Module 1 - Biological Molecules PDF

Module 1 -- Biological Molecules **1.1 - Introduction to Biological Molecules** 1. **The different types of biological molecules ** 2. **The difference between monomers and polymers ** 3. **The difference between condensation and hydrolysis reactions ** **Types of biological molecules ** Th...

Module 1 -- Biological Molecules **1.1 - Introduction to Biological Molecules** 1. **The different types of biological molecules ** 2. **The difference between monomers and polymers ** 3. **The difference between condensation and hydrolysis reactions ** **Types of biological molecules ** The cells of all living organisms primarily consist of four types of molecules: carbohydrates, lipids, proteins, and nucleic acids. These biological molecules are organic, meaning they contain the element carbon. **These molecules also contain additional elements:** - **Carbohydrates **- Carbon (C), hydrogen (H), and oxygen (O). - **Lipids **- Carbon (C), hydrogen (H), and oxygen (O). - **Proteins **- Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). - **Nucleic acids** - Carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P). +-----------------------------------------------------------------------+ | **Monomers and polymers** | | | | Most carbohydrates, proteins, and nucleic acids are polymers made up | | of small units known as monomers. | | | | - **Monomer **- Smaller units that combine to make a large molecule | | (polymer).  | | | | | | | | - **Polymer **- Large molecule made up of many monomers joined | | together.  | +=======================================================================+ | The process by which monomers join to form a polymer is known as | | polymerisation. | | | | Diagram showing monomers combining to form a polymer through | | polymerisation. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ |  | +=======================================================================+ | **Condensation and hydrolysis reactions ** | | | | Most polymers are synthesised via a condensation reaction and broken | | down via a hydrolysis reaction.  | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | Diagram showing a condensation reaction where two molecules form a | | bond and release water. | | | | **Condensation **- The removal of water to form a chemical | | bond between two molecules.  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ |  | | | | **Hydrolysis **- The addition of water to break a chemical | | bond between two molecules.  | +-----------------------------------------------------------------------+ **1.2 - Carbohydrates: Introduction** 1. **The elements that carbohydrates contain** 2. **The role of carbohydrates in living organisms** 3. **The different types of carbohydrates** +-----------------------------------------------------------------------+ | **What are carbohydrates?** | | | | Carbohydrates are biological molecules that contain the | | elements carbon (C), hydrogen (H), and oxygen (O).  | | | | 1. **\'Carbo\' **- Contains the element carbon. | | | | 2. **\'Hydrate\' **- Contains hydrogen and oxygen atoms, typically | | in a ratio of 2:1 like water (H~2~O) in most simple | | carbohydrates. | | | | The general formula for a carbohydrate is C~x~(H~2~O)~y~. | +-----------------------------------------------------------------------+ **Roles of carbohydrates** **Functions of carbohydrates in living organisms:** 1. **Energy supply for cells** - This is the main role of carbohydrates.  2. **Energy storage** - Sugars can be stored as complex carbohydrates (e.g. starch or glycogen).  3. **Structural components **- Cellulose and chitin are used in cell walls.  4. **Cellular recognition **- Glycoproteins help cells identify each other and communicate.  5. **Building blocks for biological molecules **- Deoxyribose and ribose can be used to make nucleic acids. **Types of carbohydrates** There are three types of carbohydrates: monosaccharides, disaccharides, and polysaccharides.  Table showing types of carbohydrates including monosaccharides, disaccharides, and polysaccharides with examples and functions. **1.3 - Carbohydrates: Monosaccharides & Disaccharides** 1. **The different types of monosaccharides** 2. **The difference between alpha and beta glucose** 3. **The different types of disaccharides** 4. **The reactions which form and break down disaccharides** +-----------------------------------------------------------------------+ | **Monosaccharides** | | | | Monosaccharides are the simplest form of carbohydrates, also known as | | \'simple sugars\'. Monosaccharides are soluble, sweet-tasting and are | | found in many foods such as fruits, vegetables, and grains. | | | | They have the general formula (CH~2~O)~n ~where \'n\' can be any | | number from 3 to 7. | +=======================================================================+ | **Monosaccharides are classified according to the number of carbon | | atoms in each molecule:** | | | | Hexose sugars (6 carbon atoms) | | | | - Glucose | | | | - Fructose | | | | - Galactose  | | | | Pentose sugars (5 carbon atoms) | | | | - Ribose | | | | - Deoxyribose | +-----------------------------------------------------------------------+ | **Alpha-glucose and beta-glucose ** | | | | Glucose is a hexose (6-carbon) sugar with the formula C~6~H~12~O~6~. | | The atoms in glucose can be arranged in two different ways. | | | | **This means that there are two isomers of glucose: ** | | | | 1. Alpha-glucose (α-glucose) | | | | 2. Beta-glucose (β-glucose) | | | |  | | | | The only difference between the two forms is the orientation of the | | hydroxyl group (OH) on carbon 1 (the first carbon atom in the ring). | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | Diagram showing the structures of alpha-glucose and beta-glucose with | | the difference in the orientation of the hydroxyl group on carbon 1. | | | | This diagram is showing the same molecules, but shows all the atoms.  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Properties and uses of glucose** | | | | Glucose is used as the primary energy source in animals and plants. | | | | **The following features of glucose help it to function as an energy | | source: ** | | | | 1. **It is soluble **- The hydroxyl groups can form hydrogen bonds | | with water, so it can be transported around organisms. | | | | 2. **Its bonds store lots of energy** - This energy is released when | | the bonds are broken. | +-----------------------------------------------------------------------+ **Disaccharides** Disaccharides are formed when two monosaccharides join together. Examples of disaccharides include maltose (found in grains and cereals), sucrose (used as a transport sugar in plants), and lactose (the main carbohydrate found in milk).  - Maltose is made up of glucose joined to glucose. Diagram showing the structure of sucrose with glucose and fructose molecules. - Sucrose is made up of glucose joined to fructose.  - Lactose is made up of glucose joined to galactose. +-----------------------------------------------------------------------+ | **Disaccharide formation and breakdown** | | | | Disaccharides are created via condensation reactions, and broken down | | via hydrolysis reactions. These reactions involve the formation or | | the breakdown of a covalent bond known as a glycosidic bond. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Condensation reaction** | | | | Diagram showing disaccharide formation and breakdown with glycosidic | | bond formation and water release. | | | | When two monosaccharides join, a hydroxyl group (OH) of one | | monosaccharide reacts with a hydroxyl group (OH) of another | | monosaccharide. This forms a glycosidic bond, and a water molecule | | (H~2~O) is released. | | | | In the image above, the hydroxyl groups on carbons 1 and 4 are | | reacting together, so a 1-4 glycosidic bond forms, but they can also | | form between other carbons. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Hydrolysis reaction** | | | |  | | | | When a water molecule (H~2~O) is added to a disaccharide, the | | glycosidic bond is broken to release the 2 monosaccharides. | +-----------------------------------------------------------------------+ **1.4 - Carbohydrate: Polysaccharides** 1. **The different types of polysaccharides: starch, glycogen, and cellulose ** 2. **How their structures relate to their functions** **Polysaccharides** Polysaccharides are complex carbohydrates made up of many monosaccharides joined via glycosidic bonds. Examples of polysaccharides include starch, glycogen, and cellulose.  Diagram showing the structures of polysaccharides including unbranched starch, branched starch, glycogen, and cellulose. +-----------------------------------------------------------------------+ | **Starch** | | | | Starch is an example of a polysaccharide used by plants to store | | excess glucose. This means that starch can be hydrolysed back into | | glucose when plants require energy. | | | |  | | | | Starch is made up of many alpha-glucose monomers joined via 1-4 and | | 1-6 glycosidic bonds to form chains. These chains come in two forms: | | unbranched and branched.   | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **The following features allow starch to work well as a store of | | energy: ** | | | | 1. **Insoluble **-  It does not affect the water potential of the | | cell, so water is not drawn in by osmosis.  | | | | 2. **Large** - It cannot diffuse out of cells. | | | | 3. **Many side branches **- These allow enzymes to hydrolyse the | | glycosidic bonds easily to rapidly release glucose.  | | | | 4. **Coiled **- This makes it compact so that a lot of glucose can | | be stored in a small space.  | | | | 5. **Hydrolysis releases alpha-glucose monomers** - These are | | readily used in respiration. | +=======================================================================+ | **Glycogen** | | | | Glycogen is an example of a polysaccharide used by animals to store | | excess glucose. This means that glycogen can be hydrolysed back into | | glucose when animals require energy. | | | | Glycogen is very similar to starch, but it is used by animals rather | | than plants. | | | | Diagram showing the branched structure of glycogen with alpha-glucose | | monomers. | | | | Glycogen is made up of many alpha-glucose monomers joined via 1-4 and | | 1-6 glycosidic bonds to form highly branched chains. | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **The following features allow glycogen to function as a store of | | energy:** | | | | 1. **Insoluble **- It does not affect the water potential of cells, | | and so water does not enter cells by osmosis.  | | | | 2. **Compact **- A lot of glucose can be stored in a small space.  | | | | 3. **More highly branched than starch **- Enzymes can easily | | hydrolyse the glycosidic bonds to rapidly release glucose.  | | | | 4. **Large **- It cannot diffuse out of cells. | | | | 5. **Hydrolysis releases alpha-glucose monomers** - These are | | readily used in respiration. | +=======================================================================+ | **Cellulose ** | | | | Cellulose is a polysaccharide formed from beta-glucose. Its primary | | use is to provide structural support for plant cell walls. | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ | Every other beta-glucose molecule must flip upside down | | | |  | | | | Cellulose is made up of many beta-glucose monomers joined together | | via glycosidic bonds. However, if two beta-glucose monomers line up | | next to each other, the hydroxyl groups on carbon 1 and carbon 4 are | | too far from each other to react.  | +-----------------------------------------------------------------------+ | To fix this, every other beta-glucose molecule is inverted by | | 180° (flipped upside down). This brings the hydroxyl groups (OH) | | close enough together to react. | | | | Diagram showing beta-glucose and inverted beta-glucose molecules | | close enough to react. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Many beta-glucose form long straight chains** | | | | When many beta-glucose monomers join together they form | | long, straight, unbranched chains. The alternating inversion of the | | beta glucose molecules also allows for hydrogen bonds to form between | | individual chains. Although each hydrogen bond itself is relatively | | weak, the huge number of these bonds provides great strength to | | cellulose as a whole. | | | |  | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Cellulose chains, microfibrils, and macrofibrils** | | | | Multiple cellulose chains become tightly cross linked via hydrogen | | bonds to form bundles called microfibrils. | | | | These microfibrils join together to make macrofibrils which combine | | to make strong cellulose fibres in the plant cell wall. | | | | Diagram showing the structure of cellulose including cellulose | | chains, microfibrils, and macrofibrils in a plant cell wall. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Adaptations of cellulose for its role** | | | | **The structure of cellulose is well adapted to its role:** | | | | 1. **Long, straight, and unbranched chains** - These provide | | rigidity to the cell wall. | | | | 2. **Hydrogen bonds** - These cross link the chains to add | | collective tensile strength. | | | | 3. **Microfibrils **- These provide additional strength. | +-----------------------------------------------------------------------+ | **Comparing starch, glycogen, and cellulose** | | | |  | +-----------------------------------------------------------------------+ **1.5 - Carbohydrates: Tests** 1. **The difference between reducing sugars and non-reducing sugars** 2. **How to test for reducing sugars (Benedict\'s reagent)** 3. **How to test for non-reducing sugars ** 4. **How to test for starch (iodine)** +-----------------------------------------------------------------------+ | **Testing for reducing sugars** | | | | All sugars can be grouped into two categories. | | | | **These categories are reducing sugars and non-reducing sugars:** | | | | - Reducing sugars include all monosaccharides and some | | disaccharides such as maltose and lactose. | | | | - Non-reducing sugars include some disaccharides such as sucrose | | and all polysaccharides. | +=======================================================================+ | **Steps to find out whether a sample contains a reducing sugar: ** | | | | 1. Place 2 cm^3^ of your food sample into a test tube. | | | | 2. Add an equal volume of Benedict\'s reagent. | | | | 3. Heat the mixture in a gently boiling water bath for 5 minutes. | | | | 4. If a reducing sugar is present, the mixture will change from a | | blue solution to a brick red precipitate. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Determining the concentration of reducing sugars** | | | | A positive result will form a brick red precipitate, however the | | colour seen is a mixture of the precipitate and the blue Benedict\'s | | reagent. | | | | **The concentration of reducing sugar determines the colour of this | | mixture:** | | | | - **Blue** - This indicates no reducing sugar is present. | | | | - **Green **- This indicates a low concentration. | | | | - **Orange** - This indicates a medium concentration. | | | | - **Brick-red** - This indicates a high concentration. | | | | This allows you to compare the concentration of reducing | | sugar between different samples. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Quantitative methods to determine concentration of reducing | | sugars** | | | | **More accurate methods for comparison: ** | | | | - Use a colorimeter to measure the absorbance of each solution. | | | | - Filter the solution and weigh the precipitate. | +-----------------------------------------------------------------------+ | **Testing for non-reducing sugars** | | | | Non-reducing sugars give a negative result (blue solution) for the | | normal reducing sugars test. To test for these types of sugars, you | | must first hydrolyse them into their monosaccharide components before | | we can do the rest of the test.  | | | | **Steps to find out whether a sample contains a non-reducing | | sugar: ** | | | | 1. Carry out the test for reducing sugars, and if the result is | | negative (turns blue), continue with the next steps. | | | | 2. Add 2 cm3 of the food sample to 2 cm3 of dilute hydrochloric | | acid. | | | | 3. Heat the mixture in a gently boiling water bath for 5 minutes | | (the acid will hydrolyse disaccharides into monosaccharides). | | | | 4. Neutralise the mixture by adding sodium hydrogencarbonate | | solution. | | | | 5. Retest this mixture using the test for reducing sugars. | | | | 6. If non-reducing sugars were present at the start, the mixture | | will now change from a blue solution to a brick red precipitate. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Testing for starch** | | | |  | | | | To find out if a sample contains starch, you must carry out | | the iodine test. | | | | **Steps to find out whether a sample contains starch:** | | | | 1. Place 2 cm^3^ of your food sample into a test tube. | | | | 2. Add a couple of drops of iodine solution and shake. | | | | 3. If starch is present, the solution will turn from orange | | to blue-black. | +-----------------------------------------------------------------------+ [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_aXfyfdlE)**1.6 - Lipids: Introduction** 1. **The roles of lipids in living organisms** 2. **The difference between saturated and unsaturated fatty acids** 3. **How to test for lipids** +-----------------------------------------------------------------------+ | **What are lipids?** | | | | Lipids are biological molecules that contain the elements carbon (C), | | hydrogen (H), and oxygen (O). However, lipids contain a much lower | | proportion of oxygen than carbohydrates. | | | | Lipids are not made up of long chains of monomers, meaning they are | | not considered as polymers. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Roles of lipids** | | | | **The main functions of lipids:** | | | | 1. **Energy supply** - Lipids can be oxidised to provide energy to | | cells. | | | | 2. **Structural components** - Phospholipids are used in cell | | membranes. | | | | 3. **Waterproofing **- Insoluble lipids are used to form | | water-resistant barriers. | | | | 4. **Insulation **- Lipids can help retain heat or act as electrical | | insulators. | | | | 5. **Protection **- Delicate organs are surrounded by a layer of | | fat. | +=======================================================================+ | **Fatty acids** | | | | Most lipids are made up of fatty acids combined with an alcohol | | (usually glycerol).  | | | | A diagram of a group of letters and numbers Description automatically | | generated | | | | Fatty acids consist of a carboxyl group (-COOH) attached to | | a hydrocarbon chain (R group). | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Saturated fatty acids and unsaturated fatty acids** | | | | There are two types of fatty acid: saturated fatty acids | | and unsaturated fatty acids. | | | | **Saturated fatty acids:** | | | | - These have hydrocarbon chains that are \'saturated\' with | | hydrogen, meaning all carbon atoms are bonded to the maximum | | number of hydrogen atoms. | | | | - The hydrocarbon chain has no carbon-carbon double bonds.  | | | | - Lipids that contain saturated fatty acids have higher melting | | points and so are usually solid at room temperature (fats). | | | |  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Unsaturated fatty acids:** | | | | - These have hydrocarbon chains that do not contain the maximum | | number of hydrogen atoms bonded to the carbon atoms. | | | | - The hydrocarbon chain has at least one carbon-carbon double bond, | | which causes the chain to kink. | | | | - Lipids that contain unsaturated fatty acids have lower melting | | points and so are usually liquid at room temperature (oils). | | | | A diagram of a molecule Description automatically generated | | | | **Unsaturated fatty acids may either be monounsaturated or | | polyunsaturated:** | | | | - **Monounsaturated **- One double bond. | | | | - **Polyunsaturated **- Two or more double bonds. | +-----------------------------------------------------------------------+ **Testing for lipids ** To find out whether a sample contains lipids, you must carry out the emulsion test.  **Steps to find out whether a sample contains lipids:** 1. Place your food sample in a test tube. 2. Add 2 cm^3^ of ethanol. 3. Shake. 4. Add 2 cm^3 ^of distilled water. 5. If lipids are present, a milky white emulsion will appear. [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_FBXPuCCB) **1.7 - Lipids: Triglycerides & Phospholipids** 1. **The structure and function of triglycerides ** 2. **The synthesis and breakdown of triglycerides ** 3. **The structure and function of phospholipids** 4. **The similarities and differences between triglycerides and phospholipids** +-----------------------------------------------------------------------+ | **Triglycerides** | | | | A triglyceride is a type of lipid used as a store of energy in | | animals, plants, and some bacteria. | | | | A screenshot of a video game Description automatically generated | | | | The left diagram is a simplified version of a triglyceride. The | | diagram on the right shows the atoms a triglyceride is made up of.  | | | | A triglyceride consists of a glycerol backbone attached to three | | fatty acid tails. Each fatty acid tail contains a hydrocarbon chain | | (R) which can vary in length and may be saturated or unsaturated. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Features that allow triglycerides to store energy efficiently: ** | | | | 1. **Long hydrocarbon tails **- Their many carbon-hydrogen bonds can | | be broken to release energy. | | | | 2. **Low mass to energy ratio** - Lots of energy can be stored in a | | small volume. | | | | 3. **Insoluble **- They do not affect the water potential of cells | | as they are large and non-polar. | | | | 4. **High ratio of hydrogen to oxygen atoms** - Triglycerides will | | release water when oxidised. | +=======================================================================+ | **Triglyceride formation and breakdown** | | | | Triglycerides are synthesised via condensation reactions and broken | | down via hydrolysis reactions. These reactions involve the formation | | or the breakdown of covalent bonds known as ester bonds. | +-----------------------------------------------------------------------+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Condensation reaction** | | | |  | | | | **Condensation:** | | | | - The hydroxyl groups (OH) on the glycerol and on the three fatty | | acids react together to release three water molecules (H~2~O). | | | | - This results in three ester bonds between the glycerol and the | | fatty acids. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Hydrolysis reaction ** | | | | Diagram showing the formation and breakdown of triglycerides, | | highlighting ester bonds, hydrolysis, and condensation reactions. | | | | **Hydrolysis:** | | | | - The addition of three water molecules (H~2~O) breaks the ester | | bonds. | | | | - This separates the glycerol and the fatty acids. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Phospholipids** | | | | A phospholipid is a type of lipid used as a | | structural component of the cell membrane.  | | | | They are similar to triglycerides except one of the fatty acid | | tails is replaced by a phosphate group. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Phospholipids are polar ** | | | | **A phospholipid is made up of two parts: ** | | | | 1. **A hydrophilic \'head\'** - This contains glycerol and | | phosphate. | | | | 2. **A hydrophobic \'tail\'** - This contains fatty acids. | | | | A cartoon of a hydrant Description automatically generated | | | | The phosphate group is polar and so attracts water (hydrophilic) | | whereas the fatty acid tails repel water (hydrophobic). | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Phospholipid bilayer ** | | | | When phospholipids are placed in water, they arrange themselves into | | a double layer (bilayer) so that the hydrophilic heads are facing out | | (towards the water) and the hydrophobic tails are facing in (away | | from the water).  | | | |  | | | | This arrangement creates a hydrophobic centre in the bilayer so that | | water-soluble substances cannot pass through. | +-----------------------------------------------------------------------+ **Comparing triglycerides and phospholipids ** A screenshot of a computer Description automatically generated [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_DbBeGgLg)**1.8 - Proteins: Amino Acids** 1. **The roles of proteins in living organisms ** 2. **The structure of amino acids ** 3. **The synthesis and breakdown of peptide bonds** 4. **How to test for proteins** +-----------------------------------------------------------------------+ | **Proteins are made up of amino acids** | | | | Amino acids are the building blocks of proteins, which are essential | | macromolecules involved in various functions within living organisms. | | | | Amino acids are monomers and can join together via peptide bonds to | | form dimers (dipeptides) and polymers (polypeptides).  | | | |  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **What are the roles of proteins?** | | | | **Functions of proteins in living organisms:** | | | | 1. **Enzymes **- These proteins are used to breakdown and synthesise | | molecules. | | | | 2. **Antibodies **- These proteins are involved in the immune | | response. | | | | 3. **Transport **- Some proteins can move molecules or ions across | | membranes. | | | | 4. **Structural components** - Proteins like keratin and collagen | | are used to create strong fibres. | | | | 5. **Hormones **- Some of these are proteins that act as chemical | | messengers in the body. | | | | 6. **Muscle contraction** - Muscles are made up of proteins. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Amino acid structure** | | | | There are around 20 different amino acids that are commonly found in | | living organisms.  | | | | A diagram of chemical formulas Description automatically generated | | with medium confidence | | | | **They all have the same general structure:** | | | | - A central carbon atom | | | | - An amino group (-NH~2~) | | | | - A carboxyl group (-COOH) | | | | - A hydrogen atom (-H) | | | | - An R group or a variable side group | | | | Each amino acid has a different R group which determines its | | properties. For example, amino acid cysteine contains a sulphur atom | | in its R group. This allows cysteine to form disulphide bonds. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Dipeptide synthesis and breakdown** | | | | Dipeptides are synthesised via condensation reactions and broken down | | via hydrolysis reactions. These reactions involve the formation or | | the breakdown of a covalent bond known as a peptide bond. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Condensation reaction ** | | | |  | | | | When two amino acids join, the hydroxyl (OH) in the carboxyl group of | | one amino acid reacts with the hydrogen (H) in the amino group of | | another amino acid. This releases a water molecule (H~2~O) and forms | | a peptide bond between the carbon of one amino acid and the nitrogen | | of another.  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Hydrolysis reaction** | | | | Diagram showing the synthesis and breakdown of a dipeptide, including | | condensation and hydrolysis reactions. | | | | When a water molecule (H~2~O) is added to a dipeptide, the peptide | | bond is broken to release the two amino acids. | +-----------------------------------------------------------------------+ **Testing for proteins** To find out whether a sample contains peptide bonds (and hence, proteins), you must carry out the Biuret test.  ** Steps to find out whether a sample contains proteins:** 1. Place your food sample in a test tube. 2. Add an equal volume of Biuret solution (sodium hydroxide and copper sulfate). 3. If proteins are present, the solution will turn from blue to purple. If no protein is present, the solution remains blue. [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_rRkuYteB) **1.9 - Proteins: Structures** 1. **The primary, secondary, tertiary, and quaternary structures of proteins ** 2. **The different types of bonds found within each structure ** **Proteins have complex 3D structures** Proteins are large, complex molecules with unique 3D structures. It\'s this unique structure that allows them to carry out their specific function. **We can think of protein structure in four main levels:** 1. Primary 2. Secondary 3. Tertiary 4. Quaternary Each level has specific bonds that hold it together and influence the overall shape. +-----------------------------------------------------------------------+ | **Primary structure** | | | | A diagram of a molecule Description automatically generated with | | medium confidence | | | | The primary structure is made up of the unique sequence of amino | | acids in the polypeptide chain. This structure is held together by | | peptide bonds. A change to just one of the amino acids in this chain | | can result in a change to the protein\'s structure and function. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Secondary structure** | | | |  | | | | The secondary structure involves hydrogen bonds forming between the | | amino group of one amino acid and the carboxyl group of another amino | | acid further down the chain. This causes the polypeptide chain to | | coil into either an alpha-helix or a beta-pleated sheet structure. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Tertiary structure** | | | | Diagram of a protein structure showing hydrogen bonds, ionic bonds, | | disulfide bridges, and hydrophobic interactions. | | | | The tertiary structure forms when the polypeptide chain folds and | | twists further to create a complex 3D structure. | | | | **This specific structure is held together by many bonds, | | including: ** | | | | - **Hydrogen bonds** - These are individually weak but provide | | strength in large numbers. | | | | - **Ionic bonds **- These form between positive and negative R | | groups. | | | | - **Disulfide bridges** - These form between R groups that contain | | sulphur (such as cysteine). | | | | - **Hydrophobic and hydrophilic interactions** - These are weak | | interactions between polar and non-polar R groups. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Quaternary structure ** | | | |  | | | | The quaternary structure involves two or more polypeptide chains held | | together by the same bonds found in the tertiary structure of a | | protein (hydrogen bonds, ionic bonds, disulfide bridges, and | | hydrophobic and hydrophilic interactions). | | | | It can also involve the addition of non-protein groups known | | as prosthetic groups. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Not all proteins have a quaternary structure** | | | | It is important to understand that although all proteins have | | primary, secondary, and tertiary structures, only some proteins have | | a quaternary structure. | | | | This means that some proteins consist of a single polypeptide chain, | | but others are made up of multiple chains combined.  | +-----------------------------------------------------------------------+ **Comparing protein structures** Diagram comparing primary, secondary, tertiary, and quaternary protein structures including descriptions and bond types. [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_XeBaESPz) **1.10 - Enzyme Action** 1. **The role of enzymes in living organisms ** 2. **How enzymes speed up reactions** 3. **The lock and key model of enzyme action** 4. **The induced-fit model of enzyme action ** +-----------------------------------------------------------------------+ | **Enzymes are biological catalysts** | | | | Enzymes are globular proteins with complex and unique tertiary | | structures. | | | | They are known as biological catalysts because they increase the rate | | of a chemical reaction without being used up in the reaction itself.  | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Enzymes speed up reactions** | | | | All chemical reactions require a certain amount of energy to get | | started. This is known as the activation energy, and is most often | | supplied in the form of heat.  | | | | Without sufficient activation energy, the reactant molecules will not | | have enough energy to break their bonds and form new ones to produce | | the desired products.* * | | | |  | +=======================================================================+ | Enzymes work by lowering the activation energy for a chemical | | reaction. This means that reactions are able to take place at a lower | | temperature (e.g. body temperature).  | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Intracellular enzymes and extracellular enzymes** | | | | Enzymes can be grouped into two categories: intracellular enzymes and | | extracellular enzymes. | | | | **Differences between intracellular enzymes and extracellular | | enzymes:** | | | | - **Intracellular enzymes** - These act within the cells that | | produce them. | | | | - **Extracellular enzymes** - These act outside the cells that | | produce them, and are secreted. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Enzymes bind with substrates** | | | | Diagram showing the process of enzyme binding with substrates, | | forming an enzyme-substrate complex and resulting in products. | | | | Enzymes have unique tertiary structures which determine the shape of | | their active site. | | | | This shape is complementary to the substrate.  | | | |  | | | | The substrate binds to the active site to form an enzyme-substrate | | complex. | | | | Illustration showing the process of enzymes binding with substrates, | | forming an enzyme-substrate complex and then producing products. | | | | Temporary bonds form between the R groups within the active site and | | the substrate. | | | | These bonds lower the activation energy to help break down the | | substrate into products. | | | |  | | | | -- -- -- | | | | -- -- -- | +-----------------------------------------------------------------------+ The products are released from the active site, leaving the enzyme free to be used again. +-----------------------------------------------------------------------+ | **Two models of enzyme action** | | | | Scientists originally proposed the lock and key hypothesis to explain | | how enzymes work. More recent evidence has given rise to the | | induced-fit model.   | +=======================================================================+ | **The lock and key model** | | | | Illustration showing the lock and key model of enzyme action where | | the substrate fits perfectly into the enzyme\'s active site. | | | | In this model, the substrate fits perfectly into the enzyme\'s active | | site in the same way that a key fits into a lock. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Induced fit model** | | | |  | | | | In this model, the substrate does not fit perfectly into the | | enzyme\'s active site. As the substrate enters the enzyme, the active | | site changes shape slightly. This puts a strain on the substrate\'s | | bonds which lowers the activation energy. | +-----------------------------------------------------------------------+ [\ ](https://cognitoedu.org/coursesubtopic/b3-alevel-aqa_dqLsrHVN) **1.11 - Factors Affecting Enzyme Action** 1. **What happens when an enzyme is denatured** 2. **The effects of temperature and pH on enzyme-catalysed reactions** 3. **The effects of enzyme and substrate concentration on enzyme-catalysed reactions** +-----------------------------------------------------------------------+ | **Enzyme denaturation** | | | | Changes in temperature or pH can affect the rate of enzyme-catalysed | | reactions. | +=======================================================================+ | Diagram showing enzyme denaturation where changes in temperature or | | pH cause the active site to change shape, preventing substrate | | binding. | | | | Drastic temperature increases or changes to the pH causes bonds to | | break, changing the enzyme\'s tertiary structure. | | | | This causes the active site to change shape so that the substrate no | | longer fits. This means that enzyme-substrate complexes cannot be | | formed and the enzyme is denatured.  | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Different factors affect the rate of enzyme-controlled reactions** | | | | You need to be able to describe and explain how the four factors | | affect enzyme reactions. | | | | **These factors are:** | | | | 1. Temperature  | | | | 2. pH | | | | 3. Substrate concentration  | | | | 4. Enzyme concentration | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ |  | | | | **Temperature** | | | | All enzymes have an optimum temperature, but these can vary. The | | graph below shows how temperature affects the rate of a specific | | enzyme-catalysed reaction. | +=======================================================================+ | **Explanation** | | | | 1. The molecules have more kinetic energy, causing more collisions | | and enzyme-substrate complexes. | | | | 2. The optimum temperature is the temperature this enzyme works | | fastest at.  | | | | 3. Too much kinetic energy causes the active site to change shape | | and the enzyme denatures. | | | | **Description** | | | | 1. As temperature increases, the rate of reaction increases.  | | | | 2. The maximum rate is reached at the optimum temperature.  | | | | 3. As temperature increases past the optimum, the rate of reaction | | decreases until the reaction stops. | +-----------------------------------------------------------------------+ | **pH** | | | | All enzymes have an optimum pH, but these can vary. The graph below | | shows how pH affects the rate of a specific enzyme-catalysed | | reaction. | +-----------------------------------------------------------------------+ | **Explanation** | | | | 1. In acidic conditions, H+ ions break ionic/hydrogen | | bonds and denature enzymes. | | | | 2. The optimum pH is the pH the enzyme works fastest at. | | | | 3. In alkaline conditions, OH- ions break ionic bonds or hydrogen | | bonds and denature enzymes. | | | | **Description** | | | | 1. Below the optimum pH, the rate of reaction is low or zero. | | | | 2. The maximum rate of reaction is reached at the optimum pH. | | | | 3. Above the optimum pH, the rate of reaction is low or zero.  | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Substrate concentration** | | | | The graph below shows how substrate concentration affects the rate of | | an enzyme-catalysed reaction. | | | |  | +=======================================================================+ | **Explanation** | | | | 1. There are more substrate molecules to form more  enzyme-substrate | | complexes. | | | | 2. This is the saturation point, which is when all active sites are | | occupied by a substrate and enzyme concentration becomes the | | limiting factor.  | | | | **Description** | | | | 1. As the substrate concentration increases, the rate of reaction | | increases.  | | | | 2. As the substrate concentration increases further, the rate of | | reaction plateaus (levels off). | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Enzyme concentration** | | | | The graph below shows how enzyme concentration affects the rate of an | | enzyme-catalysed reaction. | +=======================================================================+ | **Explanation** | | | | 1. There are more enzyme molecules to form more enzyme-substrate | | complexes. | | | | 2. All substrate molecules available are being acted upon and | | substrate concentration becomes the limiting factor. | | | | **Description** | | | | 1. As the enzyme concentration increases, the rate of reaction | | increases.  | | | | 2. As the enzyme concentration increases further, the rate of | | reaction plateaus (levels off). | | | | **1.12 - Enzyme Inhibition** | | | | 1. **The different types of inhibitors ** | | | | 2. **How competitive inhibitors affect enzyme action ** | | | | 3. **How non-competitive inhibitors affect enzyme action ** | | | | +------------------------------------------------------------------+ | | | **Types of inhibitors** | | | | | | | | Inhibitors are molecules that bind to enzymes to reduce their | | | | activity.  | | | | | | | | **The effects of inhibitors can be reversible or irreversible:** | | | | | | | | - **Reversible inhibitors** - These form weak bonds (e.g. | | | | hydrogen or ionic) with the enzyme.  | | | | | | | | - **Irreversible inhibitors **- These form strong bonds (e.g. | | | | covalent) with the enzyme. | | | | | +==================================================================+ | | | | | | +------------------------------------------------------------------+ | | | | +------------------------------------------------------------------+ | | | **Inhibitors can be grouped into two categories: ** | | | | | | | | 1. **Competitive inhibitors **- These bind to the active site. | | | | | | | | 2. **Non-competitive inhibitors** - These bind away from the | | | | active site. | | | | | | | | These inhibitors will be covered in more detail later in this | | | | lesson. | | | +------------------------------------------------------------------+ | | | | +------------------------------------------------------------------+ | | | **Competitive inhibitors** | | | | | | | | Competitive inhibitors bind to the active site of an enzyme to | | | | prevent enzyme-substrate complexes.  | | | +==================================================================+ | | |  | | | | | | | | Competitive inhibitors have a similar shape to the substrate and | | | | so they bind to the active site of the enzyme. This prevents the | | | | substrate from binding, and thus reduces the formation of | | | | enzyme-substrate complexes. This results in a decrease in the | | | | rate of the enzyme-catalysed reaction. | | | | | | | | Most competitive inhibitors are reversible as they | | | | only temporarily bind to the enzyme. | | | +------------------------------------------------------------------+ | | | | +------------------------------------------------------------------+ | | | **Increasing substrate concentration increases rate of | | | | reaction** | | | | | | | | Competitive inhibitors can be overcome by increasing the | | | | substrate concentration.  | | | | | | | | Graph showing the effect of competitive inhibitors on enzyme | | | | reaction rate against substrate concentration. | | | +------------------------------------------------------------------+ | | | | ------------------------------------------------------------------- | | --------------------------------------------------------------------- | | ------------------------------------------------------------ | | The higher the substrate concentration, the more likely it is that | | substrates will bind to active sites rather than inhibitor molecules. | | This will reduce the effect of the competitive inhibitor. | | ------------------------------------------------------------------- | | --------------------------------------------------------------------- | | ------------------------------------------------------------ | | | | +------------------------------------------------------------------+ | | | **Non-competitive inhibitors** | | | | | | | | Non-competitive inhibitors bind to enzymes away from the active | | | | site (allosteric site) to prevent enzyme-substrate complexes. | | | +==================================================================+ | | |  | | | | | | | | This binding changes the tertiary structure of the enzyme, | | | | causing the active site to change shape. | | | | | | | | This results in the active site no longer being complementary to | | | | the substrate, thus the substrate and enzyme cannot bind. Less | | | | enzyme-substrate complexes are formed and the rate of the | | | | enzyme-catalysed reaction decreases. | | | +------------------------------------------------------------------+ | | | | +------------------------------------------------------------------+ | | | **Increasing substrate concentration has no effect on the rate | | | | of reaction** | | | | | | | | Non-competitive inhibitors cannot be overcome by increasing | | | | substrate concentration. | | | | | | | | Graph showing the effect of non-competitive inhibitors on the | | | | rate of reaction with increasing substrate concentration. | | | +------------------------------------------------------------------+ | | | | ------------------------------------------------------------------- | | --------------------------------------------------------------------- | | ------------------------------- | | Non-competitive inhibitors do not compete with the substrate to bin | | d to the active site, so increasing the amount of substrate has no ef | | fect on the rate of reaction. | | ------------------------------------------------------------------- | | --------------------------------------------------------------------- | | ------------------------------- | +-----------------------------------------------------------------------+ **2.1 - Nucleic Acids: DNA & RNA** 1. **The structure of nucleotides ** 2. **The reactions that synthesise and breakdown nucleic acids ** 3. **The role and structures of DNA and RNA** 4. **The similarities and differences between DNA and RNA** +-----------------------------------------------------------------------+ | **Nucleotide structure** | | | | Nucleotides are the building blocks of nucleic acids such as DNA and | | RNA. Nucleotides are monomers and can join together to form dimers | | (dinucleotides) and polymers (polynucleotides). | | | | A nucleic acid is the functional molecule made of one or more | | polynucleotide chains. | +=======================================================================+ |  | | | | **Nucleotides are made up of three components:** | | | | 1. **A pentose sugar** - Contains 5 carbon atoms. | | | | 2. **A nitrogenous base** - Contains carbon and nitrogen. | | | | 3. **A phosphate group** - Contains phosphate. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Polynucleotides** | | | | Nucleotides are joined together via condensation reactions to form a | | polynucleotide. The phosphate group of one nucleotide forms a | | covalent bond with the sugar of another. This forms a phosphodiester | | bond. | +=======================================================================+ | | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | Many nucleotides can join in this way to create a chain of phosphates | | and sugars known as the sugar-phosphate backbone.  | | | | Phosphodiester bonds can be broken via hydrolysis reactions, | | releasing the nucleotide monomers. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **DNA** | | | | Deoxyribonucleic acid (DNA) is a type of nucleic acid that contains | | the instructions needed to make proteins. | +=======================================================================+ |  | | | | **Each DNA nucleotide is made up of three components:** | | | | 1. **Deoxyribose** - A pentose sugar. | | | | 2. **A, T, G, or C** **base **- Adenine, thymine, guanine, or | | cytosine. | | | | 3. **A phosphate group** | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **DNA structure** | | | | In 1953, two scientists, James Watson and Francis Crick were credited | | with working out the structure of DNA. | | | | With the help of other scientists like Rosalind Franklin, they found | | that DNA is made up of two polynucleotide strands wound around each | | other to form a double helix. | | | | Diagram showing the DNA double helix structure with sugar-phosphate | | backbone and bases | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **The following features allow DNA to pass genetic information from | | one generation to another: ** | | | | 1. **Sugar-phosphate backbone** - This protects coding bases on the | | inside of the helix. | | | | 2. **Double stranded** - This allows strands to act as templates in | | DNA replication. | | | | 3. **Large molecule** - It stores lots of information. | | | | 4. **Double helix** - This makes the molecule compact. | | | | 5. **Complementary base pairing** - This allows accurate DNA | | replication. | | | | 6. **Weak hydrogen bonds** - This allows strands to separate in DNA | | replication. | +-----------------------------------------------------------------------+ +-----------------------------------------------------------------------+ | **Purines and pyrimidines** | | | | There are four nitrogenous bases found in DNA: adenine (A), guanine | | (G), thymine (T), and cytosine (C). These bases can be grouped into | | two categories: purines and pyrimidines. | | | | **Differences between purines and pyrimidines:** | | | | - **Purines **- These are larger bases that contain two carbon ring | | structures (A and G). | | | | - **Pyrimidines **- These are smaller bases that contain one carbon | | ring structure (T and C). | | | | ![Diagram