7.5 – Proteins
7.5.1 – Explain the four levels of protein structure, indicating the significance of each level
Primary Structure (1 degree)
This is the number and sequence of the amino acids in a polypeptide, attached by peptide bonds. This structure is determined by the base sequence of the gene that codes the polypeptides. The shape of the protein is defined by the chemical interaction of each amino acid. The structure is read from the NH₂ terminal to the COOH terminal. Each amino acid is identified by its R group. Most polypeptides are between 50-1000’s amino acids long.
Interestingly, there is very little diversity in the polypeptides of cells in many organisms, as only a small fraction of these polypeptides can be found in living things.
Secondary Structure (2 degree)
This is the shape of the polypeptide chain, which takes place immediately after formation at the ribosome. Parts of the chain will become folded, twisted, or both in various ways. This may happen as a result of hydrogen bond interaction between neighbouring CO and NH groups. Not all the parts of the polypeptides form secondary structures. α helix – This is a coil formed from hydrogen bonds with a regular
α helix – This is a coil formed from hydrogen bonds with a regular helix shape. These helices often form the basis for fibrous polymers. There are 3.6 amino acids per turn.
β sheets – These are pleated sheets. They are called this because of the folds that can be seen from
the side. The polypeptide chain is more stretched than the alpha helix. These sheets often have twists to increase the strength and rigidity of the structure. Each amino acid forms two hydrogen bonds.
Open Loops – These connect alpha helices and beta-pleated sheets. They are short chains of amino acids which form neither of these structures, but simply link sections together. Often these form important regions of proteins (such as the active sites of enzymes)
Tertiary Structure (3o)
This is the way the proteins are folded and held in a particular, complex shape; also known as the conformation of the polypeptide. The folds are formed as a result of interaction between the R groups, or side chains of the amino acids. The molecule is folded around a heme group, which binds oxygen. There are four types of bonding that occur to make this happen.
Disulfide Bonding (or Bridges)
These are bridges that help maintain the structure of the molecule. They are strong, covalent bonds formed by the oxidation of SH groups of two cysteine side chains on amino acids Ionic Bonding
Ionic Bonding
This is simply electrostatic interaction between oppositely charged ions, which can be easily broken if the pH changes. Also called salt bridges.
Hydrophobic Forces
These happen between atoms that are very close. This may also be called hydrophobic interactions.
Hydrogen Bonds
This is when a hydrogen atom is shared by two other atoms. They are weak, but common, and help to stabilise the protein molecule
Quaternary Structure (4 degree)
This is the linking together of two or more polypeptides to form a single protein. Sometimes, these may contain a non-polypeptide structure called a prosthetic group. A prosthetic group is an inorganic group. The polypeptides in the case of haemoglobin are connected to a heme group (not made of amino acids – it is here that iron is found). Any proteins with a prosthetic group are called conjugated proteins.
7.5.2 – Outline the difference between fibrous and globular proteins, with references to two examples of each protein type
Fibrous Proteins
Fibrous proteins are generally long, narrow and insoluble in water. They are physically tough and may be supple or stretchy. Their tertiary structure is a much-coiled chain. Their function is often to provide strength and support to tissues.
Collagen is the basis of connective tissue and has a triple helix shape. This is the most common protein in animals, and is a component of bone, skin and tendons. When collagen does not form links to the mineral components of the bone, this leads to brittle cone disease. It strengthens the tissue.
Keratin is a common protein in animals. It is composed of seven helices and is the main protein in hair and nail structure.
Myosin causes contraction of muscle fibres, which causes movement in animals. It acts with another protein called actin.
Globular Proteins
Globular proteins are tightly folded and are usually soluble in water. They have more compact and rounded shapes. Their functions include pigment and transport proteins, and the immune system.
Examples include haemoglobin, which is a transport protein, and immunoglobin, an antibody in the immune system. Enzymes such as catalase are also globular structures, as
well as hormones, like insulin.
Haemoglobin bind to oxygen in the lungs and transport it to respiring tissues. Immunoglobin act as antibodies. Part of the molecule can be varied, so that an almost endless variety of antibodies can be produced.
Some proteins have both fibrous and globular properties.
7.5.3 – Explain the significance of polar and non-polar amino acids
The distribution of polar and non-polar amino acids in a protein molecule influence where the protein is located and its functions.
Polar Amino Acids
Polar amino acids have hydrophilic properties due to the chemical characteristics of their R groups. When these are built into protein in prominent positions, they may influence the properties and functioning of the protein in cells. Polar amino acids on the surface of proteins make them water soluble. Polar amino acids in the active site of an enzyme allow chemical interaction between
Polar amino acids in the active site of an enzyme allow chemical interaction between the substrate and enzyme to form an activated complex. This transitional state allows the weakening of internal molecular structure and therefore the reduction of the activation energy. In cell membrane proteins, the sections of the molecule that contain polar amino acids
In cell membrane proteins, the sections of the molecule that contain polar amino acids are hydrophilic, and can be in contact with water. These allow for the positioning of proteins on the external and internal surface. Both the cytoplasm and the tissue fluid are water-based regions. Polar amino acids also create channels thorough which hydrophilic substances can diffuse. Positively charged R groups allow negatively charged ions through, and vice versa.
Non-Polar Amino Acids
These have hydrophobic R groups. These amino acids in the centre of water soluble proteins stabilize their structure. The non-polar amino acids cause proteins to remain embedded in the membrane.
In the enzyme superoxide dismutase, a ring of amino acids with negatively charged R groups repel the negatively charged superoxide ions to helps direct them to the active site. The active site contains amino acids with positively charged R groups. These attract the negatively charged superoxide ions to the active site.
In the enzyme lipase, the active site contains amino acids with non-polar R groups. These bind to non-polar triglycerides. Part of the enzyme acts as a hinged lid which can cover the active site when not in use, hiding the non-polar R groups.
7.5.4 – State four functions of proteins, giving a named example of each
Hormones – Chemical Messengers
Hormones are chemical messengers produced and secreted by cells of endocrine glands. These can be polypeptides or proteins. Other hormones are steroids, which are lipids.
An example of this is insulin. It is produced in the pancreas and its target tissues are muscle cells and liver cells. It brings about the uptake of glucose across the cell membrane and the storage of it as the insoluble polymer glycogen.
Antibodies – Defence against disease
Antibodies secreted by a type of white cell (B-lymphocytes) in response to non-self substances (antigens) that may invade the body. These antibody proteins are known as immunoglobins. Great variation exists in the heavy chains which allow a response to virtually any possible antigen surface. Due to their high specificity in identifying antigen, they are used in a wide variety of biotechnologies.
Enzymes – Biological Catalysts
These alter the speed of chemical reactions, making biochemical changes possible under the normal conditions of life. They reduce the energy of activation. These are large globular proteins, often with prosthetic groups. Catalase is a very large molecule. Liver catalase has a turnover rate of 4 x 107 s-1, which
Catalase is a very large molecule. Liver catalase has a turnover rate of 4 x 107 s-1, which is the maximum number of substrate molecules that can be converted per second.
Transport of Respiratory Gases
Haemoglobin in red cells is a conjugated protein, which means that it has the non-protein heme part attached to the globin protein. This combines with oxygen in the lungs and frees it in respiring tissues (dissociation). Each heme group can carry an oxygen atom. Its formula is C3032H4816O872N780S8Fe4
Other roles include muscle movement, structure and support.