Key terms: proteins, structure of proteins, alpha helix, Beta sheet, loops, domains, motifs, folding, unfolding.
I am sure that you all must have heard this term ‘protein’ during your high school or college. But when it comes to study of proteins, sometimes it gets difficult for some people to clearly get that idea and basic concepts behind it. So have you ever imagined how exactly the protein looks like or how does it function at molecular level? Well then this article is for you. Let’s make it simple.
- What are Proteins?
They are the organic compounds which contains a long chain of amino acids (polypeptide chain) and maintains the structural components of body. They are mainly present in the muscles (eg. myosin), nails, hair (eg. keratin), immune system (eg. antibody) etc. They are also present in the food and dairy products such as egg, milk, pulses, fish etc. These proteins can be extracted and used as supplement or therapeutic purposes.
- Structure of Proteins
The structure depends on the nature of protein i. e. whether the protein is globular or fibrous in nature. But they are classified in the following four types:
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
The primary structure of protein contains a simple chain of amino acids without any loops or turns inside it. They involve formation of peptide bond. The peptide bond is covalent bond formed between carboxyl group and amino group of two amino acids.
2. Secondary structure
This involves the folding of structure with respect to polypeptide chain due to the reaction between atoms. The folding results into two most common structures, alpha helix and beta pleated sheet.
A. alpha helix
The polypeptide chain is coiled spirally in this structure. The backbone forms inner part of the coil while the side chains extend outward from the coil. In this structure the carbonyl group of amino acid is bonded with the hydrogen of amino group via hydrogen bonding. Therefore it gives the appearance of ribbon to the secondary structure.
B. Beta sheet
The linear extended zigzag pleated sheet is formed by the hydrogen bonds which is either intramolecular or intermolecular. The sheet like structure is formed when two or more segments of polypeptide chain are present next to each other and connected via hydrogen bonds. Individual segments in beta sheets are known as beta strands and they are rarely found in proteins because the structure is not stable. When two adjacent beta strands line up, they can form bridges of hydrogen bonds. This stable structure is known as Beta sheet. However there are further two types of beta sheets: a) Parellel and b) Anti-parallel.
a) Parallel beta sheet:When beta strands line up edge to edge in the same direction, it forms highly stable sheet.
b) Anti-parallel beta sheet: Beta strands runs into opposite direction with each other. The anti-parallel conformation is more stable and more common than the parallel one.
- Loops and turns in the secondary structure
- Loops and turns connect alpha helices and beta strands.
- The more common cause for a polypeptide chain to contain more loops is to make the structure more compact and stable.
- Loops that have only 4-5 amino acid residues are called as turns.
- When they have internal hydrogen bonds, loops generally have hydrophillic residues and are found on the surface of the protein. While turns and bends refer to short segments of amino acids that connect the ends of two adjacent segments of anti-parallel beta sheets.
Before moving to the tertiary structure, it is important to understand some basic concepts for the functions of protein such as domains and motifs.
- Domains, motifs and folds
The polypeptide chains with more than 100 amino acid residues often fold into two or more stable globular units are called domains. The domain is a functional area of protein which performs certain physical or chemical activity. Along with the domains there are certain motifs that represent only the structural characteristics of protein. Motif does not perform functional activity, instead they are a part of domain. In many cases a domain from a large protein still retain to its 3-D structure even if it is separated from polypeptide chain. While it is not in the case of motif because it contains short sequences of amino acids.
3. Tertiary structure
It represents the entire three dimensional conformation of protein. It indicates all the secondary structure helices, loops, turns, bends, sheets and how are they assembled to form a domain in space. It basically explains the 3-D structure of single protein(unlike quaternary structure) and how do all the small components contribute to coiling and compacting the structure to make it stable.
4. Quaternary structure
The quaternary structure of protein involves the clustering of more than one protein chains into a specific shape. This complex structure of protein is formed via various reactions and interactions such as hydrogen bonding, salt bridge formation, disulphide bonds, van der waals forces, covalent bonds etc. It contains many sub units and give rise to a complex structure held by various bonds.