Download Protein Structure and Folding Simulation

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All amino acids have a common structure, but
differ in their R groups.
The asymmetric carbon must have the four
attachments in a particular order or isomers will
be formed
By holding hands you simulate a “dehydration synthesis
reaction” by linking the amine group of one amino acid
to the carboxyl of the second amino acid. The holding
of hands represents the “peptide bond”.
Points to understand:
The amino acids (students) can be arranged in any
order. Each different arrangement produces a new
The protein has a free amine end and a free carboxyl
end (students at each end with a free hand).
The structure is flexible and can bend and fold.
A typical polypeptide or protein often has hundreds of
amino acids.
The line of students is bent so that it forms a “U”
shape with one end of the line across from the
other end. The students formed a “beta pleated
sheet” structure from this configuration. By
alternating with their arms “up” or “down” to
create the pleated sheet. One side of the pleat
(arms up or arms down) can stretch across the
gap between the two lines so that the lines
come together at these points. Hydrogen bonds
between the two lines can be formed by
extending out the thumbs (or other fingers) and
“hooking” with the counterpart on the other line.
So arms up on one side
were the double bonded C
from the carboxyl end and
the arms down were the
hydrogen from the other
sides amine group (the up
and down are not relevant
– just for the simulation).
Points to understand:
The Hydrogen bonds form at regular intervals,
between the backbone components.
The Hydrogen bonds are “weak” compared to
the peptide bonds. *The number of the H bonds
in the entire structure does give strength to the
structure (so alone H are weak, a lot of them are
The Hydrogen bonds and the pleats create a
regular structure from the amino acid chain.
Note –can’t construct alpha helixes using
students, but can you visualize this structure?
Alpha helix
Note this is not
showing R groups
The line of students (primary structure) is bent at some
point so that two amino acids (students) are physically
near each other. A sulfur-sulfur bond between these two
students was created using a bungee cord. The “S”
hooks on the ends of the bungee cord hooked through
belt loops to join these two amino acids together.
Points to understand:
The “S” shaped hooks on the bungee cord represent
sulfur atoms. The tertiary structure is formed when two
sulfur atoms are joined bonded together by the strong
non-polar covalent bond.
S-S bonds form from the interactions between the side
chains – “R” groups.
The S-S bond is more rigid than Hydrogen bonds. This
gives the protein structure more rigidity and stability.
The size of the loops created by the S-S bonds depends
on the location of the sulfur containing amino acids
(primary structure).
Form two or more small polypeptide chains. The chains
can be positioned side by side or in other configurations.
A quaternary structure is formed when two or more
polypeptides come together to make the functional
Points to understand:
Two or more separate polypeptides are needed for
this level of protein structure.
Each polypeptide has its own primary, secondary and
tertiary structure. Often these levels of structures provide
the fit between the different polypeptides in forming the
functional protein.
Genetic conditions such as Thalasemia occur when the
polypeptide units are not produced in equal amounts.
The result is that one polypeptide chain lacks a sufficient
number of partners to form the final functional protein