Eilisha Joy Bryson August16, 2007
MISEP Chem 512 – Jacobs
Enduring Understanding Essay
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EnduringUnderstanding #4 –
The bonding within amolecule determines its shape and polarity, and therefore its interactions andreactions with other molecules. Intermolecular interactions are central to thestructure and function of the biochemical systems, and the extent and rate ofbiochemical reactions govern all cellular functions. Both interactions andreactions can be understood by analyzing energetic stability of the moleculesand bonds.
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Twotypes of bonds are pertinent to this Enduring Understanding. The first is dueto intramolecular forces that makechemical covalent bonds, either polar or non-polar. Because of the octet ruleonly certain arrangements of bonds will make a stable molecule, consequentlygiving a molecule its geometric shape. Using the type of covalent bond, thepresence of lone pairs, and the symmetry of the shape of the molecule, you candetermine if the entire moleculeis polar or not (which is different than polar bonding). The polarity of themolecule determines the forces occurring between it and other molecules. These intermolecular forces are basically weak bonds, but areessential in holding molecules together. Non-polar molecules have the weakestattractions called London forces. Polar molecules have stronger intermolecular attractions, called dipole-dipole forces.The strongest intermolecularforce is a special type of dipole-dipole interaction called a hydrogen bond,formed between a molecule that contains a hydrogen atom and a molecule thatcontains a nitrogen, oxygen, or fluorine atom, which are highlyelectronegative. Intramolecularcovalent bonds are the hardest to break and are very stable, being about 98%stronger than intermolecularbonds.
The covalent and intermolecular bonds discussed above result in numerousstructures and functions of biochemical systems. This is described below usingthe multi-structures of proteins. The primary structure of the protein is thelong amino acid chain, and it is formed by intramolecular covalent bonds. Enzymes fold the primarystructure, creating regions of repeating patterns, a-helixand b-sheetsbeing the most popular. The foldsare held together and maintain their shape due to the intermolecular force of hydrogen bonds. There can beseveral differently shaped regions making up the secondary structure. Thesecondary structure then folds onto itself creating a 3-dimensional shapecalled the tertiary structure. This is held together and maintains its shapedue to all of the intermolecularforces: London, dipole-dipole and hydrogen bonds, as well as ionic anddisulfide bonds which are intramolecular.The sequence of the amino acids determines the structures of the protein andthe structures result in the proteinÕs function.
Lastsummer in our Biology course, we learned about the mechanism of hormones. Dr.WaldronÕs notes read, ÒIt begins with the binding of a hormone molecule to aspecific hormone receptor, which is a protein with a binding site whichspecifically matches the shape and electrical charge distribution of theparticular hormone molecule.Ó Focusing on the hormone receptor protein, you cansee here how shape relates to function. An excellent example that we looked atduring this class was with a protein whose job was to destroy blood cells. TheproteinÕs shape, which consisted of polar and non-polar regions, allowed it totake advantage of both the lipid and water-based properties of the cell. Whileresearching such proteins on the internet an article described a prion proteinthat was responsible for destroying brain cells. The protein Prp takes on anunexpected amyloid fold that consists of tight b-sheets that are difficultto penetrate, changing it into PrPsc. These incorrect folds cause the proteinto turn brain cells into sponge-like holes. Prion is found in patientÕs cellswho had various diseases, such as Alzheimer'sand Down's syndrome. Simply changing the shape of a region of the proteinresults in a new and dangerous function.
Reactionschange the covalent bonds within a molecule, breaking old bonds and making newones. If there is more energy released when the bonds form between the productscompared to the amount of energy absorbed to break the bonds between reactants,then the reaction is termed exothermic, and heat is given off, and the productsare more stable than the reactants. The opposite is true for an endothermicreaction, and heat needs to be added at the beginning for the reaction tooccur. This yields an unstable product at the end of the reaction. In class weanalyzed ATP and learned that ATP hydrolysis, ATP + H2O ¨ ADP+ P, is an exothermic reaction, the water breaks the oxygen and phosphorusbond, giving off essential energy for cellular functions.
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References:
http://people.sps.lane.edu/jtyser/chem/Quiz/Unit12Test.html(endothermic potential energy diagram)
http://www.simsoup.info/SimSoup/Potential_Energy_Profile.png(exothermic potential energy diagram)
Cocchetto, A. (2004). Amyloids:A Basic Primer. http://www.ncf-net.org/forum/amyloids.htm
http://en.wikipedia.org/wiki/Amyloid(Amyloids)
http://en.wikipedia.org/wiki/Prion(Prion)
Misfolding the key to proteinÕs ability to kill brain cells. ResearchNews. Ohio State University http://researchnews.osu.edu/archive/prpfind.htm
