protein
many protein characteristics depend on orientation of the protein’s molecules
Hierarchy
tertiary structure
quaternary structure
secondary structure
primary structure
the exact and unique sequence of the amino acid residues specified by genetic info
all peptides start with an amino group and end with a carboxylic acid group
the amino acid residue with
free amino group is referred to as the N-terminus residue or the amino end
free carboxylic acid group is referred to as the C-terminus residue or the carboxyl end
general three-dimensional forms of local segments of proteins
both types of structures are stabilized by hydrogen bond which form bridges between an amide hydrogen on the backbone of one peptide residue and a carbonyl oxygen on another residue
these hydrogen bonds do not involve the side chains; the side chains in a particular secondary structure could be involved in hydrogen bonding with other side chains of another structure
the chain of covalently linked amino acids is organized by forming regularly repeating patterns like designs in a tapestry
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-helix
a rigid, rodlike structure forming when polypeptide chains twists into a right-handed helical conformation
in the -helix, the residues twist in such a way that the backbone forms a shape resembling a coiled spring
the helical shape is maintained by H-bonds between backbone – C=O and -NH groups
coiling enables a carbonyl oxygen to be near a highly polar -NH bond
increased electrostatic attraction between the H of the amino group, and the nearby carbonyl O, results in hydrogen-bonding
backbone of H-bonds → between peptide bond of -C=O of i residue & -NH of i+4 residue
this is the electrostatic force that stabilizes the -helix
H -bonds are between the peptide units and do not involve the side chains which are directed away from the center axis of the helix
certain amino acids can’t form -helix → e.g. Gly, Pro, Glu, Asp, Trp
other characteristics
3.6 residues per turn and a pitch of 0.54 nm/turn
contains ~12 residues
right -handed twist (with L-amino acids)
-pleated sheet
in -pleated sheet, the peptide strands or sheets are arranged side by side; fully extended
each strand or sheet consisting of amino acid residues arranged in a zig-zag fashion
the surface of the resulting structure resembles material folded into many pleats
the H -bonds between the amide hydrogen of a chain and the carbonyl oxygen of adjacent chain, act somewhat like "staples" in much the same manner as in the -helix
these "staples" strengthen the resulting structure
2 types:
parallel → neighbouring polypeptide chains are in the same direction; less stable
anti-parallel → neighbouring polypeptide chains are in opposite direction; stable
groups of -helices and/or -sheets fold further and cross -link with one another to form a stable three-dimensional shape (include the supersecondary structures and domains)
e.g. myoglobin consists mainly of alpha helical segments which turn and fold into one another forming an extremely compact and almost spherical shape
interactions between side chains contribute to the stability of tertiary structures
four types of such interactions:
hydrogen bonding
hydrophobic interactions
electronic interactions → e.g. salt bridge
covalent bonding
several of these interactions often work together to stabilize the three-dimensional structure of a protein
e.g. disulfide bridges
sulfhydryl group of Cys undergo reversible oxidation forming a disulfide (i.e. -S-S- chain) → cystine
can occur in a single chain to form a ring or between 2 separate chains to form an intermolecular bridge
a fourth level of organization exists for proteins with more than one chain
the forces that stabilize a protein's quaternary structure are exactly the same four forces that stabilize its tertiary structure, the difference is that, in this case, the forces are between the chains
e.g. hemoglobin molecule is a tetramer; that is, it consists of four chains
Denaturation
disruption of protein’s native conformation → denaturation
denatured protein may partially or completely loses its biological activity
denaturing conditions: strong acids/bases, organic solvents, detergents, reducing agents, salt concentrations, heavy metal ions, temperature changes, mechanical stress
can regain native conformation → renaturation
Types
fibrous protein
globular protein
e.g.: collagen, keratin, fibroin
hard, long (static) & fibrous; insoluble in water
compact, folded, soluble in water, groove
e.g.: haemoglobin, enzyme, antibody
amino acid determines protein’s characteristic, structure and function based on
its number
chemical characteristics
chain sequence