Transcript Stoichiometry - Mr Field`s Chemistry Class

Biochemistry
Mr Field
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:
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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:
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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
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Lesson 1
The Energy Content of Foods
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Overview
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Copy this onto an A4 page. You should add to it as a
regular review throughout the unit.
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Assessment
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This unit will be assessed by:
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An internal assessment at the end of the topic (24%)
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A test at the end of the topic (76%)…around Lesson 19
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We Are Here
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Lesson 1: Energy Content of Foods
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Objectives:
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Reflect on prior knowledge of biochemistry
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Experimentally compare the energy value of foods
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Calculate the energy content of foods using bond-enthalpies
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Explain the difference in the energy content of fats and
carbohydrates
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Reflecting on Biochemistry
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Write down everything you already know about
biochemistry:
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You have 1 minute
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The Energy Content of Foods
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In our cells, some of the molecules we derive from food
are reacted with oxygen to release useful energy
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We will look at the process of respiration in the HL part of the
topic.
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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.
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We can compare the amounts of energy in foods by
burning them in the lab.
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Comparing Energy Content
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Design and conduct an experiment to determine whether
peanuts or crisps contain the most energy per gram.
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Calculate a value in terms of J/100 g and kcal/100g (1 kcal
= 4186 J)
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Compare your results to ones found online
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Explaining Energy Content
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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.
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Sucrose (a carbohydrate):
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A fat:
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A Ridiculous Question
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Use your answer to the previous question to answer this
(frankly silly) question:
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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:
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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
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The energy content of food can be determined using
enthalpy of combustion data
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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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Refresh
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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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We Are Here
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Lesson 2: The Structure of Proteins
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Objectives:
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Understand the structure and nature of amino acids
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Understand the four degrees of protein structure
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Use ‘Jmol’ to view real-life proteins
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Amino Acids
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General structure of an amino acid:
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Amino  the -NH2 bit
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Acid  the -COOH bit
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R  A ‘residue’ that can be a range of things
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Different R means a different amino acid, for example:
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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:
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Glycine  gly
Alanine  ala
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Zwitterionic Nature
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In the solid form, and when dissolved in water, amino
acids exist as zwitterions.
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A zwitterion is an ion with both a negative charge:
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The amine group is basic so can gain a proton:
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If you increase the pH of the solution by adding OH
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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:
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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
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Amino acids act as buffers as they can respond to changes
in pH
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Draw appropriate equations to demonstrate this
Isoelectric point:
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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
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There are 20 amino acids in the proteins of our bodies
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Check Table 19 in the Data Booklet
Try to categorise their side-chains into 4 appropriate
groups:
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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
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The –NH2 group joins to the –COOH group via a
condensation reaction.
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For example, if three amino acids join together you get:
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A chain of three amino acids is called a tri-peptide
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A chain of many amino acids is called a polypeptide
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Your Turn
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Draw displayed formulas for the following polypeptides
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gly-gly-ala
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gln-cis-his
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phe-pro-ser-met
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Protein Structure:
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Proteins are made of carefully folded and arranged strings of
amino acids.
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Go to the interactive tutorial here:
http://cbm.msoe.edu/includes/jmol/SOJmols/protienStructureH
ome.html
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Make notes on 1o, 2o, 3o and 4o structure of proteins
Use diagrams where necessary
Visit: http://proteopedia.org/wiki/index.php/Main_Page
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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:
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Research and give an example of proteins in each of the
following roles: structural, enzymes, hormones,
immunoproteins, transport proteins and as energy
source.
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Read through the experiments for next lesson
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Key Points
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Amino acid structure:
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Zwitterionic:
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Join by condensation reactions
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Proteins:
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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
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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.
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Deduce the structure of serine in
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A solution with a pH of 2.
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A solution with a pH of 12.
Deduce the structure of serine at the isoelectric point.
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We Are Here
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Lesson 3: Protein Analysis
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Objectives:
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Understand the principles of protein electrophoresis
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Understand the principles of paper chromatography
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Conduct electrophoresis to identify an unknown amino acid
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Conduct chromatography to identify an unknown amino acid
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Amino Acids
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General structure of an amino acid:
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Amino  the -NH2 bit
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Acid  the -COOH bit
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R  A ‘residue’ that can be a range of things
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Different R means a different amino acid, for example:

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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:
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Glycine  gly
Alanine  ala
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Electrophoresis
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A sample of polypeptides (or amino acids) is placed in a well in a
polyacrylamide gel
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A current is passed through the gel
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Molecules migrate towards the positive or negative electrode
depending on their charge
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Molecules migrate at speeds determined by their attraction to the
gel.
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Buffers can be used to change the ionisation of the proteins, and
thus their rates of movement.
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The molecules can be shown up by spraying with ninhydrin
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Used to analyse many macromolecules including DNA
(fingerprinting)
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Chromatography
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In chromatography, a sample dissolved in solvent makes its way through a substrate
such as:
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Paper
Silica
Resin
An alumina coated tube
Different compounds in the sample move through the substrate at different speeds
depending on:
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Their solubility in the solvent
Their attraction to the substrate
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Rf is the distance travelled by a substance divided by the distance travelled by the
solvent.
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Rf is unique for a given compound/solvent/substrate so can be used to identify
unknown compounds
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Experimentally
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You will be expected to complete an electrophoresis and
a chromatography experiment.
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Follow the instructions here and here
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This will require very careful time management
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Start electrophoresis
Do the chromatography
Finish the electrophoresis
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Key Points
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Electrophoresis use electric fields to separate
components of a mixture
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Chromatography uses solubility/attraction to a substrate
to separate the components
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Lesson 4
Carbohydrates - Monosaccharides
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Refresh
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Explain how a sample of a protein can be analysed by
electrophoresis.
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We Are Here
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Lesson 4: Monosaccharides
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Objectives:
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Understand the features of monosaccharides
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Understand the straight-chain and ring forms of glucose and
fructose
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Describe the formation of disaccharides and polysaccharides
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Carbohydrates
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General formula: CnH2nOn
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Includes:
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Sugars
Starches
Form the bulk of the energy content of most people’s
diets
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Monosaccharides – ring form
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A ‘single sugar’
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Contain a carbonyl group
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Yes really
At least two –OH groups
Empirical formula: CH2O
Glucose, C6H12O6
Fructose, C6H12O6
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Straight-chain form
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The rings exist in equilibrium with straight-chain forms:
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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
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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
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In ChemSketch, open the Templates Window (F5)
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In the left-hand drop down, select ‘Sugars: alfa-D-pyr’
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In the right-hand drop down, explore the various different
ways of representing the sugars.
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What do you think is the value of looking at the sugars in
these different ways?
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Condensation Reactions
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Disaccharides:
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Made from two monosaccharides (in the ring form) joined by a
condensation reaction
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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:
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Made from many monosaccharides joined by condensation
reactions
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Starch – α-glucose
Glycogen – α-glucose
Cellulose – β-glucose
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ChemSketch Part 2
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Use the sugars templates in ChemSketch to help you
draw:
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Lactose
Maltose
Sucrose
Three unit lengths of:
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Starch
Cellulose
Label them (use the Draw menu) and export them as an
image file.
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Homework
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Watch this: Sugar: The Bitter Truth,
https://www.youtube.com/watch?v=dBnniua6-oM
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Consider changing your dietary habits!
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Key Points
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Carbohydrates: CnH2nOn
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Monosaccharides:
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Empirical formula: CH2O
Carbonyl group
At least two -OH groups
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Disaccharides: two monosaccharides joined together
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Polysaccharides: many monosaccharides joined together
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Lesson 5
Carbohydrates - Uses
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Refresh
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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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We Are Here
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Lesson 5: The Uses of Carbohydrates
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Objectives:
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Understand why we can only make use of α-glucose
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Research and summarise the uses of carbohydrates in the body
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Starch and Cellulose
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Starch is the polysaccharide that makes up the bulk of our
staple foods
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It is a polymer of α-glucose
Two forms:
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Cellulose is the polysaccharide that forms plant cell walls and
is a major component of the bulk of plants
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Amylose
Amylopectin
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
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Enzymes run all the important reactions in the body.
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They contain an active site that is very specific to the shape of
the molecule.
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To do:
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Use molecular modelling kits to build a disaccharide from α-glucose.
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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
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Research starch (including both amylose
and amylopectin), glucose, glycogen and
dietary fibre online.You should find out:
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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
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We can’t use α-glucose as our enzymes are simply the
wrong shape
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Carbohydrates are used for:
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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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Refresh
1.
Compare the structural properties of starch and
cellulose.
2.
Explain why humans cannot digest cellulose.
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We Are Here
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Lesson 6: Lipid Structure
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Objectives:
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Understand the structure of the three types of lipid found in
the body
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Understand the difference between HDL and LDL cholesterol
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Describe the structures of the two essential fatty acids, and
their function
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Describe the formation and digestion of triglycerides
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Over to you
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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.
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Time to teach
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You have 20 minutes to teach about your topic and learn
about the others.
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You should allow about 5 minutes per speaker.
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Time to suffer be tested
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Work independently.
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You have 15 minutes.
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Lesson 7
Saturated and Unsaturated Lipids
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Refresh
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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)
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We Are Here
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Lesson 7: Saturated and Unsaturated Lipids
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Objectives:
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Understand the term saturation in relation to lipids
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Describe the use of ‘iodine numbers’ to measure saturation
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Complete an experiment to measure the iodine number of an
oil
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Saturation
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A fat or fatty acid is described as saturated when it contains
no C=C double bonds:
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For example stearic acid:
A fat or fatty acid is described as unsaturated when it contains
one or more C=C double bonds:
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For example α-linolenic acid:
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This is a poly-unsaturated fatty acid as it contains multiple C=C bonds
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Reacting with Iodine
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Iodine (I2) like all halogens, readily adds across a double
bond
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In the example below, 3 molecules of I2 react with α-linolenic,
one for each double bond.
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Iodine Number
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The reaction with iodine is used to give us a measure of saturation
called the ‘Iodine Number’
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The iodine number is defined as the mass of iodine that reacts with
100 g of a lipid, fat or oil.
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Higher iodine number  more unsaturated (more C=C)
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Lower iodine number  more saturated (fewer C=C)
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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
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
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Measuring Iodine Numbers
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In this experiment, you will measure and compare the
iodine numbers of range of different cooking oils.
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Follow the instructions here
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Key Points
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Saturated fats contain no C=C
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Unsaturated fats contain at least one C=C and often
more
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Iodine adds to double bonds
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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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Refresh
To measure the degree of unsaturation of a lipid the
iodine number can be calculated.

Define the term iodine number.
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Calculate the iodine number of linoleic acid
CH (CH ) (CH═CHCH ) (CH ) COOH
3
2 4
2 2
2 6
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M = 280.4
r
We Are Here
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Lesson 8: Lipids in the Body
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Objectives:
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Understand the important roles of lipids within the body
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Understand the potential negative effects of lipids on the body
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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 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
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Lesson 9
Micronutrients and Macronutrients
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Refresh

State three important uses of lipids in the body.
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Give two potential dangers of excess lipid
consumption
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We Are Here
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Lesson 9: Micronutrients and Macronutrients
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Objectives:
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Understand the difference between micro- and macronutrients
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Understand the structures of vitamins A, C and D
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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
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Macronutrients are needed in large amounts, >0.005% body
weight
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Proteins
Carbohydrates
Lipids
Minerals (Na, Mg, K, Ca, P, S, Cl)
Micronutrients are need in smaller amounts, <0.005% body
weight.
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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*
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A (retinol)*
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C (ascorbic acid)
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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
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Water or Fat Soluble?
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Vitamins can be categorised according to whether they
are fat-soluble or water-soluble
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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.
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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
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Macronutrients – need lots
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Micronutrients – need little
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Carbohydrate, lipid, protein
Some minerals
Vitamins
Trace minerals
Vitamins
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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
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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
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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
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The poster must include:
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Information on the causes and effects of nutrient deficiencies
Possible solutions to the problem
Information relating to a relevant charity
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Try to keep it local…Asia has problems too!
Suggestions for actions individuals could take
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Things to Consider
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Micronutrient deficiencies
such as:
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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:
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Solutions such as:
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Protein - marasmus and
kwashiorkor.
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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.
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
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Objectives:
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Understand the structure and function of hormones

Understand the how the oral contraceptive pill works
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Explore the use and abuse of steroids (theory not practical!)
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Hormones
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Chemical messengers that travel through the blood
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Produced by endocrine glands such as:
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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:
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Hormones you need to know of:
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ADH (Anti-Diuretic Hormone) – helps regulate bodily water content
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Aldosterone – regulation of blood pressure
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Estrogen – important to menstrual cycle (yes chaps: periods!)
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Progesterone – important to menstrual cycle
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Testosterone – development and maintenance of male sexual characteristics
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Insulin – regulation of blood sugar levels
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Epinephrine (adrenaline) – ‘fight or flight’
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Thyroxin – regulation of the metabolism
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Cholesterol and the Sex Hormones
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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
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Research and draw a labelled graph or diagram showing
how hormone levels vary over the course of the
menstrual cycle
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Produce a second diagram showing how the pill interferes
with hormone levels to suppress female fertility
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Steroids
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Steroids are a class of biologically active
molecules based on the steroid backbone:
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Steroids have a number of important medical uses
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Steroids can also be abused. Such abuses include:
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Homework:
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Research at least three medical uses of steroids
Research the effects of steroid abuse
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Key Points
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Hormones are chemical messengers
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The sex hormones and cholesterol share the steroid
backbone
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Progestogen and estrogen work together in the pill
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Steroids can be used, medically, but should not be abused
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Lesson 12
HL 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
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Objectives:
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Describe the function of enzymes
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Compare enzymes with inorganic catalysts
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Understand the mechanism of action of enzymes
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Enzymes you already know
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Brainstorm enzymes you already know about, and state
their function.
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What are enzymes
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Enzymes are biological catalysts.
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Enzymes are a class of protein
Key properties of enzymes
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Specific to substrate – i.e. they only catalyse one reaction
Specific to temperature
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Too cold and they don’t work very well
Too hot and they will be denatured (destroyed)
Specific to pH
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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
Function across a range of
range
pH
Specific to a single substrate Often catalyse many
reactions
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For example catalase
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Reaction catalysed:
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H2O2(aq)  H2O(l) + O2(g)
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Found in: all living things exposed to oxygen, greater concentrations
in the liver
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Optimum ph: 6.8-7.5
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Optimum temperature (human): 37oC
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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
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Research the induced fit and lock-and-key mechanisms in
more detail
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Produce an animation that shows both, include labels of
the key stages
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You could use:
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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
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Key Points
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Enzymes are biological catalysts
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They are specific to substrate, temperature and pH
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Rely on the 3D shape of their active site
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Work by the induced fit mechanism
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Lesson 13
HL 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
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Objectives:
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Describe the relationship between substrate concentration and
reaction rate
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Determine the Michaelis-Menten, Km, constant and explain its
importance
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Experimentally determine the Michaelis-Menten constant
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Explore enzyme inhibition
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State the effect of pH change, temperature change and heavy-metal
ions on enzyme activity
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Enzyme activity and substrate
concentration
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Rate initially increase
with [substrate]
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Rate levels out once
enzymes reach the point
they can’t physically work
any faster
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Max rate is called Vmax
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Michaelis-Menten Constant, Km
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The concentration of
substrate required to reach
½ Vmax
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Low Km:
 Greater affinity for
substrate
 More effective enzyme
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Higher Km:
 Lower affinity for
substrate
 Less effective enzyme
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Enzyme Inhibition
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Competitive Inhibitors
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Fit into the active site and
(reversibly) block it, preventing
substrate catalysis
Vmax unchanged but Km is
higher
Non-Competitive Inhibitors:
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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
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The Michaelis-Menten constant can be determined from a
graph of substrate concentration vs. reaction rate.
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In this experiment, you will determine Km for the catalase
enzyme, prepared from potatoes
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Follow the instructions here
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Homework:
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Complete the analysis for your Km experiment
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Sketch and label graphs to show the effect on enzyme
activity of:
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Temperature
pH
Research the effects on heavy metals on enzymes
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Key Points
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Vmax is the maximum rate of an
enzyme catalysed reaction
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Km is the substrate
concentration required for ½
Vmax
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Inhibitors reduce enzyme
activity
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Lesson 14
HL Only
The Structure of DNA and RNA
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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.
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Lesson 14: The Structure of DNA and RNA
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Objectives:
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Extract some DNA from chickpeas
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Understand the structures of DNA and RNA
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Explain the double-helix structure of DNA
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Nucleic Acids
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DNA (deoxyribose nucleic acid)
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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:
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Deoxyribose (sugar)
Phosphate
A base (either guanine, cytosine, adenine or thymine)
RNA (ribose nucleic acid)
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Translates the genetic code of DNA into useful protein
molecules
Made of a single, helical, strand of nucleotides
Each nucleotide made from:
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Ribose (sugar)
Phosphate
A base (either guanine, cytosine, adenine or uracil)
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Extracting DNA
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DNA can be extracted from chickpeas
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Follow the instructions here
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Note: this isn’t examined but is cool.
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Base Pairing
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The key to the double stranded
structure of DNA is base pairing
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Guanine pairs with cytosine
Adenine pairs with thymine
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Pairing caused by H-bonds (more on
this later)
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This:
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Holds the strands together
Allows them to replicate
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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
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Use the DNA/RNA section of ChemSketch (found in the
Template window (press F5))
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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
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DNA:
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Double stranded
G, C, A, T
Deoxyribose sugar
RNA:
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Single stranded
G, C, A, U
Ribose sugar
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Lesson 15
HL 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
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Objectives:

Understand how the role of DNA in protein synthesis
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Describe DNA profiling and its uses
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Homework: DNA Profiling
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DNA Profiling (aka DNA fingerprinting) is a technique
that can be used to analyse DNA and has many important
applications including:
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Determining the paternity of a child
Forensics
Research the key steps involved in DNA profiling
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DNA and Proteins
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DNA is a store of genetic information
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What does this mean?
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A strand of DNA comprises many genes (and
lots of other bits and pieces)
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A gene contains the instructions to make a
protein
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Genes average 27,000 base-pairs in length
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The human genome contains:
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a little over 3,000,000,000 base pairs
About 20,000 genes
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From DNA to Proteins
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The following animation explains how proteins are produced
from DNA
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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:
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Transcription
Translation
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
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Key Points
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Protein Synthesis:
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Transcription – mRNA is built from a length of DNA
Translation – tRNA brings nucleotides to the mRNA, using a 3base chemical code
DNA Profiling:
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Analyses DNA
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Identify paternity
Link suspects to crime scenes
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Lesson 16
HL 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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Lesson 16: Respiration
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Objectives:

Compare aerobic and anaerobic respiration
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Understand the roles of Copper and Iron ions in respiration
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Respiration
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The process by which cells convert ‘food’ (in this case glucose) into useful
energy
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There are two distinct pathways:
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Aerobic
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Anaerobic
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When there is plenty of oxygen
Slower
Sustainable
When oxygen is limited
Quick
Unsustainable (in animals at least)
Watch:
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http://www.phschool.com/atschool/phbio/active_art/cellular_respiration/
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Summary of Respiration
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Aerobic:
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*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
Glucose
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Carbon Dioxide and
Water
Pyruvate*
Lactic Acid
Anaerobic
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C6H12O6  2 CH3CH(OH)CO2H
Takes place in fewer small steps
Produced less energy
Glucose

Pyruvate*
For more detailed information, watch:
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http://www.mhhe.com/biosci/bio_animations/MH01_CellularRespiration_Web/index.html
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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
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Research:
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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
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Aerobic respiration
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Needs much O2
Produces CO2 and H2O
Slow
Produces much energy
Anaerobic respiration
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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
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