Chapter 2: Biological molecules

Summary:
Molecular biology is the study of the structure and function of biological molecules. Many biological molecules are formed from smaller units that bond together. These include carbohydrates, lipids, proteins and nucleic acids. Molecules which are formed from repeating identical or similar subunits are called polymers. Carbohydrates have the general formula C x(H2O)y. Monosaccharides are the smallest carbohydrate units, of which glucose is the most common form. They are important energy sources in cells and also important building blocks for larger molecules. They may form straight-chain or ring structures and may exist in different isomeric forms. These are important because they bond together in different ways and so affect the structure of polysaccharides, such as starch, glycogen and cellulose. The glycosidic bond forms between monosaccharides by condensation and is broken by hydrolysis. Benedict's reagent can be used to test for reducing and non-reducing sugars. Starch is formed form one straight and some branched chains of -glucose molecules and is an energy storage compound in plants. Glycogen is a branched -glucose chain and is an energy storage compound in animals . Cellulose is a polymer of -glucose molecules in which the chains are grouped together by hydrogen bonding to form stronger fibres that are found in plant cells. "Iodine solution" can be used to test for starch. Lipids are made from fatty acids and glycerol. They are hydrophobic and do not mix with water. They are energy storage compounds in animals, as well as having other functions such as insulation and buoyancy in marine mammals. Phospholipids have a hydrophilic phosphate head and hydrophobic fatty acid tails. That is important in the formation of membranes. The emulsion test can be used to test for lipids. Proteins are long chains of amino acids which fold into precise shapes. The sequence of amino acids in a protein, known as the primary structure, determines the way that it folds and hence determines its three-dimensional shape and function. Many proteins contain areas where the amino acid chain is twisted into an -helix; this is an example of secondary structure. Further folding produces the tertiary structure. Often, more than one polypeptide associates to form one protein molecule. The association between different polypeptide chains is the quaternary structure of the protein. Tertiary and quaternary structures are held in place by hydrogen, covalent and ionic bonding and hydrophobic interactions. Proteins may be globular or fibrous. A molecule of a globular protein is roughly spherical. Most globular proteins are soluble and metabolically active. A molecule of a fibrous protein is less folded and forms long strands. Fibrous proteins are insoluble. They often have a structural role. Biuret reagent can be used to test for proteins. Water is important within bodies where it forms a large part of the mass of the cell. It is also an environment in which organisms can live. As a result of extensive hydrogen bonding, it has unusual properties that are important for life: it is liquid at most temperatures on the Earth's surface; its highest density occurs above its freezing point so that ice floats and insulates water below form freezing air temperatures; it acts as a solvent for ions and polar molecules and causes non-polar molecules to group together; it has high surface tension which affects the way it moves through narrow tubes and forms a surface on which some organisms can live. The sum total of all the biochemical reactions in the body is known as metabolism. There are only 20 common amino acids used to make naturally occurring proteins. Why is there such an economy? One possibility is that all the manufacture and interactions of biological molecules must be controlled and regulated and, the more there are, the more complex the control becomes.

The building blocks of life

The four most common elements in living organisms are, in order of abundance, hydrogen, carbon, oxygen and nitrogen. They account for more than 99% of the atoms found in all living things. Carbon is particularly important because carbon atoms can join together to form long chains or ring structures. Organic molecules always contain carbon. Methane, carbon dioxide, hydrogen, water, nitrogen, ammonia and hydrogen sulphide are key biological molecules, limited in variety, act as the building blocks for larger molecules.

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Polymers and macromolecules

Macromolecule means "giant molecule". There are three types of macromolecules in living organisms: polysaccharides, proteins (polypeptides) and nucleic acids (polynucleotides). These molecules are polymers - macromolecules made up of many repeating subunits that are similar or identical to each other and are joined end to end. Making such molecules requires repeating the same reaction many times - polymerisation. The subunits from which polymers are made are monosaccharides, amino acids and nucleotides. Lipids and nucleotides are not polymers bur are made up of simpler biochemicals. Natural polymers are cellulose and rubber. Industrially produced polymers include polyester, polythene, PVC and nylon. All these are made up of carbon-based subunits and contain thousands of carbon atoms joined end to end.

Carbohydrates
All carbohydrates contain the elements carbon, hydrogen and oxygen. Hydrogen and oxygen come in ratio 2:1 (as in water). The general formula can be written as C x(H2O)y. Carbohydrates are divided into three groups:

Monosaccharides
-are sugars. They dissolve easily in water to form sweet solutions. Monosaccharides have the general formula (CH 2O)n and consist of a single sugar molecule. Main types: trioses (3C), pentoses (5C) and hexoses (6C;they include glucose, fructose and galactose). The names of all sugars end with -ose. Glucose is the most common monosaccharide and also the most important in energy metabolism. All monosaccharides and some disaccharides act as reducing agents. They are called reducing sugars. Molecular and structural formulae The formula for a hexose can be written as C 6H12O6. This is known as the molecular formula. Structural formula shows the arrangement of the atoms which can be done by a diagram.

Ring structures In pentoses and hexoses the chain of carbon atoms is long enough to close up on itself and form a more stable ring structure. When a glucose forms a ring, carbon atom number 1 joins to the oxygen on carbon atom number 5. The ring therefore contains oxygen and carbon atom number 6 is not part of the ring. Hydroxyl group, -OH, on carbon atom 1 may be above or below the plane of the ring. The form of glucose where it is below the ring is known as the -glucose and the form when it is above as -glucose. Two forms of the same molecule are known as isomers- This extra variety provided by - and -glucose has important biological consequences.
Roles of monosaccharides in living organisms 1. They are used as a source of energy in respiration. This is due to the large number of carbon-hydrogen bonds which can be broken to release energy which is transferred to help make ATP from ADP and phosphate. 2. They are building blocks for larger molecules. E.g. Glucose is used to make starch, glycogen and cellulose (polysaccharides). Ribose (pentose) is used to make RNA and ATP. Deoxyribose (pentose) is used to make DNA.

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(polysaccharides). Ribose (pentose) is used to make RNA and ATP. Deoxyribose (pentose) is used to make DNA.

Disaccharides and the glycosidic bond

Two monosaccharides can be joined together by condensation. Two -OH groups line up alongside each other. One combines with a hydrogen atom from the other to form a water molecule. This allows an oxygen "bridge" to form between the two molecules, holding them together and forming a disaccharide. The bridge is called a glycosidic bond. Disaccharides are sugars as well.

The reverse of this kind of condensation is the addition of water which is known as hydrolysis. This takes place during the digestion of disaccharides and polysaccharides when they are broken down to monosaccharides. These two reactions are controlled by enzymes. Different disaccharides can be formed by linking different monosaccharides; maltose = glucose + glucose; lactose = glucose + galactose; sucrose = glucose + fructose. Sucrose is a non-reducing sugar.

Polysaccharides
-are polymers whose subunits are monosaccharides which are joined together by condensation where each successive monosaccharide is added by means of a glycosidic bond. The most important polysaccharides: starch, glycogen and cellulose (polymers of glucose). Polysaccharides are not sugars. Because their molecules are so enormous, the majority do not dissolve in water. This makes them good for storing energy or for forming strong structures. If glucose itself would accumulate in cells, it would dissolve and make the contents of the cell too concentrated (which would affect the osmotic properties of the cell). It is a reactive molecule so it would interfere with normal cell chemistry as well. These problem are avoided by converting it, by condensation reactions, to a storage polysaccharide, which is a convenient, compact, inert and insoluble molecule. This is in the form of starch in plants and glycogen in animals. Glucose can be made available again by enzyme-controlled reaction.
Starch and glycogen Starch is a mixture of amylose and amylopectin. Amylose is made by many condensations between -glucose molecules. In this way a long, unbranching chain of several thousand 1,4 linked (they are linked between carbon atoms 1 and 4 of successive glucose units) glucose molecules is built up. The chains are curved and coil up into helical structures. Amylopectin is also made of many 1,4 linked -glucose molecules, but the chains are shorter and branch out to the sides. The branches are formed by 1,6 linkages. The branches mean there are many "ends", which increases the rate at which carbohydrates can hydrolyse the molecules.

Starch grains are commonly found in chloroplasts and in storage organs such as potato tubers and the seeds of legumes and cereals. Starch is never found in animal cells. A substance with molecules very like those of amylopectin is used as the storage carbohydrate. This is called glycogen, which is made of 1,4 linked -glucose with 1,6 linkages forming branches. Glycogen tends to be even more branched. Glycogen molecules clamp together to form granules, which are visible in liver cells and muscle cells where they form an energy reserve. They are found in animals and in fungi. Cellulose -is the most abundant organic molecule on the planet due to its presence in plant cell walls and its slow rate of breakdown in nature. It has a structural role being a mechanically strong molecule (unlike starch or glycogen). Cellulose is a polymer of

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in nature. It has a structural role being a mechanically strong molecule (unlike starch or glycogen). Cellulose is a polymer of -glucose, not -glucose. In order to form a glycosidic bond with carbon atom 4, where the -OH group is below the ring, one glucose molecule must be upside down (rotated by 180). Thus successive glucose units are linked at 180 to each other. The chain stays straight, rather than spiralling.

This results in a strong molecule because the hydrogen atoms of -OH groups are weekly attracted to the oxygen atoms in the same molecule and also to the oxygen atoms of the -OH groups in neighbouring molecules. These hydrogen bonds are individually weak, but so many can form, due to the large number of -OH groups, that collectively they develop enormous strength. Between 60 and 70 cellulose molecules become tightly cross-linked to form bundles called microfibrils which are in turn held together in bundles called fibres by hydrogen bonding. A cell wall typically has several layers of fibres, running in different directions to increase strength. Cellulose fibres have high tensile strength which means that if pulled at both ends they are very difficult to break, and that makes it possible for a cell to withstand the large pressure that develop within it as a result of osmosis. The microfibrils are also very difficult to digest, because few organisms have an enzyme that can break the 1-4 glycosidic bonds. Despite the strength, cellulose fibres are freely permeable, allowing water and solutes to reach the plasma membrane.

Molecules which have groups with dipoles are said to be polar. They are attracted to water molecules, because the water molecules also have dipoles. Such molecules are said to be hydrophilic (water-loving), and they tend to be soluble in water. Molecules which do not have dipoles are said to be non-polar. They are not attracted to water, and they are hydrophobic (water-hating). Such properties make possible the formation of plasma membranes.

Lipids
Lipids also contain carbon, hydrogen and oxygen, but there is a much smaller proportion of oxygen. The most common type are the triglycerides (fats and oils). The main difference between them is that, at room temperature, fats are solid whereas oils are liquid.

Triglycerides
-are made by the combination of three fatty acid molecules with three ester bonds with one glycerol molecule. Fatty acids are organic molecules which all have -COOH group attached to a hydrocarbon tail. Glycerol is a type of alcohol.

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are organic molecules which all have -COOH group attached to a hydrocarbon tail. Glycerol is a type of alcohol.

Each of the three fatty acid molecules joins to glycerol by a condensation reaction. When a fatty acid combines with glycerol, it forms a glyceride, so when all three fatty acids have been added, the final molecule is called a triglyceride. Triglycerides are insoluble in water but are soluble in certain organic solvents (ether, ethanol etc.). Triglycerides are nonpolar and hydrophobic. Saturated and unsaturated fatty acids and lipids Some fatty acids have double bonds between neighbouring carbon atoms. This double bond causes kink in hydrocarbon tail. Such fatty acids are described as unsaturated (as they do not contain the maximum possible amount of hydrogen) and form unsaturated lipids. They therefore melt more easily. If there is more than one double bond, the fatty acid or lipid is described as polyunsaturated; if there is only one it is monounsaturated. Animal lipids are often saturated and occur as fats. Plant lipids are often unsaturated and occur as oils.

Roles of triglycerides 1. Energy reserves in plants, animals and fungi: they are rich in carbon-hydrogen bonds. A given mass of lipid will yield more energy on oxidation than the same mass of carbohydrate (it has a higher calorific value). Fat is stored particularly below the dermis of the skin and around the kidneys. 2. It acts as an insulator against loss of heat below the skin. 3. Provides buoyancy. 4. It is a metabolic source of water: when oxidised in respiration they are converted to carbon dioxide and water.

Phospholipids
-are a special type of lipid. Each molecule has the unusual property of having one end which is soluble in water. This is because one of the three fatty acid molecules is replaced by a phosphate group which is polar and can therefore dissolve in water. The phosphate group is hydrophilic and makes the head of a phospholipid molecule hydrophilic., though the two remaining tails are still hydrophobic.

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Proteins
More than 50% of the dry mass of most cells is protein. All proteins are made from the same basic components - amino acids. Important functions: 1. Essential components of cell membranes 2. Oxygen-carrying pigment haemoglobin is a protein 3. Antibodies which attack and destroy invading microorganisms are proteins 4. All enzymes are proteins 5. Hair and the surface layers of skin contain the protein keratin 6. Collagen (protein) adds strength to many tissues, such as bone and the walls of arteries.

Amino acids
They all have a central carbon atom to which is bonded an amine group, NH2, and a carboxylic acid group, -COOH. The third component bonded to the carbon atom is always a hydrogen atom. The only way in which amino acids differ from each other is in the remaining, fourth, group of atoms bonded to the central atom. This is called the R group of which there are many kinds. It is these R groups that are responsible for the threedimensional shapes of protein molecules and hence their functions. There are 20 different amino acids which occur naturally in the proteins of living organisms.

The peptide bond

Two amino acids can join together. One loses -OH group from its carboxylic acid group, while the other loses a hydrogen atom from its amine group. This leaves the carbon atom of the first amino acid free to bond with the nitrogen atom of the second. The bond is called a peptide bond. The oxygen and two hydrogen atoms removed from the amino acids form a water molecule. Again, this is a condensation reaction.

Molecule made up of two linked amino acids is called dipeptide. A molecule made up of many amino acids linked together by peptide bonds is called a polypeptide (a polymer and a macromolecule). A complete protein molecule may contain just one polypeptide chain, or it may have two or more chain which interact with each other. In living cells, ribosomes are the sites where amino acids are linked together to form polypeptides. The reaction is controlled by enzymes. By hydrolysis reaction (involving the addition of water) polypeptides can be broken down to amino acids by braking the peptide bonds.

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reaction (involving the addition of water) polypeptides can be broken down to amino acids by braking the peptide bonds.

Primary structure
The types of amino acids contained in the chain, and the sequence in which they are joined, is called the primary structure of the protein. Even a change in one amino acid in the chain made up of thousand can completely alter the properties of the polypeptide or protein.

-NH3+ group and -COO- group are known as the amino and carboxyl ends, or the N and C terminals.

Secondary structure
A polypeptide chain often coils into an -helix due to the attraction between the oxygen of the -CO group of one acid and -NH group of the amino acid four places ahead of it. This is another example of hydrogen bonding. Hydrogen bonds are easily broken by high temperatures and pH changes. Sometimes a much looser, straighter shape is formed, called a pleated sheet. Other proteins show no regular arrangement at all. It all depends on which R groups are present and therefore which attraction occurs between amino acids in the chain.

Tertiary structure
The way in which a protein coils up to form a precise three-dimensional shape is known as its tertiary structure. There are four types of bonds which help to hold the folded proteins in their precise shape. 1. Hydrogen bonds form between strongly polar groups between a variety of R groups. 2. Disulphide bonds form between two cysteine molecules. 3. Ionic bonds form between R groups containing amine and carboxyl groups. 4. Hydrophobic interactions occur between R groups which are non-polar, or hydrophobic.

Quaternary structure
The association of different polypeptide chains is called the quaternary structure of the protein. The chains are held together by the same four types of bond as in the tertiary structure.

Globular and fibrous proteins

Globular proteins have molecules that fold into a roughly spherical three-dimensional shape. . In living organisms, proteins may be found in cells, in tissue fluid, or in fluids being transported (blood, phloem). All of these contain water. Globular proteins usually curl up so that their non-polar, hydrophobic R groups point into the centre of the molecule, away from their watery surroundings. Water molecules are excluded from the centre of the folded protein. The polar, hydrophilic R groups remain on the outside of the molecule. Globular proteins are therefore usually soluble, because water molecules cluster around their outward-pointing hydrophilic R groups. Many globular proteins have roles in metabolic reactions/ they are physiologically active (enzymes). Many protein molecules do not curl up into a ball, but form long strands. These

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they are physiologically active (enzymes). Many protein molecules do not curl up into a ball, but form long strands. These are known as fibrous proteins, which are usually insoluble and many have structural roles (keratin in hair and outer layers of skin, collagen). Haemoglobin Haemoglobin, oxygen-carrying pigment found in red blood cells, is a globular protein. It is made up of four polypeptide chains. Two of these make an identical pair, and are called chains. Two other make a different identical pair and are called chains. The haemoglobin molecule is nearly spherical. The four polypeptide chains pack closely together, their hydrophobic R groups pointing towards the centre and the hydrophilic one pointing outwards. Each chain has a tertiary structure very similar to that of myoglobin. The interactions between the hydrophobic R groups inside the molecule are important in holding it in its correct 3D shape. The hydrophilic R groups are important in maintaining its solubility. Having a non-polar R group on the outside of the molecule makes the haemoglobin much less soluble.

Each polypeptide chain contains a haem group which is important, permanent, part of a protein molecule but is not made of amino acids - prosthetic group. Each haem group contains an iron ion, Fe 2+. One oxygen molecule can bind with each iron ion. So a complete haemoglobin molecule, with 4 haem groups, can carry 4 oxygen molecules (8 oxygen atoms) at a time. It is the haem group which is responsible for the colour of haemoglobin. This colour changes depending on whether or not the iron ions are combined with oxygen. If they are, the molecule is known as oxyhaemoglobin, and is bright red. If not, the colour is purplish. The overall shape of the haemoglobin molecule enables it to pick up oxygen when the oxygen concentration is high, and to release oxygen when it is low. Small changes in oxygen concentration have a large effect on how much oxygen can the haemoglobin hold. Once one oxygen molecule combined with one haem group, the entire molecule changes its shape in such a way that it is easier for oxygen to combine with the other three haem groups. Collagen -is a fibrous protein that is found in skin, tendons, cartilage, bones, teeth and the walls of blood vessels. It is an important structural protein, not only in humans, but almost in all animals. A collagen molecule is made up of three polypeptide chains, each in the shape of a helix (not alpha-helix since it is not tightly wound). The three helical polypeptides then wind around each other to form a three-stranded "rope". Almost every third amino acid in each polypeptide is glycine. Its small size allows a tight coil to be formed. The three strands are held together by hydrogen bonds. Each complete, threestranded collagen molecule interacts with other collagen molecules running parallel to it. Bonds form between the R groups of lysines in molecules lying next to each other. These cross-links hold many collagen molecules together, forming fibres. The ends of the parallel molecules are staggered; if not, there would be a weak spot. Collagen has tremendous tensile strength - it can withstand large pulling forces.

Water
It is important for two reasons: 1. It is a major component of cells, typically forming between 70 and 95% of the mass of the cell. Human bodies are made up of 60% water. 2. It provides the environment for those organisms that live in water. Three quarters of the planet is covered in water.
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water. Because of its special property of hydrogen bonding to other water molecules, it is a liquid at room temperature, although, because of its size it should be a gas. It also provides a medium for molecules and ions to mix in (because of its liquid state) and hence a medium in which life could evolve. The hydrogen bonding makes the molecules more difficult to separate and affect the physical properties of water. More energy is needed to break these bonds and convert water from liquid to gas.

Water as a solvent
-for ions and polar molecules is excellent because the water molecules are attracted to them, collect around and separate them. Once a chemical is in solution, it is free to move about and react with other chemicals. If non-polar molecules are surrounded by water, they tend to be pushed together by the water since the water molecules are attracted to each other. This increases the stability of some structures (protein structure, membrane structure).

Water as a transport medium

-in blood, in the lymphatic, excretory and digestive systems of animals, and in the vascular tissues of plants. Its solvent properties are essential here.

Thermal properties
As hydrogen bonding restricts the movement of water molecules, a relatively large amount of energy is required to raise the temperature of water. This is why large bodies of water (oceans, seas) are slow to change their temperatures due to environmental conditions. This makes them more stable habitats. Human bodies also have a large amount of water in them. This is why internal temperature change is minimalized, making it easier to achieve a stable body temperature. Since a relatively large amount of heat is needed to convert water to gas, the process of evaporation transfers a large amount of energy and can be effective in the process of cooling the body. A relatively large amount of energy must be transferred from water before it is converted from a liquid to a solid (ice). This makes it less likely that water will freeze advantage both for the bodies of living organisms as well as for organisms which live in water.

Density and freezing properties

Below 4C the density of the water starts to decrease. Ice therefore floats on water and insulates the water beneath it. This reduces the tendency for large bodies of water to completely freeze, and increases the chances of life surviving cold conditions. Changes in density of water causes currents which help to maintain the circulation of nutrients in the oceans.

High surface tension and cohesion

Water molecules have very high cohesion - they tend to stick to each other. This is exploited in the way water moves in long, unbroken columns through the vascular tissue in plants and is an important property in cells. High cohesion results in high surface tension which allows certain small organisms to exploit the surface of water as habitat.

Inorganic ions
All living things need a variety of ions for their structure and metabolism. Ions are formed from individual atoms that have gained or lost one or more electrons and are therefore charged negatively or positively. Many are highly soluble in water.

Ion
Calcium, Ca2+

Some roles in living organisms

As calcium phosphate, provides a structural component of bones and teeth As ions, important in the transmission of electrical impulses across synapses, and in the contraction of muscles
Involved in the transmission of nerve impulses across neurons Constantly pumped out of cells by active transport in exchange for potassium ions Involved in the transmission of nerve impulses across neurons Contribute to the control of turgidity of guard cells (opening and closing stomata) Constantly pumped out of cells by active transport in exchange for sodium ions

Sodium, Na+ Potassium, K+

Magnesium, Mg2+ Present in chlorophyll molecules Some enzymes (ATPases) have magnesium ions at their active sites Chloride, ClNitrate, NO3
-

Help to balance the +ve charge of cations (sodium, potassium) within and around cells Plants use nitrogen from ion to make amino acids and nucleotides Used for making nucleotides, including ATP With calcium, they form calcium phosphate, that gives bones their strength The production of nucleic acids (DNA and RNA) in cells The production of phospholipids, essential in cell membranes. Haemoglobin molecules contain iron in their haem groups

Phosphate, PO43-

Iron, Fe2+

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