I have started my PhD 3 years ago with naive hopes of using Computer Science of solving global healthcare issues, curing cancer…well, you know the drill 🙂 After a year in I wrote a blog post summarising my experience so far, but I actually have never tried to summarise what my research is about to a broader audience. Now that I’m pushing the 2nd year anniversary of being a PhD student ( I’ve taken a gap year after the first 1,5 years), I thought is a good time.
When friends outside of academia (yes, I still have those, but very few) ask me what I do, I usually say something about “studying the mechanisms of generating novel protein structures and functions”. They either look puzzled or nod with understanding. Then the conversation goes back to whatever we were talking about before. I don’t want to give up though!
Let’s do it step by step!
From secondary school biology, you probably remember, that all living organisms consist of cells. In fact, cell itself is the smallest living thing. It uses energy to maintain itself and can reproduce! That is about all that we actually know regarding “what is life”. So as we said, the single cell can reproduce: it contains all the necessary information and machinery that defines the organism. This information is stored in the form of double-stranded DNAs – long molecular chains, formed always of the same subunits, nucleic acids (nucleotides).
With me so far? I’m sure you heard of DNA!
What is this information needed for the cell to function properly? What does it contain? What do we get from DNA? Well, the cell has mechanisms of reading information stored in DNA. It does it in 2 steps: first, it “transcribes” it to a different molecule type called RNAs. To simplify, to read the DNA information, the cell needs to copy it first. It’s like it was encoded for easy storing, but to read it we need to transcode it back and put on a different piece of storage. There are specific “coding rules” used for this step and they are the same across all living organisms! Once the cell has RNA, it can use it to build protein molecules. And no, proteins that cell builds, are not pieces of chicken breasts!
What are proteins anyway?
See those “ribbons” in the featured image, that is schematic representation of a protein!:D
Proteins are big and complicated molecules that perform many different functions in the cell. The cell builds protein molecules from RNA chains it got from the DNA. How does it do it? Well, there are special proteins that can do this job. Welcome to the molecular biology inception!
The diversity of proteins is amazing: some help maintain the cell shape and inner organisation, some manufacture different chemical compounds, others take care of waste by transporting it outside of the cell or make sure that certain elements get through into the cell.
Now, only a small portion of DNA actually stores information needed to make proteins. Only 2% of human genes (areas of DNA) code for proteins. But, that is another story, folks! 🙂
Back to where I come in.
My research is focused on the mechanisms of evolution of proteins. How do new proteins appear? Some proteins exist only in certain species, how did they evolve? So what scientists do is that they gather large amounts of data: DNA and protein sequences from many different species.
Computational tools are used to figure out how these different species and their respective proteins relate to each other. Which protein appeared first? How changes in sequence of the DNA lead to a completely different function of the protein it codes for? What is special about proteins that are specific to certain species?
These are just some of the questions we help answer with the research in our lab.
Got it? Have more questions? Don’t hesitate to ask in the comments!