Download Proteins have a higher order of folding known as tertiary structure

Proteins have a higher order of folding known as tertiary structure. The tertiary structure is a
description of the way the whole chain (including the secondary structural features) folds itself into a
3D shape. The structure is held in place by interactions between the side chains (R groups) of the
amino acids which made up the primary structure.
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Amino acids such as aspartic acid or glutamic acid
contain a carboxylic acid in their side chain. This can lose
a proton to give a negatively charged COO-.
Lysine, for example, contains a positively charged NH3+
group.
If the protein folds in a suitable manner, these oppositely
charged groups are able to form an ionic bond.
Aspartic acid
residue
Ionic bond
Lysine residue
Polypeptide backbone
Serine residue
H-bond
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Asparagine
residue
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You should know that hydrogen bonds between the polypeptide
backbone are responsible for maintaining a protein’s secondary
structure.
However, many amino acids have side chains which contain a
hydrogen atom attached to an oxygen or nitrogen, and can
therefore form hydrogen bonds.
For example, serine contains an OH group while asparagine
contains an amide. The diagram shows how these R groups can
form a hydrogen bond.
Several amino acids (including leucine, valine, and phenylalanine)
have non-polar hydrophobic side chains which contain just carbon
and hydrogen atoms.
Two of these groups brought close to each other will both repel
water and other polar groups, resulting in an overall attraction to
each other.
Hydrophobic
stacking
Phenylalanine
residues
Disulfide bridge
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Cysteine residues
If two cysteine residues are near to each
other, they can react to form a covalent
bond known as a disulfide bridge.
The quaternary structure of a protein is a way of describing how multiple polypeptide subunits come
together and arrange themselves. The interactions which hold the structure in place are the same as
those for tertiary structure – however now these interactions are inter-chain (between two different
chains) rather than intra-chain (between residues of the same chain).
Some quaternary structures are
made up of two or more identical
chains.
For example, HIV Protease (PDBe
entry 4je2) exists as a dimer – two
subunits of the same protein.
Chain A (shown in blue) and chain
B (shown in green) are identical –
both have exactly the same
primary structure (amino acid
sequence).
The two chains brought together
give the protein its quaternary
structure.
Other quaternary structures are made
up of two or more non-identical
chains.
An example of this type of structure is
haemoglobin (PDBe entry 2m6z).
There is a pair of α-subunits (shown in
blue) and a pair of β-subunits (shown
in yellow). The overall arrangement of
chains is roughly tetrahedral.
Each subunit binds a heme ligand
which contains an iron ion (Fe2+).
These Fe2+ ions allow oxygen binding,
so haemoglobin can carry out its
function of oxygen transport.
Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.