Choosing an option

Two major considerations for teachers in selecting the one option (of the five available) for their students to study, are first their students' likely interest in the topic and secondly their ability to cope with the amount and complexity of the material. Other considerations are likely to be how well the material integrates with and reinforces core material and how straight-forward and/or predictable are likely examination questions on the material. The availability of equipment for laboratory work is another consideration.

Judging by the number of pages I needed to cover the material in each of the three options treated in Conquering Chemistry, the Forensic chemistry option would appear to contain the most material with much of it being quite complex for students whose background in organic chemistry is just the core material. While a good option for students with a strong biological interest, it could be daunting for weaker students. The name of this option is somewhat deceptive: while there are frequent attempts to relate the material to what forensic scientists do, basically this option is an introduction to biochemistry (or biological chemistry as it used to be known in the pre-2000 syllabus). If one were genuinely after an introduction to forensic chemistry, such large slabs of the chemistry of sugars and proteins would not be included. The name is considerably more attractive to students than the material it contains, so teachers should not rush into selecting this option before having a good look at its contents. 

This option treats some fairly sophisticated instrumental techniques – electrophoresis, gas chromatography, HPLC, mass spectrometry and atomic emission spectroscopy. Teachers need to know that they will at least be able to show examples of these instruments to their students before adopting this option. Having a university or technical college nearby with a welcoming chemistry department would be a big advantage. While this would be adequate for most instrumental techniques, the school really needs to have at least very basic electrophoresis equipment to do this option. Simple chromatography experiments present no problem for the typical school lab. Also note that although the syllabus says emission spectra can be studied either with flame tests or a hand spectroscope, the spectroscope is essential, because students have to examine the spectrum of mercury and that cannot be done with a flame test (mercury is too poisonous).

Despite these difficulties, this option has been moderately popular and students who have done it have often been quite enthusiastic about it.

With the current heavy emphasis on factual recall in exam questions, the quantity of material to be assimilated is probably a key consideration in selecting an option. 

In writing Conquering Chemistry I thought that the other two options, Biochemistry of movement and Chemistry of art, contained too much material of too diverse a nature for the seven weeks available for the study of the option. Of course these options will particularly appeal to certain groups of students – those strongly interested in sport and dance and those with a strong artistic bent – and strong motivation can easily overcome barriers that may seem daunting to others.

Some general comments

1. Exam questions

HSC exam questions in the Options section of the paper differ somewhat from questions in the core section in that: 

Because of this absence of calculations and problems from the options sections of the HSC exam paper, there are no Further Exercises sections on the Options pages of this website. 
   

2. Structural formulae

Occasionally the HSC exam question has instructed students to draw the structural formula of a compound (or class of compound). Strictly speaking a structural formula shows all the chemical bonds as for example the general structure of an amino acid is (2007):

where R is a hydrogen atom or a carbon-containing group (such as an alkyl group).
Reports from the examination centres have not made it clear whether condensed structural formulae such as
or    
would get full marks, though in the absence of a comment to the contrary they probably do. Students should be encouraged to draw complete structures (unless the molecule is fairly complex) and certainly they should avoid abbreviating carboxylic acid and ester groups to –COOH and –COO–. 
   

3. Structures for saccharides

Because saccharides are fairly complex molecules, a variety of structures can be drawn for the one compound and it is essential that students can interpret any given structure and recognise  the compound in question. For example for glucose some of the structures that are commonly drawn are:

1.	Draw the hexagonal ring flat with the H and OH groups above and below the ring and show all atoms
2.	Omit the C atoms. This is a common practice for chemists: at every apex in the structure there is a C atom. The planar ring here and in 1 is drawn perpendicular to the plane of the paper; sometimes the 'front' bonds are drawn heavier than the others to denote this.
3.	Omit the H atoms also; this is another common practice, though not recommended for HSC students. At each apex there is a C atom which has enough H atoms on it to bring the valence up to four. Double and triple bonds, if present,  are always drawn.
4.	Draw the ring in its true shape which is puckered – a chair form is what chemists call this – and again the C and H atoms can be shown or just 'understood' to be present.
5.	And with any one of these the whole structure can be tipped upside down (rotated about an axis through the extreme left- and right-hand C atoms). We had to do this to alternate glucose units in cellulose in Fig 13.6 on p 470-1 though there it was the b isomer involved (not the a one as in all these structures here).
6.	Or the structure in 4 can be rotated about an axis perpendicular to the plane of the paper.

All of these structures are a-glucose – the carbonyl OH is on the opposite side of the ring from the CH₂OH. The carbonyl OH is the one at the right hand end of the structures (except in Structure 6). See p 468 and 474. b-glucose has the H and OH on the carbonyl carbon interchanged (p 474-5):


You may be required to draw a structure of glucose. The following rule may help you memorise the structure of glucose: starting from the O atom and going to the C with CH₂OH attached and keeping going around the ring in that direction, the OH groups are opp, same, opp, opp for a and opp, same, opp, same for b. Opp means on the opposite side of the ring from the CH₂OH group, and same means on the same side of the ring. Structures 2 above are the easiest to see this on, but the rule applies to all the structures drawn.

For fructose there is less variety in the structures that can be drawn because the five-membered ring is virtually planar. For 1, 2 and 3 above we have for b-fructose (the form used to make sucrose):

If we draw sucrose with glucose on the left (as is commonly done) we need to rotate our fructose molecule 180^o around an axis perpendicular to the plane of the paper through the O atom. Rotating the right-hand structure of 2 gives:
                  
(The structure of sucrose is given on p 468-9.)
      a-fructose (in the style of 2) is:
                      
   

4. Carbonyl compounds, a-b isomerism and disaccharides 

(This account contains more detail than is required for the HSC but it may help you understand better what is going on in the test for reducing and non-reducing sugars.)

Carbonyl compounds are compounds that contain the carbonyl group C=O. Two classes of carbonyl compound are aldehydes and ketones. Aldehydes have the general structure
                                
 where R₁ is a hydrogen atom or a carbon-containing group (such as an alkyl group). Ketones have the general structure
                                
 where R₂ and R₃ are carbon-containing groups; R₂ and R₃ cannot be hydrogen atoms but they can be the same group (e.g. methyl groups).
One property of these carbonyl compounds is that they react reversibly with alcohols to form hemi-acetals and acetals:
                    
The ring structures of simple monosaccharides are actually hemi-acetals (see Fig 13.10 on p 474). Rather than the carbonyl and alcohol groups being on separate molecules as in the above equations, they are both on the same molecule. When two monosaccharides combine together to form a disaccharide they are actually forming an acetal: one monosaccharide is acting as a hemi-acetal while the other is the alcohol. In Equation 13.1 on p 468 the hemi-acetal glucose (right-hand glucose) forms an acetal with an alcohol group of the left-hand one and the maltose molecule formed is an acetal.
     In carbohydrate contexts an acetal is called a glycoside and the monosaccharide–O–monosaccharide linkage is called a glycosidic bond or glycosidic link. For example the disaccharides, sucrose, maltose and galactose, are glycosides or contain glycosidic bonds.
     The hemi-acetal form of a monosaccharide can easily convert back to the carbonyl form, that is convert to the open-chain form of the monosaccharide as in Fig 13.10 on p 474. This is how a-b isomerism occurs and is why an aqueous solution of a monosaccharide contains both isomers. However once a glycoside has formed with an alcohol or another monosaccharide, the compound no longer easily reverts to a hemi-acetal; that is the glycosidic link is not easily broken. Hence sucrose does not easily revert to glucose and fructose; it needs an acid or enzyme catalyst to do it. And this is why sucrose is a non-reducing sugar (p 475-6): there is no carbonyl group to reduce Ag⁺ or Cu²⁺.
     Actually it is not strictly correct to say that carbonyl groups reduce Ag⁺ or Cu²⁺ . Certainly aldehydes do but normal ketones do not. In fact the Benedict's and Fehling's solutions tests are used to distinguish between aldehydes and ketones. However if there is a CH₂OH group beside the C=O group, then that combination can reduce Ag⁺ or Cu²⁺ as shown on p 475. If you are not convinced that going from –CO–CH₂OH to –CHOH–COOH is oxidation then write the half reaction:
                             –CO–CH₂OH  + H₂O   ®   –CHOH–COOH + 2H⁺ + + 2e^–
or more simply, there has been a gain of an oxygen atom.
     The term glycoside or  glycosidic bond does not appear in the syllabus document or in CCHSC but the latter is mentioned in the 2007 Report from the Marking Centre, so maybe it does need explanation.
     This rambling account is meant to put a little more chemistry behind the test for reducing and non-reducing sugars that is required for the HSC, though all this chemistry is not required for the HSC.

5. Peptide formation

The formation of dipeptides and tripeptides is discussed in CCHSC on p 484-5 and molecular models of on dipeptide is shown in Figure 14.2. It may be helpful to look at the formation of another dipeptide and also of a tripeptide. The dipeptide in Figure 14.2 is alanylcysteine. Now we shall consider the formation of the other peptide that can be made from these two amino acids – by using the other ends of the molecules to join them together.

Formation of the dipeptide cysteinylalanine

Using space-filling models
Using ball-and-stick models

Formation of a tripeptide using glycine, alanine and cysteine

Using space-filling models

Same thing but using ball-and-stick models

6. DNA analysis

If you compare the account of DNA analysis in CCHSC with the accounts in other HSC textbooks and study guides, you will find that CCHSC is the odd one out; the other books describe processes involving restriction enzymes and radioactive transfers from electrophoresis plates etc. Rest assured that the account in CCHSC is the standard procedure currently being used in Australia for forensic purposes, that is for identifying persons. The account in CCHSC was checked by a senior scientist in a laboratory that routinely does DNA analysis for the NSW police force and the results shown in Fig 14.16 came from a similar forensic laboratory. The procedures described in the other texts date from the 1990s before current methods were fully developed. It is a pity the HSC examiners in 2003 chose to use a very old electrophoresis plate for their exercise in Question 34(d).
    The earlier methods that cut up the DNA using restriction enzymes were not nearly as sensitive as the current methods. It is the PCR amplification (p 502) that makes current methods extremely sensitive (able to use very small samples). 
     In addition those earlier methods were not conducive to setting up DNA data banks, because they required that samples for comparison be run in parallel using identical conditions for each and then comparing the electrophoresis patterns as in the 2003 HSC exam question; these patterns were not just of a few selected introns. The current method focuses on just ten introns by magnifying (amplifying) them by a factor of over a million while leaving other introns unaffected and therefore insignificant on the electrophoresis plate. It is possible to prepare a mixture that contains all possible lengths of these ten introns and this standard mixture can be run along side the test sample to allow the lengths in the sample to be calculated (as in Fig 14.16 on p 504). Because actual lengths of introns can be measured in this way a data bank can be established. The data bank is dependent upon the introns being used. If a new procedure was adopted that used a different set of introns, then the existing data bank would become useless; DNA data banks are specific to the particular set of primers (and introns) being used.

     As explained on p 505 DNA analysis for forensic purposes is not the only type of DNA analysis. For scientific and medical purposes restriction enzymes are widely used to cut DNA molecules into smaller lengths which are then sequenced by cutting off nucleotides one by one and identifying them by electrophoresis. In such analyses radioactive labelling as an alternative to fluorescence tagging is sometimes used. A variety of techniques of DNA analysis involving clever interpretative skills is used for a range of medical and genetic studies; this work is usually more detailed and complex than what has now become a fairly routine method of DNA analysis for identification (forensic) purposes.

      The common sources of DNA for forensic testing are saliva, blood, semen and hair follicles (roots). Note that despite what you often see in TV crime shows hair itself does not contain DNA: it's pure protein. You need the hair root to get DNA.

Exercise

7. Functional groups

It may be helpful to summarise the various functional groups that we have met throughout the HSC course:
.

Functional group	Name	Endinga	Example
a Added to the stem, meth-, eth-, prop-, but- etc.

8. Which analytical technique for which classes of compounds?

This option considers several techniques for the analysis of very small samples – gas chromatography, paper chromatography, HPLC, atomic emission and absorption spectroscopies, electrophoresis, mass spectrometry. The question arises, which technique is best for a particular class of compound. The following table show which techniques are best suited to which class of compound (of those considered in this option).

     Gas chromatography requires the sample to be vaporised for the analysis to occur. This means that it is not effective for classes of compounds such as carbohydrates, amino acids and proteins because these classes of compound generally decompose before they vaporise. Carbohydrates have very high melting and boiling points because of the large amount of hydrogen bonding between molecules which arises from the large number of OH groups in the molecules. Amino acids are non-volatile because of their zwitterion (ionic) structure. While this similar presence of charges on proteins is a factor in their lack of volatility, the large molecular weight is also a major factor. Carbohydrates, amino acids and proteins can be analysed by HPLC provided the molecules are not so large that they have very low solubilities in available solvents and stationary phases.

 
Exercises
(Answers at the bottom of the page)

2.

Barbiturates are the most widely used sedatives and relaxants, though they are addictive. They are used in sleeping pills and in medications used to calm down over-excited people. Unfortunately people can overdose on them and die, and tragically some people use them for murder and suicide. Mixtures of barbiturates can be analysed by gas-liquid chromatography. Figure (a) below is a chromatogram of a mixture of seven known barbiturates. To try to identify the drug that caused the death of a person, a forensic chemist extracted any possible barbiturates from a sample of blood from the deceased and performed a GLC analysis using conditions identical with those used for chromatogram (a). The resulting chromatogram is shown at (b). What is the main barbiturate in this sample? To help investigators determine the source of the drug, identify any impurities in the drug and determine the relative composition of the mixture. (It may be helpful to print out these graphs.)

3.

An analyst wished to determine which of certain metal ions were present in the water from a particular creek. The metals of interest along with the wavelengths of their four or five strongest emission lines are shown below. An emission spectrum of a sample of the water was measured: it is shown below. Which of the metals in the table are present in the water sample? Are there any emission lines unaccounted for? Suggest some possibilities for these lines. Metal Wavelengths of emission lines (in nm) Ba 389 455 554 649   Cd 361 442 509 644   Cr 358 361 425 465   Cu 282 325 522 578   Fe 358 372 382 386   Hg 365 405 436 546 579

 
Supplementary material  (not required for the HSC)

1. Diabetes and blood sugar levels

Diabetes is a disease in which the body is unable to regulate its blood sugar levels properly. If not controlled, it can lead to fainting spells or comas, symptoms of malnutrition (despite adequate food intake) and kidney and heart damage. It arises because the pancreas is not producing sufficient of the hormone insulin.
Despite our intermittent eating habits, the human body is able to maintain fairly uniform levels of blood sugar throughout the day. 'Blood sugar' is the medical or everyday term for glucose, the predominant sugar carried by the blood. Immediately after eating (particularly a meal rich in sugar), the glucose concentration in the blood rises to quite high levels. This stimulates the pancreas to secrete insulin which is needed to convert glucose to glycogen. Glycogen is stored mainly in the liver. Glucose concentrations in the blood are thus reduced. As body cells use up the blood glucose, glycogen is converted back to glucose. In this way a fairly constant concentration of glucose in the blood is maintained for several hours after a meal. If the meal had been low in glucose but high in starch, then the body would slowly hydrolyse the starch and supply a steady supply of glucose to the blood stream without the intervention of insulin and glycogen.
     If the pancreas is unable to make insulin (or to make enough of it), glucose is not stored as glycogen in the liver. Glucose concentrations in the blood remain high and the kidneys start removing it and passing it to the urine. In this way glucose is fairly quickly removed from the body.
     This has two bad effects. First the body becomes starved of glucose, since body cells quickly use up what the kidneys have not removed. Secondly high concentrations of glucose in the kidneys lead to greatly increased urine output and cause considerable strain on the kidneys. This in turn causes heart disease.
     The brain gets all its energy from glucose and is the first body organ to suffer if glucose levels drop off dramatically. This can lead to collapse or coma.
     Diabetes may be a genetic disorder, but can also be the result of an infection in the pancreas which permanently damages its ability to generate insulin. Diabetes in very young children is generally the result of a viral infection. The genetic disposition to the disease usually shows up in middle-aged and older people. Diabetes can be exacerbated by obesity.
     Mild cases of diabetes can be controlled by diet. By eliminating or greatly reducing the intake of mono- and disaccharides (which are very quickly transferred to the blood as glucose), the sufferer prevents glucose concentrations rising to high levels after eating. The use of starch as the energy source results in a slow release of glucose to the bloodstream over a period of several hours after eating. And by having frequent small meals or snacks the lack of energy storage in the liver is overcome.
     Some cases of diabetes can be controlled by drugs which stimulate the pancreas to produce sufficient amounts of glucose. Severe cases require daily injections of insulin.
     Diabetics can suffer two types of coma, one resulting from too high a level of glucose, the other from too low a glucose level. The first type is recognised by the sweet smell of acetone on the breath and needs a shot of insulin to cure it. The second type is caused by a very low glucose concentration  which starves the brain; this coma is overcome by administering glucose. Diabetics often carry sweets (high glucose content) as a safety precaution. Because these comas can easily be mistaken for drunkenness, diabetics generally wear a bracelet or neck chain identifying them as diabetics.
     The existence and control of this disease emphasises the complex interplay of energy intake, storage and utilisation that goes on in the human body.
    

2. Glycemic index, G.I.

An important aspect of food, particularly for diabetics and people needing to watch their weight carefully is glycemic index.
    The glycemic index G.I. of a food is a measure of the speed at which glucose is released from that food by the human body to the blood stream. A high G.I. means that glucose is released quickly; a low value means it is released more slowly. 
     Essentially the G.I. of a food is the amount of glucose released to the blood stream over a two-hour period after eating a quantity of the food expressed as a percentage of the amount of glucose released after eating a mass of pure glucose equal to the mass of carbohydrate in the food being tested. So glucose has a G.I. of 100. The table below classes some common foods in terms of their G.I. (low, medium or high).
     A food with a high glycemic index rapidly produces glucose. This is a problem for diabetics as explained above but can also be a problem for other people because the glucose is rapidly converted to glycogen and as glucose levels fall the person begins to feel hungry again and may overeat and become overweight. A food with a low glycemic index releases glucose more slowly over a longer period of time and so the person does not feel hungry quite so quickly and can more easily manage food intake.
     It has been found that eating foods with low glycemic indices can help people manage their diet and weight more easily.
     It is perhaps surprising that foods with high starch contents can have quite different glycemic indices. This is because the starch can be present in different physical forms and mixed up with other substances such as cellulose in different foods and this makes it harder for body enzymes to get at it. Fructose, a major sugar in fruit, has a low G.I. because, though a monosaccharide, fructose cannot be used directly as an energy source by the body. Fructose first has to be converted to glucose and that takes time which is one reason why fruit is a very good food. 

3. How fussy can we get? Galactosemia and phenylketonuria (PKU)

The two genetic disorders, galactosemia and phenylketonuria, illustrate just how fussy the human system is.  Very slight differences in molecules can cause big problems.
     Galactose is a monosaccharide which is very similar to glucose; the two compounds differ only in the positioning of one OH group (CCHSC Figure 13.2 on p 466). Galactose and glucose are the monosaccharides that make up the disaccharide lactose that is present in many foods, particularly in milk. The cells of our body are not able to metabolise galactose directly. 'Normal' humans have an enzyme that catalyses the conversion of galactose to glucose.  While the presence of galactose in most parts of the body causes no problem, the brain is severely damaged by it. This leads to mental retardation.
    Genetically some people do not have the necessary enzymes for the conversion of galactose to glucose.  They suffer brain damage if the problem is not detected very early in life, particularly as all milk – cow and goat as well as human – contains lactose which hydrolyses to galactose and glucose.  People with this disorder called galactosemia need a special diet that excludes all foods that contain galactose (mainly dairy products).
     Phenylalanine and tyrosine are common amino acids. They differ in that tyrosine has an OH group on the benzene ring:  

     The human body does not use phenylalanine. Instead it has an enzyme phenylalanine hydroxylase that converts it to tyrosine which the body does use: it incorporates tyrosine into many of the structural and functional proteins of the body. Genetically some people lack this enzyme. Hence phenylalanine builds up to quite significant concentrations in the blood and this causes brain damage. The condition is called phenylketonuria or PKU.  If it goes undetected, it causes severe mental retardation.
     Fortunately simple blood tests are available for detecting both of these conditions.  In Australia all babies are routinely tested a couple of days after birth for four conditions – the two discussed here plus cystic fibrosis and hypothyroidism.  The combined test is called the Guthrie test or just the Blood Spot test.  Until a few years ago PKU was detected by testing the urine of young babies.
      The method of controlling PKU is to restrict very greatly the amount of phenylalanine in the diet. The widely used artificial sweetener, aspartame (trade name Nutrasweet) must be avoided, because it hydrolyses to aspartic acid and phenylalanine in the digestive tract. Controlled diet is particularly important for babies and very young children. When more mature, PKU sufferers are able to tolerate higher concentrations of phenylalanine. This means that diets can be considerably relaxed. However female PKU sufferers must revert to strict diets several months before becoming pregnant, because levels of phenylalanine which are harmless to the mother can cause irreparable brain damage to the unborn baby. 
     These two disorders illustrate just how precise the chemistry of living systems is; very small changes in structures can have quite drastic consequences.  
  

4. Hair perms

Permanent waving of hair is a simple example of how the secondary and tertiary structure of a protein can be modified. The main constituent of hair is the protein, keratin. It contains considerable amounts of the sulfur-containing amino acid cysteine (CCHSC Table 14.1 on p 482). This means that sulfur-sulfur bridges (p 487) play an important role in determining the secondary and tertiary structure of keratin.  
     The 'curliness' or 'straightness' of hair fibres can be altered by modifying these S–S bridges.  First the hair is treated with a reagent which breaks S–S links and reduces them to SH groups as in the original cysteine.  The hair fibres are then distorted by wrapping around rollers, and finally the hair is treated with another chemical which oxidises nearby SH groups to new S–S bridges. Because different SH groups become lined up when the hair is rolled, the resulting overall structure is different from the starting one. The diagram illustrates the procedure.  
     This procedure is 'permanent' in that these new S–S links remain intact, but of course as the hair grows, the new hair has the original (genetic) alignment of the fibres. Hence permanent waves eventually grow out.

Answers to exercises

260213