#01 Biochemistry Introductory Lecture for Kevin Ahern's BB 450/550

Uploaded by oharow on 26.09.2011

Captioning provided by Disability Access Services
at Oregon State University.
Kevin Ahern: Let's see.
How about now?
Can you hear me up there?
You can.
Student: No.
Kevin Ahern: No?
More volume?
Less volume?
Student: More volume.
Kevin Ahern: More volume!
How's that?
[students chuckling]
What is this?
Are you guys ready to start?
The term isn't ready to start.
This is awesome!
How are you guys doing?
What do you think of this fancy, new auditorium?
Student: It's awesome.
Kevin Ahern: I'll tell you something.
Look at this.
Something I like is I can actually walk
up here and the light's not hitting me in the face,
because I was usually blinded.
Now I can really see if you guys
are sleeping or goofing off back there.
So I know, right?
So welcome to BB 450/550.
I'm very happy to have you here.
My name is Kevin Ahern,
and I will be your instructor this term.
And what you see on the screen
is a page that you'll probably
see a lot of during the term,
and it gets updated pretty regularly.
I'll tell you a little bit about myself
and tell you a little bit about the course
and also maybe even learn a little bit about you.
So, it's a little warm in here.
They're opening some doors,
so hopefully we'll get some air in here,
which would be nice.
I've been teaching this course for,
I don't know, seven or eight years,
and have gotten to be very fond
of the course and very fond
of the number of students
and the relationships I've had
with students that have taken the course.
I really am a person who likes
that sort of personal connection.
I like to interact with you.
I like to help you in any way that I can.
I also like to see you, of course,
be responsible and do what you can,
on your part,
but I can assure you I will
also do whatever I can,
on my part,
to help you to get on top of this subject.
So, it's a difficult subject.
I know it's a subject that many
of you have a lot of anxiety about.
And I feel bad about that,
to be honest with you,
because I think that it's a subject
about which most students find
that there really is a lot of really
interesting stuff in it,
but if you come in it kind of going
you know, that's kind of a barrier
to learning, okay?
So I want to do what I can to cut through that.
I keep a lot of office hours.
And if you look at my schedule,
you'll see I don't even keep,
I don't even list them.
My policy is,
when I don't have another meeting scheduled,
I'm generally in my office
and you are welcome to come any time.
Now, you might check to see,
if I have a meeting scheduled,
I'm not going to be there,
obviously, when you come by.
But if you do that,
I'm more than happy to meet with you.
I'm more than happy to help you
in any way that I can.
That's part one of the things
that I think is very important for me
to do with you, okay?
If you want to set a meeting with me
where you want to be sure I'll be there,
of course, you're always welcome to do that.
Send me an email.
I will be happy to schedule
that with you, as well, okay?
So it's important that I be available to you.
And it's important that I be helpful to you.
If I'm not being available to you,
if I'm not being helpful to you then,
of course, you'd let me know that
and we'd deal with that.
Biochemistry is a subject
that most students take,
not because they want to,
but because they have to.
"I gotta have it for a biology degree."
"I gotta have it because I want
“to go to medical school."
"I gotta have it because I want
“to go to dental school."
And so that's the way that many
of you come into this class thinking.
And I will also tell you there are a lot
of urban legends that are out there.
I won't tell you that it's an easy course,
but I will tell you that not all
of the urban legends are true,
just as, I'm sure you know,
that not all the things that you read
on the internet are true.
So, as I get wind of those,
I do try to shoot them down.
I'll tell you the one that got started
last year was that the averages
in this course are never above 50.
Well, A, if that were the case,
you can't flunk everybody, right?
B, it's not the case.
So in the entire time
I've been teaching biochemistry,
which goes back to 1995,
I've actually had three exams
where the average was lower than 60.
Urban legends aren't always true.
So don't freak yourself out
with what's basically a bunch of bullshit.
I kind of loosened it up, right?
Bullshit, right?
I'll say it again.
How 'bout some bullshit, right?
You guys like bullshit?
Let's talk about some bullshit today, okay?
[class laughing]
So anytime you have a question,
please come see me.
That's number one.
If you don't want to come see me,
you can email me.
I don't care.
It really doesn't matter.
Before the first exam,
I'll give you my cell phone number.
You can call me.
I have no problem with that.
You can call me.
You can come see me.
You can do whatever works for you,
because my job is to help
you to learn biochemistry,
because biochemistry is going to be important
for you in whatever you want to go and do.
Medical schools, microbiology programs,
dental schools, graduate schools
don't make biochemistry a requirement
to be mean to you.
They make biochemistry a requirement
because it's going to be a very important
part of your career.
So it's important for you to get
these things down that I'll be talking about today,
and tomorrow, and the next day,
and the next day.
So, I videotape all my lectures.
I try to get the videos posted
within a couple of,
certainly within a couple of days
of the video having been made,
and they're available for streaming.
And you don't even have to come to class.
In my experience,
and I have done the experiment to test it,
those who come to class do better.
I have some very solid data for that.
But it's your tuition money.
If you decide you want to roll the dice
and take the chance,
and maybe you don't come to class
and you do well,
you can play that game.
But I don't think you want to play
that game with your career, in general.
I do reserve the right to give pop quizzes
if it looks like,
well, people are really not taking this seriously.
So a pop quiz is a possibility.
I don't do it to be mean.
I do it to encourage you to participate
and come and listen.
The best way to use the videos
are to supplement the lecture.
I tend to talk fast.
You've already seen I like to pace.
If you want to get a really humorous thing,
watch my video and speed it up
about three times,
and you'll see I'm playing tennis,
back and forth, right?
So I pace.
I will try to slow down.
If I get going too fast for you,
all you have to do is say,
"Hey, Kevin!
“Slow down!"
And by the way,
I like to be called "Kevin."
Please don't call me "Dr. Ahern," okay?
I find that really is a very stuffy term
and it gets between me and you.
So please call me "Kevin."
It's important for you to get
on top of this stuff.
And it is a subject that is rapidly expanding.
Our knowledge at the molecular level
of what is happening in cells is exploding.
There is nothing in all of the sciences
that is as exciting right now
as what's happening in biochemistry.
That's absolutely true.
We are in the middle of what's called
the "biological revolution."
Now, the biological revolution happened
as the result of several things,
the most recent of which was the ability
to determine large quantities
of genomic sequence information.
As a result of that,
we have an incredible amount
of information about cells.
You can't pick up a newspaper today
and not see some exciting new biotechnology finding.
What I hope you will get,
as a result of this course and BB 451,
is an understanding of the significance
of some of these findings,
and they are absolutely remarkable.
So I hope that one of the things
that I leave you with is an interest
and an enthusiasm for the subject,
and I hope to dispel any fears
that you have about the subject.
I know I'm coming back to that,
but that's what people have.
If you need a tutor,
if you need assistance,
I'm happy to help you to get that.
If you want to come see me,
I'm happy to help you work with me.
So, whatever works for you,
that's what I want to make sure that you do.
I want you to play an active role in your own education.
I'm not going to pound you on the head
and put the information in.
You're the one that's gotta do that.
Whatever way works for you,
works for me,
short of looking at your neighbor's,
you know, okay.
Are we clear?
So, first expectation I have of you,
you'll read the syllabus.
The syllabus is required reading.
You can download it.
You will see a question on the first exam
come straight from the syllabus.
You are responsible for reading
and knowing what's in the syllabus.
That's given.
All of the videos this term I'll be using,
I'm uploading to YouTube.
YouTube videos are a little hard to download.
If you're having some real issues
and you really,
really, really want to have a download,
I will make some other options available to you.
I also post my videos to iTunes U,
and iTunes U videos are very easy to download.
So if you're having trouble with YouTube videos,
you can go to iTunes U
and pull all of my videos down.
And, in fact,
there's a whole bunch of them there,
right now, already.
They're in a podcast format.
Every time a new one's available,
you get a notice, etc., etc.
So if you want to have a downloadable version,
iTunes U is probably the best way to go.
Well, that's enough preliminaries.
That's enough about me.
I want to ask a little bit about you.
So how many people are anxious for this term?
Be honest, or I'll cut all your arms off.
[class laughing]
That's about average.
How many people are looking forward to the term?
Some of you are probably the same people,
anxious and looking forward.
Sometimes anxiety actually
for people is adrenaline, you know?
People who have to go on live television,
they get that adrenaline rush, you know,
and a lot of anxiety,
but they go out and they do great stuff
because that adrenaline makes them do great things.
And adrenaline can do great things
for you and it can do very bad things for you.
We hope to make those things be good for you.
Hopefully, we reduce that adrenaline, right?
We get you into a place
where you can be your best
and do your best without having
to be anxious about things that you have to do.
What's the worst comment you heard
about biochemistry before you took the class?
Student: I heard that you tell people
that you don't need to know it
and then you test them on it anyway.
Kevin Ahern: Oh, yeah, yeah.
You know, you can't teach a class
in the university without hearing
that comment, right there.
"He didn't say we had to have it,
“and then he said we had to have it!"
I can tell you right now, okay?
I'll tell you what I tell everybody.
I write, at the end of every lecture I give,
I write a series of what are called "highlights."
You see them up there, highlights here.
After class, there will be a link there,
and it'll be my summary of what I talked about today.
I can assure you that I write my exams
looking at the highlights.
You're looking at the same thing
I'm looking at when I'm writing the exams.
So I hear that,
but I hope,
I certainly hope I'm not asking
you something that I haven't talked about.
I hope that that's an urban legend.
Because it's my aim,
I have no desire to be tricky.
I have no desire to be confusing to you, in any way.
I want to test your knowledge.
You had a comment here,
is that right?
Student: Yeah.
I heard you force a curve,
a bell curve.
Kevin Ahern: I force a bell curve?
Student: You only give like this many A's,
and this many B's?
Kevin Ahern: Ah, okay.
I haven't heard that one, but, okay.
So the comment is that I force a bell curve.
I force, "You're only going to have 10% A's,
“and you're going to have 20% B's,
“and the rest of you are going
“to get C's, D's and F's."
I don't do that.
I do not do it.
What you will see is that
the bell curve creates itself.
It honest to God does.
I don't force it.
I post, at the end of every exam,
I will post the distribution of the grades,
and you will see that bell curve.
And the only way that I would force
that would be if I made those numbers up,
which I don't.
So, no.
I grade according to that distribution of what's there.
The other part of that
is I don't have a fixed number
of A's, B's, C's, D's or F's.
So good.
Student: I heard that 451 is significantly
harder than 450.
Kevin Ahern: He heard that 451 is significantly
harder than 450.
I would say,
if you asked the average student,
the average student will say
it is much less difficult than 450.
Most people find 450,
at least in my experience talking to them,
most people find 450 to be more challenging.
You'll find more math in 450,
and it's because of that 450 has a recitation,
and because it has a recitation,
it has a recitation because of the math.
There's no math in 451,
so most people find 451 actually to be easier,
in that sense.
But I can't comment for everybody.
You may have talked to someone who thought that.
What else?
Student: I heard that if a cell phone goes off
you lose 10% of your grade.
Kevin Ahern: If a cell phone goes off,
you lose 10% of your grade.
Yeah, I've been known to get a little
wild on cell phones, I suppose.
Let me ask you guys,
what do you think about cell phones
going off in class?
Student: Irritating.
Kevin Ahern: Irritating.
What else?
Student: It's distracting.
Kevin Ahern: So what would you do if a cell phone
went off next to you?
Student: I'd want to throw it against the wall.
Kevin Ahern: Okay.
I haven't done that.
She wants to throw it against the wall.
I had a professor one time that did that.
He had this fake cell phone that he picks up.
And he's got it,
so he pulls it out of his pocket
and he grabs the other student's phone,
and he throws it against the wall
and everybody thinks he's thrown it, you know?
Evil professor from hell.
I'll tell you a really cool trick
I heard a professor pull one time.
He's working on a blackboard.
Back in the, you guys may not know it,
but they used to write
with chalk on blackboards, you know?
[class laughing]
It's a long time ago.
People used to write with chalk on blackboards.
And so it's the first day of class
and so he's got a bunch of freshmen,
and he's sitting there
and he's writing up on the board.
And what the freshmen don't know
is that he stuck into his pocket some candy canes
that he has licked the color off of,
so they look white, okay?
And so he's getting up here,
and he's talking,
and he's doing this,
and he's putting his hands,
and so forth, and of course,
he reaches in and he grabs one of the candy canes,
and nobody knows this.
And a student asks him a question,
and he says, "Yeah, that's a really good question."
[chomping noise]
If you guys ever go teach high school or something,
that would be a really cool trick to do.
I'm not sure how well it works at college,
but it'd be a very cool trick to pull.
Student: We had a chem teacher that would
take a hand and stick it in liquid nitrogen
and smash it with a hammer.
Kevin Ahern: Take a hand, stick it in liquid nitrogen.
Student: So it would look like it was his hand.
Kevin Ahern: See, these are instructors from hell.
I mean, I hope I'm not this bad, hopefully.
The only thing I'll do is I'll make you sing.
So you'll have to sing.
You will have to sing
for your supper in this class, okay?
What else?
What other comments?
This is the quietest you guys
are going to be, all term.
No other urban legends out there?
You want to make one up?
How come nobody ever makes up
an urban legend and says,
"Oh, man!
“That Ahern, man,
“he's the greatest guy in the world!"
You never hear that one.
You know?
It never, ever happens.
What is that?
I should start that one.
Facebook group, you know?
"Ahern's awesome!"
What's that?
Student: What are the differences
between you and the other biochem teachers?
Kevin Ahern: What are the differences between
me and the other biochem teachers?
Very good question.
I'm much better looking than they are.
You will have the same instructor.
I teach both 450 and 451.
If you take 450 next term,
which I hope you're not planning to do,
but if you take 450,
usually those aren't done by choice,
then there's somebody else that teaches that.
But I'm much better looking than he is.
You think I'm joking.
You say, "He must really be ugly, huh?"
What else?
The more we talk like this,
the less we have to talk about biochemistry.
You guys are just ready to dive into biochemistry?
Is that what it is?
It sounds like a fly flying around, doesn't it?
It's my heart.
The pacemaker's just going
You guys ready to dive into biochemistry?
Student: Yeah.
Student: I think so, yeah.
Kevin Ahern: You'll regret saying that.
Oh, there's a comment over there.
There we go.
Student: What's the weirdest thing
that's happened in your class?
Kevin Ahern: The weirdest thing that happened
in my class...
I can think of two things.
Number one, I remember being down
here lecturing one day,
and I hear this sort of shriek from the back.
And the restroom down there has started
leaking water and there's literally
a wall of water that's moving down this way.
It was not pretty.
The second one was a little bit more humorous,
and it was on Halloween.
I had a couple of young men
who decided they would disrupt class.
Well, I have been known to be the professor
from hell if people disturb
other people's learning,
whether it's with cell phones or whatever,
so I don't want to have
students' learning get disrupted.
So these two young men come in
and they dressed as really old guys.
It's a beautiful costume.
I'll give them credit.
But in the middle of my class,
they walk down,
and they come trotting down,
and they're doing the whole thing,
you know, and of course,
every eye in the class is on these guys
coming down here to come
and sit down in the front row.
And, by the way,
you're welcome to do it,
just don't disrupt the class.
That's fine.
Well, they made a big production of it,
so they kind of irritated me.
So I looked over at 'em and I said,
"Well, welcome."
[imitates old men muttering loudly]
I said, "I'm very happy that you gentlemen are here.
“And because you gentlemen are here,
“I have an announcement to make."
[imitates old men muttering loudly]
"I'd like everybody to look at these two gentlemen.
“And because these two gentlemen are here,
“you guys are going to have a pop quiz today."
[scattered gasping]
Oh, did the attitude in the class turn bad.
And it turned ugly!
And these two guys are sitting here,
and they are the focus of every eye in the room.
Needless to say,
they got their butts out of here.
So I said, after they left, of course,
"And here's your pop quiz.
“Please sign your name to the piece
“of paper and turn it in,"
which meant that they got extra credit.
Well, of course,
everybody in the class was happy,
these two yo-yos who were here got chased out,
and I was happy because I don't like people
disrupting my class.
So those were the two weirdest things
that have happened to me.
Student: You don't use Blackboard?
Kevin Ahern: I don't use Blackboard for this class.
Blackboard is an absolute kludge, okay?
If you want to see a clinker, use Blackboard.
I think the web is much more efficient,
and I can get things to you faster,
easier, without problems,
by doing what I do.
So, no.
I like HTML a lot.
I can lecture from this.
I can't lecture from Blackboard.
I mean, I'm sorry, unless you're brain dead.
Student: So you'll post grades on here, then?
Kevin Ahern: I will post distributions.
I will not post your grades.
You have to get your grades off of your exam.
I won't post your grade online, no I won't.
But you will see the distributions of grades, yes.
Because of privacy issues,
I can't post names and grades, obviously.
Other questions?
Student: This is kind of a quick one.
I'd seen where there was a new
Advanced Light Source going online
at one of the research universities.
Do you know if that's been in use
long enough for any of that material
to make it into the literature
that we're going to be using?
Kevin Ahern: I'm not even sure of what
you're talking about,
so I guess the answer is no.
But if you want to talk to me about it later,
I'd be curious to hear what it is.
Student: It was in "Popular Science" recently.
Kevin Ahern: Okay.
News to me.
News to me.
To me, this is great,
because with the real projection,
like I said, I didn't used to be able to see.
There would be a projector sitting
right there and I'd just be blinded
by the stuff here.
Comment back there?
Student: I was looking at the bookstore
and it said the online class you teach
is using the seventh edition?
Kevin Ahern: Thanks for bringing up the edition.
No, that's not true.
There was a little confusion.
My syllabus originally said "Sixth Edition."
We actually use the seventh edition.
The question is, "Can I use the sixth edition
“and get away with it?"
The answer is probably, yeah, you can.
Things don't change that much
from one edition to another.
I can't assure the problems line up appropriately,
but with your TA and/or me,
we can help you to do that.
So I think textbooks are an outrageously expensive item,
and I don't like supporting the textbook publishers,
to be honest with you.
So the online class is always behind
the classroom class,
because in the online class,
they see a whole term's worth of lectures like today.
And those lectures obviously aren't from this term.
They're from a previous term.
So they're using the textbook.
You guys are the first one to use
seventh edition of the textbook.
So that's what's up with that.
My advice to students is,
wait on the textbook, if you want.
See if you even need it.
Some people feel they don't even need it.
Student: Do you know if they're still selling it?
Because I just got mine, like, today,
and the sixth edition is still under,
like, the shelf for this class.
Student: It's probably for the online
version of the class.
Kevin Ahern: That's the online, yeah.
So the online is sixth.
This classroom version is seventh
edition of the textbook.
So I provide a lot of materials.
I actually am in the process,
and I'm not sure I'll ever do it for this class,
but I'm in the process of actually
writing my own textbook.
I hired a student last year to create
all the figures that I needed for a textbook
I will give away,
for my BB 350 class,
so the students don't have to pay $200
for a ridiculous textbook to a publisher.
I really think that's outrageous.
Paper is not that expensive!
Student: I agree.
Kevin Ahern: Okay.
It's not.
So whatever I can do to work around that,
I do try to do that.
Okay, so, as I say,
I'm paid to bore people.
Hopefully, you guys are still awake.
We should get started.
Let's do that.
So I'm going to say a few things,
in general, about biochemistry here,
that I'm not going to hold you responsible for.
And I will tell you
when I'm going to get going
about something that you are responsible for.
So, just in general terms,
and you're not responsible for this,
but, in general terms,
biochemistry is the science
of the molecular basis of life.
That's what biochemistry is.
We don't think about that so much.
We don't think about biochemistry being that new.
We think about biochemistry,
"Well, it was always around,
“like anatomy, or physiology,
“or biology, or chemistry, or something."
But it wasn't.
The roots of biochemistry literally date to the 1930s.
The modern roots of biochemistry
date to the 1930s,
when a man named Schrodinger said,
for the first time,
that the basis of life is not cells,
it's not tissues,
it's not organs.
The basis of life can be found in molecules.
And it was that fundamentally different
way of looking at things
that got people trying to understand
the molecular reactions,
the molecular basis of life in cells.
It led to the discovery of the structure of DNA,
which is truly where the roots
of the modern biological revolution can be traced.
Everything that we have,
with respect to genomic sequence,
to the topics of genomics,
proteomics, all these various "omics,"
all date to 1953,
when Watson and Crick stole data
from Rosalind Franklin to show the structure of DNA.
I've got a limerick I wrote about that.
I'll share it with you guys
when we get to that point.
They stole it.
They acknowledge they stole it.
But the point is that,
because of a variety of things,
we knew the structure of DNA,
it was quite clear that the information
that we needed to know to understand
that molecular basis of life came from that,
as a result of that, okay?
Here's a figure.
Maybe it's not.
The tree of life, okay?
We think about three major branches
of the tree of life in this class,
and we'll talk mostly about bacteria
and eukaryotic cells.
Bacteria being grouped in the category
we call "prokaryotes,"
and the higher cells,
like people, plants,
dogs, cats, fleas,
multicellular organisms will all fit into "eukaryotes."
And some unicellular organisms,
like yeast, will also fit in the eukaryotes.
All of the prokaryotes are single-celled.
They're not multicellular organisms.
So we'll see that that division
between prokaryote and eukaryote is an important one,
and we'll see that,
even though there are differences that are there,
at the molecular base,
they're not nearly as big
as you would think they are.
I'll give you an idea.
Virtually every cell on the face
of the Earth has a common set of pathways
that are virtually identical.
We burn glucose in the way,
identically to the way that
the E. coli bacteria in our gut burn glucose.
We make proteins fundamentally
the same way that the E. coli
in our gut make proteins, okay?
The molecular foundations of life are remarkably similar.
There are differences,
and we'll talk about some of those differences,
but the fundamentals are absolutely written in stone,
as it were.
And that's a really interesting thing.
It's actually a good thing.
One of the good things,
it's a simplifying feature of biochemistry.
We used to have a clock in here
that you could see,
but now I have my watch and what's on the screen.
Okay, DNA.
Memorize those structures for the first exam.
That was a joke.
[nervous laughing]
In general, I try to minimize the number
of structures that you have to memorize.
I will tell you every structure
I expect you to memorize,
and I think it's fairly small.
It's not a large number of structures
you're going to memorize.
I would much rather have you spend your time
understanding concepts than memorizing structures.
There are going to be some structures
that you will memorize,
but not a lot.
And I will always tell you what they are.
I can assure you of that.
You will never have a structure
that you have to memorize that I don't tell you about.
Covalent bonds.
You've had organic chemistry.
Covalent bonds are fundamental
to the molecular basis of life.
Covalent bonds involve reasonably
equal sharing of electrons.
They're not like ionic bonds where one,
like sodium, pretty much gives up
its electron to chlorine to make sodium chloride.
Covalent bonds, there's a sharing.
And though that sharing isn't always equal,
and there are consequences of that,
it's much more equal than what
we have in an ionic bond,
where basically one atom gives up
its electrons to another atom.
Because of that unequal sharing of electrons,
we see inequalities in terms of charge.
This is a prime example of that.
Nitrogen tends to hold electrons
closer to itself than hydrogen does.
So when nitrogen and hydrogen come together
to make a covalent bond,
the nitrogen ends up being
slightly negative and the hydrogen ends up
being slightly positive.
I know that's freshman chemistry,
but I find that people in freshman chemistry,
you know, didn't learn it.
Was it your fault or was it the professor's fault?
I think it's the damn professor's fault, okay?
We can stand around and bitch all we want
about people not learning something,
but if we don't, ourselves,
make sure that learning things
is critical to going forward,
how can we complain?
So one of the things I want us to all
start on the same page about
is something that I expect that
we will all understand.
That is that uneven sharing
of electrons leads to partial charges.
We will see this gives rise
to what are called,
in biological molecules, "hydrogen bonds."
And hydrogen bonds are remarkable things.
You're going to hear "hydrogen bonds"
over and over and over,
as we talk about structure this term,
because they're incredibly important
and they're incredibly weak,
at the same time.
And one of the reasons that they're important
is because they are weak.
If we compare the energy of a hydrogen
bond to the energy of a covalent bond,
there's no comparison.
Hydrogen bonds are much weaker.
That means it's much easier to break
hydrogen bonds than it is to break covalent bonds.
You say, "Why is that good?"
And I say, "Well, the answer's partly on the screen."
That's a base pair.
Everybody learned A pairs with T.
In your basic biology classes,
you learned that they have two hydrogen bonds,
and if we have GC,
we have three hydrogen bonds.
And you can do the math
and figure that three hydrogen bonds
take more energy to break
than two hydrogen bonds, right?
But they're still relatively easy to break.
Why is that important?
Well, think about what a cell has to do.
A cell has to replicate its DNA.
A cell has to make RNA from DNA.
And both of these processes
require pulling strands apart.
Do you want to pull apart covalent bonds
or do you want to pull apart hydrogen bonds?
But if they're so weak,
then how do the strands stay together?
There's safety in numbers, folks.
There's safety in numbers.
Millions of hydrogen bonds
held together hold DNA in a double helix.
We can take apart short stretches quite easily.
But taking apart the entirety
of a million-base-pair
or a billion-base-pair chromosome
takes an enormous amount of energy.
Cells don't bother with that.
So this weakness of a hydrogen bond,
as we will see, is critical,
not only for the structure of DNA.
It's not just an obscure thing.
But we'll see it's important
for the structure of proteins.
And we'll see that hydrogen bonds
help to stabilize the structure of proteins.
And because they stabilize the structure
of proteins and they're weak forces,
they can be fairly easily disrupted.
Hey, that's kind of good!
You know why that's good?
Because we like to kill bacteria in our food.
We can cook it and destroy
the structure of the proteins
in those bacteria and kill the bacteria.
If those are covalent bonds
that are holding those protein structures in place,
folks, we couldn't kill bacteria.
We probably wouldn't be here.
Cooking provides enough energy
to destroy the hydrogen bonds in the protein
so that those proteins don't function,
and we kill bacteria by cooking.
We can kill bacteria
by washing our hands with soap,
because we're doing the same thing.
Those hydrogen bonds can get broken
with the interactions that we're giving to them.
We'll talk more about that.
So there's a real beauty to hydrogen bonds.
I want you to understand that.
Now, we could spend a lot of time
talking about donors and acceptors,
and blah, blah, blah, okay?
To be honest with you,
I don't think it tells you much.
You can memorize that, if you want to.
I'm not going to ask you this.
What I told you to start with
was the most important thing.
The most important thing was that
there's uneven sharing of electrons.
Nitrogen has a greater electronegativity.
Remember electronegativity from freshman chemistry?
Greater electronegativity,
stronger affinity for electrons.
Nitrogen and oxygen have greater
electronegativities than does hydrogen.
Therefore, when oxygen or nitrogen
is bonded to a hydrogen,
oxygen and nitrogen will be more slightly negative.
That's that little delta sign that you see there.
It means it's partially negative, not fully negative.
And the hydrogen will be partially positive.
Well, just like a full positive
can be attracted to a full negative too,
can a partial positive be attracted
to a partial negative.
So can a partial negative repel a partial negative.
These are all important things to understand.
Now, these types of structures that you see here,
the N with an H,
the O with an H,
are very, very,
very common things that we see
in biological molecules,
proteins, DNA, fats.
There's our base pair.
Here's some examples.
Again, don't memorize this.
But you see examples about how partial
positives can interact with partial negatives.
Look at the hydrogen on the water,
partially attracted to the oxygen
on the carbonyl group, okay?
Very, very important.
[rustling continue]
What did I do.... ?
I'm not sure what I did here.
[noises continue]
Well, it shut up.
I can work on it.
[rustling noises]
Oh, I see what happened!
It's going to tear my favorite tie.
I don't want to do that.
[rustling continues]
Okay, now we're back on.
There we go.
[class laughing]
You guys were hoping that everything doesn't work
so that we'd call the day off, right?
So, we're about at a point
where we should start understanding material.
So you're responsible from here forwards, okay?
Here is a laser pointer that doesn't work.
Well, I guess it wasn't even worth all the effort.
Hydrogen on water,
partially positively charged.
Oxygen on a carbonyl group,
partially negatively charged.
And yes, oxygen has a greater electronegativity
than carbon does.
They're attracted to each other.
There's a force that holds them together.
If we want to pull them apart,
we have to provide energy to pull them apart.
That's why we have to cook food.
That's why we have to do whatever
we do to break those types of bonds.
These types of bonds are everywhere,
we find in proteins,
carbonyl with water,
we find water with an amine.
Amino acids get their name
by virtue of the fact they have amines in them.
Quite a variety of structures
that we have that's there.
Now we want to talk about van der Waals interactions,
and the main thing I want to talk
about van der Waals interactions
is just related to this one figure, right here.
Van der Waals interactions tell us
that if you try to put
two nuclei too close together,
they will fight it like crazy.
There's an ideal distance.
You put them too close together
and the energy that it takes
to put them together goes
to the power of 12 as a function of distance.
You try decreasing that distance
beyond this point at the bottom of the curve,
and you see it ain't gonna go.
Atoms are just like relationships, right?
You guys ever had the relationship, you know,
where things are going really great?
And then, after a while,
van der Waals kicks in, folks,
because what happens?
"I gotta have my space.”
“I gotta have my space!"
You can say,
"Wow, van der Waals interactions apply to relationships,"
as you're crying your way home
to mother or something, right?
"I gotta have my space."
Atoms have to have their space.
If we try to put two atoms too close together,
somebody's going to go home crying to mother.
It ain't gonna go.
So it's very important to remember
that atoms have to have sufficient space.
That drives everything that they do.
Hydrogen bonds.
You have water,
the really bizarre properties
and the wonderful properties that water does.
We think of water and we just think,
"Oh, it's a liquid."
That liquid has zillions of hydrogen bonds
that allow it to be a liquid at room temperature.
Water has an atomic weight of 18.
It's liquid at room temperature.
Methane has a molecular weight of 16.
It doesn't have hydrogen bonds.
It's a gas until way below zero.
Carbon dioxide has a molecular weight of 44,
greater than that of water.
It's a gas at room temperature
because it doesn't have hydrogen bonds.
Hydrogen bonds are a glue.
[phone ringing]
Oh, please.
Not a good way to get started.
They're a glue that literally holds things together.
That's important, very, very important.
Hydrogen bonds give water the property
that's necessary for life on Earth.
How about other effects?
Well, other effects are very important, as well.
What I've been talking about are hydrophilic things,
thing that like water,
things that interact with water.
To interact with water,
things have to be either ionic
or have some partial charges to them.
Well, what about the things that
don't have much ionic character
and don't have much in the way of partial charges?
These guys are what we call hydrophobic.
Take oil.
Take water.
Shake 'em up!
Shake 'em up!
What happens when you shake up oil and water?
Student: They separate.
Kevin Ahern: It looks, at first,
like they sort of mix, right?
And you set it down on the table
and in a very short period of time, they separate.
Do you know why they separate?
They don't like each other,
but there's a more important reason.
Yes, sir?
Student: [inaudible]
Kevin Ahern: There's no hydrogen bonding,
but there's another, more important, reason.
Student: When they aggregate
into a larger single unit,
they have less surface area for more volume.
Kevin Ahern: Ooh,ooh!
I like this!
This is good, okay?
Exactly what he said.
When they separate,
they have less surface area
that's interacting between the two.
When I have little droplets,
I add up all those surface areas,
there's a hell of a lot more interaction
between the water and the droplet
than there is when they separate.
Then we only have that immediate
interface that's there.
And if you add up those surface interactions,
they're way greater when we have little droplets
than when the layers separate.
That's kind of cool.
These things all give rise to something
we'll spend a couple of lectures talking about,
and that's an absolutely phenomenal process
called protein folding.
Protein folding, as we shall see,
arises from a variety of chemical interactions.
They include hydrogen bonds.
They include ionic bonds.
No, you don't need to write that down
right now because we'll talk about them later.
They include hydrophobic interactions.
They include metals, in some cases.
They actually, even, in a few cases,
include covalent bonds, as well.
Now, that's important, excuse me,
because structure is essential for function.
You know that.
Somebody takes your bicycle wheel off,
you don't have the structure,
the bicycle isn't going to function.
It's important to recognize that structure
is necessary for function.
If we disturb the structure of a protein,
we disturb the function of a protein,
and, hey, that's what we talked
about when we're cooking bacteria
to destroy their protein structure
and destroy the protein function.
Things that disturb protein structure
interfere with the ability of the protein
to perform its natural function.
We'll talk a lot about that as we get
talking about proteins.
Now let's see where I am.
I've got about seven minutes left.
We can actually talk very briefly
about what I'll spend an entire period
talking next time,
and that's pH in solutions.
Now, one of the places where your chemistry
teachers didn't give you your money's worth
in chemistry was teaching you about pH in solutions.
So I'm going to spend some time getting,
hopefully, everybody up to speed
regarding pH and solutions.
pH “Oh, yeah, that's the measure
“of how strong an acid is,” right?
pH is a measure of the hydrogen ion concentration,
the measure of the hydrogen ion concentration.
pH, you probably remember,
is defined as the negative log
of the hydrogen ion concentration.
But in order for you to understand that,
you have to understand what it means.
What is the hydrogen ion concentration?
Concentration is measured in moles per liter.
And here's where 50% of you in the class,
to my surprise,
will not recognize the difference
between that and moles.
And I'm not saying it's your fault.
I'm not saying it's my fault.
But I'm saying,
somewhere along the line
you didn't get that hammered into your heads.
Concentration is moles per liter.
Remember that.
Moles is a quantity.
You could say, "Okay, I'll memorize this,"
but it has to be meaningful to you.
So the way I'm make it meaningful,
well, what's the difference between,
"I'm going 60 miles an hour,"
and "I go 60 miles"?
Big difference, right?
If I go 60 miles an hour for a while,
and then I go 40 miles an hour for a while,
and then I go 30 miles for an hour,
did I go 130 miles an hour?
Of course not.
If I know how many hours I traveled each one,
I can determine how far I went, right?
Isn't that just like concentration?
If I know how many liters
of a solution I have that's 1 mole per liter,
I know how many moles I've got,
because I can multiply pretty well, right?
If I know I have 6 moles,
and somebody put it into 113.4 liters,
I could calculate the concentration
by taking the moles divided by the liters.
Don't confuse those two.
You're gonna do it.
You're gonna do it!
If you're having problems with concentration,
I know many of you will,
come see me.
I'll be happy to talk you through it.
That's something your freshman chemistry
teacher should have pounded
into your head and didn't.
You should go back and pound
on your freshman chemistry teacher's head.
"Why did you give me that grade?!"
No, you won't go do that,
I know that.
Alright, pOH is the negative log
of the hydrogen ion concentration.
That means if I know the hydrogen ion concentration,
I take the negative log of it.
What is pOH?
It sounds kind of like "pissed off" or something,
doesn't it?
"I'm P-O-H today," right?
pOH is the negative log
of the hydroxide ion concentration.
It follows.
If pH is the negative log
of the hydrogen ion concentration,
pOH is the negative log
of the hydroxide ion concentration, okay?
Same thing.
Now, there's a relationship that pops up.
You learned this in freshman chemistry.
It's very useful.
And that is that the pOH
plus the pH of a solution always equals 14.
If the pH of a solution is 6,
its pOH is 8.
So a solution that has a pOH of 8
is equivalent to a solution that has a pH of 6.
They're the same thing.
Now, one of the things,
and this is where I'm going to finish today,
one of the things that your freshman
chemistry class didn't teach you
very well is that they taught you
reasonably well about strong acids.
I've got a 1-molar solution of HCl, okay?
If I have a 1-molar solution of HCl,
it means I've got 1 mole per liter of HCl,
and when I put HCl in solution,
it completely dissociates.
It comes apart.
It means I have 1 mole of hydrogen ions
and 1 mole of chloride ions.
And I have zero moles left of HCl,
because they've completely come apart.
It's a strong acid.
Strong acids, you're going to hear me
say this over and over until you get nauseous,
strong acids completely dissociate in water.
I put HCl in water,
I end up with completely H+ and completely Cl-.
Not all acids behave that way,
meaning that not all acids are strong acids.
Well, what happens if it doesn't
completely behave that way?
Well, here's a weak acid we'll talk
a lot about, acetic acid.
Look at that.
HAc goes to H+ and Ac-.
You say, "Well, look!
“It just did it!"
Not quite.
I put a million molecules of HCl in solution,
I get a million H+'s
and I get a million Cl-'s.
If I put a million HAc's into solution,
I'll be lucky to get a thousand H+'s
and a thousand Ac-'s,
which means I have 999,000 molecules
of HAc that didn't do anything.
It's a weak acid.
With weak acids,
we have mixtures,
of dissociated and undissociated,
the undissociated being the HAc,
the dissociated being the H+ and the Ac-.
Now, why do I tell you that?
Is it to give you something to,
"Oh, my god,
“I've got something else I've got to memorize."?
Most acids that are in our body
are weak acids, folks.
Most acids are very, very weak acids.
Amino acids are weak acids.
We'll see this.
Proteins are full of weak acids.
DNA is full of weak acids.
Your cells are loaded with weak acids.
We have to understand weak acids.
Strong acids are very easy to understand.
Weak acids we'll spend more time doing.