MGD Module - Session 1 - Chemistry Lectures - PDF

MGD Module Session 1 Introduction To the Chemistry Lectures 1 16-2-2023 Dr. Ali H. Dosky 1 Session 1 References • Marks’ Basic Medical Biochemistry Chapter 6 • Medical Biochemistry Chapter 2 • Lippincott’s Illustrated Reviews: Biochemistry Chapter 1 • Lippincott’s Illustrated Reviews: Cell and Mo...

MGD Module Session 1 Introduction To the Chemistry Lectures 1 16-2-2023 Dr. Ali H. Dosky 1 Session 1 References • Marks’ Basic Medical Biochemistry Chapter 6 • Medical Biochemistry Chapter 2 • Lippincott’s Illustrated Reviews: Biochemistry Chapter 1 • Lippincott’s Illustrated Reviews: Cell and Molecular Biology Chapter 5 MGD 2017/ DR. AL-BARQAAWI 2 Session 1 Learning outcomes At the end of this session you should be able to: 1.Discuss the bonds important for macromolecular structure and interaction. 2..Explain the differences between hydrophobic and hydrophilic molecules in water. 3.Explain the concept of pH, pK and buffers. MGD 2017/ DR. AL-BARQAAWI 3 Glossary Acid: A chemical that can dissociate to release hydrogen ions (H+), i.e. it is a proton donor. Amino acid: The building blocks of proteins. They are composed of a central carbon atom attached to four other chemical groups: an amino group (-NH2), a carboxyl group (COOH), a hydrogen atom and a variable group (R). Amphipathic: A molecule that has both a polar (hydrophilic) and non-polar (hydrophobic) end is said to be amphipathic. Base: A chemical that can combine with a hydrogen ion (H+), i.e. it is a proton acceptor. Buffer: A solution of a weak acid and its conjugate base that resists a change in pH when a small amount of acid or alkali is added. Covalent bond: A bond formed between two atoms by the sharing of electrons. MGD 2017/ DR. AL-BARQAAWI 4 Glossary Hydrogen bond: A weak electrostatic interaction between a hydrogen atom bound to an electronegative atom (N, O) and another electronegative atom. Hydrophilic: A polar molecule that is able to interact with water molecules is said to be hydrophilic. Hydrophobic: A non-polar molecule that is unable to interact with water is said to be hydrophobic. Ionic bond: A bond formed between two atoms where there is a complete transfer of an electron resulting in the formation of two ions (one positive and one negative). Isoelectric point: The pH at which a protein has no overall net charge. Peptide bond: A type of covalent bond which joins amino acids in proteins. The bond forms between the carboxyl group of one amino acid and the amino group of the second. pH: A measurement of the concentration of H+ ions in solution. pH = -log10[H+] Protein: A polymer composed of amino acids joined by peptide bonds. MGD 2017/ DR. AL-BARQAAWI 5 Chemistry MGD 2017/ DR. AL-BARQAAWI 6 Subunits of Macromolecules MGD 2017/ DR. AL-BARQAAWI 7 Bonds Important For Macromolecular Structure And Interaction 1. Covalent bond: A covalent bond forms when two atoms come very close together and share one or more of their electrons. Each atom forms a fixed number of covalent bonds. MGD 2017/ DR. AL-BARQAAWI 8 Bonds Important For Macromolecular Structure And Interaction 2. Ionic bond: A bond formed between two atoms where there is a complete transfer of an electron resulting in the formation of two ions (one positive and one negative). e.g. NaCl MGD 2017/ DR. AL-BARQAAWI 9 Bonds Important For Macromolecular Structure And Interaction It should be differentiate between Ionic Bond and Ionic Interaction which may be Attraction (between two groups with different charges), or Repulsion (between two groups with the same charges). Hydrophobic Interaction: A weak electrostatic interaction between two hydrophobic groups. 3. Van der Waals Interaction: A weak interaction between any two atoms in close proximity. MGD 2017/ DR. AL-BARQAAWI 10 Bonds Important For Macromolecular Structure And Interaction 3. Hydrogen Bond: A weak electrostatic interaction between a hydrogen atom bound to an electronegative atom (N, O) and another electronegative atom. Because they are polarized, two H2O molecules can form a linkage known as Hydrogen bond. This type of bonds have only about 1/20 the strength of covalent bond. MGD 2017/ DR. AL-BARQAAWI 11 Water Properties & Functions • Weak interactions are the key means by which molecules interact with one another. • The strength and specificity of weak interactions between biomolecules are highly dependent on the medium (aqueous) in which they take place. • Two properties of water are biologically important: 1. Water is polar molecule. 2. Water is highly cohesive (hydrogen bonds between water molecules). •Water is the principal fluid medium of the cell, which is present in most cells, in a concentration of 70 to 85 per cent. Many cellular chemicals are dissolved in the water. • Water Helps in regulation of temperature since it is able to absorb large amounts ofheat. • Helps in regulation of intracellular pH since it is amphoteric solvent. • Used for transport – delivers nutrients and removes waste from cells MGD 2017/ DR. AL-BARQAAWI 12 Water As A Solvent According to the ability of water to dissolve their molecules, substances can be classified in to Hydrophilic, Hydrophobic, and Amphipathic. Hydrophilic molecules: substances that dissolve readily in water. They are composed of ions or polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule on the surface of such a solid and carry it into solution. MGD 2017/ DR. AL-BARQAAWI 13 Water As A Solvent Hydrophobic Molecules: Substances that contain nonpolar bonds and insoluble in water. Water molecules are not attracted to their molecules and so have little tendency to surround them and carry them into solution. MGD 2017/ DR. AL-BARQAAWI 14 Water As A Solvent Amphipathic Molecules: Molecules that have both hydrophilic and hydrophobic properties are said to be amphipathic MGD 2017/ DR. AL-BARQAAWI 15 Ionization of Water Water dissociates into hydronium (H3O+) and hydroxyl (OH-) ions For simplicity, we refer to the hydronium ion as a hydrogen ion(H+) and write the equilibrium as MGD 2017/ DR. AL-BARQAAWI 16 Ionization of Water K w is the ion productof water. At 25°C, K w is 1.0 × 10-14. Note that the con. of H+ and OH- are reciprocally related. If the concentration of H+ is high, then the concentration of OH- must be low, and vice versa. For example, if [H+] = 10 -2 M, then [OH-] = 10-12 M. MGD 2017/ DR. AL-BARQAAWI 17 Acids and bases MGD 2017/ DR. AL-BARQAAWI 18 Definition of pH and pK The pH of a solution is a measure of its concentration of H+. The pH is defined as: Note that if two solutions differ in pH by one unit, they differ in [H] by a factor of 10. The pH of a solution may be accurately and easily determined through electrochemical measurements with a device known as a pH meter. The ionization equilibrium of a weak acid is given by: The apparent equilibrium constant Ka for this ionization is: The pKa of an acid is defined as: The pKa of an acid is the pH at which it is half dissociated, when [A-]=[HA] MGD 2017/ DR. AL-BARQAAWI 19 Buffers Q: predict the change in the water’s pH when a 0.01-mL droplet of 1M HCl is added to 1 L of pure water. Since the properties of biological substances vary significantly with small changes in pH, they require environments in which the pH is insensitive to additions of acids or bases. To understand how this is possible, let us consider the titration of a weak acid with a strong base. An acid-base conjugate pair (such as acetic acid and acetate ion) has an important property: it resists changes in the pH of a solution. In other words, it acts as a buffer. Consider the addition of OH- to a solution of acetic acid (HA): MGD 2017/ DR. AL-BARQAAWI 20 Titration curve of acetic acid v A plot of the dependence of the pH of this solution on the amount of OH- added is called a titration curve. v There is an inflection point in the curve at pH 4.8, which is the pKa of acetic acid. MGD 2017/ DR. AL-BARQAAWI 21 Titration curves of acetic acid and another weak acids Acid–base titration curves of 1-L solutions of 1M acetic acid, H2PO -4, and NH + by 4 a strong base. MGD 2017/ DR. AL-BARQAAWI 22 What is the relation between pH and the ratio of acid to base? We know: Therefore And This equation is commonly known as the Henderson- equation. MGD 2017/ DR. AL-BARQAAWI 23 Application of Henderson Equation • The pH of a solution can be calculated from this equation if the molar proportion of A- to HA and the pK a of HA are known. Example: • Conversely, the pKa of an acid can be calculated if the molar proportion ofAto HA and the pH of the solution are known. • And, the molar proportion of A- to HA can be calculated if the pH and pKa values areknown. MGD 2017/ DR. AL-BARQAAWI 24 Thank you for attention 25