- Amino acids and proteins questions
- Central dogma of molecular biology
- Central dogma - revisited
- Peptide bonds: Formation and cleavage
- Special cases: Histidine, proline, glycine, cysteine
- Amino acid structure
- 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 are the building blocks of proteins. They contain an amino group, carboxylic acid group, alpha carbon, and side chain. Most amino acids have a chiral carbon, which allows them to rotate polarized light. Amino acids can have either an L- or D- configuration, but only the L- form is found in the human body. Created by Tracy Kim Kovach.
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- 2 configurations were mentioned, she said the "L" refers to the human body, but what does the "D" refer to?(20 votes)
- it's important to take note of her word choice here. She said that 'L' is the only one found in the human body; not that 'L' refers to the human body. 'L' enantiomers can be found in many places in the world and so can 'D', but the human body has a restriction. The human body can only make 'L'. If you were to synthesize enantiomers (like amino acids) in a laboratory, you'd find that it's possible to get a 50/50 production of 'L' and 'D' enantiomers depending on your reaction mechanism.
P.S. If you want to know more about this, you can view the lecture series on Organic Chemistry as it is elaborated further there.(63 votes)
- What is the 21st amino acid? I was always taught 20.(11 votes)
- I dont get the part where she says that u cant super impose the L and D amino acids. Cud someone explain it to me? Thank you(12 votes)
- When the L and D versions are in three dimensions they are mirror images of each other, like your hands. They look very similar, but like your hands, no matter how much you twist them you can't superimpose one on top of the other. For some reason (and I don't know what it is) in nature one form of a molecule is usually found rather than the other.(5 votes)
- I am a little confused on the geometry. On the pink drawing, saw H is going out, R is going in, and NH2 and COOH are on the same plane. That adds to be 3 planes for the groups connected to the carbon.
However, on the Fischer drawing, she explained that NH2 and H are coming towards you, and COOH and R are going away from you, that adds to only 2 plains, so aren't these different?(6 votes)
- The way I like to think about the Fischer Projection is like a stick man wearing a bow-tie facing you. The bow-tie is the horizontal line, and the guy is the vertical line. Like the lobes of a bow-tie come out towards you, so do the groups attached in the horizontal line. The vertical line leans away from you, not 180 degrees opposite, but just leans away slightly. This is why the model is still 3-dimensional.(8 votes)
- What is the difference between ATP and ADP? I hear these terms thrown around a lot...(3 votes)
- ATP(adenosine triphosphate) is the universal energy currency of cells
basically ATP has one more phosphate group than ADP, and because ATP has one more phosphate group than ADP, it contains more potential energy because more bonds could be broken
ATP forms ADP when it breaks a phosphate group to utilize its bond energy to do work, and ADP forms AMP (adenosine mono-phosphate)(15 votes)
- @5:43, approx., where would the light source come from if these processes are happening internally?(2 votes)
- There would be no light under normal conditions. It's just that if you extract and purify an amino acid and then shine polarised light through it, the light will be rotated. It's an experimental technique for analysing amino acids, not a natural process.(15 votes)
- At9:23, she indicates that L stands for Left. Just after than, she indicates that D stands for Right in Latin. Why didn't they use the Latin word for Left?(1 vote)
- The D stands for dextrorotatory or dextrorotary (from the Latin "dexter" meaning "on the right side"), meaning that plane polarized light is rotated clockwise or to the right.
The L stands for levorotatory or levorotary (from the Latin "laevus" meaning "on the left side"), meaning that plane polarized light is rotated counterclockwise or to the left. So the Latin words for both directions are used.
Hope this helps. ^ ^(13 votes)
- 6:00. Why exactly does the fact that glycine's R group is simply an H atom make its alpha carbon non-chiral, whereas the alpha carbon is chiral in all other amino acids with their different R groups? I don't quite follow this. Does having one H atom for a side chain uniquely alter glycine's optical properties? Thanks very much.(5 votes)
- A chiral C-atom means that the atom is bound to four different groups. In glycine there are two H-atoms which means there are not four different groups bound to the C-atom. In all the other aminoacids the alpha C-atom is bound to four different groups.
I'm sorry that my english is bad, but I hope i could answer your question.(2 votes)
- What does 'fischer' means exactly?(2 votes)
- type of diagram/ way of drawing. My SWAG as to the origin of the name would be the creator's last name is/was Fischer.
That said, I'm now wondering if you're just making a pun of Fischer Model vs. Fisher's Exact Test (statistical significance). Because L-amino acids would totally be present in statistically significant numbers in the human body, and you can use both Fischer and Fisher to illustrate this pun.(6 votes)
- at3:16Tracy talks about the no. of amino acid .Are there only 20 of them or are there more?(2 votes)
- There are only 20 "natural" amino acids - amino acids that are naturally incorporated into proteins by living organisms. When people refer to amino acids, they are typically referring these 20 natural ones used and created by living things.
That being said, the name, "amino acid" only requires a molecule to have both a carboxylic acid functional group and an amine functional group. So you can design an "amino acid" with almost any shape and chemistry you can imagine.(4 votes)
Hey, so we're going to be talking about amino acids, and specifically with regards to amino acid structure. And before we dive on into this topic, I think it's nice to kind of take a step back and take a big-picture view of amino acids and kind of figure out-- where do they exactly fit in the grand scheme of biochemistry and specifically human metabolism? And I think the best way to do this is to take a real-world example of a human protein called hemoglobin. Now, what is hemoglobin? Well, hemoglobin is found within the red blood cells that flow all through our bloodstream. So here's my little red blood cell. And each red blood cell is chock-full of this hemoglobin protein. I'm just going to write it out as each Hgb here. And this hemoglobin protein is what is actually responsible for picking up oxygen. When this little red blood cell flows through the vessels and the lungs, picks up oxygen, and then transports this oxygen to all the various tissues within our bodies. And so you can kind of think of hemoglobin as a car of sorts. My favorite car is a Porsche 911. If you want to be more environmentally friendly, you could think of a Prius, or something like that. So whatever your car is, oxygen is like the passenger for that car. And so hemoglobin goes by the lungs, picks up oxygen, delivers it to the tissues. And then tissues are just groups of cells that are of a similar type, and so each of the cells in these tissues then takes the oxygen and uses it to generate adenosine triphosphate, or ATP, which is the energy source for all the various metabolic processes that go on within our cells to help keep us alive. So now where do amino acids fit into all of this? Well, amino acids are the building blocks of this hemoglobin protein. And so without amino acids, this entire vitally important process wouldn't be able to occur. Now, sticking with the car analogy just a little bit longer, just like we have different types of components that come together to form different types of cars, whether it be a Porsche or a Prius, what have you, you can have different types of amino acids. And there are 20 of them-- to be exact-- that can come together to form countless, countless different types of proteins. And so now that you have an idea of where amino acids fit in this bigger picture of a metabolic process, let's go ahead and take a closer look at what the actual structure of an amino acid is. First, we have the amino group. And then we have the carboxylic acid group. And already you can start to see where the name amino acid comes from. You have amino, from the amino group, and then you have acid from this carboxylic acid group here. And then linking the two groups is this carbon atom, which we call the alpha carbon. And then bound to the alpha carbon is a hydrogen atom as well as a unique side chain, or R group. We just use R to denote any generic side chain. So each of the amino acids has this same generic structure, and what makes each of the 20 amino acids different from each other is this R group, or the side chain. So each of the side chains for the amino acids is going to look different. One thing that's important to note is that this carbon atom, the alpha carbon, is also known as a chiral carbon. And what does a chiral carbon mean again? Well, a chiral carbon is a carbon atom that has four unique groups bound to it. So if we take a look at this carbon, we can see that one group that's bound is the amino group. Another group is the carboxylic acid group. The hydrogen atom makes the third group, and then the fourth group bound to it is the R group or the side chain. And so the alpha carbon in amino acids is considered a chiral carbon. And remember that chirality really refers to optical activity. In other words, if you were to shoot plain, polarized light at an amino acid, then because this carbon is chiral, it would rotate to that light. And so that's what chirality is really referring to. It's referring to optical activity. Now, it's important to note that there is one exception among the amino acids for chirality, and that is the amino acid glycine. And that's because the side chain, or R group, for glycine is just a hydrogen atom. It is the simplest of all side chains, just one hydrogen atom. And so if you were to substitute a hydrogen atom in place of this R group, you would see that you have a duplication of atoms coming off of this alpha carbon in the case for glycine. And so glycine is the only amino acid that does not have a chiral carbon. So that's just important to make note of. So let's give ourselves a little bit more room here. Now, another way that you can portray the structure of an amino acid is with something called a Fischer projection. And Fisher projections help to highlight the relationship of the four groups around a chiral carbon. So let me draw that for you here. First, you have your amino group, and up top you have your carboxylic acid. Here is your hydrogen atom, and at the bottom is the side chain, or R group. And just to orient you a bit, here in the center is the chiral carbon, the alpha carbon here. And then you have the four groups coming off of the chiral carbon. And the horizontal bonds here-- you can kind of picture those as coming out of the plane of the computer towards you. And then these vertical bonds here are coming out of the plane of the computer away from you. And this particular configuration is called an L-amino acid. And conversely, you can have the mirror image of this, which I'll draw for you here. And this particular configuration is called a D-amino acid. And these two configurations are called enantiomers. And enantiomers are mirror-image molecules that are not superimposable. So you can picture-- these are mirror images of each other, but if you were to take this D-amino acid and try to superimpose it on the L-, you wouldn't be able to do that. You can kind of think of these two configurations like your left and right hand, and although your left and right hand are mirror images of each other, you can't superimpose them on one another. And that's the relationship between an L- and a D-configuration for Fischer projections. And these two configurations look awfully similar and are really easy to mix up, and so the way that I like to keep them straight is if I look at where the amino group is-- let's take the L amino acid. If I look at where the amino group is, I can see that it is to the left of the projection, so L is for left amino group. Now, if I look at the D amino acid, I again look for the amino group, and I see that it's to the right of this configuration. And so D, which actually means dextro, or right, in Latin, is for right amino group. That's kind of how I like to keep them straight. So why is it important to distinguish between L- and D-amino acids? Well, the L- form of an amino acid is the only form that you will find within the human body, and so that's really important to remember-- that the L-configuration is the kind that you find within humans. All right. Now how about we review a little bit about everything that we learned? First, we sort of got a big picture of where amino acids fit in a larger metabolic process, such as in the example of hemoglobin. And then we learned about the structure of an amino acid and the fact that the central alpha carbon is a chiral carbon with optical activity, and the one exception to this rule is the amino acid glycine, which just has the simplest side chain of a hydrogen atom, and therefore it is not a chiral molecule. And then we also learned about the Fischer projections for amino acids and the fact that the L-configuration of an amino acid is the only one that you find within the human body. And there you have it.