Proteins, amino acid categories, and ionization

Amino acids

The organic compounds that serve as monomers for polypeptide chains and protein formation. Contains a central α-carbon, an α-amino group, an α-carboxyl group, and an R group side chain that determines the interactions it can have.

Polypeptide

The organic compounds consisting of a large number of amino acids bonded together in a chain that forms part of a protein molecule.

Protein

The organic compound consisting of one or more polypeptide chains. Have an enormous variation in size and shape.

Nonpolar amino acids

The amino acids whose R group has mostly C-C & C-H bonds. Mostly aliphatic and aromatic, and the charges on most atoms are temporary and partial. 

Polar amino acids

The amino acids whose R group possess visible polar functional groups containing mostly O and N atoms. Some amino acids have permanent partial charges, while others possess R groups that can ionize. 

Acidic and Basic amino acids

The amino acids whose R group posses visible polar functional groups that can ionize. The R group is at full charge when the pH reaches 7. The negative or positive charge determines which group (negative for ____ groups and positive for ____ groups). 

Ionization

The process by which a neutral atom/functional group is converted into electrically charged ions through the gain or loss of electrons. 

Bronsted-Lowry Acid

The species that can donate a proton (H⁺) to another molecule. A conjugate base (A^-) is the product. 

Bronsted-Lowry Base

The species that can accept a proton (H⁺) from another molecule. A conjugate acid (B⁺) is the product. 

Acid dissociation constant (K_a)

The measure of the strength of an acid and is the equilibrium constant for the dissociation of an acid. Large ___ = stronger acid, but larger pK_a = weaker acid.

Titration curve

The graphical representation illustrating the relationship between pH (y-axis), base (x-axis), and pK_a (strength of acid). Amino acids have 2-3 ionizable groups and will have multiple points of reference for each.

• At the beginning, nearly all ionizable groups are protonated (acid keeps protons, so there is a high [H⁺]).

• As base is added, ionizable groups slowly deprotonate (acid begins to donate H⁺), resulting in a plateau/buffering region.

• Curve flattens out as the highest measurable pH is 14.

Midpoint of the plateau

The point of a titration curve at which there are equal concentrations of acid (protonated) and conjugate base (deprotonated)

• [HA] = [A^-]

• pH = pK_a

Equivalence point

The point of a titration curve at which all/most ionizable groups are deprotonated, resulting in a sharp change in pH. 

• All HA → A^-

Ribbon protein model

The protein model that highlights the backbone of proteins and key secondary structures, such as alpha helices and beta sheets. 

Stick/wire protein model

The protein model that highlights the location of atoms and their proximity to one another. 

Space-filling protein model

The protein model that highlights the location of atoms on the surface and the location of surface charges (blue represents positive charge while red represents negative charge)

Denaturation

The process where proteins unravel and noncovalent interactions can be disrupted, but the primary structure remains. 

Degradation

The process in where proteins are completely broken down across all levels of protein structure. 

Renaturation

The process where proteins are able to be restored to their original structure and function, and is only possible in certain cases/conditions.

Primary protein structure

The structure of a protein that is the linear sequence of amino acids in a polypeptide chain. Formed N-terminus (oldest AA added) → C-terminus (newest AA added). 

• <20 AA = peptide chain, >20 AA = polypeptide chain

Peptide bond

The covalent bond formed between two amino acids that links the carboxyl group of one amino acid to the amino group of another, involving the release of a water molecule. 

Secondary protein structure

The structure of a protein that refers to the spatial conformation of the polypeptide backbone, which is primarily stabilized by hydrogen bonds. Common structures are alpha-helices and beta sheets. 

Alpha-helices

The prevalent type of secondary structure that is the coiled structure formed by the sequence of amino acids. R groups point out and away from the axis, and hydrogen bonds between backbone atoms occur between N-H groups with C=O. There are 4 amino acids for every turn. 

Beta-sheets

The prevalent type of secondary structure that consists of beta strands connected laterally by at least two or three backbone hydrogen bonds between N-H groups with C=O. The direction of the sheets points towards the C-terminus, and R groups alternate to point above and below the plane of the sheet.

• Parallel: chains go in the same direction (C-terminuses match up)

• Antiparallel: chains go in opposite direction (C-terminuses point opposite of each other)

Tertiary and Quaternary protein structure

The structure of a protein that refers to the overall three-dimensional shape formed by many charge-charge (electrostatic, noncovalent) interactions that provide stability. Always includes noncovalent bonds, but sometimes has covalent bonds (disulfide bonds). Only proteins with subunits have a quaternary structure.