Lecture 2 - Main objectives + amino acid nomenclature

Classify amino acids into appropriate groups based upon the structure and properties of their unique R-group side chains.

Amino acids are classified by R-group properties into these main groups:

1. Nonpolar (hydrophobic) – e.g., Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tryptophan

2. Polar uncharged – e.g., Serine, Threonine, Asparagine, Glutamine, Tyrosine

3. Acidic (negatively charged) – e.g., Aspartic acid (Asp), Glutamic acid (Glu)

4. Basic (positively charged) – e.g., Lysine, Arginine, Histidine

Apply knowledge of the properties of amino acids to understand the structures, properties, and functions of proteins

Amino acid side chain properties—such as hydrophobicity, charge, polarity, and ability to form hydrogen or disulfide bonds—critically influence protein structure and function by dictating intra- and intermolecular interactions during folding. Hydrophobic residues typically localize to the protein core, stabilizing tertiary structure via van der Waals forces, while polar and charged residues orient toward the aqueous environment or engage in ionic and hydrogen bonding. These interactions govern secondary structural elements (e.g., α-helices, β-sheets), facilitate proper tertiary folding, and enable quaternary assembly in multimeric proteins. Functionally, specific residues within active or binding sites determine enzymatic activity, substrate specificity, allosteric regulation, and interactions with other biomolecules, underscoring the central role of amino acid chemistry in protein behavior.

Define protein primary, secondary, tertiary, and quaternary structures.

Primary structure is the linear sequence of amino acids in a polypeptide chain.
Secondary structure refers to localized folding into α-helices or β-sheets stabilized by hydrogen bonds.
Tertiary structure is the overall 3D shape of a single polypeptide, formed by interactions among R-groups.
Quaternary structure is the assembly of multiple polypeptide subunits into a functional protein complex.

Describe the types and nature of bonds and forces that stabilize primary, secondary, tertiary, and quaternary protein structure

• Primary structure: stabilized by peptide (covalent) bonds between amino acids.

• Secondary structure: stabilized by hydrogen bonds between backbone amide hydrogen and carbonyl oxygen.

• Tertiary structure: stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bridges (covalent bonds between cysteines).

• Quaternary structure: stabilized by the same forces as tertiary (noncovalent interactions and sometimes disulfide bonds) between subunits.

Predict how changes to a protein’s amino acid primary structure may alter its final structure, properties, and function

Changes to a protein’s primary structure (mutations) can disrupt folding by altering side-chain interactions, potentially leading to misfolding, loss of function, altered binding, or aggregation, depending on the location and type of substitution.

hydrophobic/non-polar neutral charge

hydrophilic/polar neutral charge

hydrophilic/polar

hydrophilic/polar

hydrophobic/non-polar neutral charge

Glycine Gly G

Proline Pro P

Valine

Leucine

Isoleucine

Alanine

Methionine

Phenylalanine

Tryptophan

hydrophobic/non-polar neutral charge

Gly

Pro

Val

Leu

Ille

Ala

Met

Phe

Trp

hydrophilic/polar neutral charge

Serine

Threonine

Tyrosine

Cysteine

Asparagine

Glutamine

hydrophilic/polar neutral charge

Ser

Thr
Tyr

Cys

Asn

Gln

hydrophilic/polar positive charge

Lysine

Arginine

Histidine

hydrophilic/polar positive charge

Lys

Arg

His

hydrophilic/polar negative charge

Aspartic Acid

Glutamic Acid

hydrophilic/polar negative charge

Asp

Glu