Create an original model of an essential amino acid that shows all atoms and bonds in both the backbone and the side chain

Below is a structured approach to completing this assignment. It provides details on how each section should be addressed and incorporates the required diagrams, models, and explanations.

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Amino Acids and Peptide Bonds, Protein Structure: Understanding BSE

A. Essential Amino Acid Model

Description of Model:

• I constructed a 3D model of lysine, an essential amino acid. This model displays the amino group (-NH₂), carboxyl group (-COOH), and side chain (ε-amino group, -(CH₂)₄NH₂).

Two Characteristics of Lysine:

1. Hydrophilicity:
   Lysine is hydrophilic due to its positively charged ε-amino group, allowing it to interact with water and form hydrogen bonds, critical for protein solubility.
2. Role in Protein Structure:
   Lysine’s side chain participates in ionic bonding with negatively charged residues, stabilizing tertiary and quaternary protein structures.

B. Levels of Protein Structure

Diagram(s) of Protein Structure:

1. Primary Structure:
   • A linear sequence of amino acids connected by peptide bonds.
2. Secondary Structure:
   • Includes α-helices and β-sheets formed through hydrogen bonding between the backbone’s -NH and -CO groups.
3. Tertiary Structure:
   • The 3D shape of a single polypeptide, stabilized by hydrophobic interactions, disulfide bonds, ionic bonds, and van der Waals forces.
4. Quaternary Structure:
   • Complexes of multiple polypeptide chains, such as hemoglobin, where each chain interacts to form the functional protein.

(Include labeled diagrams depicting each level of protein structure.)

C. Peptide Bond Formation (Dehydration Reaction)

Diagram Explanation:

• Reactants: Amino group (-NH₂) of one amino acid and carboxyl group (-COOH) of another.
• Reaction: Removal of a water molecule (dehydration) to form a peptide bond.
• Products: Dipeptide with a peptide bond (-CO-NH) and water (H₂O).

(Insert a diagram with labeled chemical structures of reactants and products.)

D. Peptide Bond Breaking (Hydrolysis Reaction)

Diagram Explanation:

• Reactants: Dipeptide and water (H₂O).
• Reaction: Water is added to break the peptide bond, regenerating the amino and carboxyl groups.
• Products: Two individual amino acids.

(Insert a diagram showing this reaction with chemical structures.)

E. Forces Stabilizing Tertiary Protein Structure

1. Hydrophobic Interactions:
   Nonpolar side chains aggregate to avoid water, stabilizing the core of the protein.
2. Hydrogen Bonds:
   Occur between polar side chains, providing structural integrity.
3. Ionic Bonds (Salt Bridges):
   Form between oppositely charged side chains, enhancing stability.
4. Disulfide Bonds:
   Covalent bonds between cysteine residues, adding robustness to the structure.

F. Molecular Basis of Bovine Spongiform Encephalopathy (BSE)

1. Protein Misfolding and Aggregation:
   • Protein Name: Prion protein (PrP).
   • Misfolding Cause: Abnormal folding into the PrP^Sc isoform, which is resistant to proteases.
   • Aggregation: Misfolded PrP^Sc aggregates, forming amyloid plaques.
   • Structural Impact: Aggregated proteins disrupt normal brain function, leading to neurodegeneration.
   • Symptoms: Behavioral changes, motor dysfunction, and eventual death.
2. Role of Prions in BSE:
   • Definition: Infectious proteins that propagate by inducing misfolding in normal prion proteins.
   • Prion Name: PrP^Sc.
   • Disease Mechanism: PrP^Sc converts PrP^C (normal prion protein) into PrP^Sc, creating a chain reaction.
3. Chaperone Protein Role in BSE:
   • Normal Role: Assist in proper protein folding and prevent aggregation.
   • BSE-Specific Chaperone: Heat shock protein (Hsp70).
   • Differences: In BSE, the chaperone fails to prevent the conversion of PrP^C to PrP^Sc.
4. Recommendations for Decreasing BSE Risk:
   • Ban the use of animal-derived feed for livestock.
   • Implement mandatory testing of cattle for prion contamination.
   • Establish protocols for safe disposal of infected carcasses.
   • Educate farmers and food processors on prion-related risks.

G. References

(Include all sources used in APA format.)

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Notes for Submission:

1. Use clear and labeled diagrams for all visual content.
2. Ensure narrative responses provide sufficient detail while avoiding unnecessary complexity.
3. Save the document as a PDF or Word file as instructed.