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PROTEIN STRUCTURE
BIOCHEMISTRY

Biological Functions
1
...
Transport and storage
Many small molecules and ions are
transported by specific proteins
eg Haemoglobin transports oxygen
Ion is stored in the liver as ferritin
3
...
Mechanical support
Tensile strength of the skin and bone is due to the
presence of collagen
5
...
Generation and transmission of nerve impulses
Receptor proteins play a role in transmission of
impulses
7
...


• The convention for the designation of the order
of amino acids is that:
• The N-terminal end (i
...
the end bearing the
residue with the free α-amino group) is to the
left (and the number 1 amino acid) and the Cterminal end (i
...
the end with the residue
containing a free α-carboxyl group) is to the
right
...


• The first amino acid contributes to the peptide
group its cabonyl carbon (C1), a-carbon
(alpha 1) and the carbonyl oxygen
(Oxygen)
...


• It is the partial double-bond character of the
peptide bond that defines the conformations a
polypeptide chain may assume
...
This means that the atoms get
in the way of each other
...


• However, the cis configuration can and does
naturally occur
...
Globular proteins are compactly folded
and coiled, whereas, fibrous proteins are more
filamentous or elongated
...


• It is a spiral structure
...


• The formation of the α-helix is spontaneous
...

• It is spaced four residues apart
...


• A complete turn of the helix contains an average
of 3
...
54 nm
• The R groups of each aminoacyl residue in an α
helix face outward

• e
...
the keratins- entirely α-helical

• Myoglobin- 80% helical
...

• The disruption of the helix is important as it
introduces additional folding of the polypeptide
backbone to allow the formation of globular
proteins
...

• The folding and alignment of stretches of the
polypeptide backbone aside one another to form
β-sheets is stabilized by H-bonding between
amide hydrogens and carbonyl oxygens
...

• β-sheets are said to be pleated in which the R
groups of adjacent residues point in opposite
directions
...


• In parallel sheets adjacent peptide chains
proceed in the same direction (i
...
the direction
of N-terminal to C-terminal ends is the same)
...


β-Bends & Loops
• Roughly half of the residues in a “typical”
globular protein reside in α helices and β sheets
• and half in loops,turns, bends, and other
extended conformational features
...


Tertiary Structure of Proteins
• Tertiary structure refers to the complete threedimensional structure of the polypeptide
units of a given protein
...

• Domain is the basic unit of structure and
function

• Tertiary structure describes the relationship of
different domains to one another within a
protein
...


• The interactions of different domains is
governed by several forces:
• These include hydrogen bonding, hydrophobic
interactions, electrostatic interactions and van
der Waals forces
...


DOMAINS:
• Polypeptide chains more than 200 amino acids
in length generally consists of two or more
domains
...


• Folding of the peptide chain within the domain
usually occurs independently of folding in other
domains
...
It is independent of
other domains
...


• The environment in which proteins are found
also contains the H-bond donors and acceptors
of the water molecule
...


Hydrophobic Forces:
• Proteins are composed of amino acids that
contain either hydrophilic or hydrophobic Rgroups
...


• The spontaneous folded state of globular
proteins is a balance between the opposing
energetics of H-bonding between hydrophilic Rgroups and the aqueous environment and the
repulsion from the aqueous environment by the
hydrophobic R-groups
...
This
driving force restricts the available
conformations into which a protein may fold
...

Typical charge-charge interactions that favor
protein folding are those between oppositely
charged R-groups such as K or R and D or E
...


Van der Waals Forces:
• There are both attractive and repulsive van der
Waals forces that control protein folding
...


• Repulsive van der Waals forces involve the
interactions that occur when uncharged nonbonded atoms come very close together
...


• Van der Waals forces are extremely weak,
relative to other forces, it is the huge number of
such interactions that occur in large protein
molecules that make them significant to the
folding of proteins
...


• The arrangement of these polypeptide
subunits is called the quaternary structure
of proteins
...


• Oligomeric proteins can be composed of
multiple identical polypeptide chains or multiple
distinct polypeptide chains
...
Proteins containing several
distinct polypeptide chains are termed heterooligomers
...


• Hemoglobin is, therefore, a hetero-oligomeric
protein
...

▫ A soluble protein that is normally secreted from the
cell is secreted in a misfolded state and converted into
an insoluble extracelluar amyloid fibre (amyloidosis)

65

• A misfolded brain protein (prion) seems to be the
causative agent of some degenerative brain disease such
as bovine spongiform encephalopathy (mad cow’s
disease)
• Prion protein is a normal constituent of brain tissue in
mammals and its function is unknown
• Illness occurs when normal prion is altered in
conformation
▫ There is progressive degeneration of the brain leading
to neurological symptoms -erratic behavior, problems
with posture, balance, coordination and loss of
cognitive function



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