A.  Daily Blog

(10/20/10)

The class started off with the presentation and the slide (since most of my notes are derived from the PowerPoint for the information to stick into my head) of how to make ATP. There are two possible ways to make ATP which include substrate-level phosphorylation and chemiosmosis. In the former, it makes 4 ATP and an enzyme directly transfers phosphate from 1 molecule to another. In the latter, it makes 28 to 32 ATP; the energy stored in an electrochemical gradient is used to make ATP from ADP. Things that store energy include ATP, carbohydrate, fats, proteins, gradients and electrons.

Like in chemistry, we went over oxidation and reduction. Though the concepts are clear to me, I still have to pause and remember which one is which. Reduction gains electrons, and it is called a reduction because the charge is reduced. And, oxidation is the opposite--it loses electrons. The reason why it's called what is called still eludes me.

Back to the main lesson of the day, which led to cellular respiration, the process where living cells obtain energy from organic molecules. The main aim of cellular respiration is to make ATP. Aerobic respiration uses oxygen, therefore oxygen is consumed whereas carbon-dioxide is released. Though it focuses on glucose, cellular respiration includes other organic molecules. Unfortunately, for the first ten steps of glycolysis (the first of the four metabolic pathways), I only have pictures and diagrams--not many notes. However, notes that I do have state that glycolysis can occur with or without oxygen, nearly identical in all species and has ten steps in three phases: energy investment, cleavage, energy liberation. Every one of these phases uses a different enzyme.

(10/22/10)

Again, in today's classes, I didn't have many notes as I did diagrams and pictures and so on. Because of that, I can only delve into the surface of what the lecture pertained to today. This included stage two and stage three: breakdown of pyruvate to an acetyl acid group and the citric acid cycle. Though Dr.Weber's lectures did clear up the hazy part of my brain when it came those stages, I couldn't help but try to look back in the e-Book. Unfortunately, that only made it more confusing and so on and so forth. I will try to use the online lectures to help clear up anything that I'm confused about.

(10/27/10)

We start off with a review of what we went over in previous classes. That is, the process of glycolysis, the breakdown of pyruvate, the Krebs (or, rather, Citric Acid Cycle). But, now, we have the last act in the wonderful performance of cellular respiration, and that would be the all important oxidative phosphorylation, which produces about 30 to 32 ATP molecules in the process. From my notes, it briefly describes this act using high energy electrons being removed, requires oxygen and the involvement of the electron transport chain--all of which occur by ATP sythase. So, as Dr. Weber described it, the NADH becomes NADH dehydronase, actively transporting H+ ions. Then, it becomes cytochrome b-c, again actively transporting H+ ions. Then, the cytochrome b-c, with transporting H+ ions, becomes cytochrome acid. Finally, this acid, again with actively transporting H+ ions becomes oxygen gas and water. Then, we briefly described lactic fermentation--respiration without oxygen. Without oxygen, NADH cannot oxidize and it glucose would staty at glucose.

The last minutes of class I talked asked how much cyanide would it take to kill someone and not be traced in the blood. And, my apologies if I annoyed Dr. Weber with the question, however, I'm curious. Mainly because of the fact that Bruce Lee, may he rest in peace, could have been killed by the Chinese TRIAD because of the use of cyanide. Not only that, but famous Mafia hitman, also known as the Iceman, was known to kill people with cyanide--never being caught for that but for his fatal flaw with the ice technique!

(10/29/10)

In class, we discussed how a cell can produce energy without the use of oxygen (though, it's very hard for humans like us). If there is no oxygen, it cannot be the final electron acceptor in the electron transport change which means an increase in NADH but a decrease in NAD+ (which is needed to oxidize organinc molecules) which then, in turn, causes the drop in the Citric Acid cycle, pyruvate acid (since glucose, fats, proteins build up and ATP is depleted) and glycolysis. Times where oxygen is depleting is during vigorous exercise.

Of course, when this popped up, I remembered an excerpt from the a book everyone in my class read (or, I hope they read since it was required reading), A Separate Peace. Being the literature nerd I am, I recalled when one of the boys was training so hard that his muscles began to hurt. That hurting was basically because of oxygen depletion and his body was telling him, "Dude, stop. Pain equals bad".  That and the fact the oxygen depletion leads to the burning of the cretin. However, being the type of dumbbell he was, he kept running because of the adrenaline. And, I was wondering if adrenaline will ever play a role in this biology class.

Moving along, there was the discussion that bacteria survived through fermentation and anaerobic respiration. So, NADH reduces pyruvate to lactate acid and the lactate acid goes to lactic acid and so on. But, in anaerobic respiration uses NO₃^-.

B.  Useful Materials

I would like to share that--since the topic does relate to fermentation (of alcohol) but, uh, not really--I did find something that pertained to how a biotech place almost managed to kill the world through booze. All right, truth be told, I found this on cracked.com, so, I had to make sure its scientific information was accurate. And, I looked it up online and didn't find any information on it. Though, in all honesty, I didn't try my hardest to find it. But, if someone could find that article, that would be great. Though, I did managed to find this  link that described a bacterium that was going to be used to make alcohol from plant debris and, uh, instead of making alcohol, this bacterium did something else.

Yeah, it killed all terrestrial plants.

Moving along, I came across another topic that was interesting. You know how we learned where ATP was produced? And that ATP was created within the cell, within the mitochondria (hence why it's commonly known as the powerhouse of the cell). So, as I was looking up ATP on cracked.com (don't blame me, there are some really good articles that links to true stories), I learned about this new cell called the brown fat cell (submitted 10/26/10). Now, the way this cell works is that the brown fat cell is heavy with mitochondria, and the various enzymes are uncoupled from it. So, the energy in glucose is released as heat.

This video was submitted on 10/26/10. And, the topic of this video is the difficult (well, at least for me) Krebs cycle, also known as the citric acid cycle. To be honesty, I preferred this brief video that described the process of the citric acid cycle because, apparently, I'm a visual learner when it comes to biology. Moving along, it shows the chains, and I can easily follow the carbons, counting how many ATP molecules, NADH molecules and FADH molecules were created.

In this PubMed article, which was submitted on 10/26/10, describes a bottom fermenting brewer's yeast. I believe (since I can never too certain with articles from PubMed due to their difficulty in reading) that the article described how the fermenting was better in heated temperatures as compared to when it was low temperatures and isolated, the proliferation of the yeast was low. Apparently, the results of the experiment helped well in the understanding of fermentation in the bottom-fermenting brewer's yeast.