Thursday, December 16, 2010

The Longest Prezi You Will See in Your Life

Well...this one's a biggie.

It's pretty self-explanatory, so I won't say much more.

However, I will point out that my energy and focus was gone by the time I got around to the Calvin Cycle, so if typos and mistakes know why.

Have fun!

Wednesday, December 15, 2010

The Joy of Making Bubbles with Enzymes

Well, we did a little experiment with enzymes to see just how they worked. Our setup was relatively simple: 3 mL of water and 3 mL of hydrogen peroxide. Our enzyme was simply yeast, and the object was to manipulate various variables with the reaction to see what the change would be. My attempt at explaining what was going on is that the yeast breaks off the oxygen from the hydrogen peroxide and releases the oxygen into the atmosphere. This created the pressure we measured with a pressure probe.

Here are the various graphs we managed to draw from the experiment. I'll explain the meaning of each as we go along. 

This graph shows the change in the rate of reaction as we changed the concentration of the enzyme. The slope of this graph is relatively constant, suggesting that the rate of reaction is directly related to the concentration of the enzyme.

This graph (although admittedly bizarre) shows the change of the rate of reaction as the pH level of the solution the reaction was occurring in changed. We used buffers to hold the pH at constant levels of 4, 7, and 10, and found that the highest rate of reaction was when the pH was the pH of water--7.

This graph shows the change of the rate of reaction as we changed the temperature of the solutions that the reaction was occurring in. We used four different temperatures, namely, 0, 25, 38, and 80 (all of which were measured in degrees Celsius). By looking at this graph, we can see that the greatest rate of reaction occurred at slightly warmer than room temperature, but that the enzymes' productivity fell dramatically as the heat increased too much. This was explained when we realized that the heat could cause the enzymes to become denatured (meaning that the shape changed).

Wednesday, December 8, 2010

Unpronouncable Words...And Lots of Them

As we've spent a large proportion of time recently discussing enzymes, I thought I'd put together a little post on a disorder of an enzyme: PKU. (I found most of this information in the Mayo Clinic article.)

Phenylketonuria (fen-ul-ke-toe-NU-re-uh) is a genetic defect that results in too much of the acid phenylalanine. It's caused by mutation within a gene that contains the instructions to make the enzyme that breaks it down. Amino acids are the fundamental building blocks of proteins, but too much of phenylalanine results in various health problems. People who have this excess of the phenylalanine, referred to as PKU, must carefully limit their diets so that they do not consume too much phenylalanine (which is found primarily in protein-rich foods).

At birth, babies within the U.S. and several other countries are screened for PKU. When it is caught soon after birth, serious complications can be prevented.
When a baby is born with PKU, he or she has no symptoms. Soon after, however, the various complications arise. These include:
  • Mental retardation
  • Behavioral or social problems
  • Seizures, tremors or jerking movements in the arms and legs)
  • Hyperactivity
  • Stunted growth
  • Skin rashes (eczema)
  • Small head size (microcephaly)
  • A musty odor in the child's breath, skin or urine, caused by too much phenylalanine in the body
  • Fair skin and blue eyes, because phenylalanine cannot transform into melanin — the pigment responsible for hair and skin tone
Let's go a little deeper with the causes of PKU:

PKU is caused by a genetic mutation. The gene that is defective is the one that carries the information used to make an enzyme that breaks down phenylalanine. Because this particular amino acid is allowed to flourish, a hazardous buildup of the acid can occur when a patient eats foods such as milk, cheese, nuts, or meats (foods that are rich in protein). This buildup leads to potentially serious health problems.

Because PKU is a genetic disease, the defective gene must be passed on to a child from both the mother and the father. This typically happens when the parents do not know that they have the defective gene. (Think of Typhoid Mary. People who have the defective gene but not PKU are known as carriers.)

Well, I think that's all for now! Who knows? I might actually stay on top of blog posts this time!

(Ha ha! How funny that is!) 

Poisonous Thoughts

Mustard gas. What is it really?

An article I found gave me a few answers. It's a poison that is particularly bad for the skin and the eyes, but can also affect the lungs and other organs if it is inhaled. Although it is typically not fatal, it does have severe effects. However, these effects do not occur immediately after exposure; rather, symptoms take up to six hours to develop. This can be a problem because permanent damage can occur before the victim even knows that they need medical treatment!

Mustard gas is a so-called "blister agent," meaning that it is a chemical that can damage the skin, eyes, and lungs. In comparison with "nerve agents," (chemicals that prevent the nervous system from properly functioning) it is not as likely to become fatal. However, the amount to which a victim is exposed plays a role in the long-term effects. Long-lasting complications (such as cancer) can be traced back to mustard gas.

Another article gave me some more in-depth information on the processes of mustard gas. As an alkylating agents, it binds to nucleophilic molecules (molecules that share electrons with another molecule to bind with them) such as both types of nucleic acids as well as proteins and various parts of cell membranes. Obviously, this can be bad. For example, when it bonds with DNA, it can cause the strands of DNA to break or develop various other problems. When mustard gas bonds with RNA, it can alter the creation of proteins that are dependent upon the RNA, which results in the death of the cell.  Because mustard gas also binds to some proteins, it can change the shape of those proteins, which can alter the enzyme activity. Finally, mustard gas can also alter the structural proteins of the membrane of the cell or cause the lipids within the cell to be damaged, both of which can cause the death of the cell.

Can anything be done for people who have been exposed to mustard gas? Unfortunately, the answer is "not too much." It seems that decontamination is the primary method of treatment for exposure to mustard gas. There is no antidote (at least at the time of publication of the latter article) and, although thiols have been suggested as possible treatment, there is not a wide acceptance of this method.

Photosynthetic Imagination

Well, after complaints from my audience (meaning: me) about the high concentration of prezis, I've reverted to Power Points. Here's a little thing I threw together about an imaginary experiment (literally, a thought experiment).

Embedding is not working well (read: not working at all) so, for now, I'll give you a link to the presentation. Hopefully, I can get it embedded sometime!

Wednesday, November 17, 2010

I'm Not Sure This One's Long Enough

Well, I've been traveling. I haven't been thinking about biology at all.

Because of this, you're about to see what should be approximately eighteen posts all merged into one prezi.

(Getting tired of prezis yet?)

Well, make sure you've got about an hour of free time ahead of you, and then click play!

Monday, October 25, 2010

The Amazing, Conceptual, Concept Map of Science!

Well, after an entire period of wrangling with different web hosts, this image file is finally ready!

I thought I'd just throw together this little concept map to show just how my mind works. Hope you enjoy it!

Wednesday, October 20, 2010

The Prestigious College of Collagen

First off, an apology: This blog has, over the last week, fallen into complete, utter, total neglect. We here at the Department of Michael 'R' Us will try and prevent this from happening again, and we apologize for the inconvenience. We will be willing to provide free tickets to two future blogs in the future.


Now, some musings on the protein of the month: collagen.

To be honest, I don't like this one as much as my prezi on the properties of water. Oh, well!

Saturday, October 9, 2010

A Question

Although up to this point, I've been extremely satisfied with the process of SBG, I've started thinking about one negative aspect it may have. I've realized that I currently have all threes and fours, which means I've earned a 95 in the class. Now, what would happen if, one day before the semester ended, I did a sloppy blog post that merited twos across the board? Would that one mistake negate the work I've done for the rest of the year?

Then, consider the flip side of this coin. Suppose a student did nothing the entire year, but one day before his or her cumulative grade was posted put together an exceptional piece of work--one that deserves entirely fours? Would this earn this person a perfect score for the class?

It seems to me that any grading system should reflect the student's knowledge of the entire curriculum--not just what content was covered most recently. But how can this hole in the system be fixed? The scores for each standard cannot be averaged--one runs into the problems that are present in the averaging system.

The more I reflect on this problem, the greater its magnitude seems. The grade that will go on my transcript should reflect my understanding of the entire world of biology, not just the content area that I have most recently learned. 

I'm curious to see how this problem will be resolved--and I hope some other SBG'ers will comment and give me some ideas. 

Wednesday, October 6, 2010

Various Popes...Or Possibly Other Kinds of Benedicts

In the past couple of days, we've been mixing various foods with Benedict's solution and iodine to observe what kind of sugars (saccharide units) were in each.

Now, I'm not the kind of guy who likes "Well, it works that way because it does!" I prefer to know everything possible going on in a reaction such as this one.

So, I tried to go a little deeper. Although I'm not quite perfect on the details yet, I'm pretty sure I have the general idea.

Benedict's solution is nothing but a copper sulphate (Cu+2) mixed with alkaline solution. When a simple sugar is heated, it loses an electron, which goes into the copper. This reduction makes the copper Cu+1. Now, it can react with oxygen to create copper oxide, creating the orange-ish color that indicates the presence of a mono-or-di-saccharide. I guess that might not have been very in depth, but hey...close enough?

Wednesday, September 29, 2010

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.

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.

Tuesday, September 28, 2010

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!

Monday, September 20, 2010

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.

Friday, September 17, 2010

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.

Monday, September 13, 2010

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!

Saturday, September 11, 2010

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.

Does that clear anything up?

Thursday, September 2, 2010

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

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?