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Intramolecular covalent bonds are the hardest to break and are very stable, being about 98% stronger than intermolecular bonds.

sas.upenn.edu - Eilisha Joy Bryson - Penn Arts & Sciences

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Eilisha Joy Bryson August 16, 2007

MISEP Chem 512 – Jacobs

Enduring Understanding Essay

Enduring Understanding #4 – The bonding within a molecule determines its shape and polarity, and therefore its interactions and reactions with other molecules. Intermolecular interactions are central to the structure and function of the biochemical systems, and the extent and rate of biochemical reactions govern all cellular functions. Both interactions and reactions can be understood by analyzing energetic stability of the molecules and bonds. Two types of bonds are pertinent to this Enduring Understanding. The first is due to intramolecular forces that make chemical covalent bonds, either polar or non-polar. Because of the octet rule only certain arrangements of bonds will make a stable molecule, consequently giving a molecule its geometric shape. Using the type of covalent bond, the presence of lone pairs, and the symmetry of the shape of the molecule, you can determine if the entire molecule is polar or not (which is different than polar bonding). The polarity of the molecule determines the forces occurring between it and other molecules. These intermolecular forces are basically weak bonds, but are essential in holding molecules together. Non-polar molecules have the weakest attractions called London forces. Polar molecules have stronger intermolecular attractions, called dipole-dipole forces. The strongest intermolecular force is a special type of dipole-dipole interaction called a hydrogen bond, formed between a molecule that contains a hydrogen atom and a molecule that contains a nitrogen, oxygen, or fluorine atom, which are highly electronegative. Intramolecular covalent bonds are the hardest to break and are very stable, being about 98% stronger than intermolecular bonds. The covalent and intermolecular bonds discussed above result in numerous structures and functions of biochemical systems. This is described below using the multi-structures of proteins. The primary structure of the protein is the long amino acid chain, and it is formed by intramolecular covalent bonds. Enzymes fold the primary structure, creating regions of repeating patterns, a-helix and b-sheets being the most popular. The folds are held together and maintain their shape due to the intermolecular force of hydrogen bonds. There can be several differently shaped regions making up the secondary structure. The secondary structure then folds onto itself creating a 3-dimensional shape called the tertiary structure. This is held together and maintains its shape due to all of the intermolecular forces: London, dipole-dipole and hydrogen bonds, as well as ionic and disulfide bonds which are intramolecular. The sequence of the amino acids determines the structures of the protein and the structures result in the protein�s function. Last summer in our Biology course, we learned about the mechanism of hormones. Dr. Waldron�s notes read, �It begins with the binding of a hormone molecule to a specific hormone receptor, which is a protein with a binding site which specifically matches the shape and electrical charge distribution of the particular hormone molecule.� Focusing on the hormone receptor protein, you can see here how shape relates to function. An excellent example that we looked at during this class was with a protein whose job was to destroy blood cells. The protein�s shape, which consisted of polar and non-polar regions, allowed it to take advantage of both the lipid and water-based properties of the cell. While researching such proteins on the internet an article described a prion protein that was responsible for destroying brain cells. The protein Prp takes on an unexpected amyloid fold that consists of tight b-sheets that are difficult to penetrate, changing it into PrPsc. These incorrect folds cause the protein to turn brain cells into sponge-like holes. Prion is found in patient�s cells who had various diseases, such as Alzheimer's and Down's syndrome. Simply changing the shape of a region of the protein results in a new and dangerous function.

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Reactions change the covalent bonds within a molecule, breaking old bonds and making new ones. If there is more energy released when the bonds form between the products compared 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 products are more stable than the reactants. The opposite is true for an endothermic reaction, and heat needs to be added at the beginning for the reaction to occur. This yields an unstable product at the end of the reaction. In class we analyzed ATP and learned that ATP hydrolysis, ATP + H 2 O � ADP + P, is an exothermic reaction, the water breaks the oxygen and phosphorus bond, giving off essential energy for cellular functions.

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 protein�s ability to kill brain cells. Research News. Ohio State University http://researchnews.osu.edu/archive/prpfind.htm

http://www.cartage.org.lb/en/themes/Sciences/LifeScience/GeneralBiology/Microbiology/PrionsViroids/Prions/Prions.htm (prions)

sas.upenn.edu - Eilisha Joy Bryson - Penn Arts & Sciences

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