Title: Unit 5 Learning Module
Course: SAT 170 Introductory Biotechnology > Section: SAT 170 Introductory Biotechnology

Unit 5 Learning Module

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- Unit 5
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- Unit 5 Glossary (Selected)

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Protein Structure and Function

The field of proteomics is dedicated to investigating the proteomes of living things in order to better understand the role of these proteins. This will allow researchers to identify the role that certain proteins play in the development and progression of diseases and disorders for the purpose of improving the treatment options for those ailments. For example, by studying different organism’s proteomes (complete set of proteins) researchers can compare a healthy and diseased individual.

Protein Function

Figure 1

Proteins carry out many important functions in cells including, but not limited to, membrane transport, cell recognition, communication, cell adhesion and catalysis.
- Proteins embedded within the cell membrane can aid in the movement of substances both into and out of the cells. These membrane proteins are sometimes known as channel proteins as they serve as a passageway for certain materials. Some membrane proteins go through a change in shape as they allow a material to pass from one side of the membrane to the other. These membrane proteins are known as carrier proteins. These transport proteins are very important in making sure that the cell can effectively exchange materials with its environment.

See Figure 1: The blue structures shown here are examples of membrane proteins. Notice how these proteins transverse the bilayer of the cell membrane (shown in gold) in order to serve as passageways for materials to get from one side of the membrane to the other.
- Another type of membrane protein known as glycoproteins (because they have carbohydrates attached to them) function in cell recognition. This is what allows us to distinguish “self” cells from “foreign” cells and is the basis of our immune response.
- Being able to receive messages from the outside world is also a function of proteins. These communication proteins receive signals from outside the cell and can then convey the information provided in that signal to the inside of the cell.
- In multicellular organisms which are composed of many cells, there are proteins that help to form tissues and organs as they bind cells together. Such proteins are known as cell adhesion proteins.
- Enzymes are also proteins. Enzymes catalyze (increase the rate of) the chemical reactions of our cells. Enzymes bind a substrate (substance on which an enzyme acts) in a specific location of the enzyme known as the active site. This active site is complementary in shape to a particular substrate. This is why enzymes are very specific and usually act upon only one substrate. Without the proper shape, an enzyme is unable to bind its specific substrate and is; therefore, ineffective at catalyzing a chemical reaction.

See Figure 2: The enzyme (shown here in blue) has a specific active site (shown as the cut out region) which is complementary to the substrate (shown in gold). Once the enzyme binds to the substrate it can catalyze the reaction that will convert that substrate into products.

Figure 2

- These are just descriptions of some of the major types of proteins present in living things. There are many other functions of proteins including movement, protection, and structure. There are approximately 80,000-100,000 proteins in human cells, each with a specific role.

Figure 3

Protein Structure

Figure 4

Most proteins have a complex three-dimensional structure which is essential for proper protein function.
- As we learned in our last unit, the subunits of proteins are amino acids. These amino acids are held together by peptide bonds. This chain of amino acids, or polypeptide, represents the first level of protein structure known as primary structure.

See Figure 3: Notice how the bands are folded back and forth forming a barrel like structure. Each band represents different regions of the chain of amino acids, when they fold back and forth in this why the structure is called a beta sheet.
- The secondary structure of a protein results from this chain of amino acids undergoing a process of folding and coiling. These folds are known as beta (β) pleated sheets and the coils are known as alpha (α) helices.
- Once the α helices and β sheets are formed they can be further organized into the three-dimensional, globular structure known as the tertiary structure of proteins.
- If a protein is composed of more than one polypeptide chain, each chain will undergo conformational changes to achieve the proper tertiary structure. These subunits can then be joined to form a larger protein complex. This level of protein structure is known as quaternary structure.

Proteins are only functional if they have the proper three-dimensional shape. This means that proteins that consist of a single subunit must have achieved tertiary structure while proteins that are composed of multiple subunits have reached the proper quaternary structure. These levels of protein structure are held together by a variety of chemical bonds and molecular interactions.

See Figure 4: As a protein’s structure becomes more complex (as it transitions from primary, to secondary, to tertiary and perhaps quaternary), the protein acquires its functional three-dimensional shape.
Protein Folding and Modifications
- As we discussed in unit 4, a protein is synthesized from an mRNA molecule during the process of translation. The protein products must undergo a folding process in order to acquire this functional, 3D shape. Proper protein folding is dependent on the interactions of the amino acids of that protein. A mutation which alters the protein even by a single amino acid, can impact the proper folding of that protein. The process of protein folding can also be impacted by the environment of the cytoplasm.
- Some proteins must be modified before they can be properly folded and functional.  These modifications are known as post-translational modifications (PTM’s) and are common in eukaryotes like us. If you recall from our discussion of cell structure, some proteins will be made on the ribosomes which are attached to the rough endoplasmic reticulum. These protein products are then sent from the rough ER to the golgi complex where they are modified and packaged and finally sent to their specific cellular destination. One of the most common protein modifications is known as glycosylation. Glycosylation is the process of adding sugar molecules (carbohydrates) at specific locations in the protein. The addition of these sugar molecules can have huge impacts on the characteristics and function of these proteins. Some proteins may also require the addition of lipids or phosphate groups in order to be active.
- Denaturation results from the unfolding of a protein which causes that protein to lose its 3D shape. Many factors can influence protein denaturation including heat and pH.
- Temperature is a measure of kinetic energy which is the energy of motion. As you increase temperature, you increase kinetic energy; thus molecules and atoms begin to move faster. At a certain point, the kinetic energy is so high that it causes the chemical bonds that are responsible for holding proteins together to break as the atoms in those molecules begin to move too fast to remain attached to one another. This includes the chemical bonds that are necessary for holding the 3D shape of a protein together which is why extreme heat can lead to protein denaturation.
- Changes to pH can also disrupt the chemical bonds responsible for a proteins 3D shape; thus changes to pH can also lead to protein denaturation.