Chemistry of Biomolecules

1. Chemistry of Biomolecules

2. Basic Concepts Chemical Bonds and Chemical Rections • Covalent bonds are attractive forces present between atoms in molecules/compounds and are formed by sharing electrons between atoms. • Covalent bonds generally do not break at room temperature. • Chemical reactions involve either forming or breaking or both of covalent bonds.

3. Consider the following reactions involving atoms A and B • Formation of covalent bond A + B → A-B • Breaking of covalent bond A-B → A + B • Both formation and breaking A + A-B → A-A +

4. Elemental Composition of the Human Body • Only about 30 of more than 100 naturally occurring chemical elements are constituent of biomolecules in the living organisms. • The elements needed for life are relatively common in the earth's crust.

5. The six most abundant elements in living organisms, • in terms of percentage of the total mass and also total number of atoms, are hydrogen, oxygen, carbon,nitrogen, calcium (Ca) and phosphorus (P), which together make up over 99% of the mass of most cells, (with most of the H and O occurring as H2O).

6. Other elements/minerals • that are significant constituents of biological molecules are • sulphur (S), magnesium (Mg), sodium (Na), potassium (K) and chlorine (Cl) – • major elements (ormacro elements/minerals).

7. In addition, living things use traces of certain other elements/minerals. • In humans they are • iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), iodine (I), fluorine (F), selenium (Se), cobalt (Co) and molybdenum (Mo) – • trace elements (micro or minor elements/minerals).

9. Besides these elements that are necessary for life, our bodies contain trace quantities of most other elements, • including some that are harmful, such as mercury, cadmium, and lead.

10. Carbon Atom • Organic compounds are the most important molecular constituents of living systems and are composed of carbon atoms. • Carbon is tetravalent and in organic compounds is covalently joined with other carbon atoms and with hydrogen, oxygen, nitrogen or sulfur. The special bonding properties of carbon permit the formation of a great variety of molecules.

11. O, N, S, P and Cl • are electronegative atoms (atoms having high affinity for electrons) on the one hand, and • Na, K, Ca, Mg, Fe, Cu andMn are electropositive atoms (atoms which readily give up electrons). This property has much influence on many physical and chemical properties of biomolecules.

12. Biomolecules Biomolecules are those molecules which are present in living organisms having one or more functions or metabolically derived from these molecules.

13. Biomolecules • Thus protein is a biomolecule because it is present in the body and has functions. Urea is also present in the body and does not have any functions. However, since it is derived from protein, it is also considered to be a biomolecule.

14. Biomolecules • Nitrogen gas (N2) is present in the blood. However, neither does it have any function nor is it metabolically produced in the body. So clearly, N2 is not a biomolecule. • There are also many other chemicals present in the body as contaminants such as mercury, lead, etc. and they are not biomolecules either.

16. Biomolecules • Human body is composed of about • 60% water, • 15% proteins, • 15% lipids, • 2% carbohydrates and • 8% minerals.

17. Basic Organic Chemistry for Biochemistry • Organic compounds = compounds composed of carbon and hydrogen or its derivatives • Organic compounds are divided into two classes: aromatic compounds, which contain benzene or similar rings of atoms, and aliphatic compounds which do not contain those rings. • Aliphatic compounds can be cyclic, like cyclohexane, or acyclic, like hexane. They also can be saturated, like hexane, or unsaturated, like hexene.

18. Functional Groups in Organic Compounds • Hydroxyl/alcohol: R–OH • Aldehyde: R-C-H O • Keto: R1-C-R2 O • Carboxyl: R-C-OH (R-COOH ) O

19. Functional Groups in Organic Compounds • Amino: R-NH2 • Imino R1-NH-R2

20. Water • All molecules and ions, in biological systems, are dissolved or suspended in aqueous medium. Virtually all biochemical reactions metabolism), therefore, take place in the aqueous medium. • Water is the medium, in which the first cells arose, and it is the solvent the properties of water that have shaped the course of evolution. Without liquid water, terrestrial life could not exist. • All living organisms on Earth depend on water and its unique chemical and physical properties.

21. Water • Everything is soluble in water to some degree and the structure and interaction of biomolecules are profoundly influenced by the aqueous solution in which biomolecules reside. The week interaction within and between biomolecules strongly is affected by the solvent properties of water. • Unique properties of water are – high latent heat, its liquid state at wide range of temperature (0 to 100◦C), ionization and its ability to form hydrogen bond and ionic bond with other water molecules and also many other molecules.

22. Non-covalent Bonds Non-covalent bonds are also attractive forces between atoms, ions or molecules and are also called weak bonds or weak interactions because they are 10 to 20 times weaker than covalent bonds. • Non-covalent bonds may be intra-molecular(occurring between different atoms of the same molecule) or inter-molecular molecular (occurring between different molecules).

23. Non-covalent Bonds • Intra-molecular week bonds cause bends in the molecule and are responsible for the molecular shape or conformation. For example, proteins though have a linear covalent structure, assume three-dimensional conformation due to the intra-molecular non-covalent bonds. • Inter-molecular week bonds, on the other hand, are responsible for supra-molecular aggregations (complexformation) of molecules. Examples of supra-molecular aggregations are – crystals; complexes of protein molecules; complexes of protein and nucleic acids (nucleoproteins – chromatin and ribosome); complexes of lipid and proteins (lipoproteins, biological membranes).

24. Non-covalent Bonds • There are basically 4 types of non-covalent bonds – • ionic bond, 2) hydrogen bond, 3) hydrophobic bonds/interactions and 4) van der Waals forces. • Ionic and hydrogen bonds are electrostatic bonds because both are formed due to charge.