Biochemistry

Goals 5.1 Amino Acids:

Be able to recognize name (including 3 letter abbreviations)
Be able to name (including the three letter abbreviation) and draw one amino acid from each of the four categories of amino acids
Be able to determine whether an amino acid is nonpolar, polar (neutral), acidic, or basic
Describe how the structure of the amino acid relates to its properties (H-bonding ability and other intermolecular interactions, nucleophilicity or other reactivity, relative basicity, etc.)

Goals 5.1, 5.2, 5.3:

Explain the role of the amine and the carboxylate in the formation of a peptide linkage (amide)
Explain the significance of resonance in the amide linkage that forms between amino acids
Describe the importance of variant and invariant residues when analyzing primary structures
Understand how chemical methods are used to sequence proteins and explain why proteins must be broken into small segments before they are sequenced
Be able to determine a sequence from "experimental" data

Goals 5.1, 5.2, 5.3:

Identify common secondary structures
Describe the role of H-bonds in the formation of secondary structures
Describe the role of other non-covalent interactions (hydrophobic interactions, ionic interactions) in the formation of the overall structure of a polypeptide or protein

Goals 5.1, 5.2, 5.3:

Describe how the unique properties of some amino acids allow them to play their roles (gly, pro, cys, his) in determining the structure of the polypeptide or protein
Recognize coenzymes, cofactors, and prosthetic groups
Analyze the amino acids used to create a polypeptide or protein and explain how the structure of a protein helps it perform its function

Goals

Explain how noncovalent interactions can be interrupted to denature proteins
Explain why one might want to denature a protein
Explain why many polypeptides are charged, and why adding acid or base can alter the charge of the molecule
Understand the basic concept behind separation of proteins or polypeptides by gel electrophoresis