4-4 SECONDARY STRUCTURE
The  Helix

Proposed in 1950 by Linus Pauling and Robert Corey, and supported by Max Perutz.
o Pauling and Corey’s model accounted for a major repeat observed in the structure
of the fibrous protein –keratin. This was the __________ (axial distance per
turn) of the -helix, and the repeat occurs on average every 0.54 nm.
o Perutz observed a secondary repeating unit every 0.15 nm while studying the Xray diffraction pattern, which was the __________ of the –helix. This refers to
the distance each _______________ advances the helix along its axis. Perutz also
showed that the –helix was present in hemoglobin.

The –Helix Structure
o The –helix can be either __________-handed or __________-handed. The –
helices found in proteins are almost always __________-handed.
o Each carbonyl oxygen is _______________-bonded to the backbone amide
hydrogen of the fourth residue toward the C-terminus. This “locks in” the and
 angles, giving the –helix a regular, _______________ structure.
o The cumulative effect of __________ hydrogen bonds within an –helix provides
structural stability.
o The __________-chains of the amino acids point _______________ from the
cylinder of the –helix. The side chains affect the _______________ of the –
helix. Most –helices have _______________ amino acids on one side and
_______________ amino acids on the other side, giving it _______________
character. This allows the hydrophilic end to remain on the _______________
and the hydrophobic end to remain in the _______________ of the protein.
o
Many times two amphipathic –helices wrap around each other (called a leucine
_______________). An example is GCN4 protein which binds to _____ for
transcription.
-Strands and -Sheets

-Strands are portions of the polypeptide chain that are almost fully _______________,
each strand has an average of _____ amino acid residues, where each residue accounts
for 0.32 to 0.34 nm of the overall length.

-strands that are arranged __________-_____-__________ form -sheets, a structure
originally proposed by Pauling and Corey when studying -helices. A -sheet can
contain between two and fifteen -strands.

-sheets are stabilized by _______________ bonds between carbonyl oxygens and amide
hydrogens on adjacent -strands.

Like -helices, -sheets that are hydrophobic cluster in the _______________ and those
that are hydrophilic cluster on the _______________ of proteins.
Parallel -sheet
Antiparallel -sheets

The diagram to the right shows a number of structural properties of -sheets:
1. -sheets have a __________ to them, and are usually
distorted and buckled.
2. The side-chains of amino acids in -sheets
protrude _______________.
3. The and  angles exhibit a __________ range of values than
those seen in -helices.
4. One side of the sheet may be hydrophobic, and the other side
hydrophilic, making it possible to make -_______________,
one of the arrangements of secondary structure.
Loops and Turns

-helices and -strands contain consecutive residues that have a similar conformation
that is repeated throughout the structure. Proteins also contain stretches of _____repeating structure – these are called _________ and __________, and cause
_______________ changes in the polypeptide backbone.

Loops and turns connect -helices and -strands, allowing the polypeptide chain to
__________ back on itself, producing the compact 3D shape seen in the native structure.

Loops often contain hydrophilic residues and are found on the __________ of proteins.

Loops that contain just a few residues (five or less) that cause an abrupt change in the
direction of a polypeptide chain are called __________.

Reverse turns – also called ___-turns because they usually connect different antiparallel
___-strands. They are stabilized by _______________-bonds.

Many turn structures are found in proteins.
They all have internal hydrogen bonds that
stabilize the structure. In many proteins, turns
make up a significant proportion of the structure.
Small amino acids like __________ allow and 
angles outside of the “permitted” regions because
there is less interference due to its small side chain.