Carbohydrates 3.1 Biological Molecules PDF

CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Monomers Polymers Condensation reaction MISSESTRUCH 2020 Hydrolysis reaction 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...

CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Monomers Polymers Condensation reaction MISSESTRUCH 2020 Hydrolysis reaction 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. Condensation and Hydrolysis Reactions For monomers to bond together a chemical reaction occurs; this is a condensation reaction. Condensation reactions involve the removal of a water molecule. 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. 1 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Monosaccharides Disaccharides Polysaccharides MISSESTRUCH 2020 Carbohydrates Glucose Galactose Carbohydrates are key biological molecules that store energy Fructose 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. Fructose Larger carbohydrates, such as sucrose and starch, are made from monosaccharides. The monomers of carbohydrates are known as monosaccharides and glucose, galactose and fructose are three common examples. Monosaccharides are sugars and are soluble in water. Their function is either to provide energy or to be a building block to create larger molecules. All carbohydrates contain three elements: carbon, hydrogen and oxygen (CHO). The general formula for a monosaccharide is CnH 2nOn, where n = the number of carbon atoms it contains. 2 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Monosaccharides Glucose Isomer MISSESTRUCH 2020 Glucose α glucose β glucose Glucose, C 6H12O6 , is a very important monosaccharide that can provide energy or be polymerised to form a structural support molecule (cellulose) or energy storage molecule (glycogen and starch). Glucose has two structural isomers. Isomers are compounds that have the same formula, but the atoms are arranged differently. The diagram on the left shows the isomer α glucose. β glucose is the second isomer. There is only one difference in the structural arrangement between these isomers. The hydrogen (H) and hydroxyl group (OH) on carbon 1 swap position. α glucose β glucose This small change has a significant impact on the bonding and final structure of the polymers that they form. 3 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Monosaccharides Disaccharides Glycosidic Bond MISSESTRUCH 2020 Disaccharides Maltose Lactose Disaccharides are two monosaccharides bonded together by Sucrose a glycosidic bond, that is 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 learned. glucose + glucose --> maltose glucose + galactose --> lactose glucose + fructose --> sucrose Condensation and Hydrolysis Reactions The diagram below demonstrates how a condensation reaction creates a disaccharide. A water molecule is being removed (highlighted 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. Disaccharides can be broken down back into monosaccharides via a hydrolysis reaction. Hydrolysis is when a water molecule is added in to break a bond, as shown in the diagram below. 4 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Polysaccharides Condensation reaction Energy store Polysaccharides MISSESTRUCH 2020 Structural support Starch Glycosidic bonds 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. 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 needed, it is converted into the polymer starch for storage. 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 (The numbers refer to which carbon atoms the bond forms between). 5 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Starch Amylose Amylopectin Structure of Starch MISSESTRUCH 2020 Glycosidic bonds Spiral Starch is made up of two polymers; amylose and amylopectin. Branched 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 in 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, as seen in the diagram to the right. Properties of Starch Starch is insoluble due to the fact it is a large molecule. This is an advantage as it means it can be stored within cells and not dissolve. Therefore it will not change the water potential of a cell and nor cause osmosis to occur. As amylose is spiral-shaped, it can be readily compacted. As amylopectin is branched, it 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 for respiration. 6 MISSESTRUCH 2020 CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Glycogen Glycosidic bonds Highly branched Glycogen MISSESTRUCH 2020 Metabolic rate Liver Glycogen is the major carbohydrate storage molecule found in Muscles 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 need for respiration it is converted into the polymer glycogen and stored. 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 access to glucose to respire and 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. Properties of Glycogen Glycogen is insoluble due to the fact it is a large molecule. This is an advantage as it means it can be stored within cells and not dissolve. Therefore it will not change the water potential of a cell nor cause osmosis, which would otherwise cause cell lysis. The fact that glycogen is a highly branched molecule means it has a larger surface area for enzymes to attach. This means that it is readily hydrolysed 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. 7 MISSESTRUCH CARBOHYDRATES 3.1 BIOLOGICAL MOLECULES Key Terms Cellulose Structural strength β-glucose Cellulose MISSESTRUCH 2020 Glycosidic bonds Unbranched Unlike starch and glycogen, the function of cellulose is to Fibril 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 (1-4 bonds create straight lines, whereas 1-6 bonds create branches). 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. Fibrils then align in parallel and are held in place by even more hydrogen bonds to form a cellulose fibres. Properties of Cellulose Key Points: Monomers join together by condensation reactions to make polymers. Polymers are hydrolysed back into monomers. Monosaccharides are the monomers of carbohydrates. Glucose, Cellulose is insoluble due to the fact it is such a large molecule. This is an advantage as it will not change the galactose and fructose are the three you need to know. Glucose water potential of a cell and affect exists as two isomers, α-glucose and β-glucose. osmosis. Due to the large number of hydrogen bonds in and between the Three key disaccharides are maltose, lactose and sucrose. Three key polysaccharides are starch, glycogen and cellulose. fibrils, cellulose is a very strong polysaccharide. Glycogen is for glucose storage in animals. Starch is for glucose storage in plants. Cellulose is for structural strength in plants. 8 MISSESTRUCH 2020 Essay Links: Glucose could link to titles on respiration, as a key respiratory substrate Glucose and glycogen could link to homeostasis and the control of blood glucose levels. Glycosidic bonds and hydrogen bonds (in cellulose) could link to titles on bonding. Monosaccharides and polysaccharides could link to titles on monomers and polymers. 8 MISSESTRUCH 2020 PROTEINS Key Terms Polypeptide 3.1 BIOLOGICAL MOLECULES Peptide bonds MISSESTRUCH 2020 Amino acids Amine group Carboxyl group Protein structure overview Proteins are large polymers made up of monomers called 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. Protein polymer chains, or polypeptides, are created on ribosomes in cells and are then further folded and modified in the Golgi apparatus. Monomer in proteins - Amino acid Proteins are large polymers, made up the monomer amino acids. There are 20 different amino acids, but you only need to learn the general structure. The general structure consists of: a central carbon an amine group (NH 2) a hydrogen atom a carboxyl group (COOH) the variable group (R group) Each of the 20 different amino acids have a different R group. Amino acids join together to make the polypeptide polymer via condensation reactions and are held together by peptide bonds. 9 MISSESTRUCH 2020 PROTEINS Key Terms Primary structure 3.1 BIOLOGICAL MOLECULES Primary Structure Sequence of amino acids MISSESTRUCH 2020 α helix β pleated sheet The first structure that forms in the creation of a protein is the Secondary structure polypeptide chain. Amino acids Proteins are all made up of one or more polypeptide chains folded into highly specific 3D shapes. The primary structure is the sequence of amino acids in a polypeptide chain. This would be a onemark 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 where bonds occur and how the protein folds. Therefore, the primary structure determines the final 3D shape and the protein's function. 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. Each amino acid is held in the polypeptide chain by peptide bonds. Secondary Structure The sequence of amino acids causes parts of a protein molecule to bend into an α helix or fold into β pleated sheets. Hydrogen bonds form between the carboxyl groups of one amino acid and the amine group of another and hold the secondary structure in place. 10 PROTEINS Key Terms Tertiary structure 3.1 BIOLOGICAL MOLECULES Tertiary Structure Hydrogen bonds MISSESTRUCH 2020 Ionic bonds Disulfide bonds The secondary structure is bent and folded to form a precise Quaternary structure 3D shape. This unique 3D shape is held in place by hydrogen Haemoglobin bonds, ionic bonds and sometimes disulfide bonds. Disulfide bonds (di meaning 2) only form between the R-groups of two amino acids that contain sulfur. Describing the tertiary structure of a protein is a 3-mark question. The 3 marks are: The further folding of the secondary structure To create a unique 3D structure Held in place by hydrogen, ionic and disulfide bonds. Make sure you always mention the bonds involved when describing protein structures, as 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 has a quaternary structure. It is still folded into a 3D shape and held by hydrogen, ionic and disulphide bonds. Haemoglobin is an example which is made up of 4 polypeptide chains. In 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. The heme group, containing 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. 11 MISSESTRUCH 2020 PROTEINS 3.1 BIOLOGICAL MOLECULES MISSESTRUCH 2020 Key points Proteins are large polymers made up of amino acids, held together by peptide bonds. There are four levels of organisation; primary, secondary, tertiary and quaternary structure. Peptide bonds hold the primary structure. Hydrogen bonds hold the secondary structure Hydrogen, ionic and disulfide bonds hold the tertiary structure. Essay Links: The primary structure can link to titles on mutations. The tertiary structure could link to titles on transport across membranes (carrier/channel proteins). The tertiary structure could link to titles on receptors. The tertiary structure could link to titles on immunity (antigens and antibodies). 12 ENZYMES Key Terms Active site 3.1 BIOLOGICAL MOLECULES Tertiary structure MISSESTRUCH 2020 Enzyme Structure Complementary Activation energy Whilst enzymes are relatively large molecules, it is only a small part of the enzyme that attaches to a substrate to catalyse a reaction. This site is known as the active site. The active site is specific and unique in shape due to the specific folding and bonding in the tertiary structure of the protein. Due to this specific active site, enzymes can only attach to substrates that are complementary in shape. Protein polymer chains, or polypeptides, are created on ribosomes in cells and are then further folded and modified in the Golgi apparatus. Enzyme Action All reactions require a certain amount of energy before they occur. This is known as the activation energy. When enzymes attach to the substrate they can lower the activation energy needed for the reaction to occur, and therefore speed up the reaction. 13 MISSESTRUCH 2020 ENZYMES Key Terms Lock and key 3.1 BIOLOGICAL MOLECULES Two models of action Induced fit MISSESTRUCH 2020 Enzyme-substrate complex There are two models to explain how this occurs: lock and key model and induced fit model. Lock and Key Model This model suggests that the enzyme is like a lock and that the substrate is like a key that fits into it due to its complementary shape. The enzyme active site is a fixed shape and due to random collisions, the substrate can collide and attach to the enzyme. This forms an enzymesubstrate complex. Once the enzyme-substrate complex has formed, the charged groups within the active site are thought to distort the substrate and therefore lower the activation energy. The products are then released, and the enzyme active site is empty and ready to be reused. Induced Fit Model This model suggests that the enzyme is like a glove and the substrate is like your hand; the empty glove is not exactly complementary in shape to your hand, but when your hand enters, it enables the glove to mould around your hand to become completely complementary. The enzyme active site is induced or slightly changes shape, to mould around the substrate. The formation of the enzymesubstrate complex involves the enzyme moulding around the substrate, which puts a strain on the bonds and therefore lowers the activation energy. The products are then removed, and the enzyme active site returns to its original shape. The induced fit model is the accepted model for how enzymes function. 14 MISSESTRUCH 2020 ENZYMES Key Terms Kinetic energy 3.1 BIOLOGICAL MOLECULES Successful collisions MISSESTRUCH 2020 Denature Factors Affecting Enzymes Enzymes, which are proteins, are sensitive to certain conditions. The following factors affect the rate of enzyme-controlled reactions: Temperature pH Substrate concentration Enzyme concentration Inhibitors Temperature If the temperature is too low, there is not enough kinetic energy for successful collisions between the enzyme and substrate. If the temperature is too high, enzymes denature, the active site changes shape and enzymesubstrate complexes cannot form. 15 MISSESTRUCH 2020 ENZYMES Key Terms Amino acids 3.1 BIOLOGICAL MOLECULES Enzyme-substrate complex MISSESTRUCH 2020 pH Denature Saturated Too high or too low a pH will interfere with the charges in the amino acids in the active site. This can break the ionic and hydrogen bonds holding the tertiary structure in place and therefore the active site changes shape. Therefore the enzyme denatures and fewer enzyme-substrate complexes form. Different enzymes have a different optimal pH Substrate and Enzyme Concentration If there is insufficient substrate, then the reaction will be slower as there will be fewer collisions between the enzyme and substrate. If there are insufficient enzymes, then the enzyme active sites will become saturated with substrate and unable to work any faster. 16 MISSESTRUCH 2020 ENZYMES Key Terms Competitive inhibitor 3.1 BIOLOGICAL MOLECULES Enzyme-inhibitor complex MISSESTRUCH 2020 Non-competitive inhibitor Inhibitors Competitive inhibitors are the same shape as the substrate and can bind to the active site. This prevents the substrate from binding and the reaction occurring. If you add more substrate this will out-compete the inhibitor, knocking them out of the active site. Non-competitive inhibitors bind to the enzyme away from the active site (the allosteric site). This causes the active site to permanently change shape, and therefore the substrate can no longer bind, regardless of how much substrate is added. 17 MISSESTRUCH 2020 ENZYMES Key Terms Competitive inhiitor 3.1 BIOLOGICAL MOLECULES Enzyme-inhibitor complex MISSESTRUCH 2020 Denature Inhibitor Graphs With a high enough substrate concentration, the competitive inhibitors are knocked out of the active site and the rate of reaction will therefore return to the same as with no inhibitor. The rate of reaction with a non-competitive inhibitor will be lower at all substrate concentrations. Key points Enzymes are tertiary structure proteins. Enzymes catalyse specific reactions due to their uniquely shaped active site How enzymes lower activation energy is demonstrated by the induced fit model Enzymes are sensitive to pH and temperature. Inhibitors, substrate and enzyme concentration affect the rate of reaction. Essay Links: Beyond the spec: Cyanide is a competitive inhibitor for an enzyme in respiration, which is why it is poisonous. Enzyme sensitivity to pH and temperature can be linked to homeostasis - thermoregulation and regulation of pH of the blood. Enzyme function and sensitivity to temperature can be linked to Rubisco in photosynthesis. Lysozyme is a hydrolytic enzyme involved in phagocytosis. 18 MISSESTRUCH 2020 LIPIDS Key Terms Triglycerides 3.1 BIOLOGICAL MOLECULES Condensation reaction MISSESTRUCH 2020 Ester bond Saturated and unsaturared Lipids Triglycerides and phospholipids are the two lipids you need to know the structure and function of. Triglyceride Phospholipids Triglycerides Triglycerides are formed via the condensation reactions between one molecule of glycerol and three molecules of fatty acid. Ester bonds are formed. The R-groups are fatty acids which can be saturated or unsaturated. Saturated fatty acids– the hydrocarbon chain has only single bonds between carbons. Unsaturated fatty acids – the hydrocarbon chain consists of at least one double bond between carbons 19 MISSESTRUCH 2020 LIPIDS Key Terms Metabolic water source 3.1 BIOLOGICAL MOLECULES Hydrophobic MISSESTRUCH 2020 Properties of Triglycerides Hydrophilic Energy storage Here is how the triglyceride structure results in its properties. 1. 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 act as a metabolic water source. Triglycerides can release water if they are oxidised. This is essential for animals in the desert, such as camels. 3. Triglycerides do not affect water potentials and osmosis. This is because they are large and hydrophobic, making them insoluble in water. 4. Lipids have a relatively low mass. Therefore a lot can be stored without increasing the mass and preventing movement. Phospholipids Phospholipids are made 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. The hydrophilic ‘head’ of a phospholipid can attract water as it is charged. Due to the phosphate being charged (polar), it repels other fats. The fatty acid chain is not charged (non-polar). It is known as the hydrophobic ‘tail’ and it repels water but will mix with fats. 20 MISSESTRUCH 2020 LIPIDS Key Terms Polar 3.1 BIOLOGICAL MOLECULES Phospholipid bilayer MISSESTRUCH 2020 Plasma membrane Phospholipids have two charged regions, so they are polar. In water, they are positioned so that the heads are exposed to water and the tails are not. This forms a phospholipid bilayer which makes up the plasma membrane around cells. Key points Triglycerides and phospholipids are lipids. Both molecules are formed via a condensation reaction and form ester bonds. Fatty acids can be saturated or unsaturated, which refers to whether there are double or single bonds between the carbon atoms. Phospholipids have a hydrophilic head and a hydrophobic tail. Essay Links: Lipids form the insulating myelin sheath on neurones to enable saltatory conduction. Lipids form the phospholipid bilayer on organelle membranes, such as mitochondria and chloroplasts Lipids form the membrane of vesicles, such as a phagosome. Lipids obtained from the membranes of host cells form an envelope around viruses (i,e, HIV) 21 MISSESTRUCH 2020 BIOCHEMICAL TESTS Key Terms Reducing sugar 3.1 BIOLOGICAL MOLECULES Benedict's reagent MISSESTRUCH 2020 Biochemical Test Overview For some of the biological molecules in this topic, you need to know the experiment to test if they are present in a substance and what a positive test result would look like. The biological molecules you need to know the test for are: Reducing sugars Non-reducing sugars Starch Proteins Lipids lipids proteins starch reducing/non-reducing sugars Reducing Sugars 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 given to sugars that can reduce Cu 2+ ions in Benedict’s reagent to Cu+ ions in the form of copper (I) oxide, which forms a brick-red precipitate. 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. 4. If the solution remains blue, there is no reducing sugar present. 22 MISSESTRUCH 2020 BIOCHEMICAL TESTS 3.1 BIOLOGICAL MOLECULES Non-reducing sugar Key Terms Non-reducing sugar Benedict's reagent MISSESTRUCH 2020 Acid hydrolysis HCl Sucrose is a non-reducing sugar because it cannot reduce Cu 2+, Sodium hydroxide this is because the chemical group needed for this reduction Glycosidic bonds reaction is involved in the glycosidic bonds between the monosaccharides. To prove that sucrose is still a sugar, but is just unable to reduce Cu2+ (a non-reducing sugar) the glycosidic bond must be hydrolysed to expose the reducing group. If a substance remained blue after the reducing sugars test, then the procedure to test to see if it is a non-reducing sugar is as follows: 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 100 oC there is not enough energy to break the glycosidic bond. 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. Add a few drops of Benedict’s reagent and heat. If a colour change of blue to yellow/green/red is observed, then this is confirmation that a non-reducing sugar is present. The rustier red the precipitate that forms after a reducing or non-reducing sugar test, the higher the concentration of sugar present. This is because more Cu 2+ has been reduced to Cu +, which forms copper oxide otherwise known as 'rust'. 23 MISSESTRUCH 2020 BIOCHEMICAL TESTS Key Terms 3.1 BIOLOGICAL MOLECULES Starch Starch Iodine MISSESTRUCH 2020 Protein Biuret reagent The presence of starch can be Lipids confirmed by adding a few drops of Ethanol iodine. Iodine is orange/brown in Distilled water colour when no starch is present, White emulsion but it turns blue/black if starch is present. Protein To test for proteins you add biuret reagent (tip - do not confuse this with a burette! It is pronounced Bi-u-ret). Biuret reagent is blue, but it will turn purple when added to a protein. Lipids To test for lipids, your sample must first be dissolved in ethanol. This is achieved by shaking the sample you are testing in ethanol. Once the sample is dissolved, add distilled water and shake again. If lipids are present, you will then observe a white emulsion. Key points For each test, you must know the name of the chemical reagent added, whether it needs to be heated and what the positive test observation looks like. Benedict's reagent must be heated for the reaction to occur. For acid hydrolysis of non-reducing sugars, the acid must be boiled. To test for lipids, you must first dissolve in ethanol and after this, you add and shake in distilled water. 24 MISSESTRUCH 2020 DNA & RNA Key Terms Deoxyribonucleic acid 3.1 BIOLOGICAL MOLECULES Nucleotide MISSESTRUCH 2020 DNA Structure Nitrogenous base Phosphate group Deoxyribonucleic Acid (DNA) codes for the sequence of amino Double helix acids in the primary structure of a protein, which in turn determines the final 3D structure and function of a protein. It is essential that cells contain a copy of this genetic code and that it can be passed to new cells without being damaged. The DNA polymer is a double helix shape. DNA Nucleotide The monomer that makes up DNA is called a nucleotide. It is made up of deoxyribose (a pentose sugar), a nitrogenous base and one phosphate group. The nitrogenous base can either be guanine, cytosine, adenine and thymine. Deoxyribose 25 MISSESTRUCH 2020 DNA & RNA Key Terms Polynucleotide 3.1 BIOLOGICAL MOLECULES Condensation reaction MISSESTRUCH 2020 Phosphodiester bond Sugar-phosphate backbone Polynucleotides Hydrogen bonds The polymer of these nucleotides is called a polynucleotide. Complementary base pairs It is created via condensation reactions between the deoxyribose sugar and the phosphate group, creating a phosphodiester bond. Phosphodiester bonds are strong covalent bonds, and therefore help ensure that the genetic code is not broken down. The polynucleotide has a sugar-phosphate ‘backbone’. This describes the strong covalent bonds between the sugar and phosphate groups that hold the polymer together. The DNA polymer occurs in pairs, and these pairs are joined together by hydrogen bonds between the bases. This is how the double helix structure is created, as the two chains twist. Hydrogen bonds can only form between complementary base pairs. This is the term given to the fact that the base cytosine can only form hydrogen bonds with guanine and that adenine can only bond with thymine. Adenine and thymine form 2 hydrogen bonds, whereas cytosine and guanine can form 3 hydrogen bonds. This complementary base pairing is important to help maintain the order of the genetic code when DNA replicates, therefore reducing the chance of mutations. 26 MISSESTRUCH 2020 DNA & RNA Key Terms Ribose 3.1 BIOLOGICAL MOLECULES Uracil MISSESTRUCH 2020 How the DNA Structure Links to its Function Single-stranded mRNA tRNA Stable structure due to the sugar-phosphate backbone (covalent bonds) and the double helix to prevent damage. rRNA Double-stranded so replication can occur using one strand as a template. Weak hydrogen bonds for easy separation of the two strands in a double helix during replication. Large molecule to carry lots of genetic information. Complementary base pairing allows identical copies to be made. RNA RNA is a polymer of a nucleotide formed of ribose, a nitrogenous base and a phosphate group. The nitrogenous bases in RNA are adenine, guanine, cytosine and uracil. RNA has the base uracil instead of thymine. In comparison to the DNA polymer, the RNA polymer is a relatively short polynucleotide chain and it is single-stranded. Ribose The function of RNA is to copy and transfer the genetic code from DNA in the nucleus to the ribosomes. Some RNA is also combined with proteins to create ribosomes. There are three types of RNA; mRNA tRNA rRNA 27 MISSESTRUCH 2020 DNA & RNA Key Terms Single-stranded 3.1 BIOLOGICAL MOLECULES Messenger RNA (mRNA) Short-lived MISSESTRUCH 2020 Codon mRNA is a copy of a gene from DNA. mRNA is created in the nucleus and it then leaves the nucleus to carry the copy of the genetic code of one gene to a ribosome in the cytoplasm. DNA is too large to leave the nucleus and would be at risk of being damaged by enzymes, therefore destroying the genetic code permanently. mRNA is much shorter because it is only the length of one gene, and can therefore leave the nucleus as it is small enough to fit through the nuclear pores. mRNA is short-lived as it is only needed temporarily to help create a protein, therefore by the time any enzymes could break it down, it would have already carried out its function. mRNA is single-stranded and every 3 bases in the sequence code for a specific amino acid; these three bases are therefore called codons. 28 MISSESTRUCH 2020 DNA & RNA Key Terms Single-stranded 3.1 BIOLOGICAL MOLECULES Transfer RNA (tRNA) Cloverleaf shape MISSESTRUCH 2020 Anticodon tRNA is found only in the cytoplasm. It is single-stranded but folded to create a shape that looks like a cloverleaf shape. This cloverleaf shape is held in place by hydrogen bonds. The function of tRNA is to attach to one of the 20 amino acids and transfer this amino acid to the ribosome to create the polypeptide chain. Specific amino acids attach to specific tRNA molecules and this is determined by 3 bases found on the tRNA which are complementary to the 3 bases on mRNA. These are called the anticodon because they are complementary to the codon on mRNA. Ribosomal RNA (rRNA) rRNA is the type of RNA that makes up the bulk of ribosomes. The rest of a ribosome is made of protein. 80S ribosome 29 MISSESTRUCH 2020 DNA & RNA 3.1 BIOLOGICAL MOLECULES MISSESTRUCH 2020 DNA compared to RNA Differences between the DNA and RNA monomer: DNA contains the base thymine, whereas RNA contains uracil instead. DNA contains the pentose sugar deoxyribose, whereas RNA contains the pentose sugar ribose. Differences between the polymers: DNA is much larger because it contains approximately 23,000 genes (the entire genome), whereas RNA is much shorter because it is only the length of one gene. DNA is double-stranded, whereas RNA is single-stranded. 30 MISSESTRUCH 2020 DNA & RNA 3.1 BIOLOGICAL MOLECULES MISSESTRUCH 2020 Key Points DNA and RNA are both polymers made up of nucleotide monomers. The polymers are made via condensation reactions and phosphodiester bonds form between the nucleotides. There are three types of RNA: mRNA, tRNA and rRNA. Hydrogen bonds form between the two bases on different chains on DNA and on RNA where the chain folds. When comparing the differences, always have the comparison within the same sentence e.g DNA has thymine whereas RNA has uracil. Read comparison questions carefully, are you being asked to compare the monomers or polymers? Essay Links: The structure of DNA can link to the cell cycle (meiosis and mitosis) and DNA technology. The function of DNA can link to inheritance, natural selection and evolution. The importance of DNA can link to mutations and cancer. RNA structure and function can link to protein synthesis. 31 MISSESTRUCH 2020 DNA REPLICATION 3.1 BIOLOGICAL MOLECULES Key Terms Semi-conservative Complementary base pairs MISSESTRUCH 2020 Before cells divide (by mitosis or meiosis) all the DNA must DNA helicase DNA polymerase replicate to provide a copy for the new cell. The process of DNA replication is semi-conservative replication (in the daughter DNA, one strand is from the parental DNA and one strand is newly synthesised). This process relies on the complementary base pairs (cytosine + guanine and thymine + adenine) and involves the enzymes DNA helicase and DNA polymerase. There are four key stages to semi-conservative DNA replication. Step 1: DNA helicase breaks the hydrogen bonds between the complementary base pairs between the two stands within a double helix. This causes the DNA double helix to unwind. 32 MISSESTRUCH 2020 DNA REPLICATION 3.1 BIOLOGICAL MOLECULES Key Terms Template Complementary base pairs MISSESTRUCH 2020 Step 2: DNA helicase DNA polymerase Each of the separated parental DNA strands acts as a Phosphodiester bond template. Free-floating DNA nucleotides within the nucleus are attracted to their complementary base pairs on the template strands of the parental DNA. Step 3: The adjacent nucleotides are joined together (to form the phosphodiester bond) by a condensation reaction. DNA polymerase catalyses the joining together of adjacent nucleotides. Step 4 The two sets of daughter DNA (the name given to the new DNA molecules) contain one strand of the parental (original) DNA and one newly synthesised strand. 33 MISSESTRUCH 2020 DNA REPLICATION 3.1 BIOLOGICAL MOLECULES MISSESTRUCH 2020 Key points DNA replication is semi-conservative. DNA helicase breaks hydrogen bonds between bases to unwind the double helix. Free-floating DNA nucleotides in the nucleus are attracted to their complementary bases exposed on the template strands. DNA polymerase joins together adjacent nucleotides to make the new strand via condensation reactions Essay Links: DNA replication can link to the cell cycle (meiosis and mitosis) and DNA technology. DNA replication is when gene mutations occur which can lead to new phenotypes, therefore natural selection and evolution. Mutations can also result in cancer. 34 MISSESTRUCH 2020 WATER Key Terms Polar 3.1 BIOLOGICAL MOLECULES The Structure of Water Hydrogen bonds MISSESTRUCH 2020 Metabolite Solvent Water is an incredibly important biological High specific heat capacity molecule, which is why about 60-70% of your body Strong cohesion is water. Large latent heat of vaporisation Water is a polar molecule. 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 a slightly positive/negative on the diagram. Five Key Properties of Water Hydrogen bonds form between different water molecules between the oxygen and a hydrogen atom. The formation of these hydrogen bonds and the fact that water is dipolar results in 5 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, and 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. 35 MISSESTRUCH 2020 WATER Key Terms Metabolite 3.1 BIOLOGICAL MOLECULES Metabolite Hydrolysis MISSESTRUCH 2020 Polar Solvent Water is involved in many reactions, such as photosynthesis, Hydrophobic hydrolysis, and condensation reactions. Hydrophilic This is one reason why it is essential that approximately 90% of the plasma in the blood and the cytoplasm in cells is largely composed of water. Solvent Water is a good solvent, meaning many substances dissolve in it. Polar (or charged) molecules dissolve readily in water due to the fact water is polar. The slight positive charge on hydrogen atoms will attract any negative ions in 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. 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 through blood or xylem. 36 MISSESTRUCH 2020 WATER Key Terms High specific heat capacity 3.1 BIOLOGICAL MOLECULES Hydrogen bonds MISSESTRUCH 2020 High Specific Heat Capacity Denature Evaporate This means that a lot of energy is required to raise the Cooling effect temperature of the water. This is because some of the heat Sweating energy is used to break the hydrogen bonds between water molecules. This is useful to organisms as it means the temperature of the water remains relatively stable, even if the surrounding temperature fluctuates significantly. Therefore, the 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 enzymes do not denature or reduce 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 due to the hydrogen bonds, as energy is needed 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 during evaporation and this provides a cooling effect. 37 MISSESTRUCH 2020 WATER Key Terms Cohesion 3.1 BIOLOGICAL MOLECULES Strong Cohesion Surface tension MISSESTRUCH 2020 Continuous water column 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. Cohesion also provides surface tension to water. This enables small invertebrates to move and live on the surface, providing them with a habitat away from predators within the water. Key points Water is a polar molecule Hydrogen bonds form between water molecules. The polar nature and hydrogen bonds result in 5 key properties: metabolite, it is a solvent, strong cohesion, high specific heat capacity and a large latent heat of vaporisation. Essay Links: The strong cohesion links to transpiration in plants. Water is a good solvent links to mass transport in plants and animals. Water as a metabolite links to many key reactions, such as photosynthesis and respiration. 38 MISSESTRUCH 2020 ATP & INORGANIC IONS Key Terms 3.1 BIOLOGICAL MOLECULES ATP synthase MISSESTRUCH 2020 ATP Immediate energy source ATP hydrolase Inorganic phosphate ATP, or Adenosine Triphosphate, is an immediate source of energy for biological processes. Metabolic reactions in cells must have a constant, steady supply of ATP. ATP contains three phosphate ions that play a significant role in energy transfer. This biological molecule is essential to metabolism, which is all the chemical reactions that take place in a cell. ATP is comprised of: Adenine is a nitrogenous base (meaning a base that contains nitrogen) Ribose (a pentose sugar) Three inorganic phosphate groups. The phosphate groups are described as being inorganic because they do not contain any carbon atoms. For this reason in chemical reactions the symbol to represent this is a P for phosphate and i for inorganic -Pi ATP is made during respiration from ADP, adenosine diphosphate, by the addition of an inorganic phosphate via a condensation reaction which uses the enzyme ATP synthase. ATP can be hydrolysed into ADP + Pi using the enzyme ATP hydrolase. ATP + water --> ADP +Pi (energy) By breaking one of the bonds between the inorganic phosphate groups in a hydrolysis reaction, a small amount of energy is released to the surroundings, which can be used in chemical reactions. Therefore, ATP is an immediate energy source as only one bond has to be hydrolysed to release energy. 39 MISSESTRUCH 2020 ATP & INORGANIC IONS 3.1 BIOLOGICAL MOLECULES Key Terms Immediate energy source Phosphorylation MISSESTRUCH 2020 Phosphorylation Soluble Hydrolysis ATP can also transfer energy to different compounds. The inorganic phosphate released during the hydrolysis of ATP can be bonded onto different compounds to make them more reactive. This is known as phosphorylation, and this happens to glucose at the start of respiration to make it more reactive. There are five key properties of ATP that make it a suitable immediate source of energy. In exam questions, the properties of ATP and glucose can be compared to emphasise the importance of ATP as the immediate source of energy for cells rather than glucose. This is explained and demonstrated in the five points below. 1. ATP releases energy in small, manageable amounts so no energy is wasted. This means that cells do not overheat from wasted heat energy and cells are less likely to run out of resources. In comparison to glucose, this would release large amounts of energy that could result in wasted energy. 2. It is small and soluble so it is easily transported around the cell. ATP can move around the cytoplasm with ease to provide energy for chemical reactions within the cell. This is a property ATP has in common with glucose. 3. Only one bond is hydrolysed to release energy, which is why energy release is immediate. Glucose would need several bonds to be broken down to release all its energy. 4. It can transfer energy to another molecule by transferring one of its phosphate groups. ATP can enable phosphorylation, making other compounds more reactive. Glucose cannot do this, as it does not contain phosphate groups. 5. ATP can’t pass out of the cell; the cell always has an immediate supply of energy. ATP cannot leave the cell, whereas glucose can. This means that all cells have a constant supply of ATP (or ADP + Pi), but a cell can run out of glucose. 40 MISSESTRUCH 2020 ATP & INORGANIC IONS Key Terms 3.1 BIOLOGICAL MOLECULES Inorganic Ions Dissolve Solutions MISSESTRUCH 2020 Inorganic ions dissolve to form solutions found within the cytoplasm of cells and other body fluids. Some inorganic ions are required in high concentrations, whereas others are required in very low concentrations. Each inorganic ion performs a different function and this is due to their different properties. You need to know the role of: Hydrogen Ions – how they determine pH (linked to enzymes) Iron ions – a compound of haemoglobin (linked to the transport of oxygen) Sodium ions – involved in co-transport (linked to the absorption of glucose and amino acids in the ileum) Phosphate ions – as a component of DNA and ATP (linked to nucleotides and nucleotide derivatives) Key points ATP is a nucleotide derivative, made of adenine, ribose and 3 phosphate groups. ATP is the immediate source of energy for a cell. Phosphorylation is the addition of an inorganic phosphate to a molecule, transferring energy to that molecule. Inorganic ions dissolve in solutions and perform different functions. Essay Links: Beyond the spec: Cholera release toxins affecting chloride ion channels. This lowers the water potential of the small intestine's lumen causing diarrhoea. Links to respiration, as glucose is phosphorylated in glycolysis. Links to respiration as ADP is phosphorylated to ATP in oxidative phosphorylation. Links to muscle contraction, as ATP is required in the sliding filament theory. Links to active transport (resting potential, co-transport in the phloem, absorption of glucose) which requires ATP. 41 MISSESTRUCH 2020 Image Credits: https://en.wikipedia.org/wiki/File:Lock_and_key.png https://commons.wikimedia.org/wiki/File:Carbonic_anhydrase_reaction_in_tissue.svg https://commons.wikimedia.org/wiki/File:Induced_fit_diagram.svg https://commons.wikimedia.org/wiki/File:CNX_Chem_12_07_Enzyme.png https://commons.wikimedia.org/wiki/File:Main_protein_structure_levels_en.svg https://commons.wikimedia.org/wiki/File:Q10_graph_c.svg https://commons.wikimedia.org/wiki/File:Effect_of_pH_on_enzymes.svg https://commons.wikimedia.org/wiki/File:Allosteric_competitive_inhibition_3.svg https://commons.wikimedia.org/wiki/File:Competitive_inhibition.svg https://commons.wikimedia.org/wiki/File:220_Triglycerides-01.jpg https://commons.wikimedia.org/wiki/File:221_Fatty_Acids_Shapes-01.jpg https://commons.wikimedia.org/wiki/File:Figure_05_01_02.jpg https://commons.wikimedia.org/wiki/File:0302_Phospholipid_Bilayer.jpg https://commons.wikimedia.org/wiki/File:1904_Hemoglobin.jpg https://commons.wikimedia.org/wiki/File:Figure_03_04_09.jpg https://commons.wikimedia.org/wiki/File:DNA_chemical_structure.svg https://www.flickr.com/photos/gemmerich/7445337412 https://commons.wikimedia.org/wiki/File:Difference_DNA_RNA-EN.svg https://www.needpix.com/photo/89414/nucleotide-dna-pyrimidine-rna-biology-chemical-chemistry-science https://commons.wikimedia.org/wiki/File:OSC_Microbio_10_03_tRNA.jpg https://commons.wikimedia.org/wiki/File:Process_of_transcription_(13080846733).jpg https://commons.wikimedia.org/wiki/File:OSC_Microbio_11_04_tRNA.jpg https://commons.wikimedia.org/wiki/File:OSC_Microbio_03_03_Ribosome.jpg Image Credits: https://commons.wikimedia.org/wiki/File:DNA_replication_split.svg https://commons.wikimedia.org/wiki/File:0323_DNA_Replication.jpg Image Credits: https://commons.wikimedia.org/wiki/File:Hydrogen-bonding-in-water-2D.png https://commons.wikimedia.org/wiki/File:Simple_Polysaccharide_Hydrolysis.png https://commons.wikimedia.org/wiki/File:NaCl_dissolving.png https://en.wikipedia.org/wiki/Egg_white https://commons.wikimedia.org/wiki/File:Sweating_at_Wilson_Trail_Stage_One_1.jpg https://www.flickr.com/photos/gails_pictures/6878227730 Image Credits: https://commons.wikimedia.org/wiki/File:ATP_chemical_structure.png https://commons.wikimedia.org/wiki/File:230_Structure_of_Adenosine_Triphosphate_(ATP)-01.jpg