How to Kill the COVID-19 Virus

By the middle of 2020 millions of people had been infected with a virus which causes a disease known as COVID-19 and hundreds of thousands of people had died.

So I was intrigued when I read that Professor Mary-Louise McLaws, an infection control expert from the University of New South Wales, had stated that, "it's relatively easy to kill compared to some other viruses".

Why is the COVID-19 virus easy to kill and how do you kill it? 

Read this edition of AUS-e-NEWS to find out more.

Subscribe to AUS-e-NEWS at https://www.ausetute.com.au/ausenews.html

Hydrolysis of Proteins

Lots of foods contain protein. When you eat them the proteins undergo hydrolysis reactions to break them down into their constituent amino acids.
AUS-e-TUTE has just added a new tutorial, game, test and exam to help you understand this.
AUS-e-TUTE Members should log-in to use these new resources (listed under Biochemical Reactions).
Non-members can currently access a "free-to-view" tutorial at
https://www.ausetute.com.au/hydrolysisprot.html

Breaking Triglycerides up into Fatty Acids

Triglycerides are found in the fats and oils you eat. They are produced in a condensation reaction between a glycerol and 3 fatty acids. So, is it possible to reverse this reaction? Can we add water to a triglyceride to break it up into glycerol and 3 fatty acids?
Good question!
AUS-e-TUTE has new resources to help you understand the hydrolysis of triglycerides.
Members should log in to access the new tutorial, game, test and exam (with worked solutions).
If you are not an AUS-e-TUTE Member, you can access the "free-to-view" tutorial at
https://www.ausetute.com.au/hydrolysistg.html

Omega Fatty Acids

"Health Food" companies are always trying to sell us something new.
Instead of eating tasty fish they recommend we consume fish oil wrapped in plastic as a pill. Apparently this is because we are suddenly deficient in "omega-3 fatty acids".
So what are omega-3 fatty acids?
Where do they come from?
Do we really need them?

AUS-e-TUTE Members should log-in to access the new omega fatty acid resources (tutorial, game, test, exam).

If you are not an AUS-e-TUTE Member you can access a free-to-view tutorial at
https://www.ausetute.com.au/omegafat.html

Rosalind Franklin and the Structure of DNA

Three men, James Dewey Watson,  Francis Harry Compton Crick and Maurice Hugh Frederick Wilkins, shared the The Nobel Prize in Physiology or Medicine 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.", that is, they  modeled DNA as a double helix, each strand of the helix has a backbone of  sugar molecules held together by phosphate groups. The two strands are twisted together and held together by hydrogen bonds. But how did they learn what DNA was made up of?

 This is where Rosalind Elsie Franklin enters the story of DNA. In 1951 she was a Research Associate at Kings College London where she worked on  X-ray diffraction studies with her colleague Maurice Wilkins. Her x-ray diffraction images of DNA led to the discovery of the DNA helix. The image on the left is known as "photograph 51" and was an x-ray diffraction image of DNA obtained by Franklin's Ph.D student Raymond Gosling.

X-ray diffraction is an instrumental technique used to elucidate the structure of crystals of chemical compounds. Incoming x-rays are diffracted by the crystal lattice and they exit the crystal at different angles. An x-ray crystallographer like Franklin can measure the angles and intensities of these diffracted x-rays to produce a 3-dimensional picture of the density of electrons in the crystal lattice. The electron density can then be used to determine the locations of atoms within the crystal lattice.

Without Franklin's knowledge, Maurice Wilkins showed this image to James Watson who used it, along with other evidence, to develop a model of DNA. Science historians still debate whether Franklin would have determined the structure of DNA on her own had her images not been shared with Watson.

Rosalind Franklin made important scientific contributions, not only to the discovery of the structure of DNA and RNA, but also in helping us to understand the structure of viruses, coal and graphite.
Unfortunately, Rosalind Franklin died of ovarian cancer in 1958. Nobel Prizes are not generally awarded posthumously so her contribution to the elucidation of the structure of DNA is not well-known.


Further Reading:
Chemistry of DNA
Intramolecular Forces
Intermolecular Forces

Suggested Study Questions:

1. Explain the terms crystalline and amorphous.
2. Give an example of a crystalline substance and an example of an amorphous substance.
3. Explain why DNA had to be crystallised before useful information could be obtained using x-ray diffraction.
4. What does the abbreviation DNA stand for?
5. What are the 4 principle bases that make up DNA?
6. These principle bases occur in pairs; what are these 2 pairs?
7. What kind of chemical bonds act between the atoms making up each base in a strand of DNA?
8. What kind of chemical forces join one of the bases on one strand of DNA to its corresponding pair on the other strand of DNA?
9. If you wanted to separate the 2 strands of a DNA double helix, what sort of chemical bonds would you need to break?
10. If you wanted to separated each base from the backbone of sugar molecules, what sort of chemical bonds would you need to break?

Fatty Acids

Do you want to answer any of the questions listed below:

• What is a fatty acid?
• What are the structures and formulae of common fatty acids?
• What is a saturated fatty acid?
• What is an unsaturated fatty acid?
• What is a monounsaturated fatty acid?
• What is a polyunsaturated fatty acid?
• What determines the melting point and solubility of a fatty acid?
• What is an essential fatty acid?
• What is an omega-3 fatty acid?
• What is an omega-6 fatty acid?

AUS-e-TUTE has new resources to help you answer these questions!
AUS-e-TUTE Members should log-in to use the new tutorial, game, test and exam.

If you are not an AUS-e-TUTE Member, a "free-to-view" Fatty Acids tutorial is currently available at http://www.ausetute.com.au/fattyacid.html for evaluation purposes.

Vitamins

Does it seem that dieticians and nutrition experts seem to make a huge fuss about eating foods that seem to contain infinitesimal amounts of those mysterious substances known as vitamins?
Well, there is some good, sound chemistry behind why this is so.
Find out about the chemistry of vitamins with AUS-e-TUTE's newest set of resources!

Members should log-in to access the Vitamins tutorial, game, test and exam.

If you are not an AUS-e-TUTE Member, a free-to-view tutorial is currently available for evaluation purposes at: http://ausetute.com.au/vitamincd.html

Lipstick Evidence

Lipstick is sticky stuff!
Kissing someone on the cheek with your lusciously lipsticked lips will invariably leave a colourful impression. And, after you've had your sip of coffee your "lips" are left behind in vivid colour on the cup. Lipstick can even end up on tissues after  a momentary touch as you blow nose, or wipe tears from your eyes. And we've all seen movies in which a wife discovers lipstick (not her own) on her husband's collar. Needless to say then that lipstick can be found at a crime scene and is considered to be an example of "trace evidence".
Researchers at  Western Illinois University have been investigating better ways to lift and analyse this lipstick evidence.
In general, lipstick is composed of

•     65% castor oil
•     15% beeswax
•     10% other waxes
•     5% lanolin (also known as wool wax or wool grease)
•     5% dyes, pigments and perfume

In other words, most of the mass of a lipstick is made up of lipids (fats, oils and waxes).
To lift the lipstick from the material, the researchers developed a two part process:

1.   Add an organic solvent to remove most of the oils and waxes.
2.   Add a basic organic solvent to extract the remaining residue.

The components of the lipstick are now present in solution.
In order to determine the chemical composition of the solutions, they will need to undergo separation and analysis. Three common methods of doing this are:

• thin layer chromatoagraphy (TLC)
• gas chromatography (GC)
• high performance liquid chromatography (HPLC)

Different brands of lipsticks have different chemical compositions so they produce different chromatographs.
Using known brands and colours of lipsticks, the researchers can produce a database of chromatographs. When lipstick evidence is found at the scene of a crime, forensic scientists can produce a chromatogram of it and compare this with the database of known brands and colours in order to find a match. In this way forensic scientists can determine the brand and colour of the lipstick. Law enforcement officials could then investigate whether a suspect uses that particular lipstick.
The researchers are still performing analyses of lipsticks, but at this stage they have reported that the best results are achieved with gas chromatography (GC).

Reference:
American Chemical Society. "Tying lipstick smears from crime scenes to specific brands." ScienceDaily. ScienceDaily, 14 March 2016.

Further Reading:
Percentage composition 
w/w % concentration
Parts per million (ppm) concentration
Lipids (oils, fats and waxes) 
Properties of Carboxylic Acids 
Preparation and Naming of Simple Esters


Suggested Study Questions:

1. A tube of lipstick contains 4.0 grams of lipstick. Calculate the mass of each of the following components of the lipstick:
   
   • castor oil
   • beeswax
   • lanolin
2.  The castor oil used to make the 4.0 grams of lipstick is itself made up of a number of fatty acids notably about 90% ricinoleic acid, 4% oleic acid and 3% linoleic acid. Calculate the mass of each of these fatty acids present in the lipstick.
3. Why do you think the concentrations of chemical compounds found in lipstick are given as % w/w (percentage by weight or percentage by mass) rather than in units of mol L^-1 or ppm?
4.  What is meant by the term "fatty acid" in chemistry?
5.  Draw and name the functional group that is present in both carboxylic acids and fatty acids.
6.  Acetic acid (ethanoic acid) is miscible (soluble in all proportions) in water,  whereas the solubility of pentanoic acid is 3.4 g mL^-1, and of hexanoic acid is 1.0 g mL^-1. Would you expect oleic acid (C₁₇H₃₄O₂) to be soluble in water? Explain your answer.
7.  What is meant by the term "triglyceride" in chemistry?
8.  Draw the functional group that is common to both triglycerides and esters.
9.  Esters are immiscible in water so an organic solvent is used to extract the triglycerides from the lipstick marks. Imagine you have been given samples of cyclohexane, ethanol, and acetone. Which of these do you think would be the best solvent to use on the lipstick mark, and explain your answer.
10.  Design an experiment that you could perform to test your hypothesis in question 9 above regarding which of the solvents would be best to use on the lipstick mark.

Cheesy Chemistry

Now here's the title of an article that sounds like it would make a great teaching and learning tool ..
"Food hacks: The science behind making perfect cheese melts and crispy cookies"
(Sydney Morning Herald, Monday 23rd November 2015)

"Science is great isn't it? ", writes the article's author.
Yes indeed, I couldn't agree more ... looks promising .....

"Even for those of us who find the periodic table of elements a foreign language, we can still reap the benefits of science's life-changing revelations."
Well, that's going a bit far (especially if you happen to teach/learn chemistry), but even so,  it still looks OK ......

"According to science, there's only one type of cheese for your toastie."
...mmm... possibly ...... "science" is rarely capable of making that kind of judgement ..... but we'll continue reading ....

until ........

" That cheese is the one with the right PH to balance the calcium, and release the casein (dairy protein) to create one big soft melty​ mess."
PH? Is that some kind of special food science thing? Could it be phosphorus monohydride?
No, it appears to simply be a mistake, which was, unfortunately repeated on the following line.
The author was referring to pH.

Nevertheless, did you know that different cheeses have different pH values?
I didn't!
So off I went to find the pH of some of my favourite cheeses:

cheese	pH
camembert	7.44
cheddar	5.90
cottage	4.75-5.02
cream	4.10-4.79
edem	5.40
gruyere	5.68-6.62
parmesan	5.20-5.30
stilton	5.70

Apparently, pH and temperature are both critical factors in the production of cheese:

• Addition of starter culture: temperature less than 20°C, pH = 5.1-5.3 (using rennet which contains enzymes for breaking down proteins)
•  Coagulation: temperature = 30°C, pH = 5.35 - 5.45
• Pressing: temperature 16-18°C (mild cheeses) or 25°C (hard cheeses), pH = 5.0-5.3
• Brining in salt solution: temperature 15°C, pH = 5.2
• Ripening: pH increases to optimum value as given in the table above.

A crumbly cheese, like a Cheshire cheese, has a low pH and low calcium content. At low pH the colloidal calcium phosphate between casein micelles becomes soluble and the size of these protein aggregates decreases, which, makes the cheese crumbly.

A low-acid cheese (high pH cheese) like Swiss cheese, has intact casein micelles which provide an extensive string of protein aggregates giving the cheese more elastic properties.

Further Reading:
http://www.ausetute.com.au/phscale.html
http://www.ausetute.com.au/phcalcs.html
http://www.ausetute.com.au/phhcalcs.html 
http://www.ausetute.com.au/enzymes.html 
http://www.ausetute.com.au/proteins.html
http://www.ausetute.com.au/aminoacid.html
http://www.ausetute.com.au/scientificm.html
http://www.ausetute.com.au/labreport.html


Suggested Study Questions:

1. What is meant by the term pH ?
2. Calculate the hydrogen ion concentration for each of the cheeses listed in the table above.
3. Arrange the cheeses in the table from lowest to highest pH.
4. Arrange the cheeses in the table from lowest hydrogen ion concentration to highest hydrogen ion concentration.
5. What is an enzyme?
6. What is a protein made up of?
7. Why do you think the temperature of the mixture during the addition of rennet and the coagulation stages is higher than at other stages during the production of cheese?
8. "According to science, there's only one type of cheese for your toastie."
    Do you think science can really tell you the best cheese to use for your toastie? Why or why not?
9. Who do you think the intended audience of this article is? Explain your answer.
10. Imagine you have just tested the pH the of various cheeses and that it is your results shown in the table above. Rewrite this article as if it were your lab report.
    

2015 Nobel Prize in (Bio)chemistry?

The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for "mechanistic studies of DNA repair".
Cells have developed mechanisms to repair damaged DNA. Four of these mechanisms are:

• photoreactivation


• dark repair (nucleotide excision repair)


• base excision repair


• mismatch repair

Photoreactivation
In the 1920s Hermann Muller found that X-rays could mutate and kill cells.
In the 1940s Albert Kelner found that visible light could stimulate growth recovery after damage caused by UV light, and this was called photoreactivation.
In 1944 Oswald Avery and co-workers showed that DNA is the material of heredity, and in the 1950s it was recognised that DNA became damaged when exposed to UV light.
Renato Dulbecco suggested photoreactivation was an enzymatic reaction dependent on light, which was demonstrated by Stanley Rupert.
In 1978 Aziz Sancar cloned the E. coli photolyase gene, an enzyme responsible for DNA repair in escherichia coli.
In the 1980s Aziz Sancar showed that photolyase can convert the energy of an absorbed photon into chemistry that produces a localised free radical that initiates thymine dimer splitting.

Dark repair (nucleotide excision repair)
In the 1960s Jane Setlow and Richard Setlow showed that thymine dimers inactivated transforming DNA in Hemophilus influenzae and that this was responsible for the biological effect of UV light.
In 1964 Richard Setlow discovered that thymine dimers disappeared from the irradiated, high molecular weight genomic DNA shortly after exposure to UV light and appeared in the low molecular weight fractions, that is, thymine dimers are excised (removed) from the DNA. This mechanism became known as nucleotide excision repair (NER).
In the 1970s Aziz Sancar working with W. Dean Rupp, developed the Maxicell technique for the rapid identification of proteins.
In 1983 Aziz Sancar used purified proteins to reconstitute essential steps in the nucleotide excision repair (NER) pathway, a "cut and patch" method for DNA repair.
Two proteins (UvrA and UvrB) track along the DNA, UvrA recognises damage and causes UvrB to stop tracking and begin unwinding the effected DNA section. Another protein, UvrC, causes the damaged section to be cut out, and then another protein UvrD, causes UvrB to bind and bridge the gap while it is repaired by resynthesising the removed segment via Pol I.

Base excision repair
In the 1970s Tomas Lindahl showed that DNA has limited chemical stability and that modification of the bases of DNA increased the risk of mutations. High levels of spontaneous cytosine deamination leads to the formation of uracil.

Uracil forms base pairs with adenine, so, high levels of cytosine demanination pose a risk of depleting the genetic material from cytosine-guanine base pairs and replacing them with thymine-adenine.
He identified the E. coli uracil-DNA glycosylase (UNG) as the first repair protein which we now know is one member of a large family of proteins that orchestrate base excision repair (BER).
A DNA glycosylase recognises and cuts the base-deoxyribose glycosyl bond of a damaged nucleotide. DNA glycosylase kinks the DNA and the abnormal nucleotide flips out and is removed and the section can then be repaired.

Mismatch repair
During the synthesis of a new DNA strand, a non-Watson-Crick base pair may be formed which distorts the double-stranded DNA helix. These types of errors are known as mismatches.
In 1983 Paul Modrich and Matthew Meselson showed that DNA methylation directed strand-specific elimination of mismatches in E. coli. Modrich developed an assay to isolate the products of the different repair genes and identify the proteins.

Further Reading:
http://www.ausetute.com.au/dna.html
http://www.ausetute.com.au/enzymes.html

Suggested Study Questions:

1. What does the abbrevaition DNA stand for?
2. What do you think when biochemists refer to damaged DNA?
3.  What is meant by the term enzyme?
4. Why do you think enzymes are required in the mechanisms available within a living cell to repair damaged DNA?
5. What is a free radical?
6. Draw the structural formula of thymine.
7. Draw the structural formula for a possible dimer of thymine.
8. What is meant by the term nucleotide?
9. With reference to DNA, what is meant by a base pair?
10. Show how uracil forms a base pair with adenine.
11. Draw the structure of a cytosine-guanine base pair
12. What do you think is meant by the statement, "cytosine deamination leads to the formation of uracil" (structural formulae may be useful in your explanation but you do not need to include chemical reactions).

Sucralose and Acesulfame potassium

Artificial sweeteners,  especially aspartame, have hit the news headlines once again with PepsiCo's decision to start selling Diet Pepsi without aspartame from August 2015 in the USA. The aspartame is to be replaced by a blend of sucralose and acesulfame potassium.

Sucralose was discovered in 1976 when Shashikant Phadnis at Queen Elizabeth College was asked to "test" a chlorinated sugar compound but he thought he'd been asked to "taste" it, so he did, and found it be very sweet! Sucralose, shown on the right, is synthesised from sucrose in a number of steps in which 3 of sucrose's hydroxyl groups are substituted for chlorine atoms.
Although sucralose is about 300 times sweeter than sucrose, it is not broken down during digestion and therefore does not contribute to ingested calories (kilojoules).
Splenda is a brand name for a common sucralose-based sweetener.


Acesulfame potassium was accidentally discovered in 1967 by German chemist Karl Clauss, who found it to be sweeter than sucrose. It is not as sweet as sucralose, however, and is often used in combination with other artificial sweeteners such as aspartame or sucralose. It has the structural formula shown below:

Acesulfame potassium is currently sold under the brand names Sunette, Sweet One and Sweet 'n Safe and is found in many "sugar-free" foods such as chewing gum, jelly (Jell-O), even in alcoholic drinks.

Reference:
http://www.smh.com.au/business/retail/diet-pepsi-dumps-aspartame-as-consumer-backlash-hurts-sales-20150425-1msz1b.html

Further Reading:

• http://www.ausetute.com.au/sugars.html 
• http://www.ausetute.com.au/proteins.html
• http://www.ausetute.com.au/fungroup.html
• http://www.ausetute.com.au/intermof.html
• http://www.ausetute.com.au/skeletal.html
• http://www.ausetute.com.au/structural2D.html
• http://www.ausetute.com.au/condensedsf.html
• http://www.ausetute.com.au/molecularformula.html

Suggested Study Questions:

1. What is the molecular formula for:
   • sucralose
   • sucrose
   • acesulfame potassium
2. Draw the structural formula for sucrose and circle the hydroxyl functional groups.
3. Draw the structural formula for sucralose and
   • circle the hydroxyl functional groups in red
   • circle the halogen functional groups in green
   • circle any other functional groups blue and name them 
4. What class of compounds does sucrose belong to?
5. Draw the structural formula for acesulfame potassium and identify the functional groups.
6. Is it appropriate to call acesulfame potassium a potassium salt? Explain your answer.
7. Aspartame is the methyl ester of a didpeptide. What functional groups do you expect the aspartame molecule to have? Explain your answer. 
8. Do you expect sucralose and acesulfame potassium to be soluble in water? Explain your answer.

Trans Fats

Some fats, such as polyunsaturated fats, are thought to be good for us.

They lower the "bad" type of cholesterol which has been linked to heart disease.

Other fats, such as saturated fats and trans fats, are considered to be bad for us because they increase this "bad" type of cholesterol.

Since the beginning of the 21st century, health authorities all over the world have been calling for the elimination of trans fats from commercially produced food products.

But what is a trans fat and where does it come from?

Go to the June 2014 issue of AUS-e-NEWS for the chemistry of Trans Fats.

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Molecule with Anti-Cancer Kick

In 2013, medical researchers found a molecule that fights cancer in animals by boosting the cell's production of a powerful natural antitumor protein known as TRAIL. The Researchers referred to this anti-cancer molecule as TIC10, short for TRAIL Inducing Compound number 10.
The structure of this molecule, as confirmed by mass spectroscopy, was published at this time as is shown below:

Chemists at The Scripps Research Institute (TSRI) found a way to synthesize this molecule in the laboratory. However, when the Chemists gave their molecule to Biologists to test on cancer cells, this molecule failed to show any anti-cancer activity!
So, the Chemists asked the Biologists to supply some of the TIC10 that had shown anti-cancer activity. The Chemists spent months analyzing both TIC10 molecules to determine their exact molecular structure. And they discovered that the molecule the biologists had shown to fight cancer did not have the structure that was originally published, so the molecule that the Chemists had synthesized in their laboratory would not fight cancer cells,.
However, the Chemists found that the molecule that DOES fight cancer cells has a very similar structure. The structure of the active molecule is shown below:

Note that the structure originally published for TIC10 had the three nitrogen containing rings in a straight line. This new, correct, structure for TIC10 has two of the nitrogen containing rings in a straight line, but the third ring sticks out at an angle from the other two. Only this "angular" isomer (the molecule with a kick) shows any anti-cancer activity.

Kim D. Janda, the Ely R. Callaway Jr. Professor of Chemistry and member of the Skaggs Institute for Chemical Biology at TSRI has been quoted as saying, "One lesson from this has got to be: don't leave your chemists behind".
(http://www.sciencedaily.com/releases/2014/05/140519184505.htm)

Reference:
Nicholas T. Jacob, Jonathan W. Lockner, Vladimir V. Kravchenko, Kim D. Janda. Pharmacophore Reassignment for Induction of the Immunosurveillance Cytokine TRAIL. Angewandte Chemie, 2014; DOI: 10.1002/ange.201402133

Further Reading
Molecular Formula  
Condensed Structural Formula 
2-Dimensional Structural Formula
Skeletal Formula
Percent Composition
Functional Groups
Benzene
Mass Spectroscopy for Structural Determination

Suggested Study Questions:

1. Refer to the structure of TIC10 as shown above. In one molecule, how many
   • carbon atoms are present?
   • hydrogen atoms are present?
   • oxygen atoms are present?
   • nitrogen atoms are present?
2.  Write the molecular formula for a molecule of TIC10.
3. For the TIC10 molecule, calculate the percent by mass of
   • carbon
   • hydrogen
   • oxygen
   • nitrogen
4. Convert the skeletal structure for the active anti-cancer molecule into a 2-dimensional structural formula.
5. Circle one benzene ring in the structure of the active anti-cancer molecule.
6. Circle and name the functional group containing an oxygen atom on the active anti-cancer molecule.
7. What value do you expect for the mass-to-charge (M/Z) peak on a mass spectrum of the anti-cancer TIC10 compound ?
8. Do you think mass spectroscopy alone could be used to distinguish between the two structures proposed for TIC10 above? Explain your answer.

Ibuprofen

Before you take that nurofen, advil, motrin,brufen, or one of the many other trade-names for ibuprofen, why not learn something about its chemistry first?

AUS-e-TUTE has just added a new tutorial, game, test and exam exploring the chemistry of ibuprofen.
Members should log-in to use these new resources.

Not an AUS-e-TUTE Member?
There is a free tutorial available at http://www.ausetute.com.au/ibuprofen.html

Methanol and the Home-Brewer

In June 2013, a young man in Queensland died as a result of drinking homemade liquor. It is believed that the liquor contained a toxic level of methanol (also known as wood alcohol). Drinking 10 mL of pure methanol can cause permanent blindness, drinking 30 mL of methanol can kill you.

The first step in the production of homemade liquors, is the fermentation of sugar.
Methanol, CH₃OH,is formed during fermentation.
When fermenting 6 kg of sugar dissolved in water for the production of distilled spirits such as whiskey or vodka, the home-brewer (and home-distiller) will typically find that the concentration of methanol in their brew is about 3 parts per million.

Many fruits are used by the home-brewer as the source of sugar to be fermented. Each fruit will lend a distinctive flavour to the final product. But fruits that are high in pectin will produce greater concentrations of methanol. Apples, apricots, guavas, quinces, plums, gooseberries, and citrus fruits like oranges, all contain high levels of pectin, typically more than 1% by mass pectin. Grapes, cherries and strawberries contain low levels of pectin, less than 1% by mass pectin.

Pectin contains  galacturonic acid which has the structural formula shown below:

In pectin, about 80% of the carboxyl groups in galacturonic acid are esterified with methanol. The remaining non-esterified carboxyl groups exist as the acid, or as salts with sodium, potassium or calcium. When pectin is broken down by enzymes during the brewing process, the methyl esters react with water to produce methanol.

The second step in the production of homemade liquor is the distillation step.
This is the crucial step in removing as much of the toxic methanol as possible.
The boiling point of methanol is about 65^oC, but the boiling point of ethanol (the desired product) is about 78^oC. During the distillation process, the first fraction collected should contain the methanol. This fraction should be collected and discarded. The next fraction should contain the desired liquor. It is highly recommended that any distillate collected after about 96^oC also be discarded.


Reference:
http://www.couriermail.com.au/news/queensland/ballandean-man-bill-lynam-who-lost-his-son-joel-to-homemade-liquor-poisoning-is-thankful-that-other-son-joshua-survived/story-fnihsrf2-1226664893229

Further Reading
http://ausetute.com.au/members/alkanolp.html (members only tutorial on alkanols)
http://ausetute.com.au/members/carboxyl.html (members only tutorial on alkanoic acids) 
http://ausetute.com.au/partspm.html 
http://ausetute.com.au/density.html 

Suggested Study Questions:

1. Draw the structural formula for methanol.
2. Locate the functional group present in methanol on the structural formula above. Name the functional group. 
3. At 25^oC methanol has a density of  0.79 g mL^-3. Calculate the mass of methanol present in a lethal dose of pure methanol .
4.  Convert the concentration of methanol given for homemade whiskey into a concentration in g mL^-1.
5. Assume the young man who died drank homemade whiskey. What minimum volume of homemade whiskey did he drink?
6. For galacturonic acid given the:
   • molecular formula
   • molar mass
7.  On the structural formula for galacturonic acid identify and name the functional groups present.
8. Draw the structure for the sodium salt of galacturonic acid.
9. Draw the structure for galacturonic acid esterified with methanol.
10. Give the molecular formula and molar mass for the structure above.
11. Apples contain about 1% by mass pectin. 10 kg of apples are to be used in the production of a homemade liquor. What mass of pectin will be present?
12. Assume exactly 100% of the carboxyl groups in galacturonic acid are esterified with methanol. How many moles of the ester are present in 10 kg of apples?
13. Write an equation representing the reaction between this ester and water to form methanol  and galacturonic acid.
14. How many moles of methanol could be produced by the break down of pectin in 10 kg of apples?
15. Assuming the young man who died had drunk this apple concoction without distilling and removing the methanol, what minimum volume of fermented apple-drink would he have had to have drunk?
16. Why do you think most countries have outlawed home-distilling?

An Itchy Polypeptide

Scientists have a discovered that a small molecule, natriuretic polypeptide b (Nppb), is responsible for that itchy feeling in mice. When natriuretic polypeptide b is removed, and mice are exposed to itch-inducing substances, nothing happens! No itching! The nervous systems of mice and humans are similar, so the scientists believe that the same molecule is probably responsible for making you feel itchy.

Natriuretic polypeptide b  is a polypeptide made up of 32 amino acid residues as shown below:

 The amino acid residues in order of appearance are:

amino acid name	structure
serine
proline
lysine
methionine
valine
glutamine
glycine
cysteine
phenylalanine
arginine
aspartic acid
isoleucine
leucine
histidine

This research could be of enormous benefit to people who suffer from chronic itch conditions like eczema and psoriasis. Unfortunately, natriuretic polypeptide b is also used in other body processes in the heart and kidneys, so its removal in humans could cause major problems.

Reference:
S. K. Mishra, M. A. Hoon. The Cells and Circuitry for Itch Responses in Mice. Science, 2013; 340 (6135): 968 DOI: 10.1126/science.1233765

Further Reading:
Amino Acids 
Proteins 

Suggested Study Questions:

1.  What is meant by the term polypeptide?
2. Refer the structure of natriuretic polypeptide b. Draw up a table giving the name and the number of each amino acid present in each molecule of natriuretic polypeptide b.
3. What two functional groups are common to all amino acids?
4. On the structure of alanine shown below, label each of the functional groups:
   
   
5. What type of bond holds the amino acids together in the chain of natriuretic polypeptide b ?
6.  Using two molecules of serine, show how they are joined together to form a dipeptide.
7. What is the name given to the type of chemical reaction in which two serine molecules combine to form a dipeptide?
8. Name the type of bond shown between two cysteines on the structure of natriuretic polypeptide b shown above.
9. What is the primary structure of natriuretic polypeptide b ?
10. How would you describe the secondary structure of natriuretic polypeptide b ?   

Drunken Fruit Flies

Wasps are a major killer of fruit flies. They inject their eggs inside fruit fly larvae, then, when the wasp egg hatches, the wasp larva starts eating the fruit fly lava from the inside!
Scientists at Emory University have found that fruit flies prefer to lay their eggs in an environment  with a "high" concentration of ethanol. The fruit flies have evolved a certain amount of tolerance to this toxic ethanol, but the wasps who inject their eggs inside fruit fly larvae find the ethanol level to be lethal. Furthermore, fruit fly lava that have been infected with wasp larva tend to prefer to eat food with a high ethanol content, this raises their blood alcohol level and helps kill the wasp larva.

The most common natural source of ethanol is rotting fruit. Yeasts on rotting fruit can ferment the fruit sugars, like fructose, to produce ethanol:

C₆H₁₂O₆ → 2C₂H₅OH + 2CO₂

This fermentation reaction takes place in anaerobic environments, that is, environments in which oxygen is not present.
The concentration of ethanol in rotting fruits has been  found to be between 0.04 and 0.72 v/v%. By comparison, the ethanol content in beer is usually between 3 and 6 v/v%, while the ethanol content of wine is between 8 and 11 v/v%.
Volume/volume (or volume) percent is a common way to refer to the concentration of alcoholic solutions. It refers to the volume of solute divided by the volume of solution which is then multiplied by 100, that is:

v/v% = V(solute)/V(solution) x 100

Beer that is 3 v/v% ethanol contains 3 mL of ethanol in every 100 mL of beer.

Wine that is 11 v/v% ethanol contains 11 mL of ethanol in every 100 mL of wine.

This preference for eating rotting fruit containing ethanol displayed by the fruit flies seems to be uncommon. Most animals, including humans, seem to prefer ripe, but not rotting, fruit.

References:

1. B. Z. Kacsoh, Z. R. Lynch, N. T. Mortimer, T. A. Schlenke. Fruit Flies Medicate Offspring After Seeing Parasites. Science, 2013; 339 (6122): 947 DOI: 10.1126/science.1229625
2. Neil F. Milan, Balint Z. Kacsoh, Todd A. Schlenke. Alcohol Consumption as Self-Medication against Blood-Borne Parasites in the Fruit Fly. Current Biology, 2012; 22 (6): 488 DOI: 10.1016/j.cub.2012.01.045

Further Reading:
Fermentation
Carbohydrates
Naming Alcohols
Density

Suggested Study Questions:

1. Calculate the volume of ethanol in a stubby (375 mL) of full strength beer (ethanol concentration 4.8 v/v%).
2. An average standard wine glass has a volume of 150 mL. What volume of ethanol is present in a standard wine glass of white wine with an ethanol concentration of 11.5 v/v%?
3. Port is an example of a fortified wine, that is, a wine that has had an additional distilled beverage like brandy added to it to increase its alcohol content to about 17.5 v/v%. A standard port glass has  a volume of 60 mL. Calculate the volume of ethanol in a standard glass of port.
4. The specific gravity (density) of ethanol is 0.789 g/mL. Calculate the mass of ethanol present in a stubby (375 mL) of
   • full strength beer (5 v/v% ethanol)
   • light beer (2.7 v/v% ethanol)
5. Spirits such as rum and vodka, have an ethanol concentration of approximately 40 v/v%. A standard "nip" is 30 mL. Calculate:
   • the volume of ethanol in a nip of vodka
   • the mass of ethanol in a nip of vodka
6. The alcohol content of Marsala wine is increased by allowing water to evaporate off it. The concentration of ethanol in Marsala wine will reach about 18 v/v%. Calculate:
   • volume of ethanol in a 750 mL bottle of Marsala
   • mass of ethanol in this bottle of Marsala wine
7. A particular type of wine barrel holds 225 L of wine. Calculate the mass of ethanol present if the wine in the barrel is
   • red wine (13 v/v% ethanol)
   • white wine (11.5 v/v% ethanol)
   • champagne (12 v/v% ethanol)