Chemical Equilibrium

This video goes in depth about the reactions in chemical equilibrium. Chemical equilibrium is a state in a chemical reaction in which the rate of formation of products is equal to the rate of formation of reactants. Vmax, activation energy, and Km are all explained thoroughly. Sal from KhanAcademy also explains the graph of the energy of a chemical reaction. You can fully understand what each curve represents and how they can be changed (how activation energy might be lowered). He explains how and what a cell might do to reach that chemical equilibrium. The potential energy that may allow an object to move is also described. He gives similar analogies as a ball at the bottom and top of a hill, that will help you remember and understand the concepts of exergonic/endergonic reactions. I found this video very helpful in understanding exergonic and endergonic reactions! 

Hammerhead Ribozymes

In my previous blog, I briefly mentioned the hammerhead ribozyme. This article talks about them in more depth. Hammerhead ribozymes are tiny, self-cleaving RNAs that boost strand scission by internal phosphoester transfer. They have two types; type I and type II. They also have two major properties which are cleavage site specificity and catalytic activity.
To identify numerous additional representatives of this ribozyme class (including the first representatives in fungi and archaea), comparative sequence analysis was used. The first natural samples of “type II” hammerheads have been uncovered. These results show that this altered form occurs in bacteria as frequently as type I and III architectures. A commonly occurring pseudoknot that forms a tertiary interaction that is very important for high-speed ribozyme activity has also been discovered. Genomic factors of many hammerhead ribozymes can tell what biological functions they perform that are different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare occurrences, nucleotide variation occurs at places within the catalytic core that are otherwise strictly conserved. Thus suggesting that core mutations are occasionally tolerated or even preferred.

Hammerhead Ribozymes have three helical stem regions and unpaired loops at the ends of two helices. Helices radiate out from central unpaired core of nucleotides. The cleavage site is next to a small, unpaired "U-turn" loop. 

This picture shows the secondary and tertiary structure of a hammerhead ribozyme.

Metal Ions that Bind and Function in RNA Enzymes

This article was about metal ions that bind and function in natural and artificial RNA enzymes. Ribozymes are catalysts that are present in RNA molecules. Recent research has shown that many new catalytic RNA concepts seem to be deviations off of common themes. This has led researchers to believe that ribozymes have evolved. They probably evolved to satisfy specific RNA-essential biological niches. Due to its small structure, many people are led to believe that ribozymes may not carry out many functions; however, analyses at the lab have proven that RNA has the ability to function in carbon-carbon reactions and even tRNA aminoacylation. 
Four naturally occurring enzymes are the hammerhead, hairpin, hepatitis delta virus, and glmS metabolite sensing ribozyme. The full article, which is not available to RVCC, would have explained these four enzymes in detail regarding their fundamental structure, metal binding properties, and the fold and ion coordination of three artificial ribozymes developed to study the boundaries of RNA catalysis (the acceleration of a chemical reaction by a catalyst). The three ribozymes under study were the leadzyme, the flexizyme, and the Diels-Alder ribozyme. The experiment compared STRUCTURE TO FUNCTION (which is uber-important in biology) but, kept in mind the idea of ideal metal-ion coordination geometry that was obtained from surveys of high-resolution small molecular structures. A newly developing theme is that natural and artificial ribozymes which catalyze single-step reactions also usually possess a pre-formed active site. Multivalent ions aid in the active site formation for RNA, but can also provide Lewis acid functionality which is required for catalysis. When this metal ion bonding is not possible, ribozymes survive/adapt by ionizing their bases, or by recruiting cofactors that increase their chemical functionality.

And the Winner is... Uh-Oh!

This article talks about a precedent in Nobel Prize history. Dr. Ralph Steinman, a biologist at Rockefeller University, was named winner of the 2011 Nobel Prize in Physiology, this Monday. Unfortunately, Steinman died of pancreatic cancer this Friday. Ironically, he had actually extended his own life using therapy that he had designed himself! The Nobel Prize Rules state that the prize cannot be awarded to someone after their death. In this situation, the Nobel committee was not aware of his death and had already declared him to be the winner. He would have received the prize of almost $1.5 million!

Steinman discovered the immune system's sentinel dendritic cells. He also demonstrated that science can productively harness the power of these cells and other components of the immune system to curb infections and other communicable diseases. Brilliantly enough, when Steinman was diagnosed with cancer, he prolonged his life using exactly this; his own dendritic cell-based immunotherapy. The Nobel Committee recognized Steinman for his discovery of the dendritic cell and its role in adaptive immunity.

In further detail, Dr. Steinman discovered dendritic cells in 1973. He found that these new class of cells are very important in activating the body's adaptive immune system. He later, found out how they function. Overall, his reasearch set a foundation for more studies in immunology and has led to advanced, new approaches to treating cancer, infectious diseases, and disorders of the immune system. Dr. Steinman applied his research on his own life. He deployed his own dendritic cells to mount an assault on his own cancer! Truly an inspiration for all.

Wee for a Wii

This article talks about Jennifer Strange, a 28 year-old woman who died due to water intoxication. Water intoxication results when the normal balance of electrolytes are disturbed and pushed out of safe limits from drinking excessive amounts of water. As we talked about in class today, cells prefer to stay in an isotonic solution. With the excess water coming in, the fluid outside the cells would get more water, becoming diluted. This would cause the fluid outside the cell to become hypotonic. Cells in hypotonic solutions start to swell up. Because, in comparison, the cells would have a higher concentration of salts and the water would rush into the cells. Eventually the cells would burst due to all the pressure. In the brain, this swelling increases intracranial pressure. This may cause headaches, confusion, and drowsiness; symptoms that Strange went through just hours before her death. Eventually, vital signs will be effected; including bradycardia which is an abnormally slow heart rate. Cerebral edema can occur; an excess accumulation of water in the intracellular and extracellular spaces of the brain. This can cause cerebral infarctions because blood vessels may collapse due to all the pressure, resulting in paralysis. In sum, the body will slowly stop working causing brain damage, coma, or even death.
Water intoxication can be prevented if your water intake does not exceed your losses. Healthy kidneys can micturate about a quarter of a gallon an hour; stress may reduce this number. Water intoxication, before it goes too far, can be treated with diuretics to help you urinate :) Another treatment is vasopressin receptor antagonists which are one of the cell surface receptors that play an important role in your body's retention of water.

Glycosylation

This article goes into depth about the process of glycosylation. Glycosylation is the attachment of carbohydrates to a lipid or protein, referred to as a glycolipid or glycoprotein respectively. Formation of the sugar-amino acid linkage is very important in the biosynthesis of the carbohydrate units of glycoproteins. the modification of proteins through enzymatic glycosylation is an event that goes beyond the genome and is controlled by factors that are very different amongst various types of cells and species. Many different glycosylation routes have been found in organisms that lead to the mature carbohydrate units on glycoproteins that are secreted by cells or become components of its membrane, cytoplasm, or nucleus. One major event in the biogenesis of peptide-linked oligosaccharides is the formation of the sugar–amino acid bond; this determines the nature of the carbohydrate units that will subsequently be formed by the cellular enzymatic machinery, which in turn influences the protein’s biological activity. This is a perfect example of structure fits function. 
This article talks about two types of glysoylation. N-glycosylation and O-glycosylation. I'm not going to go in depth about those because it is wayyyy too confusing but feel free to read the article if you're interested! It also talks about phosphoglycosylation. Phosphoglycosylation is the enzymatic attachment of a sugar to the polypeptide chain, through a phosphodiester bridge. 
Defects in the attachment of a carbohydrate to protein have lead to some human diseases. The disorders that have been present at birth are most often neurological and developmental deficiencies. 
Appreciation of the major role that oligosaccharides play in the framework of proteins with many different amino acid sequences make glycopeptide bond multiplicity more understandable. After all, it is the formation of these linkages that determines to a large extent the nature of the final carbohydrate units (where they are going to go and what role they will play in the cell) that are subsequently formed by the the many processing enzymes.