Articles by: Mark

Biochemistry – A Very Short Introduction



My new book – Biochemistry – A Very Short Introduction is available for pre-order now!

A here’s a sneak preview…

From the simplest bacteria to humans, all living things are composed of cells of one type or another. Amazingly, no matter where on the evolutionary tree they perch, those organisms all have fundamentally the same chemistry. This chemistry must provide mechanisms that allow cells to interact with the external world, a means to power the cell, machinery to carry out all the varied processes, a structure within which everything runs, and of course some sort of governance. Cells, in many ways, are like communities, but controlled and governed through a web of interlocking chemical reactions. Biochemistry is the study of those reactions, the molecules that are created, manipulated, and destroyed as a result of them, and the massive macromolecules (such as DNA, cytoskeletons, proteins and carbohydrates) that form the chemical machinery and structures on which these biochemical reactions take place.

Or, put more succinctly by the great physicist Erwin Schrödinger,

‘In biology .. a single group of atoms .. produces orderly events marvellously tuned in with each other and the environment according to the most subtle laws.’

Biochemistry is then the endeavour to understand those subtle laws governing those finely tuned orderly events, it is the study of biological molecules and their interactions, and so aims to reveal the molecular basis of life.

Of course, life in all its glory is so much more than just single cells. Cells come together to form multi-cellular organisms which then require a means for individual cells to communicate and ‘trade’ with one another. The organisms, in turn, interact to form the complex webs that are our eco-systems. And all of those interactions are modulated and facilitated through biochemical means. For example, consider the rhodopsin molecules that respond to photons of light, and so act as the first stage of a predator spotting its next meal. Or the olfactory proteins that bind a few minuscule molecules, which trigger a cascade of biochemical reactions that result in prey being alerted to the predator’s presence. Or the antibodies that act as the first guards, recognising the foreign molecules of an invading parasite and triggering the army that is the immune response. All of these processes fall within the realm of biochemistry.

It didn’t take long for an understanding of the chemistry of life to turn into a desire to manipulate it. Drugs and therapies all aim to modify biochemical processes for good or ill: Penicillin, derived from a mould, stops bacteria making their cell walls. Aspirin, with its origins in willow bark, inhibits enzymes involved in inflammatory responses. A few nanograms of botulinum toxin (botox), can kill by preventing the release of neurotransmitters from the ends of nerves and so leads to paralysis and death. Alternatively, the same botulinum toxin administered in tiny quantities results in a wrinkle free forehead. This is all biochemistry.

Detailed description of these topics could easily have made it into this book, and some readers may feel I was remiss in neglecting them and other topics as fundamental as vitamins, hormones, chromosomes, and numerous biochemical techniques. But this is after all a very short introduction, and so I had to draw the line somewhere. As a result, for much of the book I’ve focussed on some of the chemistry that occurs within cells. For therein lie the fundamental chemical processes that all life shares.

Finally, the boundaries of biochemistry are ill defined; it overlaps with genetics, molecular biology, cell biology, biophysics and biotechnology. And so I finish with a pair of chapters which explore how fundamental discoveries in biochemistry are influencing these fields and society at large.

By •April 19, 2021 •0 comments •Uncategorized

COVID-19 tests encased on coffee machine capsules

Transitioning to home working had its challenges for us all, but when your job involves researching biological applications for nanotechnology, those trials are a little more complicated than juggling the household’s broadband usage. So barred from his lab, you might reasonably expect the research by organic chemist Vittorio Saggiomo, from the Bionanotechnology group at Wageningen University & Research in the Netherlands, to have come to a grinding halt.

But Saggiomo is a creative, imaginative type, and so he began to wonder if he could turn common household appliances to good use in the fight against COVID-19. More specifically, could he create a cheap, highly sensitive home test for the virus? It turns out he could. His team has now posted the idea on a preprint server, ChemArxiv. The paper is yet to be reviewed by other scientists.

At the moment, there are two main types of COVID-19 test: the PCR test and the lateral flow test (LFT). The gold-standard PCR test checks for the presence of the virus by detecting its genetic material known as RNA. But there are vanishingly small amounts of viral material in a swab, so the material has to be converted into DNA and amplified before it can be detected. And this is achieved by the “polymerase chain reaction”, which is what PCR stands for.

The process involves repeated cycling through a range of temperatures between 50°C and 90°C. During each cycle, the amount of DNA doubles, so after 30 cycles over a billion copies of the viral material can be created from just one strand of starting material. The amplified material is then detected with fluorescent labels that attach themselves to the viral DNA sequences.

As such, PCR is a highly sensitive technique, but it needs specialist materials and equipment to perform. This is why the tests are sent off to a lab, and it takes a day or two to get the result.

The second common test is the lateral flow test (LFT). These work by detecting fragments of viral protein shells. Embedded within the strips of the LFTs are antibodies that bind to the virus. These antibodies are labelled with tiny gold particles, which appear red, allowing you to see them on the test device. The labelled antibodies accumulate on distinct bands on the LFT depending on whether the virus is present or not.

The LFTs are fast, cheap and easy to use, making them ideal for community and home testing. But they are nowhere near as sensitive as the PCR tests – they will only identify people with high viral loads. This means many people who are infected will get a false negative result from such tests.

CoroNaspresso tests

Ideally, we need a home test that’s as easy to use as the LFTs but as sensitive as the PCR test. An excellent candidate is a method called loop-mediated isothermal amplification (Lamp). This works along very similar principles to PCR, producing multiple copies of the starting genetic material – which you can get from a swab – but has some key advantages.

For example, it can be combined with a handy “colour readout”. When the Lamp reaction occurs, it causes an increase in the acidity of the sample. That means you can add a substance that changes colour according to pH value in the reaction mix, providing a visual indication of a positive or negative result. Another advantage is that Lamp reactions are carried out at a fixed temperature (about 65°C) instead of needing constant cycling through a range of temperatures.

Nevertheless, Lamp still needs fine temperature control. Temperature control systems – be they in a PCR machine, a Lamp instrument or household oven – are usually achieved with electronic thermostats. However, making and shipping new electronic devices specifically designed for home Lamp tests is impractical (especially in the middle of a pandemic). So Saggiomo tried to find a way around this. He hit upon substances called phase change materials that absorb energy (heat) as they melt and so maintain a constant temperature.

After finding a wax made of such a material that melted at exactly the required temperature, Saggiomo set about constructing a device to house the Lamp reaction tubes and chunks of wax. This then needed to be inserted into some other material that could be heated. The perfect housing turned out to be staring him in the face while making his morning coffee: Nespresso coffee machine capsules.

The final step was just finding the right way to heat the capsules. After trying the dishwasher (it worked but samples kept getting lost), the microwave oven (failed, because the tubes overheated and lids popped off) and cups full of hot water (not enough control on the temperature), Saggiomo settled on a simple pan of simmering water on a stovetop. The resulting “CoroNaspresso” device, when tested by other members of the team, with swabs from six people, correctly identified three cases of COVID-19 (these had a different colour to the negative tests).

Home covid test.
Tweet by @V_Saggiomo

The test, including the capsules, phase changing wax and vials in which to insert genetic material, would be easy to produce in millions. People could then swab for genetic material at home and heat the capsules to get their results. These devices are also cheap (about €0.20), easy to make, easy to use and largely recyclable. Maybe we’ll see the CoroNespresso tests in our homes soon, just don’t get them confused with your regular coffee pods.The Conversation

Mark Lorch, Professor of Science Communication and Chemistry, University of Hull

This article is republished from The Conversation under a Creative Commons license. Read the original article.

By •April 9, 2021 •0 comments •lab technique, science news

The Great Adamantium Heist – A chemistry themed escape room



For the last couple of years I’ve put together home escape rooms to entertain the kids over the festive period.

This year’s effort has a chemistry feel, and so I thought I’d share it in case anyone wants some inspiration for their own home-escape room. You might need to adapt things a bit depending on what you have to hand (mine includes a 3D printer!)

The Scenario:

The Lawrence Berkeley National Laboratory have succeeded in creating Unbibium, element 122! And it’s smack in the middle of the Island of Stability! Scientists are amazed by the fact it has a staggeringly long half-life of 524 thousand years. The team have even managed to make a few grams of the new element. Enough for them to test its physical properties. It looks like the Ubb has an incredible tensile strength. In fact it is so strong the press have taken to calling it adamantium. 

It turns out there are people who would like to get their hands on this new super metal. And that’s where you come in. You and your team have a reputation for being able to break into anywhere and steal anything. You’ve been approached via your dark-web chat room, to acquire the sample of adamantium. The unknown buyer will pay you £10 million for the sample that’s locked away in the Lawrence Berkeley Lab.

You quickly accept the job and hatch a plan.

The lab is world famous and lots of people want to see where new elements are made. So they regularly hold tours of their facilities. Your plan is to join one of the tours and then slip away and hide in the janitors cupboard in one of the labs. Then once all the scientists have gone home you’ll creep out, find the adamantium and make your escape. You know that the security guards come by about every 63 minutes, so if you time things right you’ll have just over an hour to get the job done. It probably won’t take that long, after all science labs aren’t known for their top-notch security!

The Set Up

I used the following to set up my escape room:

  • A padlocked box.

  • A combination lockbox (code set to 1716). Hidden in a draw.
  • A partial URL for a file on dropbox or similar e.g  https://universityofhull.box.com/v/MORSE, hidden in the combination lockbox. The URL will not work in this form. It needs to be completed by replacing  ‘Morse’ with the deciphered morse code found in the picture of Lise Mietner.
  • Computer – password protected with the ‘DEFGF’
  • Postcards, on a notice board

  • One postcard contains a description of a holiday in Sweden and particularly Ytterby.

 

  • A 3D printer and and 3D files of the key for the padlock (you can find a printable lock and key at https://www.thingiverse.com/thing:2564541). If you don’t have access to a 3D printer, then just use a combination lock for the padlocked case and replace the STL file for the key with the combination for the lock.
  • Some bismuth to represent Ubb, placed inside the padlocked box.
  • A lab coat 
  • A selection of popular science books, including Sam Kean’s The Disappearing Spoon and Simon Singh’s The Code Book
  • A USB stick – hidden in a draw.
  • Pencils, paper for note taking. 
  • Smart speaker streaming music.

I used printed copies of:

  • Ubb and a radioactive symbol to stick to the padlocked box
  • A selection of  element infographics from Andy Brunning’s Compound Chem (mainly for decoration and red herrings)
  • The periodic table of element name origins
  • A picture of Lisa Meitner, hidden within the picture (just under her name) is some Morse code. Once deciphered this gives the final part of the URL. 

 

    • Sheet music for Tom Lehrer’s Element Song. Screwed up and left in the waste bin. If none of the players can read music you may need to include a musical note crib sheet
    • A ‘signed’ picture of David Guetta (singer of Titanium) and a ticket from a David Guetta concert.

 

  • Morse code crib sheet hidden in The Code Book.
  • Definitions of isotope symbols stuck to the wall e.g.

Element - Key Stage Wiki

Clues 1-3,

Together the first 3 clues provide the number for the combination locked box. All three clues are on a handwritten note placed in a lab coat pocket. 

Combination = AxBxC

Z of my favourite song = A 

Z of lightest element named after Sonia’s 1937 holiday = B

Z of ‘Seek p15 within literature on vanishing cutlery’ = C

Each of these clues refer to the atomic number of an element.

‘My favourite song’ = Titanium (Z = 22) by David Guette. The players should get this from the signed picture and ticket to the Guette concert. If they aren’t familiar with his music they can use the smart speaker to play through his songs.

‘Lightest element named after Sonia’s 1937 holiday’ refers to one of the postcards. And along with the periodic table of element name origins should give them Yttrium (Z= 39)

‘Seek p15 of the literature on vanishing cutlery’ should take the players to page 15 of ‘The Disappearing spoon’. When the note is placed over page 15 the hole in the note reveals ‘helium’ (z=2).

Once they have all the numbers they can work out that 22 x 39 x 2 = 1716, which provides the combination of the lockbox.

Clue 4

Within the combination lock box is a scrap of paper with https://universityofhull.box.com/v/MORSE typed on it, and for an extra clue  ‘Meitner’ is written on the back.

The URL will not work until the ‘MORSE’ section is replaced with the deciphered morse code hidden in the picture of Lise Meitner. 

The Morse code crib sheet is hidden in The Code Book. Together these allow the players to complete the URL with ‘Meitnerium109’.

Clue 5

To access the URL the players obviously need a computer.  The password to the computer is on a sticky note on the back of the monitor. It reads ‘Password: Rust notes from Mr Riddle and a german teacher’s song’.  Mr Riddle refers to Tom Riddle (Harry Potter fans should get this) and  ‘teacher’ in German is ‘Lehrer’. 

Clue 6

 In the waste paper bin is a copy of sheet music of Tom Lehrer’s element song. The player’s should get iron and oxygen from the reference to rust, and then reading the notes from the sheet music to get ‘DEFGF’, which will unlock the computer.

Once the players open the computer and go to  https://universityofhull.box.com/v/meitnerium109 they will be able to download the files to 3D print the key to the lock. A USB stick can be used to transfer the data to the printer (As an alternative, hide the combination to a second lock at a URL).

Then players simply print the key, open the padlocked case, retrieve the Ubb and make their escape!

 

By •December 29, 2020 •0 comments •entertainment, fun, Uncategorized

The sort of repeating table of things that make up everything


I really like XKCD. One of the pictures I like the most is the Up Goer Five. I sometimes use it to show other people how you can explain hard ideas using just the words people use the most.

So I got to thinking whether I could explain some of the facts about the table that we all like a lot and is 150 years old,  but just using the ten hundred words people use the most.
I ended up falling down a home made by a long eared jumping animal. But it was fun and because I spent too much time doing it I thought I might as well share it with you all.
Thanks to Theo Sanderson for making the Up-Goer Five writing thing.

You can get a big picture of the table here.

EDIT: Thanks to Emma for telling me this has been done before, so please do look at it  in Thing Explainer.

By •February 3, 2019 •9 comments •fun
1 2 3 … 26