Newest Biofuel: Cow Enzymes?

Since we've realized that the waste from our excessive oil usage is detrimental to the environment, and that our oil reserves are quickly fading, scientists have been trying to think of ways to use more biofuels. Who would have thought that as this article explains, we would be looking inside of a cow's stomach?

One of the main focuses in making biofuels is cellulosic plant matter. The break down of the large molecule, cellulose, would provide the energy that we would then harness and use for whatever needs we have. Making biofuel from cellulosic plant matter would be more environmentally friendly and economical because many cheap plants contain lots and lots of cellulose (i.e. switchgrass, Miscanthus, woodchips). The only problem with this method is that the methods for breaking down cellulose are extremely expensive.
Engineers have already been using enzymes from animals like termites to degrade through tough plant material. Unfortunately, the enzymes currently available efficient enough to make the cellulose-to-fuel conversion worthwhile. The director of the U.S. Department of Energy's Joint Genome Institute, Eddy Rubin,and sixteen colleagues discovered nearly 30,000 new enzyme candidates by analyzing DNA collected from a cow's rumen, which is first compartment in the animal's four-section stomach. The researchers were able to identify 27,755 genes that were good enough to be candidates toward cellulosic biofuel practices. They then chose 90 of the candidate genes, expressed them to produce the enzymes they code for, and then applies the enzymes to the biofeul feedstocks Miscanthus and switchgrass. Over half of the selected 90 showed the capacity to degrade at least one of the feedstocks. Researchers feel that this suggests the original, larger pool of candidates is "highly enriched" with enzymes whose activity could be useful in biofuel production.

Helpful Hint: Oxidation and Reduction...

When looking at simple problems, redox reactions make perfect sense to me. As we all know, the body and life are not simple processes therefore most reactions are not quite simple, so the more complex problems have confused me a bit. I personally always love to watch Khan Academy videos in any subject applicable because they are just so helpful! So when I found this video I was ecstatic! This video has helped me a great deal because it really breaks down what is happening in redox reactions and takes you step by step when explaining what occurs. The video also gives little hints on ways to remember certain terms and concepts. The video basically is a lecture, but it is in no way boring. I also like this video because it incorporates concepts we have already learned and mastered this year (i.e. electronegativity) to explain the oxidation and reduction reactions. So, this video will help you understand the concepts more if you're a bit confused. It will also help if you want to watch a quick lecture to refresh or confirm the concepts in your mind!

Fatty Acid Oxidation Prevents Obesity in Ob/ob Mice!!

So this article talks about how scientists have found that when endogenous ligands sustain the activation of PPAR{alpha}, hepatic fatty acid oxidation is increased, resulting in the prevention of obesity in ob/ob mice. An ob/ob (or obese) mouse is a mutant mouse that eats excessively and becomes extremely obese.

Mice that lacked acyl-CoA oxidase 1 (Acox1), the first enzyme of the peroxisomal fatty acid β-oxidation system, are characterized as having an increased energy expenditure and a lean body phenotype. This is because of sustained activation of peroxisome proliferator-activated receptor α (PPARα) by endogenous ligands in liver that remain unmetabolized in the absence of Acox1.Scientists wanted to see what would happen if an ob/ob mice lacked Acox1. So, they made generated some ob/ob mice deficient in Acox1 and conducted tests comparing them to regular ob/ob mice.
When compared, the regular ob/ob mice were severely obese and had more epididymal fat content. The reason why the Acox1 deficient ob/ob mice were more resistant to obesity is because there is an increase in PPARα-mediated up-regulation of genes involving fatty acid oxidation in liver. The activation of PPARα in Acox1-deficient ob/ob mice also reduced the serum glucose and insulin levels, and improved glucose tolerance and insulin sensitivity. There are negatives as well though. For example, Acox1 deficient ob/ob mice manifested hepatic endoplasmic reticulum stress and also develop hepatocellular carcinomas. 

Wee for a Wii and Quirky Quasicrystals

The Sacromento radio station KDND 107.9 held a contest in early 2007 called "Hold Your Wee for a Wii". The person who could drink the most amount of water without using the bathroom would win the Wii. Jennifer Strange, a healthy 28-year old, participated in this contest, and unfortunately lost her life because of it. Jennifer Strange died of water intoxication just hours after the contest.

Water intoxication, as explained by this article, causes problems in electrolyte balance, resulting in a rapid decrease in serum sodium concentration and eventually leads to death. The decrease in serum sodium concentration is known as hyponatremia. As we learned in class, our cells prefer isotonic solutions. With the intake of too much water, Strange's extracellular fluid became more diluted, causing her cells to be bathed in a hypotonic solution. Water flowed into her cells to try and even out the concentration of solute to solvent. This caused her cells to swell. On the way home from the radio station, Strange was complaining of a terrible headache. This is because her brain cells contained too much water, causing intracranial pressure to increase and her to experience a headache.

This article continues to explain more symptoms of water intoxication. The electrolyte imbalance previously described also results in an irregular heartbeat, can allow fluid to enter the lungs, and not only puts pressure on brain cells, but also nerve cells. All of the symptoms are caused by the swelling of the cells. In theory, the excessive amount of water in the cell could cause it to burst.

If one is beginning to experience water intoxication, one way to quickly get it under control is to take diuretics so that one can urinate. Water intoxication should be treated promptly because it leads to damage in basically every part of the body, strokes, comas, and death.

*INSERT FETCH TRANSITION HERE*

Now, let's move on to quasicrystals! As this article explains, up until 1982 scientists believed they knew when a crystal was not a crystal. Then in 1982, came this Israeli physicist named Daniel Shechtman. He discovered these things called quasicrystals in metals. These quasicrystals were crystals with odd structures that scientists had thought were impossible structures for crystals to have. At first, his discovery of quasicrystals resulted in Schectman losing his job and drawing scorn from several colleagues. Now, his discovery has earned him the 2011 Nobel Peace Prize in Chemsitry.

So what exactly are quasicrystals? First, it would help to know what a regular crystal was. Crystals are a form of matter that in which atoms are arranged in orderly patterns that repeat themselves. In order to be a crystal,  the arrangement of atoms must be symmetrical when viewed from different angles. For example, each atom could be in the middle of a triangle formed by its neighbors. When turned, the series of overlapping triangles form a pattern that reappears with every 120 degrees of rotation. Atoms centered in a pattern of rectangles, squares, hexagons also exhibit this kind of symmetry, but at different angles. However, atoms in patterns made up of geometric shapes with five or more than seven sides, don't show symmetry at any angle. Ergo, materials with those arrangements were not considered crystals

So one day Schectman was mixing molten aluminum and manganese and cooling it quickly to study the properties of the resulting alloy. When he viewed the sample through a microscope he was flabbergasted! The atoms were arranged in pentagons. These pentagons were arranged in concentric circles each having ten dots. The geometric shape formed by the ten dots was a repeated pattern at 36 degrees but the pentagons were not. Schectman had just stumbled upon quasicrystals! At first, even Schectman did not believe his results. However, he realized the results were very real and after finding three highly respected coauthors, he published a paper about quasicrystals in 1984.

Today quasicrystals are still being studied but have been already put into use because of their unique properties. For example, researchers have been trying incorporate their unique properties into technologies as advanced as light-emitting diodes and as common as non-stick frying pans.

The figure on the left would be a crystal arrangement, the figure on the right would be a quasicrystal arrangemnt.

Great Googly Mogly, It's Glycosylation!

This article explains the process of glycosylation. Glycosylation is the process by carbohydrates are attached to protein molecules. It is a common post translational modification for protein molecules that are a part of the plasma membrane. Glycosylation involves the linking of monosaccharide units to amino acid chains. This sets up the stage for a series of enzymatic reactions which results in the formation of glycoproteins. There are 16 known enzymes that facilitate these enzymatic reactions. A typical glycoprotein has at least 41 bonds involving 8 amino acids and 13 different monosaccharide units. The major sites of protein glycosylation are the ER, Golgi , nucleus and cytoplasm.

There are 2 main types of gylcosylation.

 N-Linked Glycosylation- N-Linked Glycosylation begins with the addition of a 14-sugar precursor to an asparagine amino acid. It contains glucose, mannose and n-acetylglucosamine molecules. The whole entity is then transferred to the ER lumen. Oligosaccharyl transferase enzyme attaches the oligosaccharide chain to asparagine in the tripeptide sequence, Asn-X-Ser or Asn-X-Thr where X can be any amino acid other than Proline. The oligosaccharide attached protein sequence will now fold correctly and is translocated to the Golgi. Mannose residue is removed in the golgi apparatus.

 O-Linked Glycosylation- O-linked glycosylation begins with the addition of N-acetyl-galactosamine to the molecule by an enzyme and other carbohydrates to serine or threonine residues. O-linked glycosylation occurs at a later stage in protein processing, probably in the Golgi apparatus.