Notes on Molelecular Structure

I thought I'd just go ahead and post my notes from today. Since these are notes, taken during class, these are disjointed and not exactly a masterpiece of the English language.

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Shape matters in biochemistry! Simple structure changes have profound effects on the chemical properties of a molecule.

Monosaccharides often do not stay "mono." They bond together and become disaccharides--for example, glucose and fructose become sucrose. Double glucose is maltose, and glucose and galactose become lactose. (Lactose-intolerance is caused by lack of an enzyme that breaks the glucose and galactose bonds.)

Then, there are polysaccharides. "Simple" sugars (monosaccharides) are combined many times (a condensation reaction--water is released). For example, many glucose molecules are combined to create amylose. Amlopeclin is very similar to amylose, but has extra branches. These are considered starches.

Glucose can be combined (through condensation reactions) to create glycogen. This chemical is found in human cells, particularly muscle and liver tissue. Cellulose is when the glucose chains are "flipped." Between these chains, hydrogen bonds can be found. Because of this, these can be used to create structural support (such as a cell wall in plant cells).

Cellulose cannot be broken down (for the same reason that causes lactose-intolerance--the lack of an enzyme that can do so.)

Bugs are crunchy for the same reason--their exoskeleton is formed from chitin, which provides support because of the hydrogen bonds.

Ok...Why Not?

First off, an apology: I've been devoting quite a bit of time to trying to decide which artifact to embed in this post, and none actually doing it, so I decided to just go ahead and type this up.

We've been discussing biochemistry in far more depth than I had ever been exposed to, and I'll be honest: I'm not quite keeping up. More accurately, I haven't quite understood the intricacies of the molecular structures.

However, today especially, I started to figure out what's going on. Let's start by going all the way back to the pH scale.

Let's start by examining a simple, well known chemical formula: H20.  Everyone I've ever met knows that formula's water. You could find someone wandering around Siberia and they would know about H20.

Some more thoughts on water:

On the pH scale, it's neutral (7).  Why would this be?

To answer this question, we have to look in more depth at the pH scale. As a number gets farther and farther away from 7 (all the way to 0 and 14), it gets either more acidic (smaller numbers) or more basic (larger numbers). Acidic substances have more H⁺, while the more basic, the OH^- increases. When these two quantities are equal, the substance is H20--or water.

Then, today, I watched as a carbohydrate's bonds broke and separated water and carbon within the carbohydrate. These bonds breaking created quite a bit of heat.

Finally, I'm currently in the process of wrangling with polymers and monosaccharides and monomers and glucose, and fructose, and...well, I hope you get the idea.

The idea that a simple swap of a pair of atoms within a molecule is particularly striking to me. Mr. Ludwig explained that the only difference between glucose and galactose is one side group that is in a different location. As I understand it, this is simply because different reactions can occur with different parts of the molecule (but correct me if I'm wrong!).

Anyway, I'll keep working on the more advanced regions of biochemistry, and once again, sorry that this took so long!

Big Foaming Chemical Reactions!

Here's the write-up from our experiment on the quality of different antacids. Contributors were myself, Seth Nixon, Kiel Heerding, and Tyler White.

Random Ramblings (Mr. Ludwig, You Can Probably Ignore This.)

Having had nothing to really blog about in the past few days, I just thought I'd give a little update on my thoughts of standards-based grading (SBG).

So...what is SBG?

At first, it's the most confusing idea you can imagine (up there with string theory). But once the student (and, for that matter, the parents!) really figures out how it works, it's by far a superior grading system to the standard "averaging" system. (I have no idea what it's technically called.) What makes this so? To me, the superiority all revolves around the idea of second chances. Once a student has a grade, they can change it. Nothing is set in stone.

This system also takes some of the improvements of a system formerly employed by Mr. Ludwig: his "Binary" Grading System. This system did not overload the averages with participation points; students earned one point for turning in daily papers, and none if they did not. SBG improves along these lines because it gives specific areas for students to work in: standards. Each student has to find some way to demonstrate to Mr. Ludwig that he or she "gets" that standard. Mr. Ludwig will then evaluate the student's comprehension and give them a "level" in that standard. If the student is not happy with this level, they can try again. The whole goal of SBG (for the student, at least) is to "level up" enough times.

This is another reason that SBG is such a good idea. Grades are not formed by averaging the levels together, but simply by a combination of each. An "A" translates to all 4's and 3's, for example, and the system continues from there.

All things considered, I hope to see it implemented in many more classrooms.

A Thought

After reading through a few of my fellow classmates' posts about clinical trials, I've noticed that many people seem to criticize the fact that someone who needs a drug to survive could instead be receiving something that will do them no good.

But on the flip side of that coin, the actual drug could be killing the people taking it! That is why these clinical trials are so important: they reveal ALL the effects (good and bad) that a drug can have.

Just thought I'd throw that out there!

Molecular Anomalies

As one who finds molecular structure fascinating, I am particularly interested in the recent developments on ways to probe the structure of water. It's an interesting concept, and it's amazing that it actually works. Basically, a sheet of graphene (atomic-sized La Junta High School made of carbon atoms) acts like shrink wrap to water molecules trapped below it. By probing the shape of this anomaly, researchers can learn more about the molecules. They have discovered that, although thin layers of water are everywhere, a layer on mica originates at two molecules thick and in the structure of ice. The technique also works on other molecules. Hope more developments come soon!

Water's Wares

At one point in my life, not-so-very long ago, I didn't really know about the properties of water. For that matter, I didn't really care about the properties of water. But after examining them in depth for the past couple of days, I learned quite a few interesting things about them.

What Makes Water Water? on Prezi

Does that clear anything up?

A Study in Studies

Clinical trials.

What are they?

This question has plagued my mind for quite some time. After all, the phrase surfaces often in the news and in virtually every magazine ever published.

But what purpose do they really serve?

After reading through the summary of a study on rheumatoid arthritis, I think some of this confusion has been cleared up. A clinical trial is nothing but a research study in human beings. It's typically done to study various reactions to a medicine that is still in the trial stage.

The particular example I examined was a double-blind, placebo attempt to validate the use of a drug aimed to treat rheumatoid arthritis. What exactly do those terms mean?

To quote from http://clinicaltrials.gov:

DOUBLE-BLIND STUDY: A clinical trial design in which neither the participating individuals nor the study staff knows which participants are receiving the experimental drug and which are receiving a placebo (or another therapy). Double-blind trials are thought to produce objective results, since the expectations of the doctor and the participant about the experimental drug do not affect the outcome; also called double-masked study.

PLACEBO: A placebo is an inactive pill, liquid, or powder that has no treatment value. In clinical trials, experimental treatments are often compared with placebos to assess the treatment's effectiveness.

So a placebo is basically: nothing. It's useless. It's a waste of time. If you're the person receiving it, you can't expect anything to happen.

But if you're a placebo recipient in a double-blind study, you wouldn't know it. That's what a double-blind study is: neither the participants nor the overseers really know who is the control group and who is actually receiving a functional drug.

Now, I've mentioned something new: the control group. The control group is nothing but the placebo group. Everything else between the two groups is exactly the same. The only difference between the control group and the group actually receiving the drug is that one group actually receives the drug.

So let's set up a hypothetical situation which is an attempt to see if a drug that is hailed as fighting cancer would work. There would be two arms (groups--the control and the experimental). The control group would receive nothing but the placebo--so we could measure the results of what would happen without the drug. The experimental, on the other hand, would receive varying amounts of the drug over an extended period of time.

Once this time had expired, we could collect results. Was there a notable increase in the condition of the experimental group? If so, then perhaps the drug is notable and should be studied further. But on the other hand, if the condition of the experimental group degrades compared to the placebo group, then there are probably some adverse effects from the drug, which would need to be scrapped.

So I hope that I have cleared up some of my own confusion when it comes to what a clinical trial is. It's nothing but an attempt to carry out an experiment in humans. This is typically done to study the effects certain medicines can have on their targets. There are different setups possible, including the double-blind, in which neither the participants nor the personnel really know who receives the real drug or not.

Does anyone else not want to be in a clinical trial anytime soon?