The Science Stuff: Why am I me? Part 2

Previously, we’d spoken about how DNA contains all the information needed for our body to produce essentially, us. But how do our cells transform this genetic code from just instructions, to the real thing?  How did I end up with such frizzy hair? The answer is proteins, encoded by genes within our DNA. It is the function of proteins in our cells that make us who we are. The journey from DNA to protein is not simple, but we can simplify it into 2 main processes; Transcription and Translation.

Firstly, a protein enzyme known as RNA polymerase attaches itself to a strand of DNA and uses free nucleotides in the nucleus complementary to the nitrogenous bases in the DNA strand to make a strand of pre-messenger RNA (pre-mRNA). The pre-mRNA is an exact copy of the DNA (with the exception that Thymine is replaced by Uracil), and contains regions known as introns and exons. Exons contain the information needed to encode a gene whilst introns are just useless regions that goes into the bin. Splicing is the process responsible for taking out the introns and combining the exons in pre‑mRNA to make mRNA. The transcription of genetic information therefore refers to the production of mRNA from DNA, which includes the process of splicing.

Amino acids are the precursors of peptide chains, and the folding of peptide chains becomes protein. The process responsible for making peptide chains using mRNA is known as Translation and involves another type of RNA called transfer RNA (tRNA). Each tRNA has an amino acid attached to one end, and 3 nitrogenous bases attached to the other. The bases on the tRNA complementary to the 3 bases on the mRNA (known as a codon), will temporarily attach. For example, the codon Adenine-Uracil-Guanine (AUG) on the mRNA codes for the amino acid Methionine. As more tRNA attaches to the mRNA strand, amino acids on the end of adjacent tRNAs are brought close together and subsequently forms a peptide chain using multiple peptide bonds.

…And there you have it. Part 1 and 2 combined should have answered the question, “Why am I me?”. An explanation of how our DNA makes us, us! All of this is happening inside our bodies right now, without us even realising. Of course, I’ve probably missed out loads of details, but the point of my science posts is not to get you up to scratch for any exams but to enlighten some of you, maybe without a science background, on how amazing science truly is.

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The Science Stuff: Why am I me? Part 1

Because of my genes!

Here’s a fun fact about me. As a teenager, I decided to get 3 piercings in my left ear all at once. I mean back then it was the cool thing to do, and I admit, it did look pretty awesome. Until they got infected that is, which is when it all went downhill for my ear. What I hadn’t known back then was that because my great-grandmother was Malaysian, (making me mostly Chinese, but 1/8 Malay), the slightly darker skin that I have, had made me more prone to the production of Keloid scars. As a result, when my ear got infected, the scarring gradually built up within the space of a couple of years and became the size of a grape. Not even a small grape, but a pretty sizable one. Imagine that coming out the back of your ear lob. Hideous right? Luckily, I managed to get it surgically removed, and had radiotherapy to stop it from growing back. It worked for about a year, and then started coming back again. Now, because I am not allowed to have radiotherapy again on my ears (due to the risk of excess radiation causing cancer), doctors will not do any further surgical procedures for my Keloid scars. So now I wear a clip on my ear to keep the scars compressed and hopefully stop it from growing any further.

Yes, all this palaver because of my DNA.

Most people know that DNA is responsible for all our different physical characteristics. From my frizzy hair to my slightly darker skin colour, my DNA dictates it all. But do you really know how?

The human body is made out of millions of cells, and within the nucleus of these cells, are usually 23 pairs of chromosomes. We normally see these depicted as an X shape and they actually carry our genetic information in the form of DNA wrapped tightly around proteins known as Histones. If we unravelled the DNA from the Histones, we’d find double stranded DNA in the shape of helices, which is what we’d normally imagine when thinking about DNA. By the way, DNA stands for deoxyribonucleic acid. It’s a question that comes up often in pub quizzes, so you’re welcome. Each strand of the double stranded DNA is made up of millions of nucleotide subunits that contain a phosphate, a sugar molecule and the nitrogenous base Thymine, Adenine, Cytosine or Guanine. It is the combination of these base pairs that codes for and gives rise to gene variation from one human being to another. So how does one strand of DNA stick to the other strand to produce the double stranded structure normally seen in cells? The answer is Hydrogen bonds.  These bonds form between complementary base pairs of the two strands with Thymine binding to Adenine, and Guanine complementary to Cytosine. In addition, these hydrogen bonds cause a twist in the strands, which leads to the formation of its helical structure.

There are many other aspects involved when trying to answer the question “Why am I me?”, but what it all comes down to, is our DNA. To read about the other processes that makes us who we are, keep an eye out for part 2 of “The Science Stuff: Why am I me?”.

DNA 1

From Undergrad to PhD- My level up transition

Firstly, I would like to emphasis that no two labs are the same. From the equipments used to the ways people operate, every lab is unique and so all I can do is tell you about my own experiences in my lab.

I started in my lab as an undergraduate student for my final year project. Being only 6 months away from graduation, I still had no clue what I wanted to do with my life and because of this, I enrolled onto a Masters degree programme, which would’ve given me an extra year to discover what job I wanted, before having to face the ‘real’ world and become a working adult. Not long after I was accepted onto the Masters programme, my supervisor spoke to me about a PhD opportunity in the lab and asked if I was interested. At first, I was sceptical. After spending the last 21 years of my life in education, an extra year of my life to do a Masters was one thing, but to dedicate 4 more years to this lab was another. In the end as you’ve probably figured out, I went with the PhD rather than the Masters, mainly due to the following reasons:

  1. If I decided to do a Masters, I’d have to add at least another £10k to my student debt for my education, whereas doing the PhD would guarantee a monthly stipend for the next 3 years.
  2. If in the future I did decide to work in a pharmaceutical lab or in the field of science, a Doctorate would’ve been more advantageous than a Masters.
  3. Being called Dr. Tiff and the slight chance of getting an upgrade on a flight.

In September of 2013, I officially started my PhD journey in the same lab that I had done my undergrad project. Life was a shock. Being an undergrad in the lab, there was a PhD student guiding you through every step; all you had to do was follow instructions. Now that I was one of ‘them’, it was a whole different story. No more babysitting Tiffany. Protocols were chucked at me left, right and centre, written in a scientific language that I didn’t fully understand, and the most common thing I heard for the first 3 months of my PhD life, was “Google it”. I didn’t want to seem incompetent to my supervisor so I didn’t trouble him with my problems. I either had to figure it out myself, or bug the other PhD student so much so he would cave in and give me tips. I understand now that this was to teach me independence, but man did it suck at the beginning when I used to spent half the time unsure of whether I had done everything correctly. It didn’t take too long for me to get accustomed to the way things worked in this lab though, and so I soon grew in confidence, truly becoming one of ‘them’.

One aspect of PhD life that I really appreciated was the freedom I got. My supervisor really didn’t care when I went in, as long as I completed all my experiments and that progress was on track. Some days I might go in late, and others I might finish early, though things were not always dandy, as I did do my fair share of 10+ hour shifts and evenings where I had to stay till 10/11pm. For me, the flexibility in my PhD working hours compensated for the hard and sometime tedious work I had to do. There was even a point in time where my supervisor allowed me to swapped two of my weekdays for my weekends so that I could do my lab work when the university was the most quiet and when there would be less people fighting over the use of the machines. Flexibility was a luxury I got, one that not all PhD students have. I have heard stories of supervisors demanding that 10+hour shifts should be the norm and that “9-5 is for receptionists”. Some supervisors out there will do anything in the name of science including pushing their students to the max. So if you are thinking of doing a research-based PhD, I would make sure that you really, really love science, if not, you might find PhD life a living hell.

Hello!

Hello and welcome to DocToBeBlog. I guess I should start by introducing myself. My name is Tiffany and I’m a molecular biology PhD student hoping to gain my Doctorate by the end of 2017. As you can see if you click on the menu, the last big obstacle in my way before becoming Dr Tiffany is my Viva exam (which has been provisionally set for the end of November). For those of you who don’t know,  this is a 3, 4, maybe even 5 hour long oral exam with two examiners grilling me over the work I’ve done in the past 4 years. Fingers crossed, it will all be fine. I’ll keep you posted.

The reason I have started DocToBeBlog is mostly to reflect on my journey from a clueless and naive undergrad, to hopefully, a more clued up Dr Tiff in a few months time. I’ll be posting about my experiences, past mistakes/daily struggles in the lab and other interesting snippets of information, all in the hopes of giving undergrad students thinking of embarking on the PhD rollercoaster a better idea of what they are getting themselves into. Saying that, if you love science, then it is absolutely worth it. And of course, being a bio PhD student, my blog would be incomplete without some sort of science in it, so I will also be writing about biological theories and techniques in language that any non-science graduate can understand. This will hopefully open your eyes to the fascinating world of science and you will realise that it is not just a load of mumbo jumbo best left for the crazy scientists in the lab.

If you have any questions, then I’ll try my best to help, and if this blog sounds like something you might be interested in, then watch this space.