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Primary Structure
Proteins are made up of polypeptide chains, which are amino acids joined together with peptide bonds. The
unique sequence of amino acids that make up a protein or polypeptide chain is called the Primary Structure.
Primary Structure: The unique sequence of amino acids that makes up a protein or polypeptide chain.
Peptide bonds are created by enzyme catalysed condensation reactions and broken down by enzyme
catalysed hydrolysis reactions. Breaking down proteins is important in many areas of the body, not merely in
digestion. For example, in hormone regulation, cells that are targeted by hormones contain enzymes to break
down those hormones. This stops their effects from being permanent and allows them to be controlled.
Secondary Structure
After synthesis, polypeptide chains are folded or pleated into different shapes, called their Secondary
Structure. Two common examples of secondary structures are Alpha Helices and Beta Pleated Sheets.
Secondary structure is held together by many Hydrogen bonds, overall giving the shape great stability.
Secondary Structure: The way in which the primary structure of a polypeptide chain folds.
Tertiary Structure
The final 3D structure of a protein is its Tertiary Structure, which pertains to the shaping of the secondary
structure. This may involve coiling or pleating, often with straight chains of amino acids in between.
Tertiary Structure: The final 3D structure of a protein, entailing the shaping of a secondary structure.
Disulphide Bonds - Where two Cysteine amino acids are found together, a strong double
bond (S=S) is formed between the Sulphur atoms within the Cysteine monomers.
Ionic Bonds - If two oppositely charged 'R' groups (+ve and -ve) are found close to each other,
and ionic bond forms between them.
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Globular - These tend to form ball-like structures where hydrophobic parts are towards the centre
and hydrophilic are towards the edges, which makes them water soluble. They usually have metabolic roles,for
example: enzymes in all organisms, plasma proteins and antibodies in mammals.
Fibrous - They proteins form long fibres and mostly consist of repeated sequences of amino acids
which are insoluble in water. They usually have structural roles, such as: Collagen in bone and cartilage, Keratin
in fingernails and hair.
Quaternary Structure
Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for
example, a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if
all subunits are present.
Quaternary Structure: The structure formed when two or more polypeptide chains join together, sometimes
with an inorganic component, to form a protein.
Haemoglobin is a water soluble globular protein which is composed of two polypeptide chains, two
polypeptide chains and an inorganic prosthetic haem group. Its function is to carry oxygen around in the blood, and
it is facilitated in doing so by the presence of the haem group which contains a Fe2+ ion, onto which the oxygen
molecules can bind.
Collagen is a fibrous protein consisting of three polypeptide chains wound around each other. Each of the
three chains is a coil itself. Hydrogen bonds form between these coils, which are around 1000 amino acids in length,
which gives the structure strength. This is important given collagen's role, as structural protein. This strength is
increased by the fact that collagen molecules form further chains with other collagen molecules and form Covalent
Cross Links with each other, which are staggered along the molecules to further increase stability. Collagen
molecules wrapped around each other form Collagen Fibrils which themselves form Collagen Fibres.
Prevents blood that is being pumped at high pressure from bursting the walls of arteries
Amino Acid Constituents - Haemoglobin contains a wide range of amino acids while Collagen
has 35% of it primary structure made up of Glycine
Prosthetic Group - Haemoglobin contains a haem prosthetic group while Collagen doesn't
possess a prosthetic group
Tertiary Structure - Much of the Haemoglobin molecule is wound into helices while much of
the Collagen molecule is made up of left handed helix structures
Proteins are polymers of amino acids covalently linked through peptide bonds into a
chain. Within and outside of cells, proteins serve a myriad of functions, including
structural roles (cytoskeleton), as catalysts (enzymes), transporter to ferry ions and
molecules across membranes, and hormones to name just a few.
With few exceptions, biotechnology is about understanding, modifying and
ultimately exploiting proteins for new and useful purposes. To accomplish these
goals, one would like to have a firm grasp of protein structure and how structure relates
to function. This goal is, of course, much easier to articulate than to realize! The
objective of this brief review is to summarize only the fundamental concepts of protein
structure.
Amino Acids
Proteins are polymers of amino acids joined together by peptide bonds. There are 20
different amino acids that make up essentially all proteins on earth. Each of these amino
acids has a fundamental design composed of a central carbon (also called the alpha
carbon) bonded to:
a hydrogen
a carboxyl group
an amino group
Thus, the characteristic that distinguishes one amino acid from another is its unique
side chain, and it is the side chain that dictates an amino acids chemical
properties. Examples of three amino acids are shown below, and structures of all 20 are
available. Note that the amino acids are shown with the amino and carboxyl groups
ionized, as they are at physiologic pH.
Except for glycine, which has a hydrogen as its R-group, there is asymmetry about the
alpha carbon in all amino acids. Because of this, all amino acids except glycine can exist
in either of two mirror-image forms. The two forms - called stereoisomers - are referred
to as D and L amino acids. With rare exceptions, all of the amino acids in proteins are L
amino acids.
The unique side chains confer unique chemical properties on amino acids, and
dictate how each amino acid interacts with the others in a protein. Amino acids can
thus be classified as being hydrophobic versus hydrophilic, and uncharged versus
positively-charged versus negatively-charged. Ultimately, the three dimensional
conformation of a protein - and its activity - is determined by complex interactions
among side chains. Some aspects of protein structure can be deduced by examining the
properties of clusters of amino acids. For example, a computer program that plots the
hydrophobicity profile is often used to predict membrane-spanning regions of a protein
or regions that are likely to be immunogenic.
Peptides and Proteins
Amino acids are covalently bonded together in chains by peptide bonds. If the chain
length is short (say less than 30 amino acids) it is called a peptide; longer chains are
called polypeptides or proteins. Peptide bonds are formed between the carboxyl
group of one amino acid and the amino group of the next amino acid. Peptide bond
formation occurs in a condensation reaction involving loss of a molecule of water.
The head-to-tail arrangment of amino acids in a protein means that there is a amino
group on one end (called the amino-terminus or N-terminus) and a carboxyl group on the
other end (carboxyl-terminus or C-terminus). The carboxy-terminal amino acid
corresponds to the last one added to the chain during translation of the messenger
RNA.
Levels of Protein Structure
The primary structure of a protein can readily be deduced from the nucleotide sequence
of the corresponding messenger RNA. Based on primary structure, many features of
secondary structure can be predicted with the aid of computer programs. However,
predicting protein tertiary structure remains a very tough problem, although some
Your body contains thousands of genes, which code for thousands of different proteins. Each protein, which is made up of a sequence of
amino acids, contributes to the structure or function of your cells by supporting your metabolism, promoting cellular communication, and
supporting the shape and structure of your cells. Each of your proteins has a primary structure, which is important for how the protein
functions.
Protein Structure
Protein structure is classified on four levels: primary, secondary, tertiary and quarternary. The primary structure of proteins refers to the sequence of amino
acids that make up a protein chain, or polypeptide. Each protein has a unique primary structure that differs in both the order of amino acids in the
polypeptide and the total number of amino acids that make up the protein molecule. The secondary and tertiary structures refer to the way the polypeptide
is twisted and bent into a three-dimensional shape to make a functional protein. Quaternary structure refers to the way two or more polypeptides interact to
make up a functional protein. Every protein in your body has a primary, secondary and tertiary structure, but only some proteins have a quaternary
structure.
Hemoglobin
One example of a protein with a primary structure is hemoglobin. This protein, found on your red blood cells, helps provide the tissues
throughout your body with a constant supply of oxygen. The primary structure of hemoglobin is important because a change in only one
amino acid can disrupt hemoglobin's function. For example, a single amino acid change to hemoglobin's primary structure can cause sickle
cell anemia, a blood condition characterized by dysfunctional, sickle-shaped red blood cells.
Hexosaminidase
Another protein with important primary structure is hexosaminidase, a protein that contributes to the function of cellular compartments called lysozymes.
Maintaining lysozyme function is important to your health, since these compartments help your cells dispose of molecules that might otherwise harm the
cell. A mutation in the primary structure of hexosaminidase can disrupt lysozyme function in the brain, leading to fatal Tay-Sachs disease. As a result,
babies often undergo genetic testing for hexosaminidase mutations, to aid in early diagnosis of the disease.
Dystrophin
Dystrophin is another protein with a primary structure. The presence of dystrophin contributes to muscle functioning, and the protein helps maintain the
structure of your muscle fibers. Genetic mutations that change the primary structure of dystrophin -- such as the substitution of one amino acid for another,
or deletions of amino acids -- can harm your muscle fibers, leading to diseases such as Duchenne muscular dystrophy.
Myoglobin
The tertiary structure for myoglobin is
fairly well understood and is shown here.
Myoglobin has an alpha helix which then
can be viewed as being enclosed in this
blue sheath, the sheath doesn't exist but
we can draw it that way. That helix folds
back upon itself into what's referred to as
the tertiary structure of myoglobin. Bonds
between the side groups of the amino acid
residues are responsible for holding
together the tertiary structure of this
protein.
The kinds of bonds that can exist between the side groups include:
Van der Waals bonds if the side groups are nonpolar.
Hydrogen bonds if the side groups contain hydroxyl or amino groups.
Ionic bonds if the side groups are acids and bases that can transfer protons from one to
another making a carboxylate ion, which is negative, and essentially an ammonium or
quaternary ammonium ion which is positive.
Covalent bonds if the side groups are cysteine residues in which the sulfur atoms are
bonded together by the removal of two hydrogen atoms.
Primary Structure
The primary structure or amino acid sequence is unique for each protein.
The sequence in which the amino acids are attached to one another
ultimately is dependent on the genetic code from DNA. This primary
structure dictates the function of the protein indirectly through additional
levels of structure.
Consider this analogy, the nature of a garden is dictated by the plants that
are in it. It's function, whether it is to provide shade, protection, privacy,
food or tranquility, is going to be dictated by the individual plants selected
and the sequence and orientation of them with respect to one another.
Similarly, what a protein will be able to do is going to be determined by
what amino acids are joined to one another and the sequence in which they
are joined. However, the primary structure alone cannot carry out the
functions of protein. The amino acids bonded to one another in a line don't
make a protein function anymore than plants lined up along a roadside or in
a nursery make a garden.
Secondary Structure
Once the primary structure has been created, a secondary structure of some sort
evolves.
Alpha Helix
Beta Sheet
It is also possible for the protein's
strands to line up side by side with
one another and form hydrogen bonds
in this way. When that happens with
the strands both running in the same
direction it is called parallel.
Proteins generally have a mix of different kinds of secondary structure. They are
rarely, to my knowledge, all of a particular type. One part of a particular protein
may have an alpha helix, whereas another part can be folded back in the beta
sheet arrangement.
Whatever type of secondary structure is involved in a particular protein, the
secondary structure is held in place by hydrogen bonding interactions between
the amino group of the amino acid residue and the carbonyl group of another
amino acid residue.
Secondary strutureRESULTS in the side groups of the amino acid chain of the
protein chain sticking out to the side. Certain kinds of side groups will enhance
the formation of alpha helix, others will enhance the formation of beta sheet and
so on. But whatever the secondary structure happens to be, the side groups are
going to be sticking out.
Quaternary Structure
These chains are held together to form the larger protein by bonds that
exist between the side groups of different chains. As with tertiary structure,
the bonds involved in holding these separate chains together can be van der
Waals bonds, hydrogen bonds, ionic bonds, or at times covalent bonds.