Macromolecules - Large Molecules Part Four

Amino acids are linked together to form polypeptides and proteins.
The character of an amino acid is determined by the atoms in its side chain.
Amino acids are connected by a covalent bond called a peptide bond.
Enzymes catalyze the dehydration reaction that forms peptide bonds.
Dehydration involves the loss of atoms from two amino acids, forming water.
A polypeptide is a polymer of amino acids.
The next monomer is always added to the C terminus (carboxyl end) of the growing chain.
Polypeptides are built from the amino (N) terminus to the carboxy (C) terminus.
In a linear polypeptide, numbering starts with the most N-terminal amino acid (number one).
The most recent amino acid added has a free carboxyl end.

A protein's activity is linked to its unique three-dimensional structure.
Before becoming functional, a protein twists, turns, and folds, sometimes joining other polypeptide chains.
Deviations in structure can lead to non-functional or poorly functional proteins.
Protein structure is intricately tied to its ability to carry out its function.
Proteins have vastly different shapes and sizes.
The sequence of amino acids in the polypeptide chains determines a protein's shape.
A protein's function depends on its ability to bind to other molecules.
Recognition and binding are highly specific, requiring complementary shapes.
Defensive proteins (antibodies) bind to specific targets (e.g., viruses, cell surface proteins).
The interaction between an antibody and its target is highly specific and complementary.
Mutations in a virus can alter its proteins, preventing antibody binding and reducing protection.

The primary structure is the linear sequence of amino acids.
It specifies which amino acid is connected to which in the chain, starting from the N-terminus.
The free carboxyl group attaches to the amino group, forming a peptide bond through a dehydration reaction that releases $H_2O$ .
The number of amino acids can be counted by the number of side chains.
An oligopeptide has several, but not many, amino acids, unlike a true polypeptide.
The peptide bond can be identified by looking for the bond between the carbon and nitrogen atoms.
The first amino acid has a free amino end, indicating it is amino acid number one.
The side chains determine the amino acid identity (use three-letter abbreviations).
A polypeptide chain has a free amino end (N-terminus) connected to amino acid number one and a free carboxyl end (C-terminus) at the other end.
The next amino acid to be added would attach to the free carboxyl end.
Glycine, proline, and threonine are examples of amino acids in a polypeptide chain.
Proteins help carry nonpolar substances in the blood, which is a polar environment; the proteins make it more comfortable for the nonpolar molecules to travel within blood.
Polypeptide chains can vary widely in length, from about 15-20 amino acids to over 1,000 amino acids.

Secondary structure involves regular arrangements of shapes due to interactions between atoms of the polypeptide backbone.
Hydrogen bonds (weak, non-covalent) between backbone atoms stabilize these structures.
Alpha helices and beta pleated sheets are common secondary structures.
In an alpha helix, atoms participate between every fourth amino acid.
Hydrogen bonds form between a partially positive hydrogen atom and a partially negative oxygen atom.
The polypeptide backbone is consistent, allowing these interactions along broad stretches.
Side chains do not participate in secondary structure formation.
Hydrogen bonds form between the oxygen of a C=O group and the hydrogen of an N-H group.
Beta pleated sheets can form within a single polypeptide folded back on itself or between two adjacent polypeptide chains.
Ribbon models of proteins show the regions of helicity and beta pleated sheet.

Tertiary structure is the overall three-dimensional shape of a polypeptide or protein (if it has only one chain).
It involves interactions between side chains and the polypeptide backbone or between side chains themselves.
Tertiary structure folds on top of secondary structure.
Various types of bonds and interactions contribute to tertiary structure:
- Ionic bonds: Form between charged amino acid side chains (hydrophilic).
- Disulfide bonds: Covalent bonds (strongest) between two cysteine amino acids; also called atomic staples.
- Hydrogen bonds: Form between polar side chains or between a side chain and the backbone.
- Hydrophobic interactions: Nonpolar side chains cluster together, shielded from water, with van der Waals forces providing attraction.