Protein Primary Structure
The primary structure of a protein is its amino acid sequence. Each protein has a unique amino acid sequence, and the unique order in which the amino acids are linked together determined the higher levels of structural organization. The primary structure of the α-subunit of human hemoglobin is shown below.
Q1.
What are the
first 10 amino acids in this polypeptide chain? What are the three
letter codes for these amino acids?
Protein
Secondary Structure
In most cases the polypeptide chain of a protein does not exist as
an extended chain of amino acids. Instead amino acids adjacent to
one another interact to form segments with defined structure. These
local structural elements comprise the secondary
structure of a protein. The most
common secondary structure elements are the α-helix and the
β-pleated sheet. The α-helix and the β-pleated
sheet are regular
secondary
structure elements since the Φ and Ψ angles within each
element remains the same (or almost the same). Some segments do not
have similar Φ and Ψ angles for all amino acids in the
segment. Such segments are sometimes referred to as random coil
regions. Random coil does not (necessarily) mean that the amino
acids within this region take on random conformations from protein
to protein (i.e. that the segment is highly flexible). Rather,
random coil implies dissimilar Φ and Ψ angles within the
segment.
into the JMol window (left). The molecule is shown using
the 'cartoon' rendering scheme and is colored to show the various
secondary structure elements. Rotate the molecule around and
observe the distribution of secondary structures in the
α-subunit of human hemoglobin.
residues 53-71. It can be seen that these 19 residues
interact with each other to form an α-helical secondary
structure element. Similarly each of the other secondary structure
elements present in the protein is composed of residues that are
adjacent to each other in sequence.
The α-subunit of human hemoglobin is a predominantly
helical protein.
on the other hand is an example of a protein with both
helical and sheet secondary structures. The molecule is colored to
show the various secondary structure elements. Rotate the molecule
around and familiarize your self with the protein and its
structure.
Q2. How many β-sheets does bovine
ribonuclease have? How many β-strands are present in each of
these sheets?
Let's examine
two strands of the first sheet.
(1). Notice that, although the two strands highlighted in blue
are part of the same sheet, and lie next to each other, they are
formed from residues that are quite far apart in the protein
sequence. 35-36 residues separate the two β-strands. Although
the two β-strands are located in different areas of the
protein each strand is composed
of residues that lie adjacent to each other
(and thus
conforms to the definition of a secondary structure element).
Q3.
What forces are
responsible for maintaining the structure of α-helices and
β-sheets?
Protein
Tertiary Structure
In
a protein secondary structures are not found isolated from each
other within an extended polypeptide chain. Instead secondary
structure element interacts with each other giving rise to a
compact and folded polypeptide chain. The relative orientation of
secondary structure elements with respect to each other determines
the overall three-dimensional shape of the polypeptide chain and is
unique to a given protein. This overall three-dimensional structure
of a protein, in which the relative orientations of all the
secondary structure elements are taken into consideration, is
called the tertiary
structure of the protein.
Rotate the model of ribonuclease and observe how the different
secondary structures interact with one another. This organization
represents the tertiary structure of ribonuclease and is conserved
in all ribonuclease proteins.
Reload the α-subunit of human hemoglobin (link above)
and observe its tertiary structure. Observe how the helices are
arranged with respect to each other.
Q4.
What forces are
responsible for maintaining the tertiary structure of
proteins?
Protein
Quaternary Structure
The functional entity of some proteins are composed of more than
one polypeptide chain. Human hemoglobin is such as example. The
functional hemoglobin molecule is composed of four individual
polypeptides chains, two of which are designated as α-chains
and two of which are designated β-chains.
Rotate the molecule around and observe the arrangement
and structure of the different chains.
The two -chains are identical to each other and the two -chains are
identical to each other. The -chains are similar in structure to
the -chains but are not identical. Each polypeptide chain is
referred to as a subunit of the protein. Thus hemoglobin has four
subunits. The number subunits and the manner in which they interact
with each other is described by the quaternary
structure of the protein.
Q4.
Which structural
levels are found in all proteins?