Back to Basics: Biochemistry Part 3

Hey guys! This is the final post in my three-part series about the basics of biochemistry. This post is going to combine biology and chemistry together to show you what real biochemistry is – and to do this I’ll be using an enzyme case study. I’m first going to talk to you briefly about some enzyme theory and then we’ll get onto what chymotrypsin is and how it works in our bodies. Get your notebooks out, because this post will be an interesting one.

If you haven’t read the previous posts, you can read them here and here. I recommend reading them before this so it can help you understand this post a little better!

The Theory

Now, in my first post for this series, I talked to you guys about how amino acids can bond together to form polypeptides. These polypeptides can be transcribed and translated into enzymes. Enzymes are biological catalysts, meaning they help speed up biological processes. Enzymes contain an active site where substrates (another reagent) can come and bind to, activating the enzyme. This substrate needs to be able to fit into the active site, and usually, enzymes can change shape slightly to accommodate this. This process can be exploited for use in medicine. Enzymes also have another site called the allosteric site. This is where other substrates can bind to control catalysis. I won’t go into this, but just know that this allostery process is important for the regulation of normal enzymatic processes.

What is Chymotrypsin?

Chymotrypsin is protease enzyme that is found in the gut (in the duodenum). Just as monomers can make polymers, polymers can also be broken down into their monomers again – and this is what proteases do. Proteases are able to “cut” polypeptide chains in certain areas. This is known as proteolysis and it is used in many applications, including removing unwanted proteins from cells and digesting dietary protein. In the case of chymotrypsin, it can cleave polypeptides near a carboxylic acid sequence, near an aromatic ring or at a hydrophobic region. Chymotrypsin is also a serine protease, meaning that the amino acid serine is found in the active site.

To understand the mechanisms of chymotrypsin, we do need to look a little bit into its structure. chymotrypsin contains what we call a catalytic triad of Aspartic Acid-102 (D-102), Histidine-57 (H57) and Serine-195 (S195). These amino acids are bound together through hydrogen bonds (intermolecular bonds between hydrogen and either nitrogen, oxygen or fluorine). By itself, chymotrypsin would not be the greatest enzyme as we need a strong nucleophile to perform its reactions. In the absence of a substrate, therefore, we’re able to create an alkoxide group in the S195 of the enzyme through the polarisation of bonds. This alkoxide group is incredibly electron rich, which means that it can donate its electrons to a substrate very easily.

The alkoxide group. The small dots represent electrons and as you can see, the oxygen is very electron rich – this acts as our nucleophile.

The main purpose of chymotrypsin is to speed up the process of proteolysis – and it does this beautifully. In fact, even though proteolysis is energetically favourable, chymotrypsin still increases the rate of reaction by a factor of 1012!

The Mechanism

I’m not going to show you guys the entire mechanism of how chymotrypsin works because there are around 8 steps and frankly, it’s a little scary – I’m still traumatised by it. Instead, I’m going to show you the formation of the alkoxide (and the first step of the mechanism) because I believe this is the most important part of chymotrypsin activation, as without it, chymotrypsin just wouldn’t work. I also want to note that generally there are four catalytic techniques (covalent catalysis, acid-base catalysis, catalysis by approximation and metal-ion catalysis). Chymotrypsin utilises covalent catalysis which means that during its mechanistic action, it covalently bonds to the substrate to help stabilise any intermediates that may form, lowering overall energy to ensure that the reaction can still proceed.

An image of chymotrypsin with and without the alkoxide. I’ve also drawn the first step of the mechanism just to show you how we use curly arrows in a real life situation. If you want to know more about the mechanism of chymotrypsin, you can check this out.

And that’s all for this series guys! I hope you guys, especially non-STEM students/specialists, got a good, digestible (see what I did there 😏) glimpse into what a biochemist is required to understand and how the two separate sciences of biology and chemistry come together. This has definitely been a fun series for me to write. Comment below, did you guys enjoy this series?


Vitamin D and Depression: A Growing Field

Trigger warning – depression and suicide.

Happy World Health Day guys! Today is a day of reflection and progression – reflecting on the vast progress we’ve made in healthcare accessibility and awareness on the fact that some regions of the world still do not have adequate healthcare.  I’ll link the World Health Organisation’s page on World Health Day so you guys can get more information about it and potential ways you can help! I wanted to take a slightly different approach and talk about depression. Exam season is around the corner, and many students feel more stressed, worn out and on edge during this time. Unfortunately, suicide rates do increase during exam season due to the immense educational pressures (article linked below). So, in this post, I wanted to talk about what depression is, some signs and symptoms and some exciting research that may link vitamin D deficiency and depression.

What is Depression?

Clinically, we have a broad debate about how depression can be defined – mainly because there are so many different types and symptoms. The overarching, modern definition of depression, however, tends to be categorised as “melancholia” – a deep sadness (Beck and Alford, 2009). This may be seen as a somewhat generalised definition as there are more signs that may define depression rather than this deep sorrow. Most of these signs are:

  • A negative shift in moods, such as sadness loneliness and apathy
  • A contrary view on oneself, including self-blame and low self-worth
  • Punishing ideas, including wishes to hide, run away or to die.
  • Physiological changes such as anorexia and insomnia
  • Change in activity level

It’s important to see, therefore, that depression is a complex system of cognitive and behavioural changes alongside melancholy. Because of the similarities of low mood and depression, these two have become interchangeable, and for a long time, there has been a misconception that depression is just an exaggeration of normal sadness – this is not the case. There are various severities and types of depression, and unfortunately, there is very little knowledge on what causes depression – its aetiology is not very well known (ibid).

That being said, there is some knowledge on what causes depression. The general consensus is that there is a chemical imbalance of hormones in the brain – particularly a low level of serotonin. We now know that other hormones play a role in the onset of depression, such as dopamine and glutamic acid. The complexity of depression is unimaginable. Usually, its development is a combination of biological factors (such as the low hormones levels) and environmental factors (such as life events, stress or different types of medication (Syvälahti, 1994). New research suggests that there are a multitude of hormones that interplay to cause depression, and other physiological aspects like different parts of the brain being different in a depressed person than nondepressed (Publishing, 2009). 

The last point aforementioned is something I want to actually talk about a little bit more. There are three parts of the brain that are affected by depression: the amygdala, thalamus and hippocampus. The amygdala is a structure that is associated with anger, pleasure and sorrow and it has been seen that activity in this region of the brain is more active in a depressed person. The thalamus is the epicentre for sensory information – it receives it and relays it to the most appropriate part of the brain. There is some research to suggest problems in the thalamus could lead to feelings of overjoy or deep sadness. The hippocampus is part of the same system that the amygdala is, but its role is in long term memory. Some research suggests that the hippocampus is smaller in a depressed person, and continuous contact with stress hormones can inhibit the growth of nerve cells in the brain (ibid).

An image showing some structures of the brain, particularly those involved in depression. Taken from Harvard Public Health.

Damn – that was a lot wasn’t it? The underlying point is that depression is much more severe than feeling low. It is a complex interplay of hormonal, physiological and environmental impacts.

Symptoms of Depression

Earlier I touched a little bit on the signs of depression. Here I’ll list some of the symptoms of depression, but this list is definitely non-exhaustive (, 2016).

Earlier I touched a little bit on the signs of depression. Here I’ll list some of the symptoms of depression, but this list is definitely non-exhaustive (, 2016).

Symptoms include:

  • Continuous low mood (psychological)
  • Low self-esteem (psychological)
  • Little motivation or interest in things or hobbies (psychological/social)
  • Lack of energy (physical)
  • Disturbed sleep (physical)
  • Changes in appetite/weight (physical)
  • Avoiding contact with friends (social)

Where does Vitamin D come into this?

Vitamin D is a fat-soluble vitamin that is mainly acquired through UVB light/sun rays (hence its nicknamed “the sunshine vitamin”) and through diet. The reason scientists believe that there may be a link between vitamin D and depression is because vitamin D receptors (VDR) are found all over the body and in the brain. In the brain, VDRs are located in areas like the thalamus, amygdala and hippocampus which, if you remember from earlier, are three parts of the brain that may be involved in the onset of depression. This points to the idea that vitamin D may have a hormonal impact on the brain, especially as we find vitamin-D associated enzymes (e.g. CYP 24A1) in the brain too. This means that vitamin D could play a vital role in neuroprotection and healthy brain development and functioning (Cuomo et al., 2017).

This relationship was analysed in a few studies, and whilst there is relatively strong evidence to suggest a correlation between vitamin D and depression, there is still some uncertainty in what the data means in terms of causation. That being said, let me explain the experiments briefly and tell you what this means currently (ibid).

There was a survey of 7,970 US residents (aged 15-39) as part of The National Health and Nutrition Examination Survey. They found that those with a serum blood level of 50nmol/L or lower were at a significantly higher risk of showing symptoms of depression than those who had vitamin D levels were closer to 75nmol/L (ibid). Another study of elders aged 65-95 from the Netherlands showed that vitamin D levels in depressed persons were 14% lower than in nondepressed (ibid). These are only two studies which have demonstrated the correlation between vitamin D insufficiency/deficiency and depression, but there are many more on various different age groups and ethnicities to solidify these results. There has been some research that has not shown this link, however. A study in China comprising of 3,262 men and women aged 50 to 70 failed to confirm this relationship (ibid). Overwhelmingly, however, there is quite strong evidence that there is a link between vitamin D and depression – but what does this mean in terms of diagnosis and treatment?

The first implication we come across is that we are unsure whether low vitamin D levels causes depression or whether depression causes low vitamin D (ibid). For example, it may be that depressed persons have lower vitamin D levels due to reduced outdoor activity (when sunshine is the best way to absorb vitamin D). There is some indication that the relationship may be that low vitamin D causes depressive symptoms due to the presence of VDRs in the brain, but still very little is known about this (ibid).

The second implication is that there is very mixed evidence to suggest that vitamin D supplementation does actually help with symptoms of depression. This arises due to various reasons, such as different studies using different doses of vitamin D, different frequencies (e.g. if a supplement is taken every day or once a week) and different methods in measuring the severity of symptoms (ibid). Further standardised studies need to occur to really help us understand the treatment aspect of this link.

So, to conclude, there is a fairly strong correlation between low vitamin D levels and depression. Whether this relationship is that the low vitamin D causes depression, or whether depression causes low vitamin D is still uncertain, and in fact, quite a complicated relationship to study. This is due to behavioural factors that interplay with depression and vitamin D. Clinically, we also are not sure whether supplementation can be an effective treatment mainly due to a lack scientific literature that points towards it being effective, but even theoretically. As I’ve mentioned earlier, there are multiple reasons for the onset of depression, and it is likely that addressing one of these reasons (in this case, the low vitamin D levels) may not be an effective way to deal with depression.

I know this post was quite a heavy one, but I hope you guys understand a little bit more about depression. If you or anyone you know suffer any of these symptoms or feel like harming yourself, please seek appropriate help (I’ve linked some resources below). If you are a student who’s feeling the pressure from submitting final assignments and exam season – hang in there! Remember to take time out to chill and have fun – talk to your friends, watch some Netflix and have some “me” time!

Links Mentioned

World Health Organisation –

Mental Health Hotlines (International) –

Suicides by young people peak in exam seasons –


Beck, A. and Alford, B. (2009). Depression. 2nd ed. London: Staples Press, pp.3-9.

Cuomo, A., Giordano, N., Goracci, A. and Fagiolini, A. (2017). Depression and Vitamin D Deficiency: Causality, Assessment, and Clinical Practice Implications. Neuropsychiatry, 07(05), pp.606-612. (2016). Symptoms – Depression. [online] Available at: [Accessed 12 Apr. 2019].

Publishing, H. (2009). What causes depression? – Harvard Health. [online] Harvard Health. Available at: [Accessed 12 Apr. 2019].

Syvälahti, E. (1994). Biological aspects of depression. Acta Psychiatrica Scandinavica, 89(s377), pp.11-15.

(Photo Credit: Deborah Diem, 2018)

Back to Basics: Biochemistry Part Two

Welcome back, guys! In yesterday’s post, I talked about fundamental biological concepts that underpin biology. In today’s post I’m going to talk about basic chemistry that will help you guys understand my other science posts. Like I said in my last post – this post is ideal for non-STEM students! Hopefully, it gives you guys a friendly and approachable introduction to some advanced chemistry.

There are three subsections of chemistry: physical chemistry, inorganic chemistry and organic chemistry. In biochemistry, we’re particularly interested in organic chemistry. Organic chemistry is concerned with carbon chemistry, so any compound that contains mostly carbon is called organic.

Of course, there is knowledge from physical and inorganic chemistry that is incredibly valuable in organic. Chemistry is a subject that cannot be worked through topic by topic, but rather all knowledge is built upon so that everything flows together. I won’t be covering any of these in too much detail, but it is something important to note.

Now, there are many different organic compounds. The ones that most people are familiar with are alkanes and alkenes. Alkanes are unsaturated hydrocarbons (sequences made of carbon and hydrogen atoms only) with only single bonds. Alkenes are unsaturated, meaning they have at least one C-C double bond. We also have alkynes which are hydrocarbons that have at least one C-C triple bond. The image below should give you a visual on what they look like.

This image shows you what alkanes, alkenes and alkynes look like. The nomenclature is very similar – the top is called ethane, the middle is ethene and the bottom is ethyne. This image was taken from

There are, of course, many other types of organic molecules. In a previous post, I talked about carbonyls, but we also have things like esters and carboxylic acids. Now we’ve covered what organic compounds can look like – let’s get on to the chemistry!

I think there are two theories in organic chemistry that are important to understand: molecular orbital theory and how to understand and draw mechanisms.

Molecular orbital (MO) theory predicts what molecules will look like when atomic orbitals (AO) overlap. It is the idea that electron density is shared amongst many atoms, as opposed to localised. As we know, all atoms have orbitals that can hold at most two electrons. When reactions occur, these AOs overlap with AOs from other atoms to form MOs. If these orbitals do not overlap, a reaction does not occur.

Assuming that the geometry of the AOs allows them to overlap, the next consideration to think of when looking at organic reactions is the energy barrier. The energy barrier is the minimum energy needed for two molecules to react. This energy barrier tends to be reasonably high, and then goes lower when the product is made. This is to ensure that spontaneous reactions do not occur. So essentially, in this reaction scheme first we checked if the atoms can react together through their geometry and now we’re checking if they have enough energy to carry on the reaction – if it is energetically favourable.

The final consideration to make is whether the electrons can move from an area of high density to an area of low density – we use a curly arrow to show the movement of a pair of electrons from the nucleophile (electron donating) to the electrophile (electron accepting). It’s crucial for chemists to know which molecules make good nucleophiles and which make good electrophiles.

A good nucleophile needs to be electron rich. Organometallics (compounds that have a carbon-metal bond) can be good nucleophiles if the electronegativity difference is large. Electronegativity is the idea that electrons tend towards one atom more than the other in a molecule, and the bigger this difference is in organometallics, the better the nucleophile it will be. Here, the curly arrow will start at the polarised sigma bond.  Pi-bonds also tend to be good nucleophiles. These bonds are found in double/triple bonds as well as aromatic rings. These bonds are fairly electron rich, and the curly arrow will start at this bond.

Good electrophiles include compounds with empty AOs (as there is space for electrons), compounds with weak single bonds and compounds with multiple polarised bonds. Electrophiles need to be electron-deficient to accept electrons from a nucleophile.

Here I’ve drawn a very generalised mechanism to show you how a curly arrow is used.

And that’s it for today’s post guys! I know these last two posts have been quite heavy but I hope they’ve given you guys a small glimpse into the basic knowledge that biochemists must know to do their jobs well. I know I haven’t explained everything in excruciatingly painful detail but if you do want another post or any questions – you can always comment here or email me! The next post in this series will be about how biology and chemistry come together in a biochemistry degree – something that is a little but more complex but don’t worry – you’re ready for it!

Did you guys find chemistry interesting at school? Comment below on any fun projects you might have done!

Back to Basics: Biochemistry Part One

So, I recognise that not everyone understands what biochemistry actually is – I definitely didn’t before I got into the degree! Also, not everyone knows advanced science to understand many of the things that I want to talk about in this blog. So in the next few posts, I want to explain the absolute basics of both biology and chemistry, and how these come together in my degree discipline. So if you’re a non-STEM student or haven’t completed any science education beyond GCSE (I know, those were hard!) – this three-part series is for you! Grab some popcorn, follow this blog and enjoy the next few posts which will detail the absolute bare bones of my degree.

Firstly, what is biochemistry?

Biochemistry is the study of the chemistry of physiological and biological processes (Oxford dictionary, 2019). As an example, if we say that someone has abnormal brain biochemistry, we’re saying that the chemistry of the processes within the brain is not standard.   Undoubtedly, therefore, both chemistry and biology play a significant role in this degree. You might assume that Biochemistry is studying these two disciplines separately like in school, but it’s not really like that. In this degree, the two subjects are more intertwined, but for the sake of simplicity, I’ll separately talk about these two subjects, and in a third post I’ll talk about how these come together.

Basic Concepts: Biology

The central concept underpinning biology in biochemistry is the idea that small subunits build up to make larger molecules. Often, we call a single subunit a monomer, and we call the large molecules polymers – this is called polymerisation. Usually, these occur through a condensation reaction – where two monomers will react together, and a water molecule is lost. This will form a covalent bond (where the electrons are shared between the nuclei of the atoms) between the two monomers. I’m sure through your own education you know some examples of these! Perhaps the most important model in biochemistry is proteins. Proteins are made up of polypeptide chains – long strands of amino acids. Amino acids are the monomers in this case, and through condensation reactions polypeptide chains are formed – these are the polymers. I won’t be going further into what these do – but if you do want a post, let me know! Other examples of this monomer/polymer relationship are how nucleotides form DNA/RNA and how single sugars such as glucose (we call this a monosaccharide) can join together to form carbohydrates and starches (which we call polysaccharides).

Well done – you can now do a biochemistry degree! I’m not kidding, if you understand this process, you understand the bare basics of most concepts taught in the degree.

Now the reason we’re so interested in this is that these reactions show energy differences. Whether energy is released or absorbed is crucial for understanding why specific enzymes might be needed and how domino reactions can occur. This is often how we study the chemistry on the molecular level – I’ll take about this in the next post.

It’s important to note that biochemists work on the molecular level of understanding. If you were studying physiology, for example, you would focus on whole bodily systems. Of course, it’s essential for biochemists to have a sound knowledge of these, but the area of expertise is what happens inside cells, organelles and in macromolecules (e.g. lipids and proteins).

In relation to cells, I do have a blog post coming up that will go into detail about cell biology. For now, all we need to know is that cells are small living components are make-up larger tissues. We do have a particular hierarchy when it comes to how an organism is organised. For multicellular organisms (organisms that have more than one cell), this is the linear sequence of size and progression:

Within cells, we have these little ‘factories’ called organelles. If you will, there are like ‘mini organs’ in the sense that they have their own structures and functions. This structure and function relationship is echoed in all parts of biology and is essential for biochemists to study. These cells hold our DNA, create energy and communicate with one another to mediate a response. We do have different types of cells e.g. red blood cells, epithelial cells and white blood cells. These different cells have different functions and therefore have a different structure.

As you can hopefully see, with relation to the biological component of a biochemistry degree, there are three underpinning, vital concepts. To recap, these are:
• The idea that monomers form polymers, which are larger molecules that aid in biological function
• Energy changes in chemical reactions or polymerisation drive other chemical reactions
• Cells have various components which are studied to understand the relationship between structure and function.

If you understand these concepts, you understand a very large portion of biochemistry – so well done you! I hope you guys enjoyed this post. The next post in this series will be talking about the basic chemistry which underpins biochemical knowledge.

Comment below – did you guys enjoy any of the sciences at school? If so, which ones and why?


(Photo Credit: Michael Longmire, 2019)

Scientists Extend the DNA Alphabet

An interesting development!

The Student Scientist

Deoxyribonucleic Acid (DNA) is composed of four bases: Guanine (C5H5N5O), Cytosine (C4H5N3O), Adenine (C5H5N5), and Thymine (C5H6N2O2), or GCAT, in short.

These bases determine the information available to build and maintain an organism by bonding in specific orders: C bonds with G, and A bonds with T, forming base pairs. Each base form hydrogen bonds with the nitrogen and oxygen molecules from its respective pair.

Hydrogen Bonding In hydrogen bonding, the unbonded valance electrons in nonmetals like oxygen and nitrogen form a negative dipole, which attracts the positive dipole of hydrogen atoms, according to the Van Der Walls forces. This attractions holds DNA base pairs together.

Each base pair is also attached to a sugar molecule (C12H22O11) and a phosphate…

View original post 366 more words

Face of the Day: Drugstore Edition!

Hey guys! Being a broke university student is not fun, but that doesn’t mean you still can’t enjoy good, high-quality makeup. Before I did a post about my typical FOTD, and this post will be similar but using only drugstore products! I also will be using drugstore brushes too.


Today I will be first going in with my Rimmel Lasting Finish Makeup Primer in Shade 004 just using my fingers. While that is settling in, I used my CYO Frame of Mind Brow Sculpting Pencil (Dark) and carved out my eyebrows using Freedom Pro Camouflage Paste (shade 4) using a Primark Concealer Brush. I was feeling a decently glowy look today, so I decided to use my L’Oreal Paris Infallible Pro Glow Longwear Foundation in Natural Beige (205). I love this foundation! It’s a low-medium coverage and is a very dewy finish which is excellent for my very dry skin. So I stippled this foundation onto my face with the Morphe E31 Deluxe Flat Buffer Brush and smoothed it out with the Real Techniques Miracle Complexion Sponge. I used the Maybelline Instant Conceal Eraser Concealer (in Nude) under my eyes, between my eyebrows and on the bridge of my nose and underneath my cheekbone, blending it in with that same Real Techniques sponge. I dusted the contour shade from the Sleek Makeup Face Contour Kit (in Light) with the Fan Brush from Contour Cosmetics on my cheekbones and the perimeter of my face. I didn’t dust too much because I wasn’t going for the bronzey look today, but I did just want to warm up my face a little bit! I used a Blush Brush from Contour Cosmetics to apply some of the Bourjois Little Round Pot Blusher in Rose De Jaspe to my cheeks. I don’t usually apply much blush to the apple of my cheek as I have a round face, which can be accented if I wear blush on the apples of my cheek. I then used the Colourpop Small Fluff Brush to apply a highlighter shade from the Revolution Ultra Pro Glow Palette. Unfortunately, the palette doesn’t have individual shade names used the third shade on the bottom row on the high of my cheekbone, brow arch, down my nose bridge and over my cupids bow.

~ Eyes ~
For my eyes today. I didn’t use anything too heavy. I used the same Sleek Bronzer with the Elf Blending Eye Brush and dragged it into my crease and slightly down to my lash-line. I curled my eyelashes with the Primark Eyelash Curler and applied my Max Factor 2000 Calorie Waterproof Mascara.

~ Lips ~
I lined my lips with the Primark Lipliner (Brown) and filled in the middle part of my lips with the Nyx Liquid Suede Cream Lipstick in Soft Spoken.

And that was my makeup for today guys! Usually, I spray my face with rose water at the end to make the makeup mesh in with my skin and add a subtle glow. As you can see, I was feeling a light, pinky look today and executed that with the high-street makeup. What’s your favourite drugstore product?

(Photo Credit: Annie Spratt, 2017)


After a request, I’ve decided to link the products and list their prices down here. I hope this is helpful!

Rimmel Lasting Finish Makeup Primer in Shade 004 (currently £6.99) –

CYO Frame of Mind Brow Sculpting Pencil (Dark) (£4) –

Freedom Pro Camouflage Paste (shade 4) (currently £1.50) –—CF04/m-1804.aspx

L’Oreal Paris Infallible Pro Glow Longwear Foundation in Natural Beige (205) (£10.79) –

Morphe E31 Deluxe Flat Buffer Brush (currently £20 but I definitely got it on sale for much less) –

Real Techniques Miracle Complexion Sponge (£5.99) –

Maybelline Instant Conceal Eraser Concealer (in Nude) –

Sleek Makeup Face Contour Kit (in Light) (£6.99) –

Bourjois Little Round Pot Blusher in Rose De Jaspe (£6.49) –

Colourpop Small Fluff Brush ($7) –

Revolution Ultra Pro Glow Palette (£8) –

Elf Blending Eye Brush (£2) –

Max Factor 2000 Calorie Waterproof Mascara (£7.99) –

Nyx Liquid Suede Cream Lipstick in Soft Spoken (£7) –

Primark Eyelash Curler (£1.50) –,n35397182617597

Primark Lipliner (Brown) (£1) – There were no links for this.

Back to Basics: The Birth of Molecular Genetics

In the 1880s, August Welsmenn and Carl Nägeli suggested that there was a chemical substance in living cells that were responsible for transmission of this material. Little was known about what this material was. It’s weird to think only a century ago, we barely knew that DNA is the genetic material that did exactly what Welsmenn and Nägeli predicted. As a biochemistry student, it’s important that I learn about other sections of biology and chemistry in order to appreciate modern biochemistry. One of my Semester A modules this year, Molecular Genetics, gave me a very experimental view on how modern genetics came to be. In this post, therefore, I want to talk about how, experimentally, we found out that DNA was the substance that is responsible for protein synthesis, mitosis and genetic variance.

It’s important to recognise that there was a criterion that needed to be met to satisfy scientists in the 20th century that DNA is the genetic material. These were:

  • Information. The substance needs to have the ability to construct entire organisms through the material contained.
  • Transmission. The substance needs to be able to transmit from mother cells to daughter cells. On a broader level, the substance must be able to move from a parent to their offspring.
  • Replication. This is a relatively simple concept. As the substance needs to pass from generation to generation, it needs to have a replication mechanism.
  • Variation. The substance needs to show some variation to explain Mendel’s observations of phenotypic variation within a species.

Now the first experiment I want to talk about Fredrick Griffith’s experiment in 1928. Griffith utilised two different strains of a bacteria called Streptococcus pneumoniae. One strain was able to secrete a polysaccharide coating and had a smooth appearance (hence, known as the type IIIS strain), and the other was unable to secrete a polysaccharide and had a rough appearance (thus known as the type IIIR strain). The type IIIS strain was able to kill mice through the action of protecting the bacteria with this polysaccharide coat. This protection meant that the bacteria could enter the mice, infect it and eventually kill it. The type IIIR strain was unable to do this, as the strain would be killed by the mouse’s immune system. When Griffith injected different mice with these two strains, he recorded that the mouse injected with the type IIIS died, and the one injected with the type IIIR lived – the expected outcome. Griffith then heat treated and killed another sample of the type IIIS bacteria and injected that into the mouse, and the mouse stayed alive. Griffith then injected live IIIR bacteria and dead IIIS bacteria into the mouse. The results were strange – the mouse died! When Griffith analysed the tissues, he found live IIIS bacteria.

The conclusions from this experiment are that there is a substance (unknown at the time) in the type IIIS bacteria that transformed the IIIR bacteria through the acquisition of information on how to create this polysaccharide capsule. Griffith named this process transformation, and the substance was called the transforming principle. This experiment satisfied 3 of the above criteria I listed. It showed that the type IIIR bacteria acquired information on how to secrete a polysaccharide capsule. It also showed variation as there were two strains of the same bacteria yet one could secrete the capsule and one couldn’t. It also showed replication as the capsule information was replicated from the mother cells to the daughter cells.

(Joyce McCown, 2018)

In 1944, Oswald Avery, Colin MacLeod and Maclyn McCarty wanted to find out what the transforming substance was. They performed biochemical purifications to obtain these results. In essence, 5 test tubes were set up. The first test tube contained a solution of IIIS type DNA Extract, test tube 2 had the type IIIR bacteria and type IIIS DNA extract whilst test tubes 3,4 and 5 included the solutions mentioned above and either DNase, RNase or protease respectively. These test tubes were incubated, and antibodies were applied to promote bacterial clumping. All clumped bacteria were removed by centrifugation. Bacteria that was not recognised by the antibodies (i.e. the type IIIS) remained and were applied to agar plates. The conclusions from test tube 1 and 2 were that when there were IIIR and IIIS, some of the IIIR was transformed. This did not happen if the DNA extract was not added. As the DNA extract sample may have been contaminated with RNA or proteins, appropriate enzymes were added in test tubes 3, 4 and 5 to essentially get rid of these potential contaminants. Results from these test tubes showed that in test tubes 4 and 5, the bacteria were still transformed. It was only in test tube 3, where DNase was added, where the bacteria did not transform to type IIIS. This shows that the transforming principle is DNA.

Hershey and Chase conducted another experiment in 1952 to show that DNA is the genetic material that is transmitted. They used a phage, which is a virus that has a head containing only proteins, and DNA or RNA. They utilised the T2 phage, which infects E.coli and contains DNA. Their idea was that separation of the phage coat, and DNA could be completed through high shearing forces (e.g. a kitchen blender). Initially, they labelled their phages with two radioactive isotopes. One was 35S which was found in proteins, and the other was 32P, which was found in DNA. Each of these isotopes were radioactive labels for their respective constituents. Hershey and Chase grew bacterial cells and divided them into two flasks. In one flask, the 35S was applied and in the other 32P. They allowed time to pass for the phage to infect the bacteria and then used a kitchen blender to shear off the phage coat. They then centrifuged at 10,000 rpm. There should be a heavy bacterial pellet near the bottom of the centrifuge and lighter phages in the supernatant. The number of radioactive isotopes were then counted with a Geiger counter and compared with the starting amount. They found that most of the 35S was detected in the supernatant, suggesting that the empty phage coat is just protein. They also found that most of the 32P was found in the heavy bacterial pellet, which is consistent with the idea that phages inject their DNA into the bacteria.

If these experiments happened today, it would very much be likely that the results wouldn’t be accepted because of the simplicity and standards of the time not matching modern counterparts. At the time though, there was no other answer or reason to object to these findings. We are yet to find anything that counters them. It’s crazy how much science changes and is shaped by ground-breaking experimentation. I hope you guys enjoyed this post and it gave you a glimpse of the type of content you may expect from an undergraduate biology-related degree.


Genetics: Analysis and Principles (5th Edition) by Robert J. Brooker

Photo Credit: Drew Hays (2017)

I Took A Vitamin Blood Test!

Hi guys! Today’s post will be a bit of a lengthy deviation away from education and my degree and more into health. That being said, as a future biochemist, I am interested in vitamins and minerals – especially the role they play in your body and how they impact your health. For that reason, I wanted to take a blood test to see whether I had any deficiencies or not. I decided to go with the VITL Vitamin Level Test for a few reasons. Firstly, the test checks for ten key vitamins (Vitamin D, Iron, Zinc, Active B12 and Folate) and different markers for cholesterol health (HDL, LDL, Total Cholesterol, Cholesterol Ratio and Triglycerides). Secondly, I am somewhat familiar with VITL – I often use their app quiz to gauge where my health is at. Finally, I noticed that VITL advertise that they offer personalised nutrition information based on your blood test results – I wanted to see this for myself. The process was really simple. The test it sent to you, you prick your finger for a blood sample and send it through the post. In the next few days, your vitamin breakdown and nutrition advice should be available on the app. Below I’ve slightly detailed what my results were.

(Sharon McCutcheon, 2018)

Monday 25th March 2019

So I posted my sample last Wednesday, and received my blood test results this morning. I’ll talk to you through the results I had (whether my levels were high, low or healthy), as well as talk through what the nutritionist suggested. Please note, by no means is this any health recommendation – this is just to show you guys my results and what was said to me about them.

Active Vitamin B12 – Healthy.

Vitamin B12 is important for nerve and red blood cell health, as well as aids in the duplication of DNA. Low levels of active B12 could lead to anaemia, fatigue, weak muscles or even depression (VITL, 2019). That being said, the VITL test looked out for the active form of B!2, as opposed to general B12 levels. I liked this a lot because not all of the B12 in our diet/supplementation is not absorbed into the body.

Folate (B9) – Healthy.

Folic acid is important for red blood cell and DNA regeneration. A deficiency in folate could lead to a weakened immunity, fatigue and digestive issues (ibid).

Vitamin D – Deficient.

So my vitamin D levels are slightly lower than normal. A deficiency could lead to pain, muscle weakness, a lowered immunity and fatigue (ibid). This is the first vitamin where I was told by the nutritionist to take action. I was told to let me doctor know about these results within 2-3 weeks and that they may check my calcium levels.

Ferritin (Iron) – Healthy

Ferritin is a protein in the body that acts as the main store of iron. Iron aids in oxygen and carbon dioxide transport and it’s deficiency is associated with iron-deficiency anaemia (ibid). As my iron levels are in the healthy range I don’t need to supplement or change my diet for this, but I was still given tips on how to ensure that my iron levels remain healthy.

Zinc – Healthy

My zinc levels are within the healthy range, and zinc helps with cell division and producing new DNA and proteins. Signs of zinc deficiency include thinning hair, acne, food and environmental allergies etc. (ibid)

Cholesterol – Some Abnormal

Now this is where it gets interesting and the main reason why I wanted to get a blood test. There were 5 factors tested for this. These are listed below.

  • Triglycerides – Significantly Raised

Triglycerides are a type of fat found in the blood. These are needed for cell growth and energy in between meals. However, a high triglyceride levels could lead the to release of fatty deposits under the skin and in arteries. The levels could be elevated due to obesity, an underactive thyroid or overeating (consuming too many calories). My recommendation to improve my triglyceride levels were to supplement fish oil and improve my diet by lowering calorie intake and sugar intake. It was also suggested that I should get to a healthy weight and continue monitoring my levels.

  • Total Cholestoerol – Excess

So my total cholesterol levels (HDL and LDL) are high – I’ll go into this a bit more below. The nutritionist suggested that I see my GP within 1 week to discuss these results.

  • HDL Cholesterol – Deficient

HDL cholesterol (aka the ‘good’ cholesterol) helps transport LDL cholesterol to the liver to excrete from the body. A normal, healthy level of HDL reduces your risk of heart disease (ibid). To improve my levels, the nutritionist suggested that I increase my mono and polyunsaturated fat intake, avoid refined carbohydrates and avoiding trans fats. In terms of lifestyle, the nutritionist suggested that I do more aerobic exercise (20-30 minutes, 5 times a day).

  • LDL Cholesterol – Healthy

LDL cholesterol helps with cell growth but may lead to plaque growth in arteries, so it is good to have some but not too much (ibid). To keep my LDL levels normal, the nutritionist suggested that I have more soluble fibre (found in oats and wholegrains) and oily fish.

  • Cholesterol Ratio – Excess

So the cholesterol ratio is your total cholesterol level: HDL cholesterol level. My ratio is slightly high, suggesting that my LDL cholesterol level is too high for my HDL level. The results above do prove this.

So what do I think?

The VITL blood test was definitely useful in finding out what my blood test results mean, and now i have them to hand in the app. However, I do feel disappointed that the nutritionist advice seemed a lot more generalised. I did expect that this would be the case because of course, the nutritionist didn’t sit with me and look through my medical history and my lifestyle. But the promise of a tailored nutritionist advice is a bit misleading. The most tailored part of the test seemed to be the timeframes where the nutritionist suggested to visit the GP, and the overall conclusions from the tests. Moving forward, I think I will do another blood test in around 3-6 months, but probably with another company to see how they compare.

(Photo Credit: Pina Messina, 2017 and Sharon McCutcheon, 2018)

Back to Basics: Carbonyl Chemistry

Okay I’ll be honest, this blog post is only being written because I’m slightly bored of continuously writing out mechanisms. I do have a test coming up about carbonyl chemistry, so I should be studying. So I thought, why not talk about the theory of carbonyl chemistry – knock out some revision and a blogpost? 😅

In this blogpost then, I want to go over what the carbonyl group is and some of the chemistry behind the reactions that it can do.

What is the carbonyl group?

So the carbonyl group is when there is a carbon double bonded to an oxygen. This carbon can either be attached to two alkyl groups (a ketone) or to one alkyl group and a hydrogen (an aldehyde). You can also have carboxylic acid derivatives.  I’ve included a drawing below.

An image showing the carbonyl group. X and Y could be alkyl groups, hydrogens or other atoms.

The carbonyl group can undergo nucleophilic additions. Nucleophiles are “electron-loving” molecules and can include compounds like H2O, Cl, OHetc. The atomic orbitals of the carbon and oxygen overlap to form molecular orbitals (MO) – I won’t go into too much detail about molecular orbital theory here but I’ll link some websites below if you are interested in it! But in a carbonyl group, the valence electrons form an anti-bonding pi MO which acts as the LUMO – the lowest unoccupied molecular orbital. Electrons move from the HOMO (higher occupied molecular orbital) to the LUMO. The strange this about the carbonyl is that we usually associate It with nucleophilic additions where the C=O double bonds acts as the electrophile. The bond can actually act as nucleophile due to the lone pairs on the O, but it is usually easier for it to act as an electrophile.

Reactivity of the Carbonyl Group

We can react carbonyls with various types of nucleophiles. Good nucleophiles are often organometallics, non-bonding pairs of electrons and pi-bonds (although they are only weakly nucleophilic). So the first step of these reactions is to ensure that the nucleophile is suitable for the electrophile. The next step is to ensure that the sterics of the reaction is favourable. When nucleophilic additions occur, the old pi bond is broken at the same time as the new sigma bond is formed. This ensures that a carbon intermediate does not have 5 bonds and thus, defying the octet rule. We also have to consider the angle at which the nucleophile attacks. This is usually 107 ° and was determined experimentally by Hans-Beat Burgi and Jack D. Dunitz. This angle was determined by a compromise the maximum orbital overlap between the HOMO and LUMO and the repulsion of the HOMO electrons. This trajectory explains why some reactions do not occur.

So I hope you guys enjoyed this short blogpost which just glossed over the reactivity of carbonyls. I’m now gonna go back to practising the specific reactions and mechanisms 😢.


I did use my university lectures to write this but the lectures are based off this book:

Organic Chemisry (2nd Edition) by Jonathon Clayden et al.

Carbonyl Group Picture is from:

Feature image: Hans Reniers, 2018

If you want to learn more about MO theory:

My Typical Face of the Day

So, I’m a huge fan of makeup and its fair to say that my collection is quite…um…varied. I like mildly experimenting with makeup but I also have to be quick and efficient because I do also love my extra 5 minutes of sleep. My FOTD depends on the day depending on when my lectures are and if I have any other commitments. On this particular day, I had a lecture at 12am for an hour and I was done for the day so I didn’t wear as much makeup as I was coming home straight after.

– Base –

Today I started off with doing my base first because I wasn’t planning on wearing any eyeshadow/eyeliner. I started off with priming my face with the Rimmel Match Perfection Fix and Perfect Pro Primer and whilst that set in, I started carving out my brows with the Freedom Pro Camouflage Paste (yes before filling in!). You can’t get the Freedom concealer anymore but any concealer you enjoy would do. After the primer set, I put on the YSL Touche Éclat Foundation with the Zoeva 104 Buffer Brush and smoothed it out with the Real Techniques Miracle Complexion Makeup Sponge. I then put some of the Sephora High Coverage Concealer under my eyes, between my brows, under my cheekbones and on the bridge of my nose. I blended that out with the sponge, and went into filling my brows with the CYO Frame of Mind Brow Sculpting Pencil and setting with the Miss Sporty Clear Mascara. I slightly baked under my eyes with the Laura Mercier Translucent Loose Setting Powder and then bronzed up my face with the Urban Decay Sin Afterglow Blush in Paranoid using a Fan Brush from Contour Cosmetics. i used the translucent powder again under my cheekbones to carve them out a little bit. Using a Fan Brush from Colourpop I put on the Colourpop Super Shock Highlighter in Wisp on the high of my cheeks and under the arch of my brow.

– Eyes –

Today for my eyes I literally just wore some of the Max Factor 2000 Calorie Waterproof Mascara.

– Lips –

Today I lined my lips with the Primark Lip Liner in the shade Brown . I went over that with the Charlotte Tilbury Lipstick in Pillow Talk.

And that’s a typical FOTD! I hope you guys enjoyed this post – I definitely enjoyed writing it.

(Photo Credit: Annie Spratt, 2017)