Biological Molecules

Carbohydrates

Carbohydrates are key biological molecules that store energy and can provide structural support to plant cells. Carbohydrates can be classified into three groups determined by how many units they are made of, as seen in the flow diagram below.

Biological Molecules, figure 1

Larger carbohydrates, such as sucrose and starch, are made from monosaccharides. The monomers of carbohydrates are known as monosaccharides - glucose, galactose and fructose are three common examples. Monosaccharides are all sugars that are soluble in water. Their functions are either to provide energy or they are building blocks to create other molecules.

All carbohydrates contain three elements: carbon, hydrogen and oxygen (CHO). The general formula for a monosaccharide is CnH2nOn , where n = the number of carbon atoms it contains.

Glucose

Glucose, C6H12O6, is a very important monosaccharide that can provide energy, be polymerised to form a structural support molecule (cellulose), or energy storage molecule (glycogen and starch). It contains 6 carbon atoms, which are labelled in red on diagram (a). You could be asked to draw glucose, but luckily only in as much detail as in diagram (b).

Biological Molecules, figure 1

Glucose has two structural isomers (an isomer a compound that has the same formula, but the atoms are arranged differently). The diagrams above are of the isomer α glucose. β glucose is the second isomer. There is only one difference in the structural arrangement between these isomers, which can be seen on carbon atom 1 in the diagram below. The hydrogen (H) and hydroxyl group (OH) have swapped position. This small change has a significant impact on the bonding and final structure of the polymers that they form.

Biological Molecules, figure 2

α glucose and β glucose only differ structural on one of their carbon atoms. Which carbon atom is it that the H and OH swap position on.
Your answer should include: 1 / One
Glucose is an abundant and important monosaccharide. What is it’s function?
Your answer should include: Energy / Storage / Structural / Support
Name three common monosaccharides:
Your answer should include: Glucose / Galactose / Fructose
Which type of carbohydrates are classed as sugars?
Your answer should include: Monosaccharides / Disaccharides

Monomers and Polymers

Monomers (mono meaning one, think monobrow!)

Small, single units that act as the building blocks to create larger molecules.

Polymers (poly meaning more than two)

Made up of many monomers, usually thousands, chemically bonded together.

Biological Molecules, figure 1

For monomers to bond together a chemical reaction occurs, this is a condensation reaction. Condensation reactions involve the removal of water. This removal of water from monomers enables a chemical bond to form between the monomers.

A hydrolysis reaction is the opposite of this - Hydro (water) lysis (to split). A water molecule is added between two bonded monomers (within a dimer or polymer) to break the chemical bond.

Biological Molecules, figure 2

Disaccharides

  1. Formed from two monosaccharides
  2. Joined by a glycosidic bond
  3. Formed by a condensation reaction

There are three key disaccharides that you need to remember, and these are made from the three key monosaccharides you learnt.

  1. Glucose + Glucose –> Maltose
  2. Glucose + Galactose –> Lactose
  3. Glucose + Fructose –> Sucrose

The general formula for a disaccharide is:

(CnH2nOn) 2 – H20

Where n=the number of carbons the monosaccharide contains. This formula is simply x2 the monosaccharide formula and then minus water.

Condensation Reaction

The diagram below demonstrates how a condensation reaction creates a disaccharide. A water molecule is being removed (highlight in red) from the hydroxyl group (OH) on carbon 1 and carbon 4 on the two monosaccharides. The bond that forms is known as a glycosidic bond (highlighted in blue). This diagram shows a 1,4, glycosidic bond because it is located between carbon 1 and carbon 4.

Biological Molecules, figure 1

Disaccharides can be broken down back into monosaccharides via a hydrolysis reaction. Hydrolysis is when the water that was removed is added back again to break the glycosidic bond, as can be seen in the diagram below.

Biological Molecules, figure 2

Reducing and Non-Reducing Sugars Test

Both monosaccharides and disaccharides and described as sugars because they are sweet and soluble. It is possible to conduct an experiment to test for the presence of these sugars. All of these sugars, except sucrose, are reducing sugars. Sucrose is a non-reducing sugar.

Reducing Sugar Test

To test for the presence of these sugars Benedict’s reagent is added. This is a bright blue liquid, due to it containing copper sulfate. The name reducing sugar is giving to sugars that can reduce Cu2+ ions in Benedict’s reagent to Cu+ ions in the form of copper (I) oxide, which forms a brick red precipitate.

Biological Molecules, figure 3

The chemical procedure for this is:

  1. Add Benedict’s reagent to the sample you are testing
  2. Heat
  3. If a colour change of blue to yellow/green/red is observed, then this is confirmation that a reducing sugar is present. The more red/brown the precipitate, the more sugar it contained.

Biological Molecules, figure 4

Non-Reducing Sugar Test

Sucrose is called a non-reducing sugar because it cannot reduce Cu2+, this is because the chemical group needed for this reduction reaction is involved in the glycosidic bonds between the monosaccharides. To prove that sucrose is still a sugar, but it is just unable to reduce Cu2+ (a non-reducing sugar) the glycosidic bond must be hydrolysed to expose the reducing group.

If a substance remains blue after the reducing sugars test, then the procedure to test to see if it is a non-reducing sugar is as follows:

  1. Mix sucrose with HCl and boil – this is acid hydrolysis and it breaks the glycosidic bond so that sucrose is hydrolysed back into glucose and fructose. Hint – to get the mark you must state BOIL, as below 100C there is not enough energy to break the glycosidic bond.
  2. Cool the solution and then add sodium hydroxide to make the solution alkaline. Benedict’s reagent only works in alkaline solutions, which is why this stage is essential. You must cool the solution first to prevent excessive, dangerous fizzing.
  3. Add a few drops on Benedict’s reagent and heat.
  4. If a colour change of blue to yellow/green/red is observed, then this is confirmation that a non-reducing sugar is present.

Biological Molecules, figure 5

Polysaccharides

Polysaccharides are polymers made up of many monosaccharides. A polysaccharide is created in the same way as a disaccharide, via condensation reactions.

There are three key polysaccharides that you need to learn the structure and function of: starch, glycogen and cellulose. Starch and glycogen are both energy stores, whereas cellulose provides structural support.

Biological Molecules, figure 1

Starch

Starch is found in plants, not in animal cells, and it is the major carbohydrate store. Starch is made from the excess glucose created during photosynthesis. Glucose is used in respiration, but if more glucose is created in photosynthesis than is currently needed it is converted into the polymer starch for storage.

The presence of starch can be confirmed by using iodine. Iodine is orange/brown in colour when no starch is present, but it turns blue/black if starch is present.

Biological Molecules, figure 2

Structure of Starch

Starch is a polymer made up of α-glucose. These α-glucose monomers are joined together via condensation reactions and are held in place by 1-4 and 1-6, glycosidic bonds. (Remember, the numbers refer to which carbon atoms the bond forms between)

Amylose is the name of the structure in starch in which the glucose monomers are all joined together by 1,4 - glycosidic bonds. This results in a spiral shaped polymer, see diagram below.

Amylopectin is the name given to the other structure in starch I which the glucose monomers are joined by a combination of 1,4 and 1,6 - glycosidic bonds. The 1,6-glycosidic bonds result in branches, see diagram below.

Amylose

Biological Molecules, figure 3

Amylopectin

Biological Molecules, figure 4

Properties of Starch

Starch is insoluble due to the fact it is such a large molecule. This is an advantage to a storage molecule as it means it can be stored within cells and not dissolve. Therefore is will not change the water potential of a cell or affect osmosis.

The fact the amylose is spiral in shape means that is can be readily compacted. This is an advantage as a lot of the molecule can fit into small spaces and be stored.

The fact that amylopectin has branching strands provides a larger surface area for enzymes to attach to. This means that starch is readily hydrolysed back into glucose when plant cells are running low on glucose.

Glycogen

Glycogen is the major carbohydrate storage molecule found in animal cells. The main cells glycogen is stored in are liver and muscle cells. Glycogen is made from the excess glucose that has been eaten and absorbed into the bloodstream.

Glucose is used in respiration, but if more glucose is eaten than the cells currently need for respiration it is converted into the polymer glycogen for storage. As liver cells are responsible for removing toxins and muscles are responsible for movement, glycogen is mainly stored in these cells to ensure they always have a store of glucose to respire to release energy.

Structure of Glycogen

Glycogen is a polymer made up of α-glucose and is very similar in structure to amylopectin in starch. The α-glucose monomers are joined together via condensation reactions and are held in place by 1,4 and 1,6-glycosidic bonds. The key difference between the structure of glycogen and starch is that glycogen contains more 1,6-glycosidic bonds and is therefore a more branched structure.

Biological Molecules, figure 1

Properties of Glycogen

Glycogen is insoluble due to the fact it is such a large molecule. This is an advantage to a storage molecule as it means it can be stored within cells and not dissolve. Therefore is will not change the water potential of a cell or affect osmosis.

The fact that glycogen is a highly branched molecule means it has a larger surface area for enzymes to attach to. This means that it is readily hydrolysed back into glucose when cells are running low on glucose. Glycogen is even more branched than starch, therefore it is hydrolysed back into glucose more rapidly. This is essential for animals because they have a higher metabolic rate and therefore need more glucose. For example, they may need this glucose to provide energy to run from a predator.

Water

The Structure of Water

Water is a dipolar molecule (di meaning two and polar referring to charges). Water has an unevenly distributed charge due to the fact that the oxygen atom is slightly negative, and the hydrogen atoms are slightly positive. The delta ( δ ) symbol indicates slightly positive/negative on the diagram below.

Biological Molecules, figure 1

Hydrogen bonds form between different water molecules between the oxygen and a hydrogen atom.

Biological Molecules, figure 2

Biological Molecules, figure 3

The formation of these hydrogen bonds and the fact that water is dipolar result in 5 key properties of water.

Five Key Properties of Water

  1. It is a metabolite (e.g. in condensation and hydrolysis reactions).
  2. An important solvent in reactions.
  3. Has a high heat capacity, it buffers temperature.
  4. Has a large latent heat of vaporisation, providing a cooling effect with loss of water through evaporation.
  5. Has strong cohesion between water molecules; this supports water columns and provides surface tension

Metabolite

Water in involved in may reactions, such as photosynthesis, hydrolysis and condensation reactions. This is one reason why it is essential that approximately 90% of the plasma in blood is water and the cytoplasm in cells is largely composed of water.

Solvent

Water is good solvent, meaning many substances dissolve in it. Polar, or charged, molecules dissolve readily in water due to the fact water is dipolar. As can be seen in the diagram below, the slight positive charge on hydrogen atoms will attract any negative solutes and the slight negative charge on the oxygen atoms of water will attract any positive ions in solutes. These polar molecules are often described as hydrophilic, meaning they are attracted to water.

Biological Molecules, figure 4

Non-polar molecules, such as lipids, cannot dissolve in water and are therefore described as hydrophobic - they are repelled by water.

The fact that so many essential polar substances dissolve in water enables them to be transported easily around animals and plants, either in the blood or xylem, to cells they are needed in inside of the organism.

High Specific Heat Capacity

This means that a lot of energy is required to raise the temperature of water. This is because some of the heat energy is used to break the hydrogen bonds between water molecules.

This is useful to organisms as it means the temperature of water remains relatively stable, even if the surrounding temperature fluctuates significantly. Therefore, internal temperatures of plants and animals should remain relatively constant despite the outside temperature, due to the fact a large proportion of the organism is water. This is important so that enzyme do not denature or reduce in activity with temperature fluctuations. Finally, this provides a stable environment, in terms of temperature, for aquatic organisms.

Large Latent Heat of Vaporisation

This means that a lot of energy is required to convert water in its liquid state to a gaseous state. This is again due to the hydrogen bonds, as some energy is used to break the hydrogen bonds between water molecules to turn it into a gas.

This is advantageous to organisms as it means that water provides a significant cooling effect. For example, when humans sweat they release water onto their skin. Large amounts of heat energy from the skin is transferred to the water to evaporate it, and therefore removing a lot of heat and cooling the organism.

Strong Cohesion

Cohesion is the term used to describe water molecules ‘sticking’ together by hydrogen bonds. Due to water molecules sticking together, when water moves up the xylem in plants due to transpiration it is as a continuous column of water. This is advantageous as it is easier to draw up a column rather than individual molecules.

Biological Molecules, figure 5

Cohesion also provides surface tension to water. This enable small invertebrates to move and live on the surface, providing them a habitat away from predators within water. You can test this idea of surface tension by carefully placing a paperclip on water and it should float!

Biological Molecules, figure 6

What chemical reactions have you learnt already that involve water?
Your answer should include: Hydrolysis / Condensation
How are oxygen and hydrogen held together within a water molecule? (hint: see images above)
Covalent
How are water molecules held together?
Your answer should include: Hydrogen / Bonds / Bond
Water has an uneven distribution of electrical charges. What is the term given to describe this structural feature?
Dipolar
Which structural feature of water makes it a good solvent?
Dipolar
Which structural feature of water provides strong cohesion, a high latent heat of vaporisation and a high specific heat capacity?
Your answer should include: Hydrogen / Bonds / Bond

Inorganic Ions

Inorganic ions occur in solution in the cytoplasm of organisms, some in high concentrations and others in very low concentrations. Each type of ion has a specific role, depending on its properties and these roles the ions have are relevant in a whole range of the topics across the A-Level.

The key ions that you need to be familiar with are:

  1. Hydrogen and hydroxide ions impact on pH – this is referred to when considering enzymes and proteins denaturing, increasing heart rate and the Bohr effect on haemoglobin. Hydrogen carbonate provides a source ofcarbon dioxide to plants when dissolved in a solution, but in human blood it lowers the pH.
  2. Chloride ions and their inhibitory effect at a synapse.
  3. Sodium and potassium ions in the co-transport of glucose and amino acids – this is relevant in the absorption of glucose and resting/action potential in the nervous systems .
  4. Phosphate ions as components of__ DNA__ and of__ ATP__ – this is relevant to__ DNA, RNA__ and__ ATP__ structure
  5. Ammonium ions as a result of the decay of amino acids in decomposition and deamination
  6. Nitrate ions are absorbed through plant root hair cells and essential for the creation of proteins and nucleic acids.

Lipids

Lipids are biological molecules that contain the elements carbon, hydrogen and oxygen. These are the same elements found in carbohydrates, but unlike carbohydrates, lipids have a lot less oxygen).

Lipids are non-polar molecules, or uncharged, and therefore are insoluble in water. They will dissolve in organic solvents, such as ethanol. Due the fact that they are non-polar and not soluble in water, they are described as being hydrophobic.

Lipids are made up of two molecules, fatty acids and glycerol, and they do not form polymers.

Biological Molecules, figure 1

Biological Molecules, figure 2

Glycerol

There are many types of lipids, but triglycerides (fats and oils) and phospholipids (in cell membranes) are the two key types you need to learn.

All lipids are made up of a glycerol molecules and fatty acids.

Fatty Acids

Fatty acids are long chains of carbon and hydrogen atoms with a carboxyl group at one end (COOH). This hydrocarbon tail can vary in length.

Fatty acids can being either saturated or unsaturated, and this refers to whether there are any double bonds between the carbon atoms. Saturated Fatty Acids have no double bonds between the carbon atoms. Unsaturated Fatty Acids have at least one double bond between carbon atoms. If they have one double bond they are described as being monounsaturated, if there are many double bonds it is polyunsaturated.

Biological Molecules, figure 3

Saturated fatty acids are holding as many H atoms as possible, due to the lack of double bonds - hence the name saturated. This results in a relatively straight shape, so molecules can be tightly packed in parallel. This tight structures results in these lipids being solid, or fats.

Unsaturated fatty acid chains kink where the double bonds are, and are therefore far less straight. This means the lipid molecules can’t be as tightly packed and thus in a liquid state, oils.

Triglycerides

Triglycerides are made up of one glycerol molecule and three (tri) fatty acids. These fatty acids are each bonded onto the glycerol by a condensation reaction. The condensation reaction occurs between the carboxyl group (COOH) of the fatty acid and the hydroxyl group (OH) of the glycerol.

Biological Molecules, figure 4

The bond that forms between the glycerol and carboxyl group of the fatty acids is an ester bond.

How the triglyceride structure results in its properties:

  1. It is an energy storage. Due to the large ratio of energy-storing carbon-hydrogen bonds compared to the number of carbon atoms, a lot of energy is stored in the molecule.

  2. Due to the high ratio of hydrogen to oxygen atoms they can act as a metabolic water sauce. This is because triglycerides can release water if they are oxidised. This is essential of animals in the desert, such as camels.

  3. As lipids are large, hydrophobic molecules they are insoluble in water. This means they will not affect water potentials and osmosis.

  4. Lipids are relatively low in mass. This means a lot can be stored in an animal without it increasing the mass and preventing movement.

Phospholipids

Phospholipids are made up of a glycerol molecule, two fatty acid chains and a phosphate group (attached to the glycerol). The two fatty acids also bond to the glycerol via two condensation reactions, resulting in two ester bonds.

Biological Molecules, figure 5

How the phospholipid structure results in its properties.

The phosphate molecule, described as the hydrophilic ‘head’ of a phospholipid can interact with water as it is charged. Due to the phosphate being charged, it repels other fats. The fatty acid chain is not charged. It is known as the hydrophobic ‘tail’ and it repels water, but will mix with fats.

Biological Molecules, figure 6

Due to these two regions on a phospholipid that act differently, it is classes as a polar molecule. The impact this has is that if phospholipids are in water they will move to a position where the heads are exposed to water and the tails are not and this explains many of the properties stated below:

  1. This behaviour of the tails moving away from water results in the formation of a phospholipid bilayer membrane structure, which forms the plasma membrane around cells.

  2. The hydrophilic nature of the phosphate head enables the surface of the plasma membrane to stay in place.

  3. The phospholipid bilayer arrangement enable carbohydrates to attach and form important receptors on the membrane (glycolipids).

Biological Molecules, figure 7

Ethanol Emulsion Test

The emulsion test is how to check for the presence of lipids:

  1. A few drops of the sample are added to ethanol. This is shaken to dissolve the sample in ethanol. (You must say dissolve to get this mark).
  2. Then, distilled water is added.
  3. If a cloudy white, like milk, precipitate forms then a lipid is present.

Proteins

Proteins are large polymers.

Protein Structure

Proteins and large polymers made up of the monomer amino acids.

Biological Molecules, figure 1

Amino acid (R is the group that is different on all 20 amino acids)

These amino acids are arranged in a series of structures to create the finished 3D protein. There are up to four levels of structural arrangements in a protein, see the image below, which will each be explained fully.

Biological Molecules, figure 2

Proteins polymer chains, or polypeptides, are created on the ribosome in cells and are then further folded and modified in the Golgi apparatus.

Primary Structure

The first structure that forms in the creation of a protein is the polypeptide chain. Proteins are all made up of one or more polypeptide chain folded into highly specific 3D shapes. The exact definition of a primary structure is:

The sequence of amino acids in a polypeptide chain

This would be a one-mark question and it is essential that you state the word ‘sequence’. The order the amino acids are bonded in is determined by DNA. This specific order of amino acids will alter how the protein further folds and is bonded enabling unique functions.

There are 20 different amino acids that can form the primary structure. The polypeptide chain is created by a series of condensation reactions occurring between amino acids.

Biological Molecules, figure 3

Secondary Structure

The sequence of amino acids causes parts of a protein molecule to bend into α helix shapes or fold into β pleated sheets.

Biological Molecules, figure 4

Hydrogen bonds between the carboxyl groups of one amino acid and the amino group of another are what hold the secondary structure in place. Hydrogen bonds are individually weak bonds, but when there are large numbers of them they provide collective strength.

Describing the secondary structure would be a 2-mark question.

The two marks would be for stating:

  1. Folding the primary structure into a α helix shapes or fold into β pleated sheets

  2. Held in place by hydrogen bonds

Tertiary Structure

The secondary structure is bent and folded to form a precise 3D shape. This unique 3D shape is held in place by hydrogen bonds, ionic bonds and sometimes disulphide bonds. Disulphide bonds (di meaning 2) only form between the R-groups of two amino acids that contain sulphur.

Biological Molecules, figure 5

Describing the tertiary structure of a protein is a 3-mark question.

The 3 marks are typically:

  1. The further folding of the secondary structure

  2. To create a unique 3D structure

  3. Held in place by hydrogen, ionic and disulphide bonds.

Make sure you always mention the bonds involved when describing protein structures, there are always marks for this because without these bonds the unique shapes are not maintained.

Quaternary Structure

A protein that is made up of more than one polypeptide chain is a quaternary structure protein. It is still folded into a 3D shape and held by hydrogen, ionic and disulphide bonds. Haemoglobin is the typical example given. Haemoglobin is made up of 4 polypeptide chains.

Biological Molecules, figure 6

On the diagram of haemoglobin, you can also see extra molecules attached that are not part of the polypeptide chains. Any group that is attached to a protein, but is not made up of amino acids, is known as a prosthetic group. Iron is the prosthetic group in haemoglobin. A protein that has a prosthetic group can be described as a conjugated protein, which simply means a non-protein group is added onto it.

Fibrous and Globular Proteins

The 3D folding in tertiary and quaternary proteins generally results in either a shape that is spherical, called globular proteins, or long rope-like shape, called fibrous proteins.

Fibrous Protein Fact File:

  1. Polypeptide chains form long twisted strands linked together
  2. Stable structure
  3. Insoluble in water
  4. Strength gives structural function
  5. e.g. collagen in bone and keratin in hair

Biological Molecules, figure 7

Globular Protein Fact File:

  1. Polypeptide chains ‘roll up’ into a spherical shape
  2. Relatively unstable structure
  3. Soluble
  4. Metabolic functions
  5. e.g. all enzymes, antibodies, some hormones (e.g. insulin), haemoglobin

Biological Molecules, figure 8

Cellulose

Unlike starch and glycogen, the function of cellulose is to provide structural strength in plants. Cellulose is located in the cell wall of plants and therefore prevents cells from bursting if they take in excess water.

Structure of Cellulose

Cellulose is the only polysaccharide that is made up of β-glucose monomers. These monomers are joined by 1,4-glycosidic bonds only. For this reason, the cellulose polymer is unbranched.

These long, straight chains of β-glucose accumulate and lie parallel to each other. The parallel chains are then held together by many hydrogen bonds, and the sheer number of hydrogen bonds provides strength. This structure is called a fibril, or microfibril. Fibrils will then also align in parallel and are held in place by even more hydrogen bonds to form a cellulose fibre.

Biological Molecules, figure 1

Which polysaccharide contains 1-4 and 1-6, glycosidic bonds?
Your answer should include: Starch / Glycogen
Which polysaccharide is made up of the monomer β-glucose?
Cellulose
Which polysaccharide only forms unbranched structures?
Cellulose
Which is the only polysaccharide found in animal cells?
Glycogen
Which polysaccharide contains microfibrils?
Cellulose
Which polysaccharide contains amylose and amylopection?
Starch