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Hello. Tonight we are going to talk about basic chemistry. A bunch of this I think will
be a review from your chemistry class. Then we will get into some new information in just
a short time. Atoms are elements of a pure substance that
only contain one type of molecule, one atom. They are the smallest particle that has properties
of that element. In an atom you have the nucleus with protons and neutrons, and you have electrons
buzzing around in electron shells. The shells surrounding the nucleus: the first shell contains
2 electrons and every shell after that, if it is an out shell, can contain 8 electrons.
There are shells that have more than 8 electrons. Those are shells that are interior: the third,
fourth, fifth, sixth and seventh shells can hold more than 8 as long as they are not an
outer shell. Outer shell electrons have a special name for them; they are called valence
electrons. Those are going to be ones involved in bonding with other atoms.
There are several types of bonds we are going to talk about. The first one is called ionic
bonds. Ionic bonds are formed between a metal and a non-metal and the electrons are transferred
between the atoms. For example, sodium has 1 valence electron; chlorine has 7 valence
electrons. Each atom wants to have an outer shell that has 8 valence electrons. It is
called the octet rule. Atoms are most stable when they have 8. So sodium wants to get rid
of its 1 because then the shell that is just inside of that has 8. So it would have 8 valence
electrons. Chlorine wants to gain 1 because if it gains 1, 7 + 1 makes 8, so it would
have 8 in its outer shell. So it wants to gain 1. So to do that, sodium give 1 electron
to chlorine and then they are bonded together; they are held together. That is an ionic bond.
Covalent bonds are formed between two non-metals or a non-metal and hydrogen. What happens
to the electrons this time is they are going to be shared. Sometimes they are shared equally;
sometimes the electrons are not shared equally. We will get into that. If they are shared,
which means, each one again wants to have 8. So here are 2 oxygen atoms. This oxygen
contains 6 valence electrons and this one contains 6 valence electrons. Sometimes this
oxygen will give 2 electrons to this atom so it can have 8 valence electrons part of
the time. And part of the time this one gives 2 to the other one so it can have 8. By sharing
them they create a covalent bond. There are two types (like I said): shared equally and
not shared equally. If they are shared equally it is called a non-polar covalent bond. If
they are unequally shared it is called a polar covalent bond. Polar covalent bonds will have,
because they are not shared equally, one end that tends to be more negatively charged more
of the time and one end that tends to be more positively charged more of the time. For example,
here is a water molecule. Oxygen has 6 valence electrons. Hydrogen has 1. It only has one
shell. So hydrogen wants to have 2 electrons buzzing around. Oxygen wants to have 8 so
it borrows one from each of the hydrogens more. Then by having 8 valence electrons,
it has 2 more negatives than positive protons so it tends to have a negative charge. It
has those 2 electrons more often than the hydrogens have them. Hydrogens rarely have
them but they do a little bit. Because the hydrogen does not have its electron, it has
a positive charge because it has one less negative. So this end is positive (these ends)
and this end is negative. A polar covalent bond.
A nonpolar covalent bond is when they are shared equally and they donít have charged
regions. Molecules that are nonpolar are things like fat, oil, gasoline, things like that,
things that do not dissolve in water, waxes, different things.
That is your basic chemistry part. Now we are going to talk about four major types of
molecules found in all living organisms. The first are called carbohydrates. These are
different types of sugars. All carbohydrates contain carbon, hydrogen and oxygen atoms
in various amounts. Each type of carbohydrate has different amounts of those. There are
lots of different types. We are not going to go into all the different types. Things
like glucose, ribose and deoxyribose (found in DNA and RNA), fructose, sucrose, lactose,
maltose, starch, cellulose, glycogen, glucagonóthere are a whole bunch. These are called simple
carbohydrates. They are monomers which mean they are one single carbohydrate molecule.
These have two monomers connected. For example, maltose is made from two glucose molecules.
Sucrose is made from one glucose and one fructose. Those are disaccharides. The last group is
called polysaccharides. They are made from many of these. For example, starch is made
from hundreds of glucose molecules. To go from a monomer to a polymer you have
to connect the atoms together so there has to be a reaction. The type of reaction that
connects the two monomers is called a condensation reaction. So this glucose molecule and this
glucose molecule are going to connect and form maltose. So what happens is in this condensation
reaction, the OH on this side and the H on this side are going to connect and create
a water molecule. That will leave leaving this bonded to that oxygen right here. So
those two molecules will then be bonded together. That is a condensation reaction. You are giving
off water like condensation on the outside of a glassógiving off.
Hydrolysis is the opposite. Hydro means water; lysis means to cut. So I am going to cut a
sucrose molecule into a glucose and fructose. Remember I had that oxygen that was left in
the maltose, right there. It is there in sucrose too between these two molecules. So I add
water to the reaction. The water is cut, lysed, so an OH goes here and an H goes there. As
a result you break them apart and you have glucose and fructose. That is hydrolysis.
There are two types of glucose molecules. Letís look at the difference between them.
Look closely. What do you see as the difference between those two molecules? It is a very
subtle difference. Hopefully you noticed. The OH and the H are upside down on this one
and this one. This is an alpha glucose molecule. This is a beta glucose molecule. Because of
that subtle difference, your body is able to digest, alpha glucose is able to go through
hydrolysis and break down alpha glucose molecules. Beta glucose molecule is found in things like
cellulose and your body is not able to break down cellulose. You are not able to go through
hydrolysis with cellulose and break it apart. So we cannot digest beta glucose polymers.
We can digest alpha glucose polymers. You can digest starch all you want. You cannot
digest plant cell walls. Does it have a result? Absolutely. You canít
digest cellulose. You can digest plant material. It makes a difference. When we are looking
at various molecules if I say, oh that is a beta glucose molecule, you should start
thinking about how your body reacts to that. Even termites are not able to digest beta
glucose. You think, what a minute, termites eat wood. How can they digest it? They actually
have a little protozoan in their intestines that digests beta glucose and can eat it for
them. Then they can eat the wood. Itís a little mutualistic relationship going on.
You just canít digest it. Here is the structure of cellulose. Each of the shapes is a glucose
molecule and it is beta glucose. The strings of glucose molecules are held together not
only by a condensation reaction in between creating the oxygens, like that each of those
was condensation, but it also has hydrogen bonds between holding them together on the
sides. So it forms these very straight lines of glucose molecules.
The next major type of molecule is called a lipid. Lipids are things like fats and steroids.
They are not water soluble. They are nonpolar. One interesting thing, all four major molecules
except lipids have monomers and polymers, monomers being the basic unit, polymers meaning
multiples of the monomers. Lipids donít. They are all very different molecules. Because
they are all nonpolar, they are all put in this major group. Some have glycerol and fatty
acid chains but not all of them. They really donít have monomers and polymers.
Here are some examples. As you can see, the shapes of them are very, very different. This
is a triglyceride. Have you ever heard of triglycerides in your blood stream? It is
one of the fat molecules that flows around your body. You need some; you just canít
have too much. Steroids: estrogen, progesterone, testosterone and also things like cholesterol
are steroids. Phospholipids. Have you ever heard of a phospholipid? Phospholipids are
the major component of all cell membranes. They have a hydrophilic head region and then
they have two legs that come off. One of them is always bent. Now you say why is that bent?
What happens here is each kink is a carbon molecule, see right here, carbon-carbon-carbon-carbon,
it is just like that. Coming off from each carbons are two hydrogens, except for right
here. Here we have two carbon bonds, that means two electrons are being shared between
the two carbons. As a result it is missing two hydrogens here, one on either side of
that. So it makes it kink. It just bends it, changes the shape of the molecule. All phospholipids
have that kink. When you are looking at molecules what you can do, you look at this and you
say that looks kind of weird? Look up here where it is highlighted, that is a phosphate
group. We know in phospholipids they have a phosphate group. Lipids are going to refer
to the two tail regions where you have carbon-hydrogen, carbon-hydrogen all the way down, right here.
Those are examples of lipids. The next major molecule are called proteins.
They do have a monomer. The monomer of a protein are amino acids. There are 20 different amino
acids in your body. I think of them kind of like letters in the alphabet. I will tell
you why here in a minute. Amino acid has all the same basic shape. They all have this blue
part region identical. Then where this H is coming off, this is called the variable region;
it is called an R group. Each of the R groups has a different shape. There are different
atoms that are attached there. That is what makes them all different. These 20 amino acids
are going to build every single protein in your body. Just like you have 26 letters in
the alphabet that can build thousands and thousands of words, these 20 amino acids can
build thousands and thousands of different proteins. The order of the amino acids will
build the exact protein. That is kind of how you relate it in your mind.
There are lots of different types proteins that can be found in your body. Anything from
structural proteins like spider silk, storage proteins like egg white or albumin, transport
proteins like hemoglobin carrying oxygen, hormonal proteins like insulin or estrogen,
receptor proteins that receive nuerotransmitters in your nerve cells, contractile proteins
like actin and myocin in your muscle cells, antibodies are proteins in your immune system,
enzymesóevery enzyme that runs every single chemical reaction in your body is an enzymatic
protein. So there are several of them. To build a protein you have to create a bond
and the bond is called a peptide bond. To create the peptide bond, oh look at thisódoes
it look familiar, OH H giving off water, yup, that is a condensation reaction, a condensation
reaction resulting in a peptide bond. That is important. To put them together, you have
to go through condensation, you give off water, those two then attach and you have attached
another one. If I want to break a protein apart, what kind of reaction are you going
to go through? Hydrolysis, remember? Hydrolysis = hydro + lysis. You are going to add water,
you are going lyse it (break it, and you can break that off. Hydrolysis. As you can remember,
they all have the same basic shape, here is the same shape on each of them. But you see
the different side chains, the R groups, how each one is different. They are all different.
If you look at the structure of a protein, there are four levels of structure that we
are going to look at really quick now. The first is the order of the amino acids that
build the protein. What order are these going to be in right here? What order are the letters
of the alphabet? The amino acids, like I said, there are 20 of them. Proteins can be anywhere
from 50 amino acids long to 1500 amino acids long. They vary in length depending on what
they are going to be doing. The order of these letters, these amino acids, the order of the
amino acids will determine what protein you have. There are 20 of them. Each one is held
together by a peptide bond caused from a condensation reaction. That is your primary structure.
Peptide bonds hold them together.
The secondary structure takes those amino acids, that chain, and it does one of two
things. It either will take that chain and coil it around forming an alpha helix or it
will fold it like a fan and that is called a beta pleated sheet. Those two different
types are called secondary structures. The bond that holds those together is a hydrogen
bond. There is the word right there. Those dots represent a hydrogen attaching to an
oxygen forming a hydrogen bond. The tertiary structure is next. The tertiary
structure holds the secondary structures together. So the purple line here would be that secondary
structure here. It would be the coil, that alpha helix, or that beta pleated sheet. Here
is that coil or beta pleated sheet. Those side chains that come off now come into play.
One of the molecules has sulfur coming out of it. Because there is sulfur, sulfur is attracted to other sulfur molecules, so
anywhere along here that has another sulfur is going to be attracted to that one. It is
going to cause this to fold back over on itself. Those sulfurs connect forming a disulfide
bridge. There are lots of different types of bonds in the tertiary structure. Disulfide
is one. You can also have hydrogen bonds. You can hydrophobic interactions where these
guys hate water and so they are going to be attracted to each other so they can repel
water. You can have van der Waals interactions. You can have an ionic bond or covalent bond
forming. There are a lot of different reactions in this tertiary structure that are helping
to form the three dimension shape of your protein. Many proteins stop at the tertiary
structure and it now has a three dimensional shape that will perfectly fit another atom
or whatever it is going to react with. Whatever shape it is going to have, this tertiary shape
gives it to them. Some proteins though are built from more than
one protein molecule. If it does, it is called a quarternary structure. This particular quarternary
structure is hemoglobin. It is built from two alpha helix chains (down here in the pink
and purple) and two beta hemoglobin chains. Each of those shapes is a tertiary structure.
Four of them come together, two alpha and two beta chains, come together to create hemoglobin.
Each one of these, by the way, is the heme group, that is where the iron is. It is going
to carry the oxygen. Hemoglobin can carry 4 oxygens.
So just to review, primary structure is the order of the amino acids, that can either
be pleated or it can be a helixóthe secondary structure. Those then get folded and bent
into a three dimensional shape. If several of the three dimensional shapes come together
you can form the quarternary structure.
The last type of organic molecule is called a nucleic acid. These examples include DNA,
RNA and ATP. They are all very, very important molecules that you have to have in your body.
The monomer of each of these is called a nucleotide. A nucleotide is made from a sugar, either
deoxyribose or ribose sugar. Each of those, deoxyribose or ribose, is called a 5 carbon
sugar because they have 5 carbons in them. It is shaped kind of like a pentagon or a
house. They have one of the sugars bonded to a phosphate group and one of 5 different
nitrogenous bases. DNA and RNA are the two most common. So letís
look at their structure first and then we will look at ATP. DNA has the sugar deoxyribose.
RNA has the sugar ribose. DNA is a double helix and it is two sided like a twisted ladder.
You have two sides to your ladder. RNA is like you took a chain saw to the ladder and
cut straight down. You have half a ladder. It is single sided. The nucleic acids found
in DNA are adenine, cytosine, guanine and thymine. The ones found in RNA are adenine,
cytosine, guanine and a new one, uracil. So you have to remember which one has thymine
and which one has uracil. Examples of DNA are DNA. Examples of RNA, there are three:
rRNA which stands for ribosomal RNA and it makes up part of a ribosome, (tRNA) transfer
RNA which it is clover shaped, and (mRNA) messenger RNA. We will find out a lot about
RNA when we talk about protein synthesis. So letís look at that nucleotide structure.
You have that pentose sugar. You have one of the nitrogenous bases and you have a phosphate
group. You can look at the difference between DNA, deoxyribose and ribose and what you are
going to see is that right there. That is your major difference. Look at the difference
in the nitrogenous bases. Cytosine, thymine and uracil have a single ring and there a
slight difference between each of those. I am not going to make you memorize them. Purines
though have a double ring. Here is your DNA molecule. To help DNA make sure mistakes are
not made, when we are going to copy the DNA, adenine and thymine always go together. And
if you look at them, adenine and thymine, these guys are always going to go together.
When they go together, the hydrogens are going to form hydrogen bonds. A & T form two hydrogen
bonds. Cytosine and guanine are going to form three hydrogen bonds. Because a three does
not match up perfectly with a two, adenine will never bond to cytosine or guanine and
thymine will never bond to cytosine or guanine. They are only going to bond to the one they
are supposed to bond to. At least that is the way it is supposed to happen. We will
leave it at that for now. Twos and threes. Hydrogen bonds hold them together.
The last thing we are going to talk about, I think, is ATP, the structure of an ATP molecule.
It has ribose sugar, it has adenine and it has three phosphate groups. That looks almost
identical to the regular nucleotide. It had the ribose, the phosphate group and adenine,
but this time it has three phosphate groups. ATP is extremely important because it is the
energy storing molecule in your cell. When the cell needs energy, it breaks off one of
these phosphate groups and that releases a whole bunch of stored energy in this bond
right here. That energy is released and the cell can use that energy to do whatever it
needs to do. If the cell makes energy, like during respiration or photosynthesis, if it
is going to make some energy, what it does is it takes ADP, diphosphateódi means two
it has two phosphate groups, and it takes one of those and attaches a new phosphate
group to it. In doing so, that energy is stored and can be released when the cell needs it.
This is a really good example of how the cell uses and reuses molecules. That is an ATP
molecule and that is it for today. No homework for today. Have a great night.