IB Biochemistry

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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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