Transcript for Water: The Solvent for Biochemical Reactions

Slide 1: Title Slide

Slide 2: Water

Most biogenesis models suggest that life begins somewhere in the oceans. Regardless, life is definitely dependent on
water. Water is ubiquitous. Our planet’s surface is around 75% covered in water. Our bodies are made up of water to
the tune of 60% or more. Biochemical reactions in the cell require water as the solvent. Even the hydrophobic materials
(e.g. membranes) must be and are solvated by water. The energetics of water is unique and creates some very unusual
properties for this molecule.

Water is the medium of life.

Slide 3: Lecture goals

While this lecture is still something of a review, you still need to study it carefully. Many of the topics are fairly intuitive,
but there is some math here and you will want to practice those as they can be a bit tricky to internalize.

You will have a solid grasp on chapter 2, when you can:

 Describe polarity and explain basic solubility.

 Describe hydrogen bonds and discuss the nature of water’s properties.
 Define acids and bases in biochemical terms.
 Define pH mathematically and calculate pH for weak acids and bases.
 Explain and demonstrate the concept of titration.
 Explain and demonstrate the concept of buffering.
 Describe the blood buffering system.

Slide 4: Water: Polarity and Hydrogen Bonds (Title Slide)

Slide 5: Electronegativity

The single most important property of water is probably the fact that it is highly polar. Essentially, every other aspect of
water’s nature derives from this property. So what is polarity?

To understand polarity, we have to understand electronegativity. If you go back to chemistry and the periodic table,
you’ll recall that certain atoms exert a stronger “pull” on electrons that others. This ties back to the octet rule with
atoms attempting to achieve 8 electrons in their outer shells. Chlorine, for example a group 7 element, only needs one
more electron to achieve it’s 8. Unlike carbon, which needs four more electrons. Therefore, it’s not unreasonable to
assume that chlorine exerts more “pull” on an electron than carbon does. While we’re here, note that nitrogen and
oxygen would also be expected to pull electrons more so than carbon, and they do.

Don’t confuse this unequal “pulling” with actual electron transfer. In this case, we can complete transfer of an electron
from one species (e.g. hydrogen) to another species (e.g. chlorine) making two ions, charged atoms, and an ionic bond.
What we’re talking about here has to do with covalent bonds.

Shown in table 2.1 are the electronegativities of some elements. These are values that are relative and compared to
fluorine (the most electronegative element). Fluorine has a value of 4. One thing to note is that hydrogen has a similar
electronegativity as carbon, that’s going to be very important.

Slide 6: Polarity
Now that we have some idea about electronegativity, we can talk about polarity. The concept of polarity is an uneven
distribution of charges. Sometimes the word gets used in other ways, but in a very general sense it only means “different
ends”.

Polarity arises when we have atoms of different electronegativity sharing electrons. While the bond is covalent, because
the electrons are not fully transferred, the molecule is said to have partial charges. However, unequal electron sharing is
not sufficient. After all, carbon dioxide is not polar. Looking at the molecule you can see why. This is a linear molecule
and the partial charges perfectly balance each other.

Compare this to a water molecule. The angle of the water molecule means that the partial charges cannot cancel the
way they do in carbon dioxide. This results in water having a dipole moment and as you can see it has a sort of positive
side and a negative side. This property will enable water to interact with fully charged or partially charged species.
However, uncharged species will not interact with water at least not fully.

Slide 7: Bonds and interactions

The two most basic bonds are ionic and covalent. Both of these are far stronger than the weak interactions we’ll be
discussing next. Ionic bonds involved the transfer of electrons and for the formation of two ions. For example, a salt
cube with the associations of sodium that loses an electron to chlorine. The sodium ionizes to +1 and the chlorine (now
chloride) ionizes to -1. Notice how gaining the electron reduced chlorine’s charge from 0 (neutral) to -1 negatively
charged. This is where the term reduction comes from and we’ll be talking about that more later. Covalent bonds are
also extremely strong, and typically require special events in metabolism to break. In a covalent bond, the electron is
shared (evenly or unevenly depending on electronegativity). The hydrogens in water, for example, are covalently bound
to the oxygen even though the molecule is polar.

Weak forces are different, and of course far weaker.

Salt-bridges are similar to ionic bonds in that charged species form these. However, the difference is that we’re not
usually talking about pure ions in biochemistry but charged species on biomolecules. Sometimes these are also referred
to as electrostatic interactions. Do not mistake electrostatic for ionic, however. Remember with ionic there is a transfer
of electrons. In electrostatic there is not a transfer of electrons between the species (hence the term electro – static).

There is a small suite of interactions that fall under the heading “London Dispersion Force”. These types of interactions
appear due to the displacement or distortion of electron clouds surround atoms. In these cases, the nucleus becomes
“unshielded” allowing the positively charged nucleus to interact with a nearby electron cloud. These forces only exist in
a narrow window of distance. Too far and the atoms cannot induce the de-shielding and too close the electron clouds
overlap causing repulsion.

Slide 8: Hydrogen Bonding

Lastly on our list is hydrogen bonds. These types of interactions are rather weak but extremely common in biomolecules.
After all, the molecules are interacting in water and water itself forms a massive network of hydrogen bonds.

Hydrogen bonds are simply an arrangement where two electronegative atoms (with partial negative charges) are
attempting to share a positively charged hydrogen. The hydrogen cannot be localized to either electronegative species
so a continuous partial bond is formed. While hydrogen bonds are individually weak (about 5 kcal/mol compared to an O
– H bond (about 110 kcal/mol) they gain strength through sheer numbers.

It is the extensive network of hydrogen bonds that makes water’s melting point and boiling point dramatically higher
than other molecules of the same molecular weight, compare water’s melting point and boiling point to ammonia and
methane. This is in your book.
Slide 9: Like dissolves like
The fact that water is polar is what enables it to dissolve a host of materials. Consider the core functional groups of
biochemistry. What did they have in common? Frequently, there were oxygen and nitrogen atoms and we now know
those atoms are electronegative and polar. So we should expect hydrogen bonds to appear and they do. So most
biomolecules have some degree of solubility in water. Water creates a shell of solubility around these materials and we
term those interactions: hydrophilic.

However, some materials such as hydrocarbons do not have polarity (they are nonpolar) and so cannot interact with
water molecules. In fact, they will have a difficult time intruding into the hydrogen bond network within water because
there is nothing for these molecules to “grab” as it were. They have no charge and no charge will not remain associated
with charge. These hydrophobic molecules (found in membranes and in the cores of globular proteins) associated away
from water. This is why oil and water will not mix and will eventually separate.

There is a class molecules termed: amphipathic. These molecules typically have a substantial nonpolar side and a polar
side. Consider a fatty acid. It has a long hydrocarbon chain and a carboxylic head group. Look again at carboxylic acid.
This is polar; so the head-group will interact with water and the hydrocarbon will orient away. These molecules will
interact with water as well as non-polar materials. They are amphipathic.

Slide 10: Biochemical Hydrogen Bonds

Hydrogen bonding is a hallmark of living systems. They are everywhere. They hold proteins together in their proper
shapes. They allow enzymes to recognize substrates. Amphipathic membranes interact with water and hold a
hydrophobic core. Hydrogen bonds keep DNA base paired correctly. Even receptors and ligands need hydrogen bonding
patterns to specifically recognize each other. Hydrogen bonding is the key interaction in biochemistry.

Slide 11: Lecture Goals

At this point you should have a grasp of polarity and the idea of what can dissolve what. You should be able to describe
the hydrogen bond and other weak interactions and use this information to compare the properties of water to other
molecules of similar molecular weight.

On we go!

Slide 12: pH Acids and Bases (Title Slide)

Slide 13: Acids and Bases

Biochemically, acids and bases are simply defined. A species that donates a proton is termed an acid and a species that
accepts a proton is termed a base. In biochemical systems, an acid that loses its acidic proton is termed a conjugate
base. So acids de-protonate to conjugate bases and conjugate bases protonate to become acids.

Keep in mind that we’re discussing weak acids, typically, in biochemistry. Strong acids such as hydrochloric acid fully
dissociate in water. Weak acids, however, do not fully dissociate. Weak acids have a value that denotes their ability to
deprotonate and this is called the Ka. Table 2.6 in your book has a list of common Ka values. Be sure you understand the
table, but you don’t need to memorize it. On that table, the lower a Ka value is stronger than a higher one. For example,
look up acetic acid and pyruvic acid (their conjugate bases are acetate and pyruvate respectively), which one is the
strong acid?

Slide 14: Strong Acid / Base pH

We can take the given that pure water has [H +] is 1 x 10-7 and [OH-] is 1 x10-7. Neutral water pH 7 has equal parts protons
and hydroxides as seen here. This gives us our pH scale of 1 to 14. With 7 being neutral, below 7 being acidic and above
7 being basic.

pH itself has no units. However, it is on a log scale. This means a change of one pH unit say from 7 to 6 would be a 10-
fold increase in proton concentration. Likewise, 6 to 7 would be a 10-fold decrease in proton concentration.

Your book shows have to derive the pH equation, but let’s just skip ahead.

The pH equation is: pH equals negative 1 times the log of the concentration of proton in the solution. This is for rather
simple pH calculations that just involve strong acids and bases.

Given what we know, try to solve the following:

What is the pH of 0.001M HCl in pure water?

First, HCl is a strong acid so it will dissociate completely. This means we just added 0.001 M protons to the water. Since
we have the proton concentration we can apply the pH equation. Solving for pH we come up with an answer of 3 (don’t
forget to multiple the log result by negative 1).

Now in your book give it a try with NaOH, this one is a bit different as you’ll have to work with the ionization of water as
well. It’s not hard but it can trip you up if you’re not careful.

Slide 15: Why does pH matter?

In biochemical systems, the key players are enzymes. However, enzymes are extremely picky about their environments
and quite sensitive to change. They typically have an ideal pH for activity. Moving an enzyme outside of its pH range can
result in failure of the enzyme to be active. Therefore, in the laboratory we have to be thoughtful as to the pH of our
system if we want to accurately measure enzymatic behavior.

Look at these three enzymes: pepsin, trypsin, lysozyme. Also note their activity curves based on pH. Just by looking at
that, and the information we saw in chapter 1. Can you predict where these enzymes may be active? Give it a try!

Slide 16: Henderson-Hasselbalch

The first equation introduced is great for looking at strong acids and bases in water. However, biochemical systems
typically do not involve strong acids and bases or at the least normally involved buffered systems. A buffer is a system
that resists change. In our case, buffers resist pH changes. Remember, pH changes can dramatically affect enzymes and
enzymes are what keep life, alive.

So to work with pH in buffered systems we need to use a new equation: pH = pKa + log [A-]/[HA]. For this equation
you’ll need to calculate the concentration of conjugate base [A-] and weak acids [HA]. The pKa is found on a table such
as table 2.6.

Let’s give one a try, others are in your book to attempt but they all work similarly.

Slide 17: Titration of acetic acid

Around their pKa, weak acids and their conjugate bases do a really good job of not letting the pH move that much. After
a while though, enough acid (or base) will cause the pH to shift. We can see this happen with an acetic acid titration with
sodium hydroxide.

To do a question like this we will need to know the concentration of conjugate base and the weak acid. So we’re starting
with 1 mol of acetic acid and we’re going to add 0.1 mol of NaOH. Now, see if you can calculate the resulting pH of the
solution.

Pause the video and try to solve this before going forward.

First, remember that NaOH is a strong base so it dissociates completely. This means 0.1 mol of NaOH releases 0.1 mol of
OH- to the solution. Acetic acid immediately loses its acidic proton to the OH-. So now we have converted 0.1 mol of
acetic acid to acetate. That leaves 0.9 mol of acetic acid. We now have [HA] (0.9 mols) and [A-] (0.1 mols). Looking up
table 2.6 we see the pKa of acetic acid is 4.76. We can put all of that into the HH equation and calculate the new pH to
be 3.81. Comparing that to figure 2.15 we see that looks pretty good for how vague the figure is!

Now be sure to do the rest in your book and see how the curve turns out. It will show you the buffering behavior of
acetic acid and just how much it resists pH change. This behavior is extremely important for biochemical systems.

Also, be sure to look at 2.3 and 2.4 because this will put all the pH ideas together and show you how to use
concentrations in molar and just amounts. Apply your knowledge 2.4 is particularly interesting because it shows a
buffered vs. non-buffered system.

Slide 18: Compensatory Respiratory Alkalosis

A large number of metabolic events release protons as a product. For example, anaerobic glycolysis creates lactic acid
which deprotonates to lactate. Protons are pumped out of cell and into the blood and if enough protons are added to
the blood there is a threat of acidosis.

However, proton can bind to carbonate and eventually bicarbonate. Increasing bicarbonate results in increased gaseous
carbon dioxide and that is exhaled. Remove of this drives reduction of proton by binding it to carbon as the shown
reactions proceed backwards.

However, there is a trick that can be done and athletes do this. By hyperventilating, you can greatly increase the blood
pH (often to nearly dangerous levels). When this happens a lot more proton can be absorbed by carbonate. Remember
that lactic acid? Well, lactate is fine it’s the proton that causes the problem. Through dramatically raising blood pH by
hyperventilation an athlete can work harder and not have as much pH drop in the blood and thereby perform longer
without the lactic acid issues.

Not a bad trick!

Slide 19: Lecture Goals

So there you have it! We have now reached the end of this lecture and at this point you should be able to work on and
master each of the goals presented in the lecture.

Don’t forget to review the book especially the apply what you know exercises. I highly recommend review exercises
from 2.1 – 2.3 all of the questions. In 2.4 I recommend: 26 and 27. In 2.5 I recommend: 29, 30, 31, 32, 35, 37, 38, 41, 45,
49, 53, 59 (you may have to investigate something here), and 60.

Good luck on your work day!