Lecture notes
Amino acids and protein structure
Lecture notes summarising the main amino acids important for this module, protein structure and bonding.
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Proteins are one of the four major types of molecules The amino acids can be divided intoin cells and they contribute to the cell in many ways 4 main group
as: Group I – non-polar, hydrophobic
Enzymes amino acids (G,A,V,L,I,P,F,M,W)
Structural proteins Group II – polar, uncharged amino
Interacting with DNA to control of nucleic acids acids (S,C,T,Y,N,Q)
Lipid-bound proteins act as transport systems Group III – Acidic and negatively
Recognition of other molecules charged at physiological pH (D,E)
Group IV – Basic and positively
Certain proteins are All proteins are linear charged (R,H,K)
flexible and allow changes polymers and their
Glycine
in conformation, which monomeric unit is an
Shows no chirality as its R group is
allows other molecules to amino acid. There are
hydrogen. It adds flexibility to a
recognise their different 20 amino acids, each
molecule.
forms e.g if in the with a different R
Proline
presence of iron group.
Side chain loops to bond with the
Histidine amine group – the only cyclic amino
Found in many active sites due to its near neutral pKa and its imidazole side acid. Adds rigidity so used in e.g.
chain (3 carbons, 2 nitrogens in a ring) so it can function in acidic and basic collagen. Forms both Cis and Trans
catalysis. It can alter its charge, which is modified by other amino acids conformations that others can’t due
(Remember that amino acids join through peptide bonds.) to steric clashes.
Cysteine Amino acids
Contains a free thiol
(SH) group which allows and
Peptide protein
bonds have a partial double bond
shown via their intermediate bond length
Amino acids are zwitterionic
The carboxyl group loses its proton
it to form disulfide
bonds (via an oxidation
reaction) between 2 of
structure
between a C-N bond (1.49 Å) and a C=N (1.27
Å) at 1.32 Å. These single bonds allow for
first (pKa around 2), the dipolar
zwitterion is then maintained until
them. Found in active rotation but not all rotations are available for around a pH of 9 when the amino
sites and covalent bond certain structures as shown in the group deprotonates.
is good at maintaining Ramachandran plot. Phi = angle between Those with aromatic side chains
structures. nitrogen and alpha carbon. Psi = angle often have a strong electronic
between alpha carbon and carbon of carboxyl absorption at 280nm.
group. These angles determine the path of the
All proteins have at
polypeptide chain and restrict available
least one domain but
conformations allowing folding to take place.
many have several
sections that fold
independently and Alpha helix Beta sheets
come together to form 1 polymer chain At least 2 chains
the main molecule, Helical Pleated sheets
these are called H-bonding is within H-bonding is
domains. the chain between chains
Heteromultimers Repeats every 5.4 Å 2-residue repeat
consist of several residue per turn = every 7.0 Å
different proteins 3.6
Homomultimers consist Average length 11 Average length 15
of two or more copies residues (globular) residues (globular)
of the same protein. C=O of nth residue C=O of I residue
Haemoglobin is a H-bonds to (n+4)th bonded to I +3 in a
heterotetramer as it is reverse turn
also formed of 4 All r-groups point Can be parallel of
separate proteins. outwards anti-parallel
e.g. myoglobin E.g. Concanavalin A
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