Amino Acids and Proteins - Biochemistry

The one letter code for asparagine (asn) is N. The one letter code for aspartic acid (asp) is D. The one letter code for histidine (his) is H. The one letter code for glutamine (gln) is Q.

Cysteine is the only amino acid that forms disulfide bonds. Methionine also contains sulfur but does form these bonds.

Typically, nonpolar amino acids have side chains containing only carbons and hydrogens. The side chain on glycine contains only a hydrogen, and is nonpolar. The side chains on leucine and isoleucine contain nothing but carbons and hydrogens, so they are also nonpolar. Finally, the side chain on tryptophan does contain a nitrogen. However, tryptophan is large enough and contains enough carbons to balance out the increased electronegativity of the nitrogen within the side chain. Therefore, tryptophan, along with the rest of the answer choices, is nonpolar.

The word hydrophobic means "water fearing". Knowing this, you can eliminate the answer choice "near water". Typically, the exterior of a protein is surrounded by water, so we can also eliminate that answer choice. It is true that hydrophobic amino acids will cluster away from water. The interior of a protein typically is away from water, so the correct answer is "Both the interior of a protein and away from water."

A peptide bond is the chemical bond formed between two amino acids to create a polypeptide. The carboxyl group of one amino acid reacts with the amino group of the other amino acid, releasing a molecule of water. This is known as a dehydration reaction.

Glucose can be stored as glycogen, mostly in the liver, and fatty acids are stored in adipose cells. Amino acids, though, can not be stored for future anabolic use in the human body. Therefore, any time there is an excess of amino acids, they are broken down into their constituent parts so that they may be recycled into other molecules.

An essential amino acid is one that can not be synthesized by the human body, and so it must be consumed in the diet. Tyrosine can be synthesized, and is therefore not considered to be an essential amino acid.

Different proteins have different optimal temperature and pH ranges, values at which they function best. Outside of these ranges, they can become denatured. Thus, treatments of heat, low pH, or high pH can cause proteins to denature.

Detergents denature proteins in a different way. Detergents are amphipathic, meaning that they have both hydrophobic and hydrophilic regions. Because all membrane proteins are also amphipathic (they must be in order to remain anchored in the lipid bilayer), the detergent can be attracted to these regions and force the membrane proteins apart.

Non-proteinogenic amino acids are those which are not found in the genetic code of any organism. These are also called "unnatural" amino acids, as compared to "natural" amino acids which are found in the genetic code. Isoleucine, proline, and asparagine are three of approximately one hundred and forty "natural" amino acids. Ornithine is a non-proteinogenic amino acid that has a role in the urea cycle.

Methionine and cysteine are the only amino acids that contain sulfur.

Only two cysteine amino acids can come together to form a disulfide bridge. This disulfide bridge is a covalent bond. Disulfide bridges are a component of tertiary structure in proteins. As a side note, the name of a cysteine amino acid changes to cystine after a disulfide bridge is formed.

Only glycine is nonpolar. The rest of the answer choices are polar. Remember that being nonpolar implies that the substance is hydrophobic and, hence, insoluble in water. Besides methionine, you will notice that the rest of the nonpolar and nonaromatic amino acids have R-groups composed solely of carbon and hydrogen. Polarity of amino acids is quite important when looking at the tertiary, or three dimensional, structure of a protein.

There are only three aromatic amino acids. They are phenylalanine, tyrosine, and tryptophan. Histidine has a positively charged R-group. Proline is a nonpolar amino acid. Serine is a polar amino acid. Threonine is a polar amino acid.

Serine's R-chain contains a hydroxyl group , which is polar but uncharged, and cysteine's side chain contains a thiol (sulfhydryl) R-group which is also polar but uncharged. Each of the the other answers contain amino acids that have side groups with different functional properties, but only serine and cysteine can be classified as polar and uncharged.

All amino acids have the following main components: carbon backbone, an amine group, a carboxylic acid group, and a specific side chain to further define the particular amino acids. The other groups listed can serve as functional groups in other molecules, but an amino acid, at its baseline, is defined a a molecule with an amine and a carboxylic acid group.

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.

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.