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Comprehension of Content Enduring Understandings 

Reflection 

            Throughout the MISEP program I have had several courses that required me to work on my understanding of how molecules interact with one another and within one another.  The first time was during our chemistry class.  We discussed bonds and how they formed but I did not connect the models to real life situations and learned them in isolation.  Next I had exposure to structures again when I took biology.  I understood how the shapes of molecules at the cellular level affected their function but did not have an understanding of how the bonding affected cellular functions (see evidence below).  This class took what I had previously learned and connected it together as evidenced in my explanation below. 

MISEP Chem 512 – Jacobs

Final EU paper and reflection

Due August 16, 2007 

Submitted by Patty McCarrin

            On a pre-class assignment I was asked to comment on how bonding within a molecule determines its shape and polarity, and therefore its interactions and reactions with other molecules.  Both interactions and reactions can be understood by analyzing energetic stability of molecules and bonds.  My answer on the completed pre-class assignment shows how a molecule’s bonds affect shape and polarity.  Polar bonds result in unequal sharing while non-polar bonds share electrons equally.  The pull on the electrons and the number of pairs determines the shape.  The strength of the bond also determines its stability and how fast and easily it will react.  It was a good explanation but I couldn’t give the reason for the shape being important.        

            Throughout this course we have discussed bonding, bonding, bonding.  Each time I thought I understood it until I took my quizzes (See attached).  Each time I struggled with what types of bonds formed and how they connected.  It was not until after our final quiz that I had my “ah, ha” moment.  I finally understand when there will be a dispersion force, a hydrogen bond or dipole-dipole.  I understand that these are intermolecular and will not occur intramolecularly.  I understand that the intramolecular bonds are going to be stronger and that amino acids form covalent, peptide bonds in their linear structure and where the covalent bonds and hydrogen bonds are formed in the structure of DNA.   I understand why we spent so much time on bonding and how important it is to the fundamental structures of living and nonliving things.

              There are certain aspects with which I am still struggling but they become clearer each time I work with a problem.  This class has given me a better understanding of concepts I need to strengthen and the means to do this.

Post-Course Evidence Essay 

I have chosen the following enduring understanding to discuss for this final assignment. 

        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 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 molecules and bonds.        

            A bond is defined as anything that binds, ties, or fastens something together.  They are an extremely important part of life.  We bond with our mothers.  We bond with friends.   If it weren’t for bonds, living and non-living things would not exist.  Molecular level bonding controls the structure and function of all things.

            In biochemistry this summer we studied amino acids.  They are the building blocks of proteins and proteins are responsible for controlling all of the cellular interactions in our body.   Twenty amino acids make up the structure of all proteins.  Each protein has a unique structure which is part of our genetic code and determines how each protein will interact with other proteins to perform their specialized function. 

            The amino acids share features.  The primary features are that they all contain a carboxylate group, -COOH, at one end, an amino, -NH2, group which are covalently bonded to the same carbon atom and a side chain, R group, which is exclusive to the particular amino acid and dictates its properties. The side chains allow the amino acids to be grouped as hydrophobic or hydrophilic.  This is important to their formation and function (Denniston, 2004)). 

            There are three characteristics, primary, secondary and tertiary, which determine the structure of the amino acid and thus its function.  The primary structure is the linear arrangement which forms the backbone of the acid and contains the repeating sequence (Denniston, 2004).   It is covalently linked intramolecularly by peptide bonds which form when the carboxyl group reacts with the amino group of the other molecule in a dehydration reaction which releases water.  This first bonding of the amino acid forms the strongest of the bonds.  These bonds are fairly rigid which is important for shape maintenance needed for proper function. 

            The next bonding that takes place is in the secondary structure. This happens intermolecularly when the amide hydrogens and carbonyl oxygens of the peptide bonds form hydrogen bonds. (Denniston, 2004).  Many hydrogen bonds are needed for the amino acid to maintain a particular structure.  Two of the most common are the alpha helix and beta pleated shapes. The sides of the alpha helix shape can differ in polarity with the hydrophobic projecting in one direction and the hydrophilic projecting in another.  The beta pleated sheets are formed by folding successive planes and can be parallel or antiparallel.  These shapes determine the way the side chains will connect which occurs in the tertiary structure.

            The tertiary is the third structure responsible for creating the shape of the amino acid and is formed by the side chains and maintained by Van der Waal forces, hydrogen bonds, ionic bonds, covalent bonds or the disulfide bond of cystine.  The Van der Waals forces occur “between the R groups of nonpolar aminor acids that are hydrophobic. Hydrogen bonds form between the polar R groups of amino acids.  The Ionic bonds form between the R groups of oppositely charged amino acids and the covalent bonds between the thio-containing amino acids” (Denniston, pg. 574, 2004).   Disulfide bonds form between the cystine amino acids (Denniston, 2004). 

            The final bonding occurs as individual protein chains link together.  They are held by the same forces as the tertiary chains.  The latter two are the ultimate determiners of the proteins function.

            We also studied the bonding format of DNA.  The DNA molecule, like the amino acid, has a backbone.  This backbone is formed by a phosphate and sugar group which is linked by a covalent, phosphodiester bond with a nitrogenous base linked to the 3’ carbon of the sugar (Denniston, 2004).  Like the amino acids the backbone forms the strongest structure of the molecule. The interior of the DNA consists of bases linked together by hydrogen bonds. The four bases involved in the DNA molecule are adenine, thymine, quanine and cystosine.  They form either a double or triple hydrogen bond.  The adenine and thymine always join together forming a double bond while the quinine and cytosine form the triple hydrogen bond.  It is these hydrogen bonds that are responsible for the double helix shape of the DNA but the base pairs have other properties which are unique and are a current topic of study.  (http://www.sciencedaily.com/releases/2007/07/070712134533.htm).

            In biology class we discussed sickle cell anemia.  I obtained some background information about sickle cell anemia to do with a unit lesson for my students (see attached).  I did understand that the shape change was what caused the problem but not how it worked at the molecular level.  After studying about the structure of the amino acid and how this structure can affect its function I can better understand how the change in the shape of the red blood cell can alter the ability of this cell to function properly.  The red blood cell has hemoglobin molecules.  These molecules have a particular shape but a genetic mutation causes the shape of the hemoglobin to change. The Glutamic acid which is part of the chain, polar and soluble in water is replaced by Valine, a non-polar, insoluble protein.  The cells change from their normal donut shape to a pointed shape, hemoglobin S, which causes them to clump together making it difficult for them to pass through tiny capillaries.  This phenomenon is a clear example of how an intermolecular structure could affect the intramolecular structure of the protein causing it to malfunction (see attached).

            In Earth Science this summer we studied the nature of minerals and how their structures determine the type of mineral that will be formed.  Each mineral has a definite crystalline structure and composition which determines its physical properties.  Silicates are the most common mineral found on Earth and have a basic silicon-oxygen tetrahedron structure which consists of silicon atom being surrounded by four oxygen atoms. “In some minerals, the tetrahedral are joined into chains, sheets or three-dimensional networks by sharing oxygen atoms” (Tarbuck, pg. 40, 2006).  They are then connected by other elements.  These structures determine a minerals “cleavage[1] habits” or fracture[2] properties.  If a mineral, for example quartz, has a silicon-oxygen group with bonds that are equally strong in all directions it will not exhibit cleavage but will fracture instead.  The melting and cooling properties of minerals is also determined by its bonds and therefore determines which minerals might aggregate together to form a rock structure. 

            Bonds are important in all facets of life and drive the forces of our world and universe.   

Evidence

Two Biochemistry Quizzes and One Explanation of incorrect answers 

References

Denniston, K., Topping, J., Caret, R. (2004). General, Organic, and Biochemistry. New York: McGraw Hill.

Krogh, D. (2005). Biology: A Guide to the Natural World. New Jersey: Prentice Hall.  

Tarbuck, E., and Lutgens, F. (2006).  Earth Science. New Jersey: Prentice Hall.

Patty McCarrin - September 30, 2007                   Back to e-portfolio