Chapter 2: Water- Acids, Bases and Calculating Acidity (pH).

Among the important properties of water is its slight tendency to ionize. Pure water consists not only of H₂O but also a low concentration of hydronium ions (H₃O⁺) and an equal concentration of hydroxide ions (OH^–):

2H₂O _(l)  <–> H₃0 ⁺ _(aq) + OH ^– _(aq)

Hydronium ions are capable of donating a proton to another ion. Such proton donors are referred to as acids according to the Brønsted-Lowery concept of acids and bases.

Proton acceptors are called bases. Hydroxide ions can accept a proton and be converted back to water molecule. Therefore, what? That’s right. Hydroxide ions are bases.

The ionization of water can be analyzed quantitatively. Brace yourself for some math now. Don’t worry; it’s explained simply.

Since part of water dissociates in the water solution, we should note that the concentrations of reactants and products in a reaction will always reach equilibrium. In this case, the reactant is water H₂O and the products are hydronium ions (H₃O⁺) and hydroxide ions (OH^–).

The ratio of these concentrations defines the equilibrium constant (K_eq).

But first, we need to calculate the concentration and then its ratio. How can we calculate the concentration of water?

Formula for any concentration is M = n ÷ V, where M = concentration of solution, n = moles of substance, and V = volume of solution in litres (L).

So, to find concentration, we need to know the moles of the substance, in our case is water with one oxygen = 16gm and two hydrogen = 1 each (see periodic table), with a total of 16+1+1 = 18gms per mole of H₂O.

The volume, let’s for simplicity take 1 litre. However, since the mole is in grams, we have to convert the units of litre into grams as well. Math 101 question: how many litres are there in a gram? That’s right, 12. No idiot, go back to math class. The correct answer is 1000gms. “You Baboon! You Dracula!”,(our economics teacher).

Okay, now that we have two similar units, we must apply the formula:

(1000g of H₂O per L) / (18g of H₂O per mole) = 55.55.

The concentration of a solution is usually given in moles per litre (mol L^-1 OR mol/L) since the grams cancel each other out. This is also known as molarity.

Concentration, or molarity, is given the symbol M. Example; a short way to write that the concentration of a solution of hydrochloric acid is 0.01 mol/L is to write [HCl] = 0.01M. Got it?

So the molarity of water is 55.5 mol/L or mol L^-1 or M.

By the way, usually, the square brackets around the substance indicate concentration. So if we write [H₂O] = 55.5M, we’re trying to say that the concentration or M of water is…you get it.

Now that we have the concentration, we have to bear in mind (and as already stated) that the two products of ionization of water dissociate into equal concentrations.

Assuming that the concentrations of hydronium and hydroxide ions are very low relative to the concentration of un-ionized water, then the formula is:

K_eq ×55.5 M = [H₃O⁺] [OH^–]

The equilibrium constant for the ionization of water is 1.8 × 10^-16M at 25°C. Substituting this value in the above equation gives:

1.8 × 10^-16 M × 55.5 M = [H₃O⁺] [OH^–]

Therefore, 1.0 × 10^-14 M² = [H₃O⁺][OH^–]

[H₃O⁺][OH^–], called the ion product for water, is a constant designated K_w, and hence has a value of 1.0 × 10^-14 M².

Because water is electrically neutral, its ionization produces an equal number of hydronium ions and hydroxide ions [H₃O⁺] = [OH^–]. In the case of pure water, the above equation can therefore be rewritten as:

K_w = [H₃O⁺] ² = 1.0 × 10^-14 M².

Taking the square root of the terms gives; [H₃O⁺] = 1.0 × 10^-7 M.

Since [H₃O⁺] = [OH^–], the ionization of pure water produces 10^-7 M of H⁺ and 10^-7 M of OH^–.

One interesting point to note is that the hydronium ions are so ionic that they immediately donate a proton (H⁺)in a reaction, becoming H₂O + H⁺. Therefore, when we refer to hydronium ions, we are more specifically talking about it’s capacity to donate a proton and therefore, can neglect the H₂O and simply discuss the H⁺ to the point where the H₃O⁺ in the entire equations above can be replaced simply with H⁺ (as we did only in the end, “pure water produces 10^-7 M of H⁺and 10^-7 M of OH^–”).

Pure water and aqueous solutions containing equal concentrations of H⁺ and OH^– are said to be neutral. Of course not all aqueous solutions have equal concentrations of H⁺ and OH^–.

When an acid is dissolved in water, H⁺ increases and the solution is described as acidic solution.

Note that when an acid dissolves in water, the concentration of protons increases, conversely, the concentration of hydroxide ions decreases. This is because the ion product constant for water (K_w) in unchanged (i.e., constant) and the product of the concentrations of H⁺ and OH^– is always1.0 ×  10^-14 M².

So evidently, dissolving a base in water decreases [H⁺] and increases [OH^–] above 1.0 × 10^-7 M, producing a basic or alkaline solution.

Chapter 2: Water- Nucleophiles and Electrophiles.

Electron-rich atoms or groups are called nucleophiles (nucleus lovers) because they seek positively charged or electron-deficient species called electrophiles (electron lovers).

Nucleophiles are either negatively charged or have unshared pairs of electrons. They attack electrophiles during substitution or addition reactions.

The most common nucleophilic atoms in biology are oxygen, nitrogen, sulfur and carbon.

Because the oxygen atom of water has two unshared pairs of electrons, it is nucleophilic.

Water is relatively weak nucleophile, but its cellular concentration is so high that one might expect that many biological compounds such as polymers, would be easily degraded by nucleophilic attack by water. For example, proteins can be hydrolyzed, or degraded by water, to release their monomeric units, amino acids.

Another question immediately pops to mind here; if there is so much water in cells, why aren’t all biopolymers rapidly degraded to their components?

The linkages between the monomeric units of biopolymers, such as the amide bonds in proteins and the ester linkages in DNA, are relatively stable in solution at cellular pH and temperature (i.e., they are kinetically stable, although they are thermodynamically unstable).

Actually, there is some effect against these bonds, however, the rate of reaction is so slow under the physiological conditions (of temperature and pH) of the body that special enzymes, called hydrolases, are required to catalyze hydrolysis. Of course, these enzymes are stored in inactive forms or enclosed in special membrane-bounded compartments to avoid spontaneous hydrolysis.

Furthermore, cells can synthesize polymers in an aqueous environment by using the chemical potential energy of ATP to overcome an unfavorable thermodynamic barrier.

And, more importantly, the enzymes exclude water from the active site where synthetic reactions occur.

Chapter 2: Water- Non Covalent Bonds; Hydrogen Bonds & Hydrophobic interactions.

As we’ve already discussed these two before, here is a brief overview again.

3. Hydrogen bonds are among the strongest noncovalent forces in biological systems.

They are paradoxically strong enough to provide structural stability but weak enough to be readily broken.

In general, a hydrogen bond can form when a hydrogen atom covalently bonded to a strongly electronegative atom, such as nitrogen, oxygen, or, in rare cases, sulfur.

Examples of hydrogen bonds that can form between molecules. Click on image for credit.

Hydrogen lies approximately 0.2 nm from another strongly electronegative atom that has an unshared electron pair. The total distance between the two electronegative atoms participating in a hydrogen bond is typically 0.27 to 0.30 nm. Some common examples of hydrogen bonds are shown.

All the functional groups are also capable of forming hydrogen bonds with water molecules. In order for hydrogen bonds to form between or within biological macromolecules, the donor and acceptor groups have to be shielded from water. In most cases this shielding occurs because the groups are buried in the hydrophobic interior of the macromolecule, where water can’t penetrate.

In DNA, for example, the hydrogen bonds between complementary base pairs are in the middle of the double helix as you can see.

4. Hydrophobic interactions: When relatively nonpolar molecule or group in aqueous solution associate with other nonpolar molecules rather than with water, it is termed a hydrophobic interaction.

Although hydrophobic interactions are sometimes called hydrophobic “bonds”, this description is incorrect. Nonpolar molecules or groups tend to group-up not because of mutual attraction but because the polar water molecules around them tend to pressure and entrap them close to each other as the water molecules form hydrogen bonds.

Hydrophobic interactions, like hydrogen bonds, are much weaker than covalent bonds. For example, the energy required to transfer a -CH₂–  group from a hydrophobic to an aqueous environment is about 3kJ mole^-1.

Again, all of the interactions covered here are individually weak compared to covalent bonds, but the combined effect of many such weak interactions can be significant.

Chapter 2: Water- Non Covalent Bonds; Van Der Waals Forces.

2. Van der Waals is another weak force involving the interaction between the permanent diploes of two uncharged polarized bonds (dipole-dipole) or the interactions between a permanent dipole and a transient dipole induced in a neighboring molecule (instantaneous dipole-induced dipole).

 

Dipole-Dipole interaction between two Hydrochloric Acids (HCl). Click on image for credit.

In dipole-dipole interactions, both the molecules are uncharged yet polarized, meaning they are not ions with an extra or missing electron (anion or cation), rather, they are molecules with one end being more electropositive and another more electronegative. Such as Hydrochloric acid (HCl). When two HCl come close, they immediately configure in such a way as to have their opposite poles face each other.

 

Instantaneous Dipole- Induced Dipole 1. Click on image for credit.

Instantaneous Dipole-Induced Dipole interactions 2. Click on image for credit.

In instantaneous dipole-induced dipole, the atom’s or molecules’ electrons are in spontaneous presence around the electron orbital causing fluctuations in their polarity structure. Once a dipole is spontaneously created, the incident will induce a polarity in another neighboring molecule.

These forces are of short range and small magnitude.

The attractive forces, also known as London dispersion forces, originate from the infinitesimal dipole generated in atoms by the random movement of the negatively charged electrons around the positively charged nucleus.

Although they operate over similar distances, van der Waals forces are much weaker then hydrogen bonds.

Van der Waals forces also have a repulsive component. When two nuclei are squeezed together, the electrons in their orbitals repel each other. This repulsion increases exponentially as the atoms are pressed together, and at very close distances it becomes prohibitive.

The sum of the attractive and repulsive components of van der Waals forces, are said to be in Van der Waals contact, and the attractive force between them is maximal.

Although individual Van der Waals forces are weak, the clustering of atoms within a protein, nucleic acid, or biological membrane permits the formation of a larger number of these weak interactions.

Once formed, these cumulative weak forces play important roles in maintaining the structure of the molecules.

For example, the heterocyclic bases of nucleic acids are stacked one above another in a double-stranded DNA. This arrangement is stabilized by a variety of noncovalent interactions, especially Van der Waals forces. These forces are collectively known as stacking interactions.

Chapter 2: Water- Non covalent bonds; Charge-Charge interactions.

Four major types of noncovalent bonds or forces are involved in the structure and function of biomolecules. In addition to hydrogen bonds and hydrophobicity, there are; charge-charge interactions and van der Waals forces.

Let us discuss each.

1. Charge-charge interactions, hydrogen bonds, and van der Waals forces are variations of a more general type of force called electrostatic interactions.

Charge-charge interactions are electrostatic interactions between two charged particles. These interactions are potentially the strongest noncovalent forces and can extend over greater distances than other noncovalent interactions.

The stabilization of sodium chloride or table salt (NaCl) crystals by interionic attraction is an example of a charge-charge interaction. Water, greatly weakens these interactions as we saw earlier.

Consequently, the stability of biological polymers in an aqueous environment is not strongly dependent on charge-charge interactions, but such interactions do play a role in the recognition of one molecule by another.

For example, most enzymes have either anionic or cationic sites that bind oppositely charged reactants. Attractions between oppositely charged functional groups of proteins are sometimes called salt bridges.

Salt bridges (hydrogen & charge-charge) between Glutamic acid and Lysine. Click on image for credit.

A salt bridge buried in the hydrophobic interior of a protein is stronger than one on the surface because it can’t be disrupted by water molecules. The most accurate term for such interactions is ion-pairing.

Charge-charge interactions are also responsible for the mutual repulsion of similarly charged ionic groups. And these charge repulsions can influence the structures of individual biomolecules as they interact with other, like-charged molecules (similar to the hydrophobic effect).

Chapter 2: Water- Detergents & Chaotropes.

Detergents, sometimes called surfactants, are molecules that are both hydrophilic and hydrophobic; they usually have a hydrophobic chain at least 12 carbon atoms long and an ionic or polar end. Such molecules are said to be amphipathic.

One of the synthetic detergents most commonly used in biochemistry is sodium dodecyl sulfate (SDS), which contains a 12-carbon tail and a polar sulfate group.

Sodium Dodecyl Sulfate. Click on image for credit.

Some ions such as thiocyanate (SCN) and perchlorate (CIO₄) are called chaotropes, meaning they are structures that disrupt the structure of water, so as to promote activities inhibited by the water molecules. These ions are poorly solvated compared to ions such as ammonium (NH₄⁺), sulfate (SO₄^2-) and dihydrogen phosphate (H₂PO₄^–).

Ammonium.

Sulfate

Dihydrogen phosphate

Chaotropes enhance the solubility of nonpolar compounds in water by disordering the water molecules (there is no general agreement on how chaotropes do this). Enzymes are usually amphipathic chaotropes.

Chapter 2: Water- More on hydrogen bonds, structure of ice and polarity.

The three dimensional interactions of liquid water is difficult to study due to it’s fluid state but much has been learned by examining the structure of the ice crystals.

Ice Crystal Lattice. Click on image for credit.

Four adjacent hydrogen-bonded oxygen atoms occupy the vertices of a tetrahedron (tetra = four, hedron = plane, thus four-sided figure). The average energy required to break each hydrogen bond in ice has been estimated to be 23 kJ mol^-1.

The ability of water molecules in ice to form four hydrogen bonds and the strength of these hydrogen bonds give ice an unusually high melting point. This is because a large amount of energy, in the form of heat, is required to disrupt the hydrogen-bonded lattice of ice. When ice melts, most of the hydrogen bonds are retained by liquid water, but the bonds are distorted relative to those in ice, so that the structure of liquid water is more irregular.

Interesting point to note is that the density of most substances increase on freezing as molecular motions slows and tightly-packed crystals form. The density of water also increases as it cools until it reaches a maximum at 4°C (277K). Then, as the temperature drops below 4°C, water expands. This expansion is caused by formation of the more open hydrogen-bonded ice crystal in which each water molecule is hydrogen-bonded rigidly to four others. As a result, ice, with its open lattice, is less dense than liquid water, whose molecules can move enough to become more closely packed. Because ice is less dense than liquid water, ice floats and water freezes from the top down. This has important biological implications since a layer of ice on a pond insulates the living creatures below from extreme cold.

Furthermore, two additional properties of water are related to its hydrogen-bonded characteristics- its specific heat and its heat of vaporization.

The specific heat of substance is the amount of heat needed to raise the temperature of 1 gram of the substance by 1°C. A relatively large amount of heat is required to raise the temperature of water because each water molecule participates in multiple hydrogen bonds that must be broken in order for the kinetic energy of water molecules to increase. Btw, the abundance of water in the cells and tissues of all large multicellular organisms means that temperature fluctuations within cells are minimized. This feature is of critical biological importance since the rates of most biochemical reactions are sensitive to temperature.

The heat of vaporization of water is also much higher than that of many other liquids. A large amount of heat is required to convert water from liquid to gas because hydrogen bonds must be broken to permits water molecules to dissociate from one another and enter the gas phase. Because the evaporation of water absorbs so much heat, perspiration is an effective mechanism for decreasing body temperature; the sweat will absorb heat away from the body as it evaporates.

As discussed earlier, water molecules are permanent dipoles that are polar and can interact with and dissolve other polar compounds and compounds that ionize (the latter are called electrolytes). They can align themselves around the ions formed from electrolytes so that the negative oxygen atoms of the water molecules are oriented toward the cations (the positive ions) of the electrolytes and the positive hydrogen atoms are oriented towards the anions (the negative ions). Consider what happens when a crystal of table salt- NaCl (sodium chloride) dissolves in water. The polar water molecules are attracted to the charged ions in the crystal resulting in sodium and chloride ions on the surface of the crystal dissociating from one another, and the crystal beginning to dissolve.

Sodium Chloride dissociation (hydration) in water. Click on image for credit.

Each dissolved Na⁺ attracts the negative ends of several water molecules, whereas each dissolved Cl^– attracts the positive ends of several water molecules (see diagram).

The shell of water molecules that surrounds each ion is called a salvation sphere and usually contains several layers of solvent molecules. A molecule or ion surrounded by solvent molecules is said to be solvated. When the solvent is water, such molecules or ions are said to be hydrated.

Thus, any polar molecule has a tendency to become solvated by water molecules. Ionic organic compounds, such as carboxylates and protonated amines, owe their solubility to the amino, hydroxyl, and carbonyl groups. Molecules containing such groups disperse among water molecules, with their polar groups forming hydrogen bonds with water.

Of course, the number of polar groups in a molecule affects its solubility in water. Solubility also depends on the reaction of polar to nonpolar groups in molecule: for example, one-, two-, and three-carbon alcohols are miscible with water, but larger hydrocarbons with single hydroxyl groups are much less soluble in water.

Table measuring solubility of molecule in water as it's non-polar hydrocarbon chain grows. Click on image for credit.

In a large molecule, the properties of the nonpolar hydrocarbon portion of the molecule override those of the polar alcohol group and limit solubility.

Chapter 2: Water- Hydrogen Bonding.

All living cells depend absolutely on water for their existence. In most living cell, water is the most abundant molecule, accounting for 60% to 90% of the mass of the cell. The macromolecule components of cells-proteins, polysaccharides, nucleic acids, and membranes- get their characteristics shapes in response to interactions with water and much of the metabolic processes of cells has to operate in an aqueous environment because water is an essential solvent as well as a substrate for many cellular reactions.

A water molecule (H₂O) is V-shaped, with an angle of 104.5° between the two covalent O-H bonds.

A water molecule. Click on image for credit.

An oxygen atom has six electrons in the outer shell, but the outer shell can potentially accommodate four pairs of electrons in four sp³ orbitals. This means that oxygen can form covalent bonds involving two different hydrogen atoms, each sharing a single electron with the oxygen atom.

An oxygen nucleus (because it contains more protons or positive charge) attracts electrons more strongly towards it than the single proton in the hydrogen nucleus. This attraction of electrons defines oxygen atoms as being more electronegative than hydrogen atoms. As a result, an uneven distribution of charge occurs within each O-H bond of the water molecule, with oxygen bearing a partial negative charge and hydrogen bearing a partial positive charge (+). This uneven distribution of charge within a bond is known as a dipole, and the bond is said to be polar.

Dipolarity of water bonds.

The polarity of a molecule depends on both the polarity of its covalent bonds and its geometry. The angled arrangement of the polar O-H bonds of water creates a permanent dipole for the molecule as a whole.

A molecule of ammonia also contains a permanent diploe. Thus, even though water and gaseous ammonia are electrically neutral, both molecules are polar. The high solubility of the polar ammonia molecules in water is facilitated by strong interactions with polar water molecules.

Ammonia in the form of ammonium ions. Click on image for credit.

The reason why there’s an extra proton (H+) with ammonia is because due to the fact that it is highly polar, it will attract a hydrogen atom of a water molecule (which it has dissolved in; aqueous solution) and form a fourth hydrogen bond with it. In water, the attraction between a slightly positive hydrogen atom of one water molecule and the slightly negative oxygen atom of another produces what is referred to as a hydrogen bond.

Water is not the only molecule capable of forming hydrogen bonds; these interactions can occur between any electronegative atom and a hydrogen atom attached to another electronegative atom. In the case of ammonia, the N (Nitrogen atom) is the slightly electronegative atom and the hydrogen atom of a water molecule forms a hydrogen bond with it, converting it to ammonium ions (NH₄⁺).

The distance between this hydrogen atom and the other oxygen atom, is about twice the length of the covalent bond and hydrogen bonds are much weaker than typical covalent bonds. A single water molecule can form hydrogen bonds with up to four other water molecules.

Hydrogen Bonds in water molecules. Click on image for credit.

Orientation is important in hydrogen bonding and the bonding is most stable when a hydrogen atom and the two electronegative atoms associated with it (the two oxygen atoms in the case of water) are aligned or nearly in line.

Linear H-Bonds. Click on image for credit.

Introduction: Common Terminologies.

Some basic terminologies are brushed through in this section just for reminder’s sake.

The term metabolism describes the many reactions in which organic compounds are synthesized and degraded and useful energy is extracted, stored and used.

The study of the changes in energy during metabolic reactions is called bioenergetics.

The basic thermodynamic principles that apply to energy flow also apply to biochemistry. Thermodynamic considerations can tell us if a reaction is favored, but does not tell us how quickly a reaction will occur. The rates of the normally slow reactions are accelerated by enzymes so much so that enzyme-catalyzed reactions can be up to ×10¹⁷ greater than the rate of corresponding unanalyzed reactions!

An enzyme and a small molecule will collide one million times per second. Under these conditions, many enzyme-catalyzed reactions could be achieved if only 1 in about 1000 collisions result in a reaction.

Much of what we now know of biochemistry is attributed to the study of viruses. They are subcellular and consist of a nucleic acid molecule surrounded by a protein coat. Virus nucleic acid can contain as few as three genes or as many as several hundred. Despite their biological importance, viruses are not cells because they cannot carry out independent metabolic reactions; they multiply by hijacking the reproductive machinery of a host cell, making it form new viruses, so they’re genetic parasites.

That is all. Next chapter, water. “We made from water every living thing.” Quran, 21:30.

Introduction: Common Macromolecules- Lipids and Biomembranes.

The most distinguishing feature of lipids are the hydrocarbon chain, with a carboxyl group (C=O) at the end. This is the basic structure of lipids and called fatty acid. There are usually between 16-18 carbon atoms in the hydrocarbon chain.

Image Credit: http://schoolworkhelper.net/wp-content/uploads/2010/06/lipid.gif

In the diagram, the fatty acid is seen attached to a glycerol molecule and a phosphate group. It is known as a phospholipid. The carboxyl end of the fatty acid is highly polar and therefore water soluble (hydrophilic meaning attracted to water). Hydrocarbon chain of the fatty acid is highly non-polar and therefore water insoluble (hydrophobic, which means scared of water).

Image Credit: http://bioteach.ubc.ca/Bio-industry/Inex/

When fatty acids interact with water, the soluble carboxyl end dissolves and forms a layer with water, while the hydrocarbon tale remains outside the water surface. This quality is important in forming the bio membrane of cells which will become clearer below.

Also, another quality to remember is when all carbon atoms of the hydrocarbon chain in the fatty acid are joined by a single bond, the compound is said to be saturated, this means that every carbon atom has hydrogen atom on both sides. In unsaturated fatty acid, one or more carbon atoms form a double bond with another carbon atom. Therefore, it will not be able to hold a hydrogen atom and therefore said to be unsaturated. As you can observe from the first diagram, there are two hydrocarbon tails, one is saturated and the other unsaturated and where the carbon atom forms a double bond, there can be seen a kink in the tail. This kink provides a fluid quality to cells that allows it more flexibility in motility and structure and therefore is healthier than saturated fats that plague processed food.

Usually fatty acids are stored in the form of triglycerides– glycerol molecule + 3 fatty-acid tails. A glycerol molecule plus a fatty-acid tail is a glyceride molecule. The above diagram shows us a diglyceride consisting of two fatty-acids linked to a glycerol molecule. Triglycerides are insoluble in water and therefore group as fat droplets in the cytoplasm of the cell. When required, they can be broken down for use as energy.

Lipids provide an important form of energy storage, since they give more than twice as much energy as carbohydrates of the same mass. Also, as previously stated, they are the major components of cell membranes. Lastly, they play important roles in cell signaling. Example: steroid hormones, such as estrogen and testosterone are made of cholesterol and used in processing food and building nerve cells, apart from other metabolic functions.

Most lipids are not soluble in water, but they do dissolve in some organic solvents.

All cells are surrounded by a layer of membrane that separates their internal environment (cytoplasm) from the external environment (exoplasm or extracellular matrix). Additionally, the organelles in cells, are compartmentalized with the help of biomembranes, with similar chemical composition as that of the plasma membrane.

Cell Structure. Click on Image for Credit.

The Lipid Bilayer which is largely made of phospholipid; a glycerol molecule is joined to two fatty acid chains and the third site on the glycerol is linked to a hydrophilic phosphate group. Phospholipids are therefore amphipathic lipids, meaning they are partly water soluble and partly insoluble. This is because they have both hydrophobic (fatty acid tail) andhydrophilic (phosphate group) regions.

Phospholipid. Click on Image for Credit.

In order to understand the lipid bilayer structure of a cell, hypothetically imagine its development- If we try to dissolve one phospholipid in a water molecule, the hydrophilic head (which contains the phosphate group) will dissolve in the water, whilst the hydrophobic tail will remain outside the water. However, if two or more phospholipids get together, they will start forming a different structure; the heads will still dissolve in water, but the tails, rather than facing outwards, will face inwards towards each other shielding the water out.

Lipid Bilayer Formation. Click on Image for Credit.

This molecular character causes phospholipids to form a spherically bilayer structure called liposome. In it, all nonpolar tails in each phospholipid molecular layer is called a leaflet. Examples of phospholipids are phosphatidylcholine (the phosphate group is attached to a second small hydrophilic compound such as choline. See first image) and sphingomyelin.

Because the lipid bilayer has a nonpolar hydrophobic core that is not easily permeable, biomembranes are interspersed or separated by proteins (referred to as membrane proteins) that allow certain molecules and ions to pass and so act as gateways or pathways towards and outwards the cell cytoplasm. The best analogy here is that of a concrete house interspersed with windows and doors to allow passage of people and air.

Fluid Mosaic Model. Click on Image For Credit.

Structurally, the plasma membrane is referred to as having a Fluid Mosaic Model. This refers to the story of Prophet Moses (Mosaic) parting the sea, and crossing over. The protein gateway here provide that effect.

Cholesterol is another lipid molecule that is present in the biomembrane. It consists of four hydrocarbon rings (that are strongly hydrophobic) and a hydroxyl group (O-H) attached to one end and is weakly hydrophilic. This quality makes cholesterol amphipathic as well.

One of its main functions is that it can break down the tight connection of the biomembrane phospholipid bilayer making it more flexible for the passage of small molecules and ions. Because of this and the fact that phospholipids have the capacity of movement within the biomembrane (more on this later), it explains the presence of “fluid” in the Fluid Mosaic Model.

In the electron microscope, the cell membrane appears to have a trilaminar appearance (having three layers):

Electron Microscopy of Plasma Membrane. Click on Image For Credit.

Two dark bands indicating the lipid bilayers of the hydrophobic tail and one bright band showing the intramembranous space between the bilayers. The hydrophilic core or polar head is not visible because it has dissolved in water.