Biochemistry of Water PDF

Biochemistry of Water Cavendish University (School of Medicine)  Learning objectives Understand and outline the physical properties of water Understand that water ionizes to form hydronium ions and hydroxide ions. Understand how acids and bases affect the pH of a solu...

Biochemistry of Water Cavendish University (School of Medicine)  Learning objectives Understand and outline the physical properties of water Understand that water ionizes to form hydronium ions and hydroxide ions. Understand how acids and bases affect the pH of a solution. Understand the relationship between pH and pK for a solution of weak acid. Understand how a buffer works. Carry out calculations involving pH and pKa values of buffer systems Explain the role of buffers in biological systems Introductory Biochemistry Cavendish School of Medicine  The colorless, odorless, and tasteless nature of water belies its fundamental importance to living organisms. Water and its limitations as a solvent has important implications for the structures and functions of biological molecules. Introductory Biochemistry Cavendish School of Medicine About 70% of the mass of the human body is water. Water is central to biochemistry for the following reasons: 1. Nearly all biological molecules assume their shapes (and therefore their functions) in response to the physical and chemical properties of the surrounding water. 2. The medium for the majority of biochemical reactions is water. Reactants and products of metabolic reactions, nutrients as well as waste products, depend on water for transport within and between cells. 3. Water itself actively participates in many chemical reactions that support life. Introductory Biochemistry Cavendish School of Medicine  Water is polar. The opposite ends have opposite charges In a water molecule, each oxygen atom is partially negative. Each hydrogen atom is partially positive. This phenomenon is called charge separation. Oxygen does not share electrons well with other atoms. Oxygen takes more than its share of electron density, that is why it has a partial negative charge. The hydrogen atoms are stripped of much of their electron density and so carry a partial positive charge. In liquid water and especially in solid water, the molecules interact strongly with each other, with preferred orientations. Polarity allows water molecules to form hydrogen bonds with each other.  Hydrogen + bond Polar covalent bonds  +  +  + Each water molecule can bond to max. of 4 neighbor molecules via. hydrogen bonds Hydrogen bonds are weak bonds which are constantly reforming  IMPORTANCE OF WATER(MEDICAL AND BIOLOGICAL) 1. Water is an essential constituent of all forms of life. 2. Water is present in every cell. It is the medium in which all cellular events occurs. 3. Water is required for enzyme action and for the transport of solutes in the body. 4. Water aids the folding of biomolecules like proteins, nucleic acids. 5. Semi-fluid nature of body is due to water. 6. Water regulates body temperature. 7. Water accelerates biochemical reactions by providing ions. 8. Water content in the body alters in dehydration.  Water has all sort of strange and unusual properties. 1. Its density decreases when it freezes (ice floats). 2. It has a high boiling point and high heat of vaporization. 3. It has high surface tension. 4. It dissolves many salts (like sodium chloride) and polar molecules (like ethanol). 5. It does not dissolve non-polar substances (oil and water don’t mix). 6. It has high heat capacity 7. In the presence of amphipaths, it readily forms compartments (like in cells).  Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 70–95% water The abundance of water is the main reason the Earth is habitable Four main properties of water contribute to Earth’s suitability for life Four of water’s properties that facilitate an environment for life are 1. Adhesive and cohesive behavior 2. Ability to moderate temperature 3. Expansion upon freezing 4. Versatility as a solvent Property 1: Adhesion and Cohesion of Water Molecules Cohesion: an attraction between molecules of the same kind. – Water is very cohesive. – Cohesion causes water molecules to be drawn together. – Produces surface tension. Allows some insects and spiders to walk on water. Cohesion of water occurs due to hydrogen bonds holding water molecules together – Cohesion helps the transport of water against gravity in plants Adhesion is an attraction between different substances, for example, between water and plant cell walls  Surface tension is the elastic like force existing in the surface of a body, especially a liquid, tending to minimize the area of the surface. Surface tension is related to cohesion. A combination of both adhesion and cohesion contributes to capillarity. Property 2: Moderation of Temperature by Water Think about the weather forecast… Why does the shore stay warmer in the winter, and cooler in the summer? Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat with only a slight change in its own temperature Because water forms so many hydrogen bonds, it takes large amounts of heat energy to speed up water molecules, and increase its temperature. Causes water’s heat capacity (energy to increase Temp.) to be relatively high. Why is this important to us? Think within.  Specific heat of water is high The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC Kinetic energy is the energy of motion Heat is a measure of the total amount of kinetic energy due to molecular motion Temperature measures the intensity of heat due to the average kinetic energy of molecules Temperature measures average speed of the molecule The specific heat of water is 1 cal/g/ºC Water resists changing its temperature because of its high specific heat It takes “a lot” of heat for water to increase 1oC because of hydrogen bonds Heat first must break the hydrogen bonds, AND THEN… the molecules of water can begin to move!!! Therefore water is able to absorb heat, without increasing in temperature, better than many substances. The abundance of water in the cells and tissues of all large multicellular organisms means that temperature fluctuations within cells are minimized. This feature is of critical biological importance since the rates of most biochemical reactions are sensitive to temperature.  As a result: Water stabilizes temperatures. = acts as a heat sink H20 absorbs and stores MUCH heat from sun & air with slight changes in temperature For water to increase in temp. water molecules must be made to move faster… this requires breaking hydrogen bonds, and THAT absorbs heat. Therefore water will change temperature less when it absorbs or looses an amount of heat than other substances Water is also able to retain heat better than many substances (resists cooling) For water to decrease in temp. water molecules must be made to move more slowly. This requires forming hydrogen bonds. The forming of H-bonds gives off heat (hence counteracting cooling tendencies as heat is lost from liquid water) As a result, the air around the cooling water becomes warm  Heat of vaporization of water is high Heat of Vaporization is the amount of energy needed to convert 1.0g of a substance from a liquid state to a gaseous state to a gaseous state Water resists evaporating (vaporizing) because H-bonds must be broken in order for water to transition from liquid to the gas state. Because water has a high heat of vaporization Helps our bodies and our planet to maintain our temperature within a tolerable range. When we get hot and sweat, water evaporates from our skin and cools us. Since the evaporation of water requires a considerable amount of energy, it is very effective in cooling us. Evaporation is transformation of a substance from liquid to gas As a liquid evaporates, its remaining surface cools, a process called evaporative cooling Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water This contributes to the ability of water to serve as local heat sinks (lakes, ponds), global heat sinks (oceans)..  High melting point (0oC) Water has an unusually high melting point when compared to that of other substances close to it like hydrogen sulfide due to the hydrogen bonding between water molecules. In its solid form (ice), each water molecule is subject to four different hydrogen bonds – – two hydrogens that are capable of each being a hydrogen bond donor and an oxygen that is capable of accepting two hydrogen bonds from neighboring molecules.  High boiling point (100oC) Just like with its melting point, water molecules also have a higher boiling point than one would expect. Likewise, the reason for this is the hydrogen bonding between neighboring water molecules. Because hydrogen bonding is a relatively strong intermolecular force, high heat energy is required to break up the force. The difference between the boiling point and freezing point of water is one of the largest ranges of any compound. It is this span of temperature that mirrors the range of where life can exist, from bacteria to humans.  Property 3: Floating of Ice on Liquid Water Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense – Water reaches its greatest density at 4°C – If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth. Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable  Less dense as a solid than liquid - Bodies of H2O do not freeze from bottom up  Property 4: Water- The Solvent of Life A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution The solute is the substance that is dissolved An aqueous solution is one in which water is the solvent Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily – When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell   Na        Na    Cl Cl         – When a crystal of table salt is placed in warm water, sodium and chloride ions are attracted to the polar water molecules. Because they are attracted to, or have an affinity for water, Cl- & Na+ are said to be hydrophillic (water- loving) Cl Cl - - Na+ Na+ Water Water  – Ions break away from the crystal and are surrounded by water molecules. Cl - Cl - Na+ Na+ Water Water  – The ions gradually become dispersed in the water, forming a solution. Cl - Cl - Na+ Na+ Water Water  Water can also dissolve compounds made of nonionic polar molecules Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions +   +  Hydrophilic and Hydrophobic Substances A hydrophilic substance is one that has an affinity for water A hydrophobic substance is one that does not have an affinity for water – Hydrophobic molecules like lipids/cell membranes tend to repel water because they have relatively nonpolar bonds like A colloid is a stable suspension of fine particles in a liquid  Dissociation of Water Molecules Acidic and basic conditions affect living organisms A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other – The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) – The molecule with the extra proton is now a hydronium ion (H3O+), though it is often represented as H+ – The molecule that lost the proton is now a hydroxide ion (OH–) – Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed  Though statistically rare, the dissociation of water molecules has a great effect on organisms – Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell  Concentrations of H+ and OH– are equal in pure water – Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH– The pH scale is used to describe whether a solution is acidic or basic (the opposite of acidic)  Acids & Bases An acid is any substance that increases the H+ concentration of a solution (proton donor) A base is any substance that reduces the H+ concentration of a solution (proton acceptor)  The pH Scale In any aqueous solution at 25°C the product of H+ and OH– is constant and can be written as [H+][OH–] = 10–14 The pH of a solution is defined by the negative logarithm of H+ concentration, written as pH = –log [H+] For a neutral aqueous solution [H+] is 10–7 = –(–7) = 7  Acidic solutions have pH values less than 7 Basic solutions have pH values greater than 7 Most biological fluids have pH values in the range of 6 to 8  Buffers The internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution Most buffers consist of an acid-base pair that reversibly combines with H+. Buffers are very important because certain biomolecules are very sensitive to changes in pH. For example enzyme activity can be reduced or abolished when pH deviates from the normal range ->buffer accepts H+ from the solution when the solution is too acidic ->buffer donates H+ to the solution when the solution is too basic Henderson-Hasselbach Equation HA = weak acid 1) Ka = [H+][A-] [HA] A- = Conjugate base 2) [H+] = Ka [HA] [A-] 3) -log[H+] = -log Ka -log [HA] [A-] 4) -log[H+] = -log Ka +log [A-] * H-H equation describes [HA] the relationship between pH, pKa and buffer 5) pH = pKa +log [A-] concentration [HA] pKa: the negative logarithm of the ionization constant of an acid, a measure of the strength of an acid. The lower the pKa, the stronger the acid. Study questions 1. Which atoms make a water molecule? 2. What are buffers? 3. If a solution is too acidic, how do buffers respond to reverse the situation? 4. If a solution is too basic how do buffers ,respond to reverse the situation? 5. Why are some insects able to float on water? 6. Why is water able to flow up a capillary tube against gravity? 7. What is the pH of a neutral solution? 8. Why are buffers important? 9. What is a hydrophobic substance? 10.What is a hydrophilic substance? 11.What is a solute? 12.What is an aqueous solution? 13.Which are the four emergent properties of water?