Protein Structure = Function
Levels of Protein Structure
We have already discovered that the primary structure of a protein is the sequence of amino acids, determined by information encoded in DNA. This is not the end of protein structuring, however. This structure is extremely important - in the case of enzymes, any change to the shape of the molecule will deactivate the enzyme.
As amino acids undergo condensation reactions to form a polypeptide, the chain undergoes folding and coiling to prevent it from breaking or tangling. These substructures are held in place by hydrogen bonds - a form of intermolecular interaction stronger than van der Waal forces but weaker than covalent or ionic bonds.
When the chain coils, the structure is called an alpha helix. These coils have 36 amino acids per 10 turns of the coil, with hydrogen bonds forming between on amino acid and the one four places along the chain.
When the chain pleats, the structure is called a beta-pleated sheet.The amount of coiling or pleating depends on the primary structure (sequence of amino acids...remember?) as hydrogen bonds can only occur between certain atoms. Although hydrogen bonds are weak, there are so many of them along the polypeptide chain, they confer huge stability to parts of the polypeptide.
The structure of a protein in 3D space is what defines its function:
- A hormone must fit its receptor exactly;
- the active site of an enzyme must be complimentary in shape to its substrate;
- structural proteins must be shaped to maximise mechanical strength.
This 3D shape is the tertiary structure, and is formed when the coils and pleats of the secondary structure themselves fold or coil. This can either happen spontaneously, or with the assistance of cellular organelles such as the endoplasmic reticulum. This 3D shape is held together by a number of bonds and interactions:
- Disulphide bridges - occur between to sulphur atoms. Often occur between cysteine residues
- Ionic bonds - occur between oppositely charged R groups
- Hydrogen bonds
- Hydrophobic and Hydrophilic interactions - in the water based environment of the cell, the protein will fold so that water is excluded from hydrophobic regions (e.g. in the centre of the structure), with hydrophilic regions facing outwards in contact with water.
When more than one polypeptide chain join forces for a common cause, quaternary structure is born. This can be two identical polypeptides joining together, or several different polypeptides. This term also applies to polypeptide chains joining with an inorganic component, such as the haem group. These proteins can only function when all subunits are present. The classic examples of proteins with quaternary structure are haemoglobin, collagen and insulin. These shapes allow these proteins to carry out their jobs in the body
- The haem groups in the quaternary structure of the haemoglobin molecule combine with oxygen to form oxyhaemoglobin. This is quite handy as the function of haemoglobin is to transport oxygen from the lungs to every cell in the body. The haem group is an example of a prosthetic group - an essential part of the protein that is not made of an amino acid
- Collagen is made up of three polypeptide chains wound around one another. This hugely increases the mechanical strength over that of a single polypeptide. Also quite useful as collagen is used to provide mechanical strength to a number of areas in the body (tendons, bones, cartilage, arteries). To further increase mechanical strength, several collagen molecules wrap around each other (and cross link with covalent bonds) to make fibrils. These fibrils then repeat this to make collagen fibres: think of the overall structure like a very sturdy rope.
What happens when you drop an egg into a hot frying pan? No - apart from spit fat at you!? It changes colour - this is an example of proteins denaturing. All through this hub it has been made clear that a proteins' shape (determined by its' primary structure, in turn determined by DNA sequences) is vital to its function - but this shape can be distorted.
Heating a protein increases the kinetic energy in the molecule (scientific term for movement energy). This can literally shake the delicate structure of the protein to pieces - remember, the bonds holding this structure in place are not covalent bonds, each one is quite weak. If so much heat is applied that the whole tertiary structure unravels, the protein is said to have been denatured. This is a one-way ticket: once an enzyme has been denatured, you cannot reform the original complex structure - even if you cool it again.
Heat is not the only thing that destroys proteins. Enzymes are perfectly suited to specific pH conditions. Enzymes working in the stomach can only work in acidic pH - if you put them in neutral, or in alkaline pH, they will denature. Enzymes in the intestine are optimised for alkaline conditions - place them in acidic or neutral conditions and they will denature.
Let's review: Protein structure in 60seconds
Where Next? Proteins
So you now know loads about proteins! But how did we find this out? That is easy: through crystallography. This site gives information on proteins and on the techniques used to study them
Gordon Brown on January 18, 2015:
There is bad grammar prevalent within the secondary structure part of the page. Please fix this!
Kate P from The North Woods, USA on October 16, 2012:
Hello! You just helped me understand something in my biochem study guide that I wasn't getting--thanks! Very easy to understand, and well described. Following..
Voted up, useful, and interesting.