CELL BIOLOGY WORKSHOP

CHEMISTRY BACKGROUND

Covalent bonds

In covalent bonds, atoms share electrons. These bonds are relatively strong. eg. water is H2O, an oxygen atom, O, and 2 hydrogen atoms, H, bonded covalently together. A very simplistic explanation is that the O has 8 electrons but requires 2 more electrons to fill its outer shell of electrons, ie O has a valency of 2. H has a valency of 1, so that 2 H atoms share their electrons with the O atom, and so form a molecule of water.

covalent bond


Hydrogen bonds

Hydrogen bonds are relatively weaker than covalent bonds, and occur between polar molecules. We can use water molecules to illustrate. In the H2O molecule the O is much bigger than each H atom, and its electrons are further away from the central positively charged nucleus which consists of protons (+ve charge) and neutrons (no charge, neutral). Each electron from the 2 H atoms is pulled towards the O atom, which. produces polarity with respect to electrostatic charge, the O end of the H2O molecule becoming slightly more negative for more of the time than the H ends of the molecule, which becomes more positive for more of the time.


Ionic bond

Ionic bonds are due to an electrostatic charge between differently charged ions. For example salt (sodium chloride, NaCl solid) consist of Na+ ions together with Cl- ions. If we put the solid NaCl salt into a polar substance, like water, it (the solute) dissolves in the water (the solvent) to form a solution of Na+ and Cl- ions in solution (i.e. salty water), the ions dissociate in solution. Furthermore, the polar water molecules actually surround the +ve ions with the H end of H2O facing away from the +ve ion, and they surround the -ve ion with the O end facing away due to the electrostatic attraction between the oppositely charged particles and repulsion between same charged particles.

ionic bond
ions


Acids and bases

These are related to the concentrations of H+ and OH- ions in solution, respectively. For example, if we add HCl to water we end up with H+ and Cl- ions in solution which will be more acidic (a stronger acid) because we have more H+ ions in solution. If we add NaOH to water we end up with Na+ and OH- ions in solution which will be more basic (a stronger base) because we have more OH- in solution. Pure water, H2O, is actually in equilibrium with its ions, H+ and OH-. There are about 0.0000001 moles of H+ in one litre of pure water, ie 10-7 moles H+ per litre H2O. Similarly, there are about 10-7 moles OH- per litre H2O. Adding HCl will increase the relative concentration of H+ in solution.


pH

This is related to the concentration of H+ ions in solution. Think of the "pH" as the proportion of H, if you like. The pH is actually calculated by the following,

pH = -log10([H+])

i.e. the negative logarithm, base ten, of the [concentration] of hydrogen ions H+ in solution. A fast way to calculate the pH is to express the concentration of H+ as indices of 10, ie as 10-pH. For example, the concentration of H+ in pure water is 10-7 so the pH is simply, -(-7) = 7 (Don't forget to multiply the indices by a minus to get a positive value)

Note: pH is used readily to express the acidity of a solution, even if the acidity is very low, that is, if pH > 7, like a pH of 13, say. You should be aware that pOH is just as valid but not used as often. Furthermore,

pOH = -log10([OH-])

and hence, from what we now know about pure water,

pH + pOH = 14


Buffer Solutions

   - eg H2CO3 a weak acid

Different substances dissociate to different degrees. HCl is a strong acid because almost all of it dissociates in solution, but H2CO3 is a weak acid and only partially dissociates into H+ and HCO3- so that there are H+ , HCO3- and H2CO3 in solution,

H2CO3 <===> H+ + HCO3-

Simply stated, a buffer can be thought of as soaking up H+ ions, and forcing the reversible equilibrium reaction back the other way.

[Note that actually there is a two-way effect for this reaction. The following reactions can also occur,

H2CO3 + OH- HCO3- + H2O

to "soak up" hydroxide ions, and

CO2 + H2O <====> H2CO3

which can produce the weak carbonic acid on the left hand side of the equation. All these reactions play a very important role in maintaining a consistent pH in our blood.


Oxidation Reduction reactions

Oxidation used to be thought of as essentially adding an oxygen atom, but as time has gone by, chemists have come to realise that the essence of oxidation is not adding an oxygen atom, but it is the LOSS of an electron. Something is oxidised when it loses an electron. So by converse, something gets reduced when it gains an electron.

OXIDATION is LOSING an electron.

REDUCTION is GAINING an electron.

REDOX POTENTIAL is the potential for a substance to donate or accept an electron in a redox reaction and is measured in millivolts (mV). The redox potential Eo will tell us which way the electron is inclined to move in the reaction and by calculating the Gibbs Free Energy (ΔG) for the redox reaction we can tell whether the reaction will occur spontaneously or not.

The electron is negatively charged so it will be attracted by a positive charge and repelled by a negative charge i.e. that the electron will move from the negative towards the positive in a redox reaction. Similarly, electrons will tend to move from a negative to a more positive Eo in a redox reaction.


Gibbs free energy

ΔG = ΔH - ΔTS
where

ΔG is the change in free energy

ΔH is the change in heat

T is temperature

ΔS is the change in entropy (disorder).

A positive free energy value, +ΔG, means the reaction requires an input of energy to make it happen, +ΔG reaction is not spontaneous.

A negative free energy value, -ΔG, means that the reaction can occur spontaneously.

To calculate the ΔG of a redox reaction we can make use of the following equation and the Eo values of the substances involved,

ΔG = -nF ΔEo

where

n is the number of electrons that move in the reaction

F is Faraday's constant (96.4 kJ mol-1 volt-1)

ΔEo is the change in redox potential

For example, NADH is oxidised to NAD and the electrons passed on to FMN which is reduced to FMNH2. FMNH2. can be oxidised then back to FMN if an "electron acceptor" becomes available. A suitable electron acceptor is oxygen, O which can accept 2 electrons and combine with H+ ions to produce water, H2O. Therefore, through a series of redox reactions, in which the electrons are passed down an electrical potential we get from NADH with a Eo = -320mV to water at Eo = +815. To work out the free energy we have,

two electrons, n =2,

a change in redox potential, ΔEo = 815 - (-320) = 1.135V,

and free energy is,

ΔG = -2 x 96.4 x 1.135 ≈ -220 kJ mol-1

Since the free energy value is negative, the series of redox reactions should occur spontaneously.


Reactions can be coupled

Reactions with a -ΔG, which effectively give up energy can "couple" or happen in close proximity to another reaction which requires a small amount of energy, a +ΔG reaction - this allows the second reaction to occur. eg. redox reactions and proton pumps.