Bio Molecules PDF

# Proteins - **Tertiary structure:** The a-helix of the secondary protein structure can be folded and twisted to give a more complex, compact 3D structure. This is the tertiary structure. The shape is maintained by: - Hydrogen bonds. - Ionic bonds. - Disulphide bonds. - Hydrophobic...

# Proteins - **Tertiary structure:** The a-helix of the secondary protein structure can be folded and twisted to give a more complex, compact 3D structure. This is the tertiary structure. The shape is maintained by: - Hydrogen bonds. - Ionic bonds. - Disulphide bonds. - Hydrophobic interactions. - **Quaternary structure:** Some polypeptide chains are not functional unless they are in combination. In some cases, they may combine with another polypeptide chain, such as the insulin molecule, which has two chains. They may also be associated with non-protein groups and form large, complex molecules, such as haemoglobin. ## Globular and fibrous proteins The roles of proteins depend on their molecular shape. - **Fibrous proteins** have long, thin molecules and their shape makes them insoluble in water, so they have structural functions, as in bone. The polypeptides are in parallel chains or sheets, with many cross-linkages forming long fibres, for example keratin, the protein in hair. Fibrous proteins are strong and tough. Collagen is a fibrous protein, providing the strength and toughness needed in tendons. A single fibre, sometimes called tropocollagen, consists of three identical polypeptide chains twisted around each other, like a rope. The three chains are linked by hydrogen bonds, making the molecule very stable. - **Globular proteins** are compact and folded into spherical molecules. This makes them soluble in water and so they have many different functions, including enzymes, antibodies, plasma proteins and hormones. Haemoglobin is a globular protein, consisting of four folded polypeptide chains, at the centre of each of which is the iron-containing group, haem. ## Test for protein - the biuret test To test a solution for protein, a few drops of biuret reagent (sodium hydroxide and copper (II) sulphate) are added, although they can be added separately. The sodium hydroxide and copper sulphate react to make blue copper hydroxide. If a protein is present, the copper hydroxide interacts with the peptide bonds in the protein to make biuret, which is purple. So, the colour change for a positive biuret test is blue → purple. At low protein concentration, the colour change is difficult to detect by eye. The more concentrated the protein, the darker the purple colour, so the test is qualitative. It could be used as a semi-quantitative test, comparing the intensity of purple in two identically treated solutions. Measuring the absorbance of the purple biuret in a colorimeter, using a yellow (580 nm) filter gives a numerical estimate of relative concentration of proteins present in a sample. This is also semi-quantitative as an actual protein concentration is not measured. To measure the actual concentration, making the test quantitative, a biosensor is needed. ## Protein structure The structure of a protein can be thought of at different levels of organisation: - **Primary structure:** This is the order of the amino acids in a polypeptide chain. Polypeptides have up to 20 different types of amino acid. They can be joined in any number, order and combination, so there is a huge number of possible polypeptides. The primary structures determined by the base sequence on one strand of the DNA molecule. - **Secondary structure:** This is the shape that the polypeptide chain forms as a result of hydrogen bonding between the =O on -CO groups and the -H on -NH groups in the peptide bonds along the chain. This causes the long polypeptide chain to be twisted into a 3D shape. The spiral shape is the a-helix. Another, less common, arrangement is the B-pleated sheet. The protein keratin has a high proportion of a-helix and the protein fibroin, in silk, has a high proportion of ẞ-pleated sheet. - **Tertiary structure:** The a-helix of the secondary protein structure can be folded and twisted to give a more complex, compact 3D structure. This is the tertiary structure. The shape is maintained by: - Hydrogen bonds. - Ionic bonds. - Disulphide bonds. - Hydrophobic interactions. - **Quaternary structure:** Some polypeptide chains are not functional unless they are in combination. In some cases, they may combine with another polypeptide chain, such as the insulin molecule, which has two chains. They may also be associated with non-protein groups and form large, complex molecules, such as haemoglobin. ## Proteins Proteins differ from carbohydrates and lipids in that, in addition to carbon, hydrogen and oxygen, they always contain nitrogen. Many proteins also contain sulphur and some contain phosphorus. Proteins are polymers made of monomers called amino acids. The chains of amino acids are called polypeptides. About 20 different amino acids are used to make up proteins. There are thousands of different proteins and their shape is determined by the specific sequence of amino acids in the chain. All amino acids have the same basic structure. Attached to a central carbon atom are: - An amino group, -NH2, at one end of the molecule, called the N-terminal. - A carboxyl, group -COOH, at the other end of the molecule, called the C-terminal. - A hydrogen atom. - The R group, which is different in each amino acid. ## Test for fats and oils - the emulsion test A sample to be tested is mixed with absolute ethanol, which dissolves any lipids present. It is shaken with an equal volume of water. The dissolved lipids come out of solution, because they are insoluble in water. They form an emulsion, making the sample cloudy white. ## Implications of saturated fats for human health The main causes of heart disease are fatty deposits on the inner wall of the coronary arteries (atherosclerosis) and high blood pressure (hypertension). A diet that is high in saturated fats, smoking, lack of exercise and aging are all contributory factors and all except aging can be modified to reduce the risk of disease. Damage to the heart and blood vessels is the single leading cause of death in the UK. When food has been absorbed at the small intestine, lipids and proteins combine to make lipoproteins, which travel around the body in the bloodstream. - If the diet is high in saturated fats, low-density lipoprotein (LDL) builds up and causes harm. Fatty material called atheroma gets deposited in the coronary arteries, restricting blood flow and, therefore, oxygen delivery to the heart. This can result in angina, and, if the vessel is completely blocked, a myocardial infarction or heart attack occurs. - But if the diet has a high proportion of unsaturated fats, the body makes more high-density lipoprotein (HDL), which carries harmful fats away to the liver for disposal. The higher the ratio of HDL : LDL in a person's blood, the lower their risk of cardio-vascular and coronary heart disease. # Roles of lipids There are many different types of lipid and lipids have many different roles in living organisms. The roles are summarised here in relation to the chemical nature of the lipid molecules. | Molecule | Function | Comment | |---|---|---| | Triglycerides | Energy reserves | In both plants and animals, because lipids contain more carbon-hydrogen bonds than carbohydrates. | | | Thermal insulation | When stored under the skin, lipids insulate against heat loss in the cold, or heat gain when it is very hot. | | | Protection | Fat is often stored around delicate internal organs such as kidneys, protecting against physical damage. | | | Producing metabolic water | Metabolic water is water released from the body's chemical reactions. Triglycerides produce a lot when oxidised. | | Phospholipids | Structural | In biological membranes. | | | Electrical insulation | The myelin sheath that surrounds the axons of nerve cells. | | Waxes | Waterproofing | In terrestrial organisms, waxes reduce water loss, such as in the insect exoskeleton and in the cuticle of plants. | # Phospholipids Phospholipids are a special type of lipid. Each molecule has the unusual property of having one end that is soluble in water and one that is not. The diagram shows that one end of the molecule has a lot of oxygen atoms, in the glycerol group and the phosphate, and so this end of the molecule interacts with water and is hydrophilic. It is described as the polar head of the molecule. As in triglycerides, the fatty acid tails do not have any oxygen atoms and do not interact with water so they are hydrophobic and are non-polar. # Waxes Waxes are lipids and melt above about 45°C. They have a waterproofing role in both animals, such as in the insect exoskeleton, and plants, in the leaf's cuticle. # Properties of lipids The differences in the properties of fats and oils come from variations in the fatty acids. - If the hydrocarbon chain has only single carbon-carbon bonds, then the fatty acid is saturated, because all the carbon atoms are linked to the maximum possible number of hydrogen atoms. That is, they are saturated with hydrogen atoms. The fatty acid chain is a straight zigzag, as the photograph of the model on p23 shows, and the molecules can align readily, so fats are solid. They remain semi-solid at body temperature and are useful for storage in mammals. Animal lipids often contain saturated fatty acids. - If any carbon-carbon bond is not a single bond, the molecule is unsaturated and the chain gets a kink. The molecules cannot align uniformly and the lipid does not solidify readily. This is why unsaturated lipids are oils, which remain liquid at room temperature. Plant lipids are often unsaturated and occur as oils, such as olive oil and sunflower oil. If one carbon-carbon double bond is present, the lipids are mono-unsaturated, whereas if there are many carbon-carbon double bonds, the lipids are described as polyunsaturated. # Lipids Like carbohydrates, lipids contain carbon, hydrogen and oxygen but, in proportion to the carbon and hydrogen, they contain much less oxygen. They are non-polar compounds and so are insoluble in water, but dissolve in organic solvents, such as propanone and alcohols. ## Triglycerides Triglycerides are formed by the combination of one glycerol molecule and three molecules of fatty acids. The glycerol molecule in a lipid is always the same but the fatty acid component varies. The fatty acids join to glycerol by condensation reactions, whereby three molecules of water are removed and ester bonds are formed between the glycerol and fatty acids. # Chitin Chitin is a structural polysaccharide, found in the exoskeleton of insects and in fungal cell walls. It resembles cellulose but has an acetylamine group derived from amino acids added, to form a heteropolysaccharide. It is strong, waterproof and lightweight. Like cellulose, the monomers are rotated through 180° in relation to their neighbours, and the long parallel chains are cross-linked to each other by hydrogen bonds, forming microfibrils. # Cellulose Cellulose is a structural polysaccharide and its presence in plant cell walls makes it the most abundant organic molecule on Earth. We can think of the structure of cellulose at different levels: - An individual cellulose molecule consists of a long chain of β-glucose units. These glucose monomers are joined by ẞ-1,4-glycosidic bonds to make a straight, unbranched chain. The ẞ-link rotates adjacent glucose molecules by 180°. - Hydrogen bonds form between the (OH) groups of adjacent parallel chains, contributing to cellulose's structural stability. These parallel cellulose molecules become tightly cross-linked by hydrogen bonds to form a bundle called a microfibril. - The microfibrils are, in turn, held in bundles called fibres. - A cell wall has several layers of fibres, which run parallel within a layer but at an angle to the adjacent layers. This laminated structure also contributes to the strength of the cell wall. Cellulose is freely permeable, because there are spaces between the fibres. Water and its solutes can penetrate through these spaces in the cell wall, all the way to the cell membrane. # Glycogen The main storage product in animals is glycogen. It used to be called animal starch because it is very similar to amylopectin. It also has a-1,4 and a-1,6 bonds, *as shown on p19*. The difference is that in glycogen, the a-1,6 bonds occur every 8-10 glucose molecules. This means glycogen has shorter a-1,4-linked chains than amylopectin and so it is more branched. # Amylose Amylopectin also has chains of glucose monomers joined with a-1,4-glycosidic bonds. They are cross-linked with a-1.6-glycosidic bonds and fit inside the amylose. When a glycosidic bond forms between the C1 atom on one glucose molecule and the C6 atom on another, a side branch is seen. These occur every 24-30 glucose and the C6 atom glycosidic bonds continue on from the start of the branch. ## Testing for the presence of starch: iodine-potassium iodide test Iodine solution (iodine dissolved in aqueous potassium iodide) interacts with starch. There is a colour change from the orange-brown of the iodine solution to blue-black. The depth of blue-black colour gives an indication of relative concentration of starch. An accurate concentration cannot be determined so, like the Benedict's test, this test is qualitative. # Polysaccharides Polysaccharides are large, complex polymers. They are formed from very large numbers of monosaccharide units, which are their monomers, linked by glycosidic bonds. Glucose is the main source of energy in cells and it must be stored in an appropriate form. It is soluble in water and so it would increase the concentration of the cell contents, and consequently draw water in by osmosis. This problem is avoided by converting the glucose into starch in plant cells or glycogen in animal cells. Starch and glycogen are storage products. They are polysaccharides. They are more suitable than glucose for storage because: - They are insoluble so they have no osmotic effect. - They cannot diffuse out of the cell. - They are compact molecules and can be stored in a small space. - They carry a lot of energy in their C-H and C-C bonds. ## Starch Starch is the main store of glucose for plants. Starch grains are found in high concentrations in seeds and storage organs such as potato tubers. Starch is made of a-glucose molecules bonded together in two different ways, forming the two polymers, amylose and amylopectin. - **Amylose** is a linear, unbranched molecule with a-1,4-glycosidic bonds forming between the first carbon atom (C1) on one glucose monomer and the fourth carbon atom (C4) on the adjacent one. This is repeated, forming a chain, which coils into a helix. ## The Benedict's test Equal volumes of Benedict's reagent and the solution being tested are heated to at least 70°C. If a reducing sugar, such as glucose, is present, the solution will change colour from blue through green, yellow and orange until finally a brick-red precipitate forms. This test does not tell you the actual concentration of reducing sugar, so it is described as a qualitative test. ## Disaccharides Disaccharides are composed of two monosaccharide units bonded together with the formation of a glycosidic bond and the elimination of water. This is an example of a condensation reaction. The diagram shows water being removed between C4 of one glucose molecule and C1 of the other. The bond formed between glucose molecules is a glycosidic bond. It is between C1 and 4. Because the bond is straight and not twisted, the bond is an a-1,4-glycosidic bond. | Disaccharide | Component monosaccharides | Biological role | |---|---|---| | maltose | glucose + glucose | in germinating seeds | | sucrose | glucose + fructose | transport in phloem of flowering plants | | lactose | glucose + galactose | in mammalian milk | ## Testing for the presence of sugars Reducing sugars are sugars that can donate an electron. The Benedict's test detects reducing sugars in a solution. The reducing sugar donates an electron to reduce copper (II) ions in copper sulphate solution, which is blue. The Cu(II) ions are reduced to Cu(l) ions in red copper (I) oxide. The test is carried out as follows: *Cu2+ + e ------> Cu+ blue red Equal volumes of Benedict's reagent and the solution being tested are heated to at least 70°C. If a reducing sugar, such as glucose, is present, the solution will change colour from blue through green, yellow and orange until finally a brick-red precipitate forms. This test does not tell you the actual concentration of reducing sugar, so it is described as a qualitative test. ## Monosaccharides Monosaccharides are small organic molecules and are the building blocks for the larger carbohydrates. Monosaccharides have the general formula (CH₂O)n and their names are determined by the number of carbon atoms (n) in the molecule. A triose sugar has three carbon atoms; a pentose has five and a hexose has six. Glucose is a hexose sugar. All hexose sugars share the formula C6H12O6 but they differ in their molecular structure. The carbon atoms of monosaccharides make a ring when the sugar is dissolved in water, and they can alter their binding to make straight chains, with the rings and chains in equilibrium. Glucose has two isomers, a- and β-glucose, based on the positions of an (OH) and an (H) *as shown on p16*. These different forms result in biological differences when they form polymers, such as starch and cellulose. # Water Water is a medium for metabolic reactions and an important constituent of cells, being 65-95% of the mass of many plants and animals. About 70% of each individual human is water. The water molecule is a dipole, which means it has a positively charged end (hydrogen) and a negatively charged end (oxygen), but no overall charge. A molecule with separated charges is 'polar'. The charges are very small and they are written as δ+ and δ-, to distinguish them from full charges, written as + and -. Hydrogen bonds can form between the δ+ on a hydrogen atom of one molecule and the δ- on an oxygen atom of another molecule. Hydrogen bonds are weak, but the very large number of them present in water makes the molecules difficult to separate and gives water a wide range of physical properties vital to life. Water's properties make it essential for life, as we understand it. - **As a solvent:** living organisms obtain their key elements from aqueous solution. Water is such a good solvent that it has been called the 'universal solvent'. Because water molecules are dipoles, they attract charged particles, such as ions, and other polar molecules, such as glucose. These then dissolve in water, so chemical reactions take place in solution. Water acts a transport medium, e.g. in animals, plasma transports dissolved substances, and in plants, water transports minerals in the xylem, and sucrose and amino acids in the phloem. Non-polar molecules, such as lipids, do not dissolve in water. - **Water is a metabolite:** water is used in many biochemical reactions as a reactant, e.g. with carbon dioxide to produce glucose in photosynthesis. Many reactions in the body involve hydrolysis, where water splits a molecule, e.g maltose + water → glucose + glucose. In condensation reactions, water is a product, e.g. glucose + fructose → sucrose + water - **High specific heat capacity:** this means a large amount of heat energy is needed to raise its temperature. This is because the hydrogen bonds between water molecules restrict their movement, resisting an increase in kinetic energy and therefore resisting an increase in temperature. This prevents large fluctuations in water temperature, which is important in keeping aquatic habitats stable, so that organisms do not have to adapt to extremes of temperature. It also allows enzymes within cells to work efficiently. - **High latent heat of vaporisation:** this means a lot of heat energy is needed to change it from a liquid to a vapour. This is important, for example, in temperature control, where heat is used to vaporise water from sweat on the skin or from a leaf's surface. As the water evaporates, the body cools. # Inorganic ions Living organisms need a variety of inorganic ions to survive. Inorganic ions are also called electrolytes or minerals and are important in many cellular processes, including muscle contraction, nervous coordination and maintaining water potential in cells and blood. There are two groups: macronutrients, needed in small concentrations, and micronutrients, needed in minute (trace) concentrations, e.g. copper and zinc. Four macronutrients are described here. - **Magnesium (Mg2+):** is an important constituent of chlorophyll and is therefore essential for photosynthesis. Plants without magnesium in their soil cannot make chlorophyll and so the leaves are yellow, a condition known as chlorosis. Growth is often stunted from lack of glucose. Mammals need magnesium for their bones. - **Iron (Fe2+):** is a constituent of haemoglobin, which transports oxygen in red blood cells. Lack of iron in the human diet can lead to anaemia. - **Phosphate ions (PO43-):** are used for making nucleotides, including ATP, and are a constituent of phospholipids, found in biological membranes. - **Calcium (Ca2+):** like phosphate, is an important structural component of bones and teeth in mammals and is a component of plant cell walls, providing strength. # Carbohydrates Carbohydrates are organic compounds containing, as their name suggests, the elements carbon, hydrogen and oxygen. In carbohydrates, the basic unit is a monosaccharide. Two monosaccharides combine to form a disaccharide. Many monosaccharide molecules combine to form a polysaccharide. ## Monosaccharides Monosaccharides are small organic molecules and are the building blocks for the larger carbohydrates. Monosaccharides have the general formula (CH₂O)n and their names are determined by the number of carbon atoms (n) in the molecule. A triose sugar has three carbon atoms; a pentose has five and a hexose has six. Glucose is a hexose sugar. All hexose sugars share the formula C6H12O6 but they differ in their molecular structure. The carbon atoms of monosaccharides make a ring when the sugar is dissolved in water, and they can alter their binding to make straight chains, with the rings and chains in equilibrium. Glucose has two isomers, a- and β-glucose, *based on the positions of an (OH) and an (H) as shown on p16*. These different forms result in biological differences whent they form polymers, such as starch and cellulose. # Water (cont.) - **Cohesion:** water molecules attract each other forming hydrogen bonds. Individually these are weak but, because there are many of them, the molecules stick together in a lattice. This sticking together is called cohesion. It allows columns of water to be drawn up xylem vessels in plants. - **High surface tension:** cohesion between water molecules at the surface produces surface tension. At ordinary temperatures water has the highest surface tension of any liquid except mercury. In a pond, cohesion between water molecules at the surface produces surface tension so that the body of an insect, such as the pond skater, is supported. - **High density:** water is denser than air and, as a habitat for aquatic organisms, provides support and buoyancy. Water has a maximum density at 4°C. Ice is less dense than liquid water, because the hydrogen bonds hold the molecules further apart than they are in the liquid. So ice floats on water. Ice is a good insulator and prevents large bodies of water losing heat and freezing completely, so organisms beneath it survive. - **Water is transparent:** allowing light to pass through. This lets aquatic plants photosynthesise effectively.