Macromolecule Fundamentals - Biochemistry

A protein molecule can have four different structural levels. Primary structure consists of the sequence of amino acids making up the polypeptide. Secondary structure consists of the sequence of amino acids and the intermolecular forces and covalent bonds that form between amino acid backbone components. Examples of intermolecular forces in secondary structures include hydrogen bonding, van der Waals forces, and dipole-dipole interactions.

Tertiary structure involves covalent bonds, dipole-dipole interactions, and hydrophobic interactions between amino acid R-groups. Tertiary structure is responsible for the 3-dimensional shape of the polypeptide. An example of a covalent bond found in tertiary structure is the disulfide bond. This bond occurs between sulfur molecules in cysteine amino acids; therefore, disrupting the bonds stated in the question will alter the tertiary structure.

Quaternary structure occurs when two or more polypeptide chains interact with each other and form bonds.

Denaturing a polypeptide is the process of disrupting the secondary, tertiary, and quaternary structures. This means that denaturing a protein will lead to disruption in intermolecular forces such as hydrogen bonds. Recall that hydrogen bonds occur between a hydrogen atom and either a nitrogen, oxygen, or fluorine atom; therefore, denaturing a polypeptide will cause a disruption in the intermolecular forces between nitrogen and hydrogen (hydrogen bonds).

Secondary structures can form unique structures called beta-pleated sheets or alpha helices. The beta-pleated sheets are formed when a polypeptide chain folds in such a way that it loops back to lie adjacent to an earlier segment. Alpha helices are formed when a polypeptide chain twists and forms a helical structure. Note that both of these structures involve intermolecular forces (hydrogen bonds, van der Waals, etc.) between amino acids. Denaturing a polypeptide will disrupt both of these structures.

Recall that a denatured polypeptide will not lose its peptide bonds; therefore, the polypeptide will have its original number and sequence of amino acids (primary structure). The side chains of amino acids will not change during denaturation. The intermolecular forces and disulfide bonds between adjacent amino acids will change, but the composition of each amino acid won’t change.

To answer this question you need to know the single letter codes for the given amino acids.

D-K-A-R-H-F is aspartic acid - lysine - alanine - arginine - histidine - phenylalanine.

R-A-A-D-P-P is arginine - alanine - alanine - aspartic acid - phenylalanine - phenylalanine.

E-P-H-D-V-W is glutamic acid - phenylalanine - histidine - aspartic acid - valine - tryptophan.

To solve this question we need to figure out the overall charges of the three polypeptide chains. Recall that five amino acids are charged under physiological conditions (pH of 7.4). These five amino acids are glutamic acid (E), aspartic acid (D), arginine (R), lysine (K), and histidine (H). Glutamic acid and aspartic acid have an overall charge under physiologic pH. This occurs because their side chains are deprotonated. On the other hand, arginine, lysine, and histidine have a protonated side chain and have a charge. Knowing this information we can solve for the overall net charge on the three polypeptide chains.

Polypeptide I: overall net charge of

Polypeptide II: overall net charge of

Polypeptide III: overall net charge of

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.

Nucleic acids absorbs light at . The aromatic amino acids phenylalanine, tyrosine, and tryptophan absorb light at .

The opposite of the false statement is true: 18 of the 19 amino acids are in the S configuration, while cysteine is the only amino acid in the R configuration.

Diethylaminoethyl (DEAE) cellulose is a positive weak ion exchanger. Any molecules with a positive charge will elute through the column first, whereas molecules with a negative charge will adhere to the DEAE column and elute after the salt wash. Since protein III has a pI greater than the pH of the column, it has a positive charge and elutes first. Protein II elutes second because its pI is less than the pH but close in value. Therefore protein II contains less of a negative charge than protein I.

The amino acids histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine are considered essential amino acids as they cannot be made by the body. They need to obtained from outside sources/nutrients.

During ion-exchange chromatography, as you increase the pH of the mobile phase (the solution flowing through the column), you elute out proteins based on their isoelectric point (pI). So in this case, you first pass the pI of glutamic acid (Glu), and then that of leucine (Leu). You would never elute out the lysine, because the pI increase stops at 7 and never gets as high as lysine’s pI, 9.74. You have, however, successfully separated the three amino acids from each other, as the lysine remains in the column.

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 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.

Alpha-helices, beta-sheets, and less regular turns, loops, and coils are all of the secondary structure elements. Greek keys and Rossman folds are examples of structural motifs that are comprised of specifically arranged secondary structure elements.

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.

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.

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.

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.

Aromatic amino acids contain side chains with aromatic rings. Aromatic rings have alternating single and double bonds which form a conjugated pi system. The amino acids tryptophan, phenylalanine, and tyrosine contain aromatic ring systems. The amino acid cysteine does not have a side chain with a ring system. Instead it has a serine side chain with a sulfur in place of an oxygen.