B.2- Proteins and Enzymes

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Proteins- Biopolymers made up of monomers (amino acids)

Amino acids undergo a condensation reaction to form a long polymer chain.

Proteins are used to form structural components of an organism, such as hair, muscle, tissue, and nails. They can also be a source of energy in metabolism used to catalyze chemical reactions (as enzymes) at the cellular level.

Protein sequencing (or proteomics) allows proteins to be made synthetically. It is done by electrophoresis to diagnose abnormalities in protein structure & function.

Amino Acids

Small molecules that are made up of a central carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen (-H) and an'R' group.

--> the R group can be simple & small (like a hydrogen atom or carbonyl group) or larger and more complex (like a phenyl ring)

Amino acids are specifically 2-amino acids, since the R group and the amino group are attached to the second carbon (the first carbon is the carboxyl group). The variable R group affects the structure and properties of the amino acid and the protein that forms when amino acid monomers form in a condensation reaction to make proteins.

A 3-letter code is used to abbreviate each amino acid; since the genetic code is universal among all species, the encoded amino acids are also universal, from single-celled organisms to complex humans.

Properties of amino acids

All amino acids are amphoteric (they can behave as acids or bases in chemical reactions).

- The carboxyl group is acidic, as it can ionize and release a proton (H+ ion).

- The amino group is basic, as the nitrogen can donate its pair of electrons to accept a proton (H+ ion)

- The R group may also provide some acid-base activity

Melting point of amino acids

All amino acids are crystalline solids with high melting points (200-300C) due to their ionic charges present on the zwitterion. The presence of opposite charges allows for strong electrostatic attractions between amino acids compared to the lower attraction & 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 ionized, leading to further ionic charges, increasing the melting point.

- R groups with strong intermolecular forces can also increase the melting point.

Solubilities of amino acids

The charges present on the zwitterion also allow for high solubility in aqueous solutions, and insolubility in non polar solvents. The charged groups allow for strong ion-dipole attractions in polar solvents, but very weak attractions in non polar solvents, so the amino acids form stronger attractions with each other than with 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 groups or those with acid-base properties will show higher solubility, while non polar R groups will show lower solubility

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Zwitterion- a species that contains both a positive and negative charge (also called a dipolar ion). 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 carboxyl group will gain a hydrogen ion, making the carboxyl group neutral and still maintaining the positive charge on the amino group, making the overall species positively charged (a cation).

In very basic media, the zwitterion acts as an acid. The amino group will release a hydrogen ion, making the amino group neutral and maintaining the negative charge on the carboxyl group, making the overall species negatively charged (an anion). The pH at which these changes occur is called the isoelectric point (pI). Each amino acid has a unique isoelectric point, depending on the properties of the R group.

- 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 non polar R groups.

- R groups with acidic functional groups have an even lower pI

- R groups with basic functional groups have a higher pI.

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Polypeptide chain formation

Amino acids are joined together by a condensation reaction:

The amino group from one amino acid loses a hydrogen ion and the carboxyl group from another amino acid loses a hydroxyl group, directly bonding the nitrogen to the carbon in an amide linkage, also known as a peptide bond.

*the other product formed is water. The number of water molecules removes is always one less than the number of amino acids joined together.

When two amino acids are joined, the product is a dipeptide. Three amino acids forms a tripeptide; multiple amino acids form a polypeptide.

When a polypeptide chain is formed, one end of the linear chain still retains the amino group, referred to as the N terminal. The other remains the carboxyl group, referred to as the C terminal.

The precise sequences of amino acids is important for the overall structure and function of the protein.

*When writing a balanced chemical equation for the formation of a polypeptide chain, the number of water molecules produced is always one less than the number of amino acids.

eg. if the polypeptide chain was made from 8 amino acids, the number of water molecules produced would be 7.

Polypeptide chain formation can be reversed with a hydrolysis reaction, where water molecules are added to reverse the polymerization. The reverse reaction generally occurs with the help of enzymes to catalyze the reaction.

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Protein Structure

Proteins can contain anywhere from 20 amino acids up to 30,000 amino acids and can even include multiple polypeptide chains intricately folded together. If a single amino acid is missing or is incorrect, is can affect the structure & function of the entire protein. The structure of proteins is broken down into four levels:

Primary (1°)

The primary level of structure is the sequence of amino acid residues bonded together in the polypeptide chain by covalent bonds. The sequence is coded by genetic material.

(Amino acid reside-remains of the amino acid after it has been polymerized)

Secondary (2°)

The secondary level of structure includes the local coiling or folding of the polypeptide chain. When the chain is formed, it can take on two distinct structures: an alpha helix (coiled structure) or a beta sheet, also known as a beta pleated sheet (accordion-style folding).

The structures are held together by hydrogen bonds from distant amino acid residues. In a given protein, there will be sections of alpha helices and beta pleats as well as areas with a random structure.