Chapter 3: Biochemistry of the Molecules of Life

Talk about a scary chapter title: Biochemistry of the Molecules of Life. I don't even know if I want to keep on reading... But we're not going to let my lovely textbook's titles get the better of us.

Molecules: Organic and Not

The term Organic is used to define complex molecules (which would be all molecules) that are synthesized (a.k.a made) by life forms. Very few Organic molecules can be synthesized in laboratory settings. Most, if not all Organic Molecules contain Carbon and Hydrogen. There are four classes of organic molecules: 

1. Carbohydrates (also known as sugars)
2. Lipids (also known as fats)
3. Proteins
4. Nucleic Acids (including DNA and RNA)

These four groups come together to create all cells and organisms. 

Organic Chemistry is the study of how exactly Carbon, Hydrogen, and Oxygen help maintain the life and energy cycle. My textbook tells me that an organic molecule begins with photosynthesis, which we will remember is a method used by Producers to create sugars using the energy of the sun. Because of this, Producers are the center point of all organic molecules. 

During Photosynthesis, Producers fuse Carbon atoms extracted from the air to Oxygen and Hydrogen atoms extracted from water to build Carbohydrates. The carbohydrates are then converted by Producers and Consumers during cellular respiration into energy molecules called Adenosine Triphosphate (ATP for short. But just like with Deoxyribonucleic acid, we'll stick to the full name). The energy from these molecules of Adenosine Triphosphate are then used by the organism to fuel all of its chemical reactions. These chemical reactions are then used to create proteins, lipids, carbohydrates, and nucleic acids.

Inorganic is used to define any molecules that are not biological in origin. Normally, any molecule that does NOT include Carbon is defined by Scientists as Inorganic (remember that earlier we said most, if not all Organic Molecules contain Carbon). There are a few exceptions, but for the most part it is obvious which molecules are Inorganic by looking at their origin. Example: Diamonds contain Carbon molecules, however they are minerals and are obviously not organic.

Organic vs. Inorganic (a.k.a Here's Some More Information )

Organic molecules tend to be big in size with a large number of atoms.

vs

Inorganic molecules tend to be very small, with very few atoms involved.

- - - - - - - 

Organic molecules are always bonded using the Covalent bond.

vs

Inorganic molecules usually bond using the Ionic Bond.

- - - - - - - 

Organic molecules contain Carbon atoms.

vs

Inorganic molecules do not contain Carbon atoms (a few exceptions)

Molecular Formula and Isomers

Up until now, we've used molecular (or chemical) formulas to write down atoms "scientifically" (such as H2O and NaCl). Unfortunately, because Organic molecules have more complex combinations, the molecular formulas aren't specific enough for us to use when describing an individual molecule. The molecular formula only tells us the amount of atoms within a molecule, it doesn't include how the atoms are linked together. It'd be nice if we could just continue using this simple form of writing molecules, but if we did sooner or later we'd run into problems. Those problems are called Isomers.

Isomers are like identical twins in the molecular world. They share the same molecular formula, but are composed differently. My textbook gives the example of Butane and Isobutane. Both of these molecules have the formula of C3H10, but structurally they are quite different. 

Note the differences in appearance.

It doesn't look like much, but the way the atoms are arranged structurally is important because it changes other properties of the molecules, both Physical and Chemical. Using Butane and Inobutane, it's interesting to note that while Butane boils at -1 degrees Celsius, Inobutane's boiling point is at -12 degrees Celsius.

Isomerization is the name used by Scientists to describe multiple molecules with the same molecular formula but different structural appearances (like Butane and Inobutane). In such cases, structural formulas (like the ones in our example) are used to given more information. A structural formula shows the bonds between the atoms of a molecule, preventing any confusion about which molecule is which. At a glance it looks kind of crazy, but in reality the formula is actually quite simple.
My textbook tells me that it should be noted that the structural formula of a molecule can be used for any type of molecule, organic or inorganic. So no one's left out here.
The Bohr model still contains more information, but it's so big and burdensome (and takes forever to fill out nicely) that it would be too difficult to write it out for every single molecule (especially since most organic molecules have several hundred atoms). The structural formula, however, is a nice way to get the need data quickly.

3D... Or Just 3 Dimensional

So far, we've been define atoms and molecules in 2d (using both the structural format and the Bohr model). In reality though, atoms aren't flat like the paper in my textbook or the screen on your computer/phone. If technology allowed us to make a diagram that showed what a single molecule really looks like, there would be atoms sticking out the screen towards you and away from you. With the way things have been going in the tech-world, we just might be able to in a couple of years, but today we’re out of luck.

It’s important for us to know the 3 dimensional nature of molecules because (like we learned from the previously) organic molecules are large, and the way they work often depends on how their atoms are arranged in their structure.

Bonding Time

In the diagram of Butane and Inobutane, the structural formula was shown in all its "bloom and glory" (whatever that means). The single lines you see between atoms are representations of single Covalent bonds connecting each atom in the molecule. This is a way to show that the atoms are sharing an electron pair. So we're done here... Ha, yeah right. There's more then one way to bring two atoms together *insert evil laugh here*.

- Double Covalent Bonds

Meet Ethene (also called Ethylene). It's a colorless gas that's highly flammable and has a unpleasant, sweet smell and taste.

When there are two lines drawn between atoms, it's called a Double Covalent bond. The double bond shows us that (in Ethene's case) the carbon atoms are sharing two pairs of electron.

- Triple Covalent Bonds

This is Acetylene. It's a colorless, flammable gas that is used for cutting and welding metals.

When three lines are used between two bonded atoms, they are demonstrating a Triple Covalent bond. And, like with the others, the triple bond indicates that the atoms are sharing three pairs of electrons.


While both Ethene and Acetylene are flammable gasses, when exposed to heat Acetylene produces a flame much hotter then Ethene ever could. Why? It's because of the Triple bond. Triple bonds are harder to break then Double bonds, and likewise Double bonds are stronger then Single bonds. The strength of the bond effects the properties of the molecule. In Acetylene's case, the energy released when these bonds are broken attributes to the higher temperature in the fire. 

Cool, right?

This is Acetylene in its prime.

Chapter 2 - The Composition and Chemistry of Life - part 4

Well, we've come far! ( < that was sarcasm by the way). Actually, we're almost done with this chapter, so all in all we have come far. Kind of.

Reactants and Products

This part of the chapter starts off by describing the equation given in the previous lesson. In that distant lesson we went over Covalent and Ionic bonds, and this equation shows what happens when Sodium Chloride (the NaCl on the left) mixes with water (the H2O). In review, the water breaks apart the Ionic bond that was keeping the Sodium and Chlorine atoms together and we're left with lonely, separate Na and Cl atoms. When using this Chemical equation, Scientist use the terms Reactants and Products to distinguish the different parts of the equation. The molecules/atoms on the left side (in this case NaCl) are referred to as the Reactants, while the atoms that make them up (Na and Cl separately) are called the End Products or simply Products.

Law of Conservation of Mass

 In the equation given above, the number of Reacting atoms equal the same amount of atoms in the End Product. This balance of molecules is called the Law of Conservation of Mass. Scientist love to label things, especially things that are always true in every circumstance.

The Law of Conversation of Mass means that no matter what, you will always have the same number of atoms at the end as you did in the beginning. A random atom (or molecule) can't just appear out of no where. Okay, so right now we're probably all thinking "well obviously you're going to have the same amount of atoms as when you started out". The reason this is used in Chemistry is because, by knowing that this is a Law and therefore can't change, scientists can figure just how many molecules can be made from a given number of products. 

For example we'll take Sodium Chloride again. We know that there needs to be one Sodium atom and one Chlorine atom to make the Reactant Sodium Chloride. Say a group of 6 Sodium ions and a group of 6 Chlorine ions come together. How many Sodium Chloride molecules will be created? . . . If we all said 3 then we're all right (give yourself a pat on the back). Now, how did we know that 6 Sodium atoms and 6 Chlorine atoms would make 3 Sodium Chloride atoms? Why not 4, or 7? The answer is the Law of Conservation of Mass. We know that, no matter what, there will always be 6 Sodium atoms and 6 Chlorine atoms and when combining one of each with each other we get three pairs - 3 NaCl. New atoms could not suddenly appear and make more Sodium Chloride molecules, nor could any of the atoms we already had disappear suddenly.

Water (duh, Duh, DUH)

This part of the lesson really takes us in a different direction. I mean, we have Reactants and Products, and the Law of Conservation of Mass, and then (all of a sudden) we have water. Talk about unexpected. 

According to my lovely textbook, it's important for us to understand the molecular structure of water because it's a key role in most if not all organisms. 70%-80% of the matter of any organism is water (us included). The reason is because of how water is made up. 

We remember that, in the previous lesson, we went over how H2O is formed by Covalent Polar Bonds, and that the result is an atom with a slightly negative charge on the Oxygen side and a slightly positive charge on the Hydrogen side (note that it is not an ionic bond though). What we didn't go over what that, because of this unique structure, the water atom ends up being very compatible with many different types of atoms (including salts, sugars, and proteins). 

Also, the unique polarity of H2O allows it to form a completely new type of bond: a Hydrogen Bond.  Because the electrons shade towards the oxygen atom, and therefore the oxygen has a slightly negative charge, it attracts other slightly positive hydrogen atoms from other water molecules. Scientists refer to this as a Hydrogen bond most likely because, when you see a cluster of water molecules, the Hydrogen bond is what keeps them together.

"Another property of water that allows for hydrogen bonding is the actual structure of the molecule itself." Notice that in the model above the water molecule isn't a straight line of atoms; it looks more like a "Mickey Mouse" head (we take this time to thank Walt Disney for inventing Mickey Mouse, for without him we'd be at a loss as to how to describe the structure of a water molecule *moment of silence*).

*Ahem* Back to H2O. The water molecules structure as a "Mickey Mouse head" allows other water molecules to fit in the open spaces tightly, like so:

This special structure allows the Hydrogen bond to be much stronger then it would be normally. 

According to my textbook, the final property of water that makes them special is that that the temperature of water rises and falls very slowly (in nature). This allows organisms to obtain homeostasis.

Solutions, Solvents, and Solutes

Speaking of water, did you know that it's a solution? Well, yes, it's a solution to droughts and thirst and how to grow a good vegetable garden, but we're pretty sure that's not what the textbook meant. A Solution is a homogeneous combination of atoms, whether in the form of a liquid, solid, or gas. Homogeneous means the "same throughout". Here's an example: ocean water is a homogeneous solution of NaCl (which we'll remember is Sodium Chloride, a.k.a salt) and H2O molecules. Even though they are mixed together, the atoms are still the same (hence the "homogeneous").

Now we know how scientists love to label things, so here's a couple more labels for us. When looking at a solution, there are at least two different molecules mixing together. The Solvent is what scientists call the group of molecules that make up the bigger part of the solution (in this case the water), while the Solute is the group of molecules that make up the small part of the solution (in this case the NaCl). This is just to better organize the make up of life around us.

The reason this is important? Well, most, if not all, organisms live within solution environments. We living in a world where the air is a solution of oxygen, hydrogen, ozone, and a good many other molecules. Fish live in a world where the water is a solution of either H2O and NaCl, or H2O and whatever it is that lies in fresh water. If that's not enough to prove that this is important then: my textbook tells me it's important to understand about solutions so *ahem* it's important!

Acids and Bases and Porcelain Vases

Alright, that title was obviously just a joke. I mean: Acids and Bases no, but learning about Porcelain Vases in science? More importantly Biology? I don't think so. Now, about Acids and Bases.

In most solutions, the solvent is water, but the concentration of hydrogen ion, H+, and hydroxide ions, OH+, varies. These ions naturally build up within water, even if it's "pure" H2O, and the ratio of which one is the solvent and which is the solute changes the acidity of the solution. A solution that has more H+ ions then OH- ions is an acid, while a solution with more OH- then H+ is a base. The more H+ ions there are the stronger the acid, and likewise the more OH- there are the more basic the solution is.

pH Scale

Look a pH scale! Okay, now what is a pH scale? Simply speaking, it's a chart that allows scientists to organize the acidity of any given solution. Unlike most scales, this one doesn't start at 0, it starts at 7. 7 is the considered "neutral" in the pH Scale. This means that pure water has an equal amount if H+ ions and OH- ions and is neither acidic nor basic. It's right, smack in the middle. Oh look, blood is there too, so that means it must also be a neutral solution.

Now, in the pH scale you can go either up or down. The higher you are in the scale, the lower your number is and the more acidic you are. The lower you are on the scale, the higher you are in numbers and the more basic you are.

NOTE: My lovely textbook tells me to be aware that sometimes basic solutions are called alkaline solutions.

Hey, a Porcelain Vase! ... I just couldn't resist. 

Indicators

Scientists can add various liquids to a solution in order to tell whether it's an acid or a base. These liquids are called indicators and are usually chemicals that change color in a solution. The scientists use the color to determine the number of a solution on the pH scale.

This is the end of Chapter 2! *gasps in relief and goes to make lunch and read some more from biology textbook*

Chapter 2: Composition and Chemistry of Life - Part 3

It's not that this chapter is particularly long; there's just so much to cover in here (and it doesn't help that life doesn't take a break). Chemistry is so intense it needs its own subject, so to ask for a description of even the basics of Chemistry is a lot, right? So please don't be mad at me for settling this post so late. Please.

Molecules

Molecules are two or more atoms joined together, we know that. What we didn't know is that the reason atoms come together is because they're more stable then when their apart. Hmm, that's sort of like how it is with people. *Ahem* Back to atoms. The reason they're more stable is because when atoms come together, they're electron shells fill up (remember that an atom is stronger the more electrons it has in its shells). We already went over how the maximum number of the electrons in the outer electron shells is 8, and when atoms come together they most often fill the outer levels to the max. This is called the Octet rule.  This isn't a rule made by the Scientists (despite how it might sound), it's more like a name given by the Scientist to classify something that nature does naturally.

NOTE: Hydrogen and Helium are special cases; their outer shells can only hold 2 electrons. In their case, the Octet Rule is changed to a Duet rule.

Bonding Time

So molecules are two or more atoms when they come together to fill their own electron shells, but that's just the over view. Science is all about getting down deep and understanding just how it happens. In this case "it" is called a Chemical Bond. Now obviously atoms don't bond the same way we do. They don't scheduled little "atom outings" where they get together and go shopping or bowling. A Chemical bond occurs when the "electrons in one atom interact with the electrons in another atom, causing the two atoms to 'stick' together."

As a way to write when a Chemical bond has occurred, scientists have developed the shorthand method of writing atoms after they've "bonded".

A well-known name for water, H2O is the shorthanded way of writing:
 2 Hydrogen atoms + Oxygen atom
 Because they are all written together, we know that Chemical Bonds have taken place in order to combine these three atoms. 

I'm going to use the example given to me by my lovely textbook. In the equation  H + H = H2, "H" is the Atomic Symbol (remember those?) for Hydrogen, and the plus sign shows that the two single Hydrogen atoms have come together through a Chemical Bond to form H2 (two Hydrogen atoms stuck together).

Okay, that's a really dull explanation (I mean: two Hydrogen atoms, Huzzah!), but basically it shows us how scientists write when a Chemical Bond has occurred 

One Chlorine atom all alone.

Two Chlorine atoms after a Chemical Bond.

In the models above (called a Bohr model), two Chlorine atoms have bonded together. I've made it so we can clearly see where the bond has taken place. A Chlorine atom originally has 17 atoms (two in the third shell, 8 in the second shell, and 7 in the outer shell). Each Chlorine atom has just one electron less then the maximum electron in the outer shell. So when they come together, one electron from each atom attaches to the other's shell and fills it to the maximum complicity. Do we get it now?

Covalent and Ionic Bonds

There are actually two different versions of a Chemical Bond: Covalent and Ionic. Meaning that there are two different ways that electrons can be shared by atoms during a Chemical Bond.

Covalent Bonds

The first bond, Covalent, is formed when the electrons shared during a Chemical Bond are equal. So for example, the Chlorine atoms above are in a Covalet bond because both atoms are gaining 1 more electron.  Each Chlorine atom has 7 electrons in the outer shell, so when they share one atom with each other they suddenly have eight electrons, filling their outer shell and creating a Covalent bond. I'll put another example of a Covalent bond below.

Look at the lonely Hydrogen atom. Talk to the lonely Hydrogen atom.  

Now watch as this lonely Hydrogen atom meets another Hydrogen atom. Now these two not-so-lonely Hydrogen atoms are in a Covalent bond because they each share the same amount of electrons (1). At the same time, the Duet Rule is being fulfilled because the outer shells of both atoms are full (remember that Hydrogen and Helium can only have two electrons in their outer shell). 

*sales person voice* But wait, there's more! Within the category of "Covalent bonds" there are two separate types: Polar and Non-Polar. Non-Polar Covalent Bonds form when there's equal sharing of the electrons (the Hydrogen atoms above are an example of a Non-Polar Covalent Bond). Each atom is sharing the electrons between them equally. Polar Covalent Bonds are formed when the electrons are being shared slightly unequally. Let's take H2O as our esteemed example.

In the Covalent bond for water, notice that despite the fact that all the atoms are still connected and still sharing each other's electrons, the electrons are more attracted to the Oxygen atom. Also note that the nucleus of the oxygen atom is quite a bit larger then the nucleus of both Hydrogen atoms. This is because the Oxygen as more protons in its nucleus (giving it a slightly positive charge) that "pulls" the electrons toward it (remember that electrons have a negative charge and opposites attract). Since the electrons are closer to the oxygen atom, the oxygen's side of the bond has a slightly negative charge (which would explain the subtraction a.k.a negative sign on the bottom of the figure). At the same time, the Hydrogen atoms are left with a positive charge because the electrons have left them (and now we know why there's a plus a.k.a positive sign near the top of the figure).

Both Non-Polar and Polar Covalent Bonds are much more stable then Ionic bonds because the atoms are actually attaching to each other through their electrons, instead of simply sticking together due to their charges. It takes a lot more strength to pull a Covalent bond apart then it does to pull apart an Ionic bond. According to my lovely textbook, there's no such thing as a "perfect" Covalent or "perfect" Ionic", so basically atoms are categorized by how familiar they are to one of these classifications, though they may have characteristics of both. 

Ionic Bonds

  Ionin means that the bond has a charge added to it. Looking back to the Covalent bonds, we'll remember that each atom is made up of protons, electrons and neutrons; protons have a positive charge, electrons have a negative charge, and neutrons have no charge. An Ion is a whole atom that has a charge, and this only happens when there are more protons then electrons, or vice versa. An atom with more protons then electrons has a positive charge and is known as a positive ion, while an atom with more electrons then protons has a negative charge and is labeled as a negative ion. Simple enough, right?

Since a negative ion and a positive ion have opposite charges (and opposites attract) they are attracted to one another. This attraction is strong enough to for a type of bond purely on their charges: Ionic. So basically instead of sharing electrons and attaching to each other, like in a Covalent Bond, they are simply sticking together. Like we put down before, Ionic bonds are much easier to break apart then Covalent Bonds.

Now my lovely textbook has decided to explain itself, or rather, explain why and how Ionic Bonds form. Sadly for us it's description is quite boggled down with lots of extra words, so let's help it out a little. :)

How Do They Work?

By "they" we mean Ionic Bonds, and interestingly enough, it's not as simple as it might at first seem. Though my textbook tells me that we will be going over this again in Chemistry, I think that we should still understand it a bit more, right?

I'm going to use the atoms given as an example in my textbook for our own example. First question  why do atoms form Ionic bonds? We know that in Covalent bonds their filling out their own electron shells, but it's different in Ionic bonds, right? Wrong. When forming an Ion (which is the first thing needed in an Ionic bond) atoms become more stable, and here's how:

In Sodium Chloride (also known as table salt), the Sodium atom (with the atomic number of 11) has 2 electrons in the first electron shell (a.k.a energy level), 8 electrons in the second energy level (full), and only 1 in the third. On the other hand, the Chlorine atom (atomic number of 17) has its first and second energy levels completely full (so there are 8 electrons in each level, completing the Octet rule), and has only 1 space open for another electron in its third level.

On the left we have a Sodium atom (don't ask me why its Atomic symbol is Na, it is unknown to me). On the right we have a Chlorine atom (whose Atomic symbol makes much more sense). I've circled certain parts of the atom in order to bring our attention to them.

When these two atoms are combined, this happens:

First the lonely electron from the Sodium atom leaves (or is donated) to the Chlorine atom, filling it's third shell and completing the Octet rule. Since Sodium is "donating" an electron, Scientists have labeled it as an electron donor. Since the Chlorine atom is accepting the generous gift of the Sodium atom, it's called an electron acceptor. Now due to this little exchange of electrons the Sodium atom has less electrons then protons, it has a positive charge (so it's now known as Mr. Sodium ion). Meanwhile the Chlorine atom, since it's gained an additional electron, now has a negative charge (and is now known as Ms.Chlorine ion). Of course, like we already know, opposites attract and in this case the opposite charges of the Sodium ion and the Chlorine ion are so strong that they create a bond themselves. That's the Ionic Bond. So really, unlike the Covalent Bond where electrons are being shared by both atoms and are attaching to each other, atoms with an Ionic bond are simply sticking together due to their charges.

So why do atoms like to use the Ionic Bond? The answer: because it makes them more stable. With the Chloride atom it's easy to see that the Ionic Bond is making it stronger because its third shell is completely full. But how can it make the Sodium atom stable when it's loosing an electron? The logic behind this actually makes sense! When the lonely electron in Sodium's outer shell goes to the Chlorine atom's outer shell, Sodium's third shell disappears with it. So now Sodium is left with a full outer shell (the second shell), get it? My textbook says that we shouldn't get boggled down with this because we'll be going over this in Chemistry, so no worries if we don't get it right now.

When it comes to breaking apart Ionic bonds, here's a simple example. Who's ever put salt in water before? Maybe it's not a hobby, but for the most part I think we all have either when we're cooking or doing a science experiment. When combined with water, salt (a.k.a Sodium Chloride) breaks up and dissolves, right? The reason is because the water is breaking apart (or dissociating) the Ionic bonds between the Sodium atoms and the Chlorine atoms, leaving them once again as lonely Na and Cl atoms. (*sniff*)
Chemically, this is written as:

That's all I'm putting for part 3, but part 4's coming soon (doesn't that sound like a movie review?).

     

Chapter 2: Composition and Chemistry of Life - Part 2

-_- Science is such a bore sometimes, isn't it? Don't we just hate it sometimes? Don't we just want to throw this journal of ours' into the nearest digital trash can? Yes, yes we do; but come on, we can show those lovely textbooks that Science is made up of more than just long, dull paragraphs!

We left part 1 (a long time ago I might add) with a definition of what made up an atom... So, want to review? Um, ah, mm, meh, uh... No, we don't. Normally that would be terrible, but since this is a journal where we are putting down our lessons, we can just read the previous post so there's no need to review *pumps fists*. We're not done though, so keep reading because we're moving onto the more detailed part of Chemistry Life.

The Categories

I wonder if scientists have OCD (Over Compulsive Disorder). I mean, is that why they feel inclined to list, label, categorize, and otherwise organize every single little detail in the world of Science? We have to admit though, in the long run it does make it easier to remember everything when it's categorized just so. With that in mind I suppose its no surprise to us when we read these next few ways of organizing what-is-what and who-is-who regarding atoms.

Atomic Properties

Now we're going to go over how atoms behave when they're with other atoms, and it has a lot to do with their Electron Shells so it's a good thing we went over those very things in part 1. The properties of an atom means how one atom behaves when it meets another while strolling through the supermarket. What? That's not the case? Well, we're not that far off anyways. The true definition: the properties of an atom (or how an atom behaves when exposed to other atoms) are determined mostly by the number of electrons that atom has. According to my lovely textbook, it has been proven that atoms possessing Electron Shells with less then the maximum number of electrons it can hold (or simply put: unfilled Electron Shells) are more likely to combine (react) to other atoms with unfilled Electron Shells. Likewise, atoms with filled Electron Shells (have close to the maximum number of electrons) are less likely to react with other atoms with filled Electron Shells.

Remember that the maximum number of electrons in the first shell is 8. So obviously the atom on the right hand side has a full shell (which, FYI, is Neon. No, not Neon like "Neon Green". Neon like the element. There's an element called Neon? Yes, yes there is). Because the element of Neon has a full electron shell, it's harder for it to react to other elements because there's no place in the first shell for another electron from another atom to attach to. In the atom on the left hand side (Carbon), there's lots of room for more atoms to join in. Only four electrons are in the first shell of the Carbon atom, so another four electrons can join in.

Atomic properties depend a lot on the formation of an atom's Electron Shell. What do we mean by this? Well, say we have an atom whose electron shell is unfilled, but most of it's electrons are on the outer levels of the shell. Those electrons act as a wall towards other atoms, preventing them from reacting with each other. It's sort of like when your friend crosses his arms when you try to hug him, so your just sort of left in an awkward position... *silence*... Was that the best analogy we could come up with? -_- Never mind. The point is atoms find it difficult to react with one another if they have a lot of electrons in their outer levels.

Isotopes

What kind of a wacky name is "Isotope"? The scientist that made this one up must have been having a good morning; or it could just be that the Greek roots isos and topos mean equal and place, which would make a lot more sense. As we all know by now, an element (another word for atom) is defined by the number of protons and elections it has (as seen in the previous part of Ch 2). There is only one atom which contains 6 protons and 6 electrons, and that is Carbon. As my lovely textbook states "All elements (atoms) are defined by the number of protons and electrons the atom contains."

However there are some atoms that can contain different numbers of neutrons and still be the same element. Like we were going over before, some elements have different forms that can change in the number of neutrons they contain. These special atoms are called Isotopes. "Why is this important?" We ask, "After all it's the electrons and protons that define an atom." Well, the neutrons have a role to play too, not just the dashing little electrons and bulky protons; this "third wheel" is important!

Let's continue using carbon as an example, shall we? According to my lovely textbook, there are three isotopes of Carbon: Carbon 12, Carbon 13, and Carbon 14. Each one still contains 6 protons and 6 electrons, but Carbon 12 has 6 neutrons to go along with the 6 protons in the nucleus, so it's Atomic mass is more or less 12 (this is the isotope we put up as an example, and we didn't even know it!). Carbon 13, on the other hand, has 7 neutrons sitting next to its 6 protons, so its Atomic mass is roughly 13 . On our imaginary third hand, Carbon 14 had 8 neutrons living besides 6 protons, raising the Atomic mass of this isotope to about 14. Due to the fact that all three isotopes still have 6 protons and 6 electrons, they all behave the same way, but their build (the way they're made) is not the same because of those different neutrons (the third wheel's not such a third wheel now, hehe).

Comments

Yes! I don't know what happened, but suddenly the comments have started working. Once again, I encourage any readers who have questions, comments, or concerns on a lesson to please comment. We want to learn, don't we? Well... That answer may be a so-so, so instead we'll just say that we'll keep going over our lessons and hope for the best... *talks to self* Yes... Yes that sounds better... Okay... *continues to mumble*.

Chapter 2: Composition and Chemistry of Life - Part 1

We shall all wave "good-bye" to my textbook's lovely Introduction and wave "hello" to the next chapter in this scientific tale.

Chapter 2

Chapter 2 is focused mainly around Chemistry (as is hinted in the title), meaning that we will be spending our time in this post learning about the composition of Life's building blocks (atoms and molecules). First, though, we should go over one thing: Matter and Mass. Okay, that's two things.

Matter and Mass

Matter is anything that takes up space in the world, and mass is the amount of matter that that particular thing has. So the more an object takes up space, the more mass it has. The computer you're using to read this has a mass. If you're using a phone to read this: your phone also has a mass, but chances are its mass is a lot less than the computer's (unless you have a really big phone or a really small computer). 

Mass does not equal weight though! The weight of an object depends on the amount of Gravity pushing on that object, where as the mass of an object is the same no matter where it is because the amount of space an object takes up never changes. "Why is this important?" We ask. Let's see.

Atoms and Molecules

All matter (that would mean all objects) are made up of "basic building blocks", meaning atoms. Atoms, when they come together, form the things we see all around us; I guess that makes them the Lego's of Life.

To understand better, an atom is divided into two parts: the Nucleus and the Electron Shell. The Electron Shall is the outside of an atom, while the Nucleus is made up of subatomic parts (that's parts even small then an atom) inside of the shell. The subatomic parts that make up the inside of an atom are called Protons, and Neutrons. Now wait a minute, where are the Electrons? We'll see. First, though, here's a little of what makes up an atom:

• Neutrons - The Neutrons are located at the center of the atom (Nucleus). They have no charge.
• Protons - Protons have a positive charge and are located in the center of the atom (Nucleus).
• Electrons - The Electrons have a negative charge and are located on the outer part of an atom, in the Electron Shell (there are those Electrons, on the outside).

Here we have a diagram of a Carbon atom and can clearly see the positions of  the Protons, Electrons, and Neutrons.

Protons and Neutrons (which make up the Nucleus) are much bigger than Electrons (on a molecular level anyways), and so it makes sense to say that most of an atom's mass is found in the Nucleus. Despite their different sizes, the charges of both the Protons and Electrons are equal. So the negative charge of one Electron is just as big as the positive charge of one Proton. On another note: no matter what type of atom they are a part of, Protons, Neutrons,  and Electrons are always the same.

The Periodic Table of Elements is a system used by Scientists to list the many different types of atoms. We'll use Hydrogen to list the use of each number and symbol in the system (and we've enlarged it so as to avoid the use of magnifying glasses). On the top of each Element in the Periodic Table is the name of the Element. Each Element is given an abbreviation, or symbol, composed of letter(s). These abbreviations are called the Atomic Symbols (in Hydrogen's case, its Atomic Symbol is H). Under the name of the Element, and above the Atomic Symbol is a number (in this case the number 1) which is called the Atomic Number. The Atomic Number lists the number of Protons the Element has. Although atoms are extremely small (and Protons, Electrons, and Neutrons even smaller), they still have a mass just like everything else in the world. The number under the Atomic Symbol is called the Atomic Mass (yes, there are a lot of "Atomics" running around) and the Atomic Mass is, that's right: the amount of mass each Element has.
The amount of mass for each Proton is equal to 1 Atomic Mass unit; a Neutron is slightly more than 1 Atomic Mass; a Proton is very, very small and so have very little Atomic Mass. According to my textbook we will learn much more about this later on (don't we hate that?).

We've gone over the Nucleus part of an atom a bit (Protons and Neutrons), but haven't done much on the second part of an atom; on to the Electron Shell!

Also known as Clouds or Orbitals, the Electron Shell is made up of, wait for it: Electrons (we saw that coming). Electrons orbit around the Nucleus sort of like the way the Planets orbit around the Sun. There are several levels in the Electron Shell, depending on the atom. The Hydrogen atom has only one energy level (or shell), but there are other atoms (such as the Argon atom) that have up to three shells. Each shell is able to hold a certain amount of Electrons. The first shell can hold a maximum of 2 Electrons; the second shell can hold a maximum of 8 Electrons; the third shell can hold a maximum of 18 Electrons; and so forth and so on. Except for in the first level, Electrons travel in pairs as they orbit around the Nucleus.

The Argon atom has 18 Electrons and three shells.

That's all for part 1 *sigh*, now onto part 2.

Taxonomy System

Well look at that! Not even three minutes after my last post I suddenly gained the ability to view our wonderful Journal again! Well, now that that's over and done with on to the next lesson!

Taxonomy system

Perhaps this should be called a sub-lesson, since technically this isn't really a lesson in my textbook at all. Each class in the Taxonomy system is a rank/class, organizing each organism into their own category (and it's funny how textbooks never really get around to explaining what each rank means. So much for those long, incredibly dull paragraphs). For each Rank there are sub-categories, which are "immediate minor ranks" used to arrange organisms even further. We'll have a sample of some sub-categories for each rank, but for the most part we'll just explain the general ranks for now. If you are truly interested in these sub-categories than comment and we shall proceed in making a post about them.

• Kingdoms - The Kingdom rank is the Highest rank out of the following ranks/classes. The Kingdoms are composed of six different categories: Animalia, Plantae, Fungi, Protista, Archaebacteria (or Archae), and Eubacteria (or Bacteria). One sub-rank is Subkingdom. There is also the class of SuperKingdom which, according to my research*, is a class just above Kingdoms.
• Phylum (or Division) - In Botany (the study of plants; anything in the Plant Kingdom) the term "Division" is used instead of Phylum. A rank lower than Kingdom, organisms in this rank are arranged under different groups based on their similarity. For example: Cheetahs, Elephants, and Hippopotamus' are all members of the Phylum Chordata because they all have similar qualities (in this case the most important being the structure of their spine). Examples of sub-ranks are Subphylum and Infraphylum.
• Class - A Class is similar to the Phylum rank, grouping together animals that have similar qualities within a group in Phylum. Reptilia, Insecta, and Mammalia are three groups within the Class rank. Some sub-categories: Subclass and Infraclass.
• Order - Just as with the other ranks, Order breaks down organisms from the previous ranks into even more specific groups. In the Insecta Class there is the group Diptera, which includes insects possessing two pairs of wings (such as flies and mosquitoes). Example of sub-categories: Suborder.
• Family - Groups found in the Family rank can include a large amount of species that are extremely similar (again, like with the other ranks, these groups are all within other, larger groups in previous ranks). For example: Arecaceae is a group within the Family rank and ever one of its members is some type of Palm tree. Some sub-categories for the Family rank are Subfamily and Infrafamily.
• Genius - Each Genera (group within the Genius rank) has a designed type, something something unique to that particular organism. Subgenius and Infrafamily are two minor ranks (sub-catergories) for Genius.
• Species - We're finally at the bottom! *collapses from exhaustion and then proceeds to type from the floor* The Species is the basic rank, known by pretty much everyone. Within Families you have specific Species that define each type of organism from their closely related cousin, aunt, etc. There is only one type of organism for each species.

We're done! That took longer than I thought.