Chemistry of Life - Water, Acids, and Bases PDF

Water, Acids, and Bases Learning Objectives for this section 1. Identify water’s structure and properties 2. Explain why water is essential for life. 3. Define acids, bases, and pH. Water, Acids, and Bases Water is a common chemical substance on Earth. Almost 75% of the planet is covere...

Water, Acids, and Bases Learning Objectives for this section 1. Identify water’s structure and properties 2. Explain why water is essential for life. 3. Define acids, bases, and pH. Water, Acids, and Bases Water is a common chemical substance on Earth. Almost 75% of the planet is covered in water. - 97% of that water is salt water ocean - 3% is freshwater - 68% of all freshwater is locked in ice caps and glaciers (although that is changing) - 30% is ground water - 2% is surface water - 87% of the surface water is found in lakes - 11% is located in swamps - 2% is found in our rivers What is the nature of the substance that accounts for about 70% of the mass of most organisms? The human body, for example, is about 60% by weight water, most of It in the extracellular fluid (the fluid surrounding cells) and inside cells: The weirdness of water H2O, CH4, NH3, CO2 All small, covalently bonded molecules but methane and ammonia are gases – water is a liquid! Why??  Chemical Structure of Water Water is made up of one atom of oxygen and two Oxygen atoms of hydrogen linked by covalent bonds. Hydrogen Hydrogen The oxygen atom in a water molecule attracts electrons more strongly than the hydrogen atoms. The result of that is the oxygen side of the molecule is slightly negative and The oxygen atom bears a partial negative charge (indicated by the symbol δ-), while the hydrogen side is more positive. and each hydrogen atom bears a partial positive charge (indicated by the symbol δ+) The difference in electrical charges on different sides of a molecule is called Polarity. Water is a Polar molecule. As a result of this electronic arrangement, the water molecule is polar; that is, it has an uneven distribution of charge. This polarity is the key to many of water’s unique physical properties. Neighboring water molecules tend to orient themselves so that each partially positive hydrogen is aligned with a partially negative oxygen: This interaction, shaded yellow here, is known as a hydrogen bond. Traditionally shown as a simple electrostatic attraction between oppositely charged particles, the hydrogen bond is now known to have some covalent character. This means that the bond has directionality, or a preferred orientation. Each water molecule can potentially participate in four hydrogen bonds, since it has two hydrogen atoms to “donate” to a hydrogen bond and two pairs of unshared electrons that can “accept” a hydrogen bond  The molecule therefore has approximately tetrahedral geometry, with the oxygen atom at the center of the tetrahedron The structure of water is continually flickering as water molecules rotate, bend, and reorient themselves. In ice, a crystalline form of water, Theoretical calculations and spectroscopic data suggest that water molecules during ice formation participate in only two hydrogen bonds, one as a donor and one as an acceptor, generating transient hydrogen-bonded clusters such as the six membered ring. Hydrogen bonds usually involve N-H, O-H, and S-H groups as hydrogen donors and the electronegative N, O, or S atoms as hydrogen acceptors. therefore, can form hydrogen bonds not just with other water molecules but with a wide variety of other compounds that bear N-, O-, or S-containing functional groups.  Hydrogen bonding explains much about the various The polar nature of the properties of water. covalent bonds that hold water together, and the hydrogen bonds between the water molecules, explain the properties of water – that make it so useful to life.  Properties of water Liquid at biological temperatures Most dense, at 4°C – ice floats High latent heat Good thermal buffer - high specific heat capacity Cohesion – Adhesion- High surface tension Good solvent –reactant – acid base property o These properties can all be explained due to the polar nature of water and the H bonds o Also, in reactions it can be used e.g. as a source of hydrogen  Liquid at room temperatures Organisms can interact with it, live in and on it, use it as a solvent etc. which they couldn’t if it were a gas. As a liquid it is incompressible Therefore, it can be used for support – e.g. turgor pressure in plants Most dense, at 4°C float Ice (solid water) floats on liquid water. upon freezing, the density of water decreases by about 9% This insulates the lower levels of a pond so the entire pond doesn’t freeze It provides a habitat for penguins. It sets up currents in the water which, particularly in the sea, circulates nutrients  High Latent Heat It takes a lot of energy to change the physical state of water, therefore it is unlikely to change, so it is a stable environment for organisms to live in – it is less likely to evaporate or freeze than other liquids This also means that the evaporation of water can be used as an effective cooling mechanism e.g. panting and sweating High specific heat capacity Specific heat capacity of water is the amount of heat or energy that must be added to one gram of water to increase by one unit in temperature It takes a lot of energy to change the temperature of water Therefore, it is a stable environment to live in. Also, internal body temperatures are less likely to change  High surface tension Surface tension depends on 2 important characters Cohesion & adhesion Cohesion refers to the tendency of similar or identical particles and surfaces to attract or cohere to one another. while Adhesion is the tendency of dissimilar particles or surfaces to adhere or attract to one another. Cohesion: Water molecules attracted and stay close to each other due to the collective action of hydrogen bonds between water molecules. Water is strongly cohesive liquid. It is responsible for the formation of water droplets. Adhesion: Water also has high adhesive property because of its polar nature. On clean, smooth glass the water may form a thin film because the molecular forces between glass and water molecules. It is responsible for the spreading of water or liquid over a surface. For water, Adhesive forces are stronger than the cohesive forces.  High surface tension The tension of the surface film of a liquid caused by the attraction of the particles in the surface layer by the bulk of the liquid, which tends to minimize surface area. It is the force by which surface molecules are held together. In biological cells and organelles, water is in contact with membrane and protein surfaces that are hydrophilic; that is, surfaces that have a strong attraction to water Water has an unusually high surface tension of 71.99 mN/m at 25 °C which is caused by the strength of the hydrogen bonding between water water strider supported by the surface tension of water molecules. This allows insects to walk on water Capillary action Because water has strong cohesive and adhesive forces, it exhibits capillary action. Strong cohesion from hydrogen bonding and adhesion allows trees to transport water more than 100 m upward against gravity. Allows organisms to live on the surface of water e.g. pond skaters Is also important in capillary action e.g. in the xylem (cohesion)  Good solvent – Universal solvent As a solvent of polar molecules water can dissolve most biological molecules – except lipids (hydrophobic) Water has the ability to diminish the electrostatic attractions between dissolved ions. Therefore, reactions can easily take place within water Organisms therefore use water as the basis of their cytoplasm In multicellular organisms it can also be used as a transport medium e.g. it is the base of plasma and sap  Reactant Water is used in hydrolysis reactions to split macromolecules into smaller units by adding water. And the reverse - joining monomers to form polymers by the removal of water – condensation polymerisation. It is a source of hydrogen for the reactions of photosynthesis. Acid, Base and pH  Acid, Base and pH Buffers and Buffering  Acid, Base and pH Water is not merely an inert medium for biochemical processes; it is an active participant. Its chemical reactivity in biological systems is in part a result of its ability to ionize. This can be expressed in terms of a chemical equilibrium: Aqueous solutions do not actually contain lone protons. Instead, the H+ can be visualized as combining with a water molecule to produce a hydronium ion (H3O+):  Acid, Base and pH Pure water exhibits only a slight tendency to ionize, so the resulting concentrations of H+ and OH- are actually quite small. According to the law of mass action, the ionization of water can be described by a dissociation constant, K, which is equivalent to the concentrations of the reaction products divided by the concentration of un-ionized water: The square brackets represent the molar concentrations of the indicated species. Because the concentration of H2O (55.5 M) is so much greater than [H+] or [OH-], it is considered to be constant, and K is redefined as Kw, the ionization constant of water: has a value of about 10−14 at 25 °C. At neutral pH, the concentration of the hydroxide ion (OH−) equals that of the (solvated) hydrogen ion (H+), with a value close to 10−7 mol L−1 at 25 °C  Acid, Base and pH A solution in which [H+] = 10-7 M is said to be neutral; a solution with [H+] higher than 10-7 M is acidic; and a solution with [H+] less than 10-7 M is basic. To more easily describe such solutions, the hydrogen ion concentration is expressed as a pH: Accordingly, a neutral solution has a pH of 7, an acidic solution has a pH, below 7, and a basic solution has a pH. above 7. Note that because the pH scale is logarithmic, a difference of one pH unit is equivalent to a 10-fold difference in [H]. The so-called physiological pH, the normal pH of human blood, is a near-neutral 7.1 - 7.4. The pH values of some other body fluids are listed in a Table. Acid–base chemistry is also a concern outside the laboratory.  Concept of pH Taking together: ▪ pH is a method of expressing the acidity or alkalinity (basicity) of solution. ▪ pH stands for “potential of hydrogen” as pH is a measure of the concentration of hydrogen ions in a solution. ▪ pH is – log {H+} ▪ Measured by pH meter ▪ pH range goes from 0 to 14, with 7 being neutral. pHs of less than 7 indicate acidity, whereas a pH of greater than 7 indicates a base. pH is really a measure of the relative amount of free hydrogen and hydroxyl ions in the water. 21 Classification of substances acc. to pH 22 Classification of substances acc. to pH Amphoteric Acid Base  Acid ❑ Substance that give {H+} ions in solution or that donate proton. Strong Weak acid acid Acids 24  Strong acid ❑ It is an acid that virtually 100% ionized (completely release all of its hydrogen ) in water. Examples Sulfuric acid (H2SO4) Hydrochloric acid (HCl) Nitric acid (HNO3) ▪ Phosphoric acid (H3PO4) is intermediate 25  Weak acid ❑It is an acid which doesn't ionize fully (does not completely release all its hydrogens) when dissolved in water. Examples Carbonic acid (H2CO3) Acetic acid (CH3COOH) 26  Alkaline (Base) ❑ Substance that give {OH-} ions in solution or accept proton. Strong Weak base base Bases 27  Strong base ❑It is a base that virtually 100% ionized (completely release all of its hydroxide ions) in water. Examples Potassium hydroxide (KOH) Sodium hydroxide (NaOH) 28  Weak base ❑It is a base that partially ionized (does not completely release all its hydroxyl group) in water. Examples ❑ Ammonia (NH3)  Amphoteric substance ❑ Substance that act as acids and bases. Examples ❑ H2O H+ & OH- ❑ Amino acids 30  Importance of pH in some body fluid in our bodies Blood pH : 7.1 - 7.4 (any change is fetal) Urine pH : 6.8 (slightly acidic) Any change in pH leads to precipitate some types of salts present normally in soluble form and urinary stones formed. Gastric juice pH : 1.5 -2 (highly acidic) Increase of acidity leads to peptic ulcer Decrease of acidity lead to hypoacidity. Semen pH : 7.2 – 8 (alkaline) Any change leads to sterility The activity of most chemical reactions occurs inside the body is dependent on fluid 31 pH.  Buffers Buffers and Buffering Buffers Are solutions which can resist sudden or large change in the pH when strong acid or base are added. Buffering is the tendency of the solution to resist a change in pH following addition of a strong acid or base. 32  Buffers Composition of buffer: ▪ solutions of weak acids and their conjugate bases; i.e., Weak acids and salts of these weak acids with strong bases ▪ solution of weak bases and their conjugate acids; i.e., Weak bases and salts of these weak bases with strong acid The buffer must be in pairs 33  Examples of buffer pairs A- Acetic acid (CH3COOH) , sodium acetate (CH3COONa). B- Carbonic acid (H2CO3 ) and sodium bicarbonate (NaHCO3). C. Sodium dihydrogen phosphate (NaH2PO4 ) and Disodium hydrogen phosphate (Na2HPO4 ). D- Ammonium hydroxide (NH4OH ) and ammonium chloride (NH4Cl). E- Proteins or amino acids. 34  Example of buffering by acetate buffer pair (CH3COOH, CH3COONa) If strong acid like hydrochloric acid (HCL) is added HCl + CH3COONa NaCl + CH3COOH (strong acid) ( neutral salt) (weak acid) How do buffers “work”? 35  Example of buffering by acetate buffer pair (CH3COOH, CH3COONa) If a strong base like sodium hydroxide NaOH is added NaOH + CH3COOH CH3COONa + H2O (strong base) (salt) (water) How do buffers “work”? 36  Physiological buffers ❑ The buffer systems are “The life-saving devices'' of the body as: ❑ The pH of the arterial blood must be kept within a very narrow range between 7.35 – 7.45 and this accomplished by the buffers of the blood. ❑ It can be stated in general that all reactions of living protoplasm take place in buffer media. ❑ Any abnormality in the pH leads to sickness that could be fatal in sever conditions 37  Physiological buffers Bicarbonate buffer Phosphate Phosphate buffer buffer Hemoglobin Hemoglobin Proteins and Proteins andamino aminoacids acids 38  1- Bicarbonate buffer (H2CO3 , NaHCO3 ) Bicarbonate buffer is the most important buffer in blood If HCl is added to the media containing this buffer HCl + NaHCO3 H2CO3 + NaCl ❑ If the acidity is raised , carbonic acid will dehydrate by carbonic anhydrase enzyme to yield CO2 ,H2O which can escape through expiration. ❑ However, excessive accumulation of carbonic acid leads to acidosis 39  1- Bicarbonate buffer (H2CO3 , NaHCO3 ) Carbonic anhydrase H+ + HCO3- H2CO3 CO2 + H2O CO2 Increase Respiration rate Decrease NaHCO3 Desrease NaHCO 3 leads to acidosis N.B.: If pH of the blood ever gets below 7 , this would be fetal  1- Bicarbonate buffer (H2CO3 , NaHCO3 ) If a strong base like sodium hydroxide NAOH is added NaOH + H2CO3 NaHCO3 + H2O Weak base ❑ If a large amount NaHCO3 is formed, the excess bicarbonate is eliminated in urine. ❑ If a large amount of alkali is liberated in blood stream , the pH may raise to 7.4 – 7.5 and this condition is known as alkalosis (not common as acidosis). Alkali reserve ❑ The basic units of the blood that acting as buffers such as NaHCO3. N.B.: The ratio of bicarbonate to carbonic acid is normally 20:1 41  Phosphate buffer (NaH2PO4 , Na2HPO4 ) (The main buffer of urinary system) If a strong acid like HCl is added to this system ` HCl + Na2HPO4 NaH2PO4 + NaCl A large amount of NaH2PO4 would contribute to an acidosis and the excess of it will be eliminated in the urine.  2. Phosphate buffer (NaH2PO4 , Na2HPO4 ) If a strong base like NaOH is added to this system ` NaOH + NaH2PO4 Na2HPO4 + H2O A large amount of Na2HPO4 would contribute to an alkalosis and the excess of it will be eliminated in the urine. 43  3. Hemoglobin buffer ❑ The histidine buffer of hemoglobin control the sudden additions of acid or base. ❑ It is more powerful in the short run than the bicarbonate system. HbO2 + H+ HHb+ + O2 Increased (H+ ) will drive the reaction to the right , conversely increased PO2 will favors oxyhemoglobin formation. 4.Proteins and Amino acids ❑ Proteins act as one of the most important buffer systems in blood and tissues. ❑ Their buffering ability derives from the dissociable groups on their constituent amino acids. 44  Acid - Base balance The body has three lines of defense to regulate the body's acid - base balance and maintain the blood pH normal: ▪ Buffering agents ▪ Respiratory system ▪ Renal system Acid - base balance refers to the mechanisms the body uses to keep its fluid close to normal pH so that the body can function normally.  Acid-Base imbalance Alkalosis Acidosis Is defined as an arterial is defined as an arterial pH below 7.35 pH above 7.45  Acidosis/Alkalosis Primary respiratory Primary metabolic Disturbance in CO2 level Disturbance in bicarbonate level  Acidosis Primary respiratory acidosis It exists when there is acidosis with hypercapnia (pCO2>45mmHg) Causes: 1. Acute pulmonary insufficiency ( e.g asthma , pneumonia , pulmonary embolism) 2. Chronic pulmonary insufficiency ( e.g chronic obstructive pulmonary disease)  Acidosis Primary metabolic acidosis It is characterized by a low serum level of bicarbonate (less than 22mEq / liter) Causes: 1. Diarrhea 2. Carbonic anhydrase inhibitors 3. Lactic acidosis 4. Keto-acidosis in diabetes or in alcoholism 5. Aspirin poisoning  Alkalosis Primary respiratory alkalosis It occurs when there is alkalosis with hypocapnia (pCO2 < 35mmHg) Causes: 1. Hyperventilation due to severe anxiety, in patients on respirators 2. Fever 3. In high altitudes  Alkalosis Primary metabolic alkalosis It occurs when a high serum bicarbonate level (>29 mEq / liter) Causes: 1. Loss of gastric HCl without loss of pancreatic HCO3 e.g. vomiting 2. The administration of some diuretics  Acidosis and alkalosis compensation The two organs in the body serve as a compensatory function to acid-base balance: In case of respiratory acidosis or alkalosis In case of metabolic acidosis or alkalosis By retention or elimination of HCO3- By retention or elimination of CO2