Energy and Chemical Reactions

31/08/2010 § 1 Comment

Our last lecture of the unit was about enzymes, energy and the chemical reactions that help our bodies function. Thankfully, this class was far easier to follow, most likely because it was the last one and was not the hardest level. Next Monday, the class faces their very first test and must finally answer the essay question that we’ve all (supposed to have) been focusing on for the past week: How does complexity emerge from simplicity?

I was suggested to keep the question simple and maybe to broaden my mind first to all the possible ways to explain the answer to our essay question. I thought that protein was a good way to explain how little things, amino acids or even the information in DNA starts off a chain reaction that eventually becomes this intricate organ or individual: a human being. I thought that perhaps proteins would be a very good and a very safe way to properly explain how complex structures form from little molecules and atoms. It was one part of the unit that wasn’t hard for me to follow and to understand, so logically, it would be a good method to answer the essay question with.

In class, we studied how enzymes work, what they do, why they do it, and if I remember correctly, we were given multiple examples of molecules being broken down quickly because of the enzymes working on what needed to be collapsed or connected.

We learned that in every chemical reaction, there should first be what is called activation energy to sort of ‘push off’ the chemical reaction. The way the textbook described activation energy was to imagine a large boulder rolling down the hill. The act of the boulder rolling is the chemical reaction itself but before it starts down the hill, it needs to be push. The push is the activation energy. However, although activation energy starts the chemical reaction and is the reason that reactions occur, they sometimes take much of the time in changing or transporting energy. (As seen in the multiple charts shown in class). Sometimes, it is unhealthy for our body to transfer or transform energy slowly so we have enzymes to speed up the work.

Enzymes are substances that increase the speed of a chemical reaction accordingly. But! Enzymes, in a way, don’t just help a chemical reaction move along quickly, but they help our bodies survive. Enzymes are like problem solvers, as we saw in class with Mr. Ferguson’s story of the wise man, the camels and the three brothers who couldn’t decide how many camels their father really left them. (But really, why did the father have to leave behind such a difficult-to-understand will?) The wise man had willingly given the three brothers his camel, turning nineteen camels into twenty, therefore making life so much easier for the three brothers. This story makes a lot of sense to me, because the lucky twentieth camel’s name was Enzyme and he acted exactly like an enzyme. In assisting the substrates (the other camels), Enzyme, the camel was able to let a group of ten, a group of five, and a group of four camels go easily. Thanks to the story, I understood better what enzymes were and really how important they are.

Just a while ago, I mentioned substrates. Substrates are the substances an enzyme acts on during the chemical reaction and the substance that holds energy that needs to be transformed, transported, or changed. When an enzyme acts on a substrate, or substrates, the two different types of substances have to fit each other like a lock and key. The substrates fit into the enzyme’s active site and the chemical reaction takes place.

Returning to the essay question, though, I think the information that related most to the process of simplicity becoming complexity, was the information where amino acids came back into the picture. As Vineet repeatedly stated through the class, “Amino acids make proteins, which make enzymes. Enzymes are then used for speeding up the process of breaking down or making products.” Once again, there is a smaller unit that makes enzymes and proteins, the amino acids. And the amino acids are made, of course, with the proteins and nutrients and other enzymes that we consume. However, our bodies know how to make amino acids because of: DNA. The genetic code in our DNA and in their nucleic acids contain very important information that states what kind of proteins and enzymes we really need. In doing so, our DNA keeps us very much alive, too.

The genetic part previously mentioned wasn’t talked about much in class but will help me greatly, in my opinion. For the essay question, I will continue to develop ideas and explanations from proteins and water, because I’m also beginning to understand the characteristics of water further. Unfortunately … I think this is the last chemistry of biology unit we might have and I still don’t know what our next unit will be. Just to say it now, I liked this unit. My dad said himself that biology and chemistry are incredible topics and he was right.

Chemistry of Cells

28/08/2010 § 1 Comment

Today’s class was probably the most confusing and the hardest to follow out of the previous three classes we’ve had so far. Not only did we cover difficult topics but we covered multiple handfuls of knowledge and yes, we all felt like our minds were bursting with information that we were finding so hard to follow.

In a way, unfortunately, we all face a disadvantage in writing this blog because it was quite difficult to understand what we were taught today. How hard will it be then for us to take what we’ve learned and apply it to our essay question?

Moving back to the essay question, though, I think last class, again, we were given a chance to see examples of how complexity emerges from simplicity. A very good example of this process, this ingenuity of how such small atoms form great and diverse creatures and organisms, would be the structuring of proteins. These proteins start off small, with the amino acids that form each protein. Even then, proteins contain typically 300 amino acids per molecule. Although some proteins are small, for example, 180 or less amino acids, they are usually at least 300 amino acids in size. Since we can’t even see proteins, we can’t even see the nutrients and the little vitamins and all the small acids that are in food, we can say proteins start off very, very, very (incredibly) small but build up to some of the most important parts in our bodies.

Some of these parts include our muscles that so heavily rely on proteins to keep them functioning. Proteins are also essential in hair, collagen, and antibodies which help our bodies fight against infection. Even these parts of our bodies, even they are small things in the circle of life that protein helps to create, but they are also very complex.

In the 300 (give or take) amino acids that make up a single protein, there are an impossibly large amount of sequences that the amino acids can form into. These sequences change the type of protein that the amino acids make, therefore providing an equally impossibly large amount of proteins in the world. The number of possibilities, we learned in class, surpasses the number of amino acids in the world, if I recall the fact correctly. The diversity in the kinds of proteins then proves how life can be so complex and diverse, providing me with backup and proof that simple little things (amino acids) can form into slightly larger and much more diverse organs or body parts.

In terms of what else we learned in class, we were taught about organic compounds and the four principle compounds: carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates are organic compounds that are made up of one carbon atom, two hydrogen atoms, and one oxygen atom. The form that carbohydrates take, 1:2:1 format, shows me more proof that they mainly spend their years trying to attach themselves to other atoms and gain electrons or lose electrons to become the “ideal” molecule. We learned that carbohydrates are made of monosaccharides, which are sugars, like glucose and fructose.

We learned that lipids are not soluble and mostly insoluble non-polar molecules like oils, lard and fats. Because the molecules of lipids are non-polar, they also have no charge and don’t dissolve in the water. They simply float to the top of the glass or become bubbles after shaken. Lipids, however, store a lot of energy in our bodies and in other organisms’ bodies. Some lipids are saturated while the others are unsaturated. Saturated fatty acids are tightly packed together and are definitely unhealthy to consume for they are likely to clog up your veins and effect cardiovascular system in a bad way. Unsaturated fatty acids are better to eat because they have double covalent bonds where the hydrogen bonds have an extra ‘limb’ per se, and the fatty acid molecule is longer, thinner, and less packed.

By now, we were introduced to glycerols and triglycerides. We learned that in condensation synthesis, water is formed and that breaking things apart is hydrolysis and can be done by putting a substance or the molecule in water. This part of the class was the part where most people were asking Mr. Ferguson to “please repeat that” again and again and we were told to say the lines and to repeat the facts out loud to ourselves. Strangely, it worked.

Finally, we learned about nucleic acids. These acids are in all of our cells and make up the most important strands of information that make up who we are and what we look like. Nucleic acids are long chains of nucleotides, which are compounds made of sugar, a base, and a phosphate group which usually consist of phosphorus and oxygen atoms. The sequence of the nucleotides in DNA serves as instructions for the sequence of amino acids in proteins. Therefore, nucleotides tell the DNA to tell the amino acids how to make the proteins which will them perform many functions for the body.

As always, I was left questioning much of the lesson and as one can see, I had to write about a lot today, due to the fact that we learned a lot last class. The test is coming soon and I have yet to completely understand how complexity emerges from simplicity. What we learned about proteins helped me understand a little more about simplicity become complex, however, so that part of the lesson helped. Personally, though, the littlest atoms and molecules are so complex on their own that I can’t imagine how complex large organisms and environments could be. They could be so diverse because of little things like atoms.

Water and Solutions

26/08/2010 § 1 Comment

In class, today, we talked about the different characteristics that water molecules have. We learned a lot about what water is made out of, how they stick to surfaces, how they stay together and even more. During the class, we also learned little bits about ions started talking about acidic substances and a little bit about what happens to solutions and such.

We basically reviewed the textbook section that we were instructed to read, but it was helpful, of course, to be given a proper lesson about what we read. For me, today’s lesson only helped a little bit in the process of answering our very important essay question, (just to state it once again): How does complexity emerge from simplicity? Personally, today’s lesson about how water works and water’s abnormal properties simply provided as an example about how simplicity slowly becomes complexity.

Firstly, it’s easy to say that water is water because of the billions of molecules. (I learned that a glass of water has an average of a billion water molecules today, too). We were given a couple of examples as to how water was all just a very, very large collection of molecules that had joined hands and were moving all together.

But how did they move together and didn’t just break apart? This, I think, was the more complex part of the lesson; when learned about hydrogen bonds. To clarify, hydrogen bonds are the bonds that are made between different molecules to connect them. They are usually very weak bonds and can break many times. An example of this was water (as we saw today. Apparently, water molecules can be thought of as very ADHD little children, always bouncing and moving around), and the hydrogen bonds explained how water always moved around and didn’t stay together as one solid block (like anything solid, not liquid).

All in all, that’s how water works. Yes, there are little tweaks and additional twists that come with the properties of water, but in terms of our essay question and involving complexity and simplicity, I understand a little more about how little molecules become such large bodies of ocean. It makes more sense to me now how in the Pacific Ocean or in the Atlantic ocean, the water stays together because of the hydrogen bonds and there are bound to be a thousand groups of millions and billions of water molecules in just a small portion of the Pacific Ocean, if there are a billion molecules in a glass of water. Those numbers, I think, give us more of an idea how small simplicity really is.

Also: basic chemistry and biology that we learned today was not all that difficult to comprehend but in genuine honesty, it took some effort to get my mind wrapped up around the whole topic. Eventually though, I got to start understanding that molecules can be like people … in relationships. Within one water molecule, for example, there is one oxygen molecule and two hydrogen molecules. Each hydrogen molecule, as we’ve learned, yearns for just one more electron while one oxygen molecule needs two. If two hydrogen molecules can attach itself to an oxygen molecule, then all three molecules would be the ideal ones. I’m absolutely clear with that now.

Next, there’s the fact that those three molecules have bonded over covalent bonds but not just any covalent bonds but polar covalent bonds. I think we learn more about how simplicity borders on slightly complicated because we were enlightened about the topic of negative and positive molecules, which will then lead to multiple different bonds that might form in the process of attractions that are similar to magnetic attractions.

I’m still not perfectly clear with definitions on atoms, elements, and a few other vocabulary but that would be because we haven’t discussed the topics enough in class. We were told today that our essay question is a difficult one but with enough information from our textbook, biology students our level might just be able to begin understanding the answer to that question, whatever it may be.

Nature of Matter

23/08/2010 § 1 Comment

Earlier today, we had our very first real Biology class. We were required to really listen to the lecture given by Mr. Ferguson and were first introduced to the basic concepts of what we were to learn about biology (and little bits of chemistry) in this unit.

Today, I think we all got a slightly better idea for an answer to our essay question: How does complexity emerge from simplicity? Honestly, how does simplicity end up at all as complexity when it’s supposed to be simple in the first place?

What helped the class understand how small things build up larger complexities and structures, life and living organisms was the slideshow-picture-presentation that consisted of snapshots starting with the universe, the entire galaxy, a photo of space showing our solar system, the Milky Way as a small dot. The slideshow continued on to show the Milky Way, then the different planets, to Earth, focusing on North America, then more specifically Florida, then a university, then slowly onto a plant, into its cells, then its DNA strands and finally to one single proton.

The slideshow showed that the construction and overall structure of environments and organisms begin with the smallest and simplest particle in the simplest unit of life. Eventually, these units build up, I guess, to form what we see as organs, people, plants, animals, maybe even non-living things, with all of the chemicals and elements we learned about in class.

Now, I still don’t know exactly how the atoms form together and join and magically construct organs in an animal or such, but at least, with today’s lesson, we got the idea of how small the unit really is (in terms of micrometers, dividing nanometers into pico-meters and etc.). With this little information, we can actually begin the path to figuring out how complexity emerges from simplicity now that we know a bit about the simplicity section of the essay question.

In terms of what we learned in class, however, we slowly moved to chemistry towards the last half hour of Biology. We learned lots about the different kinds of elements, what molecules make them up, and the different bonds that the molecules make. More importantly, we learned that in an element, the first shell can only fit two electrons and the second and third shells can only fit eight electrons. These numbers are all based simply on the volume that is inside the element itself. With that, we were also introduced to a few of the ways some molecules try and become the “ideal molecule” with two electrons in the first shell and eight electrons in the outer shells.

It was all rather fascinating, really. I asked whether these units were alive because they move around so much. Apparently, they could be living, or they could be lifeless; it all depends on your point of perspective. Maybe the atoms just live on the energy that they get from their electrons, but I wouldn’t know. Hopefully we discuss the topic of how these molecules work more. Indeed, how do such small and simple units become what the world and the galaxies and the universe is today?

Musings of an Amateur High Schooler

20/08/2010 § 2 Comments

Moi. It’s all about me. No, not really. This is for school, and it’s sole purpose is to be used wisely for school. But I can spare one post, can’t I? This blog is listed under my name. Better use it as much as I can.

So anyway, Hi fellow classmates. If you’re gonna comment on anything of mine, please use the right tone of voice and appropriate use of language. I’d greatly appreciate that.

But other than that….

Welcome and enjoy reading whatever I have on this amateur blog!

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