Okay, this time we're going to do chapter 2, the second chapter in your Bio 107 course. We're going to start with atoms. I know it says molecules of cells, but we have to build with atoms before we can get to the molecules. So you're going to get a little bit of chemistry here. Dirt's certainly not your Chem 100 class, but you're going to get enough so we can talk about this.
as we go further into the rest of this course. And so matter, your first definition, is anything that takes up space and has mass. Now mass is like weight. When you take chemistry, though, you're going to see that mass and weight are going to be a little bit different.
For example, we know on the moon that there's very little gravity, so you weigh relatively less than you do. on earth, but the mass of your body is going to stay exactly the same. There are three states of matter.
These are solids, liquids, and gases. We're familiar with all of this stuff. Solid is your tabletop, liquid is the water that you drink, and the gas is the air that you breathe in and out.
Everything is made up of elements, and an element, by definition, are substances that cannot be broken down into smaller or simpler substances by normal chemical means. And if you're able to do that, you don't have the same element. You've got something else.
On this planet, there are 92 naturally occurring elements, as we know so far. And these are going to be components of everything that occupies space. It has some weight to it.
So if we look at first the globe 49 of it is oxygen some of this is in the air but by far most of it is bound up in the water that covers most of the globe silicon is an element this is going to be primarily in rock structures same thing with aluminum iron is a component found in the core and then we're going to get smaller and smaller we'll start talking about um I'll get my pointer. We'll start talking about calcium and sodium, potassium. These are actually important now to life.
And then everything else, the rest of those 92 elements, are only going to make up about 5% of the planet. In our cells, about 1% phosphorus, 1.5% calcium, 3% nitrogen, 10% hydrogen, 18% carbon. But again... By far, oxygen is going to be the most abundant.
And again, most of this is going to be bound up as water. Now, when you look at a periodic table, you'll see the 92, but you'll see it go up quite a bit higher. All of those larger elements with the larger numbers, these are human-made. These are things that we've combined on the Earth that do not occur naturally, and we don't normally find them in organic systems.
Now, 95% of us, by weight, You're just these six elements. Carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur. 95% of that is what we are. CHNOPS, that stands for the first letter of each one of these important elements.
And if you were to say this, CHNOPS, that's a great way to remember that. You can use that mnemonic. Remember these very important six elements. And so right at the core of the element is the atom.
And an individual atom is the smallest thing that we can have of an element that's going to have all the properties or characteristics of that element. But if we look into atoms a little bit closer, we're going to see that they're made up of structures called subatomic particles. The most important three are protons.
Neutrons, electrons. A proton has what's called a positive charge. A neutron doesn't have a charge.
An electron has a negative charge, and it's going to be equal to the positive charge on the protons. And so when we have these together, and we always do, they're going to cancel each other out. Now the protons and neutrons are found in the center of the atom, and that's going to be called the nucleus. Nucleus is a term we're going to use for the center of and then the electrons are going to move around the nucleus in what's called a electron cloud.
They're going to kind of rotate around it kind of like the moon rotates around the earth. And so these little orange spheres are the protons, neutrons. They have this in this light kind of green almost a gray sometimes depending on your screen and then the electrons. Electrons have that negative charge, protons have the positive charge, and a neutron is going to have a neutral charge.
So again, proton positive, neutron none, electron negative. Now when we talk about the atomic mass or the weight or what's contained within an atom, protons and neutrons are equal. They're both going to have a 1 next to them. Now an electron is a very, very small particle, and for our purposes, we're going to consider it to be zero when we're trying to figure out the mass of an atom.
Location again, both the protons and neutrons are in the nucleus. The electron is going to be in the electron orbital around that atom. So we get neutrons, protons right in the center, and then these electrons are going to circle around all around. This graphic actually shows it a little better.
All those little teeny black dots indicate where that electron can be found. It's not very predictable. It can be anywhere at any time.
They really move fast. Now to read a periodic table, there's lots of information given in it. First, the atomic symbol. The atomic symbol is usually going to have some relationship to the name.
For example, carbon, a very important element to all. Organic compounds is going to be this capital C. The atomic number is 6 and then the mass number is 12. Now the atomic mass, we're going to add up the number of protons, we're going to add up the number of neutrons found in that nucleus.
The atomic number is going to be the number of protons only. And so from this information we know that... Carbon has six protons and it has six plus six neutrons.
Usually this number, when we get the mass number, we're just going to double it. We're going to have a double number. But as we get into the larger atoms, we're going to see that this is not always the case, but especially for the little ones.
If you know the atomic number, you can probably guess the mass number. Now we arrange all of these elements in something called a periodic table, and because each of those atoms are different, we can kind of isolate them. They're going to have their own unique chemical and physical properties. This periodic table is used to group the elements according to those characteristics.
They're all kind of sorted out in groups based on their properties, and for now, the vertical columns are called groups. The horizontal rows are called periods. Here's a simplified periodic table. So again, groups are going to go up and down, and then periods are going to run across.
And so the information here is we have the atomic number, atomic mass, and then the abbreviation for the element. This one happens to be lithium. It has an atomic number.
of three that tells us that there are three protons and then when we multiply that by two we get six but this number changes a little bit it gets a little bit wonky as we go through this so this is not quite doubling this one's atomic number four this is beryllium so we have four protons we would add up four more neutrons, but it's slightly more than that. This top number is always going to be the protons, and then this is an approximate overall mass number. Oxygen plays by the rules, Nitrogen does pretty well, Carbon does pretty well, that this number is about the same as doubling the atomic number. Now we have individual atoms, but we can have something called isotopes.
Now an isotope again by definition are atoms of the same element with different number of neutrons. So we're going to change the weight for the mass. If we get too many neutrons, we can have radioactive isotopes. This is going to emit radiation as they begin to break down. These are three isotopes of carbon.
This one is called carbon 12 for the mass. This one is called carbon 13. This one is called carbon 14. All of these occur in nature. Carbon 12, carbon 13. But it's carbon 14 because now we have extra neutrons that wants to break down.
So this becomes radioactive. You can measure that energy as it starts to break down. So an isotope is the same element but different numbers of neutrons.
That's indicated in this mass number up here. Now we use this radiation for our benefit. We can scan thyroid and what the radiation does is it kind of gets soaked up in areas of higher density and then it passes through areas of lower density and then we actually can use radioactive tracers that get into the individual organs. So for this a scan of your thyroid gland iodine is an important component for that. So the areas that are more active are going to take up more iodine.
The areas that are in trouble are going to take up less. And then that information can be picked up here. In fact, it is detected that there's actually no activity here where there should be part of this thyroid gland.
So we know that there's an issue with that. Now PET scan is going to kind of do the same thing. It's looking for different densities. And again, we're going to use radiation for this. This, we can check the activity of the brain, and just like we did up here in the thyroid, we can look for areas that might be in trouble.
All right, electrons. So electron negative charge. In an electrically neutral atom, the positive charges of protons in the nucleus are balanced by the negative charges of the electrons.
And so you're going to have the same number of... protons as electrons. That's going to be a balanced atom.
Those electrons, as I mentioned before, are moving around the nucleus in structures called orbitals or an electron cloud. And again, they could be anywhere. You really can't predict where they are.
But their job is to provide a balance of the protons to the electrons. As we get larger and larger atoms, we have to have different shells in which those electrons are located. These are known as energy levels. In the first level, we're going to have only two electrons.
So this is going to be in the smallest atoms, and then at the center, even at the larger atoms. Now, once we get past two, we have to go to a second shell, and all the shells outside of that first shell are now going to hold eight electrons. up to eight electrons in those additional shells.
So if we look at it very simple, in fact the simplest atom that we have, this is hydrogen. Hydrogen is a gas that's found on the planet. Hydrogen is going to combine, we'll see in a little bit, with oxygen to make water. It has one proton, it has one electron.
You can tell that from here. So the atomic number and the mass number are exactly the same, so there's no neutrons there. We get to oxygen.
We have the symbol for oxygen. We have the atomic number, so this tells us that there are eight protons. This number tells us that there are eight neutrons, because we just doubled that.
Now to balance this out, we have to have the same number of electrons as we do protons. And so we have... Eight electrons up here.
So there's one, two, three, four, five, six, seven, and eight. Remember the inner shell can only hold two. All the other electrons after two have to go into this outer shell. This can hold up to eight. Let's go over to carbon.
Six protons, six neutrons, that gives us the twelve. We have to balance it so we know that there are six electrons, two in this inner shell. 4 in the outer. Same thing with nitrogen. 7 and 14, so there has to be 7 electrons.
Phosphorus is a larger atom. In the center we have 15 protons. So if you counted all these little blue electrons you would find 15 of those.
First shell has 2. Second shell has 8. And when that shell's full, we're starting a third shell. And then that third shell and fourth shell can hold eight as well. Sulfur, 16 protons, 16 neutrons, and then 16 electrons coming around.
Now, once we understand atoms, we can start to join those atoms or elements together. Once we do that, we have a molecule. A molecule by definition is two or more of the same elements bound together like oxygen gas.
A compound is when we join two or more different elements and we come up with something different. The simplest example here is water where we have hydrogen and oxygen. Now to bind these together we're going to have a chemical reaction. And when this happens energy may be given off. or we might actually have to put energy into it.
It's actually going to absorb energy to form the connection between these two atoms. Now there's different times of bonding. We're going to start with ionic bonding and by definition an ions form when electrons are transferred from one atom to another. So that's what an ion is.
Our example is going to be sodium. And then we're going to join it with chlorine. So sodium, with one electron in its third orbital, wants to get rid of that one electron swinging around all there by itself.
It tends to be a little bit unstable. And so sodium's going to give up its electron. It's going to be the donor.
Once it gives up that electron, because we're taking one negative charge off, this is now going to be positive. Because remember, those electrons balance out the protons. If we get rid of an electron, we're going to have a positive charge.
We have an extra proton, which is positive. Now, chlorine in its third orbital only needs one more, and it wants a full shell. That full shell is going to give it stability.
And so it's going to take sodium's extra electron. It's going to put it in that third shell. But because now it has an extra electron, it's going to be negative.
It's going to have what's said to be a negative charge. So sodium gives up an electron. It is a positive ion. Chlorine is going to take in that electron, and it's going to be a positive ion. Now, you've heard the old phrase that opposites attract.
And that's true when we're forming... ionic bonds. And so again, sodium has this one electron all by itself. It wants to get rid of it. Chlorine is missing only one.
It would love to fill this outer shell. And so what happens is sodium gives up that electron, transferred to chlorine. Sodium now has a positive charge because it lost a negative.
Chlorine took in an extra negative. So now it has a negative charge. Positive, negatives, they're going to attract and this is what's going to be called an ionic bond.
When we get that ionic bond, especially with sodium chloride, we get common table salt. And of course this is nice on these nice crispy french fries. Now covalent bonding is a little bit different.
This is where we're going to have atoms that actually share electrons. That electron is going to be shared between two different atoms, or in some cases the same type of element. So an atom may share electrons with one or more atoms. After sharing those electrons, each atom has what's called a completed outer shell, and that's what the whole game is.
We want to have... completed outer shells that's going to give us stability. Two hydrogen atoms can share their single electron and then they can form that complete inner shell with two.
electrons, so they're happy. We can have nonpolar and polar covalent bonds. So if the sharing of electrons between the two atoms is fairly equal, we have a nonpolar covalent bond.
And this usually happens with atoms of the same size. Now in water, the sharing of electrons between the oxygen and hydrogen is unequal. Oxygen is a much larger atom.
This results in something called a polar covalent bond. And then we have something called electrodictivity, which is the attraction of an atom for electrons in a covalent bond. It's actually going to want those electrons.
So here we have a nonpolar. We have two hydrogens. Remember on the earlier graph we had a single proton, we have a single electron.
When they form this bond by sharing these electrons, they fill that inner shell. This is stable, and then we get hydrogen gas. Now because these are the same size, these electrons are spending exactly the same amount of time around this hydrogen as they are in this hydrogen. A little bit of chemistry. When we draw these things, we can denote this model in simplified form.
We can simply put the H, the H, and this single line indicates a single electron or a single bond. And then to denote the gas, we're going to have two hydrogens. And we know this is two hydrogens because you have the hydrogen and then the subset 2, and you multiply this 2 into that H.
So all of these are hydrogen gas. Now methane is a carbon and then four hydrogens on the outside. This also is going to form a nonpolar bond because these are going to balance out the pull of the larger carbon.
Hydrogen has one electron each. If you go back and look at that earlier slide, we see that carbon on its outer shell has... four electrons. Remember this second shell can hold eight. And so by sharing with four hydrogens, it gets a full shell, and then hydrogen gets a full shell in its inner shell.
And then the same kind of structural formula where we see one bond, and then we see the simplified carbon with four hydrogens. Now polar covalent bonds are formed when we have different size atoms. And what happens is the larger atom is actually going to pull these electrons closer to it for more of the time.
And so what happens is since the electron is spending more time around the oxygen, it has a slightly more negative charge. Since this electron is not as much around this hydrogen, it's closer to the oxygen. This hydrogen takes on a slightly positive charge.
And this is going to be a polar covalent bond. It's kind of like the two ends of a battery where you have a negative and you have a positive end. This actually denotes that where we see these little positives next to this symbol indicating that hydrogen has a partial positive charge. Oxygen has a partial.
negative charge to it. We see this when the molecules or the atoms are actually unequal in size. Now hydrogen bonding is our third type of bonding and hydrogen bonding is actually pretty important when we start talking about biological systems and it involves water. So the polarity within a water molecule causes the hydrogen atoms in one molecule to be attracted to the negative charge on the oxygen atoms in other water molecules.
This is how we have liquid water. Each one of those individual water molecules is sticking to its neighbor so we can have liquid water and then ice. And when we have that connection between a hydrogen and an oxygen in the water, again each one of those partial charges, this is what's called a hydrogen bond. This isn't quite as strong as the ionic or the covalent bond, but when we have masses of these, they're actually pretty strong.
They have some pretty interesting characteristics, especially with water. So here's our electron model. We've seen this before. We have the sharing of the hydrogens with the oxygen.
We see the positive charges, the negative charges. And then what happens now is this positive hydrogen is attracted to the negative oxygen. And so we're going to have these little hydrogen bonds in here. That's going to happen to every molecule. that comes close to it.
Now water turns out to be pretty special. In fact we couldn't have life on this planet if it wasn't for the presence of water. We are anywhere from 70 to 90 percent water in our bodies. Water as we've established is a polar molecule and then when water molecules form hydrogen bonds which causes them to cling or kind of stick to each other We have liquid water. This is also the premise of why we have ice.
It's only when water is heated that we can get steam and water vapor in the air. It takes a lot of energy to break those bonds. For that reason, water is stated to have a high heat capacity. Now in our foods, we can talk about calories, but in chemistry, we use calories as a unit of heat. heat or a unit of energy to make something change.
And so a calorie by definition is the amount of energy needed to raise the temperature of one gram of water by one degree centigrade. The hydrogen bonds that link the water molecules are going to help to absorb the heat without a great change in temperature. This is why it takes so long for that pot of water on your stove to boil.
because the more heat you put into it, those individual hydrogen bonds are absorbing it until there's enough heat to allow it to boil. Because the temperature of water rises and falls slowly, organisms are better able to maintain their normal internal temperatures. That property comes from putting all of that energy in those hydrogen bonds, and so that's why we don't get too hot and die or we don't get too cold and die. It's all that water within our bodies. now when we sweat we're converting that liquid water to vapor and so when you get that bead of sweat on your forehead what it does is it takes so much energy to turn that liquid into steam that that energy is coming from your body heat and so that's why sweat actually is a really good way to cool yourself cool yourself off water has abilities to be called a solvent a solvent is something that allows something to be dissolved into it.
Like if you drink coffee, you put sugar in your coffee, it dissolves into it. If you put salt into a boiling pot of water, it's going to dissolve into it. That's because water is a solvent.
Now, a solution contains the solvent plus the solutes. Solutes are what you dissolve in the solvent. or the water. That would be the salt.
That would be the sugar. Now hydrophilic, hydrophobic. Hydro means water.
Philic means loving. Phobic means fearing. And so hydrophilic molecules attract the water to their surface. Hydrophobic molecules do not attract water. In fact, they can repel it.
Now when you dissolve salt, we saw on the other side where we took sodium, chlorine, and then in an ionic bond, these were joined together to form a solid table salt. But when you put that table salt into liquid water, the hydrogen or the polar charges on these individual water molecules interfere and actually can break that covalent bond. So you get... individual sodium atoms and then you get individual chlorine ions floating in the water that's why salt dissolves because you literally break that bond you get rid of that solid because of those hydrogen bonds water molecules are said to be cohesive and adhesive water molecules cling together because of hydrogen bonding And again, that's that partial positive, that partial negative.
Water's positive and negative poles allow it to adhere to polar surfaces. That's the little drop of rain that sits right on your windshield and doesn't want to go anywhere. That's the water adhering to that glass. Water is used as a transport system. Your blood is almost all water.
It acts as a solvent. and then it can transport all of those solutes to any part of the body whether it's the food going to your cells the oxygen going to your cells or the co2 coming back out or the waste products coming back out so water is an excellent way to move things around living things water also has something called a high surface tension again that has to do with the hydrogen bonds In fact, if you look carefully at water surfaces, even maybe your pool, or if you're lucky enough to have a pond in your backyard, you'll actually see insects that have the ability to land or even walk on the surface of these bodies of water. That's because that water at the surface, those molecules are really sticking together. Other properties of water include it freezes at low temperatures and This is important because when water freezes it actually expands and when it expands it becomes less dense.
It weighs less. So for example if you have 100 mls of liquid water and you have 100 mls of solid ice that you've measured out, that ice is actually going to weigh less than that liquid water. And it turns out that's important because that allows ice to float.
Now, when ice floats in lakes and oceans and streams, it actually protects the water underneath of it from freezing, and that's important so it allows all those organisms that are underneath to stay alive. If ice actually was more dense or it was heavier, all that ice would float to the bottom, and then... and all those bodies of water would literally free solid, and the diversity on this planet would go way down because none of those organisms could survive. So if we look at this example, on one side we have liquid water, on the other side we have ice.
And if we just kind of look at the liquid water, we notice that all of these individual water molecules are much closer together. This is said to be more dense because you have more of these within a given area. Now ice, when it freezes, when that water starts to chill, right before it turns to a solid, these hydrogen bonds form, but they also start to push each other apart.
So these water molecules now tend to form this crystalline structure, and it's not as dense. We don't have as many of these water molecules in the same space. as we do with liquid water. And so for that reason, that's why ice literally floats. In biological systems, we need to talk about acids and bases.
Now water is right here. And then again, this is a kind of a simplified version where we have one oxygen. We know that water has two hydrogens, single bond indicated by that solid line.
This is water. When we look at a chemical equation, these arrows mean a reaction or something's happening between this side and over on this side. Water has the ability to either break down into hydrogen ions and hydroxide ions, or it can rejoin back to water.
So that's what's indicated by this direction and this direction. When we have hydrogen ions, this is denoted as H+. When we have an OH together, this is known as hydroxide ions, and this is denoted as OH-.
This is what's going to drive differences in pH. So in acidic solutions, we have a high H+. concentrations. So acids by definitions are substances that release hydrogen ions when disassociated in water. HCL.
HCL stands for hydrochloric acid. This is a really strong acid. It would burn you in some instances if it was strong enough. But in water, it can donate these hydrogen ions, and that's going to be acidic, and then the chlorine is going to branch off there too.
And so you're getting the hydrogens from here. The more hydrogens you have in solution, the more acidic your solution is going to be. Now base, base solutions, these are low pHs and it works the same way in where we take something, we break it down in water, sodium, hydroxide, we break it down, we get sodium, and then we get this hydroxide component here, which is negative.
And the more of these, we're going to change the pH or make it more basic. So basic. is more hydroxide, acidic is more hydrogen ions.
Now here's a simple graph. It kind of outlines the difference between acidic and basic. First looking at this inner circle, the more acidic it is, it's going to be given this numerical value. The lower the number, the more acidic the more potentially harmful it is to organisms. So we have higher amounts of hydrogen ions over here.
We go up, less acidic, less acidic, until we get to a balance where there's now the same number of hydrogen ions than there is of hydroxide ions. And so we get to something called 7. This is considered neutral. We start swinging over on the other side. We go up all the way to 12, 13. In 14, this is where we have almost entirely hydroxide ions.
And again, these are very toxic to organisms. So things on the opposite scales aren't really good for biology. So if we go right here in the middle, we have pure water.
This would be distilled water. These are the tears that you make when you're happy or you're sad. Starting to work on the acidic side.
Milk is slightly root beer. urine produced by the urinary system rainwater it turns out is a little bit acidic because it picks up a lot of co2 as it drops down coffee has an acid component to it tomatoes starting to get a little more acidic vinegar soda lemon juice stomach acid is really tough stuff and then i mentioned earlier hydrochloric acid this would this would literally cause burns in your skin Starting back at that neutral, if we start going more basic, human blood. Human blood actually has a pH of about 7.45.
It needs to maintain that. Remember in Chapter 1, I talked about homeostasis. This is where human blood comes in. We have egg whites, baking soda, antacids.
Antacids are basic, so if you have an acid environment in your digestive system, you can kind of bring it back. You can neutralize it. Great Salt Lake. Ammonia cleaning products, these are all really basic.
These are all really bad for you once you get over here. So acidic, punchline, lots of hydrogen ions. Basic, lots of hydroxide ions. So acids and bases need to be balanced, and that's where buffers come in, especially in organisms.
By definition, a buffer is a chemical or combination. of chemicals that keep the pH within normal limits. So in your bloodstream, you have bicarbonate ions and carbonic acid. These are normal human blood buffers. And again, the pH of your blood needs to be around 7.4, 7.45.
You want to keep it right there.