Principles of Chemistry: Water PDF

Nutritional Biochemistry Principles of chemistry: water DIET413/BHCS1019 Dr Nathaniel Clark FHEA RNutr MRSB [email protected] 1 Previously Matter consists of chemical elements in pure form and in combinations called compounds. Ess...

Nutritional Biochemistry Principles of chemistry: water DIET413/BHCS1019 Dr Nathaniel Clark FHEA RNutr MRSB [email protected] 1 Previously Matter consists of chemical elements in pure form and in combinations called compounds. Essential elements of life include carbon, oxygen, hydrogen and nitrogen – 96%. Atomic number relates the number of protons in an atom. Isotopes of an element can differ (C), and unstable ones can decay. Electrons exist in energy levels in an atom, and they have characteristic energy levels. Strong bonds: covalent (electron sharing) and ionic (electron donating). Weak chemical bonds: van der Waals interactions and hydrogen bonding. Biology can be understood through using chemistry as a tool. 2  1. Trace elements are only required in small quantities. Last time - Quiz Microelements are required at higher levels. 2. Atomic mass = protons + neutrons (electrons negligible), atomic number = 1. How do trace elements differ from number of protons. H (1, 1), C others? (12, 6), N (14, 7) and O (16, 8). 2. What is the difference between the atomic mass and atomic number of an atom? What are these values for the major 4 elements? 3. Zinc has multiple isotopes. What is the difference between the 5 isotopes? 4. Covalent bonding = sharing 4. What is the difference between covalent of a pair of valence electrons and ionic bonding? (O2). Ionic = valence electron moves from one atom to 5. What is the importance of weak bonds? another (NaCl). 5. They form bonds between Where can these be found in macromolecules? molecules – they are found between different regions of the sample molecule e.g., a 3 protein. Learning outcomes 1. Understand the relationship of polarity and hydrogen bonding. 2. Describe the properties of water. 3. Describe how acid and base conditions are controlled in blood/cells. 4. Understand the importance of diffusion for water movement (osmosis). 4 1. The molecule that supports life: water Astronomers spent time looking for water on other planets as this is the substance that makes life as we know it on earth possible. All organisms are mostly made of water and live in an environment dominated by water. Especially Plymouth... Life on earth began in water and evolved there for 3 billion years before spreading to land where it remains tied to water. 5 1. The molecule that supports life: water (2) Humans can survive without food for a few weeks, but only a week or so without water. https://www.youtube.com/watch?v=zChe AcpFkL8 Water helps in many reactions essential to sustaining life. Most of our cells are surrounded by water and the cells themselves are about 70-95% water. It is the properties of water that allow it to support all living organisms, as we will see. 6 1. Clinical relevance The importance of things become apparent when they are taken away. Still debate over consensus for the human water requirements of different demographics. Without proper water intake, neuroendocrine defenses activate. Prolonged reduced intake will influence metabolism and chronic disease. 7 1. The polarity of water molecules Water (H2O) has oxygen which is more electronegative (lecture 1), ensuring the electrons of the covalent bond spend more time there. In other words, they are a polar covalent bond. The unequal distribution of electrons makes water a polar molecule, meaning it has two ends with opposite charges. O = negative, H = positive. https://www.youtube.com/watch?v= ASLUY2U1M-8 8 1. Water and hydrogen bonds - properties The properties of water arise from attractions between its polar molecules. The positive H of one molecule are attracted to the slightly negative O of a nearby water molecule. These two water molecules are held together by a hydrogen bond. When water is in its liquid form, its H bonds are very fragile, each about 1/20th as strong as a covalent bond. The hydrogen bonds form, break, and re-form frequently and lasts for a small amount of time (trillionths of a second). The extraordinary qualities of water are emergent properties resulting from the hydrogen bonding that orders molecules into a higher level of structural organization. 9 Activity 1. Draw 3 water molecules and label the atoms. Draw solid lines to indicate the covalent bonds. Draw dotted lines for hydrogen bonds. Add partial charge labels as appropriate (remember). 2. What is electronegativity, and how does it affect interactions between water molecules? (remember) 3. Why is it unlikely that two neighbouring water HH molecules would be arranged like this? O O (understand) HH 4. What would be the effect on the properties of the water molecule if O and H had equal electronegativity? (understand) 10 Answers 1.. 2. Electronegativity is the attraction of an atom for the electrons of a covalent bond. Because O is more electronegative than H, the O atom in H2O pulls electrons towards itself than H, resulting in a partial negative charge on the O atom (reverse on H atom). Oppositely charged ends of water molecules are attracted to each other forming a H bond. HH 3. The H atoms of one molecule with their partial O O positive charges, would repel the H atoms of the adjacent molecule. HH 4. Water molecules would not be polar, and they would not form H bonds with each other. 11 2. Properties of water: cohesion Water molecules stay close to each other form hydrogen bonding. Although the arrangement of molecules in a sample of liquid water is constantly changing, at any given moment many of the molecules are linked by multiple bonds. These linkages give water more structure than most other liquids. Collectively, the hydrogen bonds hold the substance together and is called cohesion. This can help water travel against gravity. 12 2. Properties of water: moderation of temperature Water moderates air temperature (and body temperature) by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler - sweating. Water is effective as a heat bank because it can absorb/release a relatively large amount of heat with only a slight change in its own temperature. Whenever two objects of different temperatures are brought together, heat passes from the warmer to the cooler object until the two are the same. An ice cube cools a drink because it absorbs the heat, not because it adds “coldness”. 13 2. Properties of water: temperature continued There is one convenient unit of heat. A calorie (cal) is the amount of heat it takes to raise the temperature of 1 g of water by 1 °C. Conversely, 1 cal is how much 1 g of water releases when it cools by 1 °C. A kilocalorie (kcal), 1000 cal, is the quantity of heat required to raise the temperature of 1 kilogram of water by 1 °C. This is the measurement on the back of a food packet. 14 2. Properties of water: solvent Table salt placed in a glass of tap water will dissolve (i.e., visibly disappear). The glass will (after a few moments) contain a uniform mixture of salt and water; the concentration of dissolved salt will be the same everywhere. A liquid that is completely homogenous mixture of two or more substances is called a solution. The dissolving agent of a solution is the solvent (water), and the substance that is dissolved is the solute (salt). Nothing works better than water (unless nonpolar). 15 2. Properties of water: solvent 2 Water is a very versatile solvent due to its polarity. When salt dissolves in water each crystal of salt has NaCl exposed to the solvent. These ions and the water molecules have a mutual affinity owing to the attraction between opposite charges. O is negatively charged and cling to positively charged Na ion. H is positively charged and cling to the negatively charged Cl ion. 16 2. Properties of water: solvent 3 As a result, water molecules surround the individual ions, separating and shielding them from one another (hydration shell). Working inward from the surface of each crystal, water dissolved all the ions. https://www.youtube.com/w atch?v=lIs7PAW0mlM (bigger picture) 17 2. Properties of water: solvent 4 A compound does not need to be ionic to dissolve in water. Many compounds made up of non-ionic polar molecules, such as sugars, are also water-soluble. Such compounds dissolve when water molecules surround each of the solute molecules, forming hydrogen bonds with them. Even molecules as large as proteins can dissolve in water if they have ionic and polar regions on their surface. Many kinds of polar compounds are dissolved in the water of such biological fluids as blood. 18 2. Properties of water - summary Cells are complex but water essentially provides cells with: Structure. Temperature regulation. Contain important molecules/compou nds. 19 2. Hydrophilic substances Any substance that has an affinity for water is said to be hydrophilic (Greek: hydro, water and philios, loving). In some cases, substance are hydrophilic without dissolving – they are too big to dissolve. Such a mixture is a colloid, a stable suspension of fine particles in a liquid. Think of a can of deodorant (water in air, rather than solid in water). Some substances do not have an affinity for water. 20 2. Hydrophobic substances Substances that are non-ionic and nonpolar repel water; and are said to be hydrophobic (Greek: phobos, fearing). Mixing oil and water: https://www.youtube.com/watch?v=F5HEDqzWQXE (own time) The hydrophobic behaviour of the oil molecules results from a the relatively nonpolar bonds. What does this tell you about the arrangement of the electrons in these molecules? The bonds between carbon and hydrogen share electrons equally (lecture 3). Isn’t this bad? What is the benefit of this? Hydrophobic molecules related to oils are major ingredients of cell membranes – imagine what would happen to a cell if its membrane dissolved... You wouldn’t be able to, because you wouldn’t exist... 21 2. Solute concentration in aqueous solutions Most of the chemical reactions in organisms involve solutes dissolved in water. To understand such reactions, we must know how many atoms and molecules are involved and be able to calculate the concentration of solutes in an aqueous solution (the number of solute molecules in a volume of solution). When carrying out experiments (such as your practicals) we use mass to calculate the number of molecules. We know the mass (lecture 1) of each atom in each molecule, so we can calculate its molecular mass, which is the sum of the masses of all the atoms in a molecule. 22 2. Glucose – molecular mass As an example, calculate the molecular mass of glucose, which has the formula C6H12O6. Daltons is (roughly) equal to the atomic mass and is a unit of mass. In round numbers, C = 12, H = 1 and O = 16 Daltons = 180 Da. This is impossible to weigh, so we measure things out in moles. 23 2. Calculating glucose A mol is a standard scientific unit for measuring large quantities of very small entities. The number of elements/compounds in a substance can be found using Avogadro’s constant, which is 6.02 x 1023 per mol. Just like a dozen = 12, a mole (mol) is always this value. The mass of one mole of a substance in grams is equal to the Dalton mass. Once you have the molecular mass, we can use the same number (180), but with the unit gram to represent Avogadro’s number (or 1 mol). So, to obtain 1 mol of glucose in the lab, therefore, we weigh out 180 g. 24 2. Why use moles? The practical advantage of measuring a quantity of chemicals in moles is that a mole of one substance has the same number of molecules as a mole of any other substance. If the molecular mass of substance A is 180 Daltons and that of substance B is 342 Daltons, then 180 g of A has the same number of molecules as 342 g of B. Molarity, the number of moles per litter of solution, is the unit of concentration most often used by biologists for aqueous solutions. Blood sodium concentration = 136-145 mmol/L. 25 Summary 1 Water contains an unequal distribution of electrons, giving rise to electronegativity in the oxygen and creating a polar molecule. The properties of water arise from attractions between its polar molecules. The positive H of one molecule are attracted to the slightly negative O of a nearby water molecule. The important properties of water include cohesion, moderation of temperature and solvency. Hydrophilic substance interact with water whereas hydrophobic do not. Moles is a useful unit for measuring solute concentrations in solutions. 26 10 min break 27 3. Acids and bases An acid-base reaction is a chemical reaction that occurs between an acid and a base. It can be used to determine pH via titration. Let’s consider them in isolation first. Dissociation based on electronegativity. HCl = hydrochloric acid. H+ and Cl- NaOH = sodium hydroxide. Na+ and OH- 28 3. Clinical relevance? The maintenance of acid-base conditions in the body involves the lungs, the kidneys and buffers. We will look at these systems later (DIET414/BHCS10 20) but now we need to understand the effects of them in chemistry terms. 29 3. Acid and base: water A hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other. When this happens, the H atom leaves its electron behind, and which is transferred is a H ion (H+), a single proton with a charge of 1+. The water molecule that lost a proton is now hydroxide ion (OH-), which has a charge of 1-. The proton binds to the other water molecule, making that molecule a hydronium ion (H3O+). 30 3. Acid and bas: equilibrium You can’t have one product without the other. This is a reversible reaction that reaches a state of dynamic equilibrium when water molecules dissociate at the same rate that they are being re-formed from H+ and OH-. At this equilibrium point, the water concentration greatly exceeds the other molecules. 31 3. Acid and base: reversible In pure water, only one water molecule in every 554 million is dissociated... Although this dissociation of water is reversible and rare, it is exceedingly important in the chemistry of life. H+ and OH- are very reactive. 32 3. Acid and base conditions Changes in their concentrations can drastically affect a cell’s proteins etc. The balance of H+ and OH- changes in water as you add solutes (acids and bases). Biologists use a pH scale to describe how acidic something a solution is. 33 3. Acids What would cause an aqueous solution to have an imbalance in H+ and OH- concentrations? When acids dissolve in water they donate additional H+ to the solution. Increases the H+ concentration. Hydrochloric acid (found in the stomach): HCl = H+ + Cl-. 34 3. Bases When a base dissolves in water they reduce H+ through accepting ions. Reduce the H+ concentration. Ammonia is a base: NH3 + H+ = NH4+. Other bases reduce the H+ concentration by dissociating to release hydroxide ions, which then combines with the H ions. NaOH = Na+ + OH-. A common biological buffer is bicarbonate: HCO3- 35 3. One direction versus dynamic Both the HCl and NaOH reactions occur in one direction. These compounds dissociate completely when mixed with HCl = hydrochloric acid. water, and so HCl is called a H+ and Cl- strong acid and NaOH a strong NaOH = sodium hydroxide. base. Na+ and OH- Ammonia is relatively weak (reacts with water to form a hydroxide). There are also weak acids which reversibly release and accept back H ions, e.g., carbonic anhydrase. H2CO3 ↔ HCO3- + H+. 36 3. Dynamic equilibrium H2CO3 ↔ HCO3- + H+ Here the equilibrium favours the reaction in the left direction that when carbonic acid is added to water, only 1% of the molecules are dissociate at any time. A reversible process is said to be in dynamic equilibrium when the forward and reverse processes occur at the same rate, resulting at no observable change in the system. Note, the concentrations of the products and reactants are not necessarily equal. 37 3. Acid dissociation constant In chemistry, an acid dissociation constant (Ka) is a measure of the strength of an acid in solution (pKa for amino acids , Lecture 4). It is the equilibrium constant for a chemical reaction: HA ↔ A- + H+. The chemical species HA is an acid that dissociated into A-, the base of the acid, and a hydrogen ion, H+. The system is said to be in equilibrium when the concentrations of its components will not change over time, because both forward and backward reactions are occurring at the same rate. The dissociation constant is defined by the higher the value, the stronger the acid. 38 3. The pH scale The pH scale measures how acidic a solution is. Neutral is in the middle. At neutral H+ = OH-. An acid not only adds acid to a solution, but it removes hydroxide ions because of the tendency for H+ to combine with OH-. A base has the opposite effect. Each pH unit change = a change in 10-fold difference. https://www.youtube.com/watch?v=L S67vS10O5Y (own time) Appreciate the magnitude of difference in hydrogen ion concentration... 39 3. pH in the body The internal pH of most cells is close to 7. Small changes in pH can be harmful because the chemical processes of the cell are very sensitive to the concentration of hydrogen and hydroxide ions. Human blood pH is ~7.4, which is slightly basic. You cannot survive for more than a few minutes if the blood pH drops to 7 or rises to 7.8. A chemical system exists to ensure this is maintained near this value. 40 3. Buffers If you add 0.01 mol of a strong acid to a litre of pure water, the pH drops from 7.0 to 2.0. If the same acid was added to blood, the pH would change from 7.4 to 7.3. Why is the effect less in blood than water? The presence of buffers allows addition of a relatively constant pH, despite the addition of acids or bases. They minimize changes in H+ and OH- concentrations. They do so by accepting H+ from solution when they are in excess and releasing them when they are depleted. 41 3. Carbonic anhydrase In human blood, carbonic anhydrase, stabilises the pH. H2CO3 = HCO3- + H+ H+ donor (acid) = H+ acceptor (base) + H+ (hydrogen ion). The “=“ is a response to a rise in pH or drop in pH (reversible). The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator, the reaction shifting left or right as other processes in the solution add or remove H+. If the H+ concentration rises (pH drops), the reaction proceeds to the left, with HCO3- (the base) removing the hydrogen ions, forming H2CO3. And vice versa. Thus, this buffering system is an acid-base pair. 42 4. Diffusion: molecular energy Molecules have a type of energy called thermal motion (heat). One result of thermal motion is diffusion, the movement of molecules of any substance so that they spread out evenly into the available space. Each molecule moves randomly, yet diffusion of a population of molecules may be directional. To understand this process, let’s imagine a synthetic membrane separating pure water from a solution of a dye in water. 43 4. Diffusion: semi permeable membrane Assume that this membrane has microscopic pores and is permeable to the dye molecules. Each dye molecule wanders randomly, but there will be a (overall) net movement of the dye molecules across the membrane to the side that began as pure water. The dye molecules will continue to spread across the membrane until both solution have equal concentration of the dye. Once that point is reached, there will be a dynamic equilibrium, with as many dye molecules crossing the membrane each second in one direction as in the other. 44 4. Diffusion down a gradient We can now state a simple rule of diffusion: a substance will diffuse from where it is more concentrated to where it is less concentrated. Put another way, any substance will diffuse down its concentration gradient. No “work” must be done to make this happen; diffusion is a spontaneous process, needing no input of energy. Note that each substance diffuses down its own concentration gradient, unaffected by the concentration differences of other substances. 45 4. Water diffusion: osmosis How do two solutions with different solute concentrations interact for water movement? Use a U-shaped glass tube with a selectively permeable membrane separating two sugar solutions. Pores in the synthetic membrane are too small for sugar molecules to pass through but large enough for water. How does this affect the water concentration? The solution with the higher concentration of solute would have the lower concentration of water, and that water would diffuse into it from the other side. However, for a dilute solution like most biological fluid, solutes do not affect the water concentration significantly. 46 4. Effects of osmosis on water balance Instead, tight clustering of water molecules around the hydrophilic solute molecules makes some of the water unavailable to cross the membrane. It is the difference in free water concentration that is important. In the end, the effect is the same; water diffuses across the membrane from the region of lower solute concentration to that of higher solute concentration on both sides of the membrane are equal. The diffusion of water across a selectively permeable membrane is called osmosis. The movement of water across cell membranes and the balance of water between the cell and its environment are crucial to organisms. 47 Summary 2 A water molecule can transfer H+ to another water molecules to form H3O+ and OH-. The concentration of H+ is expressed as pH. Buffers in biological fluids (e.g., blood) resist the changes in pH. A buffer consists of an acid-base pair that combines reversibly wit hydrogen ions. Diffusion is moving from an area of high concentration to low concentration, down its concentration gradient. Water specific diffusion is called osmosis, and this plays a major role in the bodies water balance. 48 Questions 1. Water is polar. What does this mean? 2. What are the three important properties of water? 3. Sucrose has the formula C12H22O11. What is its formula weight and how much do you need to weight out for make 0.5 L of 1 M sucrose? 4. What happens when water dissociates? What molecules are (briefly) made? 5. Some chemical reactions are reversible and form a dynamic equilibrium. What does this mean? 6. Which water molecules are not able to move during osmosis? 49 Before next time... Consult textbooks for further reading. Re-read the lecture notes from today. Read the next sessions lecture notes before attending. Definitions for next time: valence, isomers, enantiomers, functional groups, Daltons, ATP. Further reading: Campbell and Reece, Biology, Chapter 3. 50