The structural level of a protein refers to the way that the amino acids interact with each other to form distinct shapes. These shapes are what function to carry out actions within the cell.
Proteins can have many functions within the cell. Some examples include enzymes, receptors, transport molecules, and scaffold molecules. All of these protein types have different structural levels that contribute to their function.
The way that a protein carries out its function is highly dependent on the structure of the protein. Changing the structure of the protein can either inhibit or enhance its function, therefore structural level is very important to understand when studying proteins.
The three levels of studying proteins mentioned in this article are molecular level, structural level, and functional level. This article focuses mostly on the structural level of proteins and how to identify it.
Protein structure and function
A protein is a large, complex molecule that functions via specific structural interactions. These interactions are primarily hydrogen bonds, which can be influenced by mutation.
Proton transfers between amino acids are considered weak interactions, and they contribute to the shape of the protein and its function. For example, the function of keratin is partly determined by its internal structure, which prevents it from acting as a chemical messenger.
Other molecular interactions such as van der Waals forces and lattice structures also contribute to protein structure and function. These features are harder to disrupt than hydrogen bonding, making them part of the primary structure of a protein.
By now you should have a good grasp on the various levels of protein structure and how they relate to each other. Now it is time to learn about some common ways that proteins can become disorganized due to mutation.
The importance of hydrogen bonding
As mentioned before, hydrogen bonding is a key part of our everyday lives, from drinking water to cooking with salt. It is also present in our proteins, which are the building blocks of life.
Proteins are long, chain-like molecules that can be thought of as strings of beads. These protein chains are formed by hydrogen bonding between the atoms that make up the chain.
Hydrogen bonds occur between the atom of hydrogen and another atom or molecule. In the case of proteins, the nitrogen in one part of the chain forms a hydrogen bond with an oxygen in another part of the chain. This pulls the two parts closer to each other, creating shape and structure for the protein.
Disrupting these bonds can have serious consequences. When scientists experiment with disrupting these bonds on artificial materials, they call this testing “annealing”.
The structural level of a protein
The final level of a protein is its three-dimensional shape. This shape is determined by the secondary, tertiary, and quaternary structures of the protein.
The secondary structure of a protein is determined by interactions between amino acid residues within the protein chain. These interactions include hydrogen bonding, disulfide bridges, and van der Waals forces.
The tertiary structure of a protein is determined by interactions between secondary structures. These interactions include folding into globular shapes or rod shapes, twisting or braiding, and interlocking parts.
The quaternary structure of a protein is determined by the presence of more than one subunit in the molecule. Quaternary structures can be either independent units or parts of a larger unit that all interact to function properly.
Disruptions in any of these structural levels can cause problems with function and/or regulation of a protein.
What happens when a hydrogen bond is broken?
When a hydrogen bond is broken, the protein must find a new way to hold its structure together.
If the structural level of the protein is least affected by a disruption in hydrogen bonding, then the new structure formed may be unstable. This could lead to adverse effects in the cell.
For example, if hemoglobin loses a hydrogen bond, it will no longer be able to deliver oxygen to the body. This could possibly lead to death.
The next level of structure that is affected by a disruption in hydrogen bonding is the secondary structure. This refers to whether or not a protein curls up (the alpha helix does not). If there is a disruption in hydrogen bonding, then this can change how the protein looks.
The last level of structural affected by a disruption in hydrogen bonding is the tertiary structure. This refers to whether or not a protein folds up and how it looks (the shape and location of its domains).
What happens when a hydrogen bond is formed?
When a water molecule attaches to the nitrogen atom in a protein and the hydrogen atom attached to the nitrogen atom hooks up with a nitrogen atom in another protein, a hydrogen bond is formed.
This happens frequently within proteins, creating an environment where many hydrogen bonds are formed and broken. How quickly these happen depends on the temperature of the protein.
Higher temperatures mean more kinetic energy, or movement. This makes it easier for hydrogen bonds to be broken, so proteins are less likely to have disordered structures at high temperatures.
Lower temperatures make it harder for hydrogen bonds to be broken, so proteins are more likely to have disordered structures at lower temperatures.
Does the size of the amino acid affect the structure of the protein?
Yes, the size of the amino acid does play a role in the structure of the protein. The order and type of amino acids in the protein determine its structure.
Proline, for example, has a special exception when being ordered into the protein. It can be ordered before any other amino acid, regardless of what other amino acid it is replaced with.
This is due to Proline having a special chemical composition that does not interact with other compounds very much. Because of this, it can be ordered first without affecting any other proteins.
Other amino acids have different properties that make them more suitable for being ordered first or last in the chain. All of these factors play a role in determining which amino acids are most suitable for being a part of the structural level of a protein.
Conclusion
The structural level of a protein is the most stable level. This is due to the many hydrogen bonds that hold this domain together.
Disrupting these bonds would require very high temperatures and pressure, making it difficult to change this domain. While it may be difficult to alter the structural domain, it is possible using chemical reagents like glycerol or ethanol.
These chemicals can disrupt the interactions between the amino acids that make up the protein chain. By doing so, you can alter the shape of the protein which changes its function.
Now that you know about all three levels of protein structure and how they are affected by disruption in hydrogen bonding, you are more equipped to handle situations where proteins are not functioning properly.
References
Due to the importance of hydrogen bonding in protein structure, researchers have attempted to find ways to assess the strength of these bonds. Currently, two methods are available for assessing hydrogen bonding in proteins.
The first method is by determining the isoelectric point (pI) of a protein. pI refers to the pH where a protein’s net charge is zero.
When a protein contains both acidic and basic groups, these groups will pair with each other such that the protein has no net charge. At this pH, the protein is said to be isotonic (has the same osmotic concentration as its surroundings). At any other pH, it is said to be isoionic (has a different osmotic concentration than its surroundings).
pI can be determined through experimentally measuring the electrophoretic mobility (how easily a molecule moves through a plasma or fluid environment due to electric potential) of a solution of the protein and comparing it to known solutions with an established pI.
