IB Biochemistry


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IB Chemistry, biochemistry, proteins, enzymes, lipids, carbohydrates, nutrients, hormones

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IB Biochemistry

  1. 1. Biochemistry Mr Field
  2. 2. Using this slide show  The slide show is here to provide structure to the lessons, but not to limit them….go off-piste when you need to!  Slide shows should be shared with students (preferable electronic to save paper) and they should add their own notes as they go along.  A good tip for students to improve understanding of the calculations is to get them to highlight numbers in the question and through the maths in different colours so they can see where numbers are coming from and going to.  The slide show is designed for my teaching style, and contains only the bare minimum of explanation, which I will elaborate on as I present it. Please adapt it to your teaching style, and add any notes that you feel necessary. Main Menu
  3. 3. Menu Lessons 1-10:           Lesson 1 – Energy Content of Food Lesson 2 – Protein Structure Lesson 3 – Protein Analysis Lesson 4 – Carbohydrates - Monosaccharides Lesson 5 – Carbohydrates - Uses Lesson 6 – Lipid Structure Lesson 7 – Saturated and Unsaturated Lipids Lesson 8 – Lipids in the Body Lesson 9 – Micro- and Macronutrients Lesson 10 – Nutrient Deficiencies Main Menu
  4. 4. Menu Lessons 11-20:          Lesson 11 – Hormones Lesson 12 – HL – Enzymes and How They Work Lesson 13 – HL – Enzyme Kinetics Lesson 14 – HL – DNA Structure Lesson 15 – HL – DNA Uses Lesson 16 – HL – Respiration Lesson 17-18 – Internal Assessment Lesson 19 – Test Lesson 20 – Test Debrief Main Menu
  5. 5. Lesson 1 The Energy Content of Foods Main Menu
  6. 6. Overview  Copy this onto an A4 page. You should add to it as a regular review throughout the unit. Main Menu
  7. 7. Assessment  This unit will be assessed by:  An internal assessment at the end of the topic (24%)  A test at the end of the topic (76%)…around Lesson 19 Main Menu
  8. 8. We Are Here Main Menu
  9. 9. Lesson 1: Energy Content of Foods  Objectives:  Reflect on prior knowledge of biochemistry  Experimentally compare the energy value of foods  Calculate the energy content of foods using bond-enthalpies  Explain the difference in the energy content of fats and carbohydrates Main Menu
  10. 10. Reflecting on Biochemistry  Write down everything you already know about biochemistry:  You have 1 minute Main Menu
  11. 11. The Energy Content of Foods  In our cells, some of the molecules we derive from food are reacted with oxygen to release useful energy  We will look at the process of respiration in the HL part of the topic.  The energy comes from breaking relatively weak bonds, such as C-H and C-C and making relatively strong bonds such as H-O and C=O.  We can compare the amounts of energy in foods by burning them in the lab. Main Menu
  12. 12. Comparing Energy Content  Design and conduct an experiment to determine whether peanuts or crisps contain the most energy per gram.  Calculate a value in terms of J/100 g and kcal/100g (1 kcal = 4186 J)  Compare your results to ones found online Main Menu
  13. 13. Explaining Energy Content  Use bond enthalpies to calculate and determine the energy released on combustion of 100 g of a typical carbohydrate and 100 g of a typical fat.  Sucrose (a carbohydrate):  A fat: Main Menu
  14. 14. A Ridiculous Question  Use your answer to the previous question to answer this (frankly silly) question:    If you were trapped in this room and it was made completely airtight, would you survive longer if you had only fat to eat or carbohydrate? How many days of difference would it make to your lifespan? Assume:     The air starts at 21% O2 You die once the O2 content drops below 10% If you are a girl, assume you need 1800 kcal per day If you are a boy, assume you need 2000 kcal per day Main Menu
  15. 15. Key Points  The energy content of food can be determined using enthalpy of combustion data  Lipids store more energy than carbohydrates as they are less oxidised (and so ‘more’ combustion happens) Main Menu
  16. 16. Lesson 2 The Structure of Proteins Main Menu
  17. 17. Refresh  What would expect to release the most energy upon combustion: 100g of wheat flour or 100g cooking oil? Why? Main Menu
  18. 18. We Are Here Main Menu
  19. 19. Lesson 2: The Structure of Proteins  Objectives:  Understand the structure and nature of amino acids  Understand the four degrees of protein structure  Use ‘Jmol’ to view real-life proteins Main Menu
  20. 20. Amino Acids  General structure of an amino acid:  Amino  the -NH2 bit  Acid  the -COOH bit  R  A ‘residue’ that can be a range of things  Different R means a different amino acid, for example:    Glycine – R is an ‘H’ atom Alanine – R is a ‘-CH3’ group Amino acids are given a three letter short hand to save writing their names all the time:   Glycine  gly Alanine  ala Main Menu
  21. 21. Zwitterionic Nature  In the solid form, and when dissolved in water, amino acids exist as zwitterions.  A zwitterion is an ion with both a negative charge:  The amine group is basic so can gain a proton:  If you increase the pH of the solution by adding OH  The amine group the amine group will return to its initial NH2’ form generating a negative ion ‘- The acid group is acidic so can lose a proton:  If you decrease the pH by adding H+, the acid group will return to it’s initial ‘-COOH’ form, generating a positive ion Main Menu
  22. 22. Zwitterionic Properties  Amino acids act as buffers as they can respond to changes in pH   Draw appropriate equations to demonstrate this Isoelectric point:     This is the pH that is just the right level to protonate the amine and deprotonate the base, to form a zwitterion This is important in electrophoresis which we will look at next lesson The isoelectric point is slightly different for each This, for various reasons you do not need to know, is generally around pH 6 Main Menu
  23. 23. Meet Some Amino Acids  There are 20 amino acids in the proteins of our bodies   Check Table 19 in the Data Booklet Try to categorise their side-chains into 4 appropriate groups:    Write the names of the amino acids in the group State the characteristics of the group Hint: focus on their chemical properties Main Menu
  24. 24. Amino-Condensation  The –NH2 group joins to the –COOH group via a condensation reaction.  For example, if three amino acids join together you get:  A chain of three amino acids is called a tri-peptide  A chain of many amino acids is called a polypeptide Main Menu
  25. 25. Your Turn  Draw displayed formulas for the following polypeptides  gly-gly-ala  gln-cis-his  phe-pro-ser-met Main Menu
  26. 26. Protein Structure:  Proteins are made of carefully folded and arranged strings of amino acids.  Go to the interactive tutorial here: http://cbm.msoe.edu/includes/jmol/SOJmols/protienStructureH ome.html    Make notes on 1o, 2o, 3o and 4o structure of proteins Use diagrams where necessary Visit: http://proteopedia.org/wiki/index.php/Main_Page    Look at a variety of different proteins and try to get a feel for them Try to identify the different aspects of their structure Right click and use the Measurements menu in Jmol to take various measurements of the proteins Main Menu
  27. 27. Homework:  Research and give an example of proteins in each of the following roles: structural, enzymes, hormones, immunoproteins, transport proteins and as energy source.  Read through the experiments for next lesson Main Menu
  28. 28. Key Points  Amino acid structure:  Zwitterionic:  Join by condensation reactions  Proteins:     1o structure: order of amino acids 2o structure: folding of amino acid chains 3o structure: 3-D arrangement of amino acid chains 4o structure: assembly of individual sub-units to form whole protein Main Menu
  29. 29. Lesson 3 Protein Analysis Main Menu
  30. 30. Refresh  Individual 2-amino acids have different structures depending on the pH of the solution they are dissolved in. The structure of serine is given in Table 19 of the Data Booklet.  Deduce the structure of serine in    A solution with a pH of 2. A solution with a pH of 12. Deduce the structure of serine at the isoelectric point. Main Menu
  31. 31. We Are Here Main Menu
  32. 32. Lesson 3: Protein Analysis  Objectives:  Understand the principles of protein electrophoresis  Understand the principles of paper chromatography  Conduct electrophoresis to identify an unknown amino acid  Conduct chromatography to identify an unknown amino acid Main Menu
  33. 33. Amino Acids  General structure of an amino acid:  Amino  the -NH2 bit  Acid  the -COOH bit  R  A ‘residue’ that can be a range of things  Different R means a different amino acid, for example:    Glycine – R is an ‘H’ atom Alanine – R is a ‘-CH3’ group Amino acids are given a three letter short hand to save writing their names all the time:   Glycine  gly Alanine  ala Main Menu
  34. 34. Electrophoresis  A sample of polypeptides (or amino acids) is placed in a well in a polyacrylamide gel  A current is passed through the gel  Molecules migrate towards the positive or negative electrode depending on their charge  Molecules migrate at speeds determined by their attraction to the gel.  Buffers can be used to change the ionisation of the proteins, and thus their rates of movement.  The molecules can be shown up by spraying with ninhydrin  Used to analyse many macromolecules including DNA (fingerprinting) Main Menu
  35. 35. Chromatography  In chromatography, a sample dissolved in solvent makes its way through a substrate such as:      Paper Silica Resin An alumina coated tube Different compounds in the sample move through the substrate at different speeds depending on:   Their solubility in the solvent Their attraction to the substrate  Rf is the distance travelled by a substance divided by the distance travelled by the solvent.  Rf is unique for a given compound/solvent/substrate so can be used to identify unknown compounds Main Menu
  36. 36. Experimentally  You will be expected to complete an electrophoresis and a chromatography experiment.  Follow the instructions here and here  This will require very careful time management    Start electrophoresis Do the chromatography Finish the electrophoresis Main Menu
  37. 37. Alternative to Practical  There are a number of electrophoresis simulations on the web  None are great, but looking at a number of different ones will give you a good feel for it. Main Menu
  38. 38. Key Points  Electrophoresis use electric fields to separate components of a mixture  Chromatography uses solubility/attraction to a substrate to separate the components Main Menu
  39. 39. Lesson 4 Carbohydrates - Monosaccharides Main Menu
  40. 40. Refresh  Explain how a sample of a protein can be analysed by electrophoresis. Main Menu
  41. 41. We Are Here Main Menu
  42. 42. Lesson 4: Monosaccharides  Objectives:  Understand the features of monosaccharides  Understand the straight-chain and ring forms of glucose and fructose  Describe the formation of disaccharides and polysaccharides Main Menu
  43. 43. Carbohydrates  General formula: CnH2nOn  Includes:    Sugars Starches Form the bulk of the energy content of most people’s diets Main Menu
  44. 44. Monosaccharides – ring form  A ‘single sugar’  Contain a carbonyl group    Yes really At least two –OH groups Empirical formula: CH2O Glucose, C6H12O6 Fructose, C6H12O6 Main Menu
  45. 45. Straight-chain form  The rings exist in equilibrium with straight-chain forms:    They only spend about 0.2% of the time in this form The carbonyl (C=O) is clearly visible The ring is formed by a condensation reaction in which the –OH lone pair on the fifth carbon (from top) attacks the carbonyl carbon, forming an O-C-O bond and reducing the carbonyl to –OH  Using molecular modelling kits, try this for glucose and see if you can produce alpha and beta glucose. Main Menu
  46. 46. ChemSketch Part 1  In ChemSketch, open the Templates Window (F5)  In the left-hand drop down, select ‘Sugars: alfa-D-pyr’  In the right-hand drop down, explore the various different ways of representing the sugars.  What do you think is the value of looking at the sugars in these different ways? Main Menu
  47. 47. Condensation Reactions  Disaccharides:  Made from two monosaccharides (in the ring form) joined by a condensation reaction     Lactose: galactose/ α -glucose, 1-4 link Maltose: α -glucose/ α -glucose, 1-4 link Sucrose: α -glucose/fructose, 1-4 link Note: Start counting carbons at the C to the right of the ring-O, and work round clockwise. Polysaccharides:  Made from many monosaccharides joined by condensation reactions    Starch – α-glucose Glycogen – α-glucose Cellulose – β-glucose Main Menu
  48. 48. ChemSketch Part 2  Use the sugars templates in ChemSketch to help you draw:     Lactose Maltose Sucrose Three unit lengths of:    Starch Cellulose Label them (use the Draw menu) and export them as an image file. Main Menu
  49. 49. Homework  Watch this: Sugar: The Bitter Truth, https://www.youtube.com/watch?v=dBnniua6-oM  Consider changing your dietary habits! Main Menu
  50. 50. Key Points  Carbohydrates: CnH2nOn  Monosaccharides:    Empirical formula: CH2O Carbonyl group At least two -OH groups  Disaccharides: two monosaccharides joined together  Polysaccharides: many monosaccharides joined together Main Menu
  51. 51. Lesson 5 Carbohydrates - Uses Main Menu
  52. 52. Refresh  Glucose is a monomer of starch. a) Draw the straight-chain structure of glucose. b) Explain why two cyclic isomers are formed from the straight-chain glucose and name both isomers. Main Menu
  53. 53. We Are Here Main Menu
  54. 54. Lesson 5: The Uses of Carbohydrates  Objectives:  Understand why we can only make use of α-glucose  Research and summarise the uses of carbohydrates in the body Main Menu
  55. 55. Starch and Cellulose  Starch is the polysaccharide that makes up the bulk of our staple foods   It is a polymer of α-glucose Two forms:    Cellulose is the polysaccharide that forms plant cell walls and is a major component of the bulk of plants   Amylose Amylopectin It is a polymer of β-glucose We can extract large amounts of energy from starch; cellulose has no nutritional value. Why? Main Menu
  56. 56. It’s all about enzymes  Enzymes run all the important reactions in the body.  They contain an active site that is very specific to the shape of the molecule.  To do:  Use molecular modelling kits to build a disaccharide from α-glucose.     Just make the carbon-oxygen framework, leave off the hydrogens Using plasticine, create an enzyme that fits the link between the monosaccharides. The monosaccharide should be able to slot in and out of it. Use different colours to show where different atoms touch the enzyme. Repeat the process for a disaccharide of β-glucose Try each of your enzymes on the opposing disaccharide. What happens? Main Menu
  57. 57. Uses of Carbohydrates  Research starch (including both amylose and amylopectin), glucose, glycogen and dietary fibre online.You should find out:        Structure Source Use in the body Recommended daily intake Potential consequences of not getting enough Potential consequences of getting too much Summarise your findings in a graphic organiser (table, mind-map, diagram etc) Main Menu
  58. 58. Key Points  We can’t use α-glucose as our enzymes are simply the wrong shape  Carbohydrates are used for:     Energy production Energy storage Keeping you ‘regular’ Excess carbohydrates lead to weight gain, obesity, diabetes and other illnesses Main Menu
  59. 59. Lesson 6 Lipid Structure Main Menu
  60. 60. Refresh 1. Compare the structural properties of starch and cellulose. 2. Explain why humans cannot digest cellulose. Main Menu
  61. 61. We Are Here Main Menu
  62. 62. Lesson 6: Lipid Structure  Objectives:  Understand the structure of the three types of lipid found in the body  Understand the difference between HDL and LDL cholesterol  Describe the structures of the two essential fatty acids, and their function  Describe the formation and digestion of triglycerides Main Menu
  63. 63. Over to you      Split into groups of 4 and number each group member 1-4 All the 1s, 2s, 3s, and 4s will have to come together to produce a learning resource on a given topic. This will take 40 minutes. The original groups will then reassemble and each member will have to take it in turn teaching the others about their topic. This will take 20 minutes There will be a test at the end. This will take about 15 minutes with 5 minutes for feedback The topics are: 1. 2. 3. 4. The composition of the three types of lipid found in the body: triglycerides (fats and oils), phospholipid (lecithin) and steroids (cholesterol). The differences between LDL and HDL cholesterol and the importance of this. The structures of the essential fatty acids: linoleic (omega-6) and linolenic (omega-3) acid, and their importance. The formation of triglycerides from condensation reactions and their digestion by lipase enzymes. Main Menu
  64. 64. Time to teach  You have 20 minutes to teach about your topic and learn about the others.  You should allow about 5 minutes per speaker. Main Menu
  65. 65. Time to suffer be tested  Work independently.  You have 15 minutes. Main Menu
  66. 66. Lesson 7 Saturated and Unsaturated Lipids Main Menu
  67. 67. Refresh  Steroids and phospholipids are both classes of lipid found in the body. Cholesterol is a steroid. A structure of lecithin, a phospholipid, is shown below. a) Distinguish between HDL and LDL cholesterol. Compare the composition of cholesterol with a phospholipid such as lecithin. b) Main Menu
  68. 68. We Are Here Main Menu
  69. 69. Lesson 7: Saturated and Unsaturated Lipids  Objectives:  Understand the term saturation in relation to lipids  Describe the use of ‘iodine numbers’ to measure saturation  Complete an experiment to measure the iodine number of an oil Main Menu
  70. 70. Saturation  A fat or fatty acid is described as saturated when it contains no C=C double bonds:   For example stearic acid: A fat or fatty acid is described as unsaturated when it contains one or more C=C double bonds:  For example α-linolenic acid:  This is a poly-unsaturated fatty acid as it contains multiple C=C bonds Main Menu
  71. 71. Reacting with Iodine  Iodine (I2) like all halogens, readily adds across a double bond  In the example below, 3 molecules of I2 react with α-linolenic, one for each double bond.  Main Menu
  72. 72. Iodine Number  The reaction with iodine is used to give us a measure of saturation called the ‘Iodine Number’  The iodine number is defined as the mass of iodine that reacts with 100 g of a lipid, fat or oil.  Higher iodine number  more unsaturated (more C=C)  Lower iodine number  more saturated (fewer C=C)  Why do you think iodine number is defined like this, rather than, for example, the number of moles of iodine that react with one mole of a fat or oil? Main Menu
  73. 73. Some Iodine Numbers Fat/Oil Coconut oil Palm oil Cocoa butter Palm oil Jojoba oil Olive oil Peanut oil Cottonseed oil Corn oil Soybean oil Grape Seed oil Sunflower oil Tung oil Linseed oil Iodine number 7 – 10 16 – 19 35 – 40 44 – 51 ~80 80 – 88 84 – 105 100 – 117 109 – 133 120 – 136 124 – 143 125 – 144 163 – 173 170 – 204 Main Menu
  74. 74. Measuring Iodine Numbers  In this experiment, you will measure and compare the iodine numbers of range of different cooking oils.  Follow the instructions here Main Menu
  75. 75. Key Points  Saturated fats contain no C=C  Unsaturated fats contain at least one C=C and often more  Iodine adds to double bonds  Iodine number measures unsaturation as the mass of iodine that reacts with 100g of a fat/oil Main Menu
  76. 76. Lesson 8 Lipids in the Body Main Menu
  77. 77. Refresh To measure the degree of unsaturation of a lipid the iodine number can be calculated.  Define the term iodine number.  Calculate the iodine number of linoleic acid CH (CH ) (CH═CHCH ) (CH ) COOH 3 2 4 2 2 2 6 Main Menu M = 280.4 r
  78. 78. We Are Here Main Menu
  79. 79. Lesson 8: Lipids in the Body  Objectives:  Understand the important roles of lipids within the body  Understand the potential negative effects of lipids on the body  Prepare and conduct a debate on the health-effects of lipids Main Menu
  80. 80. Debate  This house believes that fats contained in processed foods are sufficiently bad for health that they should come with health warnings on the packets. Important Roles Potential Negative Effects Poly-unsaturated fats can lower LDL cholesterol Increased risk of heart disease from LDL cholesterol and trans-fats Insulation and protection of organs Saturated fats are the main source of LDL cholesterol…particularly lauric, palmitic and myristic acids Steroid hormones Obesity Cell membranes Omega-3 protects against heart disease Energy storage Main Menu
  81. 81. Key Points Important Roles Potential Negative Effects Poly-unsaturated fats can lower LDL cholesterol Increased risk of heart disease from LDL cholesterol and trans-fats Insulation and protection of organs Saturated fats are the main source of LDL cholesterol…particularly lauric, palmitic and myristic acids Steroid hormones Obesity Cell membranes Omega-3 protects against heart disease Energy storage Main Menu
  82. 82. Lesson 9 Micronutrients and Macronutrients Main Menu
  83. 83. Refresh  State three important uses of lipids in the body.  Give two potential dangers of excess lipid consumption Main Menu
  84. 84. We Are Here Main Menu
  85. 85. Lesson 9: Micronutrients and Macronutrients  Objectives:  Understand the difference between micro- and macronutrients  Understand the structures of vitamins A, C and D  Explain whether vitamins A, C and D are fat or water soluble  Complete an experiment to measure the vitamin C content of a fruit juice. Main Menu
  86. 86. Micronutrients vs. Macronutrients  Macronutrients are needed in large amounts, >0.005% body weight      Proteins Carbohydrates Lipids Minerals (Na, Mg, K, Ca, P, S, Cl) Micronutrients are need in smaller amounts, <0.005% body weight.    Vitamins Trace minerals (Fe, Cu, F, Zn, I, Se, Mn, Mo, Cr, Co, B) Typically help support enzymes as ‘Co-factors’ Main Menu
  87. 87. Vitamins*  A (retinol)*  C (ascorbic acid)  Vitamin structures can be found towards the back of the data booklet D (calciferol)* *Vitamins are defined by the job they do not their structure, so there will often be several ‘vitamers’ that perform the same job Main Menu
  88. 88. Water or Fat Soluble?  Vitamins can be categorised according to whether they are fat-soluble or water-soluble    Water-soluble vitamins are absorbed into our blood Fat-soluble vitamins are absorbed into our lymph system Look at the structural features of vitamins A, C and D determine whether you think they are fat- or watersoluble. Explain why. Main Menu
  89. 89. Measuring Vitamin C Content  Vitamin C readily reacts with a compound abbreviated to DCPIP, so we can determine Vitamin C concentration by titration.  Vitamin C is also readily oxidised and oxidised by iodine, which gives us an ‘iodometric’ way to measure vitamin C  In this experiment, you measure the vitamin C content of orange juice using both methods.  Follow the instructions here Main Menu
  90. 90. Key Points  Macronutrients – need lots    Micronutrients – need little    Carbohydrate, lipid, protein Some minerals Vitamins Trace minerals Vitamins    A – retinol – fat-soluble D – calciferol – fat-soluble C – ascorbic acid – water soluble Main Menu
  91. 91. Lesson 10 Nutrient Deficiencies Main Menu
  92. 92. Refresh  By comparing the structures of vitamins A, C and D given in Table 21 of the Data Booklet, state and explain which of the three vitamins is most soluble in water. Main Menu
  93. 93. We Are Here Main Menu
  94. 94. Lesson 10: Nutrient Deficiencies  Objectives:  Understand the causes, effects and possible solutions of nutritional deficiencies  Design and produce posters to raise awareness of charities that fight nutritional deficiency in the developing world Main Menu
  95. 95. Task – in groups of 3  You need to design and produce a large (minimum A2) poster that can be displayed around the school to raise awareness for a charity fighting malnutrition in the developing world  The poster must include:    Information on the causes and effects of nutrient deficiencies Possible solutions to the problem Information relating to a relevant charity   Try to keep it local…Asia has problems too! Suggestions for actions individuals could take Main Menu
  96. 96. Things to Consider  Micronutrient deficiencies such as:         Iron - anaemia Iodine - goitre Retinol (vitamin A) xerophthalmia, night blindness Niacin (vitamin B3) - pellagra Thiamin (vitamin B1) - beriberi Ascorbic acid (vitamin C) scurvy Calciferol (vitamin D) - rickets. Macronutrient deficiencies such as:   Solutions such as:      Protein - marasmus and kwashiorkor. Main Menu Providing food rations that are composed of fresh and vitamin- and mineral-rich foods Adding nutrients missing in commonly consumed foods Genetic modification of food Providing nutritional supplements Providing selenium supplements to people eating foods grown in selenium-poor soil.
  97. 97. Lesson 11 Hormones Main Menu
  98. 98. Refresh State the causes of the three deficiency diseases, beriberi, goitre and pellagra. a) Beriberi: b) Goitre: c) Pellagra: Main Menu
  99. 99. We Are Here Main Menu
  100. 100. Lesson 11: Hormones  Objectives:  Understand the structure and function of hormones  Understand the how the oral contraceptive pill works  Explore the use and abuse of steroids (theory not practical!) Main Menu
  101. 101. Hormones  Chemical messengers that travel through the blood   Produced by endocrine glands such as:   Switch on/off and regulate various cellular processes adrenal, pituitary, pancreas, thyroid, testes, ovaries Name as many hormones as you can.You have one minute: Main Menu
  102. 102. Hormones you need to know of:  ADH (Anti-Diuretic Hormone) – helps regulate bodily water content  Aldosterone – regulation of blood pressure  Estrogen – important to menstrual cycle (yes chaps: periods!)  Progesterone – important to menstrual cycle  Testosterone – development and maintenance of male sexual characteristics  Insulin – regulation of blood sugar levels  Epinephrine (adrenaline) – ‘fight or flight’  Thyroxin – regulation of the metabolism Main Menu
  103. 103. Cholesterol and the Sex Hormones  All four share the steroid backbone  Write a table to summarise for each, the functional groups they have that are not shared by all the others Main Menu
  104. 104. The Contraceptive Pill  The contraceptive contains a mixture of estrogen and progestogen which work together to suppress female fertility  Research and draw a labelled graph or diagram showing how hormone levels vary over the course of the menstrual cycle  Produce a second diagram showing how the pill interferes with hormone levels to suppress female fertility Main Menu
  105. 105. Steroids  Steroids are a class of biologically active molecules based on the steroid backbone:  Steroids have a number of important medical uses  Steroids can also be abused. Such abuses include:  Homework:   Research at least three medical uses of steroids Research the effects of steroid abuse Main Menu
  106. 106. Key Points  Hormones are chemical messengers  The sex hormones and cholesterol share the steroid backbone  Progestogen and estrogen work together in the pill  Steroids can be used, medically, but should not be abused Main Menu
  107. 107. Lesson 12 HL Only Enzymes and How They Work Main Menu
  108. 108. Refresh  Some synthetic hormones are similar in structure to progesterone and estrogen and may be used to prevent pregnancy. Outline the mode of action of these hormones as oral contraceptives. Main Menu
  109. 109. We Are Here Main Menu
  110. 110. Lesson 12: How Enzymes Work  Objectives:  Describe the function of enzymes  Compare enzymes with inorganic catalysts  Understand the mechanism of action of enzymes Main Menu
  111. 111. Enzymes you already know  Brainstorm enzymes you already know about, and state their function. Main Menu
  112. 112. What are enzymes  Enzymes are biological catalysts.   Enzymes are a class of protein Key properties of enzymes   Specific to substrate – i.e. they only catalyse one reaction Specific to temperature    Too cold and they don’t work very well Too hot and they will be denatured (destroyed) Specific to pH  Too high or low and they will be denatured Main Menu
  113. 113. Enzymes vs. Inorganic Catalysts Enzymes Inorganics Complex protein molecules Generally simple – atoms, ions or small molecules Denatured by high temperatures Function better at higher temperatures Function in narrow pH Function across a range of range pH Specific to a single substrate Often catalyse many reactions Main Menu
  114. 114. For example catalase  Reaction catalysed:  H2O2(aq)  H2O(l) + O2(g)  Found in: all living things exposed to oxygen, greater concentrations in the liver  Optimum ph: 6.8-7.5  Optimum temperature (human): 37oC  A single catalase molecule catalyses millions of H2O2 decompositions every second, making it one of the most potent known enzymes Main Menu
  115. 115. Enzymes in Motion  Research the induced fit and lock-and-key mechanisms in more detail  Produce an animation that shows both, include labels of the key stages  You could use:     Stop motion (see more here: http://www.wikihow.com/Createa-Stop-Motion-Animation) Make a flicker book (and perhaps film it) Use a smart phone flicker or general animation book app Use PowerPoint custom animations Main Menu
  116. 116. Key Points  Enzymes are biological catalysts  They are specific to substrate, temperature and pH  Rely on the 3D shape of their active site  Work by the induced fit mechanism Main Menu
  117. 117. Lesson 13 HL Only Enzyme Kinetics Main Menu
  118. 118. Refresh Pepsin is an enzyme, found in the stomach, that speeds up the breakdown of proteins. Iron is used to speed up the production of ammonia in the Haber process.  Describe the characteristics of an enzyme such as pepsin, and compare its catalytic behaviour to an inorganic catalyst such as iron. Main Menu
  119. 119. We Are Here Main Menu
  120. 120. Lesson 13: Enzymes Kinetics  Objectives:  Describe the relationship between substrate concentration and reaction rate  Determine the Michaelis-Menten, Km, constant and explain its importance  Experimentally determine the Michaelis-Menten constant  Explore enzyme inhibition  State the effect of pH change, temperature change and heavy-metal ions on enzyme activity Main Menu
  121. 121. Enzyme activity and substrate concentration  Rate initially increase with [substrate]  Rate levels out once enzymes reach the point they can’t physically work any faster  Max rate is called Vmax Main Menu
  122. 122. Michaelis-Menten Constant, Km  The concentration of substrate required to reach ½ Vmax  Low Km:  Greater affinity for substrate  More effective enzyme  Higher Km:  Lower affinity for substrate  Less effective enzyme  Main Menu
  123. 123. Enzyme Inhibition  Competitive Inhibitors    Fit into the active site and (reversibly) block it, preventing substrate catalysis Vmax unchanged but Km is higher Non-Competitive Inhibitors:    Bind (reversibly) to the enzyme away from the active site, causing the active site to change shape so it no longer works When the inhibitor is released, the active site returns to normal Vmax is reduced but Km unchanged Main Menu
  124. 124. Measuring Km  The Michaelis-Menten constant can be determined from a graph of substrate concentration vs. reaction rate.  In this experiment, you will determine Km for the catalase enzyme, prepared from potatoes  Follow the instructions here Main Menu
  125. 125. Homework:  Complete the analysis for your Km experiment  Sketch and label graphs to show the effect on enzyme activity of:    Temperature pH Research the effects on heavy metals on enzymes Main Menu
  126. 126. Key Points  Vmax is the maximum rate of an enzyme catalysed reaction  Km is the substrate concentration required for ½ Vmax  Inhibitors reduce enzyme activity Main Menu
  127. 127. Lesson 14 HL Only The Structure of DNA and RNA Main Menu
  128. 128. Refresh Enzymes are affected by inhibitors. Lead ions are a noncompetitive inhibitor, they have been linked to impaired mental functioning. Ritonavir® is a drug used to treat HIV and acts as a competitive inhibitor.  Compare the action of lead ions and Ritonavir® on enzymes, and how they affect the initial rate of reaction of the enzyme with its substrate and the values of Km and Vmax. Main Menu
  129. 129. We Are Here Main Menu
  130. 130. Lesson 14: The Structure of DNA and RNA  Objectives:  Extract some DNA from chickpeas  Understand the structures of DNA and RNA  Explain the double-helix structure of DNA Main Menu
  131. 131. Nucleic Acids  DNA (deoxyribose nucleic acid)     Store of genetic material  the code for life Made of two opposing strands of nucleotides joined by H-bonds, with a ‘double helix’ structure A self-replicating molecule Each nucleotide made from:     Deoxyribose (sugar) Phosphate A base (either guanine, cytosine, adenine or thymine) RNA (ribose nucleic acid)    Translates the genetic code of DNA into useful protein molecules Made of a single, helical, strand of nucleotides Each nucleotide made from:    Ribose (sugar) Phosphate A base (either guanine, cytosine, adenine or uracil) Main Menu
  132. 132. Extracting DNA  DNA can be extracted from chickpeas  Follow the instructions here  Note: this isn’t examined but is cool. Main Menu
  133. 133. Base Pairing  The key to the double stranded structure of DNA is base pairing   Guanine pairs with cytosine Adenine pairs with thymine  Pairing caused by H-bonds (more on this later)  This:   Holds the strands together Allows them to replicate    Strands are separated A new strand is built on each Only one possible combination for each new strand Main Menu
  134. 134. Exploring the Structure of DNA  Use the DNA/RNA section of ChemSketch (found in the Template window (press F5))     Produce a 4-nucleotide, double-stranded length of DNA, containing each of the 4 possible base pairs Use the ‘Draw’ feature to show where the H-bonds should be, and thus explain why the bases pair off Label the diagram as fully as possible Study the structure of uracil and suggest a reason that RNA is only single stranded Main Menu
  135. 135. Key Points  DNA:     Double stranded G, C, A, T Deoxyribose sugar RNA:    Single stranded G, C, A, U Ribose sugar Main Menu
  136. 136. Lesson 15 HL Only Using DNA Main Menu
  137. 137. Refresh  A nucleotide of DNA contains deoxyribose, a phosphate group and an organic base. a. Outline how nucleotides are linked together to form polynucleotides. b. Describe the bonding between the two strands in the double helical structure of DNA Main Menu
  138. 138. We Are Here Main Menu
  139. 139. Lesson 15: Using DNA  Objectives:  Understand how the role of DNA in protein synthesis  Describe DNA profiling and its uses Main Menu
  140. 140. Homework: DNA Profiling  DNA Profiling (aka DNA fingerprinting) is a technique that can be used to analyse DNA and has many important applications including:    Determining the paternity of a child Forensics Research the key steps involved in DNA profiling Main Menu
  141. 141. DNA and Proteins  DNA is a store of genetic information  What does this mean?  A strand of DNA comprises many genes (and lots of other bits and pieces)  A gene contains the instructions to make a protein  Genes average 27,000 base-pairs in length  The human genome contains:   a little over 3,000,000,000 base pairs About 20,000 genes Main Menu
  142. 142. From DNA to Proteins  The following animation explains how proteins are produced from DNA    http://www.yourgenome.org/teachers/dnaprotein.shtml Click on the ‘From DNA to Protein’ image half-way down the page Produce an A4 poster that summarises the process of protein synthesis. It should include diagrams and the following key terms:      Transcription Translation Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA) Main Menu
  143. 143. Key Points  Protein Synthesis:    Transcription – mRNA is built from a length of DNA Translation – tRNA brings nucleotides to the mRNA, using a 3base chemical code DNA Profiling:  Analyses DNA   Identify paternity Link suspects to crime scenes Main Menu
  144. 144. Lesson 16 HL Only Respiration Main Menu
  145. 145. Refresh  Describe the role of DNA in the storage of genetic information. The details of protein synthesis are not required. Main Menu
  146. 146. We Are Here Main Menu
  147. 147. Lesson 16: Respiration  Objectives:  Compare aerobic and anaerobic respiration  Understand the roles of Copper and Iron ions in respiration Main Menu
  148. 148. Respiration  The process by which cells convert ‘food’ (in this case glucose) into useful energy  There are two distinct pathways:  Aerobic     Anaerobic     When there is plenty of oxygen Slower Sustainable When oxygen is limited Quick Unsustainable (in animals at least) Watch:  http://www.phschool.com/atschool/phbio/active_art/cellular_respiration/ Main Menu
  149. 149. Summary of Respiration  Aerobic:     *Pyruvate: CH3COCO2C6H12O6 +6 O2  6 CO2 + 6 H2O Takes place in many small steps, regulated by many enzymes Glucose is oxidised and oxygen reduced Produces more energy Pyruvate*  Lactic Acid Anaerobic    C6H12O6  2 CH3CH(OH)CO2H Takes place in fewer small steps Produced less energy Glucose  Carbon Dioxide and Water Pyruvate* Glucose For more detailed information, watch:  http://www.mhhe.com/biosci/bio_animations/MH01_CellularRespiration_Web/index.html Main Menu
  150. 150. Comparing Respirations  Draw a Venn diagram to compare the two types of respiration Main Menu
  151. 151. Metal ions in respiration  Research:    The role of copper ions in electron transport (cytochromes) The role of iron ions in oxygen transport (haemoglobin) For each one, write a few sentences to explain its function. Include a diagram of the relevant molecule and describe, with labels how it works with the metal ion. Main Menu
  152. 152. Key Points  Aerobic respiration      Needs much O2 Produces CO2 and H2O Slow Produces much energy Anaerobic respiration     Needs no O2 Produces lactic acid Quick Produces little energy Main Menu
  153. 153. Lesson 17-18 Internal Assessment Main Menu
  154. 154. Internal Assessment  You should design and conduct and internal assessment on an aspect of biochemistry Main Menu
  155. 155. Lesson 19 Test Main Menu
  156. 156. Good Luck  You have 80 minutes! Main Menu
  157. 157. Lesson 20 Test Debrief Main Menu
  158. 158. Personal Reflection  Spend 15 minutes looking through your test:  Make a list of the things you did well  Use your notes and text book to make corrections to anything you struggled with. Main Menu
  159. 159. Group Reflection  Spend 10 minutes working with your classmates:  Help classmates them with corrections they were unable to do alone  Ask classmates for support on questions you were unable to correct Main Menu
  160. 160. Go Through The Paper  Stop me when I reach a question you still have difficulty with. Main Menu