Biochemistry Water, PH and Buffers Part 1 tutorial

hello I'm professor Paul Begum and this is biochemistry one our goal in this segment is take the first steps toward mastery of an understanding of water the solvent of all biochemistry and in this segment we're going to particularly talk about the structure of water how it dissolves things salvation is called and suddenly called colligative properties which we'll come to at the end of the segment so remember the status of biochemistry it's the missing piece of the jigsaw puzzles that unifies the chemical physical world with the biological world and water as we've said is the solvent in which virtually all biochemistry goes on we won't talk any more about it today but the tools that that organisms bill protein proteins can occasionally create a little tiny micro sequestered environment away from water and allow an organic reaction to go on in the absence of water as needed but in fact that's a fairly rare event most biochemistry is goes on in an aqueous environment in fact we can talk about biochemistry mostly as the as a specific subset of organic chemistry that goes on in water so let's talk first about the structure of water and as we talk about the structure of water as a solvent there's a tendency to think of the solvent is kind of fading into the background and the interesting stuff going on in the solvent and to some extent that's true but also the properties of water turn out to be properties shared with the biochemical molecules that we're going to care a lot about lighter so as we understand the property of water as the solvent we're also taking the first step toward understanding biochemical molecules in fact in a very real sense water is a biochemical molecule as you'll see over and over again going forward so this diagram is just to emphasize to you that water we live on a water planet the vast majority of the surface of the planet is covered by water life evolved in water and so it's not at all surprising that the that most biochemical reactions are designed to go on in water and in fact in seawater so we won't talk about it today but the the salt concentration of the cytoplasm of cells is remarkably similar to the salt concentration of seawater again not a big surprise all right so this is a diagram of the whole picture of a water molecule in the center is this tradition no ball-and-stick diagrams to emphasize the spatial relationships of molecules and then surrounding the clouds in blue and red blue for hydrogen in this case red for oxygen are the so-called Van der Waals radii these are the dimensions of the electron shell such that when two water molecules approach their electron shells when they get to the point that the electrostatic repulsion between their electron shells is over is overwhelming stopping further migration together you have encountered that is the definition of the van der Waals radii in most of the diagrams subsequently we're going to look at ball and stick diagrams of water molecules but remember that the van der Waals radii are ELLs are already there or always there and we'll call them back from time to time where they're relevant so this is a step toward a ball and stick model this is a water molecule with the electrons in the bonding external bonding orbitals diagrammed so there's a there there's six in the external orbitals of oxygen so to create the magic number of eight they can share one electron with each of two hydrogen atoms is diagrammed here at the bottom and then they have two unbonded electron pairs diagrammed at the top here and let's go through that so oxygen is strongly electronegative what that means is that it tends to attract electrons to itself and away from the less electronegative atoms to which it is bound of which hydrogen is a dramatic and specific example again let me emphasize something I said a moment ago this property of electronegativity pulling electrons to one atom in a bonded molecule and away from another is a generic property of many many biological molecules so as we study it in water we're learning also concepts that we're going to apply over and over again and then again the here are the unbonded electrons boxed in green at the top so let's look now at the consequences of what - the structure of water as a solvent of the strong electronegativity of oxygen kind of holding on disproportionately to electrons in water molecules so here are two water molecules water molecules are polarized we've said here are the two oxygens in the molecule so this is a slightly simplified diagram compared to the one you saw a moment ago here are the unbonded electron pairs that you saw again a moment ago and these green arrows represent the pulling of electrons toward the oxygen atom and away from the hydrogen atoms because again of the electronegativity of oxygen that creates therefore small partial positive charges on hydrogen and small partial negative charges on oxygen in a water molecule okay so as a result of that water molecules have the capacity to form what is called a hydrogen bond it is essentially like an ionic bond a small positive charge is attracted to a small negative charge but the hydrogen atom is particularly efficient at providing it in becoming involved in this kind of bond and therefore it's often referred to as a hydrogen bond again for the third time hydrogen bonds are formed by many biological molecules they are central as we'll see to the structure of biological molecules so while we're learning about water today we're also learning about some principles that are going to be crucial to the understanding of biological molecules as well as you'll see several other of the abundant elements in organisms specifically nitrogen and sulfur are also electronegative like oxygen and so in fact biological molecules that have oxygen nitrogen or sulfur will often form hydrogen bonds under the appropriate circumstances more about that in later segments today our focus is oxygen and water okay that is a hydrogen bond between two water molecules in fact water molecules can often form as many as three hydrogen bonds simultaneously and understanding that in turn helps us understand a great deal about the properties of water as a Solent let's first consider solid water and the fact that ice floats and that's a little surprising right in general when we drop a solid object of some sort into a glass of water usually we expect it to sink water ice does not it floats why because in fact ice is lighter the solid form is lighter than the liquid form how does that work well in fact ice the water molecules in ice form a highly orderly lattice structure so liquid water the molecules are moving around in ways that we'll talk about in a moment as you withdraw thermal energy from them by cooling them you eventually traverse the freezing point and they collapse into this lattice structure diagram on the image that you're looking at on the screen at the moment that highly orderly structure has some air in and so to speak some space in it the orderly molecules are held apart from one another a little bit beyond their Vander Waals radii on average because of the formation of these highly ordered structures if we start pumping more heat energy back in the molecules start vibrating more rapidly and eventually when the melting point is reached they break apart and they form liquid water a little bit of that is diagrammed here individual water molecules form and break hydrogen bonds with their neighbors but they're now doing it in kind of an insane 3-dimensional square dance where they form and break hydrogen bonds with their neighbors very rapidly in fact on a nano scale time scale so these movement of molecules at even at room temperature at the molecular scale is quite more violent than we're used to thinking of that will rarely concern us here directly but it's a kind of interesting fact to know so as liquid molecules now are going through this three-dimensional square dance forming and breaking in real time hydrogen bonds with one another it means that at certain moments in time two water molecules can bump closer than they would if they were fully hydrogen bonded in a lattice bumping up against their Vander Waals radii and therefore liquid water is about 9% denser than ice and ice floats which is a useful thing in a number of contexts our concern at the moment though is now how liquid water acts as the solvent in which virtually all biochemistry occurs and we're going to start by looking at the how water interacts with things that don't like to go into solution water the so called hydrophobic effect we'll come back later to hydrophilic molecules that like to go into solution in water but let's begin with hydrophobic we do this because the physical chemistry is interesting more generally but more importantly because the hydrophobic effect a very simple effect the interaction of a molecule with water is responsible for an enormous fraction of the structure of the macromolecules of biological system so the structure of DNA the structure of proteins the structure of lipid membranes for example are all dependent on the interaction of those molecules with water and particularly with the so called hydrophobic effect so as we go through this if it seems a little esoteric or beside the point precisely the contrary is true this is the hydrophobic effect is central to all macro molecular structure and biochemistry so let's start with a simple case this is a diagram of a benzene molecule you remember that benzene the sum of the bonding electrons delocalized around the ring and so you get a rigidly planar structure in which the carbons and the surrounding hydrogen molecules are pulled into this rigid plane notice also that carbon and hydrogen are comparably electronegative so carbon is not pulling I say again not pulling electrons off of oxygen I'm sorry off of hydrogen you you

Channel: Streaming Tutors

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Keywords: Paul Bingham, Biochemistry, streaming tutors, tutorial, Water, PH and Buffers

Id: 1k9JqWUGFCw

Length: 11min 16sec (676 seconds)

Published: Sat Feb 15 2014