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E. Coli versus HIV

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Present and discuss the differences and similarities in the structure of E. Coli and HIV. Discuss E. Coli and HIV differences in their classification - generally referred to as a natural or phylogenetic classification system. Structural differences can simply be addressed by distinguishing the physical differences between E. Coli and HIV. Characteristics that are commonly used to classify or distinguish the differences between the microorganisms may also be presented.

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I'll give you some background info on the 4 areas that seem to warrant discussion here:

1) Natural vs. phylogenetic classification of E. coli and HIV
2) Basic structural differences
3) How bacteria and viruses are classified, and where E. coli and HIV are in these categories
4) Common characteristics used to distinguish E. coli and HIV

1) Natural classification refers to classifying an organism based on a concept of descension from common ancestors while phylogenetic classification classifies based on similarity in genome. E. coli itself is a species which has many different strains, categorized into many groups. However, the entire species is genetically closest to E. fergusonii, a different species of Gram negative, ...

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The expert discusses the differences and similarities in the structures of E. Coli and HIV. The differences in their classifications are provided.

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A solution for Allosterity and Cooperativity

When a compound made up of non-polar molecules is mixed with an aqueous solvent such as water, the molecules cluster together into a ball while water tends to form a ring around them. They do so because they are hydrophobic (. Wikibooks 2015).

When more of this solute is added, the water ring is disturbed as more of the hydrophobic molecules join the non-polar core and the displaced water molecules are freed to move around. This causes high disorder in the solution environment referred to as high entropy.
According to the 2nd Law of Thermodynamics, "The total entropy of the system plus its surrounding must always be increasing"(Wikibooks 2015). In this case the release of the water molecules from the cage around nonpolar surfaces is favourable and responsible for phenomenon called the hydrophobic effect.

The degree of freedom i.e. the free movement of drugs in solution or receptor proteins also favours entropy optimization and the binding phenomenon reduces this freedom as well as the binding affinity. Creation of more rigid drug molecules with less interference on the protein degree of freedom results in compensated enthalpy/entropy environments that favour binding affinity.

1. The binding affinity of drug molecules to protein receptor sites is a function of the solubility of the drug molecule and the part of the protein bound to the drug. The less soluble the drug molecule is, the more hydrophobic it is and therefore the higher the entropy as explained in the background above which creates a favourable environment for entropic optimization. Solvation of the protein (hydrophobicity) that is buried during binding will increase binding affinity if it is more hydrophobic. Binding Affinity (Ka) is a function of Gibbs Energy which is a difference between enthalpy and entropy. A more negative enthalpy and more positive entropy are more favourable for binding affinity (Freire 2005).

2. The limitations of this approach to affinity optimization include the following:

2.1. The resulting drug molecules are insoluble in water due to their hydrophobicity

2.2. Drug resistance may result from mutations of the binding site.

3. Enthalpy/Entropy compensation is any gain in enthalpy contributions to binding is opposed by an accompanying loss in entropic contributions. Affinity optimization is accomplished by selecting chemical modifications that carry a low enthalpy/entropy compensation ((Lumry and Rajender, 1970; Eftink et al., 1983). Examples of the practical application of the entropy/enthalpy compensation principle including conformational constraints are all 1st generation HIV Protease Inhibitors Nelfinavir, Saquinavir and Ritonavir (Velasquez et.al 2003)

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