Amino Acids and Proteins - Biochemistry

Aromatic amino acids are those which contain one or more aromatic rings. There are four examples of this: tryptophan, phenylalanine, histidine, and tyrosine. Basic amino acids are those which contain basic side chains at neutral pH, and may carry a positive charge. There are three examples of this: histidine, arginine, and lysine. Hydrophobic amino acids are those which contain "water-fearing" side chains; these amino acids are found within the hydrophobic protein core. There are seven examples of this: alanine, isoleucine, leucine, phenylalanine, valine, proline, and glycine. Acidic amino acids are those which contain acidic side chains at neutral pH and may carry a net negative charge. There are two examples of this: glutamic acid and aspartic acid.

Just as with many things in biology, structure determines function. Proteins are no exception. Even though there are other things that can contribute to the functioning of a protein, such as cofactors or allosteric regulators (in the case of enzymes), a protein's unique structure can grant it unique functions.

As an example, let's look at enzymes. For an enzyme to function, it must be able to bind its substrate. A big part of what makes this possible is for the enzyme's active site to be structured in such a way that it can accept the substrate molecule. Furthermore, the enzyme's active site structure also plays a role in how that enzyme distorts the substrate and puts strain on its bonds in order to catalyze the transformation of that substrate into product.

From the molecular structure shown in the question stem, we need to be able to recognize that this is tyrosine. Furthermore, the correct one letter abbreviation for tyrosine is Y, and its three letter abbreviation is Tyr.

T is the one letter abbreviation for threonine.

I is the one letter abbreviation for isoleucine.

R is the one letter abbreviation for arginine.

C is the one letter abbreviation for cysteine.

All twenty amino acids contain the same backbone, which includes an alpha amino and alpha carboxyl group (). All amino acids also contain a variable R-group (also known as a "side chain"), and it is this group that distinguishes one amino acid from another. Therefore, the correct answer is that not all amino acids contain nitrogen in their side chains. While all 20 amino acids contain nitrogen within their backbone, only seven have nitrogen within the side chain.

Within the side chain of tyrosine, there is a phenol group. However, a phenol group contains neither sulfur nor nitrogen. Methionine and cysteine are the only two amino acids that contain sulfur, which is worth memorizing. Seven amino acids contain nitrogen, including arginine and asparagine.

Because of the unique structure of proline (its side chain is actually attached to its amino backbone group), it forms kinks within a chain of amino acids. These kinks are due to a lack of hydrogen bonding in comparison to other amino acids. Therefore, this is an example of the secondary structure of a protein being disrupted. Secondary structure is the term used to describe folding of the polypeptide chain due to hydrogen bonding between the backbone amino and carboxyl groups. Primary structure refers to the amino acid order itself. Tertiary relates to R-group interactions between residues that are farther apart in the chain. Finally, quaternary structure occurs at the most "macro" level, and refers to interactions between subunits of a protein.

Amino acids can be identified by their full names, a three-letter code, and a one-letter symbol. The one-letter symbol of glutamic acid is E. The one-letter symbol of proline is P. The one-letter symbol of isoleucine is I. The one-letter symbol of alanine is A.

A prosthetic group fits the definition listed in the question. These groups help specific proteins carry out their functions. Prosthetic groups can be inorganic (e.g. a metal ion) or organic (e.g. a vitamin, lipid, or sugar). Heme is an example of a prosthetic group (for the hemoglobin protein), but would be the wrong answer because the question asks for the general name of the defined structure. An alpha helix is a common secondary structure of proteins and has nothing to do with the function of prosthetic groups. Chaperonins are proteins that provide optimal conditions for folding of other proteins, ensuring that proteins fold correctly. These also have nothing to do with prosthetic groups.

"Asp" refers to aspartic acid; "Trp" refers to tryptophan; "Phe" refers to phenylalanine; and "Arg" refers to arginine.

A peptide bond is made from joining the amino group of one amino acid to the carboxyl group of another. A tetrapeptide is a peptide consisting of four amino acids, which are connected via peptide bonds. There are several ways in which these four amino acids could be joined. Any of the four could be located at the first position; any of the remaining three could be located at the second position; either of the remaining two at the third position, etc. Thus, there are possible tetrapeptides.

Asp-Trp-Phe-Arg

Asp-Trp-Arg-Phe

Asp-Arg-Phe-Trp

Asp-Arg-Trp-Phe

Asp-Phe-Trp-Arg

Asp-Phe-Arg-Trp

Phe-Asp-Trp-Arg

Phe-Asp-Arg-Trp

Phe-Trp-Asp-Arg

Phe-Trp-Arg-Asp

Phe-Arg-Trp-Asp

Phe-Arg-Asp-Trp

Trp-Asp-Phe-Arg

Trp-Asp-Arg-Phe

Trp-Phe-Arg-Asp

Trp-Phe-Asp-Arg

Trp-Arg-Phe-Asp

Trp-Arg-Asp-Phe

Arg-Asp-Phe-Trp

Arg-Asp-Trp-Phe

Arg-Phe-Trp-Asp

Arg-Phe-Asp-Trp

Arg-Trp-Phe-Asp

Arg-Trp-Asp-Phe

Stop the nonsense! When a base change occurs but results in the same amino acid being read, this is considered a silent mutation. When a base change results into a different amino acid (concervative-new amino acid is similar in chemical structure), this is a missense mutation. When a Frame shift mutation occurs, the change results in misreading of all nucleotides downstream, usually resulting in a nonfunctional protein.

Glutamate is an acidic amino acid. At a pH below 2.2 (acidic conditions), the side chain, the amino group, and the carboxyl backbone would all be protonated (+1 net charge). At a pH above 9.7 (basic conditions), all of those groups would be deprotonated (negative 2 net charge).

In the situation we are given, the pH is 3, which is above the , but below the . The carboxyl group on the backbone is therefore deprotonated, but not the carboxyl side chain. The amino backbone also remains protonated in these still acidic conditions. Overall, the net charge must then be zero.

To simplify this problem, remember that at any pH above the of a given group (basic conditions), that group will be deprotonated. On the other hand, at any pH below the of a given group (acid conditions), that group will be protonated.

The value of the amino groups in amino acids are around 9. On the other hand, the value of the carboxyl groups of amino acids are around 2. All biologically relevant amino acids are indeed found only in the L stereoisomer formation. There are three aromatic amino acids: phenylalanine, tyrosine, and tryptophan. All amino acids are joined together with a planar, rigid peptide bond. Glycine is the only achiral amino acid. This is due to the hydrogen found in the R-group.

Quarternary structure is the association of multiple polypeptide chains into a functional protein. Not all proteins have this level of protein structure. Subunits within the quarternary structure are held together by noncovalent bonds and disulfide bonds.

Glutamate is the primary source of ammonia. Glutamine is similar however it is the amide free form of ammonia. Glutamate plays an important role in the urea cycle. The urea cycle serves to rid the body of ammonia, which can be toxic in high amounts.

Charged hydrophilic amino acids are polar and their side chains carry a net charge at or near a neutral pH. For instance, lysine has a positive charge at a pH of 7. Examples of essential amino acids that are in this group include arginine, histidine, and lysine.

In this question, we're given the pKa of a peptide's functional group and we're told that the peptide is in a solution at a certain pH. We're asked to estimate the proportion of the functional group that we would expect to be protonated.

The first thing we can realize about this problem is that the peptide is in a solution that is far more acidic than the pKa of the functional group. Therefore, we would certainly expect a lot of it to be protonated. The question is, by how much?

We can make use of the Henderson-Hasselbalch equation to quantify the degree to which the functional group will become protonated.

In the equation above, we can take base to mean the deprotonated functional group, while acid we can take as the protonated functional group.

We can also rearrange the above expression in order to isolate the base to acid ratio.

Next, we can plug in the values given to us in the question stem.

We can rewrite this expression alternatively to make it more intuitive.

In other words, for every one equivalent of base, there are equivalents of acid. To find the proportion of acid, we can take the number of acidic equivalents and divide that by the total number of acidic plus basic equivalents.

Thus, of the functional group is expected to be in the protonated form. This makes sense, considering that the solution is significantly more acidic than this particular functional group's pKa.

A peptide bond is a covalent bond that connects adjacent amino acid molecules. The bond occurs between a carboxylic acid group on one amino acid and an amino group on the other. Specifically, the carbon atom from the carboxylic acid and the nitrogen atom from the amino group form a peptide bond; therefore, only carbon and nitrogen participate in a peptide bond.

Nitrogen and hydrogen make up the amino group (), whereas carbon and oxygen make up the carboxylic acid group (). Remember that an amino acid has a central carbon. The central carbon always has an amino group, a carboxylic acid, and a hydrogen atom. The fourth group is different for each amino acid, which gives them unique properties.

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.