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Lecture 10: Metabolism, Energy and Enzymes
Hi everyone.
0 minutes 2 seconds
Welcome to your online lecture for today where I'm going to encourage you to pull your hair back and roll your sleeves up because we're going to be talking about metabolism, which involves energy and enzymes because this is the basis for how we understand how our cells and our bodies continue to propagate our energy budget and what we use that energy on.
0 minutes 24 seconds
Now, chemistry is going to creep back up on you here as our proteins.
0 minutes 30 seconds
In the context of chemistry, we're going to be thinking about the movement of electrons, how making and breaking bonds and moving electrons around drives work processes in our cells.
0 minutes 44 seconds
So be prepared to revisit some chemistry that you may have struggled with a little bit the first time you learn it, namely redox reactions.
0 minutes 54 seconds
We have to talk about those in biological systems because that's how we move electrons around in order to make and break new bonds, to make and break new molecules, different molecules, which is basically the process of metabolism.
1 minute 8 seconds
And we're going to see in the next couple of lectures how that metabolism is applied for our replenishment of our energy budget, particularly that in plants and in animals.
Hi everyone.
0 minutes 2 seconds
Welcome to your online lecture for today where I'm going to encourage you to pull your hair back and roll your sleeves up because we're going to be talking about metabolism, which involves energy and enzymes because this is the basis for how we understand how our cells and our bodies continue to propagate our energy budget and what we use that energy on.
0 minutes 24 seconds
Now, chemistry is going to creep back up on you here as our proteins.
0 minutes 30 seconds
In the context of chemistry, we're going to be thinking about the movement of electrons, how making and breaking bonds and moving electrons around drives work processes in our cells.
0 minutes 44 seconds
So be prepared to revisit some chemistry that you may have struggled with a little bit the first time you learn it, namely redox reactions.
0 minutes 54 seconds
We have to talk about those in biological systems because that's how we move electrons around in order to make and break new bonds, to make and break new molecules, different molecules, which is basically the process of metabolism.
1 minute 8 seconds
And we're going to see in the next couple of lectures how that metabolism is applied for our replenishment of our energy budget, particularly that in plants and in animals.
1 minute 21 seconds
So metabolism has to be studied because staying alive takes a lot of work.
1 minute 26 seconds
If the Bee Gees popped into your head right now like they do into mine, you are an old soul.
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So cells are dynamic, they're constantly changing, and they have requirements in order to stay alive because living takes work, It takes energy.
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Moving around, finding a food source, communicating, making things, breaking things, recycling, dividing, all of these activities of a cell take energy.
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So imagine that compounded to the trillionth times for the number of cells that you have in your body if you're a multicellular Organism.
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And so life is based on chemical reactions.
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Remember what I told you the very first day?
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You can't escape chemistry, math and physics if you want to study biology.
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And this is where those things fundamentally meet each other.
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Chemical reactions are necessary to make the things that we need to survive.
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They're also necessary to store the energy that drives processes that other would otherwise would use energy.
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And that is physics, right?
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Being able to move and do work and create force is physics.
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And then that all happens within certain parameters in a certain amount of time and likelihood.
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And often we apply mathematics to that.
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Luckily, I'm not going to ask you to do very much math and thinking about metabolism, maybe just a smidge.
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And so the sum of all of our chemical reactions in our cells is our metabolism.
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We often use that word in our own lay context, and we think about how much fat we may have or how we burn calories or how quickly we burn off energy.
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That's generally what we think about with metabolism.
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Oh, I have a slow metabolism.
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I have a fast metabolism, but we're talking about cells.
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We're not just talking about fat metabolism or burning calories.
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Metabolism is the sum of all the chemical reactions, not only breaking bonds to break things down, but also how we rearrange those to build other things.
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And so we're going to see that making and breaking chemicals is, is what comprises metabolism.
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And in any complex biological system like you, that's going to involve a series of steps, you know, between intermediate metabolites.
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And those steps are generally catalyzed by different enzymes that are encoded by our genomes and expressed by our ribosomes to make proteins that we use to stay alive and continue doing biochemical processes.
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And many times these stepwise processes to go from a precursor molecule to some product that we want to make often require multiple different steps with multiple different enzymes.
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And we're going to see some examples of that coming up in a couple of lectures.
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But this just sort of shows you how you might start with a metabolite like a maybe a primary metabolite like a carbohydrate or a nucleic acid or an amino acid, and how some enzymatic activities sort of stepwise one at a time can convert that molecule into something else that you might need for survival.
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And you'll probably spend some time, particularly if you take biochemistry, studying some metabolic pathways and understanding how enzymes Dr.
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those forward.
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If you study genetics, you might study what happens if one of these enzymes is missing in the pathway.
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What happens if a gene is mutated and you don't produce one of these enzymes?
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What happens to the pathway?
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Does it cease altogether?
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Does something else take over?
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So genetics and biochemistry are very much at play together when we think about metabolic pathways.
So we're gonna throw it back to old school chemistry and think about the energy that is involved in chemical reactions.
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This is the business of what's happening in a cell, largely just reactions between chemicals and and seeing what kind of product results from those reactions.
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And So what we really care about in many of the molecules that we metabolize is what kind of energy is available to be released out of them or can be stored in them.
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And so we have to remind ourselves what the different types of energy are.
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So kinetic energy sounds like kinesis or kinesiology.
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Kinesiology, which a lot of people study, is the energy of movement.
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And so kinetic energy is the energy of motion, what is given off as things move around.
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And so even now I'm giving off kinetic energy in the form of movement and in the form of sound.
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The light next to me is giving off energy in the form of thermal energy as it gives off heat.
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And so these things you're pretty familiar with, right?
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Electricity is moving.
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Energy was electrons moving, as well as electromagnetic radiation.
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Now those sound like fancy words, but electromagnetic radiation is simply the light spectrums that we see and the ones that we don't.
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Things like microwaves and X-rays and visible light spectrum and UV and infrared lights, which we'll talk about a little bit later in the semester.
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The other type of energy is potential energy.
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So this is the energy that is stored that has the potential to do work.
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It's not doing any work yet.
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In fact, movement is work.
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It's giving off energy.
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You're utilizing it in some way, but potential energy means it's stored.
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And so it's the energy that's stored in something in the way that a chemical is positioned or an object is positioned or configured.
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And then what sort of motivates it can be various different things.
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Motivate that energy to be released can be various different things.
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Gravitational energy, pulling something down so it may fall from a high position to a low position, and potential energy can drive these different types of energy as well.
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Electrical energy, chemical energy.
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Think about when the light switches off versus when the light switches on, right?
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Think about what's stored in chemical bonds.
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Think about consuming an apple that has sugar in it.
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There is energy stored in the sugar molecules in an apple, and you derive those out of their bonds, the bonds of the sugar molecules, in order to get energy for yourself.
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And so there's potential energy in many, many things, and it doesn't change into a different type of energy until it's utilized or it starts moving around.
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And so what's available in something is the amount of energy that's available to do work.
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And when things start to move or when chemical reactions happen, energy often gets moved around into different states.
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And so in a minute, we'll talk about the first law of thermodynamics.
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And the energy that's available to be moved around, converted into a different type and used to drive work is the amount of free energy that's available in any reaction or any system.
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And so free energy is what we're interested in because we're going to see that some chemical reactions in cells need an input of energy.
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You have to buy the ability to do work and you need an investment of energy from somewhere.
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And other molecules have free energy stored in them so they can drive those reactions for us.
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OK.
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So here we see some examples of potential energy, kinetic movement energy and giving off energy in the form of mechanical heat and sound energy.
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And living systems do all of those things.
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And so at the molecular level, when we think about energy, what we're actually really thinking about is the energy that's stored in chemical bonds.
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And we know what chemical bonds are made of.
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They're made of electrons.
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Every single chemical bond has two electrons in it.
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So in reality, when we're thinking about stored energy in an in a molecule, all we really care about is the electrons in the bonds.
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The atoms themselves can't be split to give energy, but we can break the bonds and use the electrons to drive work for us because they will do that.
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And so electrons are the most important source in biology of chemical potential energy.
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And these electrons have the ability to do work because of the way they move around, how some atoms and molecules like them very much and how we can get them to interact with positive charges and other negative charges, OK.
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And so when we think about electrons, we have to think about the fact that they are actually excitable.
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Electrons can exist in different energy states.
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And the closer they are to the nucleus, the lower the energy state of the electron, the less sort of wild and out it can do because it's so attracted to the nucleus, so the the the protons of the nucleus.
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But you can excite electrons and actually have them jump out to higher energy states.
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Plants do this, as we're going to see later, by harnessing solar energy using pigment molecules.
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They excite electrons to do work.
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Electrons will move around and excite molecules to actually do work.
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And so when they jump up to a higher energy level, they can be used to drive work.
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Or if they're left alone, they tend to settle back down into a lower energy level where they're moving around a little less or they give up energy in the form of heat.
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But we're gonna see that electrons are sort of the most important source of chemical energy that we're going to focus on in biology.
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And so really thinking about the history of the study of, of bond making and how energy is conserved and passed around and transformed is means that you have to sort of think about the laws of thermodynamics is understanding what you can and can't do with energy, what's even possible.
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And so energy is generally conserved in a system.
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It flows through our system.
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The source is sunlight, but it can be moved around and transformed into different types.
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What you can't do to energy, though, is make it or destroy it, and so you've probably recited the first law of thermodynamics at some point in your high school or college career.
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Energy cannot be created or destroyed, it can only be transferred or transformed.
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So you can't make or break it, but you can move it around and you can convert it into a different type.
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For example, even now as I'm speaking and releasing sound energy, I'm converting what chemical energy I've stored probably from my lunch or my dinner, metabolizing that to give the do the work and give the power of vocalizing, releasing energy in the form of heat movement sound.
And so we kind of credit this initial thinking to a couple of gentlemen.
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The 1st is Nicholas Carnot.
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Carnot was a very young 30 something French military engineer and physicist and kind of a pyromaniac.
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He really liked studying fire and combustion and steam engines, understanding how it is that that steam could drive work in trains.
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How does you could combust something, create steam, and it had enough energy to produce actual work?
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He's generally referred to now as the father of thermodynamics, but was largely ignored in his time, unfortunately.
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Rudolf Clausius.
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He was a scientist who basically crafted the first law of thermodynamics partially based on what Nicholas Carnot had studied.
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He sort of eloquently put together these two tenets that energy cannot be created or destroyed, it can only be transferred or transformed through a system.
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And then Clausius together with William Thompson, otherwise known as Lord Kelvin, who's honorific, you would probably recognize the two of them together derived the second law of thermodynamics, which specifically focuses on the concept of entropy.
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And that they, they took information from Carnot's work and figured out that in any given system, if you transfer energy around entropy or the degree of disorder is going to increase.
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And there are two main types of reactions that we can study to measure the amount of potential energy of a molecule as as an output or input of heat.
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OK.
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And so this is actually looking at thermal energy.
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And so the first type of reaction is exothermic.
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Exo remembers prefix meaning out or to exit, and therm is going to be thermal energy.
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So exothermic reactions are reactions that are going to give off heat energy, whereas the opposite of that are endothermic reactions where heat is taken up from a system.
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Now, when we think about an exothermic reaction, I think those are pretty obvious.
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We recognize that we've interacted with lots of exothermic reactions.
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It wasn't really until I got into grad school that I recognized exactly how an endothermic reaction belt, you know, when we heat something, you know, a solution and a beaker and it mixes and it gives off heat, you're like, OK, cool, exothermic.
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When you mix up a buffer and you notice that it's, even though the room temperature is normal and there's no ice present, it's starting to get cold.
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That the buffer mixing is actually getting cold.
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It's taking in the heat from the room.
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And that's why it's actually endothermic.
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It's, it feels cold because it's absorbing the heat from the environment.
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And so I finally felt with that feels like when you're making a chemical that's actually endothermic.
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And so in an exothermic reaction, the products have given off their heat And so or sorry the the the reactants have given off their heat and what results from that has less potential energy because it was given off to the system in the form of heat.
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Whereas an endothermic reaction, when the reactants interact with each other, the products that are made are actually absorbing heat energy.
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So there is going to be more energy stored in the products of that particular reaction.
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An example of an exothermic reaction is shown here in this image.
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This is a picture of a Bombardier beetle.
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These guys have this special chamber in their abdomen where they can release when startled, hydrogen peroxide molecules.
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So H2O2 is hydrogen peroxide and there are enzymes along the ducts in their abdomen that have the enzyme or the that that are full of the ducts are full of catalase, which is the enzyme that metabolizes hydrogen peroxide.
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And it does.
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It so quickly, metabolizes hydrogen peroxide so quickly into water and oxygen gas that it ends up vaporizing some of the water and causing it to end up converting into steam.
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There's also a series of really stinky molecules that mix in with the solution as well.
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So the Bombardier beetle, if it is attacked, will activate the series of reactions and end up releasing scalding hot steaming water from its abdomen and some really smelly, funky chemicals that taste and smell disgusting if an animal attacks the Bombardier beetle.
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And so I've actually got a a clever video showing what can actually happen to an Organism that attacks one of these.
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You can even hear the popping sound.
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See how some of it just evaporated right away because it's basically formed steam?
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I don't know how much I believe that the toad and the beetle were both fully unharmed.
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It seemed like the beetle was covered in digestive gunk, and he clearly burned the frog's mouth and probably tasted pretty nasty.
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But, you know, you get the general idea of how even a tiny reaction can produce enough heat that it could vaporize water to make boiling water come out of an Organism.
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It protects the beetle, but it sure is painful for whatever eats the beetle.
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And we also have to remember that enthalpy also relates to entropy.
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Entropy is a measure of disorder in any system.
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When you think about molecules in a, you know, in a system sort of bouncing off of each other and moving, we think about the order of of chaos or disorder.
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As you put all those molecules together into something that's larger and cohesive, you've decreased the amount of chaos because they've formed a more organized structure than they initially were.
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And so when products in a chemical reaction are less ordered than the reactants, in other words, if you take something and you break it down, entropy is going to increase.
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One of the ways I like to think about this.
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You may be a mega nerd and have seen some of the Lego, the Lego shows, Lego Masters.
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They have these fun competitions where people build things out of Legos.
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And one of the first episodes I saw, the people on the show built these massive, massive Lego contraptions and then went up on a balcony and dropped them and they shattered and they filmed it in slow motion how everything shattered 'cause it's kind of that's what kids like to do, right?
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Build something and then break it apart.
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If you take something that's built and ordered and you shatter it all, you release the energy from it and all the parts and you increase the chaos, you increase the entropy.
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And so that's what the second law of thermodynamics pertains to, is that total entropy is always increasing in any given isolated system because energy gets moved around.
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And so that's what the second law of thermodynamics pertains to, is that total entropy is always increasing in any given isolated system because energy gets moved around.
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Now what we care about for chemical reactions that are in very small spaces where we're not particularly interested in the the, the release of heat to do work, we're gonna focus a lot on Gibbs free energy.
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So the amount of energy in a reaction that's available to do work.
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And so when we're thinking about, you know, inside of our cells, we're gonna think about reactions and moving around the bonds to create products that are different from the reactants.
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And some of the reactions we do are gonna need some additional input of energy in order to work.
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And so we have to think about what's available in any molecule in the form of free energy that's available to do work in a system.
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And so the change in free energy, which is recognized represented by delta G, is actually a function of the amount of energy available in the molecule and how that changed minus the temperature of the system and the degree of entropy.
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OK.
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And so at temperature and entropy are going to affect a chemical reaction.
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Now, I'm not going to ask you to do that kind of math and think about that again after this point.
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But I will ask you to think about the amount of free energy change in a molecule, because either a chemical reaction is going to give off that free energy where another chemical reaction can use it, or going to require an input of free energy in order to happen at all.
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And so that's why we think about free energy.
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So we're not gonna think too much about change in enthalpy because that's generally a measure of chemical potential energy.
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And that's where we think about exo and endothermic here.
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We're gonna think about exergonic and endergonic reactions.
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OK, Instead of giving off heat, we're gonna think about giving off energy.
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How we could use that to harness to another chemical reaction.
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We don't want to intentionally heat up all of our cells while we're doing chemical reactions, right?
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We wanna take a little bit of energy and we wanna transfer it to another reaction.
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And so we think about exergonic reactions and endergonic reactions when we're thinking about the change in free energy.
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And so exergonic reactions, as we're gonna see, are going to give off energy that is usable to do work.
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And they tend to be spontaneous.
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They don't need something to drive them to go.
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And so when we think about the delta G for a spontaneous reaction, we're gonna see that it's less than 0.
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It's negative, OK.
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It's like giving off energy to something else.
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And so it's like debiting some energy from a reaction to go drive another one to give it off.
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Whereas an endergonic reaction requires an input of energy to actually happen.
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That's not spontaneous.
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You gotta get that energy from somewhere.
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It doesn't just happen.
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And so the delta G in that case is gonna be greater than 0.
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Like you're buying the ability to have some energy and not having it given back to you then.
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So it requires an investment of energy, and that's going to be a positive number, OK.
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Like you're buying the reaction anytime delta G is equal to 0, Nothing's changing and your reaction is an equilibrium.
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Those are some concepts you're gonna have to know, especially what Gibbs free energy is, and you're gonna need to understand exergonic and hendorganic reactions.
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Remember, EXER suggests that energy is leaving it.
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Ender means inside, which means you energy's being invested in it.
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The reason we care about these is because we've got some molecules that we can use in our cells as energetic currency that store energy in them we can use to drive processes that are normal biochemical reactions that keep us alive.
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And anytime you're thinking about chemical reactions, what you're really talking about is a couple of reactants who rearrange their bonds with each other to make new products.
OK, So some bonds have to break, while other bonds have to form in order to make new products.
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And so we try not to just rely on these reactions to randomly happen in our cells.
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We try to encourage them to happen at a rate by which we need the products that are being produced from these things.
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Now, if you have a really high concentration of reactants and they're in a closed system like a cell, eventually they're going to interact with each other and you're gonna get more collisions and they're gonna reform certain types of bonds quickly.
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But that's not always the case.
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Sometimes you have to encourage chemicals to interact with each other and provide the energy for them to be able to do it.
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And So what we do in our cells is something called energetic coupling.
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We take a reaction that can give off energy and exergonic reaction, and we harness that to another reaction that needs the energy that was given off in order to go forward.
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And so exergonic reactions generally give off enough energy to help drive the endergonic reactions that we need to do.
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So it's a fair trade off.
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It's kind of like using one reaction to buy the other one to occur.
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OK?
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And we're gonna see that ATP is the molecule that we use to provide the excess energy to drive reactions that need them.
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OK, Now we're gonna have to stop for just a second and think about a concept that I'm sure was a struggle for people when they first learned chemistry.
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We're gonna focus on redox reactions, OK?
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And so I'll step you, walk you through every single step of a redox reaction and how to understand each little bit just in case.
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It actually was kind of intimidating the first time you learn these.
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But in reality, all we're doing is moving electrons around and getting them to do work.
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And so that's what we mean by reduction oxidation reactions.
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So don't be afraid, I'll walk you through it.
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So we got a couple of different varieties of metabolic pathways that we focus on in biology, and energy is exchanged in both types, OK.
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And so in metabolism, we often talk about different types of chemical reactions, namely catabolic and anabolic reactions.
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Now, sometimes it's confusing for people to remember which one is which.
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Generally, people struggle less with remembering what anabolic reactions are because you automatically sort of think of things like anabolic steroids.
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You know that if a person takes anabolic steroids, they get real big, right?
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So anabolic pathways build things.
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So catabolic must be the opposite metabolism which is breaking things down.
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OK, so catabolic pathways involve the breakdown of molecules and often producing ATP from those reactions.
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So imagine you have a product like a like a sugar molecule and you break it down into its individual bits.
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You have released the energy by breaking it apart, and you've gone from a more ordered system to a less ordered system.
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So you've released the energy from the system and you have increased entropy.
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So chaos is a little higher in anabolic pathways, you get the opposite.
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This is where you synthesize large things from smaller components.
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Now a catabolic reaction is spontaneous, it's exothermic.
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It's given off the energy as you break the things.
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This the parts apart.
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If I gave you a bunch of blocks and asked you to build something together, it would require an investment of time and energy.
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You actually have to work to put the things together, and so anabolic pathways require an investment of energy.
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They're endergonic.
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When you build something larger than the sum of the parts, you have done work to do that and you have decreased entropy.
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It's more ordered as this big structure on the right than it was all the little individual structures on the left, OK?
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So it's important to be comfortable with the difference between pathways that break things down and pathways that build things up, OK, And how the energy is involved in that and entropy, how it relates to those systems.
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And so sometimes it helps to think of activities that are familiar to us.
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Many people probably have gas appliances in their house.
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You might go to put the tea kettle on the stove, and you recognize that, you know, your stove produces or releases natural gas, and you're doing a reaction by combusting that natural gas.
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And in so doing, you're transferring the stored energy in the methane into heat that's transferred to your water to heat your tea kettle.
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So in any chemical reaction, you have reactants that are in the the front of the arrow where they're going to actually react with each other and sometimes rearrange.
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And at the end of a chemical reaction, you're gonna have the products, whatever is produced from that.
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And then then the products would, which is why things like gases are so valuable because they're combustible and they have a lot of electrons hiding in those hydrogen atoms that we can release for the purposes of creating, doing work and creating new products.
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And so keep in mind that's any chemical reaction.
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You're not going to be doing any balancing of equations or anything, but you are going to have to recognize what happens when atoms move around between reactants and end up in different places with the products they make new molecules.
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That's the nature of a redox reaction, OK, is moving electrons around to form new bonds that didn't exist in the reactants.
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And so when we use the short summary, the short word redox, what we're really thinking about if we expand that out is reduction oxidation reactions, OK?
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And you have to think about the the chemicals that are involved in this.
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And what you're really going to do is try to track where the electrons go in any given reaction.
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And they tend to be hidden in a hydrogen atom, OK?
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So remember that a hydrogen atom is 1 electron and one proton.
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And if you pay attention in any chemical reaction to where the HS go, this is where the electrons are hiding.
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This is generally where the energy is going to be stored in any chemical reaction that we use in a biological system.
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And so when you see these terms reduction in oxidation, sometimes it's confusing to remember, like I don't know what's being reduced or what's being oxidized.
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But when we use the term reduced, what we're talking about is reduced in charge.
33 minutes 7 seconds
If you give an element or an atom an electron, you have made it more negative than it was before you gave it the electron.
33 minutes 17 seconds
You have decreased its charge.
33 minutes 19 seconds
If you give it two electrons, its charge is even more negative now.
33 minutes 22 seconds
That's what you have reduced.
33 minutes 24 seconds
You have reduced its charge by giving it additional electrons.
33 minutes 28 seconds
The opposite of that is oxidation.
33 minutes 30 seconds
When you steal an electron from a molecule or an atom, it's now more positive than it was and so it's charge goes up, OK.
33 minutes 40 seconds
And so that's what we refer to as oxidation.
33 minutes 43 seconds
So reducing agents are going to donate electrons to oxidizing agent.
33 minutes 49 seconds
Oxidizing agents, OK.
33 minutes 51 seconds
If we use a term like that, I'm a reducing agent, I'm going to reduce my neighbor by giving them an electron.
33 minutes 57 seconds
I'm an oxidizing agent.
33 minutes 59 seconds
I steal electrons and make them more positive.
34 minutes 3 seconds
Those are some terms we don't usually use, though you may see those in chemistry.
34 minutes 8 seconds
We also use terms like electron donor.
34 minutes 11 seconds
Any type of atom or ion molecule that gives up or donates an electron is going to be oxidized and the electronic scepter who gets the electron is going to have one more negative charge, which means that their charge is reduced.
34 minutes 30 seconds
And so getting electrons makes you reduced.
34 minutes 32 seconds
Giving them up means you're oxidized.
34 minutes 35 seconds
OK.
34 minutes 36 seconds
So hopefully you'll be able to keep those straight if you are not able to.
34 minutes 40 seconds
We have a really great little acronym here, oil rig, that is used to remember the difference.
34 minutes 48 seconds
And so that helps usually with people who live on on in the Texas on Gulf Coast, it's a lot of oil businesses here.
34 minutes 57 seconds
So oxidation is loss, reduction is gain.
And so oxidation means losing an electron and becoming more positive.
35 minutes 6 seconds
Reduction means you've gained electrons and you've become more negative, your charge has been reduced.
35 minutes 12 seconds
And so that's how you remember.
35 minutes 14 seconds
And so it's the passing around of electrons to create or break bonds or to do work for us.
35 minutes 20 seconds
That's what we think about when we think about redox reactions.
35 minutes 24 seconds
Now it starts to get a little bit more complicated, though.
35 minutes 26 seconds
This is a reaction you've probably seen before.
35 minutes 29 seconds
This is basic cellular respiration, metabolism of glucose molecule.
35 minutes 35 seconds
And what you're looking for is sort of where the electrons go and where the hydrogen atoms end up.
35 minutes 44 seconds
So you've got carbon here attached to carbon and hydrogen in many cases, which is part of the reason we use glucose as a sugar, as a as an energy reservoir, because it's easy to take the electrons away from carbon and hydrogen and oxygen is happy to do that.
36 minutes
Now, what's missing in this reaction are the enzymes that are involved in helping this process actually go forward 'cause otherwise oxygen is quite happy and stable as an atmospheric gas.
36 minutes 12 seconds
But what will happen here?
36 minutes 14 seconds
And we're going to see the biochemical process of this reveals a whole big black box of what occurs in this arrow.
36 minutes 21 seconds
What happens is the hydrogen atoms are going to end up getting moved around onto oxygen on oxygen's going to be kind of stingy and take multiple hydrogen atoms for itself, while some of the carbon and oxygen bonds that were in this original molecule are going to stay that way.
36 minutes 38 seconds
So glucose itself is having hydrogens taken from it.
36 minutes 43 seconds
And So what word would you use to describe that particular process?
36 minutes 48 seconds
Glucose reacting with oxygen is a spontaneous reaction, though there are enzymes involved in this to help it go a little faster.
36 minutes 57 seconds
And so when we think about the fact that the HS are removed from carbon and given to oxygen, that must mean that carbon is oxidized.
37 minutes 6 seconds
It lost the electrons that are hidden in the HS and loses its electrons.
37 minutes 11 seconds
And so if we're gonna give some of these HS over here to oxygen, right, Which is how you get H2O, that means oxygen picked up those electrons that are hiding in the the hydrogen atoms for itself.
37 minutes 23 seconds
So oxygen was reduced and gained those electrons.
37 minutes 28 seconds
OK, So those HS are removed from the sugar molecule, they're added to some of the oxygen, and you end up getting water molecules that are produced from this.
37 minutes 39 seconds
And so those electrons get pulled toward oxygen, remember, because oxygen is really electronegatively stingy and likes to hold them quite close.
37 minutes 46 seconds
But thankfully for US, water's pretty harmless since we're all water based organisms and carbon dioxide is released as a gas that's given off as a waste along with water and a release of energy.
37 minutes 58 seconds
And so that means that this is an exergonic relationship or a reaction, right?
38 minutes 4 seconds
There's more energy stored in glucose than there is in the products because you can see that energy was released from the chemical reaction that was done, OK.
38 minutes 14 seconds
And so the potential energy in the products, carbon dioxide and water, which we know don't store much energy are, are going to be lower than what was in the glucose molecule to begin with, OK.
38 minutes 26 seconds
And so when we think about how to figure out who got the electrons, remember to keep an electron stable, you give it a proton.
38 minutes 35 seconds
And since they're attracted, they neutralize each other and everything is stable.
38 minutes 39 seconds
So the best way to handle electrons around is to give proton, to give a proton with it, which means that you're just moving around hydrogen atoms.
38 minutes 47 seconds
And so the electrons that we're looking for are generally hiding in the HS as they move around in chemical reactions.
38 minutes 53 seconds
And so the electron you're trying to follow is often company accompanied by a proton.
38 minutes 57 seconds
And remember, the negative positive together just makes a regular H And so often times whatever molecule is being reduced is going to pick up an H, it's going to get the electron and it's going to pick up a proton.
39 minutes 9 seconds
So you see all of a sudden a hydrogen atom being added to that thing.
39 minutes 13 seconds
The oxidized molecule, which is losing the electron, is also probably going to lose a proton.
39 minutes 17 seconds
You see an H disappear off of something, it's been oxidized, it's lost that electron hidden in the hydrogen.
39 minutes 24 seconds
So follow the hydrogen atoms in any chemical reaction and you'll be able to see exactly where the electrons ended up.
39 minutes 32 seconds
OK, so reduction often adds hydrogen atoms.
39 minutes 35 seconds
Oxidation often sees them removed from any chemical reactant.
39 minutes 40 seconds
This is a good example of that.
39 minutes 41 seconds
And this will come up again when we discuss cellular respiration, how it is that your mitochondria can move electrons around to do work and produce ATP.
39 minutes 52 seconds
This is a molecule that's responsible for temporarily carrying electrons from one place to another in your mitochondria.
This is called nicotinamide adenine dinucleotide, OK.
40 minutes 5 seconds
And so it's got this nicotinamide molecule on here, and then it's attached to a ribo sugar and an adenine, which is part of a nucleotide.
40 minutes 14 seconds
And this molecule is actually much more stable when it's not carrying anybody's electrons.
40 minutes 21 seconds
It's stable that way, but it's got a couple of places where it can pick up electrons and carry them with it.
40 minutes 30 seconds
To another place where it'll drop the electrons off because the receiver at that end is more attracted to electrons than it is.
40 minutes 38 seconds
OK.
40 minutes 38 seconds
And so in any chemical reaction that happens that we're reusing NA DS, we're going to see what'll often occur is you have NAD, that is that's missing an electron, so it's got a positive charge on it.
40 minutes 51 seconds
And so if you give NAD one electron, it becomes NAD minus.
40 minutes 57 seconds
No, it becomes NAD no charge.
41 minutes
If you give it a second electron, which it can hold, it's going to become NAD minus, then it's kind of reactive.
41 minutes 6 seconds
And so you want to just give it a proton to go along with that and then it'll be somewhat stable.
41 minutes 12 seconds
And so if you look at the molecule here, we can see there's a plus right here, which means it's missing an electron on this nitrogen.
41 minutes 20 seconds
And there's another place where an electron can be held as well.
41 minutes 23 seconds
See how there's a double bond here?
41 minutes 25 seconds
You can end up making the double bond move around and you can free up some room to add an H to this carbon.
41 minutes 31 seconds
And so it, this molecule can carry 2 electrons.
41 minutes 35 seconds
If you give it one electron, it's going to be held by this nitrogen right here.
41 minutes 38 seconds
Notice that it was a plus and now it's got no charge at all because you brought their charge up to neutral by giving it an electron.
41 minutes 46 seconds
You've brought their charge down to neutral by giving it an electron, and so the negative electron cancels out this positive charge.
41 minutes 51 seconds
So it's hiding an electron here in this nitrogen.
41 minutes 53 seconds
And then you'll notice that now this carbon is making four bonds instead of the double bond and two singles that was over here.
42 minutes
That forces this electron double bond to move around to the other side here.
42 minutes 4 seconds
And that allows you to add a hydrogen atom, an electron hiding in a hydrogen atom, to this carbon right here.
42 minutes 10 seconds
So it's holding one on the nitrogen and one on the carbon.
42 minutes 13 seconds
NADH is holding 2 electrons.
42 minutes 17 seconds
It's going to take them over to where it's supposed to drop them off and happily release the electrons and then go back where it started and pick up some more.
42 minutes 24 seconds
And so this particular molecule has the ability to be reduced and carry electrons, but then when it's delivering them, it has the ability to reduce the one that's the the molecule that's going to take the electrons from it.
42 minutes 40 seconds
And those electrons are going to be used either to do work or to build bonds.
42 minutes 44 seconds
OK.
42 minutes 44 seconds
And so this is an example where hydrogen atoms that get added on to a molecule are clearly hiding the electrons that are that are desired for the processes of doing work, then that's just highlighting where they are.
42 minutes 57 seconds
And so one of the energetic molecules that we produce for this purpose of storing energy in the form of bonds that we can easily break apart and then use that released energy to drive other processes is adenosine triphosphate.
43 minutes 16 seconds
And so ATP is what I often refer to as our cellular energy currency.
43 minutes 22 seconds
We make lots of ATP because it's a a currency for energy that our cells can actually utilize.
43 minutes 29 seconds
We often think that we consume foods like sugar and proteins and things than that we are directly deriving the energy and using them from those molecules.
43 minutes 36 seconds
And we're not so much we're generally breaking those apart if we metabolizing them and converting them into another type of storage molecule that actually works for us.
43 minutes 47 seconds
And so we have a pool of ATP always in our cells, lots and lots of ATP.
43 minutes 54 seconds
This particular molecule is quite exorganic.
43 minutes 57 seconds
If you break apart the phosphate groups that are on the end of this, they will release energy to the system, and that energy can be harnessed by other reactions to drive them, reactions that require an input of energy.
44 minutes 11 seconds
So adenosine triphosphate is the nucleotide which you've already learned about.
44 minutes 16 seconds
So it has adenine and the ribose sugar, right?
44 minutes 19 seconds
So this is an RNA nucleotide and it has three phosphate residues on its end.
44 minutes 25 seconds
Now, you'll notice that there's a lot of oxygens in these phosphate residues, and some of them are carrying negative charges.
44 minutes 32 seconds
And you could imagine that those things do not like each other.
44 minutes 36 seconds
They're the same atoms and they're negatively charged.
44 minutes 38 seconds
And so they very strongly repel each other.
44 minutes 42 seconds
And so you could imagine the tension that's in these bonds where you've got these oxygen.
44 minutes 48 seconds
It's just like, oh, bro, get over pushing off of each other the tension that builds up, and then by breaking one of these off, it's kind of like snapping a rubber band.
44 minutes 59 seconds
And that energy can be released from these terminal anhydride bonds.
45 minutes 4 seconds
OK.
45 minutes 5 seconds
And so that's what we do when we hydrolyze ATP.
45 minutes 7 seconds
We break off the last phosphate, sometimes the 2nd to last phosphate, and we often transfer it to a substrate that causes that substrate to get excited and to do some work.
45 minutes 17 seconds
It raises its potential energy to actually do work.
45 minutes 21 seconds
Or the the whole molecule can just be broken.
45 minutes 24 seconds
You can break off one of these phosphates and the energy that was in the bond holding it on the ATP molecule.
45 minutes 30 seconds
That energy can be transferred to another chemical reaction to drive its work.
45 minutes 35 seconds
And it's because of these repelling negatively charged oxygen atoms that there's so much energy stored in those bonds because they're really pushing off of each other.
45 minutes 45 seconds
And so when we do a hydrolysis reaction, hence the word hydrolyze, we use water to break off some of those phosphates on the end to satisfy this, these two phosphates that are left, we can remove an inorganic phosphate and we can help attach it to something to excite it, or it can simply be released.
46 minutes 7 seconds
And that energy, this is the the delta G, the amount of free energy stored in any ATP molecule is 7.3 kilocalories per mole.
46 minutes 16 seconds
And that's quite a lot of energy that's available to drive a very basic chemical reaction.
46 minutes 21 seconds
And so this is the thing that we couple as an exorganic reaction to other reactions that require an input of energy for them to go at all.
46 minutes 29 seconds
And so ATP hydrolysis can be used to drive endorganic reactions.
46 minutes 34 seconds
It's like using your energy money to to purchase an energy reaction that requires an investment.
46 minutes 43 seconds
OK, And this is how we do this energetic coupling.
46 minutes 46 seconds
We can break down and hydrolyze ATP and pair that with an endergonic reaction that needs to absorb that energy in order for it to actually occur.
46 minutes 57 seconds
OK, so here's a good way of looking at this by a graph.
46 minutes 59 seconds
So on the Y axis we have the free energy relative to reactants A&B and then on the X axis we have the progress of the reaction from reactions to product as we watch it go forward.
47 minutes 12 seconds
When you see this slope go up, it's increased in the amount of energy in the products over the reactants, which means it must be endergonic.
47 minutes 25 seconds
So delta G here is positive.
47 minutes 28 seconds
So the products are higher up on free energy than the reactants, which means you have to actually invest energy to get this reaction to go.
47 minutes 36 seconds
And so if you uncouple A&B, it's going to require that energy came from somewhere in order to get them to actually react with each other.
47 minutes 47 seconds
And by uncouple, we mean not coupled with ATP hydrolysis, OK?
47 minutes 52 seconds
What you're relying on them to do is randomly bump off of each other and rearrange bonds and make it make some kind of products on their own, OK.
48 minutes 3 seconds
And so if you couple this with ATP hydrolysis, what you can do is instead of making this an endergonic reaction, you can end up making this an exergonic reaction.
48 minutes 13 seconds
Like you had too much energy leftover.
48 minutes 15 seconds
Not only did you get the work done, but you had some change left when you did this.
48 minutes 19 seconds
And so you may take reactants A&B and couple them to the hydrolysis of ATP.
48 minutes 26 seconds
And whatever energy is released from hydrolyzing ATP can be transferred to get A&B to react with each other, OK.
48 minutes 35 seconds
And so that energy is given off.
48 minutes 37 seconds
And so this is a spontaneous reaction.
48 minutes 39 seconds
And so delta G is less than 0 watch, and you're gonna see it actually comes down.
48 minutes 44 seconds
So it's negative.
48 minutes 45 seconds
And so this phosphate is transferred from ATP onto reactant B, which helps energize it to interact with reactant A.
48 minutes 58 seconds
And so that's going to have this sort of two step peak here, right?
49 minutes 3 seconds
We've hydrolyzed and given off energy here, but then we've also energized BP or energized B and that allows them to form a reaction with each other.
49 minutes 13 seconds
And that inorganic phosphate is going to be taken back off of B because that was not part of the chemical reaction, right?
49 minutes 20 seconds
Phosphorylating it was not an intent, it's just to activate it, to get it to interact with A, and then you take the phosphate back and you put it back on to ADP.
49 minutes 30 seconds
So those are your waste products that remain.
49 minutes 32 seconds
And so by giving an input of energy from something like ATP, which you have a ton of, you can use its energy to drive the one that requires an investment.
49 minutes 42 seconds
And because there is excess leftover, you actually have this exorgonic reaction.
49 minutes 49 seconds
In other words, there's more energy stored in ATP than you even needed to drive this whole process.
49 minutes 54 seconds
And so this becomes a, this coupled reaction becomes spontaneous and exorganic.
49 minutes 59 seconds
The energy is actually given off and there's more than you needed.
Keep in mind, however, when you get to the end product on both lines, the delta G is always going to be the same, OK?
50 minutes 13 seconds
And so you're going to end up with the same delta G that you would have had you done an endergonic reaction.
50 minutes 19 seconds
It was easier to do this exorganic reaction by coupling the whole thing to ATV hydrolysis.
50 minutes 24 seconds
OK, All right.
50 minutes 26 seconds
In the process of this occurring, even though these reactions are considered spontaneous when they're exorganic, we have a whole lot of proteins that we've evolved to help get the job done considerably faster.
50 minutes 40 seconds
Remember that we're trying to stay alive and we're on a time crunch here, and we need enzymes to help make these chemical reactions proceed just a bit faster.
50 minutes 51 seconds
So enzymes are proteins, as you probably know, they have multiple different unique sites on them, and they bind to very specific reactants.
50 minutes 59 seconds
And what they do is they assist in catalyzing reactions generally by bringing reactants together in close proximity and making sure that there's an input of energy to get them to react with each other.
51 minutes 16 seconds
And this happens at meaningful rates, so faster than if you just let them wander around and try to find each other on their own.
51 minutes 24 seconds
Remember that we have all these compartments in our cells, and we're sequestering biochemical reactions in those compartments.
51 minutes 30 seconds
And you're hoping to make this process go faster.
51 minutes 33 seconds
But by sprinkling in some enzymes, you're guaranteed to make these processes go faster.
51 minutes 37 seconds
That's their job, to bring substrates together into positions where they'll interact with each other and encourage them at a faster rate to actually form the products that you are looking for.
51 minutes 51 seconds
The enzymes themselves, however, do not actually interfere with the chemical reaction.
51 minutes 58 seconds
They might bring them in close proximity, they might even provide a little ATP energy, but they don't actually interfere with the bonds that are supposed to be rearranged and produced from the reactants to the products.
52 minutes 8 seconds
OK.
52 minutes 9 seconds
And they get reused.
52 minutes 12 seconds
Now I will give you a fun analogy about enzymes in a minute.
52 minutes 19 seconds
These enzymes take on a particular shape where they have a chemical affinity for a certain substrate.
52 minutes 25 seconds
And generally the substrate sits in a pocket on the enzyme called an active site.
52 minutes 32 seconds
And when the enzyme binds to its substrate, it kind of gives it a molecular hug and causes what's called an induced fit, where it's like, I have my substrate now and I am relaxed.
52 minutes 43 seconds
And often associated with that induced fit is a second substrate, ATP.
52 minutes 48 seconds
So enzymes are proteins that do work.
52 minutes 52 seconds
They are driven by energetic hydrolysis of ATP or GTP.
52 minutes 58 seconds
Usually we're going to be talking about ATP.
53 minutes
This is an example of one called hexokinase.
53 minutes 3 seconds
So you've already learned that kinases add phosphate to things and this adds phosphates to six carbon, things like sugar, glucose.
53 minutes 13 seconds
So this enzyme actually works on phosphorylating glucose.
53 minutes 17 seconds
This is the first step in glycolysis.
53 minutes 20 seconds
And so the active site of an enzyme is very, very important.
53 minutes 23 seconds
It's where those amino acids are doing the business on whatever the substrate is.
53 minutes 28 seconds
ATP binds nearby that.
53 minutes 31 seconds
And so it's very important that the active site can bind to and recognize the substrate.
53 minutes 36 seconds
Otherwise the enzyme is somewhat dysfunctional.
53 minutes 40 seconds
And so this is the actual chemical reaction that hexokinase catabolizes or catalyzes.
53 minutes 45 seconds
So this glucose molecule, or you've got your 6 carbon sugar, this is just drawn a little differently.
53 minutes 51 seconds
Hexokinase uses ATP and transfers a phosphate onto glucose to make it glucose 6 phosphate.
53 minutes 58 seconds
And that's the first step in helping to breakdown sugar molecules in glycolysis.
54 minutes 3 seconds
And so having an enzyme helps make chemical reactions proceed at a faster rate because what they do is they lower the need, the energy needed to start the reaction to get the reactants together.
54 minutes 20 seconds
And we refer to that as the activation energy of the reaction.
54 minutes 24 seconds
So when we look at our regular reaction here, all right, we can see free energy again on the Y axis, the progress of reaction on the X axis, and we've got reactant A and reactant BC.
54 minutes 37 seconds
And when they do their chemical reaction, we can see that A&B are then going to be associated and C is going to be by itself.
54 minutes 44 seconds
But in order to get these reactants near each other and to bounce off of each other and to actually rearrange their bonds, that requires an external input of activation energy.
54 minutes 57 seconds
OK, That's separate from the actual chemical reaction.
It requires getting them close enough to each other where they could rearrange their bonds and develop this transition state where they're temporarily all bind bound together, and then the products form and then C is let go.
55 minutes 14 seconds
So you're rearranging bonds.
55 minutes 17 seconds
Now in our cells, it's very challenging to just wait around for reactants to interact with each other, form a transition state, and then, you know, make new products.
55 minutes 27 seconds
There's a little bit of a a bump that needs to get be be be ridden over here and that's a problem.
55 minutes 34 seconds
And you only have a couple of alternatives.
55 minutes 36 seconds
Number one, you can heat up your cells.
56 minutes 35 seconds
And you go find your friend or roommate.
56 minutes 37 seconds
And you say, hey, I met this really cool person.
56 minutes 39 seconds
They're absolutely your type.
56 minutes 40 seconds
You guys would get along really great.
56 minutes 42 seconds
I think you should meet this person.
56 minutes 44 seconds
And so you encourage your roommate to call and set up a blind date or maybe you would even do it for them.
56 minutes 51 seconds
And what you're doing is, is you're bringing them in close proximity to each other, decreasing the chance that they won't meet or they'll take longer, right?
57 minutes 5 seconds
The alternative is cool, I met this girl and I have this friend over here and they might be perfect, but I'm just going to let them randomly meet each other like the star of the line and faith and blah, blah, blah, blah, blah.
57 minutes 14 seconds
That's going to take a lot longer and a lot more energy right then you going OK, I'm gonna act like the enzyme.
57 minutes 20 seconds
I'm just gonna bring them in close proximity so that they're, they can, you know, go on their date.
57 minutes 25 seconds
You don't go on the date with them as the enzyme.
57 minutes 28 seconds
You know, you don't sit there and go now, Slooch.
57 minutes 30 seconds
So the enzyme really only brings them in close proximity.
57 minutes 32 seconds
What happens between the reactants is always still just between the reactants, but the enzyme has lowered the potential of the the energy needed to actually get the reactants near each other.
57 minutes 43 seconds
You know, they kind of bring them in like this.
57 minutes 45 seconds
And so that is kind of how enzymes are like, you know, a friend setting up a blind date.
57 minutes 51 seconds
You have reduced the activation energy needed to get those two people to meet by doing the work of bringing them together directly.
57 minutes 59 seconds
And so enzymes have that same effect on chemical reactions.
58 minutes 5 seconds
They lower the activation energy of a reaction and help it go faster by bringing the the reactants in close proximity to each other.
58 minutes 14 seconds
And so notice here, when you add an enzyme, the hill that you have to get over, the activation energy needed to bring them in close proximity is much lower than without the enzyme.
58 minutes 26 seconds
So the enzyme is doing part of the work of bringing them together anyway.
58 minutes 30 seconds
And that little hill they have to get over might be provided by hydrolysis of ATP by the enzyme itself.
58 minutes 37 seconds
Now you'll notice that the Delta G does not change.
58 minutes 40 seconds
Whatever happens between the reactants to make the products is going to happen the exact same way whether or not there's an enzyme.
58 minutes 46 seconds
It's just that the likelihood of it happening, the energy needed, and the rate at which the reaction happens are all going to change.
58 minutes 53 seconds
If there's an enzyme there, the enzyme is not consumed in the process.
58 minutes 57 seconds
It's not like it's spontaneously combusts.
58 minutes 58 seconds
And it was a magical, you know, blind date enzyme fairy.
59 minutes 2 seconds
They go back to whatever state they started in and they get recycled and they go do the job over and over again.
59 minutes 9 seconds
But having an enzyme present helps lower the activation energy, this hump that needs to get over in order for the the the reactants to interact and form the products.
59 minutes 18 seconds
When you read a graph like this, notice the free energy on the Y axis.
59 minutes 22 seconds
This is the line where AB and C start, and notice that the line is lower on the Y axis when you have the products.
59 minutes 30 seconds
And so delta G is the change from the reactants to the products.
59 minutes 33 seconds
There was more energy stored in the initial reactants than there are in the products.
59 minutes 37 seconds
And so some of that energy is this is an exorganic reaction that's given off to the system.
59 minutes 42 seconds
OK.
59 minutes 43 seconds
And so enzymes are going to help facilitate by driving these forward.
59 minutes 47 seconds
Generally, they do this because they have an affinity for the things that they're associating with each other.
59 minutes 53 seconds
They're not actually making these things do the reactions, they're just bringing them in close enough proximity so that they can do it.
1 hour
And so the initiation of a catalysis by an enzyme means that you've got the substrates, they find the pockets on the enzyme they're supposed to bind in, and they're oriented in the right fashion, right?
1 hour 10 seconds
If you want A&B to interact, you're going to have A&B near each other, right?
1 hour 14 seconds
And C, you're going to eventually get rid of.
1 hour 16 seconds
And so when the enzyme binds to these, often an enzyme undergoes.
1 hour 21 seconds
A a shape change, right, it actually goes A undergoes a conformational change to sort of interact with the substrates and then bring some in closer proximity than others.
1 hour 31 seconds
And so notice that it's bringing A&B close together to help form a transition state where where B is like, oh, A is over there, OK, cool.
1 hour 38 seconds
And then next thing you know, B is going to let go of C also.
1 hour 42 seconds
And so the enzyme itself did not do these reactions.
1 hour 47 seconds
It just facilitated the ease with which the reactions could occur and can provide any additional energy needed if this is an endo endergonic reaction.
1 hour 57 seconds
And then once that's finished, the products are going to release and the enzyme goes to the exact same state that initially started with and can do the process all over again.
1 hour 1 minute 5 seconds
And so when we think of chemistry and these reactions proceeding forward, we often think about how fast they can occur.
1 hour 1 minute 16 seconds
And so people have done lots of studies to figure out how different enzymes respond, how much you like your substrate, how much enzyme is there, how much substrate is there, How fast can this enzyme work given a certain amount of substrate?
1 hour 1 minute 31 seconds
And so enzymes are saturatable.
1 hour 1 minute 33 seconds
They will work as fast as they can, depending on how much substrate there actually is there.
1 hour 1 minute 39 seconds
And so the more piece, the more individual enzymes you have, the faster the reaction can go, right?
1 hour 1 minute 46 seconds
Everybody's working.
1 hour 1 minute 49 seconds
So the ratio of enzyme to substrate matters on how fast reactions can work.
1 hour 1 minute 54 seconds
And so the amount of substrate that's available matters.
1 hour 1 minute 56 seconds
The number of enzyme units actually matters as well.
1 hour 2 minutes
It also matters just how much the enzyme likes its substrate.
1 hour 2 minutes 3 seconds
The more it has an affinity for the substrate, the faster the reaction's gonna go.
1 hour 2 minutes 7 seconds
The less the affinity, the slower the reaction's gonna go.
1 hour 2 minutes 10 seconds
And so we can actually measure this, the rate of a reaction going forward and, and whether or not that that goes faster with an increase in substrate concentration.
1 hour 2 minutes 19 seconds
And so we can see here, when you have an enzyme, as you increase substrate concentration, the rate of the product formation is gonna go up really fast and hit maximum speed much faster because there's an enzyme present.
1 hour 2 minutes 31 seconds
They're just trucking, trucking, trucking, trucking, trucking working really fast.
1 hour 2 minutes 34 seconds
Whereas if you have an uncatalyzed reaction, the substrate concentration as it increases, increases the likelihood that, you know, the reactants are going to bounce off of each other, but still you're relying on them to do it themselves, OK.
1 hour 2 minutes 49 seconds
And so the the speed of the reaction is not going to be as high, the rate of product formation and the speed are not going to be as high when there's no enzyme present.
1 hour 2 minutes 59 seconds
And so enzymes show, you know, we can measure their saturation kinetics, like how much can we just overload them?
1 hour 3 minutes 6 seconds
And so they work very, very quickly.
1 hour 3 minutes 9 seconds
And at some point, their active sites just can't accept any sub substrates any faster than they're already working.
1 hour 3 minutes 15 seconds
And so we can figure out the affinity of an enzyme for a substrate by measuring sort of how fast it goes depending on how much substrate is available.
1 hour 3 minutes 23 seconds
I know that this is some kind of scary crossover between chemistry and physics, but in a biological setting it really does matter because when certain chemical reactions go too slowly for us, it can lead to problems in the cell.
1 hour 3 minutes 39 seconds
OK And enzymes are not always able to act simply on their own.
1 hour 3 minutes 43 seconds
This is where that quaternary structure of proteins comes into play.
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One of the additions to quaternary structure is sometimes different types of chemicals or molecules that have to bind inside of a protein for it to function.
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And enzymes are not exclusive of this.
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And we're going to see some examples of this later in other protein complexes when we study cellular respiration and photosynthesis and such.
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And so things that associate with enzymes to help them function might be something like a cofactor.
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Metal ions are often found as cofactors.
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We find iron in things.
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We find zinc and magnesium in things, and sometimes proteins don't work if they don't have the cofactor.
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For example, here is a polyporphyrin ring.
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You probably recognize this is heme.
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This is a protoporphyrin and in the middle of a heme molecule, this is this is called a prosthetic group, but it binds to the cofactor iron and iron holds oxygen in this prosthetic group.
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And these prosthetic groups sit inside of hemoglobin.
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So if you didn't have hemoglobin or you didn't have the iron or you if you didn't have the heme with the iron in the middle, you wouldn't be able to carry oxygen and your hemoglobin would be mostly useless.
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Some enzymes require coenzymes, which is a helper that completes a quaternary structure of the enzyme so that it functions.
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Sometimes they fit like puzzle pieces.
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So here's an example of an enzyme and it's coenzyme.
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The coenzyme is not always an enzyme.
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Sometimes it's a vitamin, sometimes it is just a regular organic molecule that binds to the enzyme and allows it to do its job.
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It doesn't necessarily have to be another protein, but the name Coenzyme is sometimes a little bit misleading.
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But either way, that fills out and creates what's called often the holoenzyme, which sounds like the whole active enzyme, and then it's got the right pocket for binding its substrate.
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And then again, some of these structures, these organic molecules that are not proteins and they're not DNA and they're not sugars, they're unique molecules that have unique functions.
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These are referred to as prosthetic groups.
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They're like an extra addition to a protein complex in order for it to work.
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They are often permanently attached to the proteins that we make, but some of them are removable.
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There are many different types of prosthetic groups.
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Often times if you study nutrition and you learn about a lot of the vitamins, the vitamins that we ingest for things are often used as coenzymes and prosthetic groups for certain proteins to function.
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Same with the the necessity to have some of these metals in your diet and usually in trace amounts, and these help you keep your enzymes functioning, otherwise they wouldn't be able to do that.
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Enzymes are also susceptible to physical conditions, OK.
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And so if environmental conditions change, it can cause enzyme functions to change.
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We've evolved as other organisms have for enzymes and proteins to function at a specific ambient temperature and pH.
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When those things fluctuate, it can cause proteins to behave differently.
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And so temperature effects how things move around.
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Slow temperatures, molecules move around slower.
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High temperatures things move around faster.
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Really high temperatures, things fall apart.
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Proteins can denature and stop functioning.
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Same thing can happen with pH when there's too low of aph.
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Often protons disrupt bonds and they can cause an enzyme shape and reactivity to change and so here are some experiments showing these.
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This on the Y axis is showing your measurement of chitinase activity.
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Chitinase is an enzyme that's gonna degrade chitin, which is a carbohydrate you've learned about already.
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And the researchers here are looking at chitinase activity relative to temperature and different types of bacteria.
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And so these guys have chitinase enzyme 1.
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Bacterium lives in a relatively cool neutral pH environment and one lives in a hot acidic environment.
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And so this first graph is actually looking at how well their proteins function at certain temperatures.
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And so the one that lives in a cool environment, its enzyme is much more functional in a a lower temperature environment.
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Actually 45°C is quite warm, quite warm, much warmer than we can stand a cool neutral environment.
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I don't know if I'd call that cool.
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45°C is still pretty hot.
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If this was Fahrenheit, I'd say yes, that's pretty cool environment.
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But notice that the guy who lives in the hot acidic environment, its enzymes are much more functional at a much higher temperature, 60°C.
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Same thing happens with pH.
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This red bacterium lives in an acidic environment and notice that pH about 3, its enzyme is the most functional.
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As you increase the pH and it becomes more basic, its enzyme functions less and less.
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You start to get down to 60% functionality when it comes to the bacterium that lives in a more neutral environment.
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Now that seven I would call neutral.
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You see that it's enzyme peaks at that neutral pH.
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And so this just indicates that those have evolved to work and be stable at these ambient temperature and pH settings.
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And changes outside of that can cause your enzymes to fall apart and stop functioning if they fluctuate too much.
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A really important thing to understand about enzymes is how they are regulated and how they may have competition.
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And we manipulate that to control what enzymes do, often using different types of chemicals that we find.
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So one example of controlling an enzyme and its behavior is using something called competitive inhibition.
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And so some molecules in nature, others that we bind and produce artificially can compete to bind in the active sites where a substrate for an enzyme would bind.
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And then the substrate doesn't ever get catalyzed.
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And so penicillin is an example of that, where you can block an enzyme and then you don't get the substrate being made, OK.
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And so you end up fighting off a bacterial infection.
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And so the other molecule here in this case, right, is competing for the binding sites so that the original substrates can't bind at all.
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The other way that you can, and this is much more common in natural situations, is regulate the activity of an enzyme is by using a site on the enzyme that's on the backside that's different than the active site, using something called allosteric regulation.
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So you can activate something allosterically, which means like you know, interacting with it in the backside and turning it on, or you can inhibit something allosterically which is interacting on the backside and turning it off.
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And so here in this case, there is the binding site, a backside binding site on this enzyme.
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And this regulatory molecule actually helps stimulate it to activate the enzyme, whereas this regulatory molecule helps inhibit it.
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So it's not going to do its chemical reaction once it's inhibited, the shape changes on the enzyme mean that it can't bind as well to its substrates.
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And so, you know, an example of that is like a GABA receptor that we have.
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And often times we use drugs to manipulate GABA receptors to circumvent pain.
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And so the GABA receptor not only has its binding sites for its substrates, but it's also got allosteric sites.
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In other places where we can use anesthesia, we use steroids, benzodiazepine, which is very strong pain reliever, barbiturates and also ethanol.
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Barbiturates are not usually recommended.
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A lot of people were addicted to benzo and barbiturates in the 80s, seventies, and 80s because it numbs the pain and you just feel delightful.
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Same thing with ethanol.
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And so all of these things can regulate an enzyme on the backside and control what it actually does.
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And so allosteric regulation is backside regulation that causes a change in shape.
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It can activate a protein in one case or deactivate an enzyme in another case.
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And so there are ways of regulating enzymes.
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We'll also see that there are pathways that may positively or negatively give feedback to regulate enzymes based on metabolites that are produced, particularly when we think about cellular respiration.
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Enzymes also are regulated by their covalent interactions, So anytime an enzyme is modified by a functional group or or binds to a prosthetic group, it can change the way the enzyme actually functions.
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Phosphorylation is a big one.
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Remember that I talked about in signal transduction in our last lecture that kinases add phosphate to things, sometimes to turn them on, sometimes turn them off.
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Sometimes multiple phosphates and phosphatases remove phosphate residues, which can turn on or off a target.
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In this case, adding phosphorylation is actually activating this particular enzyme.
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So here is a space filling model of an enzyme.
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And you can see here that there's a couple of amino acids in orange that are likely serines or threonines.
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I think tyrosine is another phosphorylatable amino acid, but phosphate groups can be added here to shift this enzyme to being in an ON state where it actually goes and find its substrate and does its job.
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And so phosphate, this looks like a tyrosine 'cause it's got a loop in it.
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Phosphates can be added here and that can actually activate.
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So covalent modifications can turn enzymes on or off to get them to find their substrates.
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And so this is sort of a toe dip into thinking about metabolic pathways and enzymes.
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Enzymes are going to come up repeatedly, especially when you study biochemistry and then later when you study human and plant Physiology because enzymes are are doers, they're getting work done and they're making things happen at a faster rate and more likely than if they weren't present at all.
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And they're the things that are stepwise controlling metabolic pathways, different enzymes.
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And we're going to see this when we think about glycolysis and cellular respiration, that there are enzymes that play at each step that are helping convert this intermediate to that one, to this one, to that one to eventually get the product you started with or you you're ending with.
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Now in a regular chemical pathway, maybe all you see are the starting molecules and the products.
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But in many biochemical pathways, there are multiple steps and enzymes that are responsible for every single step and these are regulatable.
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And so you can actually tweak the activities of these enzymes based on how many products are being produced and or how many intermediates are being produced.
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This is exactly what happens when you breakdown sugars at the very first part of breaking down glucose and cellular respiration, which is called glycolysis.
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Your cells are assessing, do we already have enough of these intermediates?
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If we do, we don't need to keep doing this.
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We can, we can shut this system off until we need to really do this.
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And that tends to be called feedback regulation.
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Some feedback regulation is positive, right when you get through a metabolic pathway and you made a product, that product is enough to keep forcing this pathway to keep going forward.
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Some metabolic pathways are inhibitory, where once you've made the products at the end of the pathway, the product is able to go back to the beginning and shut the pathway off because it's already functioned, OK.
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And so these actually can create loops where the end product feeds back on the beginning, OK?
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Some of these can feed forward, they can be positive.
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This is an example of feedback inhibition.
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So here we've got an enzyme that has low product present, whatever it is that the cell needs to make and the substrate that it binds to.
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And there are, it's going to create an intermediate and an enzyme's going to pick that one up, which creates another metabolic intermediate, which the third enzyme picks up and produces a product, OK.
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That product when it's in high enough quantity can actually end up being sensed by the 1st enzyme.
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It can allosterically bind to the first enzyme and go, hey you, we got enough.
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You can shut off, you don't need to keep working.
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And so it'll 'cause this enzyme to shut off, so it forms this feedback inhibition and that is to save your cells energy.
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You don't just keep making stuff that you don't need.
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You make usually enough, if not a little more, and then that's enough to turn the pathway off until you run out again.
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Then you can reactivate the pathway.
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And so that is what most metabolic pathways actually look like where you've got key intermediates and some of them are much longer than this.
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And many metabolic pathways send some of these metabolites offshoot into different pathways.
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If you study humans and you study plants, you'll find the metabolic pathways interact in many different places instead of how we learn.
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It is this nice, neat, neat, unique, straightforward pathway.
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It actually looks a lot more like something like this, where you see that the different sub pathways actually feed into each other and overlap.
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I mean, here we've got sugar biosynthesis and metabolism that starts to meet lipid metabolism, which makes perfect sense.
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They're both, you know, carbon, organic molecules.
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Many times you can derive sugars from lipids that are stored in tissues.
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We've got secondary metabolism, which comes after primaries.
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So primary metabolism is nucleic acids, amino acids, sugars, and lipids, and lots of other things can be derived from those.
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Here you've got carbohydrate metabolism in the middle that overlaps with amino acid metabolism and ties into obviously, energy metabolism.
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And here's your citric acid TCA cycle.
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Over here we've got nucleotide metabolism, cofactors and vitamins, overlapping metabolism, other amino acids.
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It's absolutely a crazy, crazy mess.
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And we've had to rely on pairwise interactions of geneticists and biochemists and molecular biologists trying to figure out protein, protein interactions.
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And we've had to rely on databases and computer algorithms to build us crazy maps that look like this to show us how all the metabolic pathways interact.
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It is absolutely an organic chemistry nightmare to think about how all these things interact, but it's also really fascinating that it's so well orchestrated.
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We make almost every single thing that we need except for a few things we have to take in from the external environment and things still run pretty well and spectacularly and and we have these same pathways in common with lots and lots and lots of other single and multicellular organisms on the planet.
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Metabolism can be a scary thing to think about, especially when redox is involved and we have to think about who lost electrons and who gained electrons and what were the electrons doing while they were being moved around.
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There's a whole thing that they're doing before they've even ended up where they're going to end up at the end.
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And so that's what our next couple of lectures are going to be about.
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What is the value of all those electrons that are in the bonds?
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How do we get them to do work in that mystery arrow that goes from the reactants to the products?
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They're being used for their energy to drive work before they land in the products.
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I hope that some of this was a review for you.
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I hope you're feeling a little more comfortable thinking about reactions and metabolism and where electrons go.
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This is going to be a theme that starts to come out a little bit as we continue talking about energy and metabolism, particularly in our discussions of photosynthesis and cellular respiration, which are absolutely necessary processes so that you can safely maintain your energy budget.
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And spend it on all the wonderful things that you do to stay alive.
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Thank you so much for your attention.
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I really appreciate it.
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Until next time, I hope you have a wonderful day and you'll all be hearing from me again soon.