Hydrogen bonding stabilizes secondary structure to form alpha helices and beta sheets. Hydrophobic interactions between nonpolar side groups dictate a protein's tertiary structure. Disulfide bonds are involved in the determination of a protein's tertiary and quaternary structures, but they are not the primary contributors.

The degradation of the various amino acids can produce several different compounds. But although these compounds differ, they can undergo further processing into one of two routes. Either the intermediates can be routed to become ketone bodies, or they can be routed into the gluconeogenesis pathway to become glucose. Generally speaking, amino acids that degrade to become either acetyl-CoA or acetoacetyl-CoA can potentially form ketone bodies. Thus, these amino acids are called ketogenic amino acids. Alternatively, amino acids that degrade to become pyruvate, oxaloacetate, alpha-ketoglutarate, fumarate, or succinyl-CoA can potentially form glucose. Therefore, these amino acids are called glucogenic amino acids. It's also important to note that there is some overlap between these. For instance, some amino acids are versatile because they have the potential to be both ketogenic or glucogenic. Some amino acids, however, only have the ability to do one of the two. In this case, since we are told that the amino acid in question is being converted into pyruvate, we can conclude that this amino acid is glucogenic.

Glycine contains a  as its R-group. The alpha carbon atom is bound to two hydrogen atoms. Therefore, glycine does not have a chiral center and is not optically active. 

The pKa is the pH at which half of the protons for a given site have dissociated. So when the pH is above the pKa the majority of protons will have dissociated, and when the pH is below the pKa the majority of protons will remain. There are four important protonation sites to look at in the peptide DGKA. The first site being the anime group of the N-terminus aspartate. Since the pH is greater than the pKa, this site will be deprotonated resulting in a neutral charge. The second site is the R-group of the aspartate residue. The pH is greater than the pKa resulting in deprotonation and a negative charge. The third site is the R-group of the lysine residue. The pH is greater than the pKa resulting in deprotonation and a neutral charge. The final site is the carboxyl group of the C-terminus of alanine. The pH is greater than the pKa resulting in deprotonation and a negative charge. Summing all of the charges at these locations:

The overall charge at pH 11 is -2.

The pKa is the pH at which half of the protons for a given site have dissociated. So when the pH is above the pKa the majority of protons will have dissociated, and when the pH is below the pKa the majority of protons will remain. There are four important protonation sites to look at in the peptide DGKA. The first site is the amine group of the N-terminus aspartate, which has a pKa of 9.6. The second site is the aspartate R-group which has a pKa of 3.65. The third site is the lysine R-group which has a pKa of 10.53. The final site is the carboxyl group of the C-terminus alanine, which has a pKa of 2.34. At a pH lower than all of these pKa's, all of the sites would be deprotonated resulting in an overall  charge. To achieve a charge of , it is necessary for the pH to be above just one of the pKa's. And for this reason the correct answer is 2.34 < 3.65.

The one letter abbreviation for the amino acid tyrosine is Y. T codes for threonine, S codes for serine, R codes for arginine, and N codes for asparagine.

The linear sequence of amino acids within a protein makes up the primary structure. Protein secondary structure is defined by the localized three-dimensional structure of amino acids. These localized structures are normally constructed through hydrogen bonding networks. Alpha-helices and beta-pleated sheets are examples of secondary structures. Protein tertiary structure is defined by the longer range interactions between amino acids within a single polypeptide chain. These interactions include ionic bonds, disulfide bridges, hydrogen bonds, and hydrophobic interactions. Protein quaternary structure is defined by the interactions between separate polypeptide chains. This often occurs in the formation of dimers and higher multimers.

Ionic bonds, disulfide bridges, hydrogen bonds and hydrophobic interactions are all examples of protein tertiary structure when they occur within a single polypeptide chain. If these interactions were to occur between separate polypeptide chains then they would be defining the quaternary structure of the protein. The linear sequence of amino acids within a protein makes up the primary structure. Protein secondary structure is defined by the localized three-dimensional structure of amino acids. These localized structures are normally constructed through hydrogen bonding networks. Alpha-helices and beta-pleated sheets are examples of secondary structures. 

Phosphorous is not a part of any of the standard twenty amino acids. It is however a component of other biological macromolecules such as nucleotides and metabolic intermediates. All twenty amino acids have the elements carbon, nitrogen, and oxygen found within them, and the amino acids cysteine and methionine contain sulfur.

Hydrophobic or water-fearing amino acids tend to be found in the interior of a cytosolic protein. This prevents energetically unfavorable solvation by water. Additionally, within a transmembrane segment of a protein hydrophobic amino acids can fit in alongside the hydrophobic tails of membrane phospholipids keeping them from being solvated by water.