Monthly Archives: February 2011

The Central Dogma of Molecular Biology.

Now this is a topic where I really love to let out some steam, the popular version that I was taught academically is erroneous to the extreme, for it goes “DNA makes DNA, DNA makes RNA, RNA makes Protein”, notwithstanding the fact that Howard Temin demonstrated, through the discovery of Reverse Transcriptase, that RNA can make DNA, but does this mean that the central dogma has been shown to be false? Only if one were to utilize the bastardized, dumbed down caricature of what the central dogma of molecular biology is.

At this juncture I want to introduce the abstract from Francis Crick’s original research paper in which he reiterated his statement of the Central Dogma, click the thumbnail for a larger view.

The implications of that are quite clear, the only interactions forbidden involve the transfer of sequential information in nature from Protein to nucleic acid or to another protein, which means that the Central Dogma accounts for not only the commonly occurring DNA —-> RNA —-> Protein paradigm but also a host of other documented exceptions that have been observed, without being falsified.

A list of allowed and forbidden interactions follows, again, click the thumbnail for a bigger image…

So the next time someone tells you that the Central Dogma of Molecular Biology states that “DNA makes RNA and RNA makes protein” I hope you will be well equipped to explain and demonstrate that they are wrong.


Deciphering the Genetic Code – A Classic Experiment in the Annals of Biology

The genetic code is a map of the correspondence between codons on mRNA and amino acids on proteins, this correspondence is a function of complementary base pairing between codons on mRNA and bases on the anticodon loop on tRNA, coupled with the binding of specific amino acids to the amino acid acceptor arm of tRNA, the fact that scientists were able to, with painstaking experimentation, decipher what on mRNA corresponded to which amino acid at the end of tRNA was crucial to the advent of molecular biology and its offspring, biotechnology. It enabled us to sequence proteins and produce those proteins by synthesizing DNA which made mRNA which made that specific protein, it enabled us to sequence DNA and mRNA and to predict , and to synthesize, the protein products that would result from the translation of the mRNA in question, in short, it became a foundation for much of genetic engineering.

The experiments themselves were beautiful, at least as much as beautiful can be in the world of biogeekdom…

Brenner and Crick had demonstrated using frameshift mutations that the code was triplet, so when the experiments that are described below were undertaken that was already known.

The method I shall elaborate on here is also known as the filter-assay method, and since a picture is worth a thousand words, let me introduce one here…

The Filter Assay Experiment for determining genetic code

Note that they had a simpler assay too, and the image is self explanatory in this case…

Bacterial assay for deciphering the genetic code.

Going back to the filter assay method, which is the one that I intend to explain, the experiment was carried out as follows,

[1] They chemically synthesized mRNA codons/triplets.
[2] They mixed mRNA triplets, aminoacyl tRNA and ribosomes.
[3] It so happens that complementary mRNA and tRNA bind to each other, and all the elements in [2] form a complex which includes the amino acid bound to the tRNA that is bound to the mRNA.
[4] These complexes are large and do not pass through a nitrocellulose filter, but unbound aminoacyl tRNA does.
[5] By identifying which amino acid was retained on the filter sheet, it was possible to identify which amino acid the originally synthesized codon corresponded to.

This is how one of the major breakthroughs in the history of molecular biology came to be.

All of this is explained in more detail in this Nature Scitable article , I recommend Scitable as a resource for learning biology, by the way 😉

You can find an autobiographical account of the quest to decipher the genetic code by Marshall Nirenberg here

That is it until the next post.

Rotifers, Rotifers and more Rotifers

This one is a little tangential diversion from the completely serious scheme of things that the other posts on this blog appear to fit into, and this one basically concerns Rotifers.

They’re actually microscopic animals, and that is not animal in the colloquial sense but in the Taxonomic sense, that is, they are placed under Kingdom Metazoa in the five kingdom classification, they are multicellular and have some really cool tricks up their sleeve.

I found some growing in a culture of infusoria I set up with aquarium water and a rotting banana peel in an olive jar, and since I have a little micrography setup running at home/lab I was able to get some decent shots…

Here they are…

Two Bdelloid rotifers

This one shows two bdelloid rotifers, you can actually see the cilia that are a defining morphological feature.

Three Bdelloid Rotifers Releasing Eggs

This one shows three bdelloid rotifers releasing eggs.

Sessiloid Rotifer

This one is a micrograph of a sessiloid rotifer.

A picture is worth a thousand words, and a video is worth a thousand words x the number of pictures contained therein, besides, multimedia is more effective at communicating things, I suppose, so I guess you could watch the following clip to learn more…

I hope this encourages you to seriously contemplate growing microscopic critters for observation and then actually observing and documenting them.

The microbial world is small and usually goes unnoticed, but there is literally more than meets the eye.

Essay writing tips for Scientists in the making

1.  Understanding the Question – Comprehensive analysis of the title or question:

  • Read it several times
  • How many sections are there?
  • Break up into key words/segments – Underline/highlight key words
  • What do they mean?
  • How can they be interpreted?
  • How does it link to course lectures?
  • What else do I need to find out?
  • Discuss with others

2. Research

Make a list of:

  • All the questions ideas that have arisen from analysing question/title
  • All the information that needs to be found
  • Where to get the answers: notes, books, library …

3. Read quickly to find information

  • Use contents page, index, headings, sub headings
  • Read first sentence, summary, conclusion
  • Scan for key words, phrases

4. Read carefully to improve understanding of the information

  • Pay attention to what you are reading
  • Try to prevent your mind from wandering
  • Re-read ‘missed’ material
  • Be an active reader – Make outline notes, draw sketches, boxes, doodles to organise ideas

5.  Tips on Note-taking

  • Develop good note-taking
  • Note sources for referencing
  • Put quotation marks round direct quotes
  • Have a system for keeping notes ( I use endnote. Easy way to organise your references)

6. Analyse the Information

  • Find links, themes, differences etc
  • Cross reference the information: use a map, coloured post-its’, coloured highlights
  • Draw graphs, bar charts if relevant
  • Be critical – ask: which information is important, is the question being answered? – only use relevant information
  • Look at the bigger picture
  • Be independent and draw your own conclusions

7. Writing the Essay

  • Do a rough draft – Don’t expect to it get right first time
  • Use own words – Keep direct quotes to a minimum
  • Include references to ALL work that is not your own
  • Draw diagrams/graphs to illustrate and explain, where appropriate
  • Proof read draft and edit – more than once if necessary

8. How to Acknowledge your Sources

  • Word-for-word:  quotation marks and reference [i.e. make a footnote, endnote or put information in brackets if using Harvard system].
  • Author’s idea in your own words (paraphrase):  no quotation marks, but reference.
  • No need to reference things that are common knowledge