Question

In general terms, what does the tertiary structure of a protein represent? Distinguish between the secondary and tertiary structures of a protein.

Short answer

The tertiary structure of a protein represents its overall three-dimensional shape, showing the folding and interaction of different secondary structure elements and amino acid side chains. Secondary structures, such as alpha-helices and beta-sheets, are localized folding patterns primarily driven by hydrogen bonding between the peptide backbone. On the other hand, tertiary structures are more complex, involving various interactions like hydrogen bonding, hydrophobic interactions, electrostatic interactions, and disulfide bonding among amino acid side chains and secondary structure elements.

Step-by-step solution

Defining Secondary Structure

Secondary structure represents the local, repetitive folding patterns of amino acids in a protein segment, primarily driven by hydrogen bonding between the peptide backbone. The two common secondary structure types are alpha-helices and beta-sheets.

Defining Tertiary Structure

Tertiary structure represents the overall three-dimensional shape of a protein, showing how different secondary structure elements fold and interact with each other in addition to the interactions between amino acid side chains. This folding is guided by interactions such as hydrogen bonding, hydrophobic interactions, electrostatic interactions, and disulfide bonding.

Distinguishing Between Secondary and Tertiary Structures

The primary difference between secondary and tertiary structures is the level of complexity. Secondary structures arise from repetitive folding patterns in localized regions of a protein, while tertiary structures represent the overall three-dimensional folding and arrangement of different secondary structures and amino acid side chains. Secondary structures involve hydrogen bonding between backbone atoms, while ternary structures involve various types of interactions between amino acid side chains and different secondary structure elements.

Key concepts

Secondary Structure

Secondary structure refers to the repeated patterns of folding that occur within a localized section of a protein. It is mainly stabilized by hydrogen bonds, occurring between atoms of the backbone of the amino acids. This structural level is like the first layer of organization on the way to a protein's final shape.
One key aspect of secondary structures are their recurring shapes:

• **Alpha-helices:** These structures are like a coiled spring, where the peptide chain forms a right-handed helix.
• **Beta-sheets:** In these structures, the peptide chains lie side by side, forming a flat sheet held together by hydrogen bonds. The strands can be parallel or antiparallel.

The formation of these structures is crucial as they form the building blocks that make up the more complex three-dimensional shapes of proteins.

Tertiary Structure

The tertiary structure represents the overall three-dimensional shape of a protein. This includes how the secondary structures such as alpha-helices and beta-sheets come together and interact. The arrangement in space results from the folding of the entire polypeptide chain, giving the protein its specific function.
Various interactions are responsible for stabilizing the tertiary structure:

• **Hydrogen bonding:** These occur between side chains or between side chains and backbone atoms.
• **Hydrophobic interactions:** Nonpolar side chains tend to cluster in the interior of the protein away from water.
• **Electrostatic interactions:** These occur between charged side chains.
• **Disulfide bonds:** Covalent bonds between the sulfur atoms of two cysteines stabilize the structure.

Understanding tertiary structures helps us grasp how enzymes function, how drugs interact with proteins, and how diseases associated with protein misfolding occur.

Amino Acids

Amino acids are the building blocks of proteins. Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain known as an R group.
These R groups can vary greatly and determine the characteristics and the role of the amino acids in proteins, such as being:

• Nonpolar or polar
• Charged or uncharged
• Acidic or basic

The sequence of amino acids dictates how the protein will fold into its secondary and tertiary structures. The unique side chains determine how proteins interact with each other and with other molecules. This is why amino acids are critical in maintaining the structure and function of proteins.

Hydrogen Bonding

Hydrogen bonding plays a vital role in the structure and stability of proteins. It contributes significantly to both the secondary and tertiary structures of proteins. In secondary structures, hydrogen bonds form between the carbonyl oxygen of one amino acid and the hydrogen attached to the nitrogen of another amino acid, promoting the formation of alpha-helices and beta-sheets.
For tertiary structures, hydrogen bonds can also occur between the side chains of amino acids. These bonds slightly vary in strength but collectively stabilize the overall protein structure. They also help in maintaining interactions between different parts of the protein and between the protein and other molecules, such as substrates or inhibitors in the case of an enzyme.

• The flexibility of these bonds enables proteins to undergo conformational changes, vital for their function.
• They help in maintaining the stability of protein structures under different conditions.

This bonding mechanism is a perfect example of how weak forces can create highly organized and stable structures.