Water, Weak Interactions, and Buffers - Lecture Slides PDF

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University of Saskatchewan

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water properties biochemistry hydrogen bonds biomolecules

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These lecture slides provide an overview of water's structure, its weak interactions, and its significance within biological systems. The slides cover topics such as water's unique properties, hydrogen bonds, and buffers, including their roles within biological systems. Diagrams and examples are provided to illustrate key concepts.

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Chapter 2: Water, Weak Interactions and Buffers Objectives: Dissect the structure-function relationship of water molecules. Characterize the importance of water to biological systems. Investigate the ability of water to act as a solvent. Explore how the structure of biomolecules is influen...

Chapter 2: Water, Weak Interactions and Buffers Objectives: Dissect the structure-function relationship of water molecules. Characterize the importance of water to biological systems. Investigate the ability of water to act as a solvent. Explore how the structure of biomolecules is influenced by water. Characterize the non-covalent interactions within biomolecules. Determine the mechanisms, and importance, of buffers and pH. Text Readings: Stryer 2nd or 3rd Editions: All of Chapter 2 Water -General- Water is the most abundant molecule in living organisms. Water has both passive and active roles in biochemistry. Passive: The structure (hence function) of biomolecules form in response to interaction with water. For example, protein folding is driven to bury hydrophobic residues. Active: Water is a participant in many biochemical reactions. For example, peptide bond formation releases a water molecule. Water -Matrix of Life- Water is so critical to our understanding of the molecular basis of life that it shapes the way we look for life. While the presence of water on another planet does not ensure life, it is difficult to imagine life (at least as we know it) in the absence of water. Further, the presence of water on other planets is a critical determinant of their habitability by humans. More recently, scientists have started to contemplate alternate liquids, such as ammonia or formamide, that might also be suitable for life. formamide Water -Structure/Function Relationship- The simple structure of water offers a perfect starting point to illustrate the structure-function perspective. Oxygen and hydrogen differ in their electronegativities. > nitrogen - is electronegative Oxygen is more electronegative than hydrogen, giving water a pulls e-towards permanent dipole. Oxygen has a partial negative charge and each hydrogen has partial positive charge. each water can donate/accept 2. hydrogen bonds Charge-charge ↑ The dipole of a water molecule influences it’s ability to: form electrostatic interactions with charged molecules. form hydrogen bonds (including with other water molecules). Hydrogen Bonds -General- Hydrogen bonds are electrostatic interactions between an electronegative atom with a hydrogen covalently linked (donor) to another electronegative atom with a free electron pair (acceptor). Oxygen and nitrogen are common hydrogen bonders within biomolecules. Oxygen and nitrogen can each serve as hydrogen bond donors and acceptors. The significance of the hydrogen bond for physiology is greater than that of any other single structural feature. -Linus Pauling Hydrogen Bonds -Strength and Geometry- Hydrogen bonds are relatively weak, ~5% the strength of a covalent bond. Hydrogen bonds are about double the length of a covalent bond. The strength of a hydrogen bond depends on its geometry. For example, anti-parallel beta sheets are more stable than parallel because there is better geometry of hydrogen bonding. Parallel Anti-Parallel Water -Unusual Properties- Each water molecule can donate and accept two hydrogen bonds. Within water, each water molecule has the potential to participate in four hydrogen bonds with four other water molecules. In liquid water, each molecule participates in an average of 3.4 hydrogen bonds in dynamic “flickering clusters”. The hydrogen bonds between water molecules confer great internal cohesion which influences the properties of water. perfe · Water -Unusual Properties- The large number of hydrogen bonds within water contributes to the high heat of vaporization and specific heat capacity of water. Heat of Vaporization: the amount of heat requires to vaporize a liquid at its boiling temp. Specific Heat Capacity: the amount of heat required to raise the temperature of a substance one degree. Water -Unusual Properties- Water has a higher melting point, boiling point, and heat of vaporization than most common solvents. Water -Unusual Properties- Living organisms burn tremendous amounts of energy, a by-product of which is heat. Most living organisms are isothermic, they need to regulate and maintain their temperatures. The high composition of water within our bodies, coupled with the high specific heat capacity of water, helps us to: - > ISOTHERMIC Water -Unusual Properties- In ice, each water molecule participates in four hydrogen bonds with other water molecules. This ordered arrangement of ice has a lower density than liquid water, as a consequence, ice floats on water. insulating motion slows down. 1 ayer (ice) locks in hydrogen bonds - ICE ice takes up more volume than liquid water. Polywater -A New, Deadlier Form of H20- A Soviet physicist was studying the Polywater properties of water forced through quartz Freezing Temp -40 oC tubes. Boiling Temp 150 oC This treatment resulted in a new form of Density 1.4 g/cm3 water (polywater) with a higher boiling Viscosity 15X greater than point, lower freezing point, and much regular water higher viscosity than ordinary water. Polywater was proposed to result from a novel arrangement of interaction between water molecules. Hot water freezes faster than COLD water. Polywater -A New, Deadlier Form of H20- There was considerable concern that the unusual networking of water molecules within polywater was self-propagating and could be used as a weapon. "I regard the polywater as the most dangerous material on earth. Even as I write there are undoubtedly scores of groups preparing polywater. Treat it as the most deadly virus until its safety is established.” It turned out to be B.S. (Bad Science). An American scientist demonstrated that his own sweat had properties remarkable similar to polywater, suggesting the unique properties reflected the influence of impurities. Waters Ability to Act as a Solvent -Electrostatic Interactions- Water molecules can interact, and dissolve, charged solutes through formation of layers of hydration. By virtue of their small size and permanent dipole, water molecules have great versatility in interacting with both positively and negatively charged ions. Tortiona -and Waters Ability to Act as a Solvent -Hydrogen Bonds- Biomolecules have functional groups that can form hydrogen bonds. These groups can hydrogen bond within the same molecule, other biomolecules, or with water. By virtue of their small size and ability to serve as either donors or acceptors, water molecules are ideal hydrogen bonding partners. Water -Solubility of Dissolved Molecules- The solubility of molecules in water depends on the ability to interact with water molecules. Molecules that carry charge (+ or -) and/or participate in hydrogen bonds (donors or acceptors) have the greatest solubility in water. does it carry Hydrophilic (water-loving) molecules are polar. charge ? Hydrophobic (water-fearing) molecules are non-polar. ↓ POLAR ! Yes - Amphipathic molecules contain both hydrophobic and hydrophilic portions (e.g. fatty acids). Water -Solubility of Dissolved Molecules- Many biologically important gases, such as CO2 and O2, are non-polar and therefore have limited solubility in water (and blood). Their limited solubility presents a challenge for their transport. Specialized transport proteins and strategies are required for transport of CO2 and O2 (to be discussed in a later chapter). Water -Behavior of Amphipathic Substances- POLAR When an amphipathic molecule is mixed with water the hydrophilic regions interact favorably with water but the hydrophobic regions cluster together to present the smallest NOWR surface to water. The forces that hold the non-polar regions of the molecule together are called hydrophobic interactions. Most biomolecules are amphipathic. Hydrophobic drive is a primary driving force in formation and stabilization of biomolecular structures. Weak Interactions -Crucial to Molecular Structure and Function- Most biomolecules represent stable polymers of covalently linked building blocks. The three-dimensional structures formed by these polymers are largely determined through non-covalent interactions. Interactions between biomolecules are also largely determined by non-covalent interactions. covalent breaking bonds very hard Non-covalent interactions enable: - > to do. Transient, dynamic interactions. Flexibility of structure and function. Weak Interactions -Crucial to Molecular Structure and Function- Non-covalent forces influence: formation and stabilization of structures of biomolecules. recognition/interactions between biomolecules. binding of reactants to enzymes. Non-covalent interactions within biomolecules include: hydrogen bonds. ionic (electrostatic) interactions. hydrophobic interactions. van der Waals interactions. Weak Interaction anything th m bond -Hydrogen Bonds- herogen Many of the functional groups with biomolecules have hydrogen bonding capacity. These groups can form hydrogen bonds with: Water molecules a Groups in the same molecule (intramolecular) Groups in other molecules (intermolecular) Whogebote complementary Specificity of DNA ↳ result of hydrogen bonds. Weak Interactions twoto ether -Hydrogen Bonds- Is > - which S Hydrogen bonds are critical for the specificity of biomolecular interactions but not for the formation of biomolecular structures. In the unfolded state, these groups can hydrogen bond with water, a nearly perfect hydrogen bonder. Little is to be gained, from a hydrogen bonding perspective, with formation of higher order structures. Weak Interactions -Ionic (Electrostatic) Interactions- Electrostatic interactions between charged groups can be attractive (oppositely charged groups) or repulsive (similarly charged groups). The magnitude of contribution of ionic interactions to biomolecular structures is reduced by the shielding of these groups by water molecules. Water tends to shield the charged groups, greatly diminishing the strength of the interaction. The strength of electrostatic interactions depends on the distance separating the atoms and the nature of the intervening medium. Weak Interactions -van der Waals Forces- Interaction between permanent and induced dipoles; short range, low magnitude interactions. When two atoms are separated by the sum of the van der Waals radii, the attraction is maximal. When two surfaces of complementary shapes come together a large number of atoms are brought into van der Waals contact. Abundant in the core of folded proteins. Weak Interactions -Hydrophobic Effect- Drive to have polar groups interacting with water and non-polar regions shielded away from water. For example, in protein folding: – Non-polar side chains cluster in the interior of the protein, away from water. – Polar and charged side chains remain on the outer surface facing water. Notably the folding of a protein involves creation of a more ordered state, which seems to be in contradiction of the Second Law Thermodynamics. Weak Interactions -Thermodynamics of the Hydrophobic Effect- The water molecules around hydrophobic molecules are more ordered than they would be in pure water, as such, the introduction of the non-polar molecule causes a decrease in the entropy of water. The association of non-polar molecules (or regions) releases some of the ordered water molecules, resulting in an increase in the entropy of water. The folding of a polypeptide decreases the entropy of the polypeptide but increases the entropy of the associated water. Does Water have a Memory? Andy Dufresne: You know what they say about the Pacific? Red: No. Andy Dufresne: They say it has no memory. -The Shawshank Redemption Does Water have a Memory? A paper reported that an extreme dilution of a biomolecule retained biological activity. The extent of the dilution was such that there was no possibility that even a single molecule remained. The authors suggested that water molecules “remember” what the original molecule looked like through retention of the interactions that existed between water molecules in the presence of active agent. This was published in Nature, the most respected scientific journal. In the following issue, following much uproar, Nature offered: "We conclude that there is no substantial basis for the claim that (the molecule) at high dilution retains its biological effectiveness, and that the hypothesis that water can be imprinted with the memory of past solutes is as unnecessary as it is fanciful.” Bad Science Can be Big Business Homeopathic remedies are prepared by repeatedly diluting a chosen substance; often 30 sequential dilutions of 1 in 100. This corresponds to a dilution of 1 in 1, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000. By our current understanding of the natural world, homeopathy makes no sense. Countless investigations have failed to find any scientific merit to homeopathy and yet selling water as medicine remains a multi-billion dollar industry. The disproven theory that water molecules remember the shapes of molecules has been used as support of homeopathy. Ionization of Water In solution, the structure of water is more complicated than H2O. Water has a limited tendency to ionize to hydrogen ions (H+) and hydroxide ions (OH-). H2O ßà H+ + OH- Keq = [H+][OH -] / [H2O] = 1.8 x 10-16 M and [H2O] = 55.5 M therefore 1.8 x 10-16 M x [55.5 M] = [H+][OH-] Kw = [H+][OH-] =1.0 X 10-14 M2 Kw is the ion product of water. The pH scale It is more convenient to express [H+] as pH. pH = -log [H+] = log 1/[H+] e.g. [H+] = 1 X 10-5 M or 0.00001 M pH = -log [10-5] pH = 5 e.g. [H+] = 1 X 10-6 M or 0.000001 M pH = -log [10-6] pH = 6 pH is a log scale such that the difference of 1 pH unit equals a 10-fold difference in [H+]. Weak Acids and Bases have Characteristic Dissociation Constants Strong acids and bases dissociate completely in water. Weak acids and bases do not dissociate completely in H2O and the extent of dissociation can be quantified. Weak acids can serve as buffers. Ka = [H+][CH3COO-] / [CH3COOH] Ka values often expressed as pKa’s (pKa = -log Ka). Titration Curves Reveal the pKa of Weak Acids buffer : wh resist pH changes The ratio of the acid to the conjugate acid or base being added base changes over the course of the titration curve. When pH = pKa then [A-] = [HA]. more protons = harder to donate When pH = pKa the solution is best able to resist changes in pH. lower value = stronger acid Buffering region extends one pH unit on either side of the pKa point. For a weak acid of pKa 4.76, the buffering range would be 3.76 to 5.76. Titration Curves Reveal the pKa of Weak Acids The line in red represents the weakest acid. The line in blue represents the strongest acid. The lower the pKa, the stronger the acid. Molecules can have Multiple Ionizing Groups Buffers are Important to Biological Systems Organisms need to be able to maintain a constant pH. Changes to pH could alter the protonation state of biomolecules, potentially changing their structure and function. A number of weak acids that serve to buffer biological systems. For example, the pH within blood is maintained by a bicarbonate buffer system. CO2 + H20 Hz COg + H2COg * HCOji + H ↑ blood pH hyperventaling = Compensatory respiratory alkalosis serves to maintain the ratio of H2CO3/HCO3- to maintain a constant pH. The Henderson-Hasselbalch Equation Describes the relationship between: (1) the pH of the solution. (2) the pKa of the weak acid (3) the relative concentrations of the weak acid (HA) and conjugate base (A-) PH = pKa + As 10g Given any two of these variables it is possible to calculate the third. #u Henderson-Hasselbalch Sample Questions HA 1) Calculate the pH of a mixture of 0.01 M acetic acid and 0.1 M sodium acetate. pKa of acetic acid is 4.76 base A more = PH & than pKa pH = pKa + log [A-] / [HA] pH = 4.76 + log 0.1 / 0.01 pH = 4.76 + 1.0 = 5.76 2) Calculate the pKa of lactic acid given that a mixture of 0.01 M lactic acid and 0.087 M lactate has a pH of 4.80. MA A = pH = pKa + log [A-] / [HA] pKa = pH – log [0.087] / [0.01] pKa = 4.80 – 0.94 = 3.86 Copyright Sourcing Images/Figures/Tables from Textbook – Permission: Courtesy of MacMillan Learning. Slide 3a: Source: https://en.wikipedia.org/wiki/Ammonia#/media/File:Ammonia-3D-balls-A.png Permission: Public Domain. Courtesy of Ben Mills. Slide 3b: Source: https://en.wikipedia.org/wiki/Formamide#/media/File:Formamide-2D.png Permission: Public Domain. Slide 6: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 46. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 9: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 44. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 10: Source: http://www.thlog.com/snoopy-stay-cool-sticker/ Permission: This material has been reproduced in accordance with the University of Saskatchewan interpretation of Sec.30.04 of the Copyright Act. Slide 11: Source: http://almerja.com/reading.php?idm=76592 Permission: This material has been reproduced in accordance with the University of Saskatchewan interpretation of Sec.30.04 of the Copyright Act. Slide 12: Source: http://science.sciencemag.org/content/sci/164/3887/1482.full.pdf Permission: This material has been reproduced in accordance with the University of Saskatchewan interpretation of Sec.30.04 of the Copyright Act. Slide 16: Source: http://kemkorner.blogspot.com/2012/09/ Permission: This material has been reproduced in accordance with the University of Saskatchewan interpretation of Sec.30.04 of the Copyright Act. Slide 17: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 47. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 18: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 48. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 23: Source: http://www.wikiwand.com/en/Salt_bridge_(protein_and_supramolecular) Permission: CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0/). Slide 26: Source: https://blog.generalmills.com/2014/09/have-you-experienced-the-cheerios-effect/ Permission: Courtesy of ©2018 GENERAL MILLS INC Slide 30: Source: https://immunizationalternatives.com/standard-hp-diseases/ Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 32: Source: https://en.wikipedia.org/wiki/PH#/media/File:216_pH_Scale-01.jpg Permission: CC BY 3.0 (http://creativecommons.org/licenses/by/3.0/) Courtesy of OpenStax.

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