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.

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).

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.

Introduction: Common Macromolecules- Nucleic Acids.

A nucleic acid is a polymer made up of many nucleotides. A nucleotide is generally made of;

Typical Nucleotide.

i. Nitrogen-containing base; a heterocyclic molecule, containing a closed ring of atoms of which at least one is not a carbon atom and replaced with a nitrogen atom.

ii. Pentose sugar; meaning contains five carbon atoms in the sugar molecule.

iii. Phosphate Group; usually a phosphorus atom surrounded by a double bonded oxygen atom, single bonded to two oxygen negative ions and an oxygen atom.

Since the least complicated molecule is the phosphate group, it can easily be distinguished. However, for now, the distinguishing features for the nitrogen containing base will be the nitrogen atom. If the phosphate group is absent, the sugar-base combination is called a nucleoside.

The most common two forms of nucleotides are Ribonucleotides which form the nucleic acid Ribonucleic acid (RNA) and Deoxyribonucleotides which form the polynucleotide or nucleic acid Deoxyribonucleic acid (DNA), the molecules responsible for coding the proteins in the cell. In ribonucleotides, the sugar is ribose. In deoxyribonucleotides, the sugar is deoxyribose.


The difference between the two is that the pentose sugar in DNA has one oxygen atom less in the hydroxyl group of Carbon atom 2. Also, since these two are the prime nucleic acids we shall be focusing on, their polymer structure is generally helical.

Another popular nucleotide is Adenosine Triphosphate (ATP) which is used as an energy currency in the cell. This will be clearer in later chapters.


Thus, nucleic acids are biopolymers composed of monomers called nucleotides. The term polynucleotide is a more accurate description of a single molecule of nucleic acid.

The nitrogenous bases of nucleotides belong to two families known as purines and pyrimidines.

In nucleotides, the base is joined to C-1 of the sugar and the phosphate group is attached to one of the other sugar carbons, usually C-5.

There are three phosphoryl groups; alpha(α), beta(β), and gama(γ) esterified to the C-5 hydroxyl group of the ribose. The linkage between ribose and the α-phosphoryl group is a phosphoester linkage because it includes a carbon and a phosphorus atom, whereas, the β- and γ-phosphoryl groups in ATP are connected by phosphoanhydride linkages that don’t involve carbon atoms. All Phosphoanhydride have considerable chemical potential energy, and ATP is no exception. This potential energy can be used directly in biochemical reactions.

The Phosphate Business

In polynucleotides, the phosphate group of one nucleotide is covalently linked to the C-5 oxygen atom of the sugar of another nucleotide creating a second phosphoester linkage. The entire linkage between carbons of adjacent nucleotides is called a phosphodiester linkage, because it contains two phosphoester linkages.

Nucleic acids contain many nucleotide residues and are characterized by a backbone consisting of alternating sugars and phosphates. In DNA, the bases of two different polynucleotide strands interact to form a helical structure.

DNA Back bone.

RNA contains ribose rather than deoxyribose, and is usually a single stranded polynucleotide. There are four kinds of RNA molecules: Messenger RNA (mRNA), transfer RNA (tRNA), Ribosomal RNA (rRNA), and a heterogeneous class of small RNAs that carry out a variety of different functions.

Introduction: Common Macromolecules- Polysaccharides.

Carbohydrates; As the name indicates, they consist of a Carbon atom (Carbo-) attached to a Hydrogen and an Oxygen atom in the ratio of 2:1, similar to water H2O (-hydrate from hydra in latin meaning water). They have a general chemical formula of (CH2O)n where is usually any number ranging from 2 onwards.

The most popular carbohydrates have n3 (triose) or 5 (pentose) or 6(hexose). Since most carbohydrates are sweet and sugary, sugar nomenclature end with “ose.”

They can be classified as single unit sugars which are calledmonosaccharides (mono means one, saccharide means sugar), ordisaccharide (“di” means two therefore two unit sugars joined together), or oligosaccharides (3 to 50 unit sugars joined together) or polysaccharides (“poly” means many and it is above 50 units of sugar joined together). The bond that holds the saccharides together to form carbohydrates is called glycosidic bond and is formed by the loss of a water molecule when two carbohydrates come together and are subsequently joined by the oxygen atom of one of the two saccharides molecules.

Glycosidic bond being formed by the proximity of two monosaccharides.


Carbohydrates are usually used as a food source since sugars are used to convert into energy . Example: Glucose (C6H12O6) is a monosaccharide or single unit sugar and is a common source of energy for the body. However, glucose is generally stored as an aggregated giant molecule starch in plants or glycogen in animals. They are polysaccharides or polymers (macromolecules). Actually “poly” means many, and “mer” means molecules therefore it means many molecules.

Three important disaccharides are maltoselactose, and sucrose which are used as fodder to either make the storage macromolecules or to break-down into monosaccharides for converting the sugar into energy.

In addition to it’s role as energy storage, carbohydrates are also used in plant cell wall in the form of the polysaccharide cellulose to give the cell structure, and is an important signal receptor on the plasma membrane of cells where the signal will induce the cell to perform specific functions. This is done when oligosaccharides linked to proteins on the plasma membrane work as signal receptors or markers for cell recognition and interaction.

All monosaccharides contain hydroxyl groups (OH) and are therefore alcohols. Sugar structures can be represented in many ways. Example: Ribose (the most common 5-carbon sugar can be shown as a linear molecule containing 4 hydroxyl groups and one aldehyde group.

Ribose- Fischer Projection.

This linear representation is called a Fischer projection. In its usual bio chemical form, however, the structural ribose is a ring with a covalent bond between the carbon of the aldehyde group (C-1) and the oxygen of the (C-4) hydroxyl group. This ring form is known as Haworth projection. The ring is not actually flat, it can adopt about twenty different conformations in which certain ring atoms are out-of-plane.

Ribose- Haworth’s Projection. Click on image for credit.

Another example is Glucose, which is the most abundant 6-Carbon sugar. (Insert Diagram) It is the monomer of the polysaccharide Cellulose and the storage polysacchride Glycogen and Starch.

Formation of Glycogen from Glucose. Click on image for credit.

In these polysacchrides, each glucose residue is joined covalently to the next bio covalent bond between C-1 of one glucose molecule and a hydroxyl group of another. This bond is called the glycosidic bond. In cellulose, C-1 of each glucose residue is joined to the C-4 hydroxyl group of the next residue. The hydroxyl groups on adjacent chains of cellulose interact non-covalently, creating strong insoluble fibers.


Introduction: Mass Units and Common Macromolecules- Proteins.

When we discuss molecules and bio polymers we will often refer to their molecular weight or relative molecular mass (Mr) this is the mass of a molecule relative to 1/12 the mass of an atom of carbon isotope -12 (which is exactly 12 atomic mass units. Don’t think too much into it, simply count the atom in the periodic table according to the number of protons it contains).

Now because Mr is a relative quantity, it is dimensionless and has no units associated with its value. The absolute molecular mass of a compound has the same magnitude as the molecular weight, except that it is expressed in units called Daltons; 1 Dalton = 1 atomic mass unit.

The molecular mass is also called the molar mass because it represents the mass, measured in grams, of one mole, which is Avogadro’s constant number = 6.023 × 1023. So 1 mole of an atom or molecule contains 6.023 × 1023 atoms or molecules and that in turn will give us how much the molecule will weigh in grams.

The molecular mass of a typical protein is 38,000 daltons..

The common macromolecules that we shall deal with in the coming chapters are proteins, polysaccharides, nucleic acids and lipids. We shall deal with one in each post:

a-            Proteins.

They are structurally important to the cell since they are the basic components of which the cytoskeleton is made, and functionally important since it is responsible for catalyzing reactions in the form of enzymes, have mobility functions, act as signal molecules for the cell and are part of a complex to form receptors for those signals and pretty much most other complicated functions. Due to these reasons, they are structurally complex as well.

Proteins are large polymers of amino acids joined together throughpeptide bonds to form polypeptides or in other words proteins. This is unclear unless you know what each bolded syllable is.

Amino Acid. Click on link for image credit

First, Amino Acids. Each amino acid consists of a central carbon atom bonded to a;

i-             Carboxylic-acid group (COOH); A carbon atom double-bonded to an oxygen atom and single bonded to a hydroxyl group (O-H).

ii-            Amino group (NH2); This is simply a nitrogen atom single bonded to two hydrogen atoms.

iii-           Hydrogen atom;

iv-           A distinctive side-chain that is unique to each type of amino acid, usually referred to as the “R” group. Thus, amino acids differ only in their side chains.

Amino acids get their name because of the amino group and the carboxylic acid group.

When two amino acids come close together, the hydroxyl group (OH) of the carboxylic-acid, which is polar, attracts a hydrogen atom of the amino group of the other amino acid and in the process, forms and releases a water molecule (See below image). This leads to the formation of a peptide bond which is a covalent bond between the carbon of the carboxylic-acid group of the first amino acid and the nitrogen of the amino group of the second amino acid. When many amino acids are linked together through peptide bonds, they form a polypeptide chain (or proteins).

Formation of a Peptide Bond. Click on image for credit.

Proteins are structurally complex. If you look at one (below), you can only see chaos. This is due to the fact that when amino acids begin to form peptide bonds with one another, they do not line up into a straight linear structure, rather, they begin to spiral and coil due to the interaction of their side chains with one another forming various types of (mostly) hydrogen and (sometimes) sulphur bonds.

The three dimensional shape of a protein is determine largely by the sequence of amino acid residues. This sequence of information is encoded in the gene of the protein and it is important because the protein’s 3-D structure or conformation is what does their jobs.

Many enzymes for instance contain a cleft (groove) called the active site whose function is to catalyze reactions that depend on this structure.

Enzyme with active site (cleft) shown. Click on image for credit.

Substrate is the molecule(s) that require catalysis and when bind with the active site of the enzyme, undergo specific reactions (more on it later).

Introduction- Organic Compounds, Functional Groups and Linkages.

Much of biochemistry deals with biopolymers that are macromolecules created by joining many smaller organic molecules (monomers) via condensation (removal of element of water). Each monomer that makes a macromolecular chain is called a residue.

In some cases like carbohydrates (more on it later), a single monomer or residue is repeated many times, in other cases like proteins and nucleic acids, a variety of residues are connected in a specific order.

The residues are added and converted into a polymer by repeating the same enzyme catalyzed reaction. Thus all of the residues in a biopolymer are aligned in the same direction.

Biopolymers have properties that are very different from those of their constituent monomers. Example: Starch is not soluble in water and does not taste sweet although it is a polymer of the sugar Glucose, which has both those properties.  So we can conclude that each new level of organization results in properties that cannot be predicted just from those of the previous level.

The levels of complexity in increasing order are atoms, then molecules, then biopolymers, then organelles then cells, tissue, organ, and all organisms and systems.


The types of organic compounds, functional groups and linkages commonly seen in biochemistry are;

Organic Compounds, Functional Groups and Linkages.

PS: Under most biological conditions, carboxylic acids exist as carboxylate anions: COO and amines exist as ammonium ions: NH3+ .

Please make sure you memorize the names and structures of the functional groups.

Biochemical reactions involve specific chemical bonds or parts of molecules called functional groups which we will deal with several times.

  • Ester and Ether are common linkages found in fatty acids and lipids.
  • Amide linkages are found in proteins.
  • Phosphate ester and Phosphoanhydride linkages occur in nucleotides.