Blog #4

Final Thoughts On Chem II 

Throughout the semester, the most valuable lesson learned was to take time to outline the chapters and read on your own. I struggled with keeping up with the powerpoint lectures, so I would outline the chapters on my own. Although I still struggled with test, and in class quizzes... it helped with understand the homework concepts. 

The most challenging concept was reflecting back on Chem I concepts. Chem II is built off of things learned while in Chem I. Unfortunately, it has been over two years since I have taken Chem II. I felt as though I struggled throughout the entire semester with looking back onto old concept, while trying to learn new ones as well. 

My advice for future students would be: complete all assignments on time, do your homework... even if it takes 10 tries to find the correct answer, take advantage of extra credit opportunity, and attend class!   

Blog #3 : Student Question & Answer

How do buffer solutions allow our bodies to maintain homeostasis 

consistently in the blood (keep the blood's pH constant)? 

- Question by Michael Newton

     Michael produced a question that is significance to what we have learned over the course this semester. It comes from Chapter 16, Aqueous Ionic Equilibrium, where we learned the concept of buffers and solubility equilibria. 

     A buffer  resists pH change by neutralizing added acid or added base. Our blood contains several buffering systems, with the most important one being of carbonic acid and the carbonate ion. Normal blood has pH of 7.4, this can be found by using the Henderson-Hasselbalch equation: 

[HCO3-] = 0.024 M and [H2CO3] = 0.0012 M 

pKa for carbonic acid at body temperature = 6.1 

pH=pKa + log ([base]/[acid])

= 6.1 + log ([HCO3-]/[H2CO3])

= 6.1 + log (0.024M/0.0012M)

pH= 7.4

     The concentration of the bicarbonate ion is 20 times higher than the concentration of carbonic acid and the pH of the buffer is more than one pH unit away from pKa... this is due to the higher bicarbonate ion concentration in blood makes the buffer capacity of blood greater for acid than for base, which is necessary because the products of metabolism that enter the blood are mostly acidic. A great example of this is when we exercise. Our bodies produce lactic acid (HC3H5O3), and when this enters our bloodstream it must be neutralized. The bicarbonate ion must neutralizes the lactic acid, and then an enzyme, carbonic anhydrase, then catalyzes the conversion of carbonic acid into carbon dioxide and water. Our bodies eliminate the carbon dioxide from our blood when we breathe... the larger the amount of lactic acid, the heavier we breathe. 

     All of this is in thanks to the buffers in our blood. Without them we would not be able to maintain a constant pH, which could result in life-threating issues. 

Source: 

Tro, Nivaldo J. "Aqueous Ionic Equilibrium." Chemistry: A Molecular Approach. Upper Saddle Ranch, NJ: Pearson Prentice hall, 2011. 712+. Print. 

Catalase Enzyme

A Glimpse into the Catalase Enzyme BLC... 
(Bovine Liver Catalase)

     Living organisms rely on oxygen to power our cells, but living with oxygen is dangerous. Oxygen is a reactive molecule that can cause serious problems if not carefully controlled. Oxygen can easily convert into other reactive compounds, making it very dangerous. Inside our cells, carrier molecules move electrons from site to site. If oxygen runs into one of these carrier molecules, the electrons could transfer to it. This can convert oxygen into a dangerous compound, such as hydrogen peroxide, which can attack sulfur atoms and metal ions in proteins. The free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules then attack and mutate DNA. A controversial theory is, this type of oxidative damage accumulates over the years of our life, causing us to age. 

     To fight these dangerous side-effects of living with oxygen, our cells make a variety of antioxidant enzymes. One key part in this is, catalase, which converts hydrogen peroxide into water and oxygen gas. These catalase molecules patrol the cell, and counteract the steady production of hydrogen peroxide, keep the levels in our bodies safe. 

     Catalases are some of the most efficient enzymes found in cells. Each catalase molecule can decompose millions of hydrogen peroxide molecules every second. Our own catalases use an iron ion to assist in this speedy reaction. The enzyme is compose of four identical subunits, each with its own active site buried deep inside. Iron ions are gripped at the center of a disk-shaped heme group. Catalase, are unusually stable enzymes, with four chains interweaving, and locking the entire complex into the proper shape. 

     Bovine liver catalase was one of the first enzymes to be isolated to a high state of purity and the first iron-containing enzyme to be isolated. The reaction mechanism was initially proposed to be a free radical mechanism by Oppenheimer and Stern in 1939. Throughout the next few decades, catalysis was determined to occur at the iron atom of the porphyrin . A more convenient method of preparing crystalline catalase from bovine liver was developed in 1952 by Tauber and Petit, and X-ray structure studies of the heme region of myoglobin examined the heme-containing active site.

     The reaction of catalase occurs in two steps. A molecule of hydrogen peroxide oxidizes the heme to an oxyferryl species. A porphyrin cation radical is generated when one oxidation equivalent is removed from iron and one from the poryphyrin ring. A second hydrogen peroxide molecule acts as a reducing agent to regenerate the resting state enzyme, producing a molecule of oxygen and water. Recently, catalase has been investigated as a possible agent to support methods of intracellular drug delivery. Catalase has also been incorporated into an assay for cholesterol quantification and a biosensor for alcohol determination    

     Bovine liver catalase has a molecular weight of 240kDA and a chemical formula C₂₁ H₃₀ N₇ O₁₇ P₃ . The Active site is Histidine (H74) and Asparagine (N147). Activators are Sodium Arsenate and a reaction catalyze H2O2 + H2O2 => H2O + O2

     In nature, somethings seem very simple to the naked eye. Although, when dealing with the chemical structure of things, that naked eye can not see how complex things are inside the body. Things that are as simple as living with oxygen can be as complex as the catalase enzyme that is used to support the oxygen within our bodies. 

Sources:

http://www.worthington-biochem.com/ctl/default.html

http://www.callutheran.edu/BioDev/omm/catalase/frames/cattx.htm#Topic1

http://0-www.jstor.org.library.acaweb.org/stable/10422

http://www.rcsb.org/pdb/explore/explore.do?structureId=1qqw

http://proteopedia.org/wiki/index.php/1qqw

Organic Compound

What is Vanillin?

     Have you ever wondered what gives vanilla it's sweet smell? How about in your soda, perfume, or air freshener? Where does that sweet vanilla smell come from?  All of these are thanks to an organic compound, Vanillin. This pleasant aromatic molecule occurs naturally in vanilla bean, and as mentioned above, has a wide variety of uses. The white crystalline solid, produces the odor and taste of vanilla. While vanillin is considered safe for human consumption, it can also be toxic in very large quantities. 
     Vanillin, 4-hydroxy-3-methoxybenzaldehydea, chemically is a ring compound that contains the carboxyl (-COOH) group and the hydroxyl (-OH) group. It's functional groups include aldehyde, ether, and phenol. It has a chemical formula, C8H8O3, and molecular weight of 152.15 g/mol. Stable under normal temperatures and pressures, with a boiling point of 285 degrees celsius, and melting point of 81 degrees celsius. Conditions to avoid when handling vanillin are mixing it with incompatible materials, such as, strong bases, light, air, moisture, strong oxidizing agents, bromine, perchloric acid, potassium t-butoxide, t-chlorobenzene and sodium hydroxide, formic acid and thallium nitrate. Vanillin is slightly soluble in water, 1gram dissolves in 100ml of water; also soluble in glycerol, ethyl alcohol, ether, and acetone. Vanillin is a polar molecule that has dispersion forces, however no hydrogen bonds are present.   
     Next time you are enjoying a cola, or making those delicious vanilla cupcakes... think about that little chemical molecule, Vanillin. That without it, your cola would not taste the same, those vanilla cupcakes no longer have that sweet, irresistible smell and taste, and one of the top selling spices in the world would no longer be vanilla.     

To view vanillin structure in 3D, click link below:  http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=1244576157258464967

Sources: 
http://www.chemspider.com/Chemical-Structure.13860434.html
http://www.be-longgroup.com/Human-Nutrition/Vanillin.html
http://avogadro.chem.iastate.edu/MSDS/vanillin.htm
http://en.wikipedia.org/wiki/Vanillin
http://en.wikipedia.org/wiki/Vanilla