Chapter 2: Teaching guide

Biological molecules

Resources available
Topic name Syllabus Number of Coursebook Teacher CD
outcomes lessons material resources
(suggested)

Testing for • Boxes 2.1–2.4

biological 2.1(a), (b) 6 • SAQ 2.2 Practicals 2.1–2.3
molecules • EOCQ 7f
• Pages 29–38
Carbohydrates • SAQs 2.1, 2.2,
2.2(a)–(f) 11 Practical 1.4
and lipids 2.4, 2.5
• EOCQs 4, 6, 7, 9
• Pages 39–45
Proteins 2.3(a)–(c) 7 • EOCQs 1, 2, 4, 5,
8, 10
• Pages 46–48
Water 2.3(d) 1 • SAQ 2.6 Homework 2.1
• EOCQ 3

Topic 1 Testing for biological molecules

The tests learnt in this topic have relevance to other parts of the course, particularly in syllabus section
3 on enzymes. Time spent ensuring the tests are properly understood and carried out is, therefore, well
spent.

Suggested activities
Possible starters
• This is likely to be the first opportunity for students to conduct experiments at A level standard
using standard laboratory equipment. They will not be used to the extra rigour required at A level
and some may have picked up bad habits earlier in their education. It is worth impressing on them
the standards required. Tell students the story of a biochemistry lecturer who started his course by
insisting that you should be able to carry out an experiment on top of a grand piano without
damaging it and then proceeded to demonstrate a range of techniques such as accurate pipetting
without spilling a drop. Demonstrations of such basic techniques will probably be useful. Even the
sucking up of liquid in a teat pipette is rarely done properly by students until they are shown how
to do it. (Squeeze out an appropriate amount of air from the teat before placing the end in the
solution, release the pressure on the bulb while the end is immersed and then withdraw it. Try not
to suck liquid up into the bulb. Why?)

Main lesson content

• Practical 2.2 requires some planning by the student. It could be used as a planning exercise only,
possibly at the end of Practical 2.1 or another practical for students who have finished early.
Alternatively it could be used as part of a test or for homework.

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• The tests for biological molecules can be carried out on a variety of foodstuffs. Where possible,
foods that can be ground in water using a pestle and mortar to produce a relatively clear solution
should be used.
• Practical 1.4 involves preparing slides of starch grains from potato tubers and banana fruit. Slides
of potato and banana cells showing starch grains could be set up as a demonstration to save time.
• A good test of observation is to ask students to cut a slice of banana several mm thick and to cover
it with iodine solution in a suitable container/dish. There is a particular distribution of starch,
which will show up as a blue–black colouration. Students should make a drawing to show the
distribution.

Common misunderstandings and misconceptions

• When recording observations, students often use expressions such as ‘nothing happened’, ‘no
result’, ‘negative’, and ‘positive’. They should be reminded that an actual observation is required.
Guidance is given in the 2016 syllabus (last paragraph, page 42).
• A positive result for a Benedict’s test is often recorded as a colour change only (e.g. brick-red
colour). A second observation, namely the presence of a precipitate, should also be recorded; so,
‘brick-red precipitate’ is correct.
• Students sometimes forget that the biuret test does not require heat.
• The emulsion test for lipids is only likely to work well when relatively large quantities of lipid are
present and the initial solution is transparent. Students may be tempted to record what they think
they should see when testing certain foods which they believe should contain lipid.
Supporting struggling students
• Students will gain more confidence in using the tests if they try out the tests on known solutions of
pure biochemicals first. This may slow down the practical programme, but until clear positive
results with pure solutions have been seen, students will find it hard to evaluate results which are
less clear. It is important also for subsequent topics, especially work on enzymes, that these tests
are mastered.
• Use animations to show the formation and breaking of a peptide bond, the structure of
haemoglobin and the types of bond used in secondary and tertiary structures.
Challenging high achievers
• The semi-quantitative Benedict’s test is the most challenging of the tests described here. Practical
2.3 part C is designed as an extension activity for more able students. They should be able to draw
a calibration curve if they know the glucose concentrations used for the standards. Another
variation for more able students is to provide them with an unknown mixture containing both
glucose and sucrose. The extra precipitate observed after hydrolysis with acid is a good test of
observation. Keep the concentration of glucose low (0.5% or 1%). The sucrose concentration
should be about 1%.

Homework suggestions
• SAQ 2.3
• EOCQ 7f
• Practical 2.2 used as a planning exercise

Topic 2 Carbohydrates and lipids

Carbohydrates and lipids can be categorised as molecules which have important energy and structural
functions. The structural functions are particularly associated with the barriers of cell walls and cell
membranes. This is in contrast to proteins and nucleic acids which can be regarded as ‘informational’
molecules.

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Suggested activities
Possible starters
• As part of the introduction to biochemistry, it is useful for students to understand the concept of
organic chemistry. This is the chemistry of carbon. An organic molecule could be defined as one
that contains both carbon and hydrogen, for example methane, CH4, and often other atoms, for
example glucose, C6H12O6. This definition gets round the problem of whether carbon dioxide,
normally regarded as an inorganic molecule, should be regarded as organic.
• It is also important to understand that carbon atoms can join covalently to other carbon atoms to
make the chains and rings that are the skeletons of biochemical molecules.
• Models of simple molecules should be available to hold up as demonstrations. These help to
establish confidence in understanding larger structures, particularly the role of stable covalent
bonds. Suitable examples would be water and methane. Ethanol, ammonia and ethanoic acid
(vinegar) are also useful. A ring structure (e.g. benzene or cyclohexane) is also helpful. This could
start a discussion of the biological importance of simple molecules and the concept of biochemical
evolution. It should be emphasised that although many important biological molecules are large,
they are basically just simple groups of atoms held on a carbon skeleton/scaffold.
Main lesson content
• It is very useful to have molecular modelling kits for this and subsequent topics, either ball-and-
stick or space-filling models, ideally both. An alternative to commercial products is to use
modelling clay balls joined with toothpicks, matchsticks or straws. Conventional colours are: black
for carbon, white for hydrogen, red for oxygen, blue for nitrogen, yellow for sulfur and purple for
phosphorus. Different coloured jelly beans can be used instead of modelling clay balls.
• Demonstration models of the ring structures of α-glucose and β-glucose are particularly useful.
Although the structure of the straight chain version of glucose is not required by the syllabus, the
teacher may feel that a model of the straight chain would enhance student understanding.
Demonstration of the formation of a glycosidic bond is possible with models of glucose (and
fructose if sucrose is to be made).
• The compact nature of starch can be impressed on students by making popcorn; the final popcorn
can be proved to still contain starch by adding iodine solution. Discussion about how the
transformation occurs may prove useful – does it involve breaking hydrogen bonds? The popcorn
balls can be sewn together to act as model units of glucose joined to make starch; they can be
twisted to form amylose or branched to make amylopectin.
• It is highly desirable to have models of saturated and unsaturated fatty acids. The compactness and
symmetry is best illustrated with space-filling models. They can be used in many contexts, both
here and for syllabus section 4 on membranes. A model phospholipid is also desirable.
• See Chapter 4, Topic 1 for a phospholipid role-play which could be used here, depending on the
teaching sequence.
Common misunderstandings and misconceptions
• Many students, especially those not studying A-level chemistry, fear that biochemistry will be
difficult. It is worth pointing out that the chemical reactions studied at this level are simple.
Almost all involve either hydrolysis or its reverse, condensation; both are relatively simple
reactions.
Supporting struggling students
• See ‘Common misunderstandings and misconceptions’ above.
• The concrete nature of models is particularly important in helping the less able students.

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Challenging high achievers
• Students are taught that phospholipids consist of glycerol, two fatty acids and a phosphate group.
However, other water-soluble groups, such as choline, are attached to the phosphate. Students
could investigate the variety of phospholipids and the reason for this variety.
Homework suggestions
• SAQs 2.1, 2.2, 2.4, 2.5
• EOCQs 4 (last 6 columns of table), 6, 7, 9
Other recommended resources
Alberts, B. et al. (2013) Essential Cell Biology, 4th edn. Garland Science

Chapter 2: ‘Chemical Components of Cells’ has useful narrated animations explaining the structures
of glucose, palmitic acid, ATP and non-covalent bonds using three-dimensional models. There are also
animations and video clips with narrated explanations covering the following aspects of 'Protein
Structure and Function': Viewing proteins, Alpha helix, Beta sheet, Disulfide bonds. Available at:
www.garlandscience.com/ECB4-students.

Topic 3 Proteins
The relationship between structure and function is particularly clear when it comes to proteins.
Although nucleic acids are not dealt with until syllabus Section 6, students should be made aware that
there is a direct link between proteins and the genetic code and that they are the principal tools by
which the genome controls the cell.

Suggested activities
Possible starters
• The importance of proteins can be emphasised at the start by considering their range of functions.
• After establishing that proteins are made of amino acids, provide each student with a table of the
20 common amino acids and ask questions to elicit their essential features. For example:
– What new elements are present when compared with carbohydrates and lipids?
– What chemical features are common to all amino acids?
– How can the R groups be categorised, assuming this information is available in the table
(acid, neutral, basic; straight chain or ring structures; hydrophilic or hydrophobic;
sulfur-containing) A pre-made model of an amino acid is helpful.
– Why are there only 20 amino acids? (Students probably won’t be able to answer this,
but it could be left as a hanging question after initial speculation.)
Main lesson content
• Model(s) of glycine. Students can make their own models; pairs of students can then combine to
make a dipeptide. A class polypeptide could then be made.
• Students could model the primary structure of a protein using plastic beads. They will need large
numbers of beads in 20 different colours, one colour for each amino acid type. (You may be able
to obtain fuse beads, such as Hama® or Perler® beads, which are very suitable for this activity.)
Students will also need details of the primary sequence of the proteins to be made. Proteins such as
insulin are small enough to be built by a pair of students over a lesson.
You may wish to ask different pairs of students to produce the primary sequence of the same
protein with different types of mutation. The class can then try to spot the mutations at the end of
the lesson. A useful example of a mutation would be the one responsible for cystic fibrosis, which
affects the CFTR protein. Non-mutant and mutant models of the protein could be made by
volunteers as a homework activity (however, it is rather time-consuming). The class could then be

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 asked to try to spot the mutation (difficult). This helps to stress how apparently minor changes in
structure can have a major impact on function.
• Poster presentations are an important way of conveying information at scientific conferences.
Proteins have an enormous range of functions and commercial applications. This would be an
opportunity to set a mini-project or homework on designing a poster about one or a group of
proteins. Collagen and haemoglobin are syllabus examples, but others could be used according to
the interests of the students. Some guidance will be necessary, such as keeping text to a minimum
and filling available space – a brief discussion of what makes a good poster, with some examples,
will help.
• Impressive paper models of alpha-helices can be made relatively easily, either as demonstrations
or as homework exercises. A strip (two centimetres wide) cut from the length of an A4 sheet of
graph paper is ideal. Draw a polypeptide along the strip, one amino acid every two centimetres,
showing the covalent bonds. Start with NH, and point NH up and CO down all the way along.
Twist into a helix (wrapping round a test tube or small measuring cylinder helps) so that the
relevant NH and CO groups come into contact (the fifth NH lines up with the first CO, so it is
helpful if these are coloured the same). Paper hydrogen bonds can be taped between the groups.
• EOCQ 4 could be used for a test covering Topics 1 to 3.
• The Protein Data Bank is an on-line store of data about large biological molecules such as proteins
and nucleic acids. It would be easy to use this to show examples of ribbon models of proteins, the
type used in exam questions.
Common misunderstandings and misconceptions
• Students often refer to dipeptide bonds, rather than peptide bonds.
• Quaternary structure is sometimes thought to involve four polypeptides, rather than two or more
polypeptides. This may be because students study haemoglobin, the quaternary structure of which
does involve four polypeptides. Quaternary refers to the fourth level of structure. Show students a
range of proteins including those with two, three or five polypeptide chains.
Supporting struggling students
• As with the previous topic, molecular models are helpful, particularly if they are made by students
themselves.
• Draw a pentapeptide using R to represent the R groups so the student concentrates on the repetitive
nature of the backbone.

Challenging high achievers

• Build a model protein (see ‘Main lesson content’, second bullet point).
• Design a poster (see ‘Main lesson content’, third bullet point).
• Explore the link between biological molecules (not just proteins) and materials science – how are
biological materials of interest to materials scientists?
• High achievers may be interested in finding out about proteasomes. The Protein Data Bank has
information about their structure.
Homework suggestions
• Make a paper model of an alpha-helix (see above).
• EOCQs 1, 2, 5, 8, 10
• EOCQ 4 if not used for section 2 test

Other recommended resources

www.rcsb.org
The RCSB* Protein Data Bank is a free online store for the three-dimensional structures of large
biological molecules and structures such as proteins, nucleic acids and ribosomes. It is a key resource
for biologists worldwide. It is always interesting to check out their ‘Molecule of the Month’. Many

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fascinating structures can be viewed. Videos are also available showing molecular animations, such as
the binding of oxygen to haemoglobin.

*RCSB: Research Collaboratory for Structural Bioinformatics.

www.rcsb.org/pdb/education_discussion/educational_resources
Posters of molecules and metabolic pathways, such as the Krebs cycle, are available on this section of
the RCSB site; for example, ‘What is a Protein?’ and ‘Molecular Machinery: A Tour of the Protein
Data Bank’, including nucleosome, microtubule, collagen and ribosome structures.

wwpdb.org/iycr2014.html
2014 is the International Year of Crystallography, commemorating 100 years of X-ray diffraction. The
Protein Data Bank calendar for 2014, available to view on the above link, illustrates how X-ray
crystallography has contributed to an understanding of biological molecules. There are spectacular
images of, among other things, myoglobin, a ribosome and insulin.
www.johnkyrk.com/H2O.html
www.johnkyrk.com/aminoacid.html
John Kyrk’s website has animations about water, and about amino acids and proteins.
Alberts, B. et al. (2013) Essential Cell Biology, 4th edn. Garland Science
Highly recommended. This classic book has a variety of resources for students that are freely available
at www.garlandscience.com/ECB4-students. The following are useful animations with explanatory
narration:
• ‘Protein structure and function’: Viewing proteins, Alpha helix, Beta sheet, Disulfide bonds

Topic 4 Water

Suggested activities
Possible starters
• The collective strength of hydrogen bonds in liquid water is easily demonstrated. The hydrogen
bonds between water molecules in its liquid state are responsible for a relatively high cohesion
between the molecules. This is biologically important, as in movement of water up xylem. It can
be demonstrated by floating a pin on the surface of water. The high surface tension of water that
makes this possible is a result of the high ‘cohesion’ between molecules. Add a drop of washing
up liquid to reduce the surface tension and observe the pin sink immediately.
• Add a drop of water to a clean glass surface. Compare its shape with that of a drop of ethanol on
the same surface. Discuss the difference. How much ethanol must be added to the water drop to
change its shape?
Main lesson content
• The solvent properties of water are easily demonstrated by dissolving salt in water – does this
affect its surface tension? How do you get the salt back?
• Latent heat of vaporisation can be demonstrated by setting up two clamped, inverted round-
bottomed flasks. Cover one with a wet cloth. The temperature inside this flask will fall relative to
the other. Discuss the relevance of this observation.
• A set of triangle cards could be made as an end-of-section 2 exercise. Outline six equal triangles
on a hexagonal piece of card, or eight equal triangles on a square piece of card. The triangles meet
in the centre of the shape. On each side of each line that connects the centre of the card to the
outside edge write a matching pair of statements (e.g. term for water-hating / hydrophobic, or
protein secondary structure / alpha-helix). Cut up the shape into its triangles. Then ask students to
re-create the shape by matching the statements. Students can design their own sets of triangles

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 (possibly for homework) to test each other in pairs or small groups. More complex shapes can be
assembled, with all three sides of some triangles being used for statements.
Common misunderstandings and misconceptions
• Non-chemists find it difficult to understand the difference between the full positive and full
negative charges of ions and the slight charges on water molecules caused by uneven distribution
of electrons.
Supporting struggling students
• Students could be encouraged to write a piece of prose concerning the properties of water. Various
levels of help can be provided. You could provide the student with a series of statements and
prompts about water, e.g. ‘Water has a high latent heat of vaporisation. [Explain this term and give
examples of how this property is used in cooling animals and plants]’. Ask the student to expand
on each statement using the prompt provided. Alternatively, just give the key points that should be
addressed, e.g. ‘specific heat capacity, surface tension’, etc.

Challenging high achievers

• Design their own set of triangle cards (see ‘Main lesson content’, third bullet point) or loop
activity (Chapter 1, Topic 4).

Homework suggestions
• SAQ 2.6
• EOCQ 3
• Homework 2.1
• The students could make a loop activity for biological molecules and try it out in class (Chapter 1,
Topic 4).
• In groups, students make a concept map, mind map or other form of graphic organiser for proteins,
carbohydrates or lipids (examples of mind maps can be found on the internet). It might be a good
idea to give each group the key terms that they should use in their organiser.
Other recommended resources
www.johnkyrk.com/H2O.html
John Kyrk’s website has an animation about water.
 

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