Chapter 3
Special Topics in Organic Chemistry
Special Topics in Organic Chemistry
Course code: (4024583-2)
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Lecture 5
Chapter 3
Special topics in Organic chemistry
Special Topics in Organic Chemistry
Proteins
Definitions:
Organic compounds with large molecular weight containing carbon, hydrogen, oxygen and nitrogen. It may also contain sulfur and other elements.
Sources:
Vegetable and animal sources.
Characterization:
• The main constituent of the living cells.
• Interfere in the composition of cell walls, enzymes, antibodies and some hormones.
• Proteins are specialized depending on the need of the living cells.
This means that they are found in some organism but not others;
can be found in some cells but not others in the same organism. It can also be found in a living organism but not another one for certain period according to the need of the cells.
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Proteins
The biological functions:
Proteins play a role in the:
• Immunization.
• Stimulation.
• Controlling the metabolism.
• Growth.
• Carrying some of the material.
• Controlling the structural and kinetic functions.
• Organizing the work of some genes, enzymes and the carrier of nerve signals.
• Constituent of the poisons of some snakes.
Medical and industrial importance:
Used in the diagnosis of diseases, pharmaceutical industry, preparation
Nomenclature of protein
• Start naming the protein with the name of the amino acid at the left side, which contains a free amino group (N-terminal).
• End with the name of the amino acid at the right end, which contains a free carboxyl group (C-terminal).
• Then delete the (ine) section from the end of each amino acid and add (yl); from the first one to the one before the last and the last one remains without adding (yl).
Example:
Glycyl tyrosyl histidine
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Proteins classification
1. Simple proteins: contain only amino acids and they are in two forms: fibrous and globular.
a) Fibrous proteins: insoluble in water and enter in the composition of the living tissues. Such as:
• Keratins: includes fiber constituent of hair, wool, silk, nails, horns, hooves of animals and bird feathers.
• Collagens: found in the ligaments and cartilage.
• Elastin: found in ligaments, but by less than collagen. Characterized by flexibility such as arterial walls and alveoli membranes.
b) Globular proteins: soluble in water or alcohols, include most of the blood proteins and cytoplasm soluble proteins. Such as:
• Albumins: found in milk, eggs and in blood.
• Globulins: found in milk, vegetable seeds and in blood.
• Basic proteins: such as histones.
• Glutelins: vegetable’s protein such as wheat gluten.
• Prolamines: found in zein.
Proteins classification
2. Complex proteins: like the globular simple proteins but contain non- protein molecules which gain the proteins new features. Such as:
➢ Glycoproteins: proteins containing carbohydrates found in cell membranes.
➢ Phosphoproteins: a phosphorus-containing proteins found in milk casein and egg proteins.
➢ Nucleoproteins: proteins associated with nucleic acids.
➢ Lipoproteins: proteins associated with lipids (such as cholesterol) which prevent their toxic effects and prevent their accumulation on the walls of blood vessels.
➢ Chromoproteins: proteins associated with non-protein molecules like metal. Such as hemoglobin.
➢ Metaloproteins : proteins containing metals that are found in enzymes.
3. Derived proteins: the products of breaking down of proteins.
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The general structure of proteins
Proteins characterized by a special conformation for their functions; any change in this conformation will lead to a loss in their bioactivity.
The four orders of protein structure:
1) Primary structure: the sequence of the amino acids in a polypeptide chain. This sequence will be repeated within the same protein several times. The sequence will give the proteins their shape, function and characterization. The genetic system inside the genes will control the order of the amino acids in the repeated sequence. Any defect or mutation in the gene can lead to substituting an amino acid with another and cause a change in the protein structure and function. It also leads to the occurrence of diseases such as sickle cell anemia.
2) Secondary structure: demonstrates the relation between the neighboring amino acids at the same chain or contiguous chains which are linked by hydrogen bonds. As a result the chain will be twisted and the proteins form are either a helical or sheets or both forms (alpha helix, beta pleated sheet and triple helix) .
3) Tertiary structure: spherically in shape due to the presence of a number of linkages, which gives the protein its tertiary shape; which are: hydrogen bonds, ionic bonds, hydrophobic bonds and disulfide bonds.
4) Quaternary structure: consists of more than one peptide chain in the tertiary structure linked together by non-covalent linkages such as ionic bonds, hydrophobic and polar
The four orders of protein structure
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Denaturation
Definition:
Change in the natural composition of the protein (conformation) as a result of exposure to certain conditions that lead to losing the physical and biological properties of the protein.
Affected factors:
• High heat.
• Radiation.
• The high concentration of salts and organic solvents.
• The huge difference between the hydrogen ion concentration in the media and the optimum pH of the bioactivity of the protein.
