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Protein Folding: the Orders and Steps

Updated: Oct 29, 2021

In order for protein molecules to be able to perform their functions, their structure must first be built from their basic biological building blocks: amino acids. What are the steps of this intricate process? Read to find out!

 


As substances change and acquire different properties, varying different amino acids are having bonds formed between them. The protein achieves a specific 3D shape when it completes the process of folding, which involves interactions between hydrophobic and hydrophilic amino acids and the fluctuating pH and temperature of the environment surrounding it. All of the information that determines a protein's characteristics is in the cell's DNA that contains codes in its genes. In addition, the shape of the proteins play a big role in the functions they end up performing.


To start off, there are four levels of protein structure that can help us understand how the protein gets its unique shape:


Primary Structure


The primary structure of a protein is considered the simplest level due to the fact that it refers to the amino acid sequence that makes up a protein's polypeptide chain. Each chain can have a unique set of amino acids composing it, as well as the order of how they are bonded in the chain.


Firstly, the protein's basic building block are amino acids, which are molecules formed from a central carbon atom that is linked to a side chain, an amino group, a carboxyl group, and a hydrogen atom. These amino acids are bonded together by polypeptide bonds, which form the long chain as amino acids are bonded in a specific encoded sequence.


This sequence is, in fact, determined by the DNA of the gene, which encodes the amino acids and their order in the protein with its unique sequence. Even a small difference of one amino acid greatly affects the encoding process in DNA transcription, and can drastically change the function, shape, and properties of the protein. This is what leads to mutations in organisms.


Secondary Structure


The next level, the secondary structure, consists of folded structures of the protein, such as the alpha helix and the beta sheets. They are held in that folded shape because of the hydrogen bonds that form between H and O molecules in the amino acids.


A secondary structure is an alpha helix when the hydrogen bond is formed between amino acids that are four amino acids apart from each other on the chain, creating the long curled shape of the helix structure. Beta sheets, which resemble folded pieces of paper because of how the hydrogen bonds form between amino acids that are next to each other. As a result, the strands in the sheet can be parallel or antiparallel.


Tertiary Structure

The third level of protein structure is known as tertiary structure, the overall 3D structure of the protein. It is basically a "unit" of alpha helices and beta sheets made up by amino acid sequences, and are linked together. This structure is a result of R group interactions, which include hydrogen bonding, ionic bonding, dipole-dipole forces, London dispersion forces, and other covalent bond interactions. Disulfide bonds are also another type of bond which create strong links between the protein's side chains and attach them to each other.


For instance, R groups repel each other when they have the same charge, and form an ionic bond when they have opposite charges, which creates the varying structure and folds throughout the protein. Whether R groups are polar or nonpolar also determines what forces will act upon them, creating different levels of attraction and repulsion between other molecules.


In addition, properties of the amino acids, such as whether they are hydrophobic (repellent to water) or hydrophilic (attracted to water), affect the shape of the protein. The hydrophobic R groups will avoid water by staying in the inside middle area of the protein while the hydrophilic R groups will make up the outside structure of the protein and interact with water molecules.


Quaternary Structure


Lastly, the fourth and last level of protein structure is quaternary structure. If the tertiary structure is a "unit" of protein, the quaternary structure is multiple of these units combined, creating it into a full protein with multiple chains. The multiple amino acid chains are connected to form the protein in a similar way as they were linked in tertiary structure, through the bonds and interactions of varying amino acids and R groups.


These are the four structures that, together, determine the shape of proteins. Proteins actually don't need additional energy in order to carry out this folding process, but they have chaperone proteins, which surround the protein as it folds and assist in the process.


As a result, during the process of the different levels of structure forming, the natural interactions occurring between the various components of the protein end up affecting its final shape. Things such as the temperature, how the molecules interact with water, and the DNA itself affects what type of protein will be formed, including its function and shape. Therefore, the location and sequence of these different molecules are what cause it to take on its unique structure.


Thank you for reading!


 

Written by: Janice Le

 

References:


“Protein Structure: Primary, Secondary, Tertiary & Quatrenary (Article).” Khan Academy, www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-of-protein-structure.


“Protein Structure | Learn Science at Scitable.” Scitable, 2014, www.nature.com/scitable/topicpage/protein-structure-14122136/

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