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Protein Structure
Alicia Stone
000262467
5/6/2015

A. Insert your original model of an essential amino acid that shows all atoms and bonds in both the backbone and the side chain. Click here to learn how to insert images into a Google Document.

(Insert in-text citation here).

1 Characteristics of Leucine: Hydrophobic

Oxygenation

Insert your description of two characteristics (e.g., reactivity, hydrophobicity, how it affects the structure or functions of a protein) for the amino acid model you created in part A.

(Insert in-text citation here).

B. Insert your original diagram, or series of original diagrams, of the different levels of protein structure.

1. Check to see that you labeled the primary, secondary, tertiary, and quaternary structures in your diagram(s). Primary

Secondary

Tertiary

quaterrnary (Insert in-text citation here).

C. Insert your original diagram, or series of original diagrams, that demonstrates how a peptide bond is made through dehydration.

Check to see that you used a complete chemical equation that includes the following components:

• chemical structures of all reactants
• an arrow indicating the direction of the reaction
• the chemical structures of all products (Insert in-text citation here).

D. Insert your original diagram, or series of original diagrams, that demonstrates how a peptide bond is broken through hydrolysis.

Check to see that you used a complete chemical equation that includes the following components:

• the chemical structures of all reactants
• an arrow indicating the direction of the reaction
• the chemical structures of all products (Insert in-text citation here).

E. Insert your explanation of the four forces (i.e., bonds or interactions) that stabilize a protein’s structure at the tertiary level of protein structure. Hydrophobic Interactions: Soluble globular proteins fold so that hydrophobic side chains are mostly sequestered in the core of the protein. The removal of the non-polar groups from water (i.e. the hydrophobic effect) is the primary force stabilizing tertiary structure.
Most polar amino acid side chains are on the outside surface so they can hydrogen bond to water to solubilize the protein.
Salt Bridges: Protein fold so that positively charged side chains are often located adjacent to negatively charged side chains. The salt bridge or ionic bond between the charged functional groups helps stabilize the tertiary structure.
Hydrogen Bonds: Folding is also stabilized by hydrogen bonds that form between the polar hydrogen of one amino acid and a lone pair of electrons on another (note: hydrogen atoms do not usually display in pdb files).
Covalent Bonds: Some proteins are cross-linked with covalent bonds. The most common is a disulfide b

(Insert in-text citation here).

F. Insert your explanation of how bovine spongiform encephalopathy (BSE) occurs at a molecular level.

Check to see that you explained the role of protein misfolding and aggregation in BSE, by including the following points:
• the name of the protein that is misfolding
• why the protein is misfolding
• why there is aggregation
• what structures the aggregated proteins form Sometimes, in inherited conditions, or when mutations appear in a specific protein, the amyloid protein deposits consist of the mutant protein. The