Download MCD: Metabolism – Introduction to Protein Structure

MCD – Metabolism - Introduction to Protein Structure
By Dr. Mohammad
1. Outline the reaction by which amino acids are joined together.
Chirality
Anatomy of an Amino Acid
H
H
amino
group
N
C
H
The central C carbon atom is a chiral centre (from the
Greek, meaning "handed") i.e. it has four different
substituents bound to it.
O
carboxyl
group
C
mirror
OH
R
-carbon
side chain
C
R
Substitutions at the R position or side chain, give rise to
the 20 different amino acids e.g. R=CH3 in alanine.
The whole of the amino acid minus the side chains is known
as the backbone.
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H
H
NH2
COOH
L-enantiomer
H2N C
HOOC
R
This gives rise to optical
isomers (enantiomers) of
each amino acids each
of which is a mirror
image of the other.
D-enantiomer
Glycine (Gly) has no side chain (only an H atom)
and is therefore the only non-chiral amino acid.
Side chains can be polar of non-polar – this is vital to the properties of the protein
Eg.
proline – non polar
asparagine - polar
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They can also be acidic or basic eg. glutamic acid
The state of ionisation of an amino acid provides vital biological properties to
many proteins and enzymes, and for this reason cells cannot generally tolerate
wide changes in pH.
Consequently, If the ionisation state of key amino acids within a protein is altered,
a loss of biological activity often results.
The ability to take up and release protons gives amino acids some buffering
capacity to resist some changes in pH.
Individual amino acids are joined in condensation reactions (water is lost) to form
peptide chains.
2. Sketch a trimeric peptide, illustrating the amino -terminus, carboxyl terminus
and side chains.
Anatomy of a Peptide
peptide bond
amino
terminus
H
N
H
O
C
C
H
N
C
H
R2
O
C
OH
H
R1
carboxyl
terminus
side chains
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The polypeptide chain of a protein rarely forms a disordered structure (random
coil) as proteins generally have functions to fulfil, and these functions rely upon
specificity.
In turn, functionality requires a definite 3D structure or conformation of the
polypeptide chain.
Proteins generally possess a degree of flexibility necessary for function e.g.
muscle fibres
3. Give examples of the post translation modifications of amino acids, with
reference to glycosylation, hydroxylation and carboxylation.
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Even after synthesis, (post translation), the starting set of 20 amino acids can be
modified to create novel amino acids, enhancing the capabilities of the protein.
Proline can be modified to produce hydroxyproline e.g. collagen fibres, a major
constituent of skin, cartilage, teeth & bones.
These additional hydroxyl groups help to stabilise the fibres.
The addition of sugar residues to the asparagine residues of proteins (N-linked
glycosylation) increases their solubility and also protects them from enzymatic
degradation.
Deficiency of N-linked sugar chain transfer is detected in congenital
carbohydrate-deficient glycoprotein (CGD) syndrome which affects multiple
tissues and has life threatening complications.
Similarly, g-carboxyglutamate is produced by the carboxylation of glutamate.
The formation of g-carboxyglutamate residues within several proteins of the blood
clotting cascade (e.g. factor IX) is critical for their normal function by increasing
their calcium binding capabilities.
The anticoagulant warfarin works by inhibiting the carboxylation reaction.
4. Understand the concepts of primary structure, secondary structure, tertiary
structure & quaternary structure with respect to proteins.
Folding of Proteins
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Proteins generally fold into a single conformation of lowest energy.
This can occur spontaneous or involve other molecules known as chaperones,
which bind to the partly folded polypeptide chain and ensure that the folding
continues along the most energetically favourable pathway.
By breaking the bonds that hold the protein together, we can denature the protein
into the original flexible polypeptide.
Common denaturants used within the laboratory are urea (breaks hydrogen bonds)
and 2-mercaptoethanol (breaks disulphide bonds).
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Primary structure is the linear sequence of amino acids that make up the protein.
Secondary structure is defined as local structural motifs within a protein, e.g. αhelices and β-pleated sheets.
Tertiary structure is the arrangement of the secondary structure motifs into
compact domains.
Quaternary structure is the three dimensional structure of a multimeric protein
composed of several subunits
5. Distinguish between a α-helix and a ß-pleated sheet and appreciate the bonds
that stabilise their formation.
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Neutralisation of the polar groups in amino acids is achieved by their hydrogen
bonding to each other in one of two regular structures – α helix and β pleated
sheet.
The α helix
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Hydrogen Bonds between the C=O of one residue and the N-H of another residue,
4 amino acids along the helix, stabilise the entire structure.
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The side chains of individual amino acids project out from within the a –helix.
Although theoretically helices can be either right-handed or left handed, the usage
of L-amino acids in proteins means that right-handed helices are favoured.
In proline, the last atom of the side chain is bonded to the main chain N atom.
This prevents the N atom from hydrogen bonding with the C=O groups of another
residue within the helix, thereby distorting the helical conformation, putting a
‘kink’ into it.
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The β pleated sheet
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As with the alpha helix, hydrogen bonds between the N-H and C=O groups of two
or more b-strands hold the b -pleated sheet sheet together.
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In the b-pleated sheet, the NH and C=O groups point out at right angles to the line
of the backbone. This almost two dimensional sheet is pleated, like the bellows of
an accordion.
Alternate b -strands can run in the same direction to give a parallel b-pleated sheet
or in opposite directions to give an antiparallel b -pleated sheet.
The pleating in each case allows for the best alignment of the hydrogen bonded
groups.
6. Appreciate the different types of bond that combine to stabilise a particular
protein conformation.
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Covalent bonds (in which two atoms share electrons) are the strongest bonds
within protein and exist in the primary structure itself. Covalent bonds can also
exist as disulphide bridges. These occur when cysteine side chains within a
protein are oxidised resulting in a covalent link between the two amino acids.
Hydrogen Bonds occur when two atoms bearing partial negative charges share a
partially positively charged hydrogen, the atoms are engaged in a hydrogen bond
(H-bond).
Ionic interactions arise form the electrostatic attraction between charged side
chains e.g. Glu, Asp, Lys and Arg. They are relatively strong bonds, particularly
when the ion pairs are within the protein interior and excluded from water.
Van der Waals Forces are transient, weak electrostatic attractions between two
atoms, due to the fluctuating electron cloud surrounding each atom which has a
temporary electric dipole. Although relatively weak and transient in nature,
because of the sheer number of these interactions within a protein, they can still
have a large part to say in the overall conformation of a protein.
Hydrophobic Interactions are a major force driving the folding of proteins into
their correct conformation. They juxtapose hydrophobic side chains by packing
them into the interior of the protein. This creates a hydrophobic core and a
hydrophilic surface to the majority of proteins
Summary
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Proteins are chains of amino acids linked by peptide bonds which have evolved to
fulfil specific functions within the cell.
Such functions are reliant upon the 3D structure or conformation of the protein
which is held together by a variety of forces.
The a-helix and b-pleated sheet are the two staple motifs that define the
conformation of a protein.
The nature of the amino acid side chain dictates its position within the
conformation of the protein.
Post-translational modifications of proteins add yet more diversity to protein
structure.
Dr. Mohammad A. R. Ismaiel
College for Science for Women / Babylon University