The Protein backbone is formed from the peptide bonds created from the amino and carboxyl groups of each monomer that repeat the pattern -N-C-C- or C-C-N-. The number and sequence of amino acids in a polypeptide chain is referred to as the primary structure of a protein. The free amino group and carboxyl group on opposite ends of a polypeptide chain allow proteins to act as pH buffers (resist changes in pH) inside the cell. The amino group (NH2) accepts a proton and becomes (NH3 +), and the carboxyl group (COOH) donates a proton and becomes dissociated (COO-).
Each amino acid residue in the polymer may have a different side chain or chemical group attached to it, such as hydroxyl (OH), amino (NH2),
aromatic ring (conjugate rings such as the phenol ring in phenylalanine), sulfhydryl (SH), carboxyl (COOH), or various alkyl (CHn). This variety of side chain groups on the polymer backbone gives proteins remarkable chemical and physical properties. For example, carboxylate groups can function as carboxylic acids (COO-), or amino groups can behave as bases (NH3 +). This allows protein polymers to be multifunctional molecules, with both acidic and basic behavior at the same time! Additionally, the presence of hydroxyls, carboxylates, sulfhydryls, and amino groups allows hydrogen bonding, and the alkyl groups provide hydrophobic interactions, both within the protein polymer itself and between separate protein molecules. In the case of macromolecules, such as proteins, the polymeric structure of the macromolecule allows it to simultaneously carry many different charges (on different amino acid residues). However, unlike the small single molecules, the amino acid residues are constrained by linear peptide linkages and thus cannot move freely to randomly associate with other charged molecules. Assuming that charged residues will seek to bond with the nearest convenient counter ion, it is most likely that oppositely charged amino acid residues located at different points within a single protein chain will bond. These structural differences result in the folding of proteins into a threedimensional structure, which is, in part, responsible for their functional properties as biocatalysts, structural materials, muscles, and chemical receptors. Proteins can be shaped as long flat sheets or in globular spheres. This leads to the names fibrous or globular for protein shapes. Most enzymes are globular proteins. In standard acid−base chemistry, students learn that molecules carry electrostatic charges based on the type of atoms that make up a molecule and the environment of the molecule. Given that opposite charges attract, cationic and anionic atoms can combine to form covalent bonds, in which electrons are shared between atomic orbitals, or form ionic bonds, in which only electrostatic attractions exist. In solution with smaller molecules, such as HCl (an acid) or NaOH (a base), protein molecules can freely move around and associate with each other on a more-or-less random basis. Protein polymers extend the simple acid−base charged chemical species concepts
to explain how biological systems have greater levels of complexity and can utilize simple, monomeric chemical structures (like amino acids) to create exquisitely complex biological structures like antibodies, muscle, and skin. Protein polymers have physical structure, even when dissolved in liquids. The charged and hydrophobic residues within a protein tend to associate, causing the protein to fold up. When you unfold the protein molecule (called denaturation), its charged residues can reassociate with other charged molecules (precipitation or coagulation). Protein precipitation is widely used to recover recombinant protein products, enzymes, or in the production of many common foods. Cheeses and soybean tofu are examples of coagulated protein food products.
Each amino acid residue in the polymer may have a different side chain or chemical group attached to it, such as hydroxyl (OH), amino (NH2),
aromatic ring (conjugate rings such as the phenol ring in phenylalanine), sulfhydryl (SH), carboxyl (COOH), or various alkyl (CHn). This variety of side chain groups on the polymer backbone gives proteins remarkable chemical and physical properties. For example, carboxylate groups can function as carboxylic acids (COO-), or amino groups can behave as bases (NH3 +). This allows protein polymers to be multifunctional molecules, with both acidic and basic behavior at the same time! Additionally, the presence of hydroxyls, carboxylates, sulfhydryls, and amino groups allows hydrogen bonding, and the alkyl groups provide hydrophobic interactions, both within the protein polymer itself and between separate protein molecules. In the case of macromolecules, such as proteins, the polymeric structure of the macromolecule allows it to simultaneously carry many different charges (on different amino acid residues). However, unlike the small single molecules, the amino acid residues are constrained by linear peptide linkages and thus cannot move freely to randomly associate with other charged molecules. Assuming that charged residues will seek to bond with the nearest convenient counter ion, it is most likely that oppositely charged amino acid residues located at different points within a single protein chain will bond. These structural differences result in the folding of proteins into a threedimensional structure, which is, in part, responsible for their functional properties as biocatalysts, structural materials, muscles, and chemical receptors. Proteins can be shaped as long flat sheets or in globular spheres. This leads to the names fibrous or globular for protein shapes. Most enzymes are globular proteins. In standard acid−base chemistry, students learn that molecules carry electrostatic charges based on the type of atoms that make up a molecule and the environment of the molecule. Given that opposite charges attract, cationic and anionic atoms can combine to form covalent bonds, in which electrons are shared between atomic orbitals, or form ionic bonds, in which only electrostatic attractions exist. In solution with smaller molecules, such as HCl (an acid) or NaOH (a base), protein molecules can freely move around and associate with each other on a more-or-less random basis. Protein polymers extend the simple acid−base charged chemical species concepts
to explain how biological systems have greater levels of complexity and can utilize simple, monomeric chemical structures (like amino acids) to create exquisitely complex biological structures like antibodies, muscle, and skin. Protein polymers have physical structure, even when dissolved in liquids. The charged and hydrophobic residues within a protein tend to associate, causing the protein to fold up. When you unfold the protein molecule (called denaturation), its charged residues can reassociate with other charged molecules (precipitation or coagulation). Protein precipitation is widely used to recover recombinant protein products, enzymes, or in the production of many common foods. Cheeses and soybean tofu are examples of coagulated protein food products.
