Biology 1A - Lecture 1


Uploaded by UCBerkeley on 24.08.2012

Transcript:
>>INSTRUCTOR: If you could please fill in the middle. If there is any empty seats in
the middle please fill them in. We have 750 some students. This room holds 513 if all
the chairs work. We have overflow in 10 Evans. So, right now, 10 Evans. There are still by
there as well as Iclicker receivers. Both 10 and 60 Evans. If you want to sit there
in lecture, 10 Evans. Okay? The other thing is I'm going to ask the chemistry students
when we leave I am going to ask them to make a pathway so you can exit. Because we have
500 people exiting. And we have the 500 freshmen from Chem 1A wanting to get in. It takes about
half an hour, if we make a path we'll get in and out in 10 minutes. So I'll clear that
path for you, I'll be like Moses, okay. So, we still have a minute before we start.
And then we'll make a quick couple of announcements and get going.
Welcome to Biology 1A. It's a large class, there are certain rumors
you've heard which is that this class is very hard. That is a true rumor. That is just the
way it is. Also, the live class is very hard as well.
It will help you tremendously in your future career though here and in other classes, and
study skills you learn here will be applicable to all areas of study. So my name is Mike
Meighan. I am academic coordinator for this class. I have been doing this well over 20
years, about 30,000 students. I'll deal with administrative stuff, if you're trying to
add just use TeleBears. If you are trying to switch sections, discussion sections use
TeleBears. Come this weekend we are going to turn off TeleBears for section switches
and then we'll have a form you fill out and we'll try to do it. Certain times are in high
demand as always, we can't make more space there, other times in lower demand. So there
are some sections where you can switch your discussion section into, just use the section
switch feature in TeleBears. Any questions about adding or section switches?
No, great? Yes? >>STUDENT: [Indiscernible]
>>INSTRUCTOR: So we will close down TeleBears at noon tomorrow, and then we'll have a form
available for you to fill out and then we'll process them over the weekend. Discussions
begin Monday morning. So if you put in a section switch, please check your schedule classes.
Also, even if you didn't put in a section switch, please check your schedule classes
for the correct room location. We have four discussions, for example, Monday, 11 to 12.
So if you look at the discussion classes I'm in 2062, you may not be. So please, please,
please check the correct room on your schedule of classes. So as far as a few things, We
have the overflow in 10 Evans. We have iClicker receivers there so you don't need to worry
about if I'm not in Pimentel I'm not going to earn those points. You can earn those points
in 10 Evans. Likewise we have 60 Evans set up as well. So we have both rooms if necessary.
So overflow is 10 and 60 Evans. With respect to your grades, students always ask about
grades I wish you would focus on the learning aspect of this, but we'll go over the grading,
the exams and how the grading be done. There are 3 exams that you'll be taking. The first
exam is September 24th. It's worth 100 points. That will be on Dr. Pauley's material. It's
100 hunded points. It will be multiple choice. The second exam is October 26th. That's on
Dr. Fisher's part. Again 100 points. The final exam is December 10th, 7-10 pm. The other
two exams are in the morning, 8 to 9 in various rooms. As we get closer to the exams, you'll
be given an exam handout which states where a given discussion will take the exam. We'll
have you scattered in many rooms on campus. Likewise there will be information there about
reviews that the faculty will hold and the GSIs will hold. There will be any information
about extra office hours. We're here to help you to learn the material. We have office
hours. We love it if you come to office hours. So please, please take advantage of the resources.
I absolutely love it when students come to office hours. It's our chance to interact
one on one with you to see what you get, what you don't get. Things like that. So please,
please use the resources available for you. Go to discussion. Various things like that.
If you're having difficulty email questions. Okay? We're here to help you. I can't state
that enough. Of course there are 750 of you, so we can't
be meeting with each of you everyday for an hour.
But, we'll do what we can, okay? So please take advantage of the resources you have.
The final exam as I mentioned is on December 10th at night. It's worth 300 points. It is
a comprehensive exam. It will include material from parts 1 and 2 and then part 3. Okay?
So that's the final. So 500 points worth of exam. Multiple choice. In addition, the points
that count towards your grade are as follows: iClicker, each of the three faculty will be
asking questions, iClicker questions, during lecture. You should have received a handout
on this already. It's also posted on bSpace. The way we're going to work this is each professor,
there's three of them, will have 12 iClicker points that will be distributed. We're not
going to have only 12 points awarded during the class though. You can earn up to a maximum
of 12. So we may have 14 iClicker possible points. You can earn up to a maximum. So you
don't need to email us and say, oh, my battery died today. I was there. Trust me, okay? We
don't need those emails. We have extra points built into the system. Half a point for participation.
So if you just vote, an additional half point per correct answer. So that's one point per
iClicker question possible. We will have at least 14 points during the series of lectures.
You are going to earn up to a maximum of 12. Any questions about that? So that's 36 points
the three faculty. Mastering biology. We've been doing this a long time. The number one
problem we have determined is that students fall behind. It's really difficult to state
out this material. So we're having graded assignments on line, done through mastering
biology as part of the package. So that mastering biology is typically due 4:00 p.m. the day
before the lecture. It's either 4 or 5. I'll double check. Okay? But it's due the day before
lecture. All right? And the reason for that, so that
we can look to see how you're doing on those questions, and we can focus on particular
areas students are having difficulty. The way that's going to work is each professor,
there will be 24 points for each professor for those homework assignments. Three of them
make 72 points. Again, the maximum is 24 points. So we don't have to deal, oh, I forgot this
one day. Can I get an extension, etcetera? We have 26 points built into the system. And
the way this is going to work is, we've not done this before. We don't know how many questions
there will be, etcetera. So as we go through the system, let's say in the end Dr. Pauly,
this is a made up number. No E, correct? Let's say he has let's say 114 points in terms of
mastering biology. We will then take and multiply that by what percentage you have on those
and then we'll weigh it to 26 points. So that's how the weighing system works. In theory if
you get 100%, whatever the number of questions was, you would get 26 points, but we will
award up to 24. Again, the reason why we do this is so we
don't have to worry about someone saying, oh, I missed this one assignment, etcetera,
etcetera. You don't need to email us. I've already started receiving emails from students
saying, oh, I did this question repeatedly and I always put the correct answer but it
always said I had the wrong answer. That one particular question as a subset is probably
worth less than 0.1 percent of your grade. Is it important?
Yes. Don't just email and say, oh, there's a problem with a question and I don't know
which one. Take a screen capture and then tell us. On this question it was this, here's
the screen capture, I put this answer and it marked me wrong. Because there are probably
going be mistakes in the software, and we don't know it because we haven't gone through
every question. Some are generated randomly so we won't know what question you actually
have. so please, please, if there's a problem, email us, but be specific about what the problem
is. Is that clear? And again we're working with this, so again
that's up to 72 points for a total of 608 points. At the end we do guarantee grades.
If you have 90 to 100 percent in the end, that's some form of an A, A plus, A, A minus.
We'll make cutoffs within there. That's guaranteed likewise for the 80 to 89 percent. That's
some form of a B. Those are guaranteed. We want you to work
together to do well in this class. Form study groups, very very valuable way to learn material.
So we're here again to help you to get that 100 percent. We guarantee those grades. Now,
in 20 some years, we've always done this, but we've always done this but we've always
ended up curving the class. So if for some reason only five percent of the students only
get 90 percent or above, we will curve the class and drop the percentage necessary to
get an A plus or an A or A minus. So the class can be curved and has always been curved.
So these rumors that the class is not curved not true. For over 30 years it's always been
curved. So if we need to, we will do that. So again, we're looking after you to try to
get you to the guaranteed grades, but if you, it doesn't end up that way, we're going to
curve it. Any questions about that? Rumors are always there but it's not. Now, in the
end When we make the grades to give you at end of the semester, there will be a distribution
like this. So this many students got this many points, this one's got this, this one's
got this. We make a decision and we say that's the cutoff for the A, this is the range for
the A. This is the range for the A minus. So there's always a few students who are,
oh, so close. One point, two points away. For those students who are what we call borderline,
we'll look at those students individually and we'll see how they did on the final. Because
the final is comprehensive, thus, if these students did really well on the final, we
will consider moving that student in particular to this A grade.
The decision will also be based upon the GSI's comments. For example, if they say the student
never came to discussion, they never participated blah, blah, blah, then we probably won't bump
that student. If the GSI says, yes, they actively participated, that's the reason to bump them.
Okay? So, we try to take into account for these students who are borderline and that's
what we think is a fair and equitable system. Prove it on the final and GSI input. So, any
questions about that? Okay. There will be three, yes, question?
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: Yes.
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: So mastering biology will be
covering the assigned reading for that following lecture.
Okay.? Did that answer your question? Yeah. So it's
to have you come prepared. Basically we want you to come prepared. Okay? So there will
be three faculty giving lectures. Dr. Pauly will give the first series, Dr. Fisher will
give the second series and Dr. Fisher is here. And Dr. Wiseblat in the back up there will
give the last series of lectures. Okay? They're teaching this because they want to. I've been
doing this for 20 years. I really enjoy teaching this class. I'll be doing the lab lectures
on Monday night. So, welcome to both classes and good luck. I hope to see you around office
hours and we'll begin.
>>INSTRUCTOR: Good morning. Can
you hear me? Yes, right. So good morning everybody. My name is Marcus
Pauly. I'm from the Department of Plant and Microbial Biology here on campus. I'm new
to this class as you are. This is the first time I teach this class. And I was very excited
to be able to do so because usually I continue I teach upper division biochemistry. So I
hope I tone down a notch a bit here because I'm used to upper division biochemistry. It
should work out fine. So my department chair asked me to teach this class, and I got very
excited. But I didn't read the fine print. That is that this class happens from 8 to
9:00 a.m. on Monday, Wednesday, Friday. So first takehome message, read the fine print
when you agree to teach a class, ever. So we have to stick to this together. So from
8 to 9:00 a.m. we have the honor of discussing biology. So Mike explained to you already
the various that points you can get. And really if you think of the very sections that we
have in my particular sections so that's one third of the class, you can get up to 203
points. and we really instated the iClickers and the homework to get some of these points
off the exam so you don't have to rely too much on the exam. But they still are the major
chunks of the points that you can achieve. If you have questions, if you have administrative
questions concerning iClickers, your homework, the mastering biology, your grades, the lab,
drop, etc., please write or ask Dr. Meighan. He's really the master of ceremonies of this
class. I'm just the speaker for some lectures. Scientific if you have questions please ask
your GSIs first. They are very good GSIs so they should know about 95 percent of the questions
you have. And in the case that they do not know the answer, they will forward that to
me and I will get back in touch with you directly. I also have office hours. Three office hours
per week. Monday and Wednesday immediately after this class from 9 to 10 in VLSB 2084.
And then if some people have class on Monday and Wednesday, they might also be able to
come Thursday between 2 and 3. So you can choose. Please come by and I can answer your
questions. he requests that you have, and indicates that they do not know the answer
that will forward that to me and I will get back in touch with you directly. I also have
office hours, 3 office hours per week, Monday and Wednesday immediately after this class.
Homework assignment, because this is the first week of classes, there will be slightly different.
So two of these mastering biology courses classes homework assignment in master in Biology
have already online. The prelecture, the basic biochemistry and the water and the macromolecule
section they're due next week, on August 30th at 5:00 p.m. and I will post probably this
weekend the section on cell one and cell two. They will also be due up until then. So up
until then you should able to have gotten the mastering biology password, etc., get
into the system and answer all four of them. After that with the beginning after Labor
Day with the sections on membranes and then 6 to 12 it will always be due the day before
class. So as your colleague here mentioned it's the material that will be taught the
following day when you're homework will be due.
Any questions to that? So, we start with iClickers.
So I want to test the system. Oh, yes there's a question?
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: So the question is how much
in advance will be the master biology be posted? I think probably at least two lectures before.
Yeah? So usually like five days in advance. Yeah?
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: Yes. So the due dates are listed
on the master in biology and there's, for example, now it should say August 30th. I
changed that yesterday. I hope now it is all fine. It should say August 30th for that.
Thank you. Okay.
So iClickers. This one is, you don't get any points. Usually,
when you click you can get half a point, if you choose the right answer you will get one
point. The questions that I will ask, not this one,
but the usual questions I will ask they will be example questions from the exam. So, you
get a good feel, I hope for what questions come in the exam. So the exam is all multiply
choice which is equivalent to iClicker so they should give you a good idea of what the
exam is going to look like. When I start the iClicker system, you will have 90 seconds
to answer the question and you are allowed to talk to your neighborhood. Yeah. So you,
please. So first of all before we start, say hello to your right and your left neighbor
because you're going to become really good buddies in this class. Okay.
Okay. Sorry to interrupt. You don't really have
to tell your whole life story yet. You can do that later.
Okay. I would like to continue. Doing iClicker questions
you will have 90 seconds where you can talk all the time. When you choose your answer,
you can override it by clicking another button. The only letter that counts is the one that
you click before the system shuts down. So it's your last click before the system
shuts down. Is there any questions to that? Otherwise
we're going to start and we test it now. So, also in Evans, in 10 Evans and 60 Evans
the guys are sitting there and they have the receiver there as well. And while I do not
see their results, they will be able to click and register.
So in the spirit of you guys getting to know me, which of the following statements is wrong
about me the instructor? Number one, he was born in a foreign European capital; number
two, he fed sharks at the Great Barrier Reef; three, he orchestrated a medal ceremony at
the Olympics games; D, he ranks 510th on the world wide Angry Birds charts; and E as a
boy he wanted to become a vegetable farmer, and my dream job now. So I'm going to start
the system. You see up here in the upper corner of the screen, you have a minute and a half
and you can choose now. You can discuss it with your neighbors.
Fifteen more seconds. I will always make that announcement.
Five. Click now. All right.
Stop. So 501 people voted. That's way over the capacity of this room. So what did you
guys choose? C, 288, the majority 57 percent chose C and C is the orchestrated a medal
ceremony at one of the Olympic games. So we go through this.
So number one, he was born in a former European capital. That is correct.
So, oops. Yeah. I was born in Aachen. It is in the western
side of Germany. I lived there and I studied biology there. So what capital was that of?
Any history majors here? Oh, come on guys. Nobody?
Okay. Aachen was the capital of Charlemagne, 800 A.D. I know long time ago, but okay.
There was the Empire of the Franks so that's when it use to be a capital and before you
ask I will not quiz you this on the exam, okay? He fed sharks at the Great Barrier Reef.
That is correct as well. I went when I was your age under the lower division biology
major I went for half a year to Australia to work in the lab in the molecular biology
lab, as a foreign exchange student. But we didn't have internet and we didn't have any
programs. And I went to Brisbane and worked on molecular biology in Bali. And when I was
there I also went diving in the Great Barrier Reef on Parrot Island and was allowed to feed
sharks there. So that was fun so I can highly recommend going abroad to study.
Okay. Next, he orchestrated the medal ceremony at
one of the Olympics games. That is correct. So, what happened, so what happened is I did
my Ph.D. at the University of Georgia, in Athens, Georgia here. And I did my Ph.D. in
the '90s and in 1996 the Olympics came to Atlanta and I was a volunteer, initially as
an interpreter German English. But then I became program director of protocol department.
The protocol department is the one where we have the lounges and we need to get the Olympic
family and the sports director, etcetera. And part of my job was to make sure that the
flag would hang properly. So I did not have this mishap they had in London this year where
they hung the flag wrong from the North Korean. It was a very tense moment because it dealt
with a lot of politics. And one part was also to guide through the medal ceremony. I can
tell you pain in the neck. Never do it. Anyway. Very nervous. Nerve wracking the whole
thing. Next one. He ranks 510th on the world wide
Angry Birds chart. Of course it's correct. Why would I even mention that if it would
be wrong. At least it was last week, so I have to check it again, I think it was approximately
like that. So as a boy he wanted to become a vegetable
farmer and that is wrong. I never wanted to become a vegetable farmer.
I wanted to become a zoo director. So the zoo because I really liked animals at the
time. And so, I guess there was a propensity for biology and the director because I really
didn't fancy shoveling elephant shit. So I really wanted to become a zoo director. Now
when I started to study biology just like I guess you guys, mainly and it occurred to
me that plants are much cooler because, number one, they don't bleed, they don't cry, they
don't scream and they don't run away. And therefore, it's much easier to deal with
plants, particularly when you do biochemistry than when you do animals and more importantly
also, they're much more important. If you wouldn't have plants there would be no life
on this planet and therefore I thought that's where I wanted to go and where you see here
I am teaching Bio 1A at 8:00 o'clock in the morning. All right. Next.
Here is the schedule for this first section. Which I term the molecules of life. So it's
mainly going to be chemistry, biochemistry and a little bit of cell biology. I posted
the reader on Bspace up to Chapter 7, up to here. Chapters 8 to 12 are still going to
come, I put them in one chapter. And for now I hold off to them, so I can make modifications
if I get the timing wrong, so they will come later.
The exam for this whole section will be on Monday September 24th and it will be basically
during regular lecture hours so we will have 50 minutes just like in the regular lecture
to answer the 50 50 plus multiple choice questions that you're going to get for that exam.
Any questions to that? No.
Yes? >>STUDENT: [Indiscernible].
>>INSTRUCTOR: So, again it's iClicker questions if you were to what?
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: Yeah.
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: No. You would not be able to
get them. So the iClicker questions will only happen here in the room, but the lecture is
webcast, I understand, casted to the other room and it's stored somewhere, so you know
this afternoon if you really enjoyed it you can watch it again, you know.
Anyway, and there in that webcast, you will also see the iClicker questions that, iClicker
questions, that came in this lecture. So we're going to have 12 lectures and I will
ask 14 to 15 questions, so usually per lecture it's minimum one but maximum two questions
that I ask, you will see them on the webcast. >>STUDENT: [Indiscernible].
>>INSTRUCTOR: Usually the questions are two part that's an administrative question and
I would give that to Mike but he's sitting in the other room, but generally questions
are two points and there is few exceptions when they're two points, but I give one point
and that's what makes up the 100 points. Okay.
So, science, finally we're getting there. Yeah. Nearly done. Okay.
So I don't start, you know, from the very basic chemistry, as a prerequisite for this
class you're supposed to have chemistry, and this is summarized in the book, in chapter
number two and chapter number five so I encourage you to read it. Alternative you can go to
mastering biology, I picked some questions that you should be answer able to answer and
if you answer them correctly, and you know what you're talking a about in these questions
and then you're going to be fine and then you don't have to review these chapters. So
we're going to start by means of a review, we're going to start with water actually.
So, as you know we live on the blue planet. So I need to turn on this thing here.
So water on this planet is highly abundant and very much defines the qualities of this
planet. So two thirds of our planet are covered with water. And water has been around for
more than three billion years and therefore evolution on this planet is defined by water.
And even organisms that have left water so left the oceans or left the lakes, like us,
right, we left that environment; we took the water with us.
So we are composed to 70 to 95 percent all organisms are composed of 70 to 95 percent
of water and therefore the chemistry of life, the chemistry of us and chemistry of most
of the organisms is defined by water chemistry, essentially with a few exceptions and therefore
you can understand there's excitement in the news when somebody might have found water
on another planet because that would indicate that there could be a chance that there might
be similar life here than here. So the chemistry of water, H2O we have the
oxygen, the oxygen is strongly electronegative, if you forgot this term look it up, strongly
electronegative and compared to the hydrogen and therefore it's going to pull the electrons
in this direction it's not going to attract the electrons it's just going to pull it and
therefore water can be considered a dipole molecule and these atoms have a partial charge
so the oxygen is more negative that's indicated by a minus and hydrogen is positively charged
partially charged there's a plus. And so because of this dipole character of
this molecule, these molecules can actually align, because then the opposite charges attract
each other and therefore you get what is called the hydrogen bond.
H bond. And that is one defining feature of water.
So one of these features is the cohesion and the adhesion of water molecules.
So the cohesion means that the water molecules can sort of stick together because of the
hydrogen bonds, the cohesion is water molecules stick together, adhesion is that the water
molecules can stick to other molecules if they are polar, right? The partial positive
and partial negative charge and then the water molecule adheres to the other molecules, so
far example here we have a tree, and when you think about the water flow through a tree,
it's taken up by the roots go to the vascular system here, yeah the vascular system goes
through the stem of the tree, ends up in the leaves and in the leaves it exits the vascular
system, goes threw the air space in the leaf and then there are the opening in the leaves
called stomata, you don't need to know this where the water moves out so there's a direction
of flow of the water from the soil out on the leaf.
So energetically the way the water can move through this tree is really by the evaporation
of the water in the leaf. So when the water evaporates in the leaf it pulls the water
up, yeah, so there's hardly any push from the water it pulls the water up and it can
only do so over the significant distance here because the water molecules stick together
so you a water fill and the water molecules stick to the side of these tubes, otherwise
the whole water column would collapse and you would never get water up here in the leaf.
Of course, up here in the leaf, the water is not only therefore evaporation, the water
is also required for photosynthesis. And as you know if you don't give plants water
they wilt so the water cannot be pulled up sufficiently but there's a counter force to
this if the water gets pulled up we have gravity and the gravity is going to pull the water
stream down and therefore limits so, the typical limit of a tree is 350ハfeet it cannot grow
taller because the cohesion and adhesion of these hydrogen bonds will not sustain a column
higher than that, in the architecture of these cells here, so there's an upper limit of how
this can be done. Another interesting property of water is its
high specific heat. By definition, the specific heat of water
is defined as one calorie per gram water per degree centigrade so if you want to heat up
one grade of water one sent meter higher that's a definition of a calorie and that is fairly
high so if you have alcohol, specific heat is about 0.6, if you have aluminum matter,
the specific heat is only 0.2 and if you have silver another metal, you have only 0.03,
so what does that mean specifically? Well what it means is that it takes energy to heat
up this particular compound, so you all know this if you put water and let's say in a kettle,
or in a pot, that's say made out of aluminum and heated up, it gets hotter quicker than
the water inside so you might burn your fingers ton aluminum while you don't burn your fingers
on the lukewarm water, it takes time to get the heat trance fused into the water because
water has a high specific heat. One advantage of this is the temperature certain temperature
also retain much more so it doesn't lose the temp very quickly, yeah so if you know you
have boiling water, if you pour it out of the pot into a cup, the pot cools down, because
it's low specific heat but the boiling water remains hot for a relatively long time. And
we see that macroscopically in our area, we are close to large bodies of water, the Pacific
Ocean and the bay, and they cool down our temperatures quite significantly here because
it's strongly influenced as far as if you go over the hill and go to the valley it's
extremely hot because they have little water influence because the temperature can vary
quite a bit. Another worldwide phenomenon the Gulf Stream
that goes from the Gulf of Mexico to northern Europe so Ireland and England have hardly
any snow even though they're on the same latitude even as Newfoundland of Canada and that's
because they retain a lot of the heat before they get there and they warm up these countries.
But for us, as a water organisms that is also very important, because it stabilized our
temperature. Yeah. So water organisms like us, they don't fluctuate too much in temperature,
we can of course but it takes time and it takes energy, so that's very important that
our temperatures are stabilized in various forms.
Another important feature and unique feature of waterハis that it expands upon freezing,
usually, that means solidifying when you form crystals, usually when you have molecules
that the moreハ the lower the temperature, the more dense they get, you can take more
molecules in a certain volume and when the crystallize they have the highest density.
But the water is not the case, the highest density in water is 4 degrees and if you go
below 4 degrees the water molecules expand so you see liquid water you see the hydrogen
bonds in between the water molecules that break and re break and therefore the water
can be very dense, but one once it freezes and forms the crystal structure that you see
and then there's much more space in between the water and therefore the water, the ice,
is less than and that's really important because that means that the ice flows.
So, can you imagine a world where the ice wouldn't flow? So the ice would sink to the
bottom of the lake or sin tock the bottom of the ocean so what that would mean the lake
and ocean would be frozen from the bottom up and that wouldn't sustain life so this
is important that frozen ice actually flows and you have liquid below so you can actually
do some chemistry. Another property of the water is that it's
a versatile solvent. So, because of its dipolar character it can
dissolve ions. Ions.
So here you have sodium chloride, salt, the chloride is negatively charged so you will
see that the hydrogen is aligned that's the partial positive charge to the chloride and
here the sodium which is positively charged you see the partial negatively charged is
aligned with the sodium so it can dissolve it's important for the chemistry and the salt
levels in our body it can act as a solvent to polar molecules such as proteins which
we'll discuss soon. So as you can see this is a protein and it has a polar surface and
so the water molecules align on top of the proteins, so when we discuss in the future
of protein chemistry, protein biochemistry, usually the water is omitted. So they usually
leave it out of the picture for clarity, but remember in general you should also take the
water molecules in consideration that are act as a solvent of this polar molecule.
And this again can be done because of the dipole character and depending on what police
report the water choose you will have it align with the hydrogen or where the oxygen. And
what happens in both cases the ions and the polar molecules the water formed what is called
a hydration shell so the complete molecule is surrounded by water. However water is not
a universal solvents because they're also molecules that cannot be dissolved in water.
For example, oils, oils and waxes, they are what is called hydrophobic and they cannot
be dissolved in water. Okay.
Another properties that the protons of the water can disassociate.
And this is also a very quick review, but this is very important so I hope you will
remember this one. So if you have two water molecules here, the
proton can completely disassociate and move over to the water molecule and what you get
then is the hydronium ion or H30 plus, right, H3O plus and this is commonly abbreviated
a the protein H plus but it doesn't occur in solution, so you will always have H3O plus
even though we abbreviate it as such and the water molecule where the proton came from
is a hydroxide ion so that's O H. And these two, the H3O plus and they're very
reactive molecules, and the species, and usually organisms don't want the extremes of those,
so that's why they have buffer cents. So the buffers are usually weak acids or basis that
can minimize the change in the proton concentration of the buffer, so please review what a buffer
is and how it's constituted. Be of the proton concentration is defined as the pH.
And the pH of the solution isハ ハlogarithm of the concentration of a Newton, so if you
have a pH of seven we have 10 to the molar of H plus so if you put this number in here
you will get seven out of this. And that actually reflects only one proton per 554 million water
molecules so it's relatively little protons that are in a neutral solution. And you should
keep that in mind too. Okay.
And so the last property of water it's not that it's only a solvent and has unique biophysical
properties but it can be reactant or product itself of chemistry.
So we have two important reactions, one is the dehydration reaction, which is also called
condensation. And in the condensation reaction you have a polymer that has a hydrogen yeah,
and then you have a polymer that has a hydroxy group, both spit out water and H2O is released
and then you have a polymer. Water is removed and then you link these two polymers the opposite
occurs too in organisms you have polymers you break it by introducing water again and
they then form the hydroxy group here and the hydrogen here. So we have dehydration,
concentration and we have the hydrolysis. All right. So first quiz. You can earn a point.
At least half of point all of you get half a point.
So, the bonds that are broken when water vaporizing are: Ionic bonds, covalent bond between atoms,
or hydrogen bonds between water molecules. So I'm going toハ don't click yet because
I haven't started the system. Okay. So I start the system, you're welcome
to look at your notes you're welcome to discuss it or if you know the answer, which you should,
just click it and advise your neighbors. Okay. 15 more seconds.
Okay. A few more seconds. Make your click now.
Very good. So I guess Evans Hall to stop their clickers
too. So, you guys chose E.
Yes. Very good. Excellent. So you earned already one point, only 202 to go. So it's the hydrogen
bonds that I talked about the whole time. And it's not the covalent bonds so it's not
B because it's not the covalent bond that is broken so that should have been a brief
review, any questions to the this section? Yes?
>>STUDENT: [Indiscernible]. >>INSTRUCTOR: So the question was, the dehydration
caused con sensation that has to do with the reaction mechanisms they look the opposite,
but actually energetically they're not. And we will get to that as we move through the
course of this. But, from the chemical structure from the
chemical formula wise, this is what happens. Okay.
Okay. So for the last few minutes. We're only going to do one slide.
We're going to start with the macromolecules. And for the macromolecules we're going to
start with proteins. So it turns out that when you think of organisms
such as us and then the other organisms on the planet the macromolecules that we're made
up consist of only 40 to 50 common building blocks, that's nice not so much to learn.
The key here is not the building blocks but the arrangement of the building blocks, the
sequence of the building blocks and that is true for all of these four macromolecules.
And so the first one is an amino acid. And that deals with proteins so proteins are made
out of amino acids. The protein itself is an unbranched polymer
of amino acids and there are 20 amino acids in the human body and you can see them here.
All of the amino acids have a common motive, so as the name says, they have an amino group
so they have here, NH2 but under physical logical pH this is charged so it's NH3 plus.
And they have a carboxyl group, COH but under physiological pH this is charge as well, so
we have COO. And so this is called: A zwitterion because
it's positively and negatively charged at the same ion. They're both attached to the
alpha carbon that has one proton and it has a side chain. So this section here is common
to call amino acids and the side chains are different in the amino acid.
Okay. So here you see the 20 amino acids, and then
you might ask me do I need to learn the lecture of the 20 amino acids? No, you do not.
Do I need to learn the abbreviations, the 3-letter abbreviation or the single letter
abbreviations? No, you do not. So what do you need to know? You what you need to know
is you should recognize the names so if there is a question that says, methionine there
should be a click in your brain that says, ah, amino acid. So you should know that glycine
or histidine is an amino acid, and what you need to know is how they are grouped, so you
should know that some amino acids have hydrophobic side chains so they're not really mixible
with water and these are called nonpolar side chains.
That some of the amino acids have side chains that mix very well with waterハso they're
hydrophilic so they're polar side chains. And that some side chains are charged.
And they can be either acidic, because they're negatively charged, or they can be basic because
they're positively charged and they accept protons.
Okay. So what can happen for example in the exam, I will give you structures of some of
these amino acids, and all you have to do is you will need to be able to look at the
structure and you will need to be able to classify them into polar, nonpolar, acidic
or basic. But you do not need to know the name of that
structure, or anything. Okay. But you should know the common motifs
of amino acids. Okay.
And with that we finish today. Have a nice weekend and I'll see you on Monday.