Science at Cambridge: Biochemistry

University
9D Alice Flint photo

The biochemistry of metabolism

My name is Alice and I am a 3rd year biochemist. Initially I came to Cambridge thinking I would specialise in chemistry as the less strong teaching of biology at my school had put me off the subject. However taking the Biology of Cells module as part of the Natural Sciences Tripos in first year renewed my interest in biology and persuaded me pursue it in future years. Choosing to study Natural Sciences allowed me to change my mind and develop my interests due to the array of options available.

Biochemistry is concerned with the principles underlying biology at a cellular level such as genetic regulation, cellular signalling and metabolism which are all interlinked. When I tell people I study biochemistry quite often the response is ‘but isn’t it all memorising pathways, why would you want to do that?’ However this is very far from the truth, yes there are some metabolic and signalling pathways but biochemistry is more concerned with understanding the overarching concepts rather than memorising the minute details. I find that when you look at the regulation of cellular processes it is actually very coordinated and logical which I find quite elegant.

My main interest is in metabolism. I am a sporty person so I find the changes that occur during exercise highly relevant however metabolism also has a central role in disease. For example cancer cells display anaerobic metabolism even in the presence of oxygen -the Warburg effect. This allows for detection of tumours by Positron Emission Tomography (PET) where a radioactive tracer, the glucose analogue FDG is taken up in greater amounts by tumours and can be imaged by a scanner.

In 3rd year biochemists undertake a project in their second term. My project again looks at the links between metabolism and disease. Some organisms (plants, fungi, bacteria and protists) can undergo a pathway called the glyoxylate shunt which bypasses the carbon dioxide producing steps of the Krebs cycle allowing these organisms to grow on 2 carbon substrates e.g vinegar. An enzyme essential to this pathway, isocitrate lyase (ICL) has been shown to be necessary for the upregulation of the type III secretion apparatus-this is a needle like structure that allows bacteria to inject toxins into the host cells. My project is looking at the expression of ICL in different nutrient and temperature conditions and its possible regulatory molecules. As the glyoxylate shunt does not occur in humans enzymes involved in this pathway are possible new drug targets, making research into the pathway important in this time of increasing resistance to existing antibiotics.

Carrying out a project allows you to develop key practical skills and introduces you to the lab environment. It has encouraged me to pursue a career in research and I will take further steps towards this next year by staying in Cambridge for a 4th year to do an MSci in biochemistry which will involve completing a bigger project over two terms and hopefully I will continue onto a PhD after.

Alice Flint Undergraduate student

School Winner: The Chemistry of Tea

Winning Entry Landau Forte College Derby9C Isi Moss (Landau Forte) 2SchoolWho doesn’t like a cup of tea? 6.2 billion cups of tea are consumed in the UK every year, proof that tea is Britain’s most loved beverage. But what’s the chemistry behind a brew, and what is it that makes tea so special?

It is thought that the optimum brewing temperature for tea is 92⁰C, but 58⁰C is the recommended drinking temperature.

Black tea tends to contain caffeine, which stimulates the central nervous system, hence making you feel more alert shortly after drinking. As well as caffeine, tea is a natural source of fluoride, which promotes healthy teeth. However, there are also other compounds in tea which are less well known, such as polyphenols, which are responsible for much of the taste as well as the characteristic colour of black tea.

Surprisingly, there are 180-240mg of polyphenols in a strong mug of tea, and these compounds make up approximately one third of the weight of dried tea leaves. As antioxidants, they can have a positive effect on the blood, by limiting cell damage due to oxygen that can occur due to free radicals. However, this is disputable, as it has been suggested that the protein-polyphenol complexes can be broken down in digestion, thus meaning that it cannot impact the blood concentration of polyphenols. Polyphenols are made up of catechins, and can be split into two main categories: theaflavins and thearubigins.

Theaflavins have several potential medical applications. For example, they could work to reduce blood cholesterol level, reduce obesity (by reducing the likelihood of a fatty liver), and could even reduce breast cancer cell migration. They are present in black tea due to the enzymatic oxidation of green tea to produce black tea leaves (a process referred to as fermentation). The percentage of polyphenols that are theaflavins is only 10%, yet they account for the yellowish colour of tea.

In contrast, thearubigins are reddish-brown pigments, which also contribute to the distinctive colour of tea. They are weakly ionising acids, and the anions produced are very colourful. Therefore, the addition of lemon to tea can alter the liquid’s colour, making it lighter as the citric acid is pH 2.2 as opposed to pH5 of thearubigins. This makes citric acid more strongly ionising than thearubigins, so it suppresses the ionisation of the thearubigins. Due to the opposite effect, tea brewed in alkaline water will be somewhat darker in colour.

Similarly, the chemistry of tea changes again when we add milk and sugar. While only 1 in 3 people drink their tea with sugar, 98% of Britons drink their tea with milk. The possible anti-oxidising effect of polyphenols could be reduced by adding milk, as casein proteins in milk bind to them and reduce their anti-oxidising effect.

So, next time you sit down to indulge, take a moment to remember the chemistry behind this celebrated drink, whether you like your tea milky, black with a slice of lemon, or a builder’s brew with milk and two sugars.

Isi Moss
Student at Landau Forte

“As an aspiring Chemistry student, I’m fascinated by the chemical interactions of the world around us. I would love to be a Science Journalist, communicating my passion with others, and working towards putting Chemistry in the spotlight of public interest, alongside the other popular sciences.” Isi

Science issue: The gloopy world of collagen proteins

9B Ying Chow photo1NewsI always find it a little misleading to tell people that I am a chemist; the molecules that I am studying come from biology, while the technique that I use comes from physics.

The samples I have investigated included bone, tendon, cartilage, and skin; a diverse variety of materials somehow all made from collagen proteins. Together with a range of other proteins, sugar-like molecules, and sometimes minerals, collagen proteins form the extracellular matrix — the glue-like matrix in which cells are embedded and organised. However, it is not just a passive scaffold: the cells make attachments to the matrix at an atomic level, and this attachment can trigger different cell behaviours. So what are these atomic-level “hooks” that the cell is seeing?

Perhaps a little surprisingly, it is not easy to study the atoms in the extracellular matrix. Since it is a gloopy/grainy, cross-linked, heterogeneous mix of proteins, sugars, and more, there is a mind-boggling variety of different kinds of atoms and molecules within a small piece of tissue. Often, a shortened section of pure collagen-like proteins is studied as a simpler model system. However, what if we could have a technique where we can directly compare healthy tissue and diseased tissue atomically? Perhaps we can understand how the differences in bulk property (e.g. stiffness, brittleness) came about, by understanding the molecular and atomic level organisation (e.g. different compositions, different chemical bonds). Changes in the extracellular matrix occur in many diseases, including diabetes and cancer, but also naturally over time as we age. Much of current treatment focuses upon the cells, or surgically removing diseased tissue, but perhaps there are ways to more effective treatment if we can understand, reverse or even prevent these changes at a tissue level.

Much of my research is about developing an approach to study tissues in an intact manner at an atomic level. The technique that I use, solid-state nuclear magnetic resonance spectroscopy (ssNMR), can sometimes feel like it is a world apart from biology, full of electronics, pulse programming, and liquid nitrogen. All the machinery is part of an attempt to delicately (well, as delicately as you can with a kilowatt of power) nudge the quantum mechanical states of those atoms within the sample, to find out what bonds those atoms are making, what other atoms are nearby, in order to deduce what molecule that atom is a part of. Interpreting the data is much like solving a logical puzzle, trying to fit all the pieces of information to what we know about the experiment and the sample.

At the moment, I am trying to work out why some parts of collagen proteins appear to be more flexible than others, which may help cells form attachments onto the collagen matrix. Using ssNMR, I could pick out the flexible atom pairs, which exerted a smaller magnetic (dipolar) effect on each other.

As a chemist who is working at the border between disciplines, I am always working with a range of scientists from different backgrounds: cell biologists, biochemists, computational chemists, and even engineers and doctors. It is an enriching experience, full of creative solutions, and even more creative questions.

If you are interested to find out more, feel free to ask by email or Twitter!

Ying Chow
Alumna

Further reading:

Protein Databank 101 Molecule of the month: Collagen
http://pdb101.rcsb.org/motm/4

Molecular Biology of the Cell (Alberts et al, 2002)
http://www.ncbi.nlm.nih.gov/books/NBK26810/

The Extracellular Matrix at a Glance (Frantz 2010)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995612/?tool=pmcentrez

Some introduction to solid-state NMR
http://u-of-o-nmr-facility.blogspot.de/2008/03/solution-vs-solid-state-mas-nmr.html
http://u-of-o-nmr-facility.blogspot.de/2007/11/magic-angle-spinning.html
http://u-of-o-nmr-facility.blogspot.de/2010/03/household-dust-bunnies.html
http://u-of-o-nmr-facility.blogspot.de/2011/12/13-c-nmr-of-delicious-christmas-treat.html

A set of lectures that give a fuller introduction to NMR
http://www-keeler.ch.cam.ac.uk/lectures/Irvine/
https://www.youtube.com/watch?v=nM7jQFhrvR0&list=PLE20foNk9J6L1dh9X27RaPiaul8_7wrAY

Part I of our recent attempts to understand collagen flexibility (Part II is being prepared…)
http://www.nature.com/articles/srep12556

Twitter handle @selkie_upsilon

 

Career Path: Harnessing talent and work-life balance

iop-Women in A level Physics Jan 2016
iop-Women in A level Physics Jan 2016

Career

I’ve had quite a few enjoyable and fulfilling jobs over a 40-year career, all in science education. I’ve taught physics in schools and trainee physics teachers in Universities. I’ve done some important research on children’s understanding (and many teachers’ misunderstanding) of science. Most recently I’ve been employed by the Institute of Physics to help address the very low number of girls taking Physics A-level.

Did you know that nationally only about 22% of the entrants for Physics A-level are girls. Research in 2011 showed that Physics was the fourth most popular subjects for boys to choose but the 19th most popular for girls.  In 46% of schools no young woman completed a Physics A-level.  This is a shameful waste of talent.

I was drawn to physics because it addresses big questions. How can you look at the sky and not just wonder? How can you not want to study it? And maybe it’s the wonder in a grandson’s face when he looks up at the moon which links my own passion for physics and for looking after (and teaching) children. But the great thing about studying science at University is that it lets you have your cake and eat it. Unlike some other disciplines, graduates with science degrees are rarely short of a job, even if they want to combine their career with childcare or other life passions.

You can glean insights into just a few of the jobs available within other blog entries: Sarah chose a role in creating new drugs, Angela in harvesting fuel resources, Annie in health care for women in prison, Zoe in international consultancy, Rebecca in researching the epidemiological consequences of behaviour and Jelena in developing genetic testing facilities.

Like many contributors to this blog, I went to New Hall (Murray Edwards). I was very unsure whether this was a good idea at the time as I came from a state school in Cleethorpes. The College was welcoming and friendly. I learned that we all brought different strengths and skills. And the people I met as an undergraduate became and remain my closest friends.

I haven’t got a paid job anymore. Now retired, I seem to spend most of my time looking after grandchildren. Some would see a pattern in this – I gave up a PhD to look after my own children. Having a fulfilling life is about more than what you do at work. But I don’t for a moment regret choosing to study science (mostly physics) at University. It was great for my life as well as for my career. And I’ve spent most of that career encouraging young women to do the same – and to make full use of their talent for science.

So why do I want to encourage you, to study science? Firstly, because there is so much that you will find interesting. Secondly, doing science opens up so many possibilities for what you can do with your life. Thirdly, you can be very good at it. Finally, and importantly, young women are needed.

Jenny Mant
Alumna