role in disrupting a particular pattern found in secondary protein structure called the alpha helix. And an alpha helix is just a coiled up polypeptide chain that kind of looks like this. Now, because of its secondary alpha amino group, proline introduces kinks into this alpha helix. And it ends up looking like this. And also, since glycine is so flexible around its alpha carbon, it tends to do the same thing. And thus both of these amino acids are known as alpha helix breakers. So last but not least, we have cysteine. And here's the backbone again. And then, here is our side chain. And the side chain for cysteine has a special thiol group. And all thiol is really referring to is the sulfur and the hydrogen at the end there. So cysteines have this neat little trick where, if they're in close proximity with each other within a polypeptide chain or even between two different polypeptide chains, then their side chains can form a bond together between the two sulphur atoms called a disulfide bridge. So let's bring up 2 cysteine amino acids here. And I've shown them as isolated amino acids, but remember that they are part of a greater polypeptide chain. And the formation of the disulfide bridge occurs separate from the backbone. It is just between the side chains. The cysteine at the top is flipped over to bring its side chain in close proximity with the second cysteine below it. And then, the bridge forms between the two sulphur atoms. So before we go over how a disulfide bridge is formed, let's do a quick little review of redox reactions. And really, what you want to remember is the mnemonic OIL RIG. And that's to mind you that, in oxidation, you have a loss of electrons. So oxidation is loss. And in reduction, you have a gain of electrons. So reduction is gain. So remembering that will help you understand the disulfide bridge formation. So going back to our 2 cysteines. If you look closely at their side chains, the thiols are existing in reduced form. So you're going to find these tholes in a reducing environment. Now, say those cysteines end up in an oxidizing environment. In that case, you would see the loss of these hydrogens and then the formation of a bond between these two sulphur groups, which looks like this. So this here is your disulfide bridge. So when do you see cysteines going solo, kind of like you see here in the separate thiol group form? And when do you see them forming these disulfide bridges? Well, it turns out that it depends a little bit on what the rest of the environment around them is like. And as it turns out, the exterior of the cell or the extracellular space is an oxidizing environment. So I'll write that down here. So the extracellular space will favor the formation of disulfide bridges. But in the intracellular space, you're more likely to find a reducing environment. So I'll write that down here. And the way that I like to keep this straight is that I kind of think of how the interior of the cell has these little molecules called antioxidants. And these antioxidants, which-- you can kind of tell by the name of it-- stifle any oxidizing reactions. And so they keep the intracellular space a reducing environment. So you might have seen cysteine spelled without an e, like this. And you're probably thinking to yourself, is it cysteine with an e? Is it cysteine without an e? Is it cystine? Which one is it? I'm so confused. There are actually two official ways of spelling cysteine. The version with the e refers to cysteine when it's in its reduced form. And the version without the e refers to cystine when it has been oxidized. And the way I remember this is by picturing that the e stands for electrons. And so you have the electrons when you're in the reduced form. And then, you don't have the e for electrons when you're in the oxidized form. So hopefully that helps you keep things straight a little bit.