Identifying Monomers and Dimers - Biochemistry

The conversion of tetrahydrofulate to methylene tetrahydrofulate is coupled with the amino acid conversion of serine to glycine. Serine converts to form glycine and formaldehyde. The same components are factored in with the conversion of tetrahydrofulate to methylene tetrahydrofulate.

Agarose gel electrophoresis is typically used for large molecules, not small ones like individual amino acids. Isoelectric focusing separates molecules by isoelectric point. Edman degradation only permits sequencing of about 30 amino acids, not an unlimited amount. High-performance liquid chromatography separates proteins which are peptide sequences.

Most amino acids that exist in living organisms contain an alpha-carbon that is a stereocenter (or chiral center). This means that this central carbon is bonded to four different substituents, thus allowing the amino acid to have two possible isomers. Although practically all amino acids in nature occur as the L-isomer, glycine is an exception. The reason for this is that glycine's alpha-carbon is bonded to two hydrogen atoms. As a result, this alpha-carbon is not a stereocenter, which means that glycine only has one possible conformation with no isomers.

Tryptophan contains a five membered ring and a six membered ring on its side group. Tyrosine and phenylalanine both contain one six membered ring. Histidine contains a five membered ring on its side chain. Threonine's R-group is , and does not have a ring structure.

The question states that monoamines are synthesized from aromatic amino acids. Aromatic amino acids are defined as those that have one or more aromatic rings in their structure. There are three main aromatic amino acids: histidine, tryptophan and tyrosine. Tyrosine is the precursor for many of the catecholamines (such as norepinephrine, epinephrine and dopamine) whereas histidine is the precursor for histamine. Tryptophan is the precursor for tyrosine; therefore, a lack of tryptophan will result in decreased catecholamine synthesis.

Maltose, made from the breakdown of starch, contains a 1 to 4 alpha linkage, and cellobiose, made from the breakdown of cellulose, contains a 1 to 4 beta linkage. Both are disaccharides with different shapes and different properties.

Lactose is a disaccharide that needs to be broken down to its monosaccharide components in the gut (so that it can be absorbed). Lactose is made up of galactose and glucose monosaccharide units. An enzyme called lactase, found on the intestinal walls, is used to break down lactose to galactose and glucose. A person with lactose intolerance lacks lactase and, therefore, cannot break down lactose to its components. This leads to malabsorption of lactose. However, there is no problem with galactose and glucose absorption. This means that a patient with lactose intolerance can still digest galactose and glucose if given separately.

Fructose is a monosaccharide; therefore, it is only made up of one type of carbohydrate. Disaccharides are made up of two types of monosaccharides. For example, lactose is made up of galactose and glucose whereas sucrose is made up of glucose and fructose. Polysaccharides are made up of multiple units of monosaccaharides.

While glucose, galactose, and fructose are all monosaccharides, lactose is a disaccharide comprised of two monosaccharides, glucose and galactose, joined by a -1,4-glycosidic bond.

At a pH of 12, the amino group for all of the amino acids would be deprotonated, resulting in at least a charge from the acid group. Another negative charge comes from the carboxyl group on the backbone. Tyrosine is amphipathic, and the pKa of its sidechain is 10.8, meaning it is a deprotonated at a pH of 12. This gives it a charge at a pH of 12. Tryptophan has no side-chain pKa so 3 equivalence points would not be seen. Threonine would also not have 3 equivalence points. Glutamic acid doesn't have amphipathic properties. Histidine is amphipathic, but it is a basic amino acid.

All amino acids have an amino group, a carboxyl group, a hydrogen, and an R-group that is unique to the amino acid. In this structure, the R-group is a hydrogen, which corresponds to the amino acid glycine.

Since this is an ion-exchange chromatography method, we expect that the protein found in the column has the opposite charge of the beads. Since the beads were negatively charged, we expect the amino acid to be positively charged. Lysine has a basic side chain that can easily pick up a hydrogen from solution and become positively charged.

Only aspartate and threonine have side chains capable of hydrogen bonding interactions. Aspartate has a terminal carboxylate which can act as a hydrogen bond acceptor and as a hydrogen bond donor when protonated. Threonine has a terminal hydroxyl group which can also act as a hydrogen bond donor. Alanine has an entirely aliphatic side chain which is unable to participate in hydrogen bonding, and methionine has a sulfhydryl group, that cannot participate in hydrogen bonding.

We're told in the question stem that a mutation is causing a single amino acid substitution. Originally, the amino acid encoded by this region was a lysine residue. To find the amino acid that would cause the least detriment to the organism, we need to recognize which amino acid is the most similar to lysine. Since lysine is a basic amino acid under physiological conditions, it will tend to carry a positive charge most of the time. Therefore, we are looking for an amino acid that is also basic and carries a positive charge under physiological conditions. Arginine is one such amino acid that meets this criteria, and thus it is the correct answer. Glutamate is incorrect because it is acidic under physiological conditions, and thus will carry a negative charge. Glycine, valine, and tryptophan are also all incorrect because each of these amino acids are neutral under physiological conditions.

We're told in the question that this amino acid has a pI = 10.4. Therefore, we expect this to be a basic amino acid. This means that one carboxyl group, one amino group, and one basic R-group will be present.

At the start of the titration, the solution starts out acidic at a very low pH. At a pH of 2, since so many protons are in solution at this pH, all of the important functional groups under consideration will be protonated. Thus, the amino acid will have a positive charge on each of its basic functional groups, and a neutral charge on its carboxyl group, giving the amino acid a net charge of +2.

Once the pH has climbed to a value of 8, we would expect that only the carboxyl group will be deprotonated. As a result, the carboxyl group will have a negative charge, while each of the other two basic functional groups will still retain their positive charge. Thus, the amino acid at this pH will have a net charge of +1.

And finally, once the pH climbs all the way up to a value of 12, we can expect the two basic functional groups to be deprotonated. Consequently, each of the basic functional groups will be neutral, while the carboxyl group will still be negative. Thus, the overall charge of the amino acid will be negative at this pH.

So overall, the amino acid will be positive, then positive, followed by negative.

Because proline has part of its R-group side chain attached to its amino group, it has a unique structure that differs from all other amino acids. The ring structure that it forms with its amino groups causes it to be unable to be found in alpha helix protein structures - if it were to be in one the structure would be disrupted. However, proline is important in kinks and turns because of its small, unique structure.

This problem tests knowledge of amino acid pKa values. Because the R-group of glutamic acid has a very low pKa of 4.25, which is less than the solution pH of 9.0, it will be negatively charged. Lysine and arginine are both positively charged at this pH, whereas tyrosine and methionine are both neutral.

The guanidino group of arginine is protonated in solutions with pH at or below the pKa of 12.5. It is a positively charged basic side chain that becomes neutral at a pH 12.5 or greater.

Serine and tyrosine both have uncharged polar side chains with one hydroxyl group, but only tyrosine has a pKa value for its side chain of 10.5. This indicates that tyrosine will lose its proton above pH 10.5 and is therefore neutral at pH 7.0.

All the amino acids (except glycine) are chiral, but threonine and isoleucine are the only two with a second asymmetric carbon. As a result, they give two pairs of enantiomers that have different physical properties.

Phenylalanine (F), tyrosine (Y), and tryptophan (W) all contain bulky aromatic side groups that cause proteins to absorb UV light at 280 nm.