AS Level Biology Notebook PDF

AS Level Biology Wednesday 11 September 2024 Topic 1 Molecules, Transport and Health Unit 1A Chemistry for Biologists Learning Objective- Define vocabulary related to the topic Anion- a negative ion cation - a positive ion Ionic bond- bonds that formed when atoms give or take electrons; they resu...

AS Level Biology Wednesday 11 September 2024 Topic 1 Molecules, Transport and Health Unit 1A Chemistry for Biologists Learning Objective- Define vocabulary related to the topic Anion- a negative ion cation - a positive ion Ionic bond- bonds that formed when atoms give or take electrons; they result in charged particles called ions Dipole- the separation of charge in a molecule when in the covalent bonds are not evenly shared. Polar molecule- a molecule containing a dipole Dissociation- splitting of a molecule into smaller molecules, atoms, or ions, Especially by a reverse process. Hydrogen bonds- weak electronic intermolecular formed between polar molecules containing at least one hydrogen atom. Stage 12 AS Biology Thursday 12 September 2024 Unit 1 Molecules, Transport and Health Topic 1A The chemistry of life L.O.- To compare and contrast ionic and covalent bonds Ionic Bonding The atoms involved in the reaction give or receive electrons One molecule gains one or more electrons and becomes an anion(negative) The other atom or part of the molecule, loses one or more electrons and becomes a cation (positive)  Important cations- ○ Sodium- used in nerve impulses, sweating, and many secretory systems in animals ○ Calcium- bone formation in animals and cell wall has the formation of calcium pectate in the middle lamella ○ Hydrogen ions- needed for cellular respiration and photosynthesis and many systems and pH balance ○ Magnesium ions- production of chlorophyll in plants Important anions- ○ Chloride ion- its needed for nerve impulses, sweating, and many secretory systems ○ Nitrate ions- needed by plants to grow to make DNA, and also amino acids ○ Phosphate ions- needed by all living things to make ATP and ADP ○ Hydrogencarbonate ions- these are needed to buffer blood pH and prevent it from becoming too acidic Wednesday 18 September 2024 The Chemistry of Water 1A.1 Water Essential for life and all reactions in living cells take place in water Water is a polar molecule Hydrogen bonds are slightly positive and attracted to slightly negative oxygen  ○ Weak bonds → still takes a lot of energy to break them because of waters higher boiling point Water is a polar solvent ○ Many ionic substances can dissolve in water (NaCl) ○ It is an important form of transportation b/c it is dipole and enables dissolving ○ Water is slow to absorb heat and to release it ○ Water molecules are cohesive b/c the forces between them mean they stick together ○ Water molecules are adhesive because they are attracted to other molecules that are different ○ Water molecules have a high surface tension because of the attraction of the water molecules. It forms a “skin” of surface tension. Checkpoint page 7 questions 1-4 What is dipole? 1. In some covalent compounds, the electrons in the covalent bonds are not quite evenly shared. This means the molecule has a part that is slightly negative and a part that is slightly positive. This separation of charge is called a dipole, and the tiny charges are represented as δ + and δ –. A molecule containing dipoles is known as a polar molecule. Dipoles are particularly common if one or more hydrogen atoms are involved in the bond. What are the differences between ionic substances and polar substances? 2. Ionic substances: formed when atoms are joined by ionic bonds. The positive or negative ions formed when the atoms lose or gain electrons form an ionic compound. Polar substances: compounds formed with covalent bonds where there is a slightly unequal sharing of the electrons across the bond, giving a covalent molecule with slight dipoles that can affect intermolecular bonding. How are hydrogen bonds formed between water molecules and what effect do they have on water properties? 3. Water is a polar molecule because the electrons are held closer to the oxygen atom than to the hydrogen atoms, so the oxygen has a very small negative charge and the hydrogen atoms have very small positive charges. As a result, the slightly negative region of one water molecule is attracted to the slightly positive region of another water molecule, and this weak electrostatic attraction is a hydrogen bond. Therefore,  water has relatively high melting and boiling points and solid water is less dense than liquid water. Discuss how the properties of water affect living things? 4. Excellent solvent: Its covalent nature means water dissolves covalent compounds, its polar nature means it dissolves ionic compounds, so it is an ideal solvent for chemical reactions in biological systems and makes an excellent transport medium. It is slow to absorb and release heat so is a very stable medium for life. It is a liquid at room temperature so cannot be compressed, therefore it can be used in hydraulic systems. Water molecules are cohesive (stick together) and adhesive (stick to other substances). Both are important properties in the movement of water up the xylem of plants. High surface tension means that the water surface acts as a skin; this is very important in water being drawn up the phloem of a plant and for life at the surface of ponds, lakes and other water masses. Friday, 20 September 2024 1A.2 Carbohydrates 1 : Monosaccharides and Disaccharides Page 10 L.O.- Define the meaning of the terms used in 1A.2. Vocabulary Monday, 23 September 2024 Topic 1A.2 Carbohydrates 1: Monosacharides and Disacharides L.O.- Explain the difference between a mon and disaccharide and know how mono joins to form disaccharides Organic compounds Biological molecules are often organic compounds Organic compounds all contain carbon atoms Each carbon atom can make four bonds and form a tetrahedral shape ○ Monomers- atoms or small molecules that bond together to form more complex structures such as polymers ○ Polymers- large molecule formed from many monomers joined together known as macromolecules Carbohydrates Important in cells as a usable energy source Known as sugars and starch Sucrose = table sugar Glucose → used as a fuel by the cells in our bodies Made up of carbon, hydrogen, and oxygen atoms 3 main groups ○ Monosaccharides- 1 Oxygen 2 Hydrogen for every Carbon ○ Disaccharides- 2 monosaccharides joined together ○ Polysaccharides- 3 or more monosaccharides Monosaccharides Triose sugars- (n=3) have 3 carbon atoms ex- C3H6O3 Important energy source in the mitochondria Pentose sugars- (n=5) have 5 carbon atoms C5H10O5 ○ Ex- Ribose and deoxyribose Important in the nucleic acids deoxyribonucleic acids (DNA)  Hexose sugars- (n=6) have 6 carbon atoms C6H12O6 Best known monosaccharides- glucose, galactose, fructose Note the changes in the arrangement in the alpha and beta Isomers Different forms of the same element Glucose is made from an isomer of 1 alpha and 1 beta glucose The different arrangement forms different connections other glucose molecules Dissacharides: The double sugars Two monosaccharides joined together through condensation ○ This reaction forms a disaccharide + water ○ This covalent bond is glycosidic ○ The numbers 1, 2, 3, 4, 5, 6 are used to show where the bond is located example= 1, 4 glycosidic bond says the 1 of the first is joined to the 4 of the second monosaccharide (see above for the 1-6 arrangement) Disaccharide Source Monosaccharide Sucrose Stored in plants as sugar Glucose + Fructose cane Lactose Milk sugar Glucose + galactose Maltose Malt sugar found in Glucose + Glucose germinating seeds like barley Tests for sugars Reducing sugars Benedict’s test negative result blue positive yellow/green/orange/ brick red (most sugar) Uses a water bath Exception- Sucrose is not a reducing sugar Starch Iodine test Negative result orange brown Positive black Tuesday 24 September 2024 1A.2 Carbohydrates 1: monosaccharides and disaccharides Checkpoint questions answers What are Carbohydrates? 1 Carbohydrates are important in cells as a usable energy source. They are also important for storing energy, and in plants, fungi and bacteria they form an important part of the cell wall. The basic structure of all carbohydrates is the same. They are made up of carbon, hydrogen and oxygen. There are three main groups of carbohydrates with varying complexity of molecules: monosaccharides, disaccharides and polysaccharides. Describe how the glycosidic bond is formed between two monosaccharides to form a disaccharide. 2. A glycosidic bond is formed by the removal of a hydrogen atom (–H) from one monosaccharide and a hydroxyl group (–OH) from another monosaccharide to form a disaccharide and water. Topic 1A.3 Carbohydrates 2: Polysaccharides L.O. To identify how polysaccharides are formed, how they are broken down, and the differences in structure. Polysaccharides Most complex carbohydrates Do not have a sweet taste 3-10 sugar units are known as oligosaccharides 11+ are called true polysaccharides Hydrolysis of Polysaccharides Process that breaks down polysaccharides for cellular respiration Opposite of condensation → water is added to the bond Takes place in the gut, muscles, and liver cells where carbohydrates are broken down to release sugars for cellular respiration Carbohydrates and energy Monosaccharides and disaccharides Alll chemical reactions need energy The energy is called adenosine triphosphate (ATP) ATP is created when the breakdown of monosaccharides glucose using oxygen known as cellular respiration Alpha glucose can be broken down completely with oxygen present The END Products are CO2 + Water + lots of ATP = energy for cell reactions Mono and Di ○ are good sources of instant energy ○ but cannot be stored ○ Water soluble affecting the osmotic pressure Polysaccharides Form compact molecules → need less space Physically and chemically inactive Not very water soluble → no osmotic pressure They are for energy storage Starches Amylose Unbranched chains bonded at 1, 4 They coil and take up little space Harder to release energy but keeps you going longer Amylopectin Branched chains bonded 1,4 and branching at 1,6 The difference in bonds changes the properties Releases energy faster when needed on demand but runs out quicker Glycogen Structured like amylopectin Referred to as “animal” starch Broken down rapidly to supply energy faster Checkpoint A1.3 page 13 Carbohydrate 2 1. Explain why sugars such as glucose and sucrose are useful for immediate energy, but are not suitable as a long-term energy source. 1A.3 Carbohydrates 2 – polysaccharides 1 Sucrose (a disaccharide) is easily broken down to form glucose. Glucose has a chemical structure which means it can be broken down completely with oxygen to produce carbon dioxide and water and ATP which supplies the energy needed in the chemical reactions in cells. These sugars are not suitable for long-term storage because they are too chemically active and because they are very soluble in water, so they will affect the water balance of the cell. 2. Explain how the structure of carbohydrates is related to their function as a storage molecules providing the fuel for cellular respiration Starch is formed from amylose, which is a straight-chain molecule, and amylopectin, which is a branched-chain molecule. Both are formed from alpha glucose molecules joined by 1-4 or 1-6 glycosidic bonds, and result in compact globular molecules. Cellulose is formed from beta glucose molecules held together by 1-4 glycosidic bonds. As a result, cellulose has hydroxyl molecules sticking out on either side of the molecule, so hydrogen bonds form easily between the individual, long, straight chain molecules, holding them together and making cellulose very strong. Animals can digest starch, breaking it down into glucose, which can be used in cellular respiration. Most animals do not make the enzymes needed to digest cellulose, so it is not usually an energy providing food for animals unless their digestive system contains bacteria that do have the enzymes needed to break down the cellulose molecules into glucose. VOCABULARY 1A.3 Carbohydrates 2 Thursday 26 September 2024 Unit 1A.4 Lipids pages 14-15 L.O. Identify how the bonds in lipids are made and describe the differences between saturated and unsaturated fatty acids. VOCABULARY 1A.4 Lipids Lipids They are used as an energy store Contain C, H, O (but almost no oxygen) When oxidised, the bods are broken and the products are H2O and CO2 Triglycerides store almost 3x as much energy as carbohydrates Bond is 1 glycerol with 3 fatty acids (ester bond) Long hydrocarbon chain with a folded backbone of the carbon atoms and hydrogen atoms attached and a carboxly group at one end  The bond is formed by a condensation reaction- esterfication broken by hydrolysis Saturated are usually solid at room temperature (animal fats) Long chain fatty acids are more likely to be solid Saturated fats single covalent bonded chains unsaturated fats single carbon-carbon double bond monounsaturated fatty acids unsaturated fats with more than one carbon-carbon double bond is a polyunsaturated fatty acid 1A.4 Lipids Checkpoint page 15 Answers Explain how triglycerides are formed 1 Triglycerides are formed by condensation reactions between one glycerol molecule and three fatty acids. As each of the three ester bonds is formed, one molecule of water is lost. Describe the main difference between a saturated and unsaturated fatty acid and the effect of this difference on the properties of the lipids formed from unsaturated fatty acids compared to lipids formed from saturated fatty acids. 2 A saturated lipid contains fatty acids that only have single bonds between the carbon atoms in the chain. An unsaturated lipid contains fatty acids that have one or more double bonds within their carbon chain. This means that saturated lipids are more likely to be solids at room temperature. In the body, saturated and unsaturated lipids have different effects, e.g. saturated fatty acids in the diet are more likely to lead to plaque forming in arteries. Tuesday 1 October 2024 1A.5 Proteins Pages 17-21 L.O. familiarise yourselves with the vocabulary and start to understand the structure of proteins. Vocabulary Proteins Make hair, skin, nails, enzymes, and hormones Responsible for oxygen transport in haemoglobin They are macromolecules made from smaller monomers called amino acids Made up of carbon, hydrogen, oxygen, and nitrogen + sometimes sulfur Amino Acids Bonds are formed from condensation reaction - water loss 20 naturally occurring essential amino acids Has an amino group written as -NH2 and a carboxyl group -COOH ○ It is called the R group Some have selenium and sulfur Does not help with bonds They affect the way the amino acids interact within a protein molecule Depends on if it is polar or not General formula with two different arrangements for R. Glycine R is replaced with the H Cysteine R is replaced with the CH2-SH Forming Proteins from Amino Acids When condensation occurs in proteins it is called a peptide bond ○ Two amino acids join together to form a dipeptide ○ 3 or more are called polypeptide chains ○ Polypeptides structures change by folding, coiling, associating with other chains NOTE- amino 2 -COOH group is inverted from amino 1  Wednesday 2 October 2024 Types of Bonds in Proteins Hydrogen bonds Slightly negative oxygen and slightly positive hydrogen are present in the amino groups Weaker bonds but hold firmly in the correct position Important to folding and coiling Break easily if pH and temperature change Disulfide bonds Happens when two cysteine molecules together in the structure of a polypeptide Oxidation reaction occurs between the two sulfur containing groups Strong covalent bond Important for holding folded polypeptides in place Ionic Bonds Form between some strong negative and strong positive amino acid side chains Not as common and may be buried deep in the molecule Hair is made of Keratin ○ Heat breaks the hydrogen bonds and they reform in the style chosen ○ Perms break the disulfide bond and change the structure permanently until it is cut Protein Structures Four structures- primary, secondary, tertiary and quaternary Primary structure - Sequence of amino acids that make up a polypeptide Secondary structure - Regular repeating arrangement 3D held by hydrogen bonds - Right handed helix (α-helix) - Spiral coil w/ peptide bonds as the backbone and R groups going in other directions - β-pleated sheets folds into regular pleats held together by hydrogen bonds between the amino and carboxyl group - Most fibrous proteins form this structure Tertiary structure  - Contain alpha helixes and beta pleated sheets - Folded into complicated shapes - Hydrogen, sulfur, and ionic bonds between the R group - Globular proteins are an example Quaternary structure- - More than one tertiary structure of polypeptide chains Fibrous and Globular Proteins Fibrous Proteins- ○ Little to no tertiary structure ○ Parallel polypeptide chains linked together that form fibres ○ Insoluble in water and tough ○ Where: bones matrix, tendons, spider webs, keratin in hair, nails, horns, and feathers Collagen- fibrous protein For tendons, ligaments, bones and skin Extremely strong Quaternary structure of 3 polypeptide chains Up to 1000 amino acids long alpha-Chains repeat with glycine and two other proteins (usually proline and hydroxyproline) forming a triple helix Held together by hydrogen bonds When combined with bone tissue it has the likeness of steel rods that support concrete blocks Osteogenesis imperfecta- genetic disease affecting bone strength making them break easy  Globular Proteins ○ Tertiary structures- sometimes quaternary ○ Fold into spherical balls ○ The R group plays a big role Some R groups are hydrophobic and others hydrophilic Hydrophobic- inside the cell Hydrophilic- outside of the cell ○ The -COOH and -NH2 groups give them ionic properties Don’t dissolve but form a colloid A suspension that is held in the water They do not settle to the bottom of the solution and hard to separate Holds molecules in place in the cytoplasm Important to immune system production of antibodies Haemoglobin best known globular protein ○ Large molecule 574 polypeptide bonds arranged in 4 chains connected by sulfide bonds ○ The iron haem group bind to O2 and releases it Conjugated Proteins  ○ Connected to another and called prosthetic group ○ Iron is the prosthetic group in haemoglobin ○ Haemoglobin is both globular and conjugated ○ Lipoproteins are formed when conjugated with lipids Important for blood cholesterol LDL - low density lipoproteins HDL- high density lipoproteins ○ Glycoproteins are formed when conjugated with carbohydrates Checkpoint Answers A1.5 page 20 1. Explain how the order of the amino acids in a protein affects the structure of the whole protein. The structure of a protein is determined by a variety of bonds between amino acids within the polypeptide chains. Different amino acids can form different weaker bonds (such as hydrogen bonds, sulfide bonds and ionic bonds) with other amino acids, depending on how they are placed in the amino acid chain of the protein. These bonds determine the secondary, tertiary and (possibly) quaternary structure of the protein. So, a change in a single amino acid can alter the structure of the whole protein. 2. Hydrogen bonds are weaker than disulfide bonds and ionic bonds, but they are more important in maintaining the protein structure. Why is this? There are many more hydrogen bonds because they can form between any two amino acids. 3. The body uses many resources to maintain a relatively constant internal environment. With reference to the proteins explain why constant internal conditions are so important. The tasks that proteins carry out in the body are often dependent on their three- dimensional shape. The weak bonds between amino acids in the protein create this shape. These bonds may be affected by changes in conditions, such as temperature and pH, which will change how well the protein works. So, for good protein functioning, conditions need to be kept stable. Homeostasis of pH and temperature. -