Protein Folding - Biochemistry

A single amino acid substitution from glutamic acid to lysine is responsible for sickle cell anemia. The mutation occurs in the gene that codes for hemoglobin and causes misfolding that results in a lower oxygen affinity.

With regard to protein structure, primary structure refers to the order of the amino acids, which are held together by peptide bonds. Secondary structure refers to the presence of beta pleated sheets and alpha helices within a protein. Tertiary structure refers to a protein's geometric shape as a result of the interactions between the sidechains of the amino acids in the peptide chain. Quaternary structure concerns side chain interactions within a multiple polypeptide chains.

Primary structure consists of amino acids joined by peptide bonds. Peptide bonds are between the alpha-carboxyl of one amino acid, and the alpha-amine of the next amino acid. A peptide bond is an example of an amide bond. Hydrogen bonds are found in secondary structure, tertiary structure exhibits Van Der Waals interactions.

This question is presenting us with a scenario in which a protein is being transferred to a highly acidic solution that is outside of the protein's optimal pH range. In such a situation, we would expect the protein to undergo conformational changes that would alter its function. The question, however, is which levels of protein structure would be altered by such a change in pH.

The first level of structure worth considering is primary structure. The primary structure of a protein refers to the sequence of individual amino acids that make up the protein. Upon being transferred to an acidic solution, the protein does indeed unfold, but it doesn't break apart into individual amino acids. Therefore, the unfolded protein remains as a single, long chain, but its sequence of amino acids is still intact. Thus, there is no change in primary structure.

The secondary structure of a protein refers to local conformations found within the folded protein. Such local conformations include certain commonly found structural motifs, such as alpha-helices and beta-pleated sheets. These local conformational structures are held together by various intramolecular bonds between the amino acid residues. These intramolecular interactions include hydrogen bonding and van der Waals forces, among others. When transferred to an acidic solution, these intramolecular forces are disrupted and, as a result, cause a disruption in the protein's secondary structure.

The third level of protein structure is tertiary structure, which refers to the overall conformation of a single chain of amino acids, sometimes referred to as a polypeptide. The overall three-dimensional conformation of a polypeptide is held together by some of the same intramolecular forces involved with secondary structure, such as hydrogen bonding, van der Waals interactions, and disulfide bonds. Because a highly acidic solution interferes with these interactions, the tertiary level of protein structure is indeed affected by pH changes.

And finally, the last level of protein structure to consider is quaternary structure. Not all proteins possess this level of structure, because in order to have this level of structure, two or more polypeptide chains need to come together and interact via intermolecular bonding to form the final, finished protein. An example of this level of structure can be seen in the protein hemoglobin, in which two alpha-chains and two beta-chains come together and interact to form hemoglobin. Just as with secondary and tertiary structures, the introduction of a highly acidic solution can disrupt these intermolecular interactions, thus causing a disruption in the quaternary structure of a protein composed of two or more polypeptide chains.

The primary structure of a protein is defined by the sequence of amino acid residues. It is this sequence that lays the foundation for all other higher levels of structures in a protein. Secondary structure is defined by the hydrogen bonding between the carboxyl and amino backbone of the amino acids. Tertiary is defined by amino acid side chain interactions. Finally, quaternary structure is defined by the assembly of subunits of a protein into the overall larger protein structure.

The primary structure is only composed of the sequence of amino acids in a protein. The secondary structure is the alpha or beta folding that occurs due to amino acid interaction. The tertiary structure is the three dimensional folding that occurs within a protein. Finally, quaternary structure occurs when a protein has two or more polypeptide sub-units. A perfect example of quaternary structure is found in hemoglobin.

The formation of a peptide bond is an example of a condensation reaction. This is because, when two amino acids come together, a water molecule is let go.

Because an amino acid has been altered in sickle cell anemia, we can say that the amino acid sequence for hemoglobin has been changed. The amino acid sequence is defined as the primary structure for a protein, so that is the level that has been altered. It should be noted that the subsequent levels of protein structure would be altered as well, but the manipulation of the amino acid sequence is a changing of the primary structure first.

Hemoglobin is the only available example of a macromolecule composed of multiple subunits. Hemoglobin has frou subunits, each capable of binding and transporting one molecule of oxygen in the blood.

Chymotrypsin and myogblobin are both simple proteins, each consisting of a single polypeptide. These proteins do not have multiple subunits; thus their highest level of structure is tertiary (three-dimensional). Lactose and sucrose are disaccharides, each composed of two carbohydrate monomers (monosaccharides).

Hemoglobin is a tetramer that possesses a quaternary structure containing multiple folded polypeptide structures (tertiary structures). A tertiary protein will commonly contain a single polypeptide chain with one or more secondary structures.

A protein with multiple identical subunits does indeed have a quaternary structure; in these cases, dimers and tetramers are common. The main forces holding together oligomeric subunits are weak, non-covalent interactions, specifically, hydrophobic ones, as well as electrostatic forces. Subunits do not necessarily form separate domains within a protein; in a potassium channel protein, for example, there are identical subunits which come together to form the single channel. Proteins’ 3D-structures do indeed sometimes change when ligands bind; this change help regulate the proteins’ biological activity.

Quaternary structure of a protein involves the assembly of subunits. Hemoglobin, p53 and DNA polymerase are all composed of subunits, while myoglobin is a functional single sequence. Since myoglobin does not have multiple subunits, it does not have quaternary structure.

Quaternary structure describes how polypeptide chains fit together to form a complete protein. Quaternary protein structure is held together by hydrophobic interactions, and disulfide bridges. The sequence of amino acids is known as primary structure; helices, sheets, and similar features are part of the secondary structure; and the 3-D organization is tertiary structure. "The four parts of a protein's amino acid sequence" does not refer to anything in particular.

Primary structure: linear sequence of amino acids

Secondary structure: hydrogen bonds, alpha-helices and beta-pleated sheets

Tertiary structure: disulfide bonds, single polypeptide chain

Myoglobin is a monomer, and is made of a single polypeptide chain. Thus, its highest level of protein structure is tertiary. While collagen does contain different polypeptide chains, it is an example of a protein with quaternary structure, not an explanation of what this means.

While covalent bonds create the primary structure of a protein, and hydrogen bonding and Van der Waals forces have a large impact on the secondary structure of a protein, they are not the main contributors to overall folding of a protein. This has more to do with solvation costs, hydrophobicity, and entropy. The hydrophobicity and hydrophobic portions of the protein must fold to minimize entropic costs.

Hemoglobin is a classic example of protein with a quaternary structure. The binding of oxygen to one sub unit increases the affinity of the other sub units for oxygen (cooperativity). Adult hemoglobin is made of two alpha globin and two beta globin polypeptides. Protein quaternary structure may involve both noncovalent and covalent forces.

In this question, we're asked about how disulfide bonds relate to protein folding. Let's go through each form of structure.

Primary structure refers to the sequence of amino acids in the polypeptide, from the N-terminal end to the C-terminal end.

Secondary structure refers to local conformations of protein folding. There are a number of commonly found motifs that have been recognized, such as alpha-helices and beta-pleated sheets. These motifs are stabilized by intermolecular interactions between amino acid side-chains and also between alpha-carboxy and alpha-amino groups of the peptide backbone. Some of these intermolecular interactions include hydrogen bonding, van der Waals interactions, dipole interactions, and ionic bonding.

Tertiary structure refers to the overall three-dimensional structure of the folded polypeptide. This form of structure relies on the same intermolecular interactions found in secondary structure. In addition, tertiary structure also includes disulfide bonds that are found between cysteine residues.

Quaternary structure refers only to proteins that are composed of multiple polypeptides. These separate polypeptides are held together by the same intermolecular forces found in secondary and tertiary structures. In addition, disulfide bonds are also found in quaternary structure, just like in tertiary structure.

Thus, tertiary and quaternary structure both include disulfide bonds.

Proteins do not have maximum entropy in their native state. Folding requires order which decreases entropy in the system. The energy toll needed for this decrease in entropy is more than made up with by the increase in bonds formed when the protein folds into its native state. Therefore, the native state of a protein has the lowest energy.

Protein folding diseases usually occur when beta-sheets alpha-helices misfold and precipitate into alpha-helices beta-sheets. This can lead to aggregation of amyloid deposits in the brain and neuronal apoptosis. Creutzfeld-Jacob Disease (CJD) and bovine spongiform encephalopathy (BSE, or mad cow disease) are examples of protein folding diseases.