Proteins
Proteins are the building blocks of life. They are vital to our existence and are found in every organism on Earth.
Proteins are the most common molecules found in cells. In fact, they constitute more of a cell’s dry matter than lipids, carbohydrates and all other molecules combined.
A protein is made from one or more polypeptide chains and each polypeptide chain is built from smaller molecules called ‘amino acids’. There is a total of 20 amino acids that can be arranged in trillions upon trillions of different ways to create proteins that serve a huge variety of functions.
Proteins are in fact the most structurally complex molecules known to biology.
Functions of proteins
Proteins come in a huge variety of forms and perform a wide range of functions. Examples of proteins include enzymes, antibodies and some hormones which help to speed up chemical reactions, defend against diseases and regulate the activity of cells.
Proteins also play a role in movement, structural support, storage, communication between cells, digestion and the transport of substances around the body.
Movement
Motor proteins, such as myosin and dyneins, have the ability to convert chemical energy into movement. Myosin is the protein found in muscle and causes the contraction of muscle fibers in muscles.
Dyneins provide the power that drives flagella. Flagella are long, thin structures attached to the outside of certain cells, such as sperm cells, and are responsible for their mobility.
Structure and support
Many proteins provide structural support to specific parts of an organism. Keratin, for example, is the protein found in the outer layers of skin and makes skin a strong protective layer to the outside world. Keratin is also the structural protein that makes hair, horns and nails.
Cellular communication
Cells communicate with their surrounding environment and other cells. Receptor proteins in a cell’s membrane receive signals from outside of the cell and relay messages into the cell. Once the signal is inside the cell it is usually passed between a number of proteins before it reaches its final destination (also most commonly a protein).
Digestion
Digestion is driven by, you guessed it, proteins. Enzymes are proteins that drive digestion by speeding up chemical reactions.
Digestion is the breakdown of food from large, insoluble molecules into smaller molecules that can dissolve into water. As the smaller molecules are water-soluble they can enter blood and be transported around the body.
Digestive enzymes are the enzymes responsible for breaking down food molecules into smaller, water soluble molecules. Some examples of digestive proteins include:
- Amylase – the enzyme in saliva that breaks down starch into soluble sugars
- Lipase – breaks down fats and other lipids
- Pepsin – breaks down proteins in food
Transport of oxygen
Hemoglobin is yet another hugely important protein for animals such as mammals and birds. It is the protein in blood that binds to oxygen so that oxygen can be transported around the body.
Hemoglobin contains an iron atom. The chemical structure of hemoglobin around the iron atom allows oxygen to bind to the iron and then be released to oxygen deprived tissue.
As you can see proteins are clearly extremely important to the healthy functioning of an organism. The majority of the examples I have used are animal proteins but proteins are no less important for other life forms such as plants, fungi and bacteria.
Building blocks of proteins
Amino acids are the building blocks of proteins. In total, there are 20 different amino acids found in nature. Amino acids can link together in a huge variety of ways to create different proteins.
The chemical structure of amino acids is the key to why proteins have become the foundation of life. An amino acid consists of a carboxyl group (chemical structure -COOH), an amine group (-NH₂), and a sidechain made mostly from carbon and hydrogen.
The sidechain is often referred to as the R group. Differences in the R group is what makes the 20 amino acids different from each other.
Depending on the structure of the R group, an amino acid can be water-soluble (polar), water insoluble (non-polar) or contain a positive or negative charge. These characteristics in turn affect how the amino acids behave as they link up and influences the overall shape and function of a protein.
All 20 amino acids are necessary for good health. If an organism is low in one of the 20 amino acids, certain proteins will not be able to be built and the loss of their functions will cause health issues for the organism.
Some amino acids can be created by the body using other molecules while other amino acids must be sourced from food. The amino acids that must be eaten are known as the ‘essential amino acids’ because they are an essential part of a healthy diet. The amino acids that can be made by our bodies are known as ‘non-essential amino acids’.
Polypeptides
A polypeptide is a chain of amino acids and is the simplest form of a protein. Amino acids bond together to form long, linear chains that can be more than 2000 amino acids long.
The order that amino acids are linked together determines the final shape and structure of the polypeptide chain. A protein will contain one polypeptide or multiple polypeptides bonded together to form large, complex proteins.
Amino acids are bonded together between the amine group (-NH₂) of one amino acid and the carboxyl group (-COOH) of a second amino acid.
As two amino acids bond together, two hydrogen ions are removed from the amine group and an oxygen is removed from the carboxyl group. The amine group and carboxyl group bond together and a water molecule is produced as a byproduct. The bond is known as a ‘peptide bond’.
Bonding multiple amino acids together by peptide bonds creates a polypeptide backbone with an R group extending out from each amino acid. As mentioned earlier the R groups of the 20 amino acids each have their own unique structure and chemical properties. The structure and chemical properties (such as reactivity and boiling temperature) of a polypeptide and ultimately a protein are determined by the unique sequence of R groups that extend from the polypeptide backbone. As R groups are attracted or repelled from each other, the polypeptide chain bends and twists into a uniquely shaped protein.
Protein structure
Proteins have four levels of structure, all of which we have already alluded to on this page. The four levels are known as the primary, secondary, tertiary and quaternary structure of a protein.
Primary structure
The primary structure is the specific sequence of amino acids i.e. the order that they are bonded together. The exact order that amino acids are bonded together is determined by the information stored in genes.
Through processes called transcription and translation, DNA provides all the necessary information for cells to produce the exact primary structure for thousands of different proteins. The primary structure determines the secondary and tertiary structures of proteins.
Secondary structure
The secondary structure of a protein is formed by hydrogen bonds between atoms along the backbone of the polypeptide chain.
Remembering each amino acid has a carboxyl group and an amine group, the slight negative charge on the oxygen of the carboxyl group forms a weak bond with the slight positive charge of a hydrogen atom on the amine group of another amino acid. Hydrogen bonds are weak but many of them create enough strength to influence the shape of a polypeptide chain.
The hydrogen bonds cause the polypeptide backbone to fold and coil into two possible forms – the α helix and the β pleated sheets. An α (greek letter ‘alpha’) helix is a spiral, similar to the double helix of the iconic DNA strand but with only one coil, and is formed by hydrogen bonds between every fourth amino acid. The α helix is common in structural proteins such as keratin.
The β (greek letter ‘beta’) pleated sheets are formed when hydrogen bonds occur between two or more adjacent polypeptide chains and are common in globular proteins (see below in ‘Types of proteins’).
Tertiary structure
The tertiary structure is the final shape that the polypeptide chain takes and is determined by the R groups. The attraction and repulsion between different R groups bends and folds the polypeptide to create the final 3D shape of a protein.
Quaternary structure
Not all proteins have a quaternary structure. A quaternary structure only results when multiple polypeptide chains combine together to form a large complex protein. In such cases, each polypeptide is referred to as a ‘subunit’.
Hemoglobin is an example of a protein with quaternary structure. In most animals, hemoglobin is made from four globular subunits.
Types of proteins
There are four main types of proteins. The most commonly known are the globular proteins. The other three types of proteins are fibrous, membrane and disordered proteins.
Globular proteins
A globular protein is any protein that takes a spherical shape in its tertiary structure. These include many enzymes, antibodies and proteins such as hemoglobin.
Globular proteins are water-soluble and are created due to the attraction and repulsion of different R groups with water. Polar R groups of the amino acids in proteins are water-soluble while non-polar R groups are water insoluble. Globular proteins form because non-polar R groups hide in the internal sections of the protein and polar R groups that arrange themselves on the outer surface that is exposed to any surrounding water.
Fibrous proteins
Fibrous proteins are elongated proteins that lack any tertiary structure. Instead of bending and folding to form a globular protein, fibrous proteins remain in their linear secondary structure. They are often important structural and support proteins.
Fibrous proteins are insoluble in water and often have repeating patterns of amino acids along their polypeptide chain. Examples of fibrous proteins include collagen, keratin and silk.
Membrane proteins
A membrane protein is any protein found within or attached to a cell membrane. They are unique proteins due to the unique environment that they exist in.
Cell membranes are made from a double layer of phospholipids. The inner parts of a cell membrane is non-polar but the exterior is polar. In order for membrane proteins to successfully exist across a cell membrane they must contain specific non-polar and polar sections.
Disordered proteins
The discovery of disordered proteins in the early 2000s challenged historical thinking of proteins. Until then it had been believed that the function of a protein was dependent on its fixed 3D structure. Disordered proteins however exhibit no ordered structure to their shape.
Some proteins can be fully unstructured whilst other are partially structured with certain unstructured sections. Other proteins have the ability to exist as disordered proteins only to form a fixed structure after bonding to other molecules.
Last edited: 23 April 2016
