Professional Documents
Culture Documents
7.5
Proteins
Protein structure
! Primary structure
! Secondary structure
! Tertiary structure
! Quaternary structure
Primary structure
The primary level of protein structure is the unique sequence of amino acids held together by
peptide bonds in each polypeptide chain (Fig. 1). There are 20 amino acids and there many
be any number of these and they may be arranged in any order this means that that there is
effectively an infinite number of possible proteins. The order or sequence in which the amino
acids are arranged is determined by the nucleotide base sequence in the DNA of an organism.
Because every organism has its own DNA, every organism has its own unique proteins.
Simply put, the primary structure is a chain of amino acids attached by peptide bonds (CN
bonds), and there may be hundred of amino acids in these polypeptide chains (some repeated).
H O
H OH
The primary structure of a protein determines the next three levels of its organisation. Changing
one amino acid in the chain can completely alter the structure and function of the protein, for
example in sickle cell disease. In this condition, just one amino acid is changed in an otherwise
normal protein of red blood cells (haemoglobin). This is because the R group is changed, so R
group interaction at higher levels of structure is also changed. The result is that red blood cells
are unable to carry oxygen.
Secondary structure
This level of protein structure is created by the formation of hydrogen bonds between the
oxygen from the carboxyl group (COOH, in particular the oxygen in C=O) of one amino acid and
the hydrogen from the amino group (NH2, in particular a single hydrogen atom) of another.
~ 1~
Biology HL
7.5
Proteins
N.B.: !This is not R group interaction secondary structure is made by the formation of
! hydrogen bonds between the carboxyl and amino groups that are present in all
! amino acids, whereas the R group interaction is part of tertiary structure.
The two most common configurations of secondary structure are the -helix and the -pleated
sheet (Fig. 2, Fig. 3 and Fig. 4), and both have regular repeating patterns.
O H
At this point, R groups are not involved they are put on the outward side of -helices.
~ 2~
Biology HL
7.5
Proteins
H N C O
C H H N
O C C H
N H O C
H C N H
C O H C
H C O
N
C H H N
O C C H
N H O C
H C N H
C O H C
Hydrogen bond
Fig. 4: Chemical display of -pleat
structure
Tertiary structure
Tertiary structure is the overall three dimensional structure of the entire polypeptide. The
structure is formed by R group interaction. As there are many different R groups, there are many
ways in which the R groups can interact (or bond).
Quaternary Structure
Fig. 5: Visual Sausage model of
tertiary structure Quaternary structure is the three dimensional
structure of proteins that are composed of two or
more polypeptide
chains (called
subunits). Quaternary
structure may also
!
involve the binding of a
prosthetic (non-
polypeptide) group to
form a conjugated
protein.
Several polypeptide
chains interact to form
a single structure and
a functional protein.
These subunits are
held together by weak,
n o n - c o v a l e n t
interactions. Some
Prosthetic group proteins with
Fig. 6: Visual Sausage model of a quaternary structure
conjugated protein in quaternary structure
may include prosthetic or non-polypeptide groups. These proteins are called conjugated
proteins (Fig. 6).
Not all proteins consist of multiple polypeptide chains, so not all proteins have quaternary
structure. Collagen (mentioned earlier) is an example of a secondary structure protein, and has
no quaternary structure.
~ 4~
Biology HL
7.5
Proteins
Fibrous proteins are composed of many polypeptide chains in a long, narrow shape. They are
usually insoluble in water. One example is collagen, which plays a structural role in the
connective tissue of humans. Actin is another example. It is a major component of human
muscle and interacts with myosin to bring about muscle movement in animals.
Globular proteins are more three-dimensional in their shape and are mostly water soluble.
Haemoglobin, which delivers oxygen to body tissues, is one type of globular protein. The
hormone insulin is another globular protein.
Actual sequences may very slightly between Sequence highly specific and never varies
two examples of the same protein between two examples of the same protein
Polypeptide chains form long parallel strands Polypeptide chains folded into a spherical
shape
Length of chain may vary in two examples of Length always identical in two examples of
the same protein the same protein
Examples include collagen and keratin Examples include all enzymes, some
hormones (e.g. insulin) and haemoglobin
~ 5~
Biology HL
7.5
Proteins
Inorganic chemicals The ions of heavy metals such as Many enzymes are inhibited by
mercury and silver are highly being denatured in the presence
electropositive. They combine of certain ions, e.g. cytochrome
with COO- groups and disrupt oxidase (respiratory enzyme) in
ionic bonds. Similarly, highly inhibited by cyanide
electronegative ions, e.g. cyanide
(CN-) combine with NH3+ groups
and disrupt ionic bonds
Mechanical force Physical movement may break On stretching a hair, the hydrogen
hydrogen bonds bonds in the keratin helix are
broken. The helix is extended and
the hair stretches. If released, the
hair returns to its normal length. If,
however, it is wetted and then
dried under tension, it maintains
its new length the basis of hair
styling.
~ 6~
Biology HL
7.5
Proteins
Amino acids are often grouped according to the properties of their sidechains (R groups).
Amino acids with non-polar sidechains are hydrophobic. Non-polar amino acids are found in the
regions of proteins that are linked to the hydrophobic area of the cell membrane.
Polar amino acids have hydrophilic properties, and they are found in regions of proteins that are
exposed to water. Membrane proteins include polar amino acids towards the interior and
exterior of the membrane. These amino acids create hydrophilic channels in proteins through
which polar substances can move.
Polar and non-polar amino acids are important in determining the specificity of a enzyme. Each
enzyme has a region called the active site. Only specific substrates can combine with particular
active sites. Combination is possible when fitting occurs. The fitting involves the general
shapes and polar properties of the substrate and of the amino acids exposed at the active site.
Functions of proteins
Function Example
Hormones Insulin: a hormone secreted by the pancreas that aids in maintaining the
blood-glucose levels vertebrates
Movement Actin and Myosin: proteins that interact to bring about muscle movement
in animals
Transport Haemoglobin: protein containing iron in its haem groups that transports
oxygen from the lungs to all parts of the body in vertebrates
~ 7~