1. Lecture 3 Chemicals of Life
Biochemistry

2. Content Elements Chemical Bonds Acids, Bases, Salts, pH and buffers
Organic chemistry
Water

3. Elements-1
All matter is composed of varying amounts of about 106 elements.
An element is a substance that cannot be split into a simpler substance by chemical means e.g carbon, nitrogen, and oxygen
Each element has its own unique properties.
The smallest particle of an element is an atom.
Elements combine to form compounds.
All matter is composed of atoms,a molecule is a combination of atoms.

4. The Periodic Table
The Periodic Table is the collection of all known elements, they are organized into groups based on shared properties according to their atomic number.

5. Elements - 2 Life requires 25 of the 106 elements
96% living things made of O (oxygen), H (hydrogen), C (carbon) and N (nitrogen).
4% Ca (calcium), P (phosphate), K (potassium), and S (sulphur).
Trace elements
Atom, elements, compound a substance of two or more elements, atoms linked by chemical bonds e,g water H2O, table salt NaCl, carbon dioxide CO2

6. Atomic Structure Made up of the following particles.
Particle Location Mass Charge
Proton central 1 unit 1.7x10-24 g +1
Neutron core 1 unit
Electron orbits 1/1870 unit
Atomic number represents the no. of protons in an element
Mass number the number of protons + neutrons
Isotope atoms of elements with different no. of neutrons.

7. Atomic Structure - Example6n
20p
20n
Calcium = Ca
Atomic no. = 20
Mass no. = 40
Electrons = 2, 8, 8, 2
Carbon = C
Atomic no. = 6
Mass no. = 12
Electrons = 2, 4

8. Chemical Bonds Electrons arranged in shells around nucleus:
1st shell 2 electrons,
2nd shell 8 electrons,
3rd shell 8 electronss,
4th shell 18 electrons,
5th shell 32 electrons.
Outer shell complete set of electrons – unreactive.
Tendency is to try and obtain a full set of electrons through reaction with other elements.
Two types of interactions or bonds can be formed:
Ionic bonds
Covalent bonds

9. Ionic Bonding - 1 A transfer of electrons from one atom to another.e.g
Sodium + Chlorine
Na + Cl
11 electrons (2,8,1) 17 electrons (2,8,7)
11 protons 17 protons
10 electrons 18 electrons
11 protons 17 protons
Na+ Cl-
Cation Anion

10. Ionic Bonding - 2 Resulting compound is sodium chloride NaCl.
Compounds from the transfer of electrons are called ionic compounds
Usually when metal reacts with a non-metal
The metal produces a cation and the non-metal an anion.
The number of electrons transferred (loss/gain) is the valency of the element.e.g Na and Cl have a valency of 1 this is usually shown for ions Na+ Cl-

11. Covalent Bonding - 1 Electrons are shared
E.g 2 Chlorine atoms, each has 7 electrons in outer shell.
Each atom contributes an electron making a Chlorine molecule (Cl2), covalency of 1.
Structural Formula
Cl Cl
Cl Cl

12. Covalent Bonding - 2 Methane, CH4 Ethene, C2H4 H H H H H C H H C H C C

13. Acids and Bases Hydrogen ions in a aqueous solution, H+
An acid is a substance that can act as a proton donor in an aqueous solution.
When it completely dissociates into its constituent ions in water you get a strong acid.
When a small proportion of the hydrogen ions dissociate a weak acid is produced.
A base is a substance that reacts with an acid to form a salt and water only, it is a hydrogen acceptor.
Most bases are insoluble in water, when they do dissolve they produce a alkalis. E.g sodium hydroxide

14. pH
The acidity and alkalinity of a solution is related to the concentration of hydrogen ions in the solution.
The pH is defined as the log to the base of 10 of the reciprocal of the hydrogen ion concentration.
Pure water contains 1x10–7 moles of H+ /L
pH of water therefore log (1x107) = 7
A pH of 7 = neutral solution < = acid > = alkali
Range 0-14

15. Buffers Mixture of a weak acid and its soluble salt
Resists changes in pH.
If acidity increases the free anion from the salt will mop up any free hydrogen ions.
If acidity decreases hydrogen ions released by the anion.
E.g HPO H H2PO4-
Proteins act as buffers and they are particularly important in blood.
Low pH
High pH

16. Organic Chemistry Organic chemistry based on the element carbon.
Organic compounds are usually defined as containing carbon and at least one hydrogen atom.
Living organisms primarily composed of organic molecules e.g carbohydrates.

17. Carbon Small atom with low mass. Able to form strong covalent bonds.
Carbon atoms can join each other to form rings or chains.
Very strong bonds hence very stable molecules.
Has the ability to form multiple covalent bonds with other carbon atoms, oxygen and nitrogen.
Variation in organic molecules occurs through:
Size (no. of carbon atoms)
Chemistry (elements or functional groups attached to carbon atoms)
Shape (angles of the bonds formed)

18. Functional Groups Hydroxyl OH
Carbonyl C=O, if oxygen on outside it is an aldehyde
if oxygen on the inside it is a ketone
Carboxyl COOH, the hydrogen tends to dissociate from
oxygen to produce organic ion and H+ ion
Amino NH amines
Sulfhydrl SH forms disulfide bridges in proteins chains
contribute toward function as enzyme
Phosphate (PO4)3 important in metabolism and information
storage
Methyl CH3

19. Isomers
The same atoms can often be arranged in various ways to form compounds with different chemical properties.
Compounds that have the same molecular formulae but different structures are known as ISOMERS.
There are 3 types:
Structural – differ in relationship between atoms in molecule
Geometric – atoms bonded to same partners but arranged differently around double bond.
Stereoisomers – mirror image
Stereoisomers- one active form one inactive, most sugars right handed (D-sugars), left handed can be made commercially. Human enzymes that break down sugars do not recognise L-sugars, but taste buts do. They are used as a sugar substitute, where they produce sensation of sweetness not metabolised hence do not contribute to weight gain.