ib biochemistry
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IB Chemistry, biochemistry, proteins, enzymes, lipids, carbohydrates, nutrients, hormonesTRANSCRIPT
Biochemistry
Mr Field
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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.
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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
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Menu Lessons 11-20: Lesson 11 – Hormones Lesson 12 – HL – Enzymes and How They Wor
k 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
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Lesson 1
The Energy Content of Foods
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Overview Copy this onto an A4 page. You should add to
it as a regular review throughout the unit.
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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
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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
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Reflecting on Biochemistry
Write down everything you already know about biochemistry:
You have 1 minute
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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.
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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
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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:
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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
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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)
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Lesson 2
The Structure of Proteins
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What would expect to release the most energy upon combustion: 100g of wheat flour or 100g cooking oil? Why?
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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
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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
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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
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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
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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
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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
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Your Turn
Draw displayed formulas for the following polypeptides
gly-gly-ala
gln-cis-his
phe-pro-ser-met
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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/protienStructureHome.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
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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
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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
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Lesson 3
Protein Analysis
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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.
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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
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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
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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)
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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
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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
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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.
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Key Points
Electrophoresis use electric fields to separate components of a mixture
Chromatography uses solubility/attraction to a substrate to separate the components
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Lesson 4
Carbohydrates - Monosaccharides
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Explain how a sample of a protein can be analysed by electrophoresis.
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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
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Carbohydrates
General formula: CnH2nOn
Includes: Sugars Starches
Form the bulk of the energy content of most people’s diets
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Monosaccharides – ring form A ‘single sugar’
Contain a carbonyl group Yes really
At least two –OH groups Empirical formula: CH2O
Glucose, C6H12O6 Fructose, C6H12O6
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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.
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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?
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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
Polysaccharides: Made from many monosaccharides joined by
condensation reactions Starch – α-glucose Glycogen – α-glucose Cellulose – β-glucose
Note: Start counting carbons at the C to the right of the ring-O, and work round clockwise.
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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.
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Homework
Watch this: Sugar: The Bitter Truth, https://www.youtube.com/watch?v=dBnniua6-oM
Consider changing your dietary habits!
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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
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Lesson 5
Carbohydrates - Uses
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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.
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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
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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:
Amylose Amylopectin
Cellulose is the polysaccharide that forms plant cell walls and is a major component of the bulk of plants It is a polymer of β-glucose
We can extract large amounts of energy from starch; cellulose has no nutritional value. Why?
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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?
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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)
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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
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Lesson 6
Lipid Structure
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1. Compare the structural properties of starch and cellulose.
2. Explain why humans cannot digest cellulose.
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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
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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. The composition of the three types of lipid found in the body: triglycerides
(fats and oils), phospholipid (lecithin) and steroids (cholesterol).2. The differences between LDL and HDL cholesterol and the importance of
this.3. The structures of the essential fatty acids: linoleic (omega-6) and linolenic
(omega-3) acid, and their importance.4. The formation of triglycerides from condensation reactions and their
digestion by lipase enzymes.
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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.
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Time to suffer be tested
Work independently.
You have 15 minutes.
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Lesson 7
Saturated and Unsaturated Lipids
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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.b) Compare the composition of cholesterol with
a phospholipid such as lecithin.
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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
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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
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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.
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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?
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Some Iodine Numbers
Fat/Oil Iodine number
Coconut oil 7 – 10Palm oil 16 – 19Cocoa butter 35 – 40
Palm oil 44 – 51Jojoba oil ~80Olive oil 80 – 88
Peanut oil 84 – 105Cottonseed
oil 100 – 117Corn oil 109 – 133
Soybean oil 120 – 136Grape Seed
oil 124 – 143Sunflower
oil 125 – 144Tung oil 163 – 173
Linseed oil 170 – 204
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Measuring Iodine Numbers
In this experiment, you will measure and compare the iodine numbers of range of different cooking oils.
Follow the instructions here
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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
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Lesson 8
Lipids in the Body
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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
CH3(CH2)4(CH═CHCH2)2(CH2)6COOH Mr = 280.4
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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
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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
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Key PointsImportant 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
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Lesson 9
Micronutrients and Macronutrients
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State three important uses of lipids in the body.
Give two potential dangers of excess lipid consumption
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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.
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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’
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Vitamins* A (retinol)*
C (ascorbic acid) D (calciferol)*
Vitamin structures can be found towards the back of the data booklet
*Vitamins are defined by the job they do not their structure, so there will often be several ‘vitamers’ that perform the same job
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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 water-soluble. Explain why.
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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
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Key Points
Macronutrients – need lots Carbohydrate, lipid, protein Some minerals
Micronutrients – need little Vitamins Trace minerals
Vitamins A – retinol – fat-soluble D – calciferol – fat-soluble C – ascorbic acid – water soluble
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Lesson 10
Nutrient Deficiencies
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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.
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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
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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
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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: Protein - marasmus and
kwashiorkor.
Solutions such as: 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.
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Lesson 11
Hormones
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State the causes of the three deficiency diseases, beriberi, goitre and pellagra.
a) Beriberi:
b) Goitre:
c) Pellagra:
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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!)
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Hormones
Chemical messengers that travel through the blood Switch on/off and regulate various cellular
processes
Produced by endocrine glands such as: adrenal, pituitary, pancreas, thyroid, testes,
ovaries
Name as many hormones as you can. You have one minute:
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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
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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
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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
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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
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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
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Lesson 12HL Only
Enzymes and How They Work
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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.
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Lesson 12: How Enzymes Work
Objectives:
Describe the function of enzymes
Compare enzymes with inorganic catalysts
Understand the mechanism of action of enzymes
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Enzymes you already know
Brainstorm enzymes you already know about, and state their function.
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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
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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 range
Function across a range of pH
Specific to a single substrate
Often catalyse many reactions
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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
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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/Create-a-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
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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
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Lesson 13HL Only
Enzyme Kinetics
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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.
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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
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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
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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
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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
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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
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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
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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
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Lesson 14HL Only
The Structure of DNA and RNA
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Enzymes are affected by inhibitors. Lead ions are a non-competitive 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.
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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
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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)
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Extracting DNA
DNA can be extracted from chickpeas
Follow the instructions here
Note: this isn’t examined but is cool.
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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
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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
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Key Points
DNA: Double stranded G, C, A, T Deoxyribose sugar
RNA: Single stranded G, C, A, U Ribose sugar
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Lesson 15HL Only
Using DNA
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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
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We Are Here
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Lesson 15: Using DNA
Objectives:
Understand how the role of DNA in protein synthesis
Describe DNA profiling and its uses
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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
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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
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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)
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Key Points
Protein Synthesis: Transcription – mRNA is built from a length of DNA Translation – tRNA brings nucleotides to the mRNA,
using a 3-base chemical code
DNA Profiling: Analyses DNA
Identify paternity Link suspects to crime scenes
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Lesson 16HL Only
Respiration
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Describe the role of DNA in the storage of genetic information. The details of protein synthesis are not required.
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We Are Here
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Lesson 16: Respiration
Objectives:
Compare aerobic and anaerobic respiration
Understand the roles of Copper and Iron ions in respiration
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Respiration
The process by which cells convert ‘food’ (in this case glucose) into useful energy
There are two distinct pathways: Aerobic
When there is plenty of oxygen Slower Sustainable
Anaerobic When oxygen is limited Quick Unsustainable (in animals at least)
Watch: http://www.phschool.com/atschool/phbio/active_art/cellular_respiration/
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Summary of Respiration Aerobic:
C6H12O6 +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
Anaerobic C6H12O6 2 CH3CH(OH)CO2H Takes place in fewer small steps Produced less energy
For more detailed information, watch: http://www.mhhe.com/biosci/bio_animations/MH01_CellularRespiration_Web/ind
ex.html
Glucose Pyruvate* Carbon Dioxide and Water
Glucose Pyruvate* Lactic Acid
*Pyruvate: CH3COCO2-
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Comparing Respirations
Draw a Venn diagram to compare the two types of respiration
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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.
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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
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Lesson 17-18
Internal Assessment
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Internal Assessment
You should design and conduct and internal assessment on an aspect of biochemistry
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Lesson 19
Test
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Good Luck
You have 80 minutes!
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Lesson 20
Test Debrief
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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.
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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
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Go Through The Paper
Stop me when I reach a question you still have difficulty with.
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Targeted Lesson PREPARE AFTER MARKING THE TEST
SHORT LESSON ON SPECIFIC AREAS OF DIFFICULTY