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.  

Difficulties

I've not been able to post these past couple of days due to some difficulty with my Journal. I can no longer view my own "blog" and so I am annoyingly unaware of how my own posts are looking. I've never had this problem before and am hoping that it'll clear up in a couple of hours, or days... At the rate it's going though, I think it'll be the latter. I apologize for the lack of posts during this time!

                                           My sincerest apologies,
                                                              Unknown

Introduction Part 2: Classification and the Scientific Method

As with all textbooks, the chapters in my 2-inch-thick book are extremely long (and also particularly dull). Never the less, we shall prevail! The rest of the Introduction is dedicated to the explanation of the methods used by scientists to organize the many different forms of life on this planet, as well as explain a little bit about how scientists do their work.

Classification

In the world there are trillions of animal and plant species, not to mention the many bacteria species that are living alongside us. In order to keep track and organize the many different organisms in the world, scientists developed a system used to classify each species. This system is called Taxonomy, and we just might have heard about it before. In it there are seven levels, and we'll go over them here:

• Kingdoms
• Phylum (or Division)
• Class
• Order
• Family
• Genius
• Species

The farther down the list we go, the more specific the Taxonomy system gets. First, the Kingdoms. While we read up on them we can also go over some examples. Why? It's because we think examples are great! *glares at textbook which lacks considerable amount of examples*

•  Archaebacteria - Also known as just Archae, these are incellular organisms (they have only one cell). Archae have no cellular nucleus and are able to survive in extreme environments such as active volcanoes and sulfur springs. There are not many organisms classified under this kingdom.

Methanogens - These one-celled organisms are Classified under the Archaebacteria Kingdom.  They can appear as either a sphere (like in this picture) or in more of a "rod" shape. 

•  Eubacteria - Organisms classified under the Eubacteria Kingdom are also incellular, like those in the Archae Kingdom. Most bacteria are classified under this Kingdom (so chances are that if we're studying a type of bacteria, it's in the Eubacteria Kingdom). On top of being in this Kingdom, Bacteria are also classified as Decomposers (remember the previous lesson?); some decompose animals (and are therefore carnivores), others only decompose plants (and therefore are herbivores), and then we have those that aren't picky about what they eat, and so are classified as omnivores.

Escherichia coli (E. coli) - These bacteria are also one-celled (like the Methanogens) but are classified under the Eubacteria Kingdom. They are a well-known bacteria that can be found in the intestines of mammals and cause illness.

Protista (Protist) - The Protista Kingdom is probably the most diverse of all Six Kingdoms. Organisms classified under this Kingdom are not bacteria, animals, or plants. Most organisms in this Kingdom are incellular, however there are also organisms that are multicellular (contain multiple cells). Protists are found in most watery environments (such as ponds, lakes, oceans, etc).

 

Padriastrum - Green Algae is one of the most common organisms in the Protista Kingdom.

• Fungi - Like Bacteria, Fungi are Decomposers and break down dead organisms. Mold and Mushrooms are common forms of Fungi. Most organisms in the Fungi Kingdom are Multicellular.

Penicillium - Before it's used to create the antibiotic Penicillin, Penicillium is just one of the many molds in the Fungi Kingdom. 

• Plantae - All plants are organized into this Kingdom. All organisms in the Plantae Kingdom are multicellular and are capable of creating there own food (Photosynthesis). When plants are referred to in the Taxonomy system, Phylum is changed to Division.

Saint Paulia Violets - Also known as African Violets, these flowers are just one of the many different species of plants  in the Plantae Kingdom.

• Animalia - This is probably the one kingdom (other than the Plant Kingdom) that is most commonly known about. The Animal Kingdom is the largest out of all Six Kingdoms, containing more than a billion different species. All organisms classified under this Kingdom are multicellular.

Labrador Retrievers - Labrador Retrievers are dogs (obviously). There are many different kinds of dogs besides Labradors, and a dog is just one of the millions of species of animals throughout the world.

Every living thing is organized into each of these Kingdoms, but on top of that we have the rest of the Taxonomy system to help arrange all these living things even further. When the Taxonomy system is filled out, it looks like this:

• Kingdom - Animalia
• Phylum - Chordata
• Class - Reptilia
• Order - Squamata
• Family - Serpentes
• Genius - Calliophis

First, say hi to Mr. Coral Snake on the left. Now look to the right. There we can see a complete classification of Mr. Coral Snake, so that he will never forget who he is and so that we will never forget who he is either. Each classification (from Kingdom, all the way to Genius) is used so that scientists can be as specific as possible. Unlike my textbook, who so lovingly left me hanging here, we'll go over what each of the classifications represent... Unfortunately we've looked back and seen how very long this post is getting, and how little time we have left for our beloved Science Journal today, so instead we will promise to get back to this in a future post. Now, onto the next topic!

Scientific Method

We might have once thought that scientists are allowed to jump from one subject to another, ask whatever questions might occur to them, and just play around with all that cool equipment they've got in their laboratories. This is not the case! Just like with the classification of organisms, scientists also have an organization in the way they work. First comes a question, any question (so long as it is on the topic at hand and not about something random like "who wants coffee?"). This question takes hold, and soon an observation is conducted; the scientists observe in order to gain ground on how to get the answer to their question. Once some data has been gathered, a hypothesis (which is "an educated statement that explains the observations up to a point") is made. Experiments are then conducted in order to prove the hypothesis. If the hypothesis is proven wrong by the experiments, then a new hypothesis is made and more experiments follow. This goes on until the scientists have finally created a hypothesis that is valid; the hypothesis becomes a Theory. A theory is the closest thing you can come to the truth without having enough proof to make it a Law. For example, Newton's First Law (an object in motion stays in motion, and an object in rest stays in rest, until a force acts against it) is a Law because all evidence shows it being the absolute truth. Making a theory a Law is the final step in the Scientific Method. Everything in Science is completely organized, from Classification to the Scientific Method. 

Well, that finishes up the lovely Introduction in my lovely textbook. Now, what's next? *goes to have lunch and do some more Biology reading*

Introduction Part 1:Biology, Cells, Deoxyribonucleic Acid (DNA)

There's an Introduction in my textbook (there's always an Introduction in a textbook).

Did I read it? Yes, yes of course I read it (that's what an Introduction is for). It went something like this:

Biology: The Study of Life

Biology is the science used to explore the makings of life: how it works, how it relates to other things in the world, and so on. All living things have somethings in common: they are made of cells; they contain Deoxyribonucleic Acid (DNA); they reproduce; they're connected to the environment in which they live; they  extract energy (eat); they are complex and organized (sounds like a certain textbook I know).

Deoxyribonucleic Acid (DNA)

As you probably have noticed, I don't use the abbreviation (DNA) when referring to Deoxyribonucleic Acid. The reason is hardly anyone knows what DNA even stands for, myself included. So I figured that, if I only referred to Deoxyribonucleic Acid by its full name, then I would finally remember it no matter what (and perhaps someone else might too if I say it enough times). Deoxyribonucleic Acid is passed down from the parents to the offspring during reproduction and is the "building block" of life, so to speak. The Deoxyribonucleic Acid of every living thing contains all the information needed for a cell to work properly. I guess you could say that Deoxyribonucleic Acid is the Supervisor of all the cells, making sure than everything is running smoothly on a cellular level. According to my textbook, I will be discussing this much more later in my posts.

Reproduction

All living things can reproduce (come together to create another life). In my opinion, it is a beautiful thing and can almost seem like magic. As the Introduction states, there are two types of Reproduction, and whether a species uses one method or another depends on the formation of their Deoxyribonucleic Acid.

Connected to the Environment

All living things are connected to the land they live in. Meaning that if the environment is cold than anything living there must be built to live in the cold (otherwise it would die). If the environment is hot, than anything living there must be built to live in the heat (otherwise it would also die, like its cousin in the cold). Everything is built with the abilities to live in the particular place they live in. Being connected to the Environment also means that those living in the area are able to change with the environment, since the environment is constantly shifting. 

The picture on the top captures Yosemite in the Summer. There are lots of plants, and since most animals live near water it's likely there are a lot of animals in the area too. The animals and plants in Yosemite in the Summer are built to live in the environment we see in the top picture.

Now for the bottom picture. It's still Yosemite but during the Winter, and now the plants look half dead and the water partially frozen. The environment has changed a lot, yet there are still living things here. The animals have either gone into hibernation or are traveling through Yosemite to find more food. The plants are all hibernating until Spring, when they can flourish again. Coming Summer, this frozen river will probably look just like the picture on the top again. Even though there was a change in the environment, everything living in Yosemite is able to continue living despite the change because they adapted. That is the connection to the environment that every living thing has.

Okay, reading back that sounded rather dull, so from now on I'm going to see if I can be a bit more animated through my journal. *flexes fingers and gets ready to type*

Energy Extraction

Going down the list let's see what we have next. Oh yes, Energy Extraction. I'm going to see if I can shorten the long paragraph in my textbook since, relatively speaking, this topic should be a simple one.

All living things must extract (or take in) energy for themselves. Like most living things, eating is our way of extracting energy (and by "our" I mean all human beings). The process of taking energy from our surroundings is called Metabolism (met-a-bole-ism). You've heard that word before? Perhaps you have. I think I have too somewhere, long ago... Maybe it was in P.E... I'm off topic now!

Metabolism is the amount of food that goes through an organism's body to use as energy.

As my textbook clearly (or not so clearly) states as an example, Photosynthesis is the metabolic process used by plants (meaning the Metabolism of plants is known as Photosynthesis). 

Unlike plants, neither humans nor animals can create their own sugar molecules (also known as carbohydrates, also known as the fuel of the universe. I'll get back to this in another post).

 Both animals and humans have to eat other organisms (whether animal or plant) to gain sugar molecules, which our bodies then turns into the energy molecules needed to continue living. The process of turning sugar molecules into energy molecules is called Cellular Respiration. 

The following facts are rather common knowledge, but as I've promised to put down my findings in this journal I'd best put them down now shouldn't I?

• Organisms that only extract sugar (and therefore energy) from eating plant organisms are called Herbivores (such as Horses, Rabbits, etc).
•  Organisms that only extract sugar from eating animal species are called Carnivores (such as lions, wolves, eagles, etc).
• Organisms that extract sugar from eating both plant organisms and other animal species are called Omnivores (such as Humans, bears, and a few others).

The Food Chain is a simple way of discovering what animals are Carnivores, which are Herbivores  and which are Omnivores. In the Food Chain, organisms are separated into three different groups (and nope; they are not Carnivores, Herbivores, and Omnivores). 

Note: The Red arrows in the chart above show the flow of sugar molecules (which will become energy molecules through Cellular Respiration) as they pass from one living organism to another .

• Producers - Plants - With the use of the Sun and Water, plants use Photosynthesis to "produce" they're own sugar molecules which then turn into energy molecules to sustain the life of the plant.
• Consumers - Herbivores, Carnivores, and Omnivores (Unfortunately the chart above does not contain any Omnivores) - Consumers "consume" (eat) other organisms in order to obtain sugar molecules. In the chart above, the Grasshopper is the herbivore, consuming the plant to gain sugar molecules (and therefore energy molecules). The Snake is the second consumer, eating the Grasshopper to extract energy; then comes the Hawk, who will eat the Snake in order to consume the necessary sugar molecules. 
• Decomposer - Fungi and Bacteria - Decomposers break down the remains of dead organisms, whether plant or Animal (therefore they can be either Carnivores or Herbivores).  The nutrients that is left behind from the Decomposers becomes the perfect material for future plants to grow in, starting the cycle all over again. Decomposers are the last part of the circle that makes up the Food Chain.

Complex and Organized

I guess I'll finish up Part 1 with this last paragraph. Even the simplest looking of living organisms are incredibly complex, and everything not just jumbled up: there's an order to everything in life. For once, I'm going to quote my text book here, since I think it does a pretty good job of describing the organization of life.
"Life forms are organized specifically in regard to their atoms, atoms are specifically arranged into molecules, molecules are organized into cells, cells are organized into tissue, tissue is organized into organs, and organs are specifically arranged into organisms." All that specific arrangement and design, makes it kind of hard to believe that there isn't an Intelligence behind the creation of all things in the world. Life is like a gigantic, complex jigsaw puzzle, one that no human could possibly put together. It's incredible!

Please feel free to comment on anything that you might disagree with or find incorrect.

This is not a Blog, this is a Journal.

I must get this right the first time. First of all, I am not writing a blog, I find that I cannot keep up with such a thing as of right now (perhaps later?). This is my Science Journal: a place to write down my notes, my questions, and my frustration at Textbook writers who enjoy writing in complex sentences filled with big words and strange diagrams.

My only goal out of this is to be able to put down all that I am learning and all that I question, and perhaps get some of my questions answered along the way. I'm not a scientist, I'm a simple student who wants to learn; this journal isn't going to be filled with elaborate theories and fantastical wonders *sigh*.

So now the pages are open, the pen is ready, and the textbook is close at hand.