Lec 1 Chemistry Of Water Biochemistry Medicine Biochemistry

Lec. 1 Chemistry Of Water

Biochemistry & Medicine • Biochemistry can be defined as the science concerned with the chemical basis of life. • Biochemistry can be described as the science concerned with the chemical constituents of living cells and with the reactions and processes they undergo.

A reciprocal relationship between biochemistry & medicine • Normal biochemical process are the basis of health. • The Aim of biochemistry is to describe & explain, all chemical processes of living cells. • Most & perhaps all disease has a biochemical basis.

Water • Water plays a central role in the chemistry of all life • The chemical properties of water are related to the functions of biomolecules, entire cells, and organisms 4

The Water Molecule is Polar • Important properties of water arise from its angled shape • Angle of 104. 5 o between two covalent bonds • Polar O-H bonds due to uneven distribution of charge (oxygen (d-), hydrogen (d+)) • Angled arrangement of polar bonds creates a permanent dipole for a water molecule 5

(a) Space-filling structure of water (b) Covalent bond angle of water 6

Hydrogen Bonding in Water • Water molecules attract each other due to their polarity • A hydrogen bond is formed when a partially positive hydrogen atom attracts the partially negative oxygen atom of a second water molecule • Hydrogen bonds can form between electronegative atoms and a hydrogen attached to another electronegative atom 7

Hydrogen bonding between two water molecules 8

Hydrogen bonding by a water molecule • A water molecule can form up to four hydrogen bonds • Hydrogen bonds shown in yellow 9

Ionic and Polar Substances Dissolve in Water • Hydrophilic (water-loving) substances (polar and ionic (electrolytes)) readily dissolve in H 2 O • Polar water molecules align themselves around ions or other polar molecules • A molecule or ion surrounded by solvent molecules is solvated • When the solvent is water the molecules or ions are hydrated 10

Solubilities of molecules in water • Solubility in water depends upon the ratio of polar to nonpolar groups in a molecule • The larger the portion of nonpolar groups the less soluble the molecule is in water • The larger the portion of polar groups (e. g. hydroxyl groups (-OH)) the more soluble the molecule is in water 11

Nonpolar Substances Are Insoluble in Water • Hydrophobic nonpolar (water-fearing) molecules are • Hydrophobic effect - the exclusion of nonpolar substances by water (critical for protein folding and self-assembly of biological membranes) • Amphipathic molecules have hydrophobic chains and ionic or polar ends. 12

Water Is Nucleophilic • Nucleophiles - electron-rich atoms or groups • Electrophiles - electron-deficient atoms or groups • Water is a relatively weak nucleophile • Due to its high cellular concentration, hydrolysis reactions in water are thermodynamically favored 13

Covalent & Noncovalent Bonds Stabilize Biologic Molecules. Covalent bond, e. g. : 1. Peptide bonds. 2. Disulfide bond. b. Non-covalent bond, e. g. : 1. Hydrogen bond. 2. Electrostatic or ionic bond or salt bridge 3. Hydrophobic bond or interaction 4. Vander Waals interactions.

1 - The covalent bond is the strongest force that holds molecules together and it involves the sharing of pairs of electrons. A- Peptide Bonds (-CO-NH-): Ø A peptide bond is formed by the condensation of the amino group (NH 2) of one amino acid with the carboxyl group(COOH) of an another amino acid with the removal of a water molecule. B- Disulfide bond (-S-S-) Ø covalent bond formed between the sulfhydryl group ( -SH) of side chain of cystein residues in the same or different peptide chains.

2 - Noncovalent bond is a type of chemical bond that does not involve the sharing of pairs of electrons, but rather involves more dispersed variations of electromagnetic interactions. • Noncovalent bonds are critical in maintaining the three-dimensional structure of large molecules. A- Hydrogen bond: Ø A hydrogen nucleus covalently bound to oxygen can interact with an unshared electron pair on another oxygen atom to form a hydrogen bond. Bond formed between (–NH) and (–CO) groups of peptide bond by sharing single hydrogen.

B- Electrostatic or ionic bond or salt bridge: Ø These are formed between oppositely charged groups when they are close. Such as amino (NH 3+) terminal and carboxyl (COO-) terminal groups of the peptide. C- Hydrophopic bond or Interaction: - Ø Hydrophobic interaction refers to the tendency of non-polar compounds to self-associate in an aqueous environment. D- Vander Waals Interactions: Ø Van der Waals forces arise from attractions between transient dipoles generated by the rapid movement of electrons on all neutral atoms. Significantly weaker than hydrogen bonds.

The role of water in biological systems. Ø All known forms of life depend on water. A human body 60– 70%, plant body up to 90% water. Ø Water is vital both as a solvent in which many of the body's solutes dissolve and as an essential part of many metabolic processes within the body. Ø In anabolism, water is removed from molecules in order to grow larger molecules (e. g. starches and proteins for storage of fuels and information). Ø In catabolism, water is used to break bonds in order to generate smaller molecules (e. g. glucose and amino acids to be used for fuels for energy use or other purposes).

Ionization of Water • Pure water consists of a low concentration of hydronium ions (H 3 O+) and an equal concentration of hydroxide ions (OH-) • Acids are proton donors (e. g. H 3 O+) and bases are proton acceptors (e. g. OH-) 19

The p. H Scale • p. H is defined as the negative logarithm of the concentration of H+ 20

Acid is defined as any substance that is capable of producing hydronium ion (H 3 O+) in aqueous medium p. H=-log(H 3 O +) Base is defined as any substance that is capable of producing hydroxyl ion [OH-] in aqueous medium. p. OH=-log(OH-)

Buffer solutions • Solutions of weak acids or bases and their conjugates exhibit buffering, the ability to resist a change in p. H following addition of strong acid or base. • It is often necessary to keep the p. H value nearly constant despite the addition of acids and bases. • The oxygen carrying capacity of the hemoglobin in your blood and the activity of the enzymes in your cell are very sensitive to the p. H of your body fluids.

A- Acidic buffer solutions It is a combination of a weak acid and its salt and the p. H of this solution is < 7 Examples of this type of buffer are the combination of acetic acid and sodium acetate. B- Basic buffer solutions It is a combination of a weak base and its salt and the p. H of this solution is > 7 Examples of this type of buffer are the combination of ammonia solution and its ammonium salt as ammonium chloride.