Critical Thinking

It an amide bond is situated on both

It
is formed between two amino acids when an amide bond is situated on both sides
by carbon atoms. Peptide bonds show how the electrons are distributed between
atoms because of their differences in hybridizations in their bonding orbitals
and the polarity of atoms. If the peptide group consists any of these four
atoms, two are more electronegative (O and N) and two of them should be less
electronegative atoms (C and H) then we can say the structure is in resonance. Thus,
it forms double bond partially with an intermediate bond length. Polypeptide
chains which are across the bond can be in two forms cis and trans. Additional
consequences are added to the polypeptide structure when peptide bond has
planarity.

Bond Rotation and it’s
Restrictions

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There
are some restricted and free rotations in peptide bonds. These two rotations
play a pivotal role for the polypeptide structure. On the Ramachandran plot we
can see G space for each amino acid. Restrictions are reserved for some
branched residues and for the G space only little fraction is allowed. Between
the helix and strand region there is an energy barrier. Most of the residues
are allowed in both these regions but also the conversion is restricted between
helical and strand region. In large cases planarity is slightly deviated into
fractions from the peptide bond. Angles of peptide bond effect enlarging the
space for G space and it reduces the strand barrier. In protein structures,
some residues are tending to have polar residues which are small, and they are
outside the allowed regions.

Secondary
Structures

Steric
hinderance between the backbone and side chain is due to the restrictions on G
space. And that’s how helical and strand regions are originated in secondary
structures. No sequence dependence is allowed on the two regions because g
restrictions are more happened in between the residues not within each separately.
These secondary structures are favorable for the chain under all conditions and
they are independent about bonding. Helix is having spring structure and it is
right handed. Opposite charges get neutralize in the middle of helix when pitch
and dimensions of the helix bring dipole moments of peptide residues into
proximity. But the peptide dipole cannot be neutralized at the ends and they
result in net helix macrodipole. Maybe these charges get neutralized by side
chains which are nearer. When amide proton is brought into the proximity by
pitch and dimensional helix hydrogen bond is formed with carbonyl oxygen of
residue. Helical segments are in the central part not at the end when peptide
group hydrogen bonds are satisfied. But the structure is saying that all the
hydrogen bond acceptors and donors are highly populated in helical segments of
proteins. G restriction plays a role in helical confirmation by enhancing the
concentrations of acceptors and donors.

Strands are also
important in these secondary protein structures. In this structures dipole
moment is altered because these structures are extended. G space is larger than
the G steric hinderance because it is reduced in the strand region. Unlike
helical structures the hydrogen bond donors and acceptors are not satisfied but
they have an independent existence. These strand segments can also come from
the distant segments of the chain. And these sheets can occur only in one
strand and they have parallel and antiparallel mixture of the two strands. Thus,
when forming hairpin structure chain structures and residues which are distinct
brought at the ends of N and C terminals. So, this may be the reason strand
sheet can be called as tertiary structure

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