CAPE PROTEINS
Ms. Seejoor
AMINO ACIDS
o Contain a central carbon, a hydrogen, an amino group and a carboxylic
acid group
o Amphoteric
o Act as acids in basic medium
o Act as bases in acidic medium
o Form zwitterions in neutral medium (act as both acids and bases, overall
charge neutral)
o All are identical except for the R group
o The R group is largely hydrocarbon in composition
o Classified according to the nature of the R group
o Acidic/negative amino acids have a carboxylic acid group in their R
o Basic/positive amino acids have an amino group in their R
o Polar amino acids have an -OH group or an -NH group in their R
o Positive, negative and polar amino acids are hydrophilic amino
acids
o Non-polar/uncharged amino acids have a large hydrocarbon
component in their R
o The R group of nonpolar amino acids may be aliphatic (straight
chain or branched structures) or aromatic (ring structures)
o Non-polar amino acids are hydrophobic
o Condense to form dipeptides and polypeptides
o Condensation results in formation of a covalent (and therefore strong)
bond (the peptide bond)
o Formation of the peptide bond results in formation of the peptide group
o The peptide group consists of part of the carboxylic acid group from one
amino acid and part of the amino group of the other amino acid
PRIMARY STRUCTURE
o The primary structure is the sequence of amino acids in a polypeptide
chain, stabilised by peptide bonds between the carboxylic acid group and
the amino group of adjacent amino acids.
o Asp----Lys---Arg---Gly---Cys is an example of primary structure
o Asp---Lys---Arg---Gly---Cys---Glu---Trp---His is an example of a longer
primary structure
o Molecular weight varies from 5000 to more than 1 million
o Proteins with molecular weight of more than 36000 tend to be
composed of more than one polypeptide chain
o Condensation of amino acids occur at the ribosomes. The primary
structure is formed at the ribosomes
SECONDARY STRUCTURE
o The secondary structure of a protein is the regular arrangements (alpha
helix and beta pleated sheet) of sections of the polypeptide chain,
stabilised by hydrogen bonding between the peptide groups of the chain.
o Hydrogen bonds (and therefore secondary structure) are broken by high
temperatures and pH changes
o The size and charge of the R groups may sometimes prevent formation of
secondary structure in parts of the chain. These parts will show no
secondary structure and are said to be in random coil.
o Hydrogen bonds are formed between a peptide group and the fourth
peptide group down the chain
o Alpha helix:
o There are 3.6 amino acids in each turn of the helix
o R groups point outside, perpendicular to the main axis of the helix
o Each hydrogen bond is weak but the cumulative effect is strong
o The helix is flexible and elastic
o 3 or 7 helices may be twisted together to form a fibre, e.g. in hair
or wool
o Involves intrachain hydrogen bonding (bonding within one
polypeptide chain)
o Found commonly in proteins that are required to have precise 3D
shape and contour, e.g. keratin in hair, wool, claws, horns and
feathers
o Beta pleated sheet:
o Sections of the polypeptide chain are antiparallel to each other
o R groups project above and below the chain, forming a zig zag
pattern
o Peptide groups are hydrogen bonded to peptide groups of the
adjacent antiparallel strand
o Flexible and inelastic
o Occurs less commonly than alpha helices
o Common in proteins requiring strength, e.g. fibroin in silk
TERTIARY STRUCTURE
o Tertiary structure is the three-dimensional shape of a polypeptide chain,
stabilised by intrachain bonding (hydrogen, ionic, hydrophobic
interactions and disulphide bonds) among the R groups
o The diversity of R groups in a polypeptide chain allow the diversity of
bonds in the tertiary structure
o The polypeptide folds such that hydrophobic R groups are within the
structure and the hydrophilic R groups are on the outside (where they
are exposed to the aqueous environment)
o Proteins showing tertiary structure are described as globular
o Proteins showing tertiary structure are water soluble, since hydrophilic R
groups are exposed to the solvent water and the hydrophobic R groups
are tucked away inside the polypeptide
o Responsible for maintaining the three dimensional shape of the active
sites of enzymes
o Tertiary structure can be disrupted by breaking the bonds among the R
groups
o pH changes break ionic bonds
o high temperatures and pH changes break hydrogen bonds
o reducing agents break disulphide bonds
QUATERNARY STRUCTURE
o Quaternary structure is the three-dimensional arrangement of the
constituent polypeptide chains of an oligomeric protein, and is stabilised
by interchain bonding (hydrogen, ionic, hydrophobic interactions and
disulphide bonds) among the R groups
o A small amount of hydrophobic interactions occur (since the
hydrophobic groups are tucked away in the interior of the tertiary
structure
o Quaternary structure can be disrupted by breaking the bonds among the
R groups
o pH changes break ionic bonds
o high temperatures and pH changes break hydrogen bonds
o reducing agents break disulphide bonds
homework:
compare fibrous and globular proteins
compare collagen, haemoglobin
