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Chemistry: Proteins


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  • Type: Video Tutorial
  • Length: 9:44
  • Media: Video/mp4
  • Use: Watch Online & Download
  • Access Period: Unrestricted
  • Download: MP4 (iPod compatible)
  • Size: 105 MB
  • Posted: 07/14/2009

This lesson is part of the following series:

Chemistry: Full Course (303 lessons, $198.00)
Chemistry: Biological Molecules (4 lessons, $5.94)

This lesson was selected from a broader, comprehensive course, Chemistry, taught by Professor Harman, Professor Yee, and Professor Sammakia. This course and others are available from Thinkwell, Inc. The full course can be found at The full course covers atoms, molecules and ions, stoichiometry, reactions in aqueous solutions, gases, thermochemistry, Modern Atomic Theory, electron configurations, periodicity, chemical bonding, molecular geometry, bonding theory, oxidation-reduction reactions, condensed phases, solution properties, kinetics, acids and bases, organic reactions, thermodynamics, nuclear chemistry, metals, nonmetals, biochemistry, organic chemistry, and more.

Dean Harman is a professor of chemistry at the University of Virginia, where he has been honored with several teaching awards. He heads Harman Research Group, which specializes in the novel organic transformations made possible by electron-rich metal centers such as Os(II), RE(I), AND W(0). He holds a Ph.D. from Stanford University.

Gordon Yee is an associate professor of chemistry at Virginia Tech in Blacksburg, VA. He received his Ph.D. from Stanford University and completed postdoctoral work at DuPont. A widely published author, Professor Yee studies molecule-based magnetism.

Tarek Sammakia is a Professor of Chemistry at the University of Colorado at Boulder where he teaches organic chemistry to undergraduate and graduate students. He received his Ph.D. from Yale University and carried out postdoctoral research at Harvard University. He has received several national awards for his work in synthetic and mechanistic organic chemistry.

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Biochemistry is the study of chemical processes of living systems. Living systems are very complicated systems, obviously. There are lots of chemistry and chemical reactions that have to occur to get a living organism to actually reproduce and be alive.
Central to the study, is the study of proteins. Everybody knows what proteins are in the context of the basic food groups. You know that you should eat a certain amount of protein everyday. But the question is, do people really know what the definition of a protein is? Well, a protein is a natural polymer that is made up of an amino acid or an amino acid sub unit. Amino acids are bonded to each other via amide bonds to make proteins.
Now an amino acid is a molecule that contains and amine and a carboxylic acid, as the name would imply. To make an amide bond, this molecule, for example, would condense with itself to make that bond right there, to make that amide bond right there. So amide bonds are bonds that have the nitrogen in them, and the nitrogen is bound to a carbonyl. The C double bond O. That defines an amide. Proteins are polyamides. They are polymers of amino acids that are bonded together to form many, many amides.
Now there are a lot of natural amino acids, about 20 essential amino acids that your body produces naturally and so on. Many of these amino acids are chiral. Essentially what happens is that you have a molecule that is an amino acid that has an R group here and the word R group, by the way, is simply the chemist notation for the term X in mathematics. The word R, means any carbon group that you want to have attached here that might be attached to this position. But these molecules are chiral because this carbon here contains four different substituents attached to it. It contains the carbon r group, the carbonyl, the carboxylic acid, nitrogen, and don't forget that there is an H bound to that carbon as well to complete its valency, so these molecules are chiral. They have the stereo? center and there are two general types of R groups that are found in these amino acids. The are the non-polar R groups, that contain only carbon and hydrogen. An example of which, is this molecule here, which is valine. It has an isopropyl group as a side chain. And here is another example, which contains a CH[3], which is the alanine side chain.
So these are the non-polar amino acids. The other kind of amino acids that you have are the polar amino acids. The polar amino acids have a heteroatom like sulfur, oxygen or nitrogen in their side chain. This is an example of an amino acid called serine and this is an amino acid called lysine. The serine contains an OH and the lysine and NH[2].
Whether an amino acid is polar or non-polar, can have a profound influence on the structure of a protein and the function of a protein. Here is a portion of a protein. Here is the polyamide structure that I was referring to earlier. This nitrogen is an amide nitrogen bonded to that carbonyl. That is an amide nitrogen bonded to that carbonyl and so on and so on. Amino acids that are the constituents of this protein are shown right here. Here is one amino acid. Here is another amino acid sub unit, here is another one, and there is the fourth one. So you can see what happened is, that we basically polymerized these amino acids and made amide bonds. Now these amide bonds hold this protein together, this portion of the protein together. Then the protein extends onwards, these squiggly lines are meant to indicate.
Now we talk about the structure of protein. There are different levels of structure that we can talk about. We can talk about the primary structure. The primary structure is simply the amino acid sequence. What is the identity of the groups R[1], R[2], R[3], R[4] and so on and so on in the protein? That is called a primary structure of the protein. But more important, or as important, is the secondary structure. The primary structure influences the secondary structure, because the protein has a certain primary structure it will fold up into a certain secondary structure. By secondary structure, what I mean is how the backbone of the protein actually organizes itself and folds into a certain shape. Here is an example of one important secondary structural unit. It is an alpha helix. An alpha helix is a helix structure that rotates around like this and that has hydrogen bonding between the NH of the amide and the carbonyl of a different amid. This hydrogen bonding is what holds the molecule together. In other words, when the molecules hydrogen bond they will fold up in a certain way and they will be able to get good strong hydrogen bond when they are folded up that way. If they were to unfold, they wouldn't have these nice strong hydrogen bonds. So the presence of these hydrogen bonds is what dictates the structure of the protein. Also here is a picture of a secondary structure element, the alpha helix, and here it is in model form. And you can see that the dashed red lines are the hydrogen bonds between that carbonyl and the oxygen, let's say and the hydrogen of that nitrogen. So there is an NH bond right there and there is a carbonyl right there. This dashed line represents that hydrogen bond that is hold this molecule together in that shape.
Another very important secondary structure that is called the beta sheet. And beta sheets are extended zigzag confirmations of proteins and they are held together by hydrogen bonds between the two beta sheet strands. So here is one beta sheet strand; here is another beta sheet strand. These two strands are held together by these red hydrogen bonds. You can see what happens is that the NH of one molecule points towards the CO of the other, and the oxygen is basic. NH is acidic. Here is an oxygen, and here is an H, NH acidic, oxygen basic. NHO, NHO. And so all these interactions are hydrogen-bonding interactions that will hold the beta sheet together as it is. You can also see that there is room for another beta sheet to come up here let's say. If I had written up here I could have written another one up here. And you can still have the same functionality that is required for making the hydrogen bond on the topside. We have the carbonyl, NH, carbonyl, oxygen, NH. This can be hydrogen bond acceptor, hydrogen bond donor, acceptor, donor, acceptor, donor and so on. So this can then form a third strand and so on. You can get a number of strands in beta sheets.
Here is an example of that. In this representation the black dashed lines represent hydrogen bonds. So the yellow would be a carbonyl, oxygen that color there, whatever that might be, orangish would be the NH. Yellow, orange, yellow, orange and wherever you have the carbonyl and the NH you have the potential to form a hydrogen bond and you can see how these arrays stack on top of each other or side by side with each other to form this sheet-like structure.
Now proteins also have what is known as tertiary structure. Tertiary structure is the way the secondary structure packs. So here is the helix, another helix and a beta sheet. These things might pack where you will have one helix like this and the other helix like that, and then the beta sheet might fill in between the two helices. Often times what happens is, that proteins pack in a tertiary structure, such that there is a pocket and this might be the pocket for this particular rendition of a protein. This pocket might be where a molecule might fit in and do some chemistry. So the proteins are catalytic and catalyze reactions. They have to be able to bind the molecules that they are going to react with. A good way of doing that is by forming a little pocket such that the molecule can bind and the reaction can occur.
So that is the important thing about proteins that they can adopt these tertiary structures and they can do lots of things like catalysis and recognition and so on. Well we have a name for proteins that can do catalysis and that name is enzymes. Basically an enzyme is nature's catalyst. It will catalyze all kinds of reactions. Different enzymes catalyze different reactions and they catalyze all their reactions that are important for life. One example of a very important catalysis is the HIV protease. Of course everybody has heard of HIV. HIV is the positive agent of AIDS. HIV is formed in the cell. HIV is a virus and the virus is formed in the cell, and when the virus replicates, it produces what is known as a polyprotein. What happens is you have a protein here that is linked to another protein, that is link to another protein and so on. And these proteins are linked by amide bonds. HIV protease comes in and cleaves to amide bonds and liberates the proteins so that they can go off and do their thing within the virus. That is an essential step in the life cycle of the HIV virus.
So specifically what the enzyme does is it takes this amide bond. The amide bond is part of the polyprotein structure and it catalyzes the addition of water to this amide bond and the cleavage of amide bond to give you carboxylic acid and an amine. So this oxygen would be that oxygen over there. And the HIV protease catalyzes this reaction, normally a very stable bond, amide bond, but the protein catalyzes the hydrolysis to give you this product and that product. Like I said, that is required for HIV replication.
Now medicinal chemists at drug companies are very smart and they can come in and what they can do is try and engineer molecules that will bind to the HIV protease and inhibit its replication. And in so doing you can slow down the replication of the virus. This class of compounds is known as HIV protease inhibitors. And recently there have been several of these that have hit the market and they have had a profound effect on HIV infected patients. These compounds are so effective that in some patients the levels of the HIV virus itself is slow low that it can not be detected by modern methods. That does not mean that the patients are cured by any sense, because the way HIV works is something of a retro virus and it is incorporated into the body in a way that it is not going to be cured by the protease inhibitors. But the life cycle has slowed down so much that the virus particles are undetectable in the blood stream.
So now to summarize what we have learned. Proteins are an essential component of living systems. Proteins can be catalysts and when they are they are called enzymes. Proteins are made of amino acids that are linked together by amide bonds to make a polymer and these amino acids are chiral and they have different side chains on them that are either polar or non-polar. And the identity of these side chains determines structural features of the protein whether the protein are pulled into giving you alpha helical structures or beta sheet structures as well as the catalysis that the protein can undergo.
Biological Molecules
Proteins Page [1 of 3]

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