Question

An amino acid on a protein strand forms a hydrogen bond to another amino acid that is four amino acid units away. The next amino acid on the chain does the same, hydrogen-bonding to an amino acid that is four amino acids away from it. This pattern repeats itself over a significant part of the protein chain. The resulting pattern in the protein is an example of which kind of structure? (primary, secondary, tertiary, or quaternary)

Short answer

The resulting pattern in the protein is an example of a secondary structure.

Step-by-step solution

Understanding Protein Structure Hierarchy

Protein structures are organized into four levels: primary, secondary, tertiary, and quaternary. The primary structure is the sequence of amino acids. The secondary structure includes local configurations like alpha helices and beta sheets formed by hydrogen bonding. Tertiary structure refers to the overall 3D shape of a single protein molecule. Quaternary structure is the arrangement of multiple protein subunits.

Identifying the Relevant Structure Level

Since the amino acids are forming hydrogen bonds to other amino acids at a regular interval along the chain, this indicates a patterned folding typical of alpha helices or beta sheets, which are forms of secondary structures.

Determining the Specific Structure Type

As the exercise describes a repeating pattern of hydrogen bonds within a single protein chain, the structure formed is part of the secondary level of protein structure.

Key concepts

Amino Acids

Amino acids are the building blocks of proteins. Each amino acid has a central carbon atom attached to a hydrogen atom, an amino group, a carboxyl group, and a distinctive side chain, or R-group, that determines its properties. In proteins, amino acids are linked together by peptide bonds to form a polypeptide chain. The sequence of amino acids in this chain is the primary structure of a protein, and this sequence dictates how the protein will fold into its more complex shapes - including secondary structures like alpha helices and beta sheets.

It is the unique combination of amino acids that allows proteins to carry out a vast array of functions within our cells, from catalyzing metabolic reactions with enzymes to providing cellular structure. Different side chains can cause the amino acids to repel or attract each other, influencing the protein folding process that establishes its secondary structure.

Hydrogen Bonding

Hydrogen bonds are a type of non-covalent interaction crucial for the structure and function of biomolecules. In proteins, they occur when a hydrogen atom, covalently bound to an electronegative atom like nitrogen or oxygen, exhibits a partial positive charge that attracts a nearby electronegative atom with a partial negative charge. Although individually weaker than covalent bonds, hydrogen bonds are collectively strong and play a major role in stabilizing the protein's secondary structure.

These hydrogen bonds can form between atoms within a single protein chain or between different protein chains. As depicted in the exercise, regular patterns of hydrogen bonding along the protein chain contribute significantly to the formation of predictable secondary structures, such as the alpha helix and beta sheet, by holding specific parts of the polypeptide chain in place.

Alpha Helix

The alpha helix is a common element of secondary protein structure, shaped like a right-handed coil. The structure is stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of an amino acid that is four residues earlier in the sequence. This results in a helical structure where the R-groups of the amino acids protrude outward from the helix, allowing the backbone to snug closely together.

One alpha helix alone can serve a function, but often, helices are part of more extensive, complex protein structures. The repetitive nature of the hydrogen bonding that defines an alpha helix makes it easy to identify based on the regularity of the pattern, just as described in the exercise. This pattern of hydrogen bonds confers considerable stability to the overall protein structure and can affect the protein's physical properties, such as its elasticity or flexibility.

Beta Sheet

The beta sheet is another type of secondary structure found in proteins. It is comprised of beta strands, which are almost fully extended rather than coiled as in an alpha helix. These strands align alongside one another, and hydrogen bonds form between the strands, holding them together into a sheet-like array. Beta sheets can be parallel, where the strands run in the same direction, or antiparallel, where adjacent strands run in opposite directions.

Depending on the sequence and spatial orientation of the beta strands, the resulting beta sheet can be flat or can adopt a more twisted or pleated configuration. The R-groups of amino acids residing in beta sheets alternate facing above and below the plane of the sheet, which can impact how beta sheets interact with other elements of the protein's structure. As with alpha helices, patterns of hydrogen bonding play a crucial role in maintaining the integrity of the beta sheet structure. The description in the exercise of amino acids bonding at regular intervals is indicative of the regular hydrogen bonding pattern seen in these secondary structures.