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The formation of a peptide bond between glycine
and alanine is shown in Figure 5.8. The product is
called dipeptide, the reaction can be
eliminated a water molecule.
E
G
A
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The portion of each amino acids remaining in
the chain is called an amino acid residue
Chains containing a few amino acid residues
are collectively referred to as oligopeptides.
If the chain is very long, it is called a
polypeptide. Oligopeptides and polypeptides
are formed by polymerization of amino acids
via peptide bonds
In writing the sequence of an oligopeptide or
polypeptide that the convention is to always
write the N-terminal amino acid (the residue
has a free α-amino group) to the left, and the
C-terminal to the right. (the residue has a free
α-carboxyl group)
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Large peptide chain. Protein polypeptide
chain are typically more than 100 amino acid
residue. All proteins are polypeptides. This is
why understanding the nature of polypeptides
and the peptide bond is so important a part of
biochemistry.
Small peptide chains are common and often
have important biologic roles. For example the
hormone glucagon has 29 residues, vasopressin
has 9 residue and thyrotropin- releasing
hormone has 3 residue
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CONFORMATION OF PROTEINS
Every protein in its native state has a unique threedimentional structure, which referred to as its
conformation.
The function of a protein arises from its
conformation.
Protein structures can be classified into four levels
of organization : primary, secondary, tertiary, and
quartenary.
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 The primary structure is the covalent
“backbone” of the polypeptide formed by the
specific sequence. This sequence is coded for by
DNA and determines the final three dimensional
from adopted by the protein in its native state
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
The secondary structure is the spatial
relationships of neighboring amino acid residue.
1.
Secondary structure is dictated by primary
structure. The secondary structure arises from
interactions of neighboring amino acids. Because
DNA –coded primary sequence dictated which amino
acids are near each other, secondary structure often
form as the peptide chain comes off the ribosome.
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2. Hydrogen bonds, these formation very
important characteristic of secondary
structure, (H-bond) between the CO- group
of one peptide bond and the –NH group of
another nearby peptide bond.
(a). If the H-bonds form between peptide bonds in
the same chain, either helical structure such as
the α-helix develop or turn such as β-turns are
formed.
(b). If the H-bonds form between peptide bonds in
different chains, extended structures form, such
as the β-pleated sheet.
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3. The α-helix is rod like structure with the
peptide bond coiled tightly inside and the side
chain of the residue protruding outward.
(a). Characteristics
(1.) Each –CO is hydrogen-bonded to the –NH of
a peptide bond that is four residues away
from it along the same chain
2.) There are 3.6 amino acid residue per turn of
the helix, and the helix is right-handed (turn
in a clockwise around the axis)
(b). Helical structures in proteins were predicted by
Linus Pauling from his studies of fibrous proteins.
However, the α-helix can also be important in the
structure globular proteins, although those chains are
much shorter than the chains in fibrous proteins
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-Sheet
-Helix
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 Tertiary structure refers to the spatial
relationships of more distant residues
1. Folding. The secondary ordered polypeptide
chains of soluble proteins tend to fold into globular
structure with the hydrophobic side chain in the
interior of the structure away from the water and
the hydrophilic side chains on the outside in contact
with water. This folding is due to associations
between segments α-helix, extended β-chains, or
other secondary structures and represent a state of
lowest energy (greatest stability)
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2. The conformation result from:
a. Hydrogen bonding within a chain or between chains
b. The flexibility of the chain at points of instability,
allowing water to obtain maximum entropy and thus
govern the structure to some extent
c. The formation of other non covalent bonds between
side chain groups, such as salt linkages, or ηelectron interaction of aromatic rings
d. The sites and numbers of disulfide bridges between
Cys residues within the chain
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 Quartenary structure refers to the spatial
relationships between individual polypeptide
chains in a multi chain protein; that is, the
characteristic noncovalent interaction between the
chains that form the native conformation of the
protein as well as occasional disulfide bonds
between the chains
1. Many proteins larger than 50 kdal have more than
one chain and are said to contain multiple subunits,
with individual chains known as protomers.
2. Many multisubunit proteins are composed of different
kinds of functional subunits.
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Denaturation
 Denaturation is the organization of the overall
molecular shape of a protein. It can occur as an
unfolding of uncoiling of helices, or as separation of
subunits.
 Denaturation is usually is accompanied by a major
loss in solubility.
 Several reagents or physical force like heat, UV
radiation, shaking, ethanol, heavy metals, and strong
acids and bases that cause denaturation.
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denaturation
renaturation
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 The gene-encoded primary structure of
polypeptide is the sequence of its
amino acids. Primary structure are
stabilized by covalent peptide bonds.
 Its secondary structure results from
folding of polypeptide into hydrogenbonded motifs can form
supersecondary motifs. Secondary
structure (higher orders) are stabilized
by weak force-multiple hydrogen bond,
electrostatic bond (salt bond), and
association of hydrophobic R groups.
 Tertiary structure concern the
relationships between secondary
structure domains.
 Quartenary structure of proteins with
two or more polypeptides (oligometric
proteins) is a feature based on the
spatial relationships between various
types of polypeptide
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