Water_Structure_and_Properties_2024.pdf

BCCB2000 Foundations of Biochemistry Water: Structure and Properties Ricardo L. Mancera WARNING This material has been reproduced and communicated to you by or on behalf of Curtin University in accordance with section 113P of the Copyright Act 1968 (the Act) The material in this communication may be...

BCCB2000 Foundations of Biochemistry Water: Structure and Properties Ricardo L. Mancera WARNING This material has been reproduced and communicated to you by or on behalf of Curtin University in accordance with section 113P of the Copyright Act 1968 (the Act) The material in this communication may be subject to copyright under the Act. Any further reproduction or communication of this material by you may be the subject of copyright protection under the Act. Do not remove this notice. 1 Learning objectives  When you complete this lecture you will be able to  Appreciate the importance of water for biology  Understand the relationship between weak molecular forces and the chemical and physical properties of water  Describe the concept of diffusion  Describe the concept of osmosis  Understand the concepts of pH and buffers  Use the biochemical knowledge you learned to answer questions and solve problems The roles and regulation of water  Water regulates body temperature    Ectothermic (cold-blooded) and endothermic (warm-blooded) organisms Water reduces friction between surfaces (lubricant)  Between bones in joints  In mucous and saliva Water maintains cell shape Synovial fluid (mostly water) 2 The roles and regulation of water  Water is a shock absorber   In the brain through other water-filled cavities Water transport is carefully regulated in most organisms  Changes in water content, especially in animals, are often not well tolerated and can be life threatening  The cell wall in plants offers protection against changes in water content Water as a solvent  Most organisms are comprised of 60-75% of water (by weight)  About 2/3 of the body’s water resides in cells  No organism is known to be active without water  All known life forms use water for the bulk of their chemical reactions  Many of the organic chemicals and ions required for biochemistry dissolve in water  Water as a liquid allows molecules to come close together in a myriad of forms to react and interact  Impossible in a solid because molecules cannot move (there is no diffusion)  Difficult in a gas because molecules are too far apart 3 Water as a reactant and mediator  Water interacts with other molecules   Forms hydrogen bonds and other non-covalent interactions Water takes part in chemical reactions  As a chemical reactant  As a renewal intermediate  Can release and accept protons, acting as an acid and a base Water as a reactant Condensation reaction Dehydration Hydrolysis reaction Synthesis Hydration Degradation Protein synthesis Protein synthesis Protein degradation 4 Water as a reactant Condensation reaction Dehydration Hydrolysis reaction Synthesis Hydration Degradation Polysaccharide synthesis Glycosidic bond formation Glycosidic bond hydrolysis Water as a reactant Condensation reaction Dehydration Hydrolysis reaction Synthesis Nucleotide synthesis Hydration Degradation Phosphodiester bond formation Phosphodiester bond hydrolysis 5 Water as a reactant Condensation reaction Dehydration Synthesis Hydrolysis reaction Hydration Degradation Triglyceride synthesis Ester bond formation Ester bond hydrolysis Peculiar physico-chemical properties of water  Water expands when frozen    Water is more dense as a liquid  Most solids are more dense than their corresponding liquids  Maximum density at about 4ºC Water has a melting point about 100ºC higher than expected   Most solids contract when frozen Compared to similar hydrides (e.g. H2S and H2Se) Water has a boiling point about 200ºC higher than expected  Stable H-bonds, crystalline arrangement of molecules when frozen Transient H-bonds, molecules more densely packed in liquid near 4°C (but less densely packed at higher temperatures) Compared to similar hydrides 6 Peculiar physico-chemical properties of water  Water has the highest surface tension of any liquid   Water in liquid form has a high specific heat   Only mercury (Hg) has a similar surface tension More heat (energy) required to increase the temperature of 1 g of water by 1°C than any other liquid All of these properties can be explained by the structure and physical properties of water!  In particular, the polarity and hydrogen-bonding characteristics of water molecules The chemistry and structure of water  Oxygen has a valence of 2 O8 Protons: 8 Electrons: 8 Electronic configuration: 1s2 2s2 2p4 Two unpaired electrons in the 2p orbital  Water has two sets of electron lone pairs on the oxygen atom that create an electron dense (electronegative) part of the molecule Electronic distribution and dipole representation 7 The chemistry and structure of water  Water also has two O-H polar covalent bonds, each forming electron-deficient (electropositive) parts of the molecule  Therefore, there are exactly the same number of electron dense lone pairs (2) as there are partial positive charges (2) Two sets of electron lone pairs Water has a permanent dipole due to the bonds being at an angle The chemistry and structure of water  Each water molecule can form, in principle, four hydrogen bonds to other water molecules or other molecules that can also form hydrogen bonds 8 The hydrogen bonds (H-bonds) of water  Arise from the polarity and polarisability of water  H-bond strength is much smaller than a covalent bond but larger than dispersion forces: 2-20 kJ/mole  In the liquid, the strength of H-bonds is about 23 kJ/mole  One water molecule can form four H-bonds  H-bonds are continuously broken and formed  Strength is ideally suited for water to exist as a liquid   There would be no liquid water if H-bonds were 7% stronger or 29% weaker Liquid water is essential and unique for life!  Allows chemical reactions to take place at sufficient rates for biochemical processes to occur and to repair damage (e.g. radiation damage, chemical and thermal decay) The non-covalent interactions of water  Hydrogen bonds  Ion-dipole interactions (also known as charge-dipole)  Dipole-dipole (water can interact with other dipoles)  Dipole-induced dipole (water can induce a dipole in a non-polar molecule)  Dispersion interactions  Hydrophobic interactions Multiple occurrences of these interactions in biochemical processes 9 Interaction of water with gases    Biologically important gases are non-polar  Carbon dioxide (CO2) – two dipoles cancel each other  Oxygen (O2) – electrons shared equally  Nitrogen (N2) – electrons shared equally These important gases have poor solubility in water  Solubility of O2 in water at 37°C is 6.7 mg/L  By comparison, solubility of glucose in water at 37°C is ~900,000 mg/L Some organisms need special carrier proteins to transport O2 in water (haemoglobin, myoglobin) Water-mediated H-bonds between polypeptides The green bonds represent hydrogen bonds Water Polypeptide covalent backbone of protein (side chains not drawn) Water acts as a bridge between the two polypeptide chains 10 Water-mediated disruption of H-bonds between polypeptides Water disrupts hydrogen bonds on the left to create the situation on the right Water-mediated disruption of H-bonds between polypeptides Water disrupts hydrogen bonds on the left to create the situation on the right 11 Water and ion separation  Water dissolves polar and ionic molecules (thus salt crystals do not form in our body) Separated (hydrated) ions Sodium chloride (NaCl) ionic lattice Nelson & Cox (2005) Water and ion separation  Water dissolves polar and ionic molecules (thus salt crystals do not form in our body)  Water separates (hydrates) ions, shielding them from each other  This is referred to as the dielectric effect of water  Reduces electrostatic interactions (attraction and repulsion) between ions or other charged molecules Nelson & Cox (2005) 12 Interaction of water with amphipathic and nonpolar molecules A fatty acid is an example of an amphipathic molecule Amphipathic molecules have polar and non-polar groups Highly ordered H2O molecules form cages around the hydrophobic alkyl chains Nelson & Cox (2005) Interaction of water with amphipathic and nonpolar molecules Dissolution of lipids in water Each lipid molecule forces surrounding H2O molecules to become highly ordered (low entropy) Physico-chemically not possible! Gives rise to the phenomenon known as the hydrophobic effect Nelson & Cox (2005) 13 Interaction of water with amphipathic and nonpolar molecules Clusters of lipid molecules Only lipid portions at the edge of the cluster force the ordering of water. Fewer water molecules are ordered and entropy increases Dissolution of lipids in water Each lipid molecule forces surrounding H2O molecules to become highly ordered (low entropy) Micelles All hydrophobic groups are sequestered from water; ordered shell of water is minimised and entropy increases further A similar mechanism used to form the membranes of cells and cellular organelles Nelson & Cox (2005) Interaction of water with proteins  Hydration of proteins  Water surrounds proteins and other biomolecules as a ‘hydration shell’, making them soluble  Interaction of water on both the surface and interior of the protein  ‘Conserved’ water molecules – specific locations on and within the protein that are always occupied by water across different species   Have a structural (stabilisation) or functional role Similar ‘hydration shells’ can form around other macromolecules  Polysaccharides have a high level of hydration  Nucleic acids have specific hydration sites Accessed from MolMol image gallery at: http://hugin.ethz.ch/wuthrich/software/molmol/gallery.html 14 Interaction of water with proteins  Conformational flexibility depends on degree of hydration   Protein folding is largely determined by the interaction of water with the polypeptide backbone and side chains and hydrophilic interactions   Furthermore, hydrophobic interactions are entirely water-induced forces! Water molecules in the active site of enzymes often mediate biochemical reactions   ‘Hydration shell’ is a hydrogen-bonded network with glass-like properties that influences protein dynamics (i.e. how flexible proteins are) Water molecules are often reactants that give away hydrogen atoms and act as nucleophilic reagents Water molecules are often important for ligand binding to proteins  Hydrogen bonding interactions  Modify shape and size of binding site Interaction of water with proteins  Example: binding of ergosterol to a lipid-binding protein Ordered water molecules Im et al., 2005 15 Water, diffusion and thermal energy  Diffusion is the random movement of molecules (solutes) in a solvent (e.g. water) from a region of high concentration to a region of low concentration  Diffusion results in mixing of the solute molecules within the solvent Water, diffusion and thermal energy  Diffusion is the random movement of molecules (solutes) in a solvent (e.g. water) from a region of high concentration to a region of low concentration  Diffusion results in mixing of the solute molecules within the solvent  The solute and solvent molecules are constantly moving and are self-propelled by thermal energy gained from their environment     Water and other molecules have kinetic energy and are always moving (thermal motion) Total amount of kinetic energy (thermal energy) determines amount of movement Temperature is the average kinetic energy in a system Thermal motions are responsible for initiating many biological (non-covalent) interactions 16 Water, diffusion and thermal energy  Diffusion is the random movement of molecules (solutes) in a solvent (e.g. water) from a region of high concentration to a region of low concentration  Diffusion results in mixing of the solute molecules within the solvent  The solute and solvent molecules are constantly moving and are self-propelled by thermal energy gained from their environment     Water and other molecules have kinetic energy and are always moving (thermal motion) Total amount of kinetic energy (thermal energy) determines amount of movement Temperature is the average kinetic energy in a system Thermal motions are responsible for initiating many biological (non-covalent) interactions Diffusion — Energy of thermal motion Energy Thermal motion and its relation to other energies (kJ/mol) 104 There is sufficient energy in the thermal motion of water at 37°C to affect most of the van der Waals interactions, including some (weak) hydrogen bonds 103 Combustion of glucose (2808 kJ/mol) Covalent bonds in biomolecules (150 to 600 kJ/mol) 102 101 100 Higher energy non-covalent interactions, such as salt bridges and hydrogen bonds (5 to 20 kJ/mol) Thermal motion at 37°C (average about 2.5 kJ/mol) van der Waals interactions (0.5 to 2 kJ/mol) 10-1 17 Water as a solvent and colligative properties  A solution is a mixture of solvent (water) and solute (ions or molecules)  The number of solute molecules affect the physicochemical properties of water:  Elevation of boiling point  Lowering of vapour pressure  Lowering of freezing point  Osmotic pressure  These are referred to as the ‘colligative properties’ of water Osmolarity  The number of solute particles contributes to the osmotic pressure of a solution and is measured by it osmolarity:  Osmolarity of a non-dissociable solute   Osmolarity of a dissociable solute   This is directly the molarity of the solute This is the number of dissociable ‘particles’ of the solute x molarity Osmol is the unit of osmolarity  Equal to the moles of dissociable solute per litre  The osmolarity of a cell is about 308 mOsmol 18 Osmosis  Osmosis is the movement of water across a semi-permeable membrane   The plasma membrane and membrane-bound organelles in the cell are semi-permeable Driven by the differences in osmotic pressure across the membrane  Differences in the total number of osmotically active particles across the membrane  Osmotic pressure is defined as the hydraulic pressure that needs to be applied to prevent the migration of solvent from a region of low solute concentration to a region of high solute concentration Taken from https://derangedphysiology.com/main/cicm-primary-exam/Chapter%20011/colligative-properties-liquids-osmosis-and-osmotic-pressure Osmotic pressure  Osmotic pressure () is directly proportional to the concentration of solute, defined by van’t Hoff’s equation:  = n(C/M)RT where n = number of dissociable particles C = concentration M = molecular weight of the molecules R = universal gas constant T = absolute temperature  The total osmotic pressure of the human plasma calculated with this equation is 5535 mmHg (~7.1 atm)  This is the pressure that would need to be applied to prevent water from moving into the plasma 19 Isotonicity  Isotonic solutions have equal osmolarity to the inside of the cell  Hypertonic solutions have higher osmolarity than the inside of the cell  Hypotonic solutions have lower osmolarity than the inside of the cell Water dissociation and equilibrium  Water can dissociate into two ions: 2H2O ⇌ H3O+ + OH- (H3O+ is the hydronium ion and OH- is the hydroxide ion)  This reaction is simplified as H2O ⇌ H+ + OH- (H+ is commonly referred to as a hydrogen ion or proton)  The equilibrium constant for the dissociation of water (Ka) is Ka = [H+] [OH-] / [H2O] = 1.8 x10-16 M  The magnitude of Ka indicates that minuscule amounts of ions are formed, such that the chemical equilibrium is better represented as H2O ⇌ H + + OH- 20 Importance of proton concentration  The hydrogen ion/proton (hydronium ion) is very reactive and affects many biochemical reactions and processes  The structure and function of macromolecules, such as proteins, is very sensitive to the concentration of hydrogen ions  Many chemical reactions depend on, or are sensitive to, the concentration of hydrogen ions  Most organisms can only operate and survive in a relatively narrow range of hydrogen ion concentrations Water reactions – acid and base  Water is amphoteric   It can function as both an acid and a base Water can exchange protons with other chemical groups  Uncatalysed proton exchange  Catalysed proton exchange  For example, the action of the enzyme D-amino acid transaminase 21 Proton concentration and pH  Proton/hydronium ion concentration is measured by the pH (potential of hydrogen): pH = -log10 [H+(H3O+)]   pH is thus the negative log10 of proton (hydronium ion) concentration At a neutral pH (pH = 7.0 at 25°C) there is an equal concentration of hydrogen and hydroxide ions: [H+] = [OH-] = 1.0 x 10-7 M  This is because the self-ionisation constant of water (Kw) is Kw = [H+] [OH-] = 1.0 x 10-14 Proton concentration, pH and pKa  The pH scale is logarithmic and non-linear  This means that pH = 8 is not twice as large as pH = 4!  A solution at pH = 4 has 104 (10,000) the amount of H+ as a solution at pH = 8.   Generally advisable to first convert pH to actual concentrations before performing mathematical operations with pH values (e.g. averaging) The acid dissociation constant (Ka) is an example of an equilibrium constant. For a monoprotic acid HA and its conjugate base A- in water this can expressed as HA + H2O ⇌ A- + H3O+ which can be simplified to HA ⇌ A- + H+ such that Ka = [A-] [H+] / [HA]  For practical reasons, the logarithmic constant, pKa, is more convenient: pKa = -log10 (Ka) 22 Weaks acids and bases – buffers  An acid can be considered a proton donor and a base a proton acceptor  A proton donor always has a corresponding proton acceptor, and this ‘pair’ is called a conjugate acid/base pair  Weak acids and bases do not completely dissociate in water and hence play an important role as buffers  A buffer is a solution of a weak acid or base that can “resist” a change in pH  Buffers are effective in a range of pKa ± 1 of the weak acid or base  Buffers are critical for controlling the pH inside cells Conjugate acids and bases  A conjugate acid is the species formed by the reception of a proton  A conjugate base is the species formed by the removal of a proton from an acid Acid + NH4+ + CH3COOH +  Base OHOH- ⇌ ⇌ ⇌ Conjugate acid H 2O H 2O + + + Conjugate base NH3 CH3COO- Important conjugate acids and bases in biology Acid Conjugate base Base Conjugate acid H3O+ H2O H3PO4 H2PO4- NH3 NH4+ CH3COOH CH3COO- C6H5CO2- C6H6CO2 NH4+ NH3 PO43- HPO42- HCO3- CO32- OH- H 2O 23 How do buffers work? pKa = -log10Ka where Ka is the acid dissociation constant pKa is a measure of the strength of an acid and is the tendency of the acid to ionise (produce H+) The lower the pKa value the stronger the acid Relatively large additions of OH- do not drastically change the pH over the range pKa ± 1. This means that the weak acid acts as a ‘buffer’ to changes in pH OH- added (fraction titrated) Nelson & Cox (2005) Henderson-Hasselbalch equation  Describes the relationship between the pH of a solution of a weak acid and its base to the concentrations of these species: pH = pKa + log10 [base]/[acid] or pH = pKa + log10 [A-]/[HA]  Used to estimate the pH of a buffer solution containing given concentrations of an acid and its conjugate base, or of a base and its conjugate acid  At half-neutralisation, the ratio [A-]/[HA] = 1; since log10 (1) = 0, at halfneutralisation pH = pKa. Conversely, when pH = pKa, [HA] = [A-]  The numerical value of the acid dissociation constant (pKa) of the acid must be known  Commonly used in biochemistry to prepare a buffer at a particular pH 24 Further reading  Structure of water and hydrogen bonding (Khan Academy): https://www.khanacademy.org/science/ap-biology/chemistry-of-life#structure-ofwater-and-hydrogen-bonding  Garret R.H. and Grisham C.M. (2010) Biochemistry, 4th Edition.  Levitt, M., and B. H. Park. (1993). Water: now you see it, now you don't. Structure 1 (4): 223R226.  Mohammad, O et al. (2005) AcidRBase Reactions Sequential Proton Transfer Through Water Bridges Science 310: 83R86.  Molecular dynamics simulation of molecular motion in water and hydrogen bonding: https://www.youtube.com/watch?v=t5ZFoU0S5iE  Frequently Asked Questions (FAQ) about Dihydrogen Monoxide: http://www.dhmo.org/facts.html (Funny way of looking at water!)  Logarithms and pH: https://web.mst.edu/~gbert/logs/logarithm.html 25