Secondary structure is slightly more complex than Primary. This refers to the way the polypeptide chains are twisted and folded due to hydrogen bonding. Within Secondary structure there are two types of bonding: Alpha Helix and Beta pleating.
Alpha helix proteins are twisted into an alpha helix formation by hydrogen bonds forming between different amino acids. This happens as the hydrogen bonds are not long enough to reach the amino acids in the linear, primary structure and so they force polypeptide chain into the new structure. This provides a stronger more stable structure than a simple polypeptide chain would provide. Proteins can contain more than one alpha helix.
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Beta pleating is the other form of secondary structure, where polypeptide chains run parallel to each other and are cross linked by hydrogen bonds, again the length hydrogen bonds affect the shape of the molecules however this time it causes it to fold rather than twist. This provides a flat folded structure that is very strong, i.e. silk, which is produced naturally by silk worms.
Secondary structure proteins are generally fibrous proteins. Fibrous proteins such as collagen and keratin have a structural function, for which the alpha helix arrangement is ideal because its hydrogen bonding and helical shape provide mechanical strength. Keratin is found in hair, nails, horn, feather and hoof where the hydrogen bonds in the polypeptide backbone provide elasticity.
Secondary structure proteins are essential to all living organisms as they provide the molecules that make up the structure of most plants and animals, such as tendons, hair, skin, etc. Fibrous Proteins could be described as the building blocks of life.
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Tertiary structure is even more complex than secondary, and this refers to the way proteins are twisted and folded into a 3D shape. The new 3D shape, which is roughly spherical, is caused by projecting variable groups running down the polypeptide backbone interfering with the alpha helix and beta pleating arrangements of secondary structure proteins and forming bonds, such as hydrogen, ionic and di-sulphide bonds, with each other. This causes the molecule to twist and form into a 3D roughly spherical arrangement.
Quaternary structure is when more than one polypeptide chain bond to form a large protein molecule. Quaternary proteins make up the majority of metabolically active proteins. Such as haemoglobin, found in the blood and used to carry chemicals, i.e. oxygen, round the body.
Tertiary and Quaternary structure proteins tend to be globular proteins, and have a metabolic function, such as: Hormones, antibodies, and enzymes.
Enzymes are present in all living organisms and are described as biological catalysts as they speed up chemical reactions (i.e. the bonding or splitting of molecules) with living organisms. These are essential to all life as without enzymes simple reactions such as digestion and respiration would be so slow that most if not all life would die off.
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Enzymes are stereo specific, and so only catalyse one specific substrate. This is explained using the lock and key theory, where the enzyme molecule temporarily bonds to the substrate, via certain atoms on the protein which are placed in the exact place to bond to the substrate; these are known as active sites. The lock and key theory provides a direct link between the structure and function of proteins, i.e. the structure enables the enzyme to work via active sites, if the structure of the protein were to change even slightly, the enzyme would be de-natured and would not work.
Antibodies are immune system-related proteins called immunoglobulins. Each antibody consists of four polypeptide chains joined to form a "Y" shaped molecule. Antibodies are used by the body for defence against any harmful antigens which may enter the body. Antibodies fight disease by attaching itself to any invading antigens and by breaking it down into its individual polymers and amino acids. Antibodies are also stereo specific, i.e. they only fight one particular antigen, this is similar to the lock and key mechanism. Therefore the structure of antibodies is also directly linked to its function, i.e. a minute change in structure would lead to loss of immunity to the antigen for which the antibody is specific.
Hormones are chemical substances made by . These pass the hormones directly into the bloodstream, which carries them around the body. In this way, a can cause a change anywhere within the body. Some hormones can have long term effects, such as testosterone, others can have very short term effects, such as adrenalin produced in the adrenal glands.
Hormones are essential to life because they regulate all processes within the body, from metabolic rate to hair growth. A good example of this is adrenaline, which is released from the adrenal gland when the body perceives that it is in danger, the hormone is released into the blood stream and is pumped around the body.
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When the hormone reaches the heart, it attaches itself to special receptor sites on the lining of the heart, to which its structure fits similar to a jigsaw, and triggers the heart to work faster therefore pumping more blood round the body therefore providing more oxygen for the muscles. Each hormone is specific to certain receptor sites around the body, be it near hair follicles or on the lining of the heart, this is due to the structure of the protein only ‘fitting’ that particular site, similar to the lock and key theory.
It is possible to de-nature all globular proteins because they are susceptible to heat, pressure and acidity. If the temperature rises excessively or the globular protein is put under immense pressure kinetic energy within the molecule will increase causing vibrations within the molecule to increase also. Eventually the hydrogen bonds holding protein in its 3D shape break irrevocably causing the molecule to ‘unfold’ and lose its shape. Also excess acidity causes the hydrogen bonds to break and has the same effect as excess heat. This is known as de-naturation of the protein.
When this happens the proteins can no longer perform their functions because they no longer have the structure to do so; the key no longer fits the lock. This further proves a direct link between structure and function in that when the structure is proved even minutely, the protein can no longer carry out its metabolic function.
Matt Wilkinson