Biological Molecules

The cells of all living things are made up of three main types of biological molecules: carbohydrates, proteins and lipids. By understanding more about these important molecules we can learn about how living organisms function on the molecular level.

Water

Water is a polar molecule - this means that the electrons are shared unequally within the bonds that hold a water molecule together. Oxygen is greedy when it comes to electrons and is able to pull the electrons closer towards it (we say it is more electronegative). This gives oxygen a slight negative charge and hydrogen a slight positive charge. A hydrogen bond forms between the slightly negative oxygen atom of one water molecule and the slightly positive hydrogen atom on another molecule. The ability of water molecules to hydrogen bond gives it some special properties:

1. It is an excellent solvent: water is a good solvent because it can form hydrogen bonds with other polar molecules or charged ionic compounds. Water dissolves more substances than any other liquid so is referred to as the ‘universal solvent’. This is handy for humans, since our blood consists mostly of water which is able to dissolve hydrophilic molecules such as glucose, ions and some amino acids.

2. It has a high latent heat of evaporation - this means that a lot of energy is used to convert water from a liquid to a gas. This is why we feel cooler when we sweat, since the evaporation of water from our skin’s surface takes a lot of heat energy with it.

3. It has a high specific heat capacity - all those hydrogen bonds within water are great at absorbing energy, which means you have to add a lot of it to heat water up. This is really useful for marine life since it means that bodies of water are fairly resistant to changes in temperature, making it a stable habitat in which to live.

Carbohydrates

Carbohydrates are long chains of sugar molecules (the technical term is ‘polysaccharides’) formed from lots of individual sugar molecules (monosaccharides) joining together. When two monosaccharides react to form a disaccharide, a condensation reaction occurs. During the condensation reaction, a molecule of water is removed (from a hydroxyl group on one sugar and a hydrogen on another) and a glycosidic bond forms. When polysaccharides are broken down during digestion, a hydrolysis reaction occurs in which a water molecule is added to break the glycosidic bond.

Ribose is another example of a monosaccharide - it’s a component of RNA molecules. It is a pentose sugar with five carbon atoms in the ring.

Polysaccharides

The polysaccharides found in plants are starch and cellulose. Starch is broken down by the plant when it needs energy and cellulose is the major component of plant cell walls. Starch exists in two different forms: amylose and amylopectin. In animals, the energy storage carbohydrate is glycogen.

• Amylose: unbranched spiralling chains of alpha-glucose molecules. Its coiled structure means that it is very compact so lots of amylose can be packed into a cell.

• Amylopectin: branched chains of alpha-glucose molecules. Its branches increase its surface area which means that enzyme can quickly break it apart when glucose is needed for respiration.

• Cellulose: long unbranched chains of beta-glucose molecules. Multiple chains are linked together by hydrogen bonding to form strong structures called micofibrils. The strong microfibrils in the cell wall help to give plant cells their shape and structural support.

• Glycogen: branched chains of alpha glucose, similar to amylopectin but with more side-branches. This gives it a large surface area for enzyme action to release glucose when energy is needed. It is more compact that amylopectin, which means more can be stored in a cell.

Lipids

Triglycerides, phospholipids and cholesterol are all types of lipid. Triglycerides and phospholipids have similar structures as they are both made up of glycerol connected to fatty acids molecules through ester bonds. However, triglycerides contains three fatty acid ‘tails’ whereas phospholipids only have two. Phospholipids also possess a phosphate group which is absent in triglycerides. The fatty acid tails of triglycerides or phospholipids can be saturated (only single carbon-carbon bonds) or unsaturated (contain at least one double carbon bond).

The synthesis of a phospholipid or triglyceride from glycerol and fatty acids involves the formation of an ester bond. Just like we saw for the formation of a glycosidic bond, the synthesis of ester bonds is a condensation reaction in which a water molecule is released. Breaking apart a triglyceride or phospholipid involves the addition of water in a hydrolysis reaction.

Different types of lipids have different functions in living organisms:

• Triglycerides: used as an energy store. A lot of energy is released when the ester bonds are hydrolysed - around twice as much compared to the breakdown of carbohydrates. Inside cells, triglycerides group together into lipid droplets where the hydrophobic tails face inwards and the hydrophilic heads face outwards. These insoluble droplets make good energy storage molecules since they do not affect the osmotic potential of the cell.

• Phospholipids are the main component of cell membranes. They form a phospholipid bilayer with the hydrophobic tails facing each other and the hydrophilic heads facing outwards, forming a barrier to prevent any polar molecules from entering or leaving the cell.

• Cholesterol is also found in cell membranes and helps to strengthen the membrane. Cholesterol pushes the hydrophobic tails of phospholipids closer together, making the membrane more rigid.

Proteins

Proteins are polymers of amino acids joined together by peptide bonds. There are 20 different amino acids that our body needs to stay healthy, all of which have the same general structure. They consist of a central carbon atom attached to four different groups: an amine group, a hydrogen atom, a carboxyl group and an 'R’ group which is different in each amino acid. The identity of the R group will influence how the amino acid interacts with other amino acids, therefore influencing protein folding. For example, lysine has a charged R group and is able to form ionic bonds with negatively charged amino acids.

Just like we saw for the formation of glycosidic and ester bonds, peptide bond formation also involves the removal of water in a condensation reaction. The water is formed by removing a hydrogen atom from the amine group and a hydroxyl (-OH) group from the carboxylic acid. What’s left behind is a peptide bond (-CONH) which can be broken with the addition of water in a hydrolysis reaction.

Once a long polypeptide chain is synthesised from the formation of numerous peptide bonds between adjacent amino acids, the polypeptide undergoes multiple stages of folding. These stages of protein origami are defined as the primary, secondary, tertiary and quaternary structures which describe a protein from its most unravelled to its final compact structure.

• Primary structure: peptide bonds have formed between amino acids to form a long, straight chain (polypeptide).

• Secondary structure: hydrogen bonds form between nearby amino acids (from the amine group on one amino acid to the carboxyl group of another) to form either an alpha helix or a beta pleated sheet. Proteins which form neither of these two structures will form a random coil.

• Tertiary structure: more bonds form between the different R groups to give the protein a 3D structure. R-group interactions involve hydrogen bonds, disulfide bonds, ionic bonds and polar interactions. If proteins are made of a single polypeptide chain, this is their final overall structure.

• Quarternary structure: this is the structure formed from the interaction of multiple polypeptide chains held together by bonds. Haemoglobin is an example of a protein with quaternary structure. It consists of four polypeptide chains (two alpha chains and two beta chains) bonded together. Each chain surrounds an iron-containing haem group. The haem group is referred to as a prosthetic group - non-protein components which are required for protein function.

Globular vs fibrous proteins

All proteins can be organised into one of two broad categories: globular proteins and fibrous proteins. Globular proteins are spherical and arranged with their hydrophobic amino acids tucked inside and the hydrophilic amino acids exposed on the outside. This means globular proteins are soluble and can be transported easily from one part of the cell to another. They perform functional roles and include things like enzymes (such as amylase), hormones (such as insulin) or proteins like haemoglobin. Globular proteins unravel and denature when the temperature or pH deviates from optimum levels. Globular proteins with prosthetic groups attached (such as haemoglobin) are referred to as conjugated proteins.

Fibrous proteins are long and thin and their primary structure consists of a repetitive sequence of amino acids. They perform structural roles so they are strong and insoluble. Examples of fibrous proteins include collagen, keratin and elastin. Collagen consists of three polypeptide chains wrapped tightly around each other to form a stable quaternary structure held together by numerous hydrogen bonds. Collagen is found in connective tissue, such as skin, muscle and bone. Fibrous proteins tend to be less sensitive than globular proteins to changes in temperature and pH.

Nucleic acids

Nucleic acids are long chains (polymers) of lots of nucleotide monomers joined together by phosphodiester bonds. Each nucleotide is made up of three components:

1. Pentose sugar (either deoxyribose or ribose),

2. Nitrogenous base (guanine, cytosine, adenine, thymine or uracil)

3. Phosphate

DNA consists of two nucleic acid strands bonded together by complementary base pairing, the strands twisted around each other to form a double helix. The two strands have the same sequence running in opposite directions so we say they are anti-parallel. The bonding between bases is predictable, since guanine always pairs with cytosine with three hydrogen bonds holding them together. Adenine always bonds with thymine (in DNA) or uracil (in RNA) with two hydrogen bonds between them. Adenine and guanine are purines, which means they have a large double ring structure. Cytosine and thymine are pyrimidines, which are smaller as they are composed of a single ring. Notice that a purine always base pairs with a pyrimidine - this happens because it’s the only way DNA can keep a regular shape and not become too bulky or narrow.

There are some important differences between a molecule of DNA and RNA:

1. They contain different sugars - the pentose sugar in DNA is deoxyribose and in RNA is ribose. The difference is that deoxyribose has one less oxygen atom.

2. RNA contains uracil instead of thymine

3. DNA is double-stranded whereas RNA is single-stranded

4. DNA has hydrogen bonds between the two complementary strands

During DNA and RNA synthesis, nucleotides are connected through the formation of phosphodiester bonds (a type of covalent bond) between the phosphate group on one nucleotide and the pentose sugar of the next nucleotide. It is a condensation reaction which means that water is formed during the reaction and it is catalysed by an enzyme called DNA polymerase or RNA polymerase depending on whether a DNA or RNA strand is being synthesised. Breaking phosphodiester bonds requires the addition of a water molecule, so it is a hydrolysis reaction.

Inorganic ions

There is an array of cations (positive ions) and anions (negative ions) which are necessary for many biological processes:

Biochemical Tests

Testing reducing sugars using Benedict’s solution

A reducing sugar is any sugar that can act as a reducing agent because of its aldehyde or ketone group. All monosaccharides are reducing sugars, along with some disaccharides (such as maltose and lactose). If the sugar you are testing is a reducing sugar, it will change colour from blue to green/yellow/orange/brick red, depending on the concentration of sugar you are testing. Low concentrations of reducing sugar will cause a green or yellow precipitate to form whereas a reducing sugar of higher concentration will appear orange or brick red.

If the test for reducing sugars is negative and you want to confirm the presence of a non-reducing sugar, such as sucrose, you need to break down the sample into monosaccharides using hydrochloric acid which breaks the glycosidic bonds. The sample is neutralised with sodium hydrogencarbonate and the Benedict’s test can be carried out. Since sucrose will have been broken down into glucose and fructose (both reducing sugars), you should now see a positive result if your original sample contained sucrose.

If you want to accurately measure the amount of reducing sugar in a sample, you can use calorimetry. Calorimetry works by measuring how much light is able to pass through the solution. The less light that passes through, the higher the absorbance of the sample and the higher the concentration. Before measuring the unknown sample, you first need to measure the absorbance readings of a series of solutions of a known concentration. You would plot a calibration curve of absorbance against concentration then measure the absorbance of the sample of unknown concentration. You can read off your graph to find the concentration which corresponds to this particular absorbance reading.

Testing for starch using iodine

Starch is the storage carbohydrate in plant cells. If you want to test a part of a plant (such as a potato) for starch, you need to add iodine dissolved in potassium iodide solution. A positive result occurs when the solution changes colour from orange/brown to blue/black.

Testing for proteins using Biuret reagent

The Biuret test involves adding sodium hydroxide to a sample followed by copper sulfate solution (together these compounds are referred to as Biuret reagent). A colour change from blue to purple indicates a positive result.

Testing for lipids using the Emulsion test

To test for the presence of lipid in a sample, you need to add ethanol to a sample and mix thoroughly by shaking. Add an equal volume of water and if lipid is present a milky white suspension should form. If the solution remains colourless, no lipid was present in the sample.

Separating biological molecules using chromatography

Chromatography is used to separate a mixture of soluble molecules, such as amino acids, vitamins, nucleic acids and carbohydrates. It involves placing the mixture to be separated onto a stationary phase which could be a sheet of chromatography paper, silica gel or a glass plate. A liquid solvent, such as ethanol or water (which is referred to as the mobile phase) moves over the stationary phase. As it travels up the stationary phase, it causes the molecules from the mixture to separate out. This is because they spend different amounts of time in the mobile phase and the stationary phase - the ones that spend longer in the mobile phase are able to travel further up the stationary phase. We use Rf values to identify the separated molecules.

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