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Biology: Amino Acids: The R Groups

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About this Lesson

  • Type: Video Tutorial
  • Length: 10:52
  • Media: Video/mp4
  • Use: Watch Online & Download
  • Access Period: Unrestricted
  • Download: MP4 (iPod compatible)
  • Size: 116 MB
  • Posted: 07/01/2009

This lesson is part of the following series:

Biology Course (390 lessons, $198.00)
Biology: Inorganic and Organic Chemistry (34 lessons, $51.48)
Biology: Proteins (6 lessons, $9.90)

Taught by Professor George Wolfe, this lesson was selected from a broader, comprehensive course, Biology. This course and others are available from Thinkwell, Inc. The full course can be found at http://www.thinkwell.com/student/product/biology. The full course covers evolution, ecology, inorganic and organic chemistry, cell biology, respiration, molecular genetics, photosynthesis, biotechnology, cell reproduction, Mendelian genetics and mutation, population genetics and mutation, animal systems and homeostasis, evolution of life on earth, and plant systems and homeostasis.

George Wolfe brings 30+ years of teaching and curriculum writing experience to Thinkwell Biology. His teaching career started in Zaire, Africa where he taught Biology, Chemistry, Political Economics, and Physical Education in the Peace Corps. Since then, he's taught in the Western NY region, spending the last 20 years in the Rochester City School District where he is the Director of the Loudoun Academy of Science. Besides his teaching career, Mr. Wolfe has also been an Emmy-winning television host, fielding live questions for the PBS/WXXI production of Homework Hotline as well as writing and performing in "Football Physics" segments for the Buffalo Bills and the Discover Channel. His contributions to education have been extensive, serving on multiple advisory boards including the Cornell Institute of Physics Teachers, the Cornell Institute of Biology Teachers and the Harvard-Smithsonian Center for Astrophysics SportSmarts curriculum project. He has authored several publications including "The Nasonia Project", a lab series built around the genetics and behaviors of a parasitic wasp. He has received numerous awards throughout his teaching career including the NSTA Presidential Excellence Award, The National Association of Biology Teachers Outstanding Biology Teacher Award for New York State, The Shell Award for Outstanding Science Educator, and was recently inducted in the National Teaching Hall of Fame.

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  • 3964_amino_acids.pdf 3964_amino_acids.pdf

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Thinkwell lessons feature a star-studded cast of outstanding university professors: Edward Burger (Pre-Algebra through...

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Recent Reviews

Nopic_blu
Perfect
08/26/2012
~ Igor7

This is great. Just watching from the nucleic acids intro up to here I've learnt more than I did spending half a semester in molecular biology at uni. And for that person who gave it 2 stars 'cause "the professor doesn't explain polar and nonpolar", he explains it in an earlier video of this course, and if you don't know what it is and you're watching about proteins with *functional groups*, then you seriously need to open up your textbook every once in a while. No one's gonna spoon-feed you.

Nopic_grn
Why couldn't I have learned everything this...
08/16/2012
~ Sabrina8

I want a do-over.... everything. With these professors.

Nopic_tan
Polar vs. Non polar
10/30/2011
~ David157

The professor never tells us what polar and non polar means. He points to a lot of R Groups saying which ones were polar and which were non polar but he never did define what a non polar/polar molecule is, or what it was about the molecule that made it non polar or polar or neutral. I still don't know and listened carefully. That's not fair when the focus of the lecture is nonpolar/polar distinctions.

Nopic_blu
Perfect
08/26/2012
~ Igor7

This is great. Just watching from the nucleic acids intro up to here I've learnt more than I did spending half a semester in molecular biology at uni. And for that person who gave it 2 stars 'cause "the professor doesn't explain polar and nonpolar", he explains it in an earlier video of this course, and if you don't know what it is and you're watching about proteins with *functional groups*, then you seriously need to open up your textbook every once in a while. No one's gonna spoon-feed you.

Nopic_grn
Why couldn't I have learned everything this...
08/16/2012
~ Sabrina8

I want a do-over.... everything. With these professors.

Nopic_tan
Polar vs. Non polar
10/30/2011
~ David157

The professor never tells us what polar and non polar means. He points to a lot of R Groups saying which ones were polar and which were non polar but he never did define what a non polar/polar molecule is, or what it was about the molecule that made it non polar or polar or neutral. I still don't know and listened carefully. That's not fair when the focus of the lecture is nonpolar/polar distinctions.

You know, some of you out there are hoping to be engineers one day. You may have started out in engineering. Engineers all started out, perhaps, thinking that, "You know, I just want to design things." So, they really never understood, perhaps, early in their careers why they had to take these, what seem to be trivial courses. I have a friend who wanted to be a ceramic engineer. He wanted to design computer chips and things like that and one of the first courses he had to take was called, kind of like, in the background they called it Mud 101. He had to learn about mud. He had to learn about the basics of mud and how you put mud together to make ceramics and what's the consistency of mud and what happens when you do this to mud and that mud. Mud became his life in Mud 101.
Well, welcome to Protein 101. Yes, proteins those true secrets to life. The things that run your body are made out of mud. Well, that's kind of an analogy. They're truly not made out of mud, but what they are made of are building blocks. Building blocks I know you know about. Building blocks called amino acids. Remember, proteins are polymers of amino acids. Which means that they basically are going to be thrown together in a dehydration synthesis, one right after the other forming peptide bonds between a carboxyl group of one and the amino group of the other. You're going to make these long chains of those. Remember that there are twenty amino acids that give you your proteins.
Now, proteins have hundreds, if not thousands, if not more amino acids in them. Oh, wait a minute, is there a contradiction there? How can you have hundreds or thousands or more and only have twenty. Well, you know the answer to that. The bottom line is you're going to have these twenty repeated over and over and over again an all of them are equally important. Not only that, as they are repeated over and over and over again, they're going to interact with each other. You know, Chemistry is a reaction of electrons. Remember that there are certain things that happen in Chemistry that are important. Remember that atoms, therefore molecules tend to have positive and negative interactions. But there's other forces in nature, too.
You know, you thought that words like hydrophobic had to do with like fats and oils--whew, boy I'm glad I'm out of that, but hydrophobic and hydrophilic interactions become important. So, if you're really going to understand ceramics, you need to know about mud and if you're really going to understand proteins, you need to know about amino acids. Now, we have this great chart. I want you to download if you haven't downloaded this thing yet. We're going to go through all twenty amino acids and we're going to lump them into three categories. This is going to loom huge as we start talking about that aspect of proteins called protein confirmation, protein shape. What gives a protein its shape is the interaction of its amino acids.
Imagine, if you will, a chain of amino acids and I want you to imagine and we're going to go to the bottom of this chart, right here. Where we have what are called electrically charged amino acids. I want to line those up. Now, remember, what am I talking about? Very briefly, we're talking about those R groups. So, let me draw a generic amino acid right up here. We'll put the H here and the carboxyl group here. This is just going to be to remind you throughout this whole discussion where we are in the amino acid and what's important. So, what we are doing is we are taking the R group and we're going to take a look at the R group.
So, here's the R group and I want to jump to the bottom of the chart, because these are kind of easy to visualize. Imagine, if you will, you have a chain of amino acids and one over here is positive and one over here is negative. What are they going to do? Well, they're going to attract. We find that there are several amino acids that have charges at the bottom of it. So, if you're looking at that chart and you're looking at the bottom of that chart--we're going to be talking about this. This R group right now. So, look at the bottom f the chart--the electrically charged ones and we're going to start out with the electrically charged aspartic acid and work our way through.
Aspartic acid, there it is. Now, once again, show you what we're doing. That's an R group. You see? So, R group--and take a look at how that goes. That electrically charged R group is CH[2], there's no charge there, but you have the electron--the oxygen with its electron coming off and therefore it's going to be charged. Okay, that's why that one's charged. Glutonic acid. Glutonic acid, same thing. An oxygen with a negative charge. Glycine. Now, this one has a slightly longer chain, but again, now down here we have an NH[3] group. That NH[3] group takes on a positive charge. So, you can imagine, for example, a molecule of lysine attracting to a molecule of aspartic acid, with its negative charge. How's that? This is just great stuff.
Who ever thought that you'd get a charge out of charge. There's a longer chain still. Once again, look at that. Two potentially charged, one definitely charged NH[2] group down there. Whey is this one charged and not this one? Well, look, there's a double bond there That must have something to do with it. Continuing on, histadine. Now, histadine has one of these rings on it, but again we see a positive charge. So, all in all, what's the message here? Charged amino acids are going to interact when they're on that big old protein polymer.
Well, some amino acids are charge. In other words, they're polar. So, they're not going to have ions, but they're going to be polar. Now, let's take a look at our polar amino acids, right now. So. On your chart, we're in that middle group. That polar group of amino acids. We're going to start out with Syrian. We'll put polar here, so we remember. Syrian--do you notice by the way, we're going from simpler to more complex. See, an OH group--and you remember that OH groups tend to be unbalanced. Oxygen tends to get more of the negative, hydrogen more of the positive.
So, we have this kind of like charge situation, a polarity, if you will. So, in this case we're going to have a kind of a polar situation, where the Syrian is going to be able to interact with other polar molecules. Thrianine is another one. You see that next on your chart. Again, the Carbon coming off, that's not polar and CH[3] is not polar. But OH is polar. You see and you know what I'm hoping you're learning through all this, that sometimes an understanding of Chemistry is more important than a memorization of Chemistry. I know very few people who have all twenty amino acids and their structures memorized.
This is an important one. This one, Systine--you see that Sulfur? Okay, it's the only one--well, there's two with Sulfur in it, but this one is going to be every active in Sulfhydro bridges, but that comes later. For now, I want you to remember that this particular one, Systine, has that Sulfur group and that's going to cause a polarity. Pyrisine--OH, there you go, polarity. NH[2], double bonded Oxygen. Polarity, we don't have a charge, but we o have polarity. The last one of these, Glutamic acid. Glutamic acid, in this polarity--let's take a look at this. Glutamine, not Glutamic--I knew that didn't look like it. You see, now I'm going to teach you a lesson here. I looked at this thing and I'm not as dumb as I look. I have the names on the back. I looked at this thing and I think I called it Glutamic acid or at least I thought Glutamic acid. I said, "That's not an acid. This is Glutamine." Polarity, but it's not an acid. So, it's not going to be a Hydrogen donor.
I proved my point, knowing a little bit and being able to understand these things is as important as memorizing everything. So, those are the polar amino acids. Last but not least, I want to show you--and I saved these for last. They're the biggest group, but I saved these for last because I want you to first think about, "Well, if polars are going to interact and charges are going to interact. What are non-polars going to do?" Just the fact that they are nonpolar, means they're not going to interact with each other. Remember something about nonpolar molecules. They're hydrophobic. Well, if you're living in a cell and the cell is mostly water and you're hydrophobic, that's going to make an interesting situation, isn't it.
Let's take a look at some non-polars here. Nonpolar--there's a simple nonpolar. A simple nonpolar, such as Glycine, right there. Now we move to Alemine, CH[3], nonpolar. This is a good review of what we mean between polar and nonpolar. Again, nonpolar, CH[3]. You're going to be so smart after this. Look, more nonpolar, CH[3], CH[3]. Do you see a tendency here? All right, Isolucine, CH[3], CH[3], nonpolar. Methyanine, CH[3]. Are you getting the idea that a Carbon covered with Hydrogen is nonpolar? If you haven't' gotten that idea--well, let's continue. Let's try Phenolalenine. I got you. Phenolalenine doesn't have CH[3] at the bottom, but it has this ring. A tightly covered ring with double bonds in there, no polarity to speak of. This is going to be nonpolar also.
Triptephan--you think it's got a CH[3]? Well, remember, we're getting more complex. No. But once again we see the ring situation. Last but not least on your chart, number twenty, Proline, no CH[3], but nevertheless, a very nonpolar situation. Two lessons I want you to take from this lesson. Number one, understand Chemistry and you'll understand Biology. Number two, polars are going to react hydrophilically, they're going to react with other materials. Charges are going to interact plus, minus and non-polars are going to be hydrophobic. Wait until you see the implication of all that later on.
Inorganic and Organic Chemistry
Proteins
Amino Acids: The R Groups Page [1 of 2]

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