Protein Folding - Biochemistry

The side chains of the amino acid residues within an alpha helix point "out" and "back" relative to the turns of the helix. Despite differing polarity's of side chains, this pattern holds true. This first reason this pattern is important is in order to minimize steric hindrance. Finally, this pattern allows for a maximization of hydrogen bonding between the side chains and the backbone amides.

Large side chains have increased Van der Waals interactions repelling each other, which is unfavorable. To minimize this steric clash, these residues must be kept far apart, and "They are kept far apart from each other." is the correct answer.

Large residues being near each other in a beta sheet would be very unfavorable. If these large residues alternated in a "every other" manner, they would still be relatively close to each other. Finally, if these residues were kept parallel to each other, they would be on different. But these chains would still be in close proximity to each other, and unfavorable interactions would occur.

The two most common secondary structures within a protein are alpha helixes, and beta-sheets. However, remember that there are multiple types of alpha helixes and beta-sheets, and all have slightly different properties. Overall, alpha helixes and beta sheets are in approximately equal amounts.

Anything not regarded as an alpha helix or a beta sheet is typically referred to as a "irregular structure". This can include random coil, coil structures, Beta-hairpin turns, in addition to a seemingly infinite number of unnamed structures. Overall, there is as much irregular structure as beta sheet and alpha helix within a protein, and the correct answer is 33% for all three.

All the answer choices are different examples of protein supersecondary structures. Beta barrels are commonly found in transmembrane porin proteins.

Alpha helices and beta pleated sheets are two forms of secondary structure. Alpha helices can be either right handed (counterclockwise) or left handed (clockwise). Beta pleated sheets can be either parallel (amino and carbonyl groups do not line up) or anti parallel (amino and carbonyl groups line up).

Glycine and proline are the two amino acids that are found in beta turns. These 180 degree turns are composed of four total amino acids.

Covalent bonding is when two nonmetals share electrons in order to form a bond. This type of bonding can be observed in the primary (peptide bonds), tertiary (disulfide bonds), and quaternary (disulfide bonds) levels of protein structure. The secondary structure of proteins only uses hydrogen bonding as the folding force.

Polypeptide chains in proteins fold to attain a more compact secondary structure. The two forms of secondary structures are alpha helices and beta sheets. Amino acids that are separated by three or four residues in a polypeptide chain within a secondary alpha helix structure are spatially close and can form hydrogen bonds.

Secondary structures in proteins consist of alpha helices and beta sheets. Proline has an additional amino group that interferes with the formation of an alpha helix. Amino acids such as lysine and arginine can form ionic bonds due to their charges. Other amino acids, like isoleucine, tryptophan, or valine disrupt the helix due to big side chains. However, amongst the amino acid mentioned in the answers, proline has the most disruptive effect.

Beta bends are part of secondary protein structures. They serve as a link between alpha helices and beta sheets. Beta bends are composed of proline and glycine, amino acids that usually are not found in alpha helices.

Motifs are supersecondary protein structures. Motifs are combinations of secondary structures such as alpha helices and beta sheets.The beta-alpha-beta and the beta hairpin motifs are some of the most common.

A beta sheet (a secondary structure) has parallel strands when the N-terminal and C-terminal are in the same orientation for all the strands. When the orientation alternates between beta strands they are considered to be anti-parallel. Hydrogen bonds stabilize the structure between polypeptide strands.

Proline is necessary for the beta bend (along with a glycine). This beta bend is needed for the polypeptide to turn 180 degrees and come back to form a parallel beta sheet. Proline disrupts the hydrogen bonding of alpha helices, and is not needed for antiparallel beta sheets, since there is no beta turn required.

Not all proteins have a quaternary structure; quaternary structure refers to the arrangement and number of subunits, and not every protein has multiple subunits. Disulfide bonds make proteins less susceptible to unfolding; typically, they will link -sheets, -helices, and loops, which means that they primarily maintain tertiary structure, not secondary, which refers to local conformations, and is maintained largely by hydrogen bonds. Protein charges do change with pH; as a solution’s pH increases, acidic groups on proteins deprotonate. A protein’s function depends, however, very much on its spatial conformation. Its native conformation permits it to recognize and bind to specific molecules, and thus perform its specific function.

During the formation of a disulfide bond, two free groups lose their bond to hydrogen and form an bond. This loss of bonds to hydrogen means it is an oxidation reaction.

Tertiary structure is stabilized by multiple interactions, specifically side chain functional groups which involve hydrogen bonds, salt bridges, covalent disulfide bonds, and hydrophobic interactions. Amide bonds do not contribute to the stability of a protein's secondary structure, rather, peptide bonds are amide bonds that stabilize a protein's primary structure..

In order for a protein to stay soluble in the cell, it needs to have a hydrophilic surface that can interact with water and and hydrophobic regions need to be contained in its center. Therefore polar, hydrophilic amino acids are mostly found on the surface of a protein's 3D structure while non polar hydrophobic residues are usually found on buried in the core of a proteins 3D structure.

Proteins are made of primary, secondary, tertiary, and sometimes quaternary structure. The primary structure of a protein involves the amino acid sequence in the polypeptide chain. The amino acids in this chain are held together by peptide bonds. The secondary structure of a protein involves the pattern of hydrogen bonds along the its peptide bond backbone, such as alpha helices and beta pleated sheets. The tertiary structure of a protein is the final specific shape of one subunit; this is determined by bonding interactions between the amino acid side chains. Some proteins consist of quaternary structure, which is the number and arrangement of multiple folded subunits.

The tertiary structure of a protein is the three dimensional shape of the protein. Disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic interactions all influence the shape a protein takes. Quaternary structure is the level that deals with multiple sub-units folding together. An example of quaternary structure is hemoglobin, composed of four sub-units.

A disulfide bond is created by two cysteine residues coming together and creating a sulfur-sulfur linkage. This type of linkage contributes to the tertiary structure of proteins. It can also be seen in quaternary structure between peptide subunits, but tertiary structure is the first level where this force can be observed.