CLASS: Fundamentals Scribe: Amy Ratclif

CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 1 of 6

I. Intro Slide [S1] Water the Medium of Life a. Today should be a review, if not read ch. 2 of Garrett and Grisham 4th edition b. I’m going to lecture right out of the book, so if you know someone who misses a lecture they can follow up with just reading the book II. Chapter 2 [S2] a. If there is magic on this planet, it is contained in water.” b. Basis of this chapter is all about water. Title of lecture is about pH. That is one characteristics of water that is incredibly important for biological systems c. This is a picture from the book. d. Water is absolutely essential to life. e. We try to keep control of it. f. Anyone who has water damage realizes that mold can grow and creates neurotoxins that harm entire families. III. Essential Question [S3] a. Water chemically has several properties that allow life to take place. b. We’re going to talk about pH, how pH is controlled in biological systems and in the laboratory. c. We’re going to talk about some of the other properties of water. IV. Outline [S4] a. What are the properties of water? b. What is pH? c. What are buffers, and what do they do? d. Does water have a unique role in the fitness of the environment? V. What are the properties of water [S5] a. Water has a high boiling point and high melting point, mainly because of weak hydrogen bonds. And the many hydrogen bonds that form. b. It is a polar substance, it allows the dissolving of ions. c. It is a polar molecule so it has a difference of charge that causes hydrogen bonds to be able to form. d. Has potential to form 4 hydrogen bonds per water molecule. VI. What are the properties of water [S6] a. Structure of water gives it this difference in charge. There’s a dipole moment. That just means one side of molecule has a net + charge and the other side has a net – charge. b. Electrostatic interactions between water molecules, or molecule such as a solute molecule that is dumped into water, example salt. Sodium Chloride. The Chloride ions will be negative so they tend to organize water so that the positive charge of water will surround them. The sodium would be the opposite, negative side. VII. What are the properties of water [S7] a. There are 3 states that water can be in: solid, liquid, and vapor form. b. In water, hydrogen bonds form but they can break fairly easily, every 10 picoseconds there’s a breaking and joining of a hydrogen bond. c. Hydrogen bond is just that positively charged, electrostatic interaction between a positively charged hydrogen and negatively charged oxygen. Not a full negative charge, but a partial charge, a tendency toward charge. VIII.What are the properties of water [S8] a. This just shows you the bonds that can be formed, supposed to be in 3D. b. You can see where the little blue balls are the hydrogen’s and the red is the oxygen. c. You can see where the blue and the red stick together. There is a very weak bond that occurs. Obviously not a covalent bond but its stronger than the other forces and bonds that would occur in the water. These interactions. d. Hydrogen bond is not covalent at all. IX. What are the properties of water [S9 + 10] a. This just goes through the idea of the fluidity of water b. You have a psec clock, you can see that in water you have this breakage and rejoining of these bonds which gives it it’s fluid nature. X. The Solvent Properties of Water Derive from Its Polar Nature [S11] a. The polar nature, that is that there’s a dipole moment across this molecule, polar nature of water, being negatively charged on one side and positive on the other, allows it to dissolve ions. XI. The Solvent Properties of Water Derive from Its Polar Nature [S12] a. If you dump a salt into water, the crystal of salt can be broken apart and will form a solution of the water. b. That’s because hydrogen bonds can form with these solutes. CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 2 of 6 c. If you take sodium chloride, for example, and drop a crystal into water, it will reorganize the water around it. d. When you have a negatively charged chlorine atom what will happen is the positively charged hydrogen’s of the water will then surround it, will form a cage which in the book is called the clasthrate structure around the molecule. e. Those are much stronger in the case of sodium chloride than the bond between the chloride and the sodium, the electrostatic interaction between those. The sodium chloride will tend to dissolve very readily in water, up to a saturation point, which is about 5 molar. XII. The Solvent Properties of Water Derive from Its Polar Nature [S13] a. Ability of water to dissolve things is not present in many other solvents. We take this for granted. b. High dielectric constant = It’s ability to dissolve these crystalline forms of solutes c. Go down to hexane and benzene , you would not be able to get a lot of sodium chloride in hexane and benzene but you would in water and even more in formamide just because it has a higher dielectric constant. XIII.Hydrophobic Interactions [S14] a. We were just talking about a highly polar or charged solute but there are many times when you don’t have that. You have a nonpolar molecule, for example a fatty acid that doesn’t like to dissolve very well in water. That tends to organize the water. b. In the book, it mentions entropy. c. Entropy drives chemical reactions d. Free energy = enthalpy – (temperature)(entropy) G = H-(T)(S) e. Way to remember this is “goldfish are hell without tartar sauce” f. Systems or chemical reactions are driven forward thermodynamically when the free energy goes down. g. Increasing entropy, which is just disorder, then the lower the free energy. Kind of like potential energy for a reaction. It drives the reaction forward. h. If you take heat (enthalpy) out of the equation, what ever we are dissolving into water doesn’t create or lose any heat (this dissolving is not endothermic or exothermic reaction) then really entropy is what dictates whether something will dissolve in water or not. i. Entropy of the water is what matters quite a bit XIV. Amphiphilic/Amphipathic Molecules [S15] a. Going to talk about Amphiphilic and Amphipathic, they’re essentially the same terms because they are molecules that can be dissolved in water. b. But they have a hydrophobic part. They have hydrophilic part – means like to be in water c. The water likes to interact directly with that with hydrogen bonds. That would be a good solute. XV. The Solvent Properties of Water Derive from Its Polar Nature [S16] a. Figure 2.5 Charged entity at the end there, in this case is not even charged but has a carbonyl group that can lose its hydrogen and become charged. b. The water likes to interact directly with that with hydrogen bonds. That would be a good solute. c. Carbon backbone in yellow is a fatty acid. This fatty acid tends to organize water around it. That organization is order. The opposite of entropy, the opposite of disorder. XVI. The Solvent Properties of Water Derive from Its Polar Nature [S17] a. That can happen and this caged structure comes around and called a clathray cage. A cage of bonded water around that. b. Water doesn’t like to be ordered that way. Entropy is disorder. You want to increase disorder in this system so ordering is bad. It thermodynamically unfavorable. c. What tend to happen is these large carbon tails of fatty acids tend to stick to each other. They exclude water. That exclusion of water creates a situation where entropy of the water can be maximized. This is a property of water that allows a lipid bilayer to form which is the cell membrane of all of our cells. XVII. The Solvent Properties of Water Derive from Its Polar Nature [S18] a. Fatty acids look somewhat like this. This is palmitate. It has an acid group at the end, which is the polar head which would dissolve readily in water and a nonpolar tail which is just carbons. b. If you put that in water it will tend to form a little ball structure with all the polar groups on the outside. This is called a micelle. So you have in the center – something doesn’t like water, or hydrophobic and outside you have hydrophilic, loving water, the sphere form. XVIII. The Solvent Properties of Water Derive from Its Polar Nature [S19] a. Inside the cell you have a lipid bilayer – would have 2 fatty acids and your cell membranes would all look like this (drew on chalk board), with the charged groups on the outside. Much more ordered than the micelle, which is like a little blob that forms, almost like a grease blob that form in the water XIX. The Solvent Properties of Water Derive from Its Polar Nature [S20] CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 3 of 6 a. There are what are called colligative properties of water. Very important for biological systems. A colligative property is just how water reacts when something is dissolved in it. b. When there is ice on the roads they dump salt on there. It lowers the melting temperature of water by adding sodium chloride. That’s a colligative property of water. c. Another colligative property that deals with ice is that the density of water, liquid water, is higher, more dense, than it is when its in a frozen state. d. If you put on ice skates, and your skating, the pressure of your body on those skates, melt water and allows you to ice skate. This is another property of water. e. This next colligative property of water is very important for biological systems. You can take water and add a solute to it. The number of molecules in that solvent will drive a reaction that can create pressure. This is the osmotic pressure of 1 molal solution. This is equal to 22.4. f. Do you remember what molar is? It’s 6.022 x10^23 molecules per L of water. Molal is just an easier way to make the solution up. You just take 1 mole of, lets say sodium chloride, or any other solvent, and you dump it into 1L of water. So the molar means the volume is 1L after you dump a mole in it. But if you have a mole of sodium chloride it takes up space and you dump that in there. Then you might have more than one L of water but you started with 1 L of water from molal. Kind of a lazier way of doing things so you don’t have to calculate the final volume. g. The way this is done is if you have a semipermeable membrane, where the solute cannot go in, or go through the membrane, but the water can. What will happen is if you take a solution of high osmolarity, means has a lot of solute in it, it’s the number of molecules that matters. Not anything else. Not what the molecules shaped like, whether its charged, it has nothing to do with that. You put that into pure water and only water can go through that membrane, what will happen is water will create the column of water, it will suck water up into it. Its trying to dilute that solute. And maximize the entropy of the system. That creates a force which can be measured by just taking a piston or providing air pressure on top of that. Air pressure equal to 22.4 atmospheres. We are living in 1 atm. That is a lot of pressure. h. Say you’ve done a tissue culture in lab or learned about this in textbooks –, say you have a cell – its in an isotonic solution, which means osmolarity on inside and outside re about the same, 290 milliosmoles. If you increase the salt concentration outside, or solute concentration, dump anything in solution on outside that cannot get into the cell, what will happen , water will be drawn out and the cell will shrivel up. The concentration of everything inside the cell will go up and the cell will die. Called a HYPERTONIC solution. Don’t want that happening inside your body. i. If on the other hand, you put this into pure water, water will rush in, like it does for that semipermeable membrane, because this is a semipermeable membrane essentially. The cell will get bigger and ultimately explode. HYPOTONIC. j. In tissue culture cells, in my lab, if someone takes their tissue culture cells and decide to dilute the cells and they use water instead of something that’s isotonic, like physiologically buffered saline, which is good for the cells, they will kill all their cells by popping them, HYPOTONIC solution. Then their experiment doesn’t work and I have to figure out why their cells died, that’s one of the reasons they die. k. Important colligative property of water that is essential to life. XX. 2.1 What Are the Properties of Water? [S21} a. Water itself can ionize. This is one of the reactions that occurs. b. This is the basis of acid/base chemistry. This reactions and how it’s skewed toward one direction or the other is absolutely important for biological functions. An enzyme that works inside a cell has an optimum hydrogen ion concentration that it works in. c. There are some pockets inside the cell called lysosomes that chew up proteins and other molecules. These have a low pH, or high hydrogen ion concentration. d. This is the chemical reaction. e. Water itself is 55.5 molar, so 1L of water has 55.5 moles of water. f. A mole is a large number, the number of molecules. Instead of saying 55 times Avogadro’s number, we say 55 molar. The number of molecules that would be in a liter of water. g. You remember that in chemical reactions there is a mass balance that occurs. There is this way to figure out equilibrium constants. That is once you have the equilibrium things going on inside a steady state, you put the concentrations of the products and the numerator you put the concentration of substrates. That’s the convention that’s used. So that’s how we come up with the Keq. h. Pure water is mostly H2O – very little H ions, very little hydroxide. This concentration of hydrogen ions would be 10^-7 in pure water. i. The concentration of H ion will be 10^-7 in pure water, with nothing else there XXI. Water Can Ionize to Form H+ and OH[S22 +23] CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 4 of 6 a. This shows what the reaction would look like on the chalkboard, but not really what happens. b. In solution there are not very many free ions. c. Those ions immediately stick to another water molecule and form this hydronium ion - H3O+. d. H3O+ creates polar interactions with other molecules around it and tends to organize them. Have structure that looks like this inside water. e. Since the H ion concentration is so low in pure water (10^-7) this guy Sorenson came up with the pH scale XXII. What is pH? [S24] a. pH is negative the log of hydrogen ion concentration b. H ion concentration can be replaced with H3O+, we’ll use these interchangeably. Even though there’s not free hydrogen ions. c. pH is the negative logarithm of the hydrogen ion concentration d. The way logarithms work, if you have two numbers that are multiplied together, if you take the log of the entire equation, you actually add those 2 together to get the log of the other side. That’s a mathematical way logarithms work. e. The pKw is essentially this Keq, but you know that you arnt going to change the molarity of water, you just take that into account. f. If you take the logarithm of 10^-7 times 10^-7 then you ultimately end up with the pKw of the water. pKw is defined as the pH + pOH. g. The pKw is essential this Keq but you know that you wont change molarity of water (take this into account). Take log of this…you ultimately end up with pKw…which equals pH + pOH = 14 XXIII. What is pH? [S26] a. This gives you an idea of pH scale. Its like the ickter scale for earthquakes. Earthquake of magnitude of 6/0 is 10 fold less than 7.0, because its on a log base scale. b. If the hydrogen ion concentration is always reciprocal to hydroxyl ion concentration. c. These always turn out to be 10^-14. If you take this scale here you can see that if you take the pH on the top it would be zero to 14 because you are taking the hydrogen ion concentration, the negative log of that. It’s just the number of decimal points. d. Here are the pHs of common fluids inside biological systems. Pancreatic fluid has slightly high pH to neutralize acid coming out of your stomach e. For dentists, saliva is 6.6. f. When we grow bacteria in the lab, one of the things that always happens is the pH decrease as we grow the bacteria. The solution becomes more acidic. More hydrogen ion concentration. g. The pH going down can cause tooth decay. XXIV. Dissociation of Weak Electrolytes [S27] a. There are some acids, like HCl, that if you dump into water it will totally dissociate. The amount of hydrogen ions is virtually the same as how many molar HCl you put in. How much moles of HCl you put in is the molarity of H ions in solution. b. This is not always the case. Sometimes you have partially dissociated acids. c. What we’re showing here is that each acid has a property, a KA value, which is taking the products multiplied by the concentrations of those and divided by the concentration fully formed acids that’s in solution at steady state. XXV. The Henderson-Hasselbalch Equation[ [S28] a. This is the Henderson-Hasselbalch equation which is a way to predict, knowing the pKa of a weak acid, what the final pH will be of the solution. b. Also a way, knowing the pKa, need to know how much is dissociated. A- is hydrogen acceptor, this is the base form. The associated forms is what’s thrown of is the Hydrogen ion. c. This pH can be calculated because pKa value is known, can be looked up in a book or derived by a titration. d. This is a way to titrate something XXVI. 2.2 What is pH? [S29+S30] a. This is a way to titrate something b. Have acetic acid, a weak acid. What you want to do is put in enough hydroxide ion from sodium hydroxide. Sodium hydroxide will just tirely all go in. Have a 1 molar solution of weak acid. If you put in ½ a mole of sodium hydroxide then these 2 should be equal. The log base 10 of water is 0. c. That eliminates this and then the pH equals the pKa. d. Can determine what the pKa based on that experiment. e. The way this is usually done, is you have a burette and you measure how much sodium hydroxide and you’re going up and up and up and you know how much your putting in because you know the concentration of the base and you know the concentration of what you are trying to titrate. What will happen is at first you will CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 5 of 6 have an acidic solution and it will very rapidly increase in pH as you add more base. When it come to pKa value, that will slow down. If you keep on putting in the base, the reaction, the acid that you have in the solution will suck up the base at that point. It will do so over a range and then about 1 pH past there you will have a vast increase. This is actually a buffer system. f. When you had 0.5 equivalence, an equivalence means you have a 1 molar solution of weak acid, your putting in ½ mole of base, that’s ½ equivalent. XXVII. Consider the Dissociation of Acetic Acid [S31] a. This is to give you an idea of how to use the Henderson Hasselbalch equation b. If you put in 0.1 equivalence of a base to a fully protonated solution of acetic acid then you can calculate what the pH of the final solution will be using Henderson Hasselbalch equation. c. The pKa of acetic acid is 4.76 or you can do the titration curve and see the inflexion point. The inflexion point is equal to pKa. You can do the math, a figure out the pH to be 3.81. XXVIII. Consider the Dissociation of Acetic Acid [S32] a. I did this before, I showed you that if you put in half of an equivalent of a base then ultimately that log ten of 5.50/5.50 will give you 0. The pH will = pKa. This is the opposite when you add .9 equivalence of a base then you are going to increase the pH of that solution. XXIX. Consider the Dissociation of Acetic Acid [S33] a. This is the opposite when you add .9 equivalence of a base then you are going to increase the pH of that solution. XXX. The Dissociation Behavior of Weak Electrolytes [S34] a. Here are the pKa’s of several acids that are biological relevant and are used in labs as buffers. b. When you use a buffering system, you want to pick it , want to maintain pH of 7 and didn’t want it to fluctuate wildly when you added anything to the solution. You pick something that had pKa value around 7. It would be good buffer in the range that you need. c. Phosphoric acid is one here. d. There’s ammonia that has a pKa of 9.25. That’s outside of physiological range. You might use it in a lab. It tend to hold on to its protons pretty well. Acetic acid holds on to protons a little bit. Mitizol, present in histamine, present in a lot of proteins, when it’s free has a pKa of 6.9. e. These types of things are important in creating an environment within the cell or laboratory such that you can carry the reactions out that are important. f. What to keep the pH around 7.2-7.4 inside biological system. g. That is typically done inside the cell with histadines and mostly by phosphoric acid. Phosphoric acid can give up 3 different hydrogen’s and does so at different pHs. The titration curve has 3 inflexion point and 3 pKa values. The one that’s important for biological systems is when it gives up the 2nd out of the 3 hydrogen’s. The one in the middle. The pK 2 important for maintaining pH balance inside the cell, a buffer inside the cell. XXXI. The Dissociation Behavior of Weak Electrolytes [S35] a. The buffers that are outside the cell are much different, more complicated. b. The extracellular pH is maintained by carbonate ions. Concentration of Carbon Dioxide that you breath out is very important in keeping your serum levels of pH constant. c. Someone that hyper/hyperventilates, their pH changes drastically inside serum. XXXII. Titration Curves Illustrate the Progressive Dissociation of a Weak Acid [S36] a. Add methicillin to list of penicillin derivatives. In MSRA, that staph aureus has developed resistance to methicillin. b. Extended spectrum drugs have better coverage. These drugs are the ones that would benefit from having a lactam added to them. c. Know this slide to memorize all the classes and kinds of antibiotics. XXXIII. 2.3 What Are Buffers, and What Do They Do? [S37] a. This is a little bit redundant. XXXIV. 2.3 What Are Buffers, and What Do They Do? [S38] a. This is a little bit redundant. XXXV. Enzyme Activity is Influenced by pH [S39] a. Shows 3 different enzymes that have different pH optimums. These different enzymes do different things. They are very sensitive in changes of pH. If you were trying to carry out these reactions outside the cell, you would want to find out what it’s pH optimum is. b. Then you would alter the pH with a buffer system with a pKa value around that. c. Inside the cell there is compartmentalization with different pHs and different compartments within the cell, I mentioned lysozyme earlier. CLASS: FUNdamentals Scribe: Amy ratclif 8-8-2011 Proof: Gary Cramer DETLOFF Water: the Medium of Life Page 6 of 6 d. Pepsin might work well inside lysozyme but not work well outside the lysozyme. Think of that as a way to control. Pepsin chews up proteins, you don’t want it chewing up all the proteins in the cell. You only want them chewing up proteins when its inside the compartment designated for chewing up proteins. That’s one way of controlling the activity of pepsin. XXXVI. What Are Buffers, and What Do They Do? [S40] a. Anserine is really in its one form of histadine. Histadine looks like its linked to glysine. With histadine itself the metizol group doesn’t have proper pH to maintain balance at 7.2 pH. When it’s linked to something else the metizol groups capacity to give up hydrogen ions changes slightly. It being proteins and other amino acids is one way the buffering works. Of course the other buffering system with the phosphates is very important XXXVII.What Are Buffers, and What Do They Do? [S41] a. Inside the laboratory there was once a need for different chemical compounds with different pkA values up and down a range and molecules that wouldn’t inhibit chemical/enzymatic reactions that are normal b. Heaps is one to the buffers that is commonly used inside. This is fully protonated form. XXXVIII. What Properties of Water Give It a Unique Role in the Environment? [S42] a. Whole point of lecture is that water itself has properties that allow many different things to take place b. We’re approximately 80% water – your weight. c. You are organizing the water into little pockets with lipids, chemical reaction. All this things go on within water, inside your body.