241Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York. This document may have been altered from the original.

TLTHE THREAD OF LIFE

Concept mapThis concept map shows how the major chemical ideas in this teaching module develop throughout the course.

Concept First introduced in module

Developed in module(s)

Assumed in module(s)

Relative atomic mass and relative formula mass EL all

Amount of substance EL DF allChemical formulae and inorganic nomenclature EL ES allBalanced chemical equations EL DF allAtomic structure EL allCovalent bonding EL DF, ES, PR allShapes of molecules EL DF allRelationship between properties, and bonding and structure

EL MR, TL, AI, CD, O DF, ES, PR, SS

Catalysis DF A, TL, SS, AI severalIsomerism DF PR, TL MDHomologous series DF PR severalNomenclature of organic compounds DF ES, PR, WM, MR,

TL, CDMD

Structural formulae (full, shortened and skeletal) DF ES, PR all organic modules

Organic functional groups DF ES, PR, WM, MR, TL, CD

MD

Properties of alkanes DF severalStructure of benzene DF CD WM, MR, TL, MDIonic equations ES SS severalIonic substances ES O severalElectronegativity and bond polarity ES PR, O severalIntermolecular bonds ES PR, MR, TL, O AI, CD, MDRedox ES SS, AI severalIndustrial applications ES WM, MR, TL, SS,

AIMD

Atom economy ES WM TL, AI, MDRates of reactions A TL, AI Bond ssion A PR severalElimination reactions PR severalCarboxylic acids PR WM, MR TL, AI, CD, MDPolymers and polymerisation PR MR, TL MDChromatography WM TL, CD AI, MDAcids and bases WM O TL, SS, MDCondensation reactions WM MR, TL MDDelocalisation of electrons WM CD severalAmines MR TL CD, MDAmides MR TL CD, MDGreen chemistry MR TL, AI CD, MDAmino acids TL MDProteins and enzymes TL MDDNA and protein synthesis TL Molecular recognition TL MD

242Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

TL Advance warning

Advance warningThe following items needed for activities in this module may not be in your school currently, and might take a little time to obtain.

Activity Item(s) Essential/optional Typical quantity per activity

TL2.1 glycineethanoyl chloride

EssentialEssential

2 g2 cm3

TL2.3 aspartame (e.g. Canderel) tabletsaspartic acidphenylalanine

EssentialEssentialEssential

13 tabletsSmall amounts for chromatographySmall amounts for chromatography

TL2.4 mirror Essential access to 1

TL3 small sweets e.g. Micro Mix or Jelly Bearsstrawberry sweet lacescocktail sticks

EssentialEssentialEssential

1016

TL4.1 glucose test strips (such as Clinistix or Diastix)* Essential 510

TL4.2 potassium peroxodisulfate(VI) (K2S2O8) Essential 0.0400 mol dm3 (10 cm3)

TL4.5 set of graphs and description boxes Essential 1 set per group

TL5 plastic-coated wire (e.g. Radio Spares 30 0.25 mm strand: code RS360239 to RS360295 depending on colour)*Minit molecular model peg type a: Ref 7a293 (white) to 7a300 (green) depending on colour*21 cm plastic tubes: Ref 72289 (red)*RASMOL or other electronic molecular structure les

Essential

Essential

EssentialOptional

1 m

30

81

* Current suppliers are listed on the Salters Advanced Chemistry website.

Storyline: answers to assignments 1 a i Amino acids with non-polar side chains are: Gly Ala Val Leu Ile Phe Pro (Trp Met) ii Amino acids with polar side chains are: Ser Thr Cys Asp Glu Asn Gln Tyr His Lys Arg iii Amino acids with ionisable groups on their side

chains are: Asp Glu His Lys Arg Tyr b The side chains in Leu and Ile make them structural

isomers. c i Ser ii Thr iii Tyr iv Either Asp or Glu2 a

CH COOHCO NH CHH2N

HCH3 b i Ser ii Ala3 a Butenedioic acid. b

Z E c No, since butanedioic acid will bind to the active site in

only one way, so only one E/Z isomer will be formed.

d HOOCCH2CH2CH2COOH It might if the relevant parts can t on to the active

site. This is unlikely, however, so it probably would not react and might be an inhibitor. If a product were formed it would be pentenedioic acid.

4 a Franklin was close. The DNA structure is helical, with phosphate groups on the outside. She did not postulate a double helix, though.

b

O

O

O

OMg2

H

H

H H

H

H

H

H

Mg2+ already hydrated so unable to bond to phosphate groups.

c

O

OH

PHO

OH All the OH groups.

Activities: notes and answers to questions TL

243Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York. This document may have been altered from the original.

TL2.1 Investigating an amino acid

Safety note Information about hazardous chemicals is given on the activity sheet.1 Glycine is soluble in water. It is largely present as

zwitterions, which are solvated by water resulting in iondipole interactions.

2 Glycine solution is close to neutral (slightly acid). The pH should remain fairly constant throughout the additions of acid and alkali. The theory is covered in the Chemical Ideas section on amino acids.

3 Only butylamine reacts with ethanoyl chloride. Both dissolve in water. Butylamine is basic but glycine is neutral. The zwitterion form of glycine is responsible for its different behaviour. There is no NH2 group with its lone pair of electrons to react with the acid chloride. The zwitterion can be either a proton donor or a proton acceptor in solution, which is why the amino acid is neutral. Butylamine dissolves in water as a result of hydrogen bonding, glycine dissolves as a result of iondipole bonds.

4 Only relatively weak intermolecular bonds (dipoledipole bonds, dipoleinduced dipole bonds and hydrogen bonds) between molecules of butylamine. Glycine exists as zwitterions with strong ionic bonds between the particles.

TL2.2 The structures of peptides

This activity provides an opportunity for students to practise using molecular models and molecular drawing software to reinforce their ideas about molecular structures.

1 The structural formulae of the three amino acids are:

CH

H

COOH

CH

CH3

COOH

C

COOH

H2N CH

CH3

CH3H

H2N H2N

5 One possible dipeptide is:

Gly Ala

COOH

CH3

C

H

H

CH2N

H

C

H

N

O

The six dipeptides are: Gly Ala, Gly Val, Ala Gly, Ala Val, Ala Val, Val Ala6 One possible tripeptide is:

C

C

H H O

C CC COOHCNN

H CH

CH3H3C

H2N

H H HCH3Gly Ala Val

The six tripeptides are: Gly Ala Val, Gly Val Ala, Ala Gly Val, Ala Val Gly, Val Gly Ala, Val Ala Gly

Activities: notes and answers to questions

5 a Both condensation. b

H

H

C

H

H

H

H

HH

CO

C

C

HH

C

O

O

6 a Only two bases are important in coding for: Ser Leu Pro Arg Thr Val Ala Gly b Three bases are important for: Phe Tyr Cys Trp His Glu Ile Met Asn Lys Asp Gln7 a i Lys Lys ii Arg Ala Arg Ala iii Tyr Leu Thr b i ACC ii CUA or CUG8 a GUCA b GTCA9 There are a few correct answers here. The object of the

assignment is to start the students thinking about these matters. A few suggested answers are given to the right to open discussion.

a i The individual him/herself. Their doctors, for diagnosing genetic diseases but

see below. The police, for solving crimes this is of benet to

the whole community, although many might disagree.

ii Anyone else not mentioned above this is condential personal information.

b Should parents have the right to have their children tested?

Yes could help them to make decisions about how their children could be treated for genetic diseases.

No children may object to it later on. Should testing be performed for genetic diseases for

which there is no cure? Yes know areas where care is needed; cure may be

discovered soon. No just makes an individual anxious and they may

not suffer as a result of the condition. Should an individual be given his/her personal genetic

information? Yes its his/her right, the information relates to

themselves. No it may make the individual anxious (possibly

without cause). Should insurance companies make use of the data to

x premiums? Yes its only an extension to different premiums on

grounds of age and gender, for example; those with healthy genes will benet.

No they should distribute the risk equally for all.

TL Activities: notes and answers to questions

244Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

TL2.3 Whats in aspartame?

Safety note Information about hazardous chemicals is given on the activity sheet. Check that the articial sweetener you use contains aspartame and not saccharin. Also, avoid aspartame tablets such as Hermesetas, which also contain leucine.Peptide hydrolysis normally requires reux for several hours with moderately concentrated acid. However it is possible to get adequate results after 30 minutes reux with 4 mol dm3 HCl.1

NH

Acidhydrolysis

aspartame

aspartic acid phenylalanine methanol

O

OH2N OCH3

HO

O

H2N

HO

OH2N

OH

O

O

OHCH3OH+

2 It is important that the hydrolysed aspartame is checked against both amino acids. Aspartame itself, being only a dipeptide, will travel up the paper, and could be confused with an amino acid. Also, some tablets contain phenylalanine along with the aspartame. Both phenylalanine and aspartic acid must be detected to be sure hydrolysis has occurred.

TL2.4 The shapes of A-amino acidsThe model building in step 3 can be shared round members of a group to save time. If you have molecular modelling software this can be used to good effect alongside the model kits, and students can be given print-outs of, say, D-alanine and L-alanine at the end of the session.1

109109

109 120

N CC

H HO

OH

H

H

2 a

C H All angles 109H CC

H H

H

H

H

b

All angles 109C HO

H

H

c

H All angles 109C S

H

H

C

H

H

C

H

H

d

109

109 120

CC

H HO

OH

5 a

COOH

C(H3C)2HC

HH2N

HOOC

CCH(CH3)2

HNH2

b

7 Molecules that are non-superimposable on their mirror images are chiral. A carbon atom that is surrounded by four different groups is called a chiral centre.

TL3 Modelling protein structures

This activity aims to reinforce students ideas about the structures of proteins in a more unusual way. If students are allowed to eat the sweets they have used after completing the activity, it is recommended that this activity does not take place in a laboratory unless careful measures have been taken to ensure that the sweets cannot become contaminated with chemicals.1 The small sweets represent amino acids.2 Peptide links join the amino acids together (the lace).3 Condensation reactions are involved in creating peptide

links.4 The sequence of amino acids is the primary structure of

the protein.5 The helix or pleated sheet is the secondary structure of

the protein.6 The structure created when sections of the helix or

pleated sheet is folded upon itself is the tertiary structure of the protein.

7 The cocktail sticks could represent instantaneous dipoleinduced dipole, permanent dipolepermanent dipole, hydrogen, ionic and sulfursulfur covalent bonds.

8 Phenylalanine and leucine are likely to form instantaneous dipoleinduced dipole bonds.

9 Serine and asparagine are likely to form hydrogen bonds.

H

H

CN

CH2 H2C

OH

O10 Aspartic acid and lysine are likely to form ionic bonds.

H2C

H2C CH2H2C

H3N CH2

O

OC

Activities: notes and answers to questions TL

245Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York. This document may have been altered from the original.

TL4.1 Testing for glucose

Safety note Information about hazardous chemicals is given on the activity sheet. In a simple experiment, the test strips could be placed in dilute acid or alkali, or in boiling water, before being used to prove that these conditions deactivate the enzyme. More careful investigation might make use of solutions of different pH or water at different temperatures, and students might try to time how long a particular depth of colour takes to develop. The pH of urine is 4.87.5. The enzyme has no effect on other sugars. The use of test strips makes this activity quicker and more convenient than some other methods of studying enzyme catalysis. They can, however, be expensive for large groups. It helps to cut the test strips into thinner pieces.

TL4.2 Using the iodine clock method to nd the order of a reaction

Safety note Information about hazardous chemicals is given in the activity sheet.2 Iodide concentrations vary from 0.5 mol dm3 to

0.1 mol dm3. The corresponding times should be between about 80 s and 400 s.

3 I is always in excess.4 8 s 105 mol I2 can be produced in each case.5 a 2 s 105 mol S2O32 b 1 s 105 mol I2 c 12.5% of the total reaction is studied.7 The reaction is rst order with respect to iodide.8 a Rate = k[I] [S2O82] b Second order

c k = Rate _________ [I][S2O82]

units of k are dm3 mol1 s1

Rate ____ [I] can be found from the gradient of the graph.

d The value of k depends on the temperature.

TL4.3 Methods of following reactions

Safety note Information about hazardous chemicals is given in the activity sheet.

Two methods are described for following the course of this reaction; by titration and by using a colorimeter. Teachers may arrange for groups of students to use different methods, so that they can compare the methods and the results they obtain. The graph of concentration of iodine against time is a straight line. This indicates that the rate of reaction is the same at different iodine concentrations. The results show that the reaction is zero order with respect to the iodine and the students should conclude that iodine is not involved in the rate-determining step.

TL4.4 Enzyme kinetics

1 At high substrate concentration the process is almost zero order with respect to the substrate.

2 If the rst step in the mechanism were the rate-determining step, the rate of the reaction would depend on [S]. (It would be rst order with respect to the substrate.)

3 At saturation, [ES] will be constant, and so the rate of conversion of bound substrate to unbound product (ESmP + E) remains constant. It is independent of [S], i.e. the reaction is zero order with respect to substrate.

4 At lower substrate concentrations, the rate at which the substrate binds to the enzyme decreases as the [S] falls. Enzyme active sites will no longer be full. The stage E + SmES eventually becomes rate-determining and the reaction becomes rst order with respect to substrate.

5 The reaction is always rst order with respect to enzyme.6 The enzyme concentration is always low compared with

the substrate concentration. The concentration of ES formed depends on [E]. So the rate always depends on the enzyme concentration, no matter which step is rate-determining.

TL4.5 Kinetics graphs

In this activity students choose from a set of eight graphs the one which best matches what they expect from a number of different situations related to rates of reaction (see below).

Description Graph Reason

[reactant] v time for a zero-order reaction (with respect to this reactant)

C rate of change of concentration with time is constant

[reactant] v time for a rst-order reaction (with respect to this reactant)

E graph illustrates a change of concentration with a constant half-life

[reaction product] v time F concentration increases from zero and reaches a constant value as the reaction is completed

rate of reaction v [reactant] for a zero-order reaction (with respect to this reactant))

A the rate is constant

rate of reaction v [reactant] for a rst-order reaction (with respect to this reactant)

B straight line, because rate is directly proportional to [reactant]

rate of reaction v [reactant] for a second-order reaction (with respect to this reactant)

D an exponentially increasing line

rate of reaction v [reactant]2 for a second-order reaction (with respect to this reactant)

B a straight line, because rate is directly proportional to [reactant]2

rate of reaction v [substrate] for an enzyme-catalysed decomposition reaction

F the reaction is rst order at low substrate concentrations and changes to zero order at higher substrate concentrations

number of collisions with Kinetic Energy E v Kinetic Energy (E) at temperature T K

G same prole as graph H, but is more narrow and has a higher peak

number of collisions with Kinetic Energy E v Kinetic Energy (E) at temperature (T + 10) K

H same prole as graph G, but is wider and has a lower peak

TL Activities: notes and answers to questions

246Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

TL5 Modelling DNA

Students gain a much better understanding of the structure of DNA if they draw and build models of the bases and the double helix. By doing this activity they should also realise that hydrogen bonding and instantaneous dipoleinduced dipole bonding are important for holding the structure together.

O

OH

OH

O

O

O

O

O

P

OH

OH

sugarphosphate backbone

O

OH

OH

O

O

O

O

O

POH

N

NO

HO

CH3

sugarphosphate backbone with base thymine

H

N

NN

NN

O

N

CH3

O

N

HH

base pair thymine and adenine

N

NN

NN

N

O

O

NH

N

CH3

H

H

H

H

base pair cytosine and guanine

1 The centre of the double helix is full; there is no empty space. This contrasts with the traditional ladder representation of DNA, which gives the mistaken impression that there are large gaps between the bases.

2 The helix could not be twisted more tightly because the bases are already at their closest.

3 Instantaneous dipoleinduced dipole bonding.4 Less twisting would take the bases further apart and the

structure would lose the instantaneous dipoleinduced dipole bonding. This bonding may be weak between any pair of bases, but it is signicant over the whole polymer.

TL7 Check your knowledge and understanding

This activity ensures that students are aware of the learning outcomes (specication statements) that their assessment will be based on, and provides an opportunity for them to reect on how well they understand the ideas that they have covered in this module. Crucially, it enables teachers to identify areas where individual students are less condent, and to provide appropriate additional support to improve their understanding. This activity could be used as part of the preparation for an end of module test.