L2 - Amino Acids

objectives

Understandings:

• Proteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds).
• Amino acids are amphoteric and can exist as zwitterions, cations and anions.
• Protein structures are diverse and are described at the primary, secondary, tertiary and quaternary levels.
• A protein’s three-dimensional shape determines its role in structural components or in metabolic processes.
• Most enzymes are proteins that act as catalysts by binding specifically to a substrate at the active site.
• As enzyme activity depends on the conformation, it is sensitive to changes in temperature and pH and the presence of heavy metal ions.
• Chromatography separation is based on different physical and chemical principles.

Applications and skills:

• Deduction of the structural formulas of reactants and products in condensation reactions of amino acids, and hydrolysis reactions of peptides.
• Explanation of the solubilities and melting points of amino acids in terms of zwitterions.
• Application of the relationships between charge, pH and isoelectric point for amino acids and proteins.
• Description of the four levels of protein structure, including the origin and types of bonds and interactions involved.
• Deduction and interpretation of graphs of enzyme activity involving changes in substrate concentration, pH and temperature.
• Explanation of the processes of paper chromatography and gel electrophoresis in amino acid and protein separation and identification.

Guidance:

• The names and structural formulas of the amino acids are given in the data booklet in section 33.
• Reference should be made to alpha helix and beta pleated sheet, and to fibrous and globular proteins with examples of each.
• In paper chromatography the use of Rf values and locating agents should be covered.
• In enzyme kinetics Km and Vmax are not required.

• Proteins are biopolymers formed from monomers called amino acids.
• Amino acids are small molecules that are made up of a central carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (-H) and a variable 'R' group.
• There are 20 different amino acids that vary in structure and properties depending on the identity of the R group.
• The R group can be simple and small like a hydrogen atom or carbonyl group, or larger and more complex like a phenyl ring.

Amino Acids

2-Amino Acids

• Amino acids are specifically known as 2-amino acids, since the variable R group and the amino group are attached to the second carbon (carbon #1 is the carboxyl carbon).

Zwitterions

• The structure of amino acids leads to several unique properties.
• All amino acids are amphoteric, that is, they can behave as acids or bases in chemical reactions.
• The carboxyl group (-COOH) is acidic, as it can ionise and release a proton (H+ ion).
• The amino group (-NH2) is basic, as the nitrogen can donate its pair of electrons to accept a proton (H+ ion).
• In addition, the R group may also provide some acid-base activity.

• This unusual property allows amino acids to exist as zwitterions.
• A zwitterion is a species that contains both a positive and negative charge, sometimes called a dipolar ion.
• Zwitterion comes from the German word 'zwitter', meaning hybrid.
• Amino acids generally exist in the zwitterion form in a pH range close to neutral.
• Since most biological aqueous environments are buffered to maintain a pH range close to neutral, amino acids are generally found in their zwitterion form.

• In very acidic media, the zwitterion acts as a base.
• The COO– group gains a hydrogen ion to form a COOH group, however, the positive charge on the NH3+ group remains, making the overall species positively charged (a cation).
• In very basic media, the zwitterion acts as an acid.
• The NH3+ group releases a hydrogen ion to form an NH2 group, however, the negative charge on the COO– group remains, making the overall species negatively charged (an anion).
• The pH at which these changes occur is known as the isoelectric point (abbreviated pI). Each amino acid has a unique isoelectric point, depending on the properties of the R group.

• The properties of the R group affect the isoelectric point (pI).
• R groups that have no acidic or basic properties have an isoelectric point near 6, with polar R groups having a slightly lower pI than nonpolar R groups.
• R groups that have acidic functional groups have an even lower pI and those with basic functional groups have a higher pI.

Melting Points of Amino Acids

• Since amino acids are generally found in the zwitterion form in biological conditions, all amino acids are crystalline solids with high melting points (200-300°C) due to the ionic charges present on the zwitterion.
• They show Ionic Bonding
• The presence of opposite charges allows for strong electrostatic attractions between amino acids, compared to the lower attraction and melting points for amino acids that are not in their zwitterion form.
• The properties of the R group can further increase or decrease the melting points.
• R groups that are acidic or basic can also be ionised, leading to further ionic charges, increasing the melting point.
• R groups with strong intermolecular forces can also increase the melting point.

Solubility of Amino Acids

• The charges present on the zwitterion also allow for high solubility in aqueous solutions, which are typically present in biological environments, and insolubility in nonpolar solvents.
• The charged groups allow for strong ion-dipole attractions in polar solvents, but very weak attractions in nonpolar solvents, so the amino acids form stronger attractions with each other than the solvent, resulting in low solubility.
• The properties of the R group can also increase or decrease the solubility of the amino acid in water.
• Highly polar R group or those with acid-base properties will show higher solubility, while those R groups that are nonpolar will show lower solubility.