Water: The Solvent for Biochemical Reactions
Chapter 2
Outline
• what is polarity and how does it affect water? • why is water the universal solvent?
• hydrophilic vs. hydrophobic
• hydrogen bonds and van der Waals interactions • acids, bases, pH & buffers
Water: a Polar Molecule
• we are all, quite literally, bags of ___________________ • life evolved in the oceans
- and the chemistry of life evolved to work best in that environment
• when life crawled out of the water and onto land, it had to take the ocean with it (otherwise all that chemistry would fail)
• through the course of this semester, you will see how important and critical water is for life and biochemistry
• to understand how water influences all of the chemical reactions that allow life, we must first understand water itself
• water is a _________________ molecule
- this means that it has an unequal ___________________________________________ - said more simply, one side of water is a bit negative while the other side is a bit positive • like this…?
… I said, “a bit”
• how can something possibly become ‘a bit’ charged?
- through ____________________________________ • here’s water…
• oxygen is ELECTRONEGATIVE – this means it exerts a strong attraction for the ______________ in the covalent bond it shares with hydrogen (remember: all covalent bonds are shared
electrons )
• if oxygen is acting as a magnet for electrons, towards what do you think those electrons will be attracted?
• and, if electrons are negatively charged, what will be the charge near oxygen? - near hydrogen?
• this is why water is a ___________________ molecule
- it has a partial positive charge on one side and a partial negative charge on the other
- FYI: ___________________ behaves very much like oxygen in this way… • now, think about this…
- what will happen when another water molecule floats by like this…? - remember: it’s another water molecule – identical to the first, so…
• a hydrogen bond is a weak bond (non-covalent) between a partially positive hydrogen (donor) and a partially negative electronegative atom (e.g., oxygen, nitrogen) involved in a polar bond (acceptor)
• H-bonds are responsible for much of life including enzyme function and holding DNA together
• it’s important for you to know that many molecules are __________________ • carbon dioxide has no polarity, no partial charges and is therefore not polar! • these nonpolar molecules have no charge characteristics of any kind
• a single water molecule has two hydrogens that can each be H-bond donors and an oxygen that can accept two H-bonds
- so each molecule can be engaged in as many as ______________ H-bonds • this means water molecules really like to stick to water molecules
- strength in numbers
- lots and lots of weak interactions make a difference
• water molecules are constantly making and breaking H-bonds with each other - but overall, there are tons of H-bonds occurring in any volume of liquid water • this results in a very interesting thing about water…
• if you found a chemist from another world and showed him the structure of the water
molecule chances are he (it?) would tell you that water is a _________
• water is a liquid solely because of the H-bonds holding water molecules to other water molecules
• H-bonds in water are responsible for another cool trick of water
- _________________________________
• again, H-bonds between water molecules impede other things getting between them
Water: the Universal Solvent
• many things dissolve in water and this is how biochemistry can be water-based • polar molecules dissolve in water (these include fully and partially charged molecules)
- I like to think of this as “water speaks the polar language –
anything that doesn’t speak that language can’t interact with water”
• when you put table salt (NaCl) in water it is literally picked apart – ion by ion – by water - note the orientation of the water on each ion
- this is the process of ___________________
- ___________________________ SHELL
• anything polar – anything fully or partially charged that can dissolve in water (speak water’s language) is said to be HYDROPHILIC
- literally translating to “water loving”
• for the most part, in biochemical reactions, hydrophilic things are our friends…
• anything nonpolar – that can not dissolve in water (does not speak water’s language) is HYDROPHOBIC
Things that Don’t Like Water
• hydrophobic molecules are often ______________________ - molecules that contain only hydrogen and carbon
- fats, oils, etc.
• when placed in water, they blob together and separate themselves from water (think of a salad dressing)
- why does this happen…?
• “the universe tends towards chaos” - randomness defeats all
- ___________________
• water can’t interact with oil, so it holds hands with other water molecules around the glob of oil
- this is order!!! not random!!!
• by corralling the oil together, the ____________________ number of waters are ordered • this is a good thing; the universe likes this
• the tendency of hydrophobic molecules to cluster together in water is known as HYDROPHOBIC INTERACTIONS
• it’s important for you to know that these are not bonds or interactions the way that H-bonds are
- these are simply nonpolar things all trying to get away from water together • we did not like Russia in WWII…
- both the US and Russia hated and feared Nazi Germany - that is why the US and Russia were allies
- a common enemy
• hydrocarbons do not like each other
- it just that their common enemy is _________________
Amphipathic Molecules
• a small family of molecules contain both polar and nonpolar regions
- these are called ______________________________
• part of this molecule speaks the language of water and part of it does not • drop this in water and…
• … MICELLES form – the polar head groups are • interfacing with water while the nonpolar tails • are tucked safely away
Brief Discussion of van der Waals Interactions
Induced Dipole Interactions
• remember that an atom is a positive center being orbited by a negative cloud • the negative cloud of one atom repels the negative cloud of another
- literally pushing the electrons to the other side of the atom
• that leaves a relatively positive area where the electron cloud has been repelled • then, as usual, opposites attract… positive region with negative
• at very short distances, repulsive forces win and no attraction occurs • and, of course, at far distances dipoles cannot be induced
• but it’s a small amount of energy summed up across many many atoms that gives van der Waals its strength
- just like H-bonds
Acids and Bases
• an acid – simply put – is a hydrogen ion ____________________
• a base – simply put – is a hydrogen ion ___________________
- hydrogen ions are also referred to as ______________________
• strong acids and bases lose or gain protons very rapidly and/or to completion – we call this DISSOCIATION
• the ACID DISSOCIATION CONSTANT (Ka) is a measure of acid strength • here, [_] refers to the concentration in molarity
• each acid has its own particular Ka - it’s a characteristic
• the _________________ the Ka, the more dissociation in water, the _______________ the acid • FYI: there are never true H+ protons in water
- water itself acts as a base, absorbs the H+ and becomes H3O+ - HYDRONIUM ION
• water itself can also dissociate into an acid and a base (thereby neutralizing itself) • water dissociates to equal concentrations of H+ and OH- (obviously)
- approximately 10-7M of each
• other acids dissociate to proton concentrations of 10-1 to 10-14M and everything in between - this is a real PIA… so we make it easier to write, look at, and say
• pH = -log10[H+] • in water, [H+] = 10-7
• pH of water is –log10[10-7] or 7
• big surprise… the pH of water is neutral
• acids have pH’s ______________ than 7
• bases have pH’s __________________ than 7
• 10-3M HCl (a very strong acid = complete dissociation) [H+] = 10-3
pH = -log[10-3] = 3 the pH is 3
• 10-4M NaOH (a very strong base = complete dissociation) [OH-] = 10-4 (… we need [H+]…)
remember water! [H+][OH-]=10-14 ALWAYS!!! [H+] = 10-10 (because [10-10][10-4] = 10-14) pH = -log[10-10] = 10
• we make things easier for ourselves with Ka as well pKa = -log10Ka
• the smaller this value the stronger the acid, the higher this value… • here’s how I like to think of pKa…
• if the pKa is 11, then the pH must be 11 for 50% of this acid to dissociate
- that means A LOT of OH- ions need to be around to forcibly PULL those protons off the acid! - does that sound like a strong acid (readily dissociates) to you?
• in biochemical systems (including the human body) most acids encountered are weak acids
The Henderson-Hasselbalch Equation (because we have to…)
• this equation connects the pH of a solution of acid with the pKa of that acid and the concentrations of the acid and its conjugate base
• pH is critically important to us because much of biochemistry and the chemical reactions that govern life occur in a very narrow range of pH
- any deviation towards too acidic or too basic can cause those reactions to stop entirely
Polyprotic Acids
• some molecules have ________________________________________________ and are called - POLYPROTIC ACIDS
• each dissociatable proton has its own pKa - can you tell me why…?
AS REVIEW
• if an acid has a pKa of 5 and the pH of the solution that acid is in is 3 - will that acid have donated its proton or not?
• if an acid has a pKa of 8 and the pH of the solution that acid is in is 10 - will that acid have donated its proton or not?
Buffers
• a buffer is anything that resists _____________________
• for us a buffer is something that resists a ________________________ • a buffer is a solution of a weak acid and its conjugate base
- weak acids have strong conjugate bases - makes common sense
- if you have to pull and fight and wrestle and bite and yell to get your poor stuffed bunny away from your pal…
… chances are your pal will rapidly take your bunny back if offered, right? - if you have to pull and fight and wrestle and bite and yell to get a proton off of an acid
… chances are that conjugate base will take that proton back if offered - and something that readily accepts protons is a strong base!
• so, we’ve got a solution of a weak acid (that really isn’t doing anything) and a strong base that’s hungry to accept free protons
• if we add strong acid to this buffer, the protons released by the acid will be ‘eaten’ by the conjugate base of the buffer
- pH will not change because there are no protons in the solution - this solution is resistant to change in pH
• compare this to water and you see a big difference
- without a buffer, the pH changes dramatically even when relatively little strong acid is added - this is because all those protons are dissociated and contributing to [H+]
• to keep pH stable and constant in the lab, we use buffers all the time (chemistry depends on pH)
• when the animation ended, there were two molecules of conjugate base left in solution • what if we added 4 or 6 or 8 more molecules of HCl…?
• pH would begin to change!
• all buffers can be ‘broken’ where all available conjugate base has been converted back to weak acid by absorbing a free proton
• with no base left to soak up protons, pH changes dramatically upon the addition of acid (just like it would in water)
• therefore, we always try to pick a buffer that has a pKa near the pH we want to keep stable - why…?
- at this pH, the buffer will be close to 50/50 weak acid/conjugate base and so there will be plenty of base available to absorb free protons
• a buffer is usually effective for one pH unit on either side of its pKa - a range of two pH units total
- buffer’s pKa is 7; the buffer will be effective from pH6-8
• in living cells, a phosphate based buffer functions to keep the pH near 7 • in the blood, CO2 itself acts as a buffer
Summary
• water is a polar molecule – this is due to the electronegativity of oxygen • the polar nature of water allows it to hydrogen bond with itself
- this is enormously important for liquid water, DNA, proteins, etc. • polar molecules (hydrophilic) dissolve in water
• nonpolar molecules (hydrophobic) do not; then instead cluster together • acids give up protons while bases accept them
• strong acids and bases fully dissociate in water … we did some math…
• pKa is a measure of the strength of an acid; the lower the value the stronger the acid (the less OH- needed to pull the proton off…) • buffers are solutions of a weak acid and its conjugate base
- this base absorbs added protons making the buffered solution resistant to changes in pH
FRIDAY: LAB in SCS 105
