#53 Biochemistry Sensory Systems II Lecture for Kevin Ahern’s BB 451/551

#53 Biochemistry Sensory Systems II Lecture for Kevin Ahern’s BB 451/551


Kevin Ahern:
Okay folks, let’s get started! A lot of last minute
questions about this figure. So the figure is showing you, this is what I showed at
the end of the last period, this figure is showing
you the relative places where these individual
opsins are absorbing. And as the young man
pointed out to me earlier, this isn’t really the
ideal place to get red. Red is actually further out here. However, if we look at
the absorption spectrum we have a, the…wrong one. Here we go. So this guy is able to
get things further out here and so is going to be more
sensitive to longer wavelengths than this guy is here. It’s not perfect. Is there overlap? Yes, there’s overlap. Do we have a perfect
system for absorption? We don’t. We can chemically go
out and make a color TV that has perfect ways
of putting these out, but our eyes don’t have
perfect ways of seeing those. Our brain does sort that out. And so as I will show you today,
the red and green receptors are very closely related to each other. And it’s that close relationship
that ultimately results in colorblindness for some people. It’s not this absorption
difference though. That’s not what’s happening
with colorblindness. So even though you see this
guy over here just about thirty nanometers in wavelength
higher for an optimum, you still get that distinction. Obviously, if you didn’t,
you wouldn’t be seeing red. Let’s go back here. So as I pointed out last time, these, when we look in different organisms, we see somewhat different
receptors and we see different differences in the
evolutionary relationships. If we look at rhodopsin,
look at rhodopsin, rhodopsin, rhodopsin, rhodopsin. But we see different color receptors that have evolved from
them in different ways along the evolutionary
trail rather differently. We see chickens have a very wide range with which they see stuff. They see things down here and up here. Mouse has a very odd one
way down here in the blue. Blue or violet, you can call it what you want to at this point. And chickens, as I said,
have an ability to see somewhat in the infrared. So they see what we
would think of as heat a little bit more than we do. We don’t see that as such. Well, the red and the
green in human beings, as you see here they’re
evolutionarily not very far apart. And we measure evolutionary
distance by sequence of proteins which means that the sequence
of the proteins in the red and green opsins that we have
are very similar in sequence, and that actually itself is the way that colorblindness arises. So it turns out that the
red, the genes for the red and the green opsins
are on the X chromosome. So it means we have, if we’re guys, we have one good set of copies. Women have two good sets of copies. Well, if I’m a guy and
I have something that happens to one of my sets of copies,
I can have some issues. And one of the most
common things that happens to one of my sets of
copies is recombination. Now if you remember when
I talked back about recombination, I talked about the fact
that we have homologous recombination as the most
common type of recombination, and this is a recombination that occurs between related sequences. So when we have two sequences
that are very closely related such as these guys are, it’s
not unreasonable to think that they might, during
the time when recombination can occur, they might crossover
with respect to each other. If we see a scenario happening
like we see on the top, then an individual who’s
suffered recombination across their opsin genes, and if they’re a male they
may end up with only one copy, they don’t have a green receptor. They may only have a red receptor. It may go the other way. They may only have a green
and not have a red receptor. The important point being that they don’t have three receptors. They have two. So it turns out that colorblindness, A, is most common in
males, not surprisingly, and the most common type of
colorblindness is red/green. And again it arises from this likelihood of recombination that happens. So that’s why colorblindness happens or one of the ways
colorblindness happens, and it’s why we see it
more predominantly in males than we see it in females. Clear as mud? Connie? Connie: When developmentally
does this happen, like this recombination? Kevin Ahern: Well, developmentally
recombination can happen in a cell at anytime. But if this happens in
a developing embryo or in gametes that lead to a developing embryo, then all the cells of the
embryo’s going to have that. Connie: So you’re not going
to wake up one day and go, “Oh, I can’t tell if
this is green or not?” Kevin Ahern: You’re not
going to wake up one day and be colorblind unless
you magically destroyed all of your receptors
of a certain type, no. And that’s not going to
happen by this mechanism. You would have had to,
let’s say you had a, I don’t know a weird
situation, a chemical that only affected
green ones, for example. So you don’t have to worry
about waking up colorblind. Yes? Female student: What
happens to people who are, I guess you could call
it color deficient, where they see the colors but
sometimes they have a hard time perceiving different
shades of the same color? Kevin Ahern: So what
she is asking about is are people color deficient,
what’s the difference with that? I’m not an expert in
this, but I would say that is really a manifestation
of the same thing. All this is processing
in terms of signal that the brain gets, so
if the brain’s not getting the signal, it can’t
distinguish between the two. Short of that, somebody else asked me about kinesthesia earlier. Kinesthesia’s where you
have connections that largely mix up the signals of,
let’s say color with numbers, for example, or colors and music. Some people say that they
have crosses with those. And this isn’t happening
at the level of the neurons. This is happening in the
brain so that there’s changes in the way that those
signals are being processed and they’re crossing at
some section in the brain. So it has nothing to do with
what we’re talking about here. Okay good questions. I really like the fact
you guys had a bunch of questions on this. It’s kind of cool stuff, so
senses are pretty awesome. Well, the last two senses
that I have to talk about I won’t say as much about, but they’re nonetheless
cool and interesting. One of them is hearing, and hearing arises as
a result of manipulation. And when I say manipulation, I’m talking about mechanical changes, that is physical movement changes, that are happening to hair
cells inside of your ear. And you see these little cones or cone-like structures
that are at the top. These are actually the structures that are being moved
during the mechanical agitation that happens with sound waves. So a sound wave, this is now that sort of pyramidal
thing that’s on top. The nerve ending is right here. All these are nerve
endings relating to sound. And what happens is sound
is one of the senses that is as I said mechanical,
touch being another one. But sound happens because of soundwaves that are being
propagated, and soundwaves can physically move things. And that’s what’s
happening with these very, very delicate ear cells that are, these cells in your ear, hair
cells that are in your ear. And what happens is, let me
show you a better figure here, is right here. This is a close up of
those individual cells that were in that bundle
that you saw in that pyramid. And if you look very carefully, you see that the bundle of one hair cell is physically attached
to the one adjacent to it. There’s a similar one
right here that you can see. And that attachment is real. And so what happens when
a sound wave hits this bundle of hair cells is that the
bundle gets slightly displaced. This is schematically shown here. So here’s two of the cells
that are in that bundle. We see a sound wave come along
and it physically moves it. So we see this movement. Since we have an
attachment that’s there, shown as a little spring, the attachment is able to
physically open up this nerve cell, and into this nerve cell,
ions can flow as a result. So let’s go back to that figure. Alright, so we see right here. So here’s that opening, and
mechanical movement happens. This guy slides very slightly as a result of a soundwave coming. This opens up an opening,
and it’s no different than when we opened up an opening to let sodium ions in or potassium
ions in in nerve signaling. This, and these are yes, in fluid. These guys are then
allowing in sodium ions, and that starts a signal that
says, “Hey, I heard something,” or, “Hey, I got hit by a soundwave.” What’s remarkable is that
our brain again puts all those together and we perceive
those as coherent sounds. We cannot only perceive
them as coherent sounds but we can also tell direction. And the reason we can
tell direction is our brain can sort out which ear
got the most information and as a consequence of that go,
“Oh, that happened over there,” or, “That happened in front of me. “That happened behind me.” It’s remarkable the directions that we can perceive with sound. Questions about that? The last sense I’ll talk about is touch. I alluded to it earlier, and touch is the least understood sense. We study touch mostly from
the sense of pain receptors, but there are many components of touch. There’s a mechanical component to touch. There’s a temperature
component to touch. There are chemical components to touch. And we can sense all of these
things with our sense of touch. The most work that’s
been done, as I said, is with pain receptors. One of the students in the class
at the end of the last period sent me a very neat link,
thank you, Ellen, for that, for talking about how
capsaicin receptors that are in our tongue
were there evolutionarily for the purpose of protecting our tongue against very hot substances. So they were there on our
tongue as a pain receptor. So if we had something
very hot, they evolved, upon our tongue at
least, from that sense. Capsaicin is a compound
that on our tongue or on our membranes of our,
I shouldn’t say membranes, the sort of fluid membranes of our cell, like our sinuses or something like that. Capsaicin is a compound
that will actually activate those pain receptors. So capsaicin is the
compound that’s found inside of habanero peppers, hot
peppers, and so forth. And what it’s doing is it’s
activating those pain receptors by opening them up and allowing
calcium to move into them. So calcium is actually
the ion that’s moving with these receptors,
and the calcium signal that’s going in through this
receptor tells the brain, “Okay, I’ve got something going on,” and the brain senses this as, in the case of a hot food,
as a pain-like substance. Now it’s kind of neat, and
I love evolutionary analyses. It’s kind of neat
looking at the evolution of this receptor that’s out there. So human beings have this receptor. Dogs, cats have this receptor. If you give an animal a hot food, a spicy hot food that
has capsaicin in it from hot peppers or something, they’re going to feel very
much like what you feel. But interestingly, birds don’t have it. And the reason it appears
that birds don’t have it is that the plants that carry
capsaicin evolved capsaicin so that it wouldn’t affect the birds because the birds distribute the seeds. And so the birds, if the
birds were affected by this, they go to a habanero
plant, for example, and they grab the seeds,
and they eat the seeds. And for many plants the way
that seeds get distributed is that the bird eats them, it passes through
their digestive system, and then they poop it out somewhere, and the plant grows as a result. Birds don’t have those receptors. So a very cool piece of
evolutionary interest there, I think. Capsaicin is actually used. The receptor is not a 7TM, by the way. The receptor is actually shown here. It has a pore, and that
pore can open, as I said, and allow calcium ions to flow into it. Capsaicin will cause the pore to open, and there are other
things that probably will also cause that pore to open. The next figure shows
the effect of heat and pH. So as we alter the pH we can, in fact, activate those receptors that are there. We see the same thing
happening with temperature, and that’s not totally surprising because again when we think
of the effect of temperature and pH on protein structure,
this is a membrane protein. As it gets exposed to
either of these things, we’re going to see some
slight changes in structure, and those slight changes in
structure are going to allow ions to flow in this
case and give that signal, “Hey, I’m hot. “I’m telling you to be careful here.” Questions about this? Yeah? Male student: I have a question actually back on the hearing part. Is the temporary hearing loss you get from loud noises a function
of those little threads being snapped, or…? Kevin Ahern: Yeah, so is the
temporary hearing loss you get from hearing a loud
noise a result of damage to those hair cells? Probably to some extent
I would say, and again, I’m not an expert,
I would say probably yes. There was a very interesting
study that was reported in the past ten days about
hearing that may relate to this, and this interesting study
relates to actually a structure that they have found in hair cells that they didn’t know was there. And it’s a structure that
allows a hair cell to basically sort of become stiffer,
and they think that what it’s doing is it is, that if you stimulate something for a long time with a signal… So the example I give in class is you spill a very smelly
chemical in the lab. At first it stinks like crazy. After you work around it for
awhile, you don’t notice it, but people walking in notice it. And so what’s happening is
that signaling is stopping. The brain is also stopping
paying attention to it. It appears that the hair cell
has this stiffening mechanism after it’s been
stimulated for a long time to sort of resist that. And so that may play
a role in this process. It’s very newly discovered. Like I said, it’s come
up in the past ten days. That’s how recent it is. So it may relate to what you said. Well, we’ve got a lot to cover in the rest of the period today, so we want to make sure
we don’t skip any of that. I’m going to ask you guys to make sure that you read through everything
that I don’t get through, and then we’ll have that on the final. Nobody protested that? [class laughing] Female student: I protest. Kevin Ahern: This is the
easiest group I have ever taught. [class laughing] Now you’re smiling. How do you know that
I’ve changed my mind? I just said read through it and you’re responsible for whatever I don’t get through here. Laura? Laura: We just assumed
that you weren’t kidding so we were going to [inaudible]. Kevin Ahern: Just phisssht! That’s what happened
to my hair, “Phisssht!” Many years ago, phisssht! [class laughing] Some student came by, and I
said that, and they scalped me, and that’s what happened to my… [class laughing] It’s funny for you! [class laughing] The immune system. The immune system is I think
in comparison to the senses equally magical and equally mysterious, and the immune system is something that when scientists first
started studying it there were some enormous, enormous technical considerations. How in the world can the
immune system function? Now I’m going to tell
you what one of those is. Our immune system can make 10
to the 12th different antibodies. One trillion different antibodies. Now when people first
came to grips with that back in the ’80s, they said, “How in the world can a genome
that only has a few billion “base pairs code for over
a trillion different antibodies?” That means you’re getting
a thousand antibodies for every base pair of the genome! That doesn’t make any sense! It doesn’t make any sense. And so there was this element of, “Wow. “There’s just, how can that possibly be?” Well, we know today mechanisms
whereby the immune system can actually make that
number of antibodies. And I’m going to tell you,
you already know those. You’ve seen them by mixing
and matching of exons. When we mix and match exons, what we see is an ability
to create combinations that we didn’t otherwise
have the ability to do. Let’s take a quick look at that. Here is a coding
sequence for an antibody. We see that the coding
sequence has various regions that I’ll actually come back and
talk about in just a little bit. But it has these various coding regions. Some of them end up in an
antibod, some of them don’t. And the more mixing and
matching that a cell can do with respect to these regions, the more possible antibodies
that a cell can make. So the answer is yes,
a cell, or the body can make 10 to the 12th antibodies, but it does it by mixing
and matching things. Mixing and matching through
splicing is one mechanism. Mixing and matching
through recombination is another mechanism. And there’s a third mechanism
that’s kind of interesting. It’s a mechanism that results
in generation of mutations. Immune cells have a DNA
polymerase that they will invoke that isn’t very good at
copying at certain points during their development
which means that they make mistakes as
they’re going along. And those mistakes in these
antibody coding regions actually help to increase the diversity of these segments as well. That’s absolutely incredible. The result is that
cells really can make, or a body can make 10 to the
12th different antibodies. Yes sir? Male student: Without
computer-aided technology, how did the early researchers
even determine that that was the upper limit? Kevin Ahern: Without
computer-aided technology, how did they determine
that was the upper limit? I can’t answer that question. But they certainly can tell
that they have a diversity of antibodies within a given organism, and they can see how that
would change over time. And my expectation is they
just simply extrapolated, but I don’t know that. The antibodies that you’re making today may not be the same as the
antibodies you’re making tomorrow. Your immune system is
continually evolving antibodies as we’re going along. Anesia? Anesia: Is that what contributes
to autoimmune diseases? Kevin Ahern: Is that what contributes to autoimmune diseases, yeah. So autoimmune diseases
arise as a result, it’s kind of a complicated process. So let me just since
you’ve asked the question very briefly answer that for you. When we’re an infant, our immune
system is sort of evolving. Our immune system is
starting to put together those cells that will make
antibodies and protect us. The child that’s nursing is
getting antibodies from mom, and that’s helping in
that process of protection while the infant’s
immune system is evolving. And part of that evolution
of the infant’s immune system is selecting away,
that is destroying cells that will bind to the body, to the proteins in that
infant’s own system. Autoimmune diseases arise
because cells that bind to proteins in the body’s
system start recognizing and binding to them. So it can result from
a lack of selection that happens very early during infancy. It may happen as a result
of some odd recombination that happens that wouldn’t
have otherwise happened that’s generated those. But autoimmune, autoimmunity happens because your own immune
system is attacking you. Autoimmunity comes about with lupus. I have psoriasis. I get various spots that appear, and that psoriasis is a product
of an autoimmune response where the body is
basically attacking itself. There’s other examples of that as well. Well, when we think about antibodies, antibodies are the main line
of defense of the immune system. They’re the primary way through which the immune system works. That isn’t the one I wanted. Antibodies are structurally
looking like this guy. They have a Y-shaped structure. They have a short chain
called a light chain. It’s relatively short. It goes to these two segments here. And we have something
called the heavy chain. You can see this here. The heavy chain over here is the same as the heavy chain over here. The light chain over here is the same as the light chain over here. Starting from left to right
we go from amino to carboxyl, and starting over here we go from amino down to carboxyl down here. You’ll notice that the light chains are joined to the heavy chain
by a green bond right there, and that green bond is a disulfide bond. And similarly the two heavy chains are held together by a green bond that is also a disulfide bond. So the whole thing is held
together by disulfide bonds. You’ll also notice on
this structure that you see various regions called VL, VH. Well, “H” stands for “heavy.” So this is a variable, and
“V” stands for “variable,” a variable region of the heavy chain. VL stands for a variable
region of the light chain. It’s out in these variable
regions that antibodies have specific structures that recognize and bind to other specific structures. Usually they’re proteins,
but they don’t have to be. So the binding region
of an antibody is out in the variable regions, and
the places where one antibody will differ from another are
primarily in these regions. What we see is that if we
look in the constant regions, they’re not absolutely constant. There are different
classes of antibodies, and one class will have
one type of constant region, another class will have another type, but all antibodies will
vary considerably out in their variable region
as shown right here. Jodi? Jodi: And that’s indicated
by the “C” on those? Kevin Ahern: And the “C”
stands for “constant,” I’m sorry yeah. So it’s constant light, constant heavy, constant heavy, et cetera. So that’s structurally
what an antibody has. When we look at antibody diversity, as I mentioned previously, what we see is that the
coding region for these in our chromosomes has
little exons that get mixed and matched to make
a functional antibody. You see here’s a variable
region that you saw in that last schematic, and
this is for a light chain. So this variable region has
forty different possible exons. Well, if you start thinking about the number of combinations,
the number of ways you can put those guys together,
it’s an enormous number. Just for that alone. And we’re not talking about
heavy chains or anything else. We’re talking about one
segment of one antibody. The variable regions are
spliced, and recombined, and mutated to give a tremendous amount of diversity out here. And then that spliced product
is spliced to different regions called joining regions, and that’s what the “J” stands for here. So the joining region
that we had on that antibody a moment ago are
this little segment right here. That little segment
is the joining region. So we see a variable being
joined to a joining region. And finally we have a constant
region that’s out there, and the ultimate product
puts all those together to make that light chain. As we can see, we’ll
have a lot of variability out in the variable region. The joining regions really
don’t mix and match much. And the constant region
doesn’t have anything to mix and match at all. If we look at the heavy
chains, by contrast, the heavy chains have a similar setup. They have more variable regions. So there’s 51 right there. There’s 27 more. And these are called D regions. D’s are the other portion of
that variability that happens. There are some joining regions, and we see different
constant regions out here. And the constant regions will vary a bit according to antibody type. So there are five major
classes of antibodies, and they will vary in
the structure of their constant regions partially. The five different classes of antibody you see on the screen here. They are known as IgG,
IgA, IgM, IgD, and IgE. IgE is, IgG is the most
abundant class of antibodies that we have in our cells, and it’s that nice Y-shaped structure that I showed you previously. IgM is a structurally somewhat different class of antibodies. It has a pentameric
structure as you can see here. It is usually the first class
of antibodies that is produced in response to an infection. First class produced in
response to an infection. The IgA is commonly
found in mucous or tears. They’re very common there. People describe IgA as
being a first line of defense because if we think about
it, when we breathe things in, the mucous in our lungs
is going to have this class of antibodies in it, or the
tears of our eyes, et cetera. IgD, the function isn’t
completely understood what it does. And IgE plays a variety of roles. From a health perspective
one of the most important ones that we see is it
actually gets stimulated in allergic responses. So if you have a very
nasty allergic response, IgE is actually going crazy
with being synthesized there. So that’s an important consideration. Let’s see. When we talk about the
cells of the immune system that make antibodies we have
two main classes of cells. The so-called B cells and the T cells. The T cells themselves get
broken into two divisions as well. Helper T cells and
cytotoxic killer T cells. So the immune, they all can
make, and do make, antibodies. What you see here is a B cell, and the B cell has on
its surface an antibody, in this case an IgM. That antibody is out there to
recognize and protect the body, and B cells get activated
by binding to an antigen. So your body’s making a whole
bunch of antibodies right now that aren’t doing anything,
and that pattern that it’s making today is atleast a little bit different from that pattern it
was making yesterday. Immune cells in your immune system, unless they’re part of
what’s called immune memory, usually have a halflife
of a couple of weeks. If they don’t bind something
in that couple of weeks, then they haven’t in fact encountered any antigens that are there. The body says, “Well, I’m not
going to make any more of this. Why waste my time? Let’s make something else.” There are memory cells
of the immune system that, in fact, are produced at
a low level constantly; and that’s what gives us immunity. When we give a vaccination
and we give immunity, we’re stimulating the
production of these memory cells that are there. Those memory cells will be around. They argue for how long that is, but on average we say that
ten years is a reasonable time. If it’s been ten years since
you’ve had a vaccination or more than ten years since
you’ve had a vaccination, you may not have those
memory cells around. When I was a kid everybody
got vaccinated for polio and also for smallpox, and I probably have no
resistance to polio or smallpox because they didn’t give
boosters over a period of time. They do that for tetanus, for example, because tetanus is out
there and going to get us. Polio kind of disappeared,
smallpox kind of disappeared, and we got lazy, and we
didn’t boost and protect people as a result of that. So what’s happening here? Well what’s happening
in the immune response is this particular
antibody has recognized the structure on this antigen. An antigen is a structure
bound by an antibody. It has a specific structure. And what’s happening in
this process is the binding of the antigen is actually
stimulating a signaling process that’s going on. This signaling process that’s going on is in fact going through
these various domains here. We’ve seen once we get a signal
inside in a signaling process that cells can respond
to it appropriately, and in this case what’s
going to happen is this cell is going to be stimulated to divide. So once I’ve got an immune
cell that’s out there that is bound to an antibody and I want to mount a
defense against what might be an invading virus, the
first thing I want this cell that has this antibody
to do is start dividing. Because if it starts dividing
it’s going to make a lot more antibodies to fight a lot more virus. And that’s what’s
happening when we get a cold or an infection and our immune
system kind of catches up. That’s what’s happening in that process. You’ve heard of immunosuppressants. There are chemicals
that we give to suppress an overactive immune system. These are given for
a couple of purposes. One of the purposes being that of an overactive immune system. In other cases we give them
to suppress immune responses for things like transplants. Cyclosporin A is a compound
that is given to suppress the immune response and is
very functional in doing so. Now the last thing I’ll
mention is that once, let’s say I’ve got a
cell that has an immune, it is bound to an antigen. It has recognized that
I’ve got this antigen, and this was let’s say
an IgG that recognized and bound to this. I would like to be able to use
that knowledge of that binding of that IgG variable region
and put that onto other classes of antibodies, for example,
some that might appear in my tears or some that might
be protecting other things. Well, that can happen if
the immune cell goes through what’s called class switching, the same sort of thing you’re thinking you wish you had done
two terms ago here. [class laughing] I went for the whole
term to get to that joke. Do you realize that? [class laughing] [class applauding] Thank you. Thank you. You’re thanking me for waiting until the very end to
tell it I’m thinking, too. [Kevin Ahern and class laughing] But class switching, that’s
actually what this is called. It is called class switching. Class switching involves
basically replanting a specific variable region onto a
different class constant region so that that can also
give additional protection. Now as I said, I will expect you, anything I haven’t gone through here, to read through for the final; and you’ll see that on the final, okay? [laughing sarcastically] Jodi: That class
switching looked a lot like a viral resistance cassette. Is there a similarity? Kevin Ahern: A viral
resistance cassette, meaning? Jodi: Like antibiotic
resistance cassettes where it loops out a section… Kevin Ahern: No. No. No. People are still smiling. I don’t know. So I promised you some surprises today, and so I think it’s perhaps time that I bring up the surprises. So the first surprise is that you are going to be responsible. No, okay. Alright. It’s not April Fools’. And in fact, what I
will do is I will stop what you’re responsible
for with the senses. You’re not responsible
for the immune system that I talked about today. [class cheering] [class applauding] So I saved a joke,
and I got the laughter. And now I know how to get applause, and it’s the last day of class. I waited too long to
get all these things. [class laughing] You guys should have
said something sooner! Well, as is traditional in the class, you guys were in class last term. You know that on the last day of class I like to have a little surprise, and I’ve got some new things to do and some excitement with that. So we’re done with the term. If you want to stick
around, and hear, and sing, and join in on the fun;
we’re going to do some fun. So last term, at the end of the term, you may recall that you
heard the Biocomical Choir. You heard them right here;
and I have to tell you, I know the anticipation is just, you’re giddy with anticipation that is it going to happen again? Well, you heard them… Now you get to experience
the only campus group, the only campus group, that
practices hydrogen bondage. [class laughing] That’s what we’re into folks. I’m sorry; but we’re a DNA based group, so we practice hydrogen bondage. That’s a joke, Ahem. With that said, let me
introduce the Hydrogen Bonds! [class applauding] Are we only two? Come on. Come on down. Come on. Everybody can come join. You guys in the back can come join. Alright, so I have joining us
I have Emily, I have Oresteia, I have Linda, I have Lisa; and I hope these guys
sing louder than I do. So we have some songs for you. We actually have four songs. This is a record of some sort. And I’m going to need the words myself. So I hope that you will
join us in singing loudly. And what’s the rule on singing? Class: Extra credit! Kevin Ahern: Extra credit, okay. So if I hear you well enough we will have a nice extra
credit question on the exam. Alright. Everybody ready? The first tune. Alright, I’ve got to
set this up a little bit. The first tune. What was with that weather yesterday? Right? Everybody love that weather? I mean we’ve had snow, we’ve had rain, we got a day of the term called off. Are you tired of that? You’re supposed to say, “Yes!” Class: Yes! Kevin Ahern: Okay. Well, we have a song to deal with that. It’s to the tune of Let It
Snow and it goes, Make It Stop. [Make It Stop by Kevin Ahern
to the tune of Let It Snow] Lyrics: So the forecast
says much more raining It’s of this that I’m complaining I get cranky from all the slop Oh make it stop, make
it stop, make it stop It is dark and it’s gray and gloomy The climate is out to screw me I go crazy with drip, drop, drop Please make it stop,
make it stop, make it stop Every time that I look outside And I spot the sun then I know That our weather is Jekyll/Hyde When it goes out and makes a rainbow Now I know if the rain is dropping That my clothing will be sopping I don’t care if it’s good for crops Just make it stop, make
it stop, make it stop Kevin Ahern: Okay. Thank you. That’s very good. [class applauding] We have two new songs today. They’ve actually been on my website, but we’ve never sung them in class. This is the world
premier of these songs, and the first of those is next. It’s to the tune of
Good King Wenceslaus. And that’s a Christmas song. [humming tune] The Sprite Song, right? And it’s called, Good Protein Synthesis. [Good Protein Synthesis by Kevin Ahern to the tune of Good King Wenceslaus] Lyrics: Amino acids cannot join By themselves together They require ribosomes To create the tether All the protein chains get made ‘Cording to instruction Carried
by m-R-N-A In peptide bond construction Small subunit starts it all With initiation Pairing up two RNAs At the docking station Shine-Dalgarno’s complement In the 16 esses Lines the
A-U-G up so Synthesis commences Kevin Ahern: Oh, sorry. [class and Kevin Ahern laughing] Lyrics: Elongation happens in Ribosomic insides Where rRNA creates Bonds for polypeptides These depart the ribosome Passing right straight through it In the tiny channels there Of the large subunit Finally when the sequence of One of the stop codons Parks itself in the A site Synthesis can’t go on P-site RNA lets go Of what it was holding So the polypeptide can Get on with its folding Kevin Ahern: Alright. [class applauding] The next one is another new
song, and this is a tune everybody knows, and it’s one of
the hardest songs to sing. It’s our national anthem. So you want to put your
hands on your heart again. This is a different
song than we had before. This is The Star Spangled Banner. It’s about sight. [The Vision Thing by Kevin Ahern to the tune of The Star Spangled Banner] Lyrics: Did you know you can see In the dimmest of light With your rods and your cones And their retinaldehyde Found in rhodopsin it’s Got a bond shaped as cis But it changes its state When a photon gets it straight Then the sign’ling kicks in Thanks to a transducin Cuz its GTP ways Turn on diesterase So gated ion channels stop Charges from passing through Such as
sod-i-um plus one And cal-ci-um
plus two [class cheering] Kevin Ahern: Excellent. [class applauding] That was good! I like that. That’s good. Now before I get to the last song, I realized there was one
announcement I didn’t make that you all want to hear. I do have a review session
scheduled that is Sunday evening, 7:30pm, ALS 4001. I will videotape that and
make it available as before. Sunday, ALS 4001. Exam in here Wednesday at noon. And you know how to sit and everything. Now for the last song, I need some help; and the help I need is from you. I need… [begins clapping rhythmically] [class clapping throughout song] Not too fast. [Thank God There’s a
Video by Kevin Ahern to the tune of Thank
God I’m a Country Boy] Lyrics: There’s a bundle of
things a student oughta know And Ahern’s talk isn’t really very slow Learnin’ ain’t easy /
the lecture’s kinda blow Thank God there’s a video Well we’ve gone through the
cycles and their enzymes, too Studying the regulation
everything is new I gotta admit that I haven’t got a clue What am I gonna do? So I got me a note card
and bought me a Stryer I got the enzymes down
and the names he requires I hope I can muster
up a little more desire Thank God there’s a video Just got up to speed about the NAD Protons moving through Complex Vee Electrons dance in the cytochrome C Gotta hear the MP3 Fatty acid oxidation
makes the acetyl-CoA Inside the inner matrix
of the mitochondri-ay It’s very complicated,
I guess I gotta say Thank God there’s a video So I got me a note card
and bought me a Stryer Got the enzymes down
and the names he requires I hope that can muster
up a little more desire Thank God there’s a video Replication’s kind of easy
in a simply kind of way Copyin’ the bases in the plasmid DNAs Gs goes with Cs and Ts go with As Thanks to polymerase And the DNA’s a template for the RNA Helices unwinding
at T-A-T-A Termination happens,
then the enzyme goes away Don’t forget the poly-A So I got me a note card
and bought me a Stryer Got the enzymes down
and the names he requires I think that I can muster
up a little more desire Thank God there’s a video [class cheering] [class applauding] Kevin Ahern: Extra credit. Extra credit. Alright. [Kevin Ahern laughing] Thank you guys. [END]

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