Water PDF - Biochemistry Lecture Notes

2. Water Recommended reading: Chapter 2 (Lehninger Principles of Biochemistry. Nelson & Cox-7th Edition) Course Proficiencies covered: 1. Describe the relationships between water, pH, solutes and biological molecules 2. Interpret tabular and graphical information rel...

2. Water Recommended reading: Chapter 2 (Lehninger Principles of Biochemistry. Nelson & Cox-7th Edition) Course Proficiencies covered: 1. Describe the relationships between water, pH, solutes and biological molecules 2. Interpret tabular and graphical information relating to biochemistry Jayshree Mishra Office: Rm. 213 Poll Everywhere login: mishra Learning goals: Describe chemical and molecular properties of water Describe the types of interactions between molecules. Describe behavior of: (a) charged, (b) polar, (c) non- polar, and (d) amphipathic molecules in water Discuss the concepts of micelles, membranes, and lipid bilayer model in aqueous environment. Describe ionization of water and its significance. Key concept: The just-right polarity and extraordinary ability of hydrogen-bonding are key to biological essentialness of water molecule.  Water Is the Medium for Life Life evolved in water due to the protection it provides from UV light & heat. (heat capacity and heat of vaporization) Organisms typically contain 70–90% water. Chemical reactions occur in aqueous milieu. Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes.  Structure of the Water Molecule The octet rule dictates that there are four electron pairs around an oxygen atom in water. Two of these pairs covalently link two hydrogen atoms to a central oxygen atom. The two remaining pairs remain nonbonding (lone pairs). Water geometry is a distorted tetrahedron. The electronegativity of the oxygen atom induces a net dipole moment. Because of the dipole moment, water can serve as both a hydrogen bond donor and acceptor.  Hydrogen Bonds Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a covalently bound hydrogen and lone pair of electrons. They typically involve two electronegative atoms (frequently nitrogen and oxygen). Hydrogen Bonding in Water  Importance of Hydrogen Bonds Source of unique properties of water Structure and function of proteins Structure and function of DNA Structure and function of polysaccharides Binding of substrates to enzymes Binding of hormones to receptors Matching of mRNA and tRNA 1. What does matching of mRNA and tRNA do? Biological Relevance of Hydrogen Bonds  Water as a Solvent Water is a good solvent for charged and polar substances: – amino acids and peptides – small alcohols – carbohydrates Water is a poor solvent for nonpolar substances: – nonpolar gases – aromatic moieties – aliphatic chains Dissolving Salts Involves Breaking Ionic Interactions 2. Why are nonpolar molecules poorly soluble in water? Solubility of Polar and Nonpolar Solutes 3. Which one is more polar H2O or H2S and why?  Water Surrounding Nonpolar Solutes Has Lower Entropy High entropy Low Entropy Low entropy is thermodynamically unfavorable, thus hydrophobic solutes have low solubility. Fluid Mosaic Model of Membrane Structure: The Lipid Bilayer CFTR: Cystic Fibrosis Transmembrane Conductance Regulator: An example of how a protein is located in the lipid membrane  CFTR: Cystic Fibrosis Transmembrane Conductance Regulator: An example of how a protein is located in the lipid membrane Common location of mutation leading to cystic fibrosis  Cystic Fibrosis Affects Several Organs Always Seldom Often nih.gov 5. What is the diagnostic test to confirm CF?  Ionization of Water Concentrations of participating species in an equilibrium process are not independent but are related via the equilibrium constant: → H+ + OH⎼ H2O  [H+] [OH⎼] Keq = __________ [H2O] Keq can be determined experimentally, it is 1.8 x 10–16 M at 25C. [H2O] can be determined from water density, it is 55.5 M. Ionic product of water: K w = K eq  [H 2 O] = [H + ][OH - ] = 110 −14 M 2 In pure water, [H+] = [OH–] = 10–7 M.  At this time you should know 1. Describe the differences between hydrogen bonds, and ionic, hydrophobic and van der Waals interactions. 2. Describe polarity in water molecule and how it hydrogen bonds with itself, charged solutes, and biological molecules. 3. Describe the properties of non-polar and amphipathic molecules in water. 4. Describe the relationship between polarity and water solubility. 5. Describe micelles, membranes, and the lipid bilayer models. 6. Describe CFTR molecule, its role in cystic fibrosis, and the common symptoms observed in CF. 7. Describe the ionization of water and relationships between Keq and Kw