Proteins are polymers of
amino acids joined by peptide bonds. They have a wide range of functions in the
body including; structures such as hair, channel proteins in the cell
membranes, antibodies in the immune system and enzymes that allow metabolic
reactions to occur at a higher rate. The amino acids are the monomers that
proteins are made up of, amino acids themselves are molecules that contain an
amine group, a carboxy group and a side chain known as the R group (Feher, 2016).
R groups differ depending on the amino acid. The sequence of different amino
acids is controlled by the sequence of nucleotides on the messenger RNA. In
translation, transfer RNA nucleotides carrying amino acids pair with their
complementary codons while ribosomes catalyse the formation of peptide bonds.
This is the primary structure of the protein. The R groups on the different amino
acids, of the same protein, interact with each other as they have different
properties, this causes the formation of structures. The main structures that
form are alpha helices and beta pleated sheets, this is the secondary
structure. The tertiary structure is the three-dimensional arrangement of the amino
acid in space, it forms due to the folding of the different regions of the
proteins into a stable structure (Feher, 2016). The protein may then interact
with other proteins forming the quaternary structure, this interaction can
change the tertiary shape of the protein and alter its function (Feher, 2016).

The tertiary structure of
a protein can be split into domains, these are chains of amino acids that are
able to fold independently to form stable three-dimensional structures. A
protein may have one or several domains, these are important for the function
of the protein (Branden and Tooze, 2009). The formation of these domains, and
therefore the tertiary structure, cannot be predicted from the primary
structure as we cannot see which amino acids will interact, and therefore fold,
to create the 3D structure. There are multiple interactions that can occur
between the R groups of the amino acids. One of these is a hydrophobic
interaction, this is where non-polar side chains are repelled by water
molecules. The hydrophobic amino acid side chains are then forced to cluster at
the centre of the protein, they are held together by van der Waals interactions
(Campbell et al, 2017). Further
stabilisation of the 3D structure occurs as hydrogen bonds forms between polar
molecules and ionic bonds form between charged side chains that are close to
each other (Campbell et al, 2017).
Another interaction that helps to strengthen the final structure are covalent
bonds, such as sulphide bridges. Cysteine amino acids contain a sulfhydryl
group which form a sulphide bridge with another cysteine sulfhydryl group, this
is a strong bond that holds part of the protein together (Campbell et al, 2017).

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To determine the
tertiary structure of the protein, techniques such as x-ray crystallography,
electron crystallography or nuclear magnetic resonance spectroscopy must be
used (Branden and Tooze, 2009). X-ray crystallography requires a pure protein
sample to be crystallised, as x-rays pass through the crystal they are
scattered and picked up by a digital detector (Campbell et al, 2017). The result is a pattern of spots that can be
processed by a computer to produce a 3D model (Campbell et al, 2017). This does not show the native hydrolysed form of the
protein as the crystal version is analysed. It is also difficult to determine
the exact 3D structure of proteins that are insoluble, such as membrane
proteins, as they cannot be easily crystallised (White, 2004). Nuclear magnetic
resonance spectroscopy requires a pure protein sample but does not crystallise
the protein. Instead, magnets are used to produce a 2D pattern of the chemical
shifts of a pure protein in solution (Wuthrich,1989). This information can then
be processed by a computer to produce the 3D structure; however, this method
produces a family of possible protein structures (Wuthrich,1989). Identifying
the structure allows us to see the mechanisms the protein uses for its function.The investigations of
Giannoglou et al tested the effect of
increasing pressure on the activity and structure of the enzyme X-prolyl
dipeptidyl aminopeptidase found in bacteria (Giannoglou et al. 2018). Some of their results are shown in fig. 1, this
conveys that at high temperatures and pressures the enzyme was inactive, an
analysis of the structure of the protein at these high temperatures and
pressures showed changes and eventual denaturing of the enzyme (Giannoglou et al. 2018). This demonstrates how the
3D structure of a protein, like an enzyme, allows it to perform its function
and how changing this structure causes it to no longer operate as it is
supposed to. However, there are examples of proteins that do not form a
tertiary structure and remain as non-globular chains of amino acids (Wright and
Dyson, 1999). All organisms seem to have a high proportion of these unfolded
proteins in their genomes many of which have regulatory functions (Wright and
Dyson, 1999). This indicates that, although the tertiary structure of a protein
is a key part of its function, it is not necessary for all biological
functions.

The tertiary
structure of a protein is, therefore, important for the function of the protein
and specificity, although there are some exceptions to this. The spontaneous
folding into domains creates the stable 3D structure enabling interactions
between the amino acids and putting amino acids in the correct positions to
interact with a substrate or molecule. Research has shown that changing the
structure of the protein impedes its activity so that it can no longer perform
its function. This supports how important the 3D structure is to its function. 

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