Protein Structure and Physics
What I will talk about today…
-Outline protein synthesis and explain the basic steps
involved.
-Go over the Chemistry of a peptide bond
-Define and exemplify a secondary structure of a
protein.
-Define a Protein motif and relate structure to
function.
-The protein folding “problem” and why it has
become one of the most basic intellectual
challenges in Molecular Biology.
Protein Synthesis
• Proteins are macromolecules
(heteropolymers) made up from
20 different L-a-amino acids,
also referred to as residues
• Two amino acids are combined
in a condensation reaction.
• The sequence of the different
amino acids is considered the
primary structure of the
peptide or protein.
How is the primary structure of a protein determined
in the first place?
• DNA is transcribed
into mRNA which is
then translated into
protein.
• A codon is a sequence
of 3 nucleotide bases
that codes for 1 amino
acid.
• The “genetic code” tells us (based on the sequence of the
mRNA) what the sequence of amino acids will be within
the protein.
Back to primary structure…
• Now that we understand how
the sequence of amino acids is
determined here is how the
amino acids are linked together.
• A bond between two amino
acids is called a peptide bond.
Protein Secondary Structure
• Once the primary structure
has been established it is
referred to as the “backbone”
of the protein.
• The secondary structure can
be defined as the regular,
repeated patters of folding of
the protein backbone. The
two most common folding
patterns are the alpha helix
and the beta sheet.
• Patterns result from regular
hydrogen bond patterns of
backbone atoms.
A Protein Motif
• Secondary structure
elements of a protein are
connected together to
form protein motifs.
• An example of a protein
motif is calmodulin.
• The shape of the molecule
allows calmodulin to
recognize and bind
calcium.
• A similar motif is found in
Parvalbumin (a muscle
protein that also binds
calcium).
Physics and molecular biology
• Proteins recognize
thousands of molecules
within the cell through 3D
interactions.
• Understanding biological
functions of a protein
requires knowledge of the
structure.
• The structure of the protein
cannot be predicted by
simply looking at the amino
acid sequence.
W.L. Bragg won the
nobel prize in physics in
1915 for the first crystal
structure analysis using x
rays.
To Review…
• The amino acid sequence of a
given protein is translated from
mRNA and is inferred by the
genetic code.
• Each protein has its own
specific primary, secondary and
tertiary structure and the
structure of the protein
determines its function within
the cell.
• Present day biology relies
enormously on tools that have
been largely developed by
physicists (protein
crystallography experiments)