Unit 2 Water Unit 1 PDF

UNIT 2 WATER Structure 2.1 Introduction 2.4 Ionization of Water Expected Learning Outcomes pH 2.2 Noncovalent Inte...

UNIT 2 WATER Structure 2.1 Introduction 2.4 Ionization of Water Expected Learning Outcomes pH 2.2 Noncovalent Interactions in 2.5 Buffers Aqueous Systems Henderson-Hasselbalch Hydrogen Bond Equation Hydrophilic and 2.6 Water as a Reactant and Hydrophobic Interactions Fitness of the Aqueous Vander Waals Environment Interactions 2.7 Susmmary Electrostatic Interactions 2.8 Terminal Questions 2.3 Unique Properties of Water 2.9 Answers 2.10 Further Readings 2.1 INTRODUCTION In Unit 1, you have learned about foundations of Biochemistry. You know living organisms are composed of water, organic molecules and inorganic ions. Water is the most abundant molecule in living organisms. It is essential for life. Life first arose in an aqueous environment. Water makes up 70% or more of the body weight of all living organisms. The unique properties of this ubiquitous substance have a profound influence on the chemistry of life. However, water acts as an aqueous medium in which living organisms carry out their biological functions such as metabolism. It can dissolve or dissociate most compounds and is considered as a universal solvent. Water acts as a reactant and is also a product in many metabolic reactions. Therefore, we can say that existence of living beings would not have been possible without water. This unit begins with a brief discussion on noncovalent interactions in aqueous systems (Sec. 2.2). Here, you will learn about structure of water, hydrogen bond, hydrophilic, hydrophobic, Vander Walls and electrostatic interactions. The Sec. 2.3 will discuss the unique properties of water. You will learn about ionization of water and the concept of pH in Sec 2.4. The Sec. 2.5 will explain you about buffers and Henderson-Hasselbalch equation. At the end of this Unitwater as a reactant and fitness of the aqueous environment will be discussed. 19 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... Objectives After studying this unit, you should be able to:  describe the noncovalent interactions i.e. hydrogen bond, hydrophilic and hydrophobic, Vander Walls and electrostatic interactions;  explain the unique properties of water;  explain ionization of water and define pH;  define buffers and derive the Henderson Hasselbalch equation; and  justify water as a reactant and fitness of the aqueous environment. 2.2 NONCOVALENT INTERACTIONS IN AQUEOUS SYSTEMS You might have studied about water in your school chemistry courses. A molecule of water consists of two hydrogen atoms and one oxygen atom. It is represented by chemical formula H2O. However, it constitutes an aqueous medium in which almost all biological processes take place. The solubility of a substance in water depends upon the nature of forces of the functional groups of the substance with water. The unusual properties of water make it an ideal medium for living organisms. Therefore, water is considered as a universal solvent as it dissolves many substances. Water is the principal component of biological systems. Most functions of biomolecules depend upon aqueous medium as they interact with water molecules by weak interactions. Weak interactions, called noncovalent interactions include hydrogen bond, hydrophilic, hydrophobic, vander Waals and electrostatic interactions. These interactions are weak but collectively show significant effects in biological systems. These are involved in maintaining the structure of proteins, nucleic acids, polysaccharides and membrane lipids. Therefore, you will learn about noncovalent interactions involved in aqueous systems such as: l Hydrogen bond l Hydrophilic and Hydrophobic interactions, l Vander Waals interactions, and l Electrostatic interactions. Let us study these interactions one by one. 2.2.1 Hydrogen Bond Hydrogen bond is very common in biological systems. It plays a significant role in biochemical reactions as well as formation of biological structure. Therefore, let us first understand the molecular structure of a water molecule which reveals the cause of the hydrogen bonding. Look at Fig. 2.1 (a) it shows the molecular geometry of a water molecule in 20 which two hydrogen atoms are covalently bonded to one oxygen (O) atom and Unit 2 Water.......................................................................................................................................................................... each hydrogen (H) atom are at the two corners (two bonding electron pairs) and the two nonbonding electron pairs (unshared electron pairs) of oxygen atom are at the other two corners. This geometry looks like a tetrahedron. These nonbonding electron pairs repel each other. As a result, these repulsive forces act to push the hydrogens closer together. Thus, the H-O-H bond angle decreases to 104.5o as compared to 109.5o for a perfect tetrahedron (see Fig. 2.1b). Hence, the structure of water molecule acquires a bent angular geometry or V-shape structure. In a water molecule, the oxygen atom is more electronegative than the hydrogen atom; therefore, the oxygen nucleus attracts the shared pair of electrons than the hydrogen nucleus. The unequal sharing of electrons results in two electric dipoles in water molecule, (one along each O-H bond). The oxygen atom bears a () partial negative charge and each hydrogen atom bears (+) partial positive charge. The presence of opposite charges in a water molecule allow it to form interactions with other water molecules. This interaction is specifically called the hydrogen bond. Hydrogen bond is an electrostatic interaction between partial negatively charged oxygen atom of one water molecule and partial positively charged hydrogen atom of another. Hydrogen bond with the three parallel lines as shown is Fig. 2.1(c). The distance between the participating atoms for hydrogen bonding is around 0.17 nm and distance of a covalent bond (H-O) is approximately 0.096 nm. (a) (b)             (c) Fig.2.1: (a) Tetrahedral geometry of a water molecule; (b) H-O-H bond angle (104.5O); and (c) Hydrogen bonding between two water molecules and the symbol delta () shows a partial weaker charges on a water molecule. 21 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... However, each water molecule can theoretically form H bonds with four nearby water molecules. This feature of water can be viewed in ice formation. Look at Fig. 2.2 showing the network of hydrogen bonding in the crystal structure of ice (solid state). Hydrogen bonds are weak and very unstable. They keep forming and breaking at all times and so most water molecules in liquid state are always hydrogen bonded. Hydrogen bonds provide the stability to water molecules which are accounting for unusual properties of water. Extensive hydrogen bonding is responsible for water being a liquid at room temperature. Fig. 2.2: Hydrogen bonding in ice. However, hydrogen bonding is not unique to water. Water molecules also readily form hydrogen bonds with other kind of biological molecules such as proteins and nucleic acids. Besides, hydrogen bonding is frequently encountered between water and biomolecules and within biomolecules. The electronegative atoms, usually oxygen (O) and nitrogen (N) are involved in forming hydrogen bonds. These atoms primarily occur in amino group NH2) and hydroxyl group (OH). In biological systems, the presence of amino and hydroxyl groups in polypeptides (proteins) and nucleic acids (DNA and RNA) allows to form hydrogen bonding. Look at Fig. 2.3 showing biologically important hydrogen bonds within polypeptide chains as well as de-oxy ribonucleic acids (DNA). Therefore, hydrogen bonding is crucial for the formation of three-dimensional structures of proteins, nucleic acids and other biological molecules. H-bond H-bond (a) Hydrogen bonding between (b) Hydrogen bonding between nitrogenous two polypeptide chains bases of two stands of DNA 22 Fig. 2.3: Hydrogen bonding between biological molecules. Unit 2 Water.......................................................................................................................................................................... 2.2.2 Hydrophilic and Hydrophobic Interactions Hydrophilic means ‘water loving’ and hydrophobic means ‘afraid of water’. Hydrophilic interactions are found between two polar or charged molecules and they interact by forming hydrogen bonds. Hydrophilic molecules (polar) such as glucose, amino acids etc. that experience hydrophilic interactions and readily dissolve in water. On the other hand hydrophobic, (non-polar) molecules such as lipids, oils tend to aggregate together via hydrophobic interactions in order to avoid contact with water. A non-polar molecule is virtually insoluble in water and cannot form hydrogen bonds with water. Thus, they have tendency to self-associate in an aqueous environment. However, there are some compounds in biological systems which have both ‘polar groups’ and ‘non-polar groups’ are called amphipathic molecules (amphi meaning ‘‘both’’ and philos meaning ‘‘loving’’). Amphipathic molecules exhibit both hydrophobic and hydrophilic interactions which play an important role in the formation of biological membranes. For example, phospholipid molecules are amphipathic in nature which contain polar and charged head groups with phosphate and a hydrophobic group as a non-polar tail. You can see in Fig. 2.4 how these molecules are arranged such that their polar hydrophilic regions (shown in blue color) interact with water molecule while non-polar hydrophobic regions (shown in red color) interact with each other with minimum exposure to water molecules. As a result, amphipathic molecules aggregate themselves in an aqueous solution and form micelle (spherical in shape). This shape involves in the formation of cell membrane. Fig. 2.4: Micelle formation 2.2.3 Vander Waals Interactions Vander Waals Interactions are the weakest of all intermolecular attractions and arise due to attraction of the nuclei and electron clouds between atoms or molecules. As you know, electrons are negatively charged and nucleus bears positive charge, so when two uncharged atoms come close together, the 23 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... nucleus of one atom attracts the electron cloud of the other, and vice versa. As a result, the transient dipoles develop in them. Such dipoles are called induced dipoles and the attractions between them are called Vander Waals interactions as shown in Fig. 2.5. These forces require the two atoms to be present at a characteristic optimal distance called vander Waals radius. This interaction contributes in protein interactions with other molecules such as enzyme-substrate interaction, antibody-antigen interaction as well as protein folding. Vender waals' interaction  Fig. 2.5 : Vander Waals interactions. (The delta sign + and  show weaker positive charge on nuclei cloud of one atom and a weaker negative charge on electronic cloud of another atom respectively). 2.2.4 Electrostatic Interactions These interactions occur between polar or ionic compounds for example sodium chloride (NaCl) ions which are held together by strong electrostatic forces. As you know water is a polar molecule, it readily dissolves charged or polar molecules. When crystal form of NaCl (salt) dissolves in water, it  dissociates into the sodium ions (Na+) and the chloride ions (Cl ). These opposite ions are surrounded by water molecules. Fig. 2.6 (a) shows that negative end ( ) of water molecules attracts the sodium ions and the positive end (+) of water molecules attracts the chloride ions. Since water has a high dielectric constant, it dissolves ionic compounds such as NaCl by effectively weakening the electrostatic interactions between them. These ions then get hydrated or solvated by a large number of water molecules which surround them. In biological systems, simple inorganic ions such as sodium (Na +),  potassium (K+), calcium (Ca2+), magnesium (Mg2+), and chloride (Cl ), do not exist as free and each ion is bound by electrostatic interaction between the ion and the oppositely charged end of the water dipole. Fig 2.6 (b) shows the electrostatic interaction between a K+ ion and a water molecule (H2O). Solid Crystal   H+ K.... O + H+ Dissolved ions (a) (b) Fig. 2.6 : (a) Electrostatic interactions between NaCl and water molecules. 24 (b) Electrostatic interaction between K+ ion and a water molecule. Unit 2 Water.......................................................................................................................................................................... SAQ 1 a) Fill in the blanks with suitable words. i) The oxygen atom in water molecule has........unshared electron pairs. ii) The bent shape of a water molecule is due to........... between nonbonding electron pairs of oxygen atom. iii) The oxygen atom in water molecule acquires partial negative charge and hydrogen atom a partial positive charge because of high............. of oxygen atom. iv) A water molecule has permanent electric............................because of partial positive charge on hydrogen atoms and partial negative charge on oxygen atom. v) In a DNA double helix the hydrogen bonds are formed between hydrogen and oxygen and between hydrogen and.................of two bases. b) Choose the correct answer given in the brackets. i) Hydrogen bonds are (weaker/stronger) than covalent bonds. ii) A water molecule in ice can form maximum of (3/4) hydrogen bonds with neighboring molecules. iii) Hydrogen bonds are (unstable/permanent). c) Fill in the blanks with suitable words: i) Lipid molecules have tendency to.......... in an aqueous environment. ii) The inter molecular force of attraction between nuclei and electron cloud of two atoms, results in..................... interactions. iii) Molecules that have both polar and non-polar groups are called........................... molecules. d) Choose the correct answer given in the brackets. i) Water dissolves salt by effectively (weakening/strengthening) electrostatic interaction between ions. ii) In amphipathic molecules, (polar/non-polar) groups aggregate so that they are (in contact with/avoid of) water. 2.3 UNIQUE PROPERTIES OF WATER The unique properties of water are due to hydrogen bonds present in it. We will now learn some of the physical properties of water and relate them to its usefulness for supporting life. 25 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... Table 2.1: Physical properties of Water Property Constants with units Melting point 0o C Boiling point 100oC Heat of vaporization 2260 J/g Dielectric constant 78.5 at 25oC Density (maximum) 999.97 kg/m3 at 4oC Specific heat capacity 1 Hydrogen bonding between water molecules can explain the unusual nature of many physical properties listed in Table 2.1. Let us discuss them one by one: l Melting point: Unless a significant proportion of H bonds are broken the crystal structure of ice cannot be destabilised. The thermal energy required to do so accounts for the melting point. Melting of ice is a spontaneous process. l Water is expected to have a high boiling point. This is supported by the high heat of vaporisation that provides a direct measure of the energy required to overcome the attractive forces between water molecules. Many higher organisms lose excess body heat by evaporation of sweat. l The high dielectric constant of water makes it an effective solvent for dissolving polar (such as sugars) and charged molecules (amino acids such as lysine). It dissolves these compounds by reducing their electrostatic interactions and form hydrogen bonds. On the other hand, non-polar substances tend to cluster together in the presence of water. l Water has the maximum density at 4oC. When it freezes, it is less dense than liquid water. This is advantageous for the survival of aquatic organisms. When water freezes in ponds, ice floats on the surface and life still continues in the liquid water underneath. l Water has a high specific heat. It needs to absorb 4.814 Joules of heat in order to raise the temperature of 1g of H 2O by one degree Celsius (1oC). This is beneficial for organisms to withstand temperature fluctuations. SAQ 2 Fill in the blanks with suitable words: i) Ice floats on surface of water because it is less............................... than liquid water. 26 Unit 2 Water.......................................................................................................................................................................... ii) Water is a good solvent for polar or ionic compounds due to its …...........…. O iii) 1 gram of water needs 4.814 joules of heat to raise the temperature by 1 C is due to................................………… iv) Unique properties of water are due to....................... ……………… 2.4 IONIZATION OF WATER You might have learnt about ionization of water in your 10+2 chemistry courses. You know that water molecules ionize to a limited extent. This  ionization or dissociation produces H + (proton) and OH (hydroxy) ions which is given below:  H2O H + + OH Eq. (1.1) H2O + H + H3O + In reality protons (H+) are not ‘‘free’’ in solution and they immediately associate  with another water molecule to form hydronium ions (H3O ). The hydronium ions are routinely represented as H+. So we can write H+ in place of H3O+. The equilibrium constant (Keq) for Eq. 1.1 is represented as: [H+], [OH ] Eq. (1.2) Keq = [H2O] Keq = equilibrium constant for dissociation of water. From electrical conductivity measurement of water, the value of Keq is 1.8×10 16 M (moles L1 ) at 25°C. Molar: The term molar or molarity is a unit [H + ], [OH ] and [H2O] in brackets represent molar concentration.  used to express the Let us now define another useful constant called the ionic product of water, it is concentration of a 1 substance dissolved represented by Kw. The molecular weight of water is 18 g mole. Therefore, in a solution. It is the concentration of water at 25°C is grams of H2O in 1 Litre (L) is divided by denoted by M. 1 gram molecular weight, i.e.,1000/18 = 55.5 moles L. Thus, the molar Therefore, 1 M is concentration of pure H2O is 55.5 M (molar). gram molecular weight of a substance Substituting the values for Keq and molar concentration of H2O in the Eq. (1.2) per litre of solution  (g mole 1) [H+] [OH ] 1.8 × 10 16 = 55.5 Rearranging, we gets  [H+] [OH ] = (55.5) (1.8 × 1016) To simplify,  [H+] [OH ] = 1.0 × 10 14  The ionic product [H+] [OH ] of water is represented by Kw, thus   14 Kw = [H+] [OH ] = 1.0 × 10 at 25 °C Eq. (1.3) 27 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... According to the Eq. 1.3, the product of hydrogen ion concentration and hydroxyl ion concentration is the constant value of 1.0 × 10 14 at 25°C. The  value of Kw can be used to calculate the concentration of H+ and OH of water.  Kw = [H+] [OH ] = 1.0 × 10  14 [H+] 2 = 1.0 × 10  14 or Solving for [H+], we get [H+] = 1.0 × 10  7 Eq. (1.4) or [H+] = [OH  ] = 1 x 10  7 Moles/L  The Eq. 1.4 states that the concentrations of H+ and OH of pure water at  25°C are equal (10  7 Moles/L). When concentrations of [H+] and [OH ] are equal in any given solution, as in pure water, the solution will be neutral. In acidic solution the concentration of H+ ions is more than the concentration of   OH ions. Similarly, alkaline solution will have higher concentration of OH ions than the H+ ions. As an example let us calculate hydrogen ion concentration in a given solution using the ionic product of water (Kw).  Example 1: (a) What is the concentration of H ions in solution of 0.01 M NaOH.  Kw = [H+] [OH ] = 1.0 × 10 14 M2  Solving for [H ] Kw 1.0 × 10 14 M2 10 14 M2 [H + ] = = =  [OH ] 0.01 M 10 2 M  To simplify, the concentration of H ions will be 1x10 12 M in a given solution.  (b) Calculate the concentration of OH in a solution of 0.1M HCl.  Kw = [H + ] [OH ]  Solving for [OH ] Kw 1.0 × 10  14 M2 10  14 M2  [OH ] = = = + [H ] 0.1 M 10 1 M   13 To simplify, the concentration of OH ions will be 1x10 M in a given solution. 2.4.1 pH Recall from your school chemistry books the concept of pH. The ionization 28 products of water have an important role to define the pH of any solution. The Unit 2 Water.......................................................................................................................................................................... pH is defined as the negative logarithm of the hydrogen ion (concentration in moles/ litre) and can be represented by the following expression: 1 pH = log [H+] = log [H+] where [H+] is hydrogen ion concentration in mol/L. In 1909, S.P.L Sorenson introduced the concept of pH to express hydrogen ion concentration of aqueous solutions. You know that pure water contains an equal amount of hydrogen ions and hydroxyl ions,  [H+] = [OH ] = 1 x 10  7 M at 25°C. The pH of pure water at 25°C can thus be calculated as follows, 1 pH =log = log (1.0  10 ) 1.0  10 7 = log 1.0 + log 10  (log 1 = 0) = 0+7 pH = 7 Therefore, pH of pure water is 7.0 at 25°C. Sometimes, pOH is used to  describe basicity or OH concentration  pOH=  log [OH ] Therefore, the acidic or basic nature of a solution is experssed in terms of pH scale, ranges from 0 to 14 as shown in Fig. 2.7.    [H ] > [OH ]  [OH ] > [H ] Neutral   [H ] = [OH ] · l pH of 7 is a neutral · l pH < 7 is an acidic · l pH > 7 is a basic · Fig. 2.7: pH scale. On pH scale, a pH of 7.0 represents neutral solution in which the number of hydrogen ions is balanced by the same number of hydroxyl ions. The pH of an acidic solution is less than 7 and that of a basic or alkaline solution is more than 7. There is an inverse relation between pH value and hydrogen ion 29 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... concentration. The lower pH value corresponds to higher H+ concentration  [H+]>[OH ] and the higher pH value corresponds to higher concentration of  hydroxyl ions [OH ]>[H+]. However, most of the biochemical reactions are sensitive to pH. The biomolecules such as proteins and nucleic acids carry functional groups that will be charged or neutral depending on the pH. The changes in pH may influence the catalytic activity of enzymes as well as functioning of the cells. Table 2.2 enlists the pH values of some cellular organelles and body fluids of living system. Table 2.2: pH values of some important organelles and body fluids Cellular Organelles and body fluids pH Mitochondria matrix 7.5 Cytosol 7.2 Nucleus 7.2 Blood 7.4 Peroxisomes 7.0 Urine 6.0 Saliva 6.3-6.8 Human skin 5.5 Lysosomes 4.5 Gastric juice 1 SAQ 3 Fill in the blanks with correct words: i) Hydronium ions are routinely represented as......... ions. ii) Lower pH value indicates............concentration of H+ ions. iii) The value of Kw of water is........... iv) The molar concentration of pure water is....... v) pH of a solution indicates the acidic or........nature of solution. vi) pH scale ranges from........... to............ 2.5 BUFFERS A buffer is an aqueous solution that resists a change in pH when small quantities of an acid or a base are added to it. The property of resistance is called buffer action. Most commonly used buffers are made up of a conjugate acid-base pair. Acidic buffer is a mixture of a weak acid and its conjugate base 30 e.g. acetate buffer system. Alkaline buffer contains a weak base and its salt. If Unit 2 Water.......................................................................................................................................................................... hydrogen ions are added to the buffer solution, they are neutralized by the base and similarly on addition of hydroxyl ions they will be neutralized by the acid. As a result of these neutralization reactions, the pH of buffer solution, remains unchanged. In general, an acid is a proton donor and a base is a proton acceptor. An acid and its corresponding base are called conjugate acid-base pair. For example, acetic acid is a weak acid, which dissociates into a proton and acetate ions and vice versa in an aqueous solution as follows. CH3COOH H+ + CH3COO¯ HAc Ac To simplify, acetic acid has been represented by HAc while acetate has been represented by Ac. This is a reversible reaction where acetic acid acts as a proton donor and the acetate acts as a proton acceptor. The ionization of acetic acid is designated by dissociation constant (Ka), thus Ka = [H+] [Ac ] / [HAc] This conjugate acetic acid-acetate pair acts as a buffer system if we add small amounts of either acid or bases to this buffer solution. The acid and base are themselves ionized and releases protons and hydroxyl ions respectively in the buffer solution. Look at Fig. 2.8 to understand how this buffer system works.  Added OH H2O  CH3COOH CH3COO Added H+ Fig. 2.8: Acetic acid-acetate buffer system. If small amount of H+ added to the buffer solution, it will react with acetate ion and form acetic acid.  CH3COO + H+ CH3COOH Likewise, if small amounts of OH added to the buffer solution, H+ of acetic acid will react with the hydroxyl ion and form H2O and acetate ion.   CH3COOH + OH CH3COO + H2O 31 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... In the above reaction, water is formed and no free H+ or OH ions are available. The buffering capacity Thus, the acetic acid-acetate buffer system acts as a conjugate acid-base pair of any buffer system and tends to resist change in pH if little amount of acid or base is added to it. depends on two Thus, a buffer system is capable of absorbing the free H+ or OH. reversible reaction equilibria occurring in Buffers play important roles in maintaining the pH of cells and cellular a solution of nearly organelles to carry out their biological processes. The important biological equal concentrations of a proton donor and buffers in the human body are phosphate buffer and bicarbonate buffer. The its conjugate proton phosphate buffer is an intracellular buffer in the cells which is maximally acceptor. The final effective at pH 6.86 and it has buffering range from 5.9 to 7.9. The bicarbonate outcome is a small buffer is a physiological buffer system in human blood which plays a crucial change in both the pH and the ratio of role to maintain the blood at pH 7.4. conjugate acid and its Let us learn about the equation which has significant role for buffers. base. Buffer system is 2.5.1 Henderson-Hasselbalch Equation effective at a narrow Henderson-Hasselbalch equation is important equation to express the pH range. In general, the buffering region relationship between pH, pKa and conjugate acid-base pair in a buffer system. is one unit on either Let us derive this equation: side of pKa. When Consider a weak acid (HA) that ionizes into a proton (H+) and a base (A ) in an  pH = pKa, the ratio of conjugate acid to aqueous solution: conjugate base is  equal and at this pH HA H+ + A the buffering power is maximal. The equilibrium constant for this ionization is often represented by dissociation constant (Ka), thus + [ H ] [ A ]  pKa: Is the negative Ka = [ HA] logarithm of proton Eq. (i) dissociation constant, and it is Solving [H ] in the Eq. (i),  equal to the pH, at 1[ A ]  1 which half of the = + acid has Eq. (ii) dissociated. [ H+ ] [ Ka][ HA] Taking the logarithm at both sides in the Eq. (ii), 1[ A ]  1 log = log + log [ H+ ] [ Ka][ HA] by substitution of log 1/[H+] = pH and log 1/ [Ka] = pKa, thus we obtain [A ] pH = pKa + log Eq. (iii) [HA] In general it can be represented as: [Base] pH = pKa + log [Acid] The Eq. (iii) is known as the Henderson-Hasselbalch equation, this used to 32 calculate the pH of a buffer solution and the ratio of conjugate base and conjugate acid at a given pH. Unit 2 Water.......................................................................................................................................................................... SAQ 4 Fill in the blanks with correct words: i) Buffers are made up of …………. ii) The ability of a buffer solution to resist the pH change in a solution is known as.................................... ……….. iii) Acids are ……………and bases are ……………… iv) Bicarbonate buffer system maintains the pH at................................. in human blood. v) Henderson-Hasselbalch equation defines the relationship between.......................and pKa of a......................... vi) The ratio of conjugate acid and conjugate base in a solution can be determined by....................... 2.6 WATER AS A REACTANT AND FITNESS OF THE AQUEOUS ENVIRONMENT So far you have learned about the biological importance of water, pH and buffers in maintaining life. In this section, you will study about water as a reactant and the fitness of the aqueous environment. 1. Water as a reactant: Water not only acts as a solvent b is often actively participates as a reactant in various biochemical reactions. These reactions include condensation, hydrolysis, and oxidation-reduction reactions. According to biological needs water acts as a proton donor and proton acceptor. This ability of water is very significant in maintaining life. Let us discuss the ability of water as a reactant with following examples: (i) Fig. 2.9 shows the formation of adenosine tri phosphate (ATP) from adenosine di phosphate and inorganic phosphates (Pi ) is an example of condensation reaction in which a molecule of water is released. The reverse of this reaction, ATP is break down into ADP and Pi by the addition of water, which is a hydrolytic reaction. Condensation reaction Hydrolytic reaction Fig. 2.9: ATP formation and its breakdown (R = Adenosine). 33 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... (ii) In animals, water (H2O) and Carbon dioxide (CO2) are the end products of oxidation of glucose and fatty acids. The dissolved CO2 in blood reacts with water to form bicarbonic acid (H2CO3). Where water is not only acting as a substrate but also serves as a proton donor which helps in maintaining the blood pH at 7.4. The reversisble of this reaction is catalyzed by the enzyme carbonic anhydrase. Carbonic anhydrase CO2 (d) + H2O H2CO3 Where (d) denotes dissolved CO2 in Blood (iii) In plants, water donates electron (e) to chlorophyll and itself undergoes ioxidizes to produce molecular oxygen during photosynthesis. light 2H2 O + 2A O2 + 2AH2 In above reaction, ‘‘A’’ is an electron-accepting species and water serves as electron donor. Inside cell extended networks of H bonded water molecules with other biomolecules exist. This will allow interactions to occur over distances. This network has been used by plants to transport dissolved nutrients during transpiration from roots to the leaves. Water molecules are tightly bound to certain proteins such as cytochromes-f by hydrogen bonding and they assist in the movement of protons through the membrane. 2. Water as a fitness of the aqueous environment: Most living organisms require water more than any other substance. Water is the only essential substance that supports life on the earth as well as in the aqueous environment. Recall the unique properties of water such as high specific heat and high heat of vaporization which are dissussed in the section 2.3. In general, these two properties are very significant in maintaining aquatic life, specifically in maintaining relatively constant body temperatures of aquafic organism irrespective of their surrounding environment. Have you ever noticed that small organisms float or walk on water surface? The floating on surface of water is due to the high surface tension of water. The high degree of internal cohesion of liquid water, due to hydrogen bonding. Water has low density on freezing. It has maximum density at 4°C and it becomes less dense below 4°C. Water supports life at very low temperatures in aqueous environment because the density of ice, is less than that of liquid water. This is an important natural phenomena that occurs in the aquatic ecosystem. The floating layer of ice on the top effectively insulates the water below it, allowing most aquatic organisms survive in extreme winter. Therefore, we can say that the unique properties of water have a determinative 34 role in the process of biological evolution. Unit 2 Water.......................................................................................................................................................................... SAQ 5 Fill in the blanks with correct words: i) Water not only acts as a …………….. but it also serve as a …………….. ii) Water serves as a………….. and a............................................ iii) In plant photosynthesis, water molecule under goes oxidotion to release................................. iv) The unique properties of water such as ………………………. are crucial to support aquatic life in an aqueous environment. v) Water has a high ………which allow small organism to float on …………… vi) Water has lower and maximum density at ….°C. 2.7 SUMMARY In this Unit you have studied: l Water is the main constituent of biological systems. It is a polar molecule due to the presence of opposite charges. The presence of opposite charges on each water molecule allows formation of hydrogen bonding. Hydrogen bonding property of water makes it a unique molecule. Hydrogen bonding in water accounting for several physical properties such as melting point, high boiling point, and high dielectric constant. Hydrogen bonding property of water determines solubility of many substances. Due to polar nature of water, it forms hydrogen bonds with other polar or charged molecules. Noncovalent interactions are crucial for the formation of biological structures specially proteins and DNA. l The ionic products of water [H+] and [OH ] define the acidic and basic nature of a substance in an aqueous system. Weak acid-conjugate base pairs act as a buffer system. Henderson-Hasselbalch equation is useful for determining the quantitative relationships between pH, pKa and the ratio of acids and bases in buffer systems. Biological buffers are essential in maintaining constant pH in the human body. Important biological buffers such as phosphate and bicarbonate buffers which are vital to maintain pH intracellula and in blood respectivley. l Water molecules participate in various metabolic reactions where they serve as proton donor and proton acceptor. Owing to the physical properties of water it acts as a vital molecule in maintaining life both terrestial and aquatic environments. 35 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... 2.8 TERMINAL QUESTIONS 1. Describe the structure of water. 2. Explain polar nature of water molecule. 3. Define the terms hydrophilic, hydrophobic and amphipathic. 4. What do you understand by the term buffer? 5. Explain the Henderson-Hasselbalch equation and its use. 2.9 ANSWERS Self-Assessment Questions 1. (a) (i) Two (ii) electrostatic repulsion (iii) electronegativity (iv) dipole moment (v) nitrogen (b) (i) weaker (ii) 4 (iii) unstable (c) (i) aggregate (ii) Vander Waals (iii) amphipathic (d (i) weakening (ii) non-polar, avoid of 2. (i) dense (ii) polar nature (iii) high specific heat (iv) Hydrogen bonding 3. (i) H3O+ (ii) high (iii) 1 x 10 -14 M2. (iv) 55.5 moles/ liter or 55.5 M. (v) basic (vi) 0 to 14. 4. (i) weak acids or bases and their conjugates. (ii) buffer action. (iii) proton donors, proton acceptors. (iv) 7.4 (v) pH, conjugate acid-base pair. (vi) Henderson-Hasselbalch equation. 36 Unit 2 Water.......................................................................................................................................................................... 5. (i) universal solvent, reactant. (ii) proton donor, proton acceptor. (iii) oxygen (O2) (iv) high specific heat, heat of vaporization and low density. (v) surface tension. (vi) 4°C. Terminal Questions 1. Water has bent shape structure due to presence of two nonbonding electron pairs (unshared/lone pairs) on oxygen atom. These electrons tend to arrange themselves symmetrically at the vertices of a regular tetrahedron around the oxygen atom. Due to the electronic repulsion, the bond angle of H-O-H decreases to 104.50 as compared to 109.5° of a perfect tetrahedron. 2. In a water molecule, the oxygen atom has more electronegativity as compared to hydrogen atoms resulting in electronegativity difference. Therefore, oxygen atom tends to withdraw the shared electrons towards itself of each hydrogen atom. As a result, oxygen atom bears a partial negative charge () and each hydrogen atom bears partial positive charge (+). The presence of opposite charges on a water molecule is said to be a permanent polar molecule. These opposite charge on a water molecule allow it to form hydrogen bonding between water molecules. Being a polar molecule, water dissolves many polar, uncharged, ionic and charged molecules by forming hydrogen bonding with them. Hence, it is considered a biological solvent. 3. Hydrophilic molecules form hydrogen bonding with water molecules. Water readily dissolves polar and ionic molecules such as sugar (glucose), amino acids and sodium chloride etc. Hydrophobic molecules do not make hydrogen bonding with water molecules. These molecules such as lipids and hydrocarbons are nonpolar. Such molecules avoid interacting with water molecules and aggregate in aqueous solution. Amplipathic Molecules are having both the hydrophilic and hydrophobic groups are called amphipathic molecules. 4. A buffer system comprises of conjugate acid-base pair of a weak acid or a weak base. This system is able to resist a change in pH following addition of small quantities of strong acid or base. 37 Block 1 Introduction to Biochemistry.......................................................................................................................................................................... 5. Henderson-Hasselbalch equation is useful to expres the quantitative relationship between pH and pKa of the weak acid and conjugate acid-base pair. The following forms of equation have several applications as: pH = pKa + log [base/acid] (useful to calculate the pH of the buffer solution) pH – pKa = log [base/acid] (useful to calculate the ratio of concentration of base to acid) pKa = pH + log acid/base (useful to calculate the pKa of weak acid in a buffer system) pKa – pH = log [acid/base] (useful to calculate the ratio of concentration of acid to base) 2.10 FURTHER READINGS 1. Albert L. Lehninger: Principles of Biochemistry, Worth Publishers, Inc. New York, 1984. 2. Harper’s Illustrated Biochemistry, 29e. Robert K. Murray, David A Bender, Kathleen M. Botham, Peter J. Kennelly, Victor W. Rodwell, P. Anthony Weil, USA. 3. J. L. Jain: Fundamentals of Biochemistry, S. Chand & Company Ltd., India 4. U. Satyanarayana and U. Chakrapani: Biochemistry, UBS Publishers Distributors Pvt. Ltd., Kolkata, India. 38