Proteins

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Summary

  • Proteins carry out the majority of the functions of the cell
  • Proteins have hugely diverse components, sizes, structures, and functions
  • Proteins are made up of chains of amino acids, which progressively fold to form the final structure of the protein
  • Primary, secondary, tertiary and quaternary structures classify the distinct layers of polypepide folding structures, from the polypeptide sequence to the final 3D structure

Proteins are the building blocks of cells. They perform a variety of functions, and are the key executers of the instructions held within the DNA. Enzymes are examples of proteins, and are crucial in catalysing reactions within the cell and allowing cells to carry out their jobs. Proteins also regulate the transport of molecules within and outwith the cell, sense cellular environments and signal responses at the cell and organism level, and perform structural/scaffolding roles. The specialisation of proteins and diversification of their function relies on the unique and abundant structures that proteins can adopt.

What are proteins made of?

All proteins in the cell are synthesised by the process of translation. The information coded within DNA is transmitted into a message RNA, which is translated into a sequence of amino acids, through the actions of tRNAs, a process covered in the topic of DNA and protein synthesis.

Amino acid chains

Amino acids have a basic amino group (NH2) and a carboxylic acid group (COOH). Amino acids also possess a side chain called the ‘R’ group, which gives each amino acid its specificity. The R group is a different molecule in each amino acids, giving them their unique properties. This side chain can give the amino acid different 3D structures, charges or polarity.

The translated sequence of these amino acids creates a unique protein with specific structural and functional properties. The amino acids and their properties are summarised in the table shown.

Amino acids are linked together to form a chain – the carboxy group of one amino acid is joined to the amino group of another, forming a peptide bond, (also called an amine bond). These are examples of covalent chemical bonds, and are stable. When two amino acids are joined, the reaction releases a molecule of water. This is type of reaction is called a condensation reaction. Hydrolysis is the reverse of the condensation reaction, involving breaking the peptide bond using a molecule of water.

Protein structures

The way scientists classify structures of proteins increases in complexity in a hierarchical manner, from the underlying chain of amino acids (the primary structure), right up to the overall 3D structure of the protein and the incorporation of other polypeptides and accessory molecules.

Primary structure

The most basic level of structure of a protein is the sequence of the polypeptide chain. This chain will be made up of a particular order of amino acids with their unique properties, forming the initial polypeptide chain. This chain is the first layer of structure, and is dictated by the information contained within the DNA.

Secondary structure

The next layer of structural organisation is the local folding shapes that the polypeptide chain adopts. The two most common structures are the α-helix and the β-pleated sheet. Certain amino acid sequences tend to form particular secondary structures due to the properties of the peptide backbone. These structures are held together by hydrogen bonds.

Tertiary structure

The protein tertiary structure refers to the overall 3D structure of the polypeptide chain. This level of structure is principally due to the properties and interactions between the side chains of the amino acids, and depends on the nature of the chemical groups present on each amino acid. The properties of these side chains can attract or repel interactions with other side chains.

These interactions occur primarily through non-covalent bonds such as hydrogen and ionic bonds. Disulphide bonds are a unique example of a covalent bond that can form part of a tertiary structure, acting as strong bridges that form when two amino acids contain sulphur groups in their side chains. These stable bonds hold the tertiary structure in place.

Quaternary structure

Some proteins are made up of several polypeptide chains that form one structure. The final layer of structure is the way these polypeptides are arranged together, the quaternary structure. The quaternary structure is held together by interactions similar to those at the tertiary level.

Proteins can also have additional non-protein components that are incorporated into their structure and to help in the execution of their functions. These components are called prosthetic groups, and examples include vitamins, sugars and metal ions. A good example of a protein requiring a prosthetic group is the iron component of haemoglobin, which is essential for oxygen transport in the bloodstream

Further reading and references:

[1]. http://www.genome.gov/Pages/Hyperion//DIR/VIP/Glossary/Illustration/amino_acid.shtml Image primary protein structure

[2]. http://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/amino-acids.html Image amino acid tables

[3]. https://simple.wikipedia.org/wiki/Protein_structure#/media/File:Main_protein_structure_levels_en.svg Image protein structure

[4]. https://www.ncbi.nlm.nih.gov/books/NBK22364/

[5]. https://www.nature.com/scitable/topicpage/protein-structure-14122136