Biology 1A - Lecture 6: Metabolism: energetics


Uploaded by UCBerkeley on 07.09.2012

Transcript:
>>INSTRUCTOR: Okay. Good morning everybody. Good morning.
You guys are awake. The weekend is close. So hang in there.
So, for the next 2 lectures, we are going to discuss bioenergetics.
Now, there's a light chance with on Monday, when we are in lecture 7, I will already start
with lecture 8, because it's a very long lecture. Now lecture 8 is in the second reader that
I posted on bSpace, so please make sure that on Monday, you also bring the reader for lecture
8, etc. Yeah, because we might flow over this.
We might not. It depends on what questions you have.
Okay. Bioenergetics. So, if you think of life on this planet, essentially
all living organisms, require energy and the ultimate source for the energy is the sunlight
and so the sunlight, exerting energy to our planet in form of electromagnetic waves or
photons is captured by photosynthetic organisms, so photosynthetic organisms are plants and
photosynthetic bacteria and they capture this energy and they convert it to chemical energy
and so these organisms are called autotrophs. So autotrophs come from Greek and mean self
nourishing, because seemingly it seems that these organisms do not require any other chemical
energy but sunlight that. Is not completely true. As you mow when you have plants in the
garden they do require fertilizer so they do require other compounds too. But by and
large they capture energy from the sun and convert it into chemical energy, which is
organic product and as by products, they release CO2, which is essentially for life on this
planet and the organics plan plants are taken up by the heterotrophs. So heterotrophs is
the consumers so it's Greek for nourishment from others. So the heterotrophs feed on plant
material, for example, the autotrophs, and they get they're energy from taking these
organic product and breaking them down into CO2, and in into water. Essentially and then
these two CO2 and water they're captured again by the autotrophs to be fixed to make organic
molecules and out of water they make oxygen and so this will be the theme for I think
the next 5 lecturesハ 6 lectures will be all about this cycle here. So light energy
is converted, and chemical energy can then be used by organisms including the autotrophs,
to perform work. So, what we're going to discuss this metabolism,
metabolism is Greek for to change. And metabolism encompasses all chemical reactions
and transformations that happen in a cell. Metabolism is the sum of two distinct pathways
one is the synthesis of molecules and that is called: Anabolism.
Anabolism, where precursor molecules, such as sugars are the nucleotides are used to
make macromolecules. Where you make polysaccharides, lipids and sugars. Precursor molecules move
into macromolecules. Now for this anabolism to occur, energy is required, and the chemical
energy in our body, the currency that our body uses or organisms use is mainly ATP.
[Indiscernible] and we will get into the structure and the function a little bit later in this
lecture. So ATP delivers the energy, and this hydrolyzed to ADP using diphosphate + inorganic
phosphate so this is where the energy comes from for these molecules.
Now to get ATP, you need to degrade molecules. So degradation is also called catabolism.
And so in catabolism, energy containing nutrients such as carbohydrates, fats and proteins that
will we ingest with our food will be degraded to energy depleted molecules such as carbon
dioxide, water and ammonia. Ammonia comes from the proteins. So this catabolic
pathway, these pathways here they provide the energy for the cells in form of forming
ATP and then the ATP can be used to build up the organism through anabolism.
Now before we go into metabolism, a few words about thermodynamics.
Who of you had physical chemistry? Okay.
So that's quite a few. So you should know this already, because there
that's quite tricky to explain in about 10 minutes.
So, the reactions in the cell have to abide by the laws of thermodynamics. And there's
no way around it. Okay, they always have to abide by that. So
the first law of thermodynamics is the conservation of energy.
And that basically states that energy may change form or it may be transported, but
it cannot be created or destroyed. Yeah, so energy in our body can be transformed so we
can take chemical energy from a food molecule and make it into ATP, ATP powers our muscles,
so the chemical energy is transformed into mechanical energy but it cannot be destroyed.
And rule No.ハ2: Entropy so it stands for disorder.
In all natural processes the entropy of the universe increases.
And there's nothing you can do about it. So the entropyハ the disorder of the molecules
in theハ and the universe always increases. And so this was what I told my dad when he
visited by apartment, when my apartment looked like an mess, the entropy of the universe
here and my dad is an electroengineer so he said son donate some heat to the universe
and clean up this place and this is exactly how this works. So you don't have this slide,
sorry, you don't have this slide, but I just wanted to tell you a little about order and
disorder. So what is order? And what is disorder? So, order for example, would be a macromolecule.
The macromolecule is this disorder when it's its in single monomer, such as the amino acids
in this case, so this would be a case of disorder so this is what the universe tends to go to.
A chemical reactions, you have high-energy compounds such as glucose here and glucose
is degraded towards energy depleted compounds such as carbon dioxide and water so this would
be disorder and this is something that the universe tries to toss.
Diffusion is a disorder if you have molecules that are very tight in space they tend to
diffuse out. That's an increase in disorder.
That was my argument when my room was a mess, that's a diffusion of molecule. So that's
also disorder and if you have molecules that have a certain movement, so certain amount
of heat, they tend to speed up and they need to accept heat and that would also be disorder.
So all of these pathways, all one direction to increase disorder in the universe so how
it is then that we can increase order, which would be the opposite, right, where we take
amino acids, and we move them into polymers so this thermodynamics possible or not? And
of course it is possible even though it isハ it seems that it is against the second law
of thermodynamics. But actually it is not, because this reaction
is not alone on the planet. So if you create order, in an organism, or
if you create order in a molecule, all you have to do is create even more disorder in
your environment. And we do this usually by exuding heat, and
so heat will create disorder in the environment. Literally the universe and then we still by
abide by the law of thermodynamics even if we build things. And so back to your slides
so see here joy a nicely ordered tissue of a plant, this would be order.
And this order can only happen because you create more disorder in its environment and
that is the release of heat and you can also see this here with this bear that jumps through
the water, so it takes the energy and converts it to mechanical order but this seemingly
order of entropy can be compensated by the bear releasing heat and creating more disorder
in the universe and its environment. So hands, I didn't have an excuse anymore
I had to clean up my room. Oh well. So, the one variable that you need to know,
when we talk about metabolism, is the free energy, or gene. And thermodynamically ask
the energy that is released in a system. So there's a formula that's pretty much the
only formula that we use here is the delta G that's the free energy of the Gibb's free
energy. Equals the entropy, and that's the difference the entropy is the heat consent
of a reaction and when distinguishes between an exothermic reaction, where this delta H
is negative, around that means that heat is released from the reaction, or endothermic
where the delta H is positive and that means heat is taken up by the reactants. So free
energy is the delta H, the change in entropyハミハT. T is the absolute temperature of the system
in Calvin and delta S is the change in entropy so a change in disorder of a system. So this
delta G is very important because it can tell us something how a reaction proceeds.
So if the delta G is smaller than 0, then it is referred to as an exergonic reaction
and that means that the reaction will proceed forward and energy can be released. And can
be transformed into something else it cannot be destroyed remember. If the delta G is positive,
then this is an endergonic reaction, the energy is required for this reaction to occur in
this direction. So these are the two things you need to remember.
Delta G positive is needed for this reaction to occur.
So, if we have here an example, of reactants and product, and you look at the free energy
of the reactants they have a certain value for example this...
And if you look at the free energy of the product they have a certain value and in this
first case you see the product energy free energy is lower so therefore the delta G,
the difference between these two is smaller than 0, so the reaction will proceed, the
reaction is spontaneous and energy will be released. Here joy the opposite, here you
have an example of the endergonic reaction the reactants are low, free energy the product
have a high free energy and so the difference between the two the delta G is positive. Therefore
energy is required for this reaction to occur. Okay.
Good. So, first question today.
We're going to have two. So please get out your iClickers.
Okay. Which of the following statements is true
about the change of entropy, so delta H of a reaction that is spontaneous atハ25ハdegrees
centigrade and so here you the possible answers it is = to T delta S. It is negative and the
reaction is endergonic it must be equal to 0 or it can be either positive or negative.
So, that was also from an exam, although I think I wouldn't have asked that, but anyway,
it was from an exam, so I guess you're supposed to know that.
Okay. Go. Oh. Time is up sorry. Give you another 5 seconds.
Okay. Time is up. Okay.
So let's go through it. So obviously the equation that we need to look at is delta G = delta
Hハ ハT delta S. Right?
So, is it equalハ so whatハ the only thing that this statement actually says is so we're
looking at a change in entropy and the reaction should be spontaneous so that mean it is delta
G should be smaller than 0. Right.
So, is the delta H = to delta S, so if delta H is = to T delta S and then this difference
here would be 0. And it would not be smaller than 0, so this
is certainly wrong. Is it positive in the reaction is exergonic?
Yes, because it's negative. That is correct.
But is the delta Hハ does it have to be positive? Well that depends on if theハ ハT delta
S is hugely negative to make this into a negative value. So in this case, it can be, but it
doesn't have to be. So, this one is also wrong.
Is it negative and the reaction is endergonic it can be negative and then the term would
be more slightly negative but endergonic is not smaller than 0, so this one is wrong.
It must be = to 0 if delta H is 0, and then you only haveハ ハT delta S.
A then it depends on whatハ weather the delta S is positive or negative, the delta S ask
also be negative and if you haveハ ハsomething negative it is positive so that means that
the delta G is not smaller than 0 this one is also wrong it can be but doesn'tハhave
to be. It can be positive or negative and that is correct, because both of those depending
on what the T delta S term is, can happen, so reaction can be exothermic and endothermic
and in most case it might occur spontaneous it depends on the entropy term. Okay is this
clear? I think most of you got this right. Which is very impressive.
Because I got mostly got my thermodynamics questions always wrong when I was a student.
So, very good. My compliments.
You know thermodynamics. Good.
At least for what you need to know for this class here.
So, when we think about metabolism, and equilibrium, and then the delta G, the book came up with
this sort of model where you have two water containers and then here you have a turbine
and because there's a higher level than this, the water will power the turbine and then
you energy and that's the equivalence of the dealt G being negative, but if you have an
isolated system the water will drop and then lit be equal and then the delta G will be
0. And so this is one thing you should note. The delta G is not a constant; the delta G
will change depending on the reactants. Okay.
So, in this particular system the delta G is 0.
So that means we have reached an equilibrium, and there will be no energy that can be released
the light bulb is dark and therefore no work can be performed. Fortunately for us as we're
made out of cells the cells are not never at equilibrium, there's always something we
need to add, as indicated by the [Indiscernible] so we always need to take up food, that is
converted and there's always molecules that are with drawn from us.
So we excel carbon dioxide, we [Indiscernible] water, so we're an open system and this open
system is never at equilibrium and therefore energy can be generated and can be utilized
in the body. And so you can think of our body has this
multi-step open system because we don't have one reaction we have thousands of reactions
in the cell. So, one way to put this metabolism in equilibrium
in a framework, is to look at the concentrations of your reactants and the product of a reactant,
of a reaction, and the term that one can calculate from this is the equilibrium constant.
The equilibrium constant KEQ is the concentration of the product divided by the concentrations
of the reaction, reactants. So it's product divided by reactants.
So if we have a reaction here, where reactants are mostly converted to the product, and only
very little, very rarely converted to the reactants. And then the equilibrium is larger
than 1. So if you put certain concentration, let's
say 1 millimolar of reactant in a solution, and you have 0 product you will see the reactants
will be depleted the product will be made and eventually you reach this equilibrium.
And of course, in this equilibrium, because of the [Indiscernible] strength of this, if
the K equilibrium is larger than one, the reactant concentration will be much lower
than the product concentration, which will be up here somewhere.
Okay. So if we have the notion that the reactant
concentration or the reaction form is equal back a wards and forward and then the equilibrium
constant = 1, and when it = 1 and you put, again the same concentration of your reactant
in the solution, so 1 millimolar it will also deplete, it will come to an equilibrium, and
at the equilibrium, the concentration of the product and the reactant are equal so they're
both 0 and 5 millimolar. If in a reaction, reactant to product the reverse is more dominant,
so actually the formation of a reactant than the equilibrium constant is smaller than one.
And if you add now, a reactant to the solution it will still go down because you don't have
any product initially, the product concentration initially is 0.
So it will go down, but it willハ the equilibriumハ equilibrium will reside at a much higher level
than here. So you will have a much higher level of product of product, yes, than of
reactants. And so these equilibrium constants can tell
you what concentrations are you looking at? You should note that in all of these cases,
these reactions proceed because the delta G is negative but once the equilibrium is
reached the delta G is 0. Yeah, so again, the delta G can change dependent
on your concentrations of reactant and product. So that's not always given as a value.
So, now here weハ I'm going to discuss the same case. Right.
More product than reactant, both at the same concentrations, more reactant that product,
larger than one, or smaller than one, but we take the same equal molar, concentration
of reactant and product. So, what will happen, if I start then with
1 and I just monitor the reactant concentration, and the K equilibrium constant is larger than
1, that means that theハ because you have more of the reactant than the product it will
still go down. Because you will have at the end more product.
If in this case, you add the same equal molar amountハin product, the equilibrium constant
is 1, what will happen is nothing, the concentrateハ there should be a straight line it will be
a straight line, okay. Nothing will happen because you have it already at equilibrium.
And if you haveハ now, at the same concentration to a reaction where you get favoriteハ the
formation of the reactant to back to the reactant and then this will go up.
And so, what happens then if you think of the delta G initially here the delta G is
negative, and it will favor this reaction. Here, the delta G is 0.
And in this last case, the delta G is positive. And it will not favor the reaction that you
want, that is the product formation. And so, what you look at, of course again
once you have reached equilibrium, your dealt G is going to be 0, but initially it has these
values so what the chemists and the thermodynamic people do, what the book doesn't do is that
the delta G can fluctuate, depending on the concentration, but what people use in when
they describe reactions is the delta G 0. And the delta G 0, is a constant.
And the delta G 0 is the constant of the delta G when you have equal molar amount of concentrations
of your product and your substrates. So when you see in the book and we will do this also
inハ during the remainder of the lecture there is a delta G for reaction ofハ ハ30,
or a delta G of + 5. And then that doesn't mean that this is the
delta G that willハ that is there for the entire reaction time. It only means is the
delta G 0 assuming that your reactants and your product have a concentration of 1.
Okay and so this value is constant. For a particular reaction.
And that's what we will actually mainly discuss. Excuse me.
So, in cellular work, we discuss that energy is required.
And the energy has to come somewhere. And some of the reactions that are performed in
our bodies are endergonic so they actually do require energy. And so fortunately what
happens is these endergonic reaction that require energy and the exergonic reaction
that release energy they can be coupled to overcome the endergonic reactions.
So as you know energy is required for chemical work that means making macromolecules for
example for transport work, we have the sodium potassium pump to pump ions in and out of
the cell and also mechanical work if you think of muscle movement and so here's an example
of how you can couple the endergonic and the exergonic reactions so here we have glucose
1 phosphate that's converted to glucose 6 phosphate and glucose 6 phosphate and that's
converted to fructose 6 phosphate. So this reaction has a delta G 0 value, of 1.7 kilojoule
per mol. So that means this reaction here is endergonic and it would not happen spontaneously.
However if you couple it to another reaction the proceeding reaction in this case, the
glucose 1 phosphate converted to glucose 6 phosphate the delta G 0 for this reaction
isハ ハ7.3 so it's negative. Negative means it's exergonic it will be spontaneous and
if you couple these two reaction it is total form glucose phosphate 1 phosphate, fructose
2 phosphate it's the sum of this, and the sum of this isハ ハ5.6 kilojoule per mol.
So overall the reaction will actually be spontaneous because it's exergonic and you to add up the
constants here. So this is a way of how you can overcome and
endergonic reaction, you to put in an exergonic reaction that gives more energy than your
reaction here and then the reaction would occur spontaneously.
So, if you think again of this water system that they're present in the book, here's the
first reaction that is highly exergonic so there's a huge drop in water, so you can produce
a lot of energy the delta G is negative, but then there's this reaction here which is positive
which would mean that theハ that actually the water would move uphill, which of course
it doesn't. And then here is a third reaction, in this example that the energy is negative
again because it moves downhill and so this reaction wouldn't occur because the delta
G is positive, but if you connect these two, the delta G from this one is steeper than
the increase over here so the total delta G for these two reactions combined is negative.
And you see the water level hereハ here is lower than the water level here so it would
actually occur. And then lit continue through out here. So if you think of this model, essentially
what will happen is the tank will fill up until it's higher than average No.ハ3, and
then the reaction would occur. Okay.
Any questions to this topic? It's quite complicated so I would encourage
you to read the appropriate chapters and you don't need toハ
>>STUDENT: [Indiscernible] >>INSTRUCTOR: The difference between delta
G? >>STUDENT: [Indiscernible]
>>INSTRUCTOR: Oh, delta G 0, is constant, that is the free energy that occurs when you
have the reactant and the product at one molar concentration.
So the delta G 0 never changes, so when you have over here, in these reactions, you the
delta G 0 of 1.7 and the delta G 0 of this reaction isハ ハ7.3, these are constants
they will not change. But if you take this for example just this
system, glucose 1 phosphate and glucose 6 phosphate you have 1 mol of each because it's
negative it will increase the reactant concentration will decrease and there will be at equilibrium
and then your delta G 0. But this is the constant so we use always delta G 0 because that's
the constant that tells you something about the reaction it doesn't tell you what the
delta G currently in the reaction is. That can change. Depending on the concentrations.
Is this clear? Good.
>>STUDENT: [Indiscernible] >>INSTRUCTOR: Yes?
>>STUDENT: So what you're basically saying when you a [Indiscernible] of I = 1 [Indiscernible].
>>INSTRUCTOR: Um, so there was a question about how do theハ this one or the one before.
>>STUDENT: The one before. >>INSTRUCTOR: The bun before.
So, how is it all of these proceed, all of these reactions proceed?
>>STUDENT: [Indiscernible] >>INSTRUCTOR: So in all cases delta G is less
than 0 because in all cases your product concentration is 0.
So even if you have an equilibrium that favors your reactants you will produce in equilibrium
first product. But the level of product it's much higher
than here. But in both cases there they will proceed,
and in both cases the delta G is initially 0. Smaller than 1, smaller than 0, so it's
negative, initially it's negative and then it will become 0.
In all of these reactions. Yes, please?
>>STUDENT: [Indiscernible] >>INSTRUCTOR: So the question was if one considers
the couplings of reactions, endergonic and exergonic reactions do they have to occur
at the same time or do they have to be close in space?
Um, that's a good question, so I'm thinking ofハ so it can be. Okay. So for example in
the example that I showed here, with the glucose 1 phosphate, we acting to fructose 6 phosphate
they occur because they come next to each other that's a continuous reaction they will
occur close in space. Yeah.
But it doesn't have to be, what also can happen is that the energy that is released can be
captured by a molecule, for example, ATP and we're go going to get to that and then the
ATP can move and then at another position in a cell or even in another organelle they
can do the work so they do not have to occur at the same time and they do not have to be
especially very close. But they can and most of the time they do. But you have molecules
that can capture energy and donate that energy at a different place at a different time.
Okay. So that was with a good segue into the next
topic, for the structure and hydrolysis of the structure.
So here you have the structure of ATP. ATP consists of the [Indiscernible] adenine,
that's a ribose in this case and the 3 phosphate groups they're labeled from the outside to
the inside gamma, beta and alpha, and if you look at the bonds of the phosphate groups
you will notice that this one here, is anハester bond, because you have an alcohol from the
sugar. And theハ an acid group from the phosphate but these two bonds here, between the beta
and the gamma, they're in hydrolyze bond, and so these hydrolyze bonds, so the phosphate
it starts with the gamma phosphate when it's cleaved off, add seen phosphate ATP is converted
to ADP so one phosphate is hydrolyzed. And then energy is released and so that energy
is approximatelyハ ハ30 kilojoule [Indiscernible]. In the book they mention this number as kilocalories
but I'm a metric guy so I'm going to use kilojoules and that's the only number you need to know
for the exam. The energy that is released when it's hydrolyzed.
And so ATP is used by the cell in copious amount as the currency. To transfer energy
from one part of metabolism into another part of metabolism.
It's like when we use money so the cell uses ATP.
It pays for it by using this molecule. We have seen ATP before. Where have we seen
ATP before? Anybody?
>>STUDENT: [Indiscernible] >>INSTRUCTOR: Say it again, please?
>>STUDENT: [Indiscernible] >>INSTRUCTOR: Active transport, yes. That's
correct we have seen it in activity transport, but there already it was used as an energy
molecule. Yeah.
Yes, please? >>STUDENT: [Indiscernible]
>>INSTRUCTOR: RNA. Perfect. Yes. So we also have seen ATP as a nucleotide in
RNA synthesis. Yeah, it contains a ribose, so it goes into RNA not DNA and there also
this will be used as a nucleotide to make the A base in an RNA molecule.
So, we can utilize ATP and ATP hydrolysis to couple it to reactions that the are endergonic
that require energy. For example here you have glue tonic acid, glue tonic acid accepts
ammonia to form the acid glutenin, this reaction is positive so the delta G 0 is + 14ハkilojoules
per mol. So, what it can do is take the glutamic acid,
ATP is hydrolyzed to ADP and then the phosphate group is replaced by the ammonia that leads
to glutamine so that's exactly what we have here, + ATP + ADP + phosphate so in that reaction
ADP is hydrolyzed and the ammonia is transferred so we have the ammonia forming glutenin that
have the delta G of up here + 14ハkilojoules per mol, and we have the ATP hydrolysis, which
has a delta G ofハ ハ30, kilojoules per mol and therefore the net delta G, 0, isハ
ハ16ハkilojoules per mol. And so therefore, this reaction will proceed.
Because it's negative now. Yeah, so with the coupling of ATP hydrolysis,
you can make an endergonic reaction, exergonic and therefore the reaction will proceed. And
again it's additive, just like the case that we discussed before, you just have to add
the two numbers and then you'll be able to calculate whether the reaction will proceed
or not. So there goes the use of ATP for chemical
reactions. ATP hydrolysis can also be coupled to transporters, as we mentioned earlier,
the sodium potassium pump where ATP is hydrolyzed the pump is for phosphorylated changing its
confirmation and the solute can be transported against its concentration gradient.
Again and ATP is hydrolyzed to ADP to phosphate in the end. So phosphorylation can lead to
phosphorylation of transport proteins but the hydrolysis of ATP can provide the energy
for active transport. Right. Moving of molecules against a concentration gradient.
And we had also when we discussed the cellular structures we had the mechanical for, example
the motor proteins that move a vesicle along a microtubule and also those transport reactions
require ATP to be hydrolyzed to ATP and phosphate they change the confirmation of the motor
protein so the motor protein can move along the microtubules. So that again is an example
of ATP is utilized by the cell to perform work.
In addition to the chemical reactions that we just discussed.
So, coming back to the very beginning of the lecture if you think about how energy works
in the system, we have ATP, can be hydrolyzed to ADP and phosphate that releases energy
of aboutハ ハ30ハkilojoules per mol. And that energy can be used for cellular work.
So it can drive endergonic reactions. But, ATP also needs to be formed.
And that's what I refer to as earlier as catabolism where energy which molecules are converted
to energy depleted molecules and the energy out of this conversion is captured by the
formation of ATP. So, again, the delta G of the reverse reaction
ADP + phosphate to ATP is now + 30ハkilojoules per mol and that endergonic reaction can only
occur because energy is released from other reactions from catabolism so these would be
exergonic reactions. And this pathway will be the talkハ I will
talk about the next 5 lectures after we're done with the enzymes.
Yeah. So, again if you think of the dealt G 0, in
both cases, it's the opposite, if you want to go the opposite direction.
But the value is the same. So, last questions for today.
Also an exam question from an exam question. For the following reaction, [Indiscernible]
phosphate, to acetate and phosphate the delta G 0 isハ ハ36ハkilojoules per mol so what
will be the delta G 0 for the following phosphate transfer? Phosphate + ADP and phosphate ATP.
Here are some of the answer and you go now. Okay. 15 more seconds.
Okay. Few more seconds.
Okay. And then I stop.
And all right. 95% got it right. Very good.
So how does it work? Acetate phosphate to acetate phosphate this
reaction isハ ハ36. The ADP formation + phosphate to ATP because
it's not ATP hydrolysis but formation is + 30,ハ ハ36 + 30 isハ ハ6 and therefore
the reaction is exergonic and it will occur, but most of you got that right. Very good.
And I think with that we finish so we'll finish 5 minutes early so enjoy your weekend.