InfoChem

Elements of life

Akshat Rathi wonders if the elements in DNA are the same throughout
the universe

ISSUE 131 | NOVEMBER 2011

In this issue
Seeing in the dark
-carotene, chlorophyll
and autumn

Can chemistry help

you to forget?

Eternal sunshine of the

spotless mind

Restoring the family

silver

Prof Hal presents an

experiment you can do on
your own

Working for the

Atomic Weapons
Establishment
A day in the life of
Imran Khan

Plus

NASA

Prize puzzles

++A planet orbiting two suns, 200 light years from earth the first confirmed alien world found by NASAs Kepler telescope

As far as we know, there are very few planets in the

universe which are just like our planet Earth. The
elements it is made from have played a critical role
in allowing life to exist here. However, there may be
planets out there whose composition is very different.
There is a huge range of possibilities perhaps there is
no oxygen, only sulfur or very little phosphorus but a lot
of arsenic. Could life exist on such planets? Scientists
have thought about this question for decades. To
answer it, we need to understand more about DNA, the
molecule of life, the elements it is composed of and
consider the results of some unusual experiments.
DNA: The molecule of life
Since its discovery, DNA has been at the centre of many
great scientific discoveries and its critical role in the
development of life has pushed the boundaries of our

understanding. Exploring the chemistry of DNA holds

potential for creating new and alien forms of life, and
maybe even the chance of spreading life beyond our
little planet.
DNA is made up of carbon, hydrogen, oxygen, nitrogen
and phosphorus (see The DNA box). Currently, our
knowledge of living things is limited to what we know
about life on earth and the role these elements play in
it. As we expand our reach into outer space, curiosity
about life beyond our Earth increases. In attempts
to understand whether life could exist elsewhere,
researchers need to explore the role of these essential
elements of life. Tinkering with the elements that make
up this fascinating molecule has been on the minds of
scientists for many decades. Only recently have they
made progress towards that dream.

Editor
Karen J Ogilvie
Assistant editor
David Sait
Production
Scott Ollington and Emma Shiells
Publisher
Bibiana Campos-Seijo
InfoChem is a supplement to
Education in Chemistry and is
published six times a year by
the Royal Society of Chemistry,
Thomas Graham House,
Cambridge,
CB4 0WF.
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email: eic@rsc.org
www.rsc.org/infochem

The Royal Society of Chemistry,

2011. ISSN: 1752-0533

www.rsc.org/infochem
Registered Charity Number 207890

0611INFO - Feature - DNA.indd 1

10/31/2011 9:10:31 AM

SCIENCE PHOTO LIBRARY

Robot picking bacteria

containing human DNA
for the Human Genome
Project

Thymine

Tinkering with the elements

One way of better understanding the roles played by
these important elements is by replacing them in key
biomolecules and observing the changes that occur in
the organism. Although the proposition seems straightforward, this has been very difficult to achieve in the
lab. As with the beginning of every major scientific work,
attempts start small. Most work done in the past has
been on replacing enzyme cofactors with other elements.
Enzymes are proteins that help catalyse chemical
transformations within living cells. You can think of
enzyme cofactors as molecules which help the enzyme
to perform its actions. Inorganic enzyme cofactors are
usually metal ions. Some common metal ions that are
found working in human enzymes as cofactors are iron,
magnesium, manganese, cobalt, copper, molybdenum,
selenium and zinc.

Chlorouracil

The successful attempts at swapping elements in

different enzymes are the replacements of molybdenum
by tungsten, iron by copper and zinc by cadmium. All
these swaps have been possible because the replacing
elements are closely related chemically and structurally
to the original element.
For example, cadmium and zinc are both from group 12
and have the same valency (2). This makes it possible for
an enzyme to bind to another element which is closely
related to the original one.

InfoChem

0611INFO - Feature - DNA.indd 2

Building on this work, scientists started the more

challenging task of tinkering with the most important
biomolecule DNA. The first few attempts made on

DNA outside living cells were successful but attempts at

replicating those results in living cells had failed
until recently.
Messing with DNA
In 2007, researchers from the Massachusetts Institute of
Technology in Cambridge, US (MIT), made a surprising
discovery. They found that certain strains of bacteria
can modify its DNA by replacing one of the oxygen
atoms attached to the phosphorus with a sulfur atom.
The process is known as phosphorothioation and until
recently, this transformation was only ever achieved
outside a living cell in a lab. Peter Dedon, the lead
researcher in the study said, We are very excited about
the implications of this observation.
A few years later, the research group reported that these
genes which caused the modifications occur widely
in many other bacteria. Surprising as it may seem, the
researchers believe that these genes must have been
carried through bacterial evolution from its earlier days
when they lived in sulfur-rich environments.
Earlier this year, researchers in Europe and the US
reported the incorporation of chlorouracil, an analogue
of thymine that contains chlorine, in the DNA of a
bacterium. They fed the bacterium larger doses of
chlorouracil while giving small doses of thymine to
ensure that the bacterium did not starve to death.
They found that the bacterium that mutated to
incorporate chlorouracil, instead of thymine, was
naturally selected. Lowering the levels of thymine put
pressure on the bacterium to evolve to adapt. In five

10/31/2011 9:10:54 AM

The DNA box

DNA was first isolated in 1869 by the
Swiss physician Friedrich Miescher but
its structure was not confirmed until
1953. At the time, British molecular
biologists Francis Crick and James
Watson suggested that DNA exists
in the form a double helix (like a
twisted ladder) which consists of two
complementary strands of nucleobases
held by a support structure.

EMMA SHIELLS

The elements that constitute DNA are

carbon, hydrogen, oxygen, nitrogen
and phosphorus. Interesting, but not
surprising, is the fact that along with
sulfur, this forms a set of six elements
which are the basis of all life on earth.
An easy to remember mnemonic for

months the bacterium underwent considerable change.

It became much more elongated and had 98 per cent of
the thymine in the DNA replaced by chlorouracil.
This is the first organism of a new biology. No organism
has ever been discovered or made that has a different
nucleobase altogether and the impact of this study is
yet to be understood. What it proves though is that it
may be possible to form new species with DNA that
incorporates atoms of chlorine.

DNA is considered to be the blueprint of

an organism. If an organism is a simple
single cell bacterium then its code holds
instructions to build cellular organelles, all
the proteins, cellular walls and pretty much
everything that is needed by the bacteria to
live and flourish. Similarly, if the organism
is as complex as a human being, then the
DNA holds information not only for building
each cell in the human body, it holds
instructions on how these cells will make
up different elements of the body such as
organs and bones and how they function
as a whole.

Arsenic in DNA
In another interesting paper published in June this
year, US astrobiologists, funded by NASA, reported the
existence of a bacterium species which they claimed
had incorporated arsenic in its DNA backbone to replace
the phosphorus. It was found in Mono Lake, a highly
salty and arsenic-rich lake in California, US. Arsenic is
an element from the same group as phosphorus and
possesses similar chemical properties. Unlike phosphates
which form strong bonds to provide support for the DNA
structure, arsenates can only form weak bonds.
The scientific community in general has shown heavy
scepticism towards these results as the presence
of arsenic may be very unstable in cells. Further
experiments are needed to verify the claim made by the
astrobiologists. Samuel Webb, one of the researchers
in the study, says, Even if we are proven wrong about
arsenic in the DNA, its definitely doing something thats
crazy and cool. The sentiment expressed by Webb shows
the excitement in this field of study.

SHUTTERSTOCK

SCIENCE PHOTO LIBRARY

All DNA is made up of only four building

blocks called nucleobases that are held
together by a sugar and phosphate
backbone. The four nucleobases are
adenine, thymine, guanine and cytosine.

these elements is CHNOPS. The importance

of these elements cannot be overstated as
the various arrangements of these essential
elements give us other vital molecules
such as carbohydrates, proteins and lipids.
These biomolecules, along with DNA, are
essential for the functioning of a cell and
are critical to life itself.

0611INFO - Feature - DNA.indd 3

The origin of life on Earth is still largely a mystery. The six

essential elements of life possess some unique chemical
properties that give them the ability to interact in a
manner that is conducive to life as we know it. And yet, it
does not mean that other elements could not do that job.
We have seen bacteria that can replace oxygen with sulfur
and scientists have created an organism with chlorine
atoms in its DNA. This is only the beginning. There is much
to explore in the chemistry of life and if nothing else,
research has shown us that with such an exciting start,
there is surely an even more exciting future.

Did you
know?
Mono Lake, California
formed at least 76 000
years ago. It has no outlet
and due to evaporation,
dissolved salts have built
up creating a very alien
environment. The lake is
now 2.5 times as salty
and 80 times as alkaline
as the ocean!

Mono Lake, California, US

InfoChem

10/31/2011 9:11:17 AM

Magnificent molecules
Phillip Broadwith highlights one of his favourite molecules.
In this issue: -carotene

The world record

for the most carrots
peeled and chopped
in one minute is held
by Rosalia Addis from
Italy. She prepared
591 g of carrots in sixty
seconds in April 2009.

Talking of -carotene (1) will almost always bring

to mind bright orange root vegetables. But while
the carrot has lent its name to this highly coloured
compound and several related carotenes and
carotenoids, it is not the only place where it is found.
Carotenes occur all over the place in nature some
of the more obvious places are the orange flesh
of fruits and vegetables like mangoes, pumpkins
and sweet potatoes; but it is also an important
compound in green plants like spinach and in the
green leaves of deciduous trees. During the summer,
its vibrant colour is swamped by the strong green
of light-harvesting chlorophyll. As autumn comes,
and the chlorophyll decays, the orange and red
hues of carotenes are revealed, turning forests into
enchanting vistas of gold and dappled red.
Carotenes association with chlorophyll in leaves is
no accident. It is also a light-harvesting molecule,
and absorbs blue and indigo wavelengths which
help in photosynthesis. It is its chemical structure
which allows it to do this. The chain
arrangement of single and double
bonds allows the electrons from
the double bonds to spread,
or delocalise, over the whole
string, a bit like how the electrons
in a benzene ring are spread
evenly around the whole ring. This
delocalisation also means that the
electrons are perfectly set up to absorb light energy.
The length of the chain dictates the wavelength of
light absorbed, and carotenes are tuned in to the
blue end of the spectrum.

(1)
This absorption is what makes carotenes appear
orangey-yellow. The blue light is absorbed, while
the longer wavelength yellow and red are not, and
so are picked up by the light-sensitive molecules
in our eyes. Those light-sensitive molecules are, in
fact, closely chemically related to the carotenes.
Retinal, an oxidised form of vitamin A, is responsible
for detecting light in our eyes, and is formed by
chopping molecules of -carotene in half.
Since carotene is a good dietary source of vitamin A
(and therefore retinal), you might think that this

SHUTTERSTOCK

Did you
know?

is the origin of the myth that eating lots of carrots

gives you better night vision. However, you would be
much better off eating liver, which has exceptionally
high levels of vitamin A; or raw palm oil, which is
particularly rich in -carotene. In fact, unless you
are deficient in vitamin A, eating large amounts of
-carotene will not do anything to improve your
eyesight, but it could turn your skin orange if you
manage to eat enough!
The night vision myth was seized on by the UK
government during the second world war. It claimed
that it was the carrot-induced keen eyesight of Royal
Air Force pilots that allowed them to shoot down
enemy aircraft. This helped to hide the effectiveness
of radar. It also persuaded the population to
eat carrots, which were easy for people to grow
themselves, and of which there was a relative
surplus at the time.
The intensely strong colour of -carotene has also
meant it has found uses as a food colouring it is
added to some margarines to make them look more
like butter, which is naturally coloured by the small
amounts of carotenoids dissolved in the fats in milk
and cream.
While they may not have helped the masses see
better in the blackout as the Ministry of Foods
posters proclaimed, the humble carrot and its bright
orange molecular namesake play an important part
in vision and health.

Check out the podcasts from Chemistry World. Each

week a leading scientist or author tells the story
behind a different compound.
www.chemistryworld.org/compounds

InfoChem

0611INFO - Magnificent molecules.indd 4

10/31/2011 9:12:53 AM

On-screen chemistry
Heading in here
Can chemistry help you to forget?
In the film Eternal Sunshine of the Spotless Mind,1 Joel
(Jim Carrey) is very hurt when his girlfriend Clementine
leaves him. He is astonished and depressed when he
learns that she actually underwent medical treatment
on her brain to remove memories of him! This film is
definitely in the science fiction genre. For example, the
medical apparatus used to remove the memories looks
like it came straight from a fantasy comic strip. Putting
the weird machine aside, is there any modern scientific
basis for the concept of the film; is it possible to remove
troublesome memories using science and technology?

PICTURE CREDIT

Jonathan Hare explains...

There is currently a lot of research taking place to try

and develop treatments for people with post traumatic
stress disorder, phobias and even addictions.2 Soldiers
coming back from wars and car crash victims can take
years, sometimes decades, to recover from ordeals they
have experienced. Some never make a full recovery.

THINKSTOCK

Recent research claims that the beta blocker blood

pressure drug propranolol modifies the way memories
are retrieved and re-stored in the brain. This provides
a way in which problem memories, and our reaction to
them, may be tackled. A very simplistic explanation is
that remembering is at least a two step process. Firstly,
a stimulus causes the memories to be replayed (with
much of the discomfort associated with the original
trauma). In the next step, these memories are
re-stored back in the memory. This means that going
over memories again and again effectively enhances the
very memories you might wish to forget.
Taking propranolol, while being stimulated to remember
certain memories, apparently reduces the effectiveness
of the second part of this process. In other words, the
memory cells associated with the traumatic memories
behave normally (ie you remember) but the drug stops
the same memories from being replaced (you dont
keep remembering). Propranolol probably temporarily
effects neurone communication between memory cells
that facilitate the memory restorage.

you forget the emotional response that ultimately

causes so much pain and suffering. With a skilful
combination of drugs and special mental exercises, (to
select the correct parts of the memory to be modified)
the researchers claim that it may be possible to tackle
long term reactions to trauma.

The researchers claim that the memory cells are not

damaged by the drug. Propranolol seems to target the
cells in the part of the brain called the amygdala often
associated with emotional memories. The treatment
may not mean you actually forget the trauma but that

References
1 Eternal Sunshine of the Spotless Mind, Focus Features,
2004 http://imdb.to/obX8v2
2 Chemistry World, July 2010, p46

With this current research in mind, this film plot, could

in fact, be plausible.

InfoChem

0611INFO - On screen chemistry.indd 5

10/31/2011 9:17:59 AM

Did you
know?
Silver ions have
antibacterial
properties. Socks
are now being made
which include threads
coated with silver to
prevent the growth of
the bacteria that cause
smelly feet!

Prof Hal Sosabowski presents

experiments you can do on your own

In this issue: restoring the family silver

Hala Jawad

We commonly associate certain

metals with high value the normal
examples are gold, silver and
platinum. As it happens the most
expensive commodity metal isnt
gold or platinum, its normally
rhodium, which reached record
prices of $10000 per ounce, in
2008. The reason we use the word
normally, is that the price of
commodity metals are fluid and
change with supply and demand.

Health &
Safety
This experiment
involves hot water.
You need to use oven
gloves when handling
vessels containing
hot water. Have your
sleeves rolled down
and safety glasses on
during the experiment.

Backyard chemistry

InfoChem

aluminium foil
two litres of water
a saucepan
75 g baking soda
safety glasses, oven gloves and a laboratory coat/apron
Method
Line the bottom of the casserole dish with the aluminium
foil. Put the tarnished spoon on top of the foil ensuring
that the as much as possible of the surface of the spoon
touches the aluminium.

Heat the water in the saucepan to boiling and then place

the saucepan in the sink. Carefully add the baking soda to
Rhodium is one of the noble
the hot water. The mixture may boil over the edge of the
metals, which includes ruthenium,
saucepan which is why you must be very careful.
rhodium, palladium, silver,
osmium, iridium, platinum, and gold. These metals are Pour the hot baking soda and water mixture into the
noble inasmuch as they are, relative to other metals, inert casserole dish, so it completely covers the silver.
(unreactive) or chemically aloof. However as we shall see,
Almost immediately, the tarnish will begin to disappear.
some are more unreactive than others. Gold reacts with
If the silver is only lightly tarnished, all of the tarnish
very few other elements or compounds, and the only acid
will disappear within a few minutes. If the silver is badly
in which it will dissolve is aqua regia (royal water). This is a
tarnished, you may need to reheat the baking soda and
concentrated mixture of nitric and hydrochloric acids, and
water mixture, and give the silver several treatments to
derives its regal name from the fact that it is uniquely able
remove all of the tarnish.
to dissolve gold.
Chemistry
Silver is more reactive than gold, and will tarnish over
The equation for this reaction is:
time because it reacts with the small amounts of sulfur3 Ag2S
+
2 Al 6 Ag
+
Al2S3
containing compounds in the air. This results in a black
silver
aluminum
silver
aluminum
colouration developing. Silver polish reacts with the
sulfide
sulfide
tarnish to restore the shine of the silver. In this experiment
we are going to use household materials to emulate silver The more reactive aluminium has reduced the silver
polish and restore the shine to an item of tarnished silver. sulfide back to silver, and chemically restored its lustre.
This is how most corrosion-removers work, they remove
Materials
whatever oxidant has oxidised the base metal. Tarnish is
a tarnished piece of silver (you may have silver cutlery
the silver equivalent of rust. You may notice yellow flakes of
but ask the owner before using it). For this experiment,
aluminium sulfide on the bottom of the pan.
assume we are using a tarnished spoon
This is adapted with permission from an article by
a large casserole dish to completely immerse the
Bassam Shakhashiri.
silver in

ochem
You can download InfoChem at www.rsc.org/inf
and copy it for use within schools

A Day in the life of

Imran Khan
IMRAN KHAN

Sensors and spectroscopy

development scientist
at AWE
Imran uses his expertise in chemistry to do
research on hazardous materials. He tells
Josh Howgego what its like to do fundamental
research for the government.
Excited about finding things out
Imran first became excited about science listening to
Johnny Ball and Richard Feynman people with an
insatiable curiosity about the world around them. Listen
to people like that, he says, and you cant fail to be
inspired to do some experiments.
Imran spent much of his early career in academia,
carrying out not only a PhD but also postdoctoral
research where he worked on the pioneering technique
of surface enhanced raman spectroscopy (SERS). He
has now finally moved out of academia, and works for
the Atomic Weapons Establishment (AWE) in Berkshire.
AWE manufactures and maintains warheads for the
UKs nuclear deterrent on behalf of the Ministry of
Defence. Imran enjoys his job as it still allows him time
to enjoy looking into problems and finding out whats
going on.
He explains that the great thing about AWE is that it
provides a happy medium between academic and
industrial research. There are similarities with industry,
but also an intellectual atmosphere reminiscent of
academia. Imran is able to pursue research because
it furthers understanding about materials and doesnt
always have to justify with an opportunity for a profit.
Investigating materials
Imrans job is all about using spectroscopy on
materials to understand their properties and control
their performance. At AWE we must understand and
underwrite the safety of nuclear weapons, as well
as building them, he says. SERS is a relatively new
technique, but it can provide scientists with interesting

and valuable information about materials. SERS is

sometimes temperamental though, and Imran is focusing
on how to make the technology more robust.
He also works with fibre optic sensors, which make it
possible to analyse materials remotely. This means its
possible to study dangerous materials from a distance
or safely through a barrier. It takes all sorts of specialists
to create these new fibre optic tools and ensure they are
capable of functioning properly in the field. Imran has
to be good at working in a team with technologists and
engineers to help develop the new devices.

Pathway to
success
2007present, Sensors
and spectroscopy
development scientist at
AWE.
20032006, Postdoctoral
research on electron
microscopy of silver
nanostructures, Imperial
College, London.
19992003, PhD studying
surface enhanced Raman
spectroscopy, University of
Strathclyde, Glasgow.
19941999, BSc in
chemistry, University of
Strathclyde, Glasgow.
Industrial sandwich
placement at ICI Chemicals
working on catalyst
testing.
19921994, Scottish
Highers in chemistry,
physics, biology, maths,
history and english,
Chryston High School,
Glasgow.

Communication
Once he has made discoveries and carried out practical
work its important that Imran can communicate
what hes found out. In fact he spends about half of
his time doing the practical science and the other
half communicating it. He publishes his work in
peer reviewed journals and attends international
conferences so he can tell others about what he has
done. It is a great way to get feedback and inspiration
from other experts and to learn about their approaches
to the problems Imran is trying to solve.
Get inspired
Imrans passion for science has led him to an exciting
job at the cutting edge of research. He recommends
anyone wanting to be a research scientist should
try getting a summer placement in a lab selected
universities offer this then theyll see what its really
like. Nothing beats getting some experience in a real
research group, he says.

InfoChem

A DAY IN THE LIFE_BACKYARD CHEMISTRY.indd 7

10/31/2011 9:16:16 AM

50 of tokens to be won

New magazine

Puzzles

In January 2012 we launch our new student magazine

The Mole.
This will bring your regular features about cutting edge chemistry, how
this affects our daily lives and lots more. New content includes news
coverage of exciting new research, chemistry you can do at home, careers
and university advice and information about events in your area.

Prize wordsearch no. 59

Thanks to all who entered the competition to help choose the name.
The winner is Jack Langley, who wins a 25 Amazon voucher.

Find the 32 words/expressions associated with genome sequencing

hidden in this grid contributed by Bert Neary. Words read in any
direction, but are always in a straight line. Some letters may be used
more than once. The unused letters, read in order, will spell a further
9-letter word.

Chemical acrostic no. 21

Send your answers to the editor by Monday 5 December. A randomly

chosen correct answer will win a 25 Amazon voucher.

Complete the grid (contributed by Simon Cotton) by answering the

nine clues to find the answer in the shaded box, which is the name
of an isotope of an element found in heavy water.

1. Valuable metal sometimes found in quartz deposits.

M M O

2. First noble gas to have chemical compounds isolated.

O M M O M O

3. Heavy metal that caused poisoning in Japan, following

consumption of toxic fish.

O M

O M

W O

AMPLIFIED IN SITU
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NOISE
CHAIN
FRAGMENT
NUCLEOTIDE
CLUSTERS
GENERATE BASE CELLS
ONE
COMPUTER
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PCR
COST
HUMAN GENOME
PROGRAM
DNA
IMAGE
PYROPHOSPHATE
DNA SEQUENCING
IMMOBILISED
SEQUENCING
ELECTROPHORESIS

5. Transition metal that is purified by electrolysis.

6. Element used to test for unsaturation in organic compounds.
7. One of the two elements that makes up quartz.
8. Metal found between zinc and mercury in the periodic table.
9. Metal used to supply yellow glow in street lighting.

The winner was Alexander Kounoupias from Surrey. The 8-letter word was SWELLING.

10

ION
SINGLE MOLECULE DNA
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September prize wordsearch no. 58 winner

Name

4. Name given to radioactive isotope of hydrogen.

Please send your answers to the usual address to arrive no later than
Monday 5 December. The first correct answer out of the editors hat
will receive a 25 Amazon gift voucher.

School name

School address
Your email

0611INFO - PUZZLES.indd 1

10/31/2011 9:09:48 AM