#6- The Macromolecules of Life (II): Nucleic Acids

Like seriously, it’s about time you peeps know the difference between RNA and DNA

First of all, good work on reading and understanding my posts so far, even if you understood some of them 👏 You can always go back to read them again and take your time to get the hang of such concepts. It's fine to be slow since I am a slow-poke at grasping new and complicated stuff, but with time, I did great, even to this day, and so can you 🙌

Alrighty then! I wanted to discuss nucleic acids as soon as I could because I am upset by the number of conspiracy theories about “mRNA vAcCiNeS wILl AlTeR oUr DNA!”, which is not even one bit true.

It saddens me that some don’t even question the media they consume on various social media platforms these days. I will not blame the common people for being like that when schools need to really teach every student how to think critically, i.e., question everything around them and to rely on credible sources. Not to forget some people with degrees who like to gatekeep science and make others feel that they are not smart enough to understand (NOT COOL!)

Those who are here, I am glad that you are doing your best to learn real science. Is it complicated? Yes, most of science is. Can you still learn it? Also yes, if you put your mind to it, and with the help of a good encouraging teacher.

Here in this post, I will be talking about the differences between RNA and DNA (see more on DNA here), how DNA is replicated, and the type of code hidden in it.

Let’s go! ✊

DNA and RNA, it’s Everywhere

The structure of uracil is a  single 6-membered ring. Source in caption.
Figure 1- Structural formula of uracil. Source- By NEUROtiker — Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=2230876

DNA, a.k.a., deoxyribonucleic acid, is found in all living organisms as a genome, influencing every behavioural and physical feature in them. I did mention an exception in Post #3 that some groups of viruses have RNA (ribonucleic acid) as their functioning genome. What can I say, the world has a lot of exceptions which makes it all the more interesting to learn.

You may remember that DNA has the bases adenine, thymine, guanine and cytosine. In the case of RNA, 3 out of 4 bases match with those found in DNA, except for thymine which is replaced by uracil (U), a pyrimidine just like thymine and cytosine (See Fig. 1). That is the first difference between them.

Secondly, DNA is a double helix while RNA is a single alpha helix. Since this is biology, we have an exception here: single-stranded DNA, double-stranded RNA, and other interesting forms normally seen in certain groups of viruses.

Thirdly, the pentose sugar called deoxyribose in DNA has one hydroxyl group ( — OH), and in RNA, the ribose sugar has two hydroxyl groups.

Lastly, DNA is pretty stable due to the absence of a second — OH group, which contrasts to that of ribose sugar in RNA (See Fig. 2). However, DNA cannot withstand UV radiation very well as it will suffer double-strand breaks, unlike the RNA which can hold its own against it.

Chemical structure of the two pentose sugars, deoxyribose (left) and ribose (right) sugars. Notice that deoxyribose is labelled as 2-Deoxyribose due to the lack of an oxygen atom with carbon 2 atom. Source in caption.
Figure 2- Chemical structure of deoxyribose (left) and ribose (right) sugars. Notice that deoxyribose is labelled as 2-Deoxyribose due to the lack of an oxygen atom. Source- https://www.mun.ca/biology/scarr/Ribose_sugar.html

You are now familiar with the structural differences between DNA and RNA and some more general information about RNA.

Moving on to the next interesting part, DNA replication!

How Does the DNA Replicate? Definitely Semiconservatively

DNA is a whole different kind of macromolecule, so it must have some way to replicate since it is the bearer of genetic information that needs to be replicated, and split between cells whenever the cell divides (Mitosis and Meiosis will be discussed soon!).

There is a little story I would like to share on how DNA is replicated in a semi-conservative manner. It involved two scientists named Matthew Meselson and Franklin Stahl, and a rather elegant experiment published in 1958 (See Fig. 3).

Meselson-Stahl experiment description in main text. Source in caption.
Figure 3- Experimental proof of DNA’s semiconservative replication. Source- The Cell: A Molecular Approach, by Geoffrey M. Cooper, 8th Edn.

The scientists first grew Escherichia coli (E. coli) bacteria in a medium rich in ammonium chloride as the only source of nitrogen for making nitrogenous bases during DNA replication. Keep in mind that the nitrogen used here was nitrogen-14 (¹⁴N), a.k.a., regular nitrogen. After several generations replicating in that medium, the bacteria was collected for DNA extraction and centrifuged in caesium chloride (CsCl) solution. This led to the light DNA settling at the top. The process conducted was the density-gradient centrifugation or isopycnic centrifugation where the DNA was sorted solely on its density.

Afterwards, they took the bacteria grown in a medium having ¹⁴N to the one containing a heavier isotope known as nitrogen-15 (¹⁵N) and were allowed to grow for several generations. Later on, the bacteria was taken, density gradient centrifugation was carried out again which got them heavy DNA that settled almost to the bottom of the tube.

Bacteria grown for many generations on heavy ¹⁵N medium was transferred back to ¹⁴N medium but only allowed to replicate for a single generation. Matthew and Franklin, once again, extracted the DNA and centrifuged the sample. They discovered that the DNA was a hybrid with one strand having ¹⁴N incorporated in its bases and the other having heavy ¹⁵N isotope. This experiment came to be known as the Meselson-Stahl Experiment and here is the ORIGINAL PAPER.

A simple summary showing how DNA is replicated starting with a single parental DNA molecule (in orange) whose strands separate and receive complimentary strands (in red), creating two newly synthesised daughter DNA molecules. Source in caption.
Figure 4- A simple summary showing how DNA is replicated starting with a single parental DNA molecule (in orange) whose strands separate and receive complimentary strands (in red), creating two newly synthesised daughter DNA molecules. Source- The Molecular Biology of the Cell, by Alberts et al., 6th Edn.

DNA replication sounded easy so far, but it is a bit more complicated since I did not mention the main players involved in doing this lengthy process. Do not fret! It is easy once you know it by watching an awesome video by the Amoeba Sisters (should have watched it when I was at school 😅).

Video 1- DNA Replication process by Amoeba Sisters on YouTube + good captions.

To the school and university peeps out there, be sure to remember your enzymes and their respective functions correctly!

Final stop, the code in DNA.

Decoding the DNA

The A-T-G-Cs surely must have some meaning behind them, right? They sure do! All instructions are hidden behind a set of trinucleotide sequences known as codons. Each codon in the DNA codes for a single amino acid. For example, three codons, or nine individual bases, code for three amino acids.

Triplet codon code from RNA showing the 20 amino acids. Just replace the ‘U’ with ‘T’ and you will get the codons that correspond to a strand in a DNA molecule.
Figure 5- Triplet codon code from RNA showing the 20 amino acids. Just replace the ‘U’ with ‘T’ and you will get the parts that correspond to a strand in a DNA molecule.

You may think that one codon codes for one amino acid, but the code is redundant, i.e., more than one codon can code for a single amino acid. For example, amino acid valine (Val) can be coded by four codons (See Fig. 5).

Here is the expanded code on the 20 amino acids, single- and triple-letter codes:

Figure 6- The 20 amino acids with triple- and single-letter codes. Source- http://baronerocks.com/index.php/mnemonics/mnemonics-biochemisty/716-amino-acid-codes-cheatsheet

Points to Remember!: Amino acid methionine (Met; green in Fig. 5) is coded by a start codon AUG in the RNA. The ones in red are stop codons, to indicate the end of making a protein chain.

That’s quite enough information I have given you guys so I will be stopping here. You now at least know some differences between DNA and RNA, and even more interesting stuff on nucleic acids. There is still more about them and it shall be discussed in my future posts once you know what proteins and fatty acids are, how enzymes work, and so on.

Thank you for reading my posts! Make sure to comment, and follow/subscribe for more simplified microbiology every Saturday 😄👍

Glossary

mRNA- Messenger RNA; the kind of RNA that contains a message to make proteins

UV radiation- Ultraviolet radiation; can be deadly if exposure is too long outside on a sunny day without sunscreen or covering yourself or not taking any protection at the lab

Double-strand breaks- When DNA double helix is broken through and through; fatal for the cell if it’s not fixed right away

Medium (plural: media)- A substance, be it solid agar or liquid broth that have different substances to support the growth of various organisms in a controlled environment, like a lab

Centrifuged- The act of spinning a biological sample in a tube at very high speeds to induce strong G forces for sedimentation

Isotope- An element that is the same but has a slightly heavier atomic mass

Trinucleotide- Three nucleotides

Amino acid- The basic building block for proteins

Enzymes- Special proteins that act as catalysts to speed up biological reactions

Sources

  • Chapter 2: The Chemicals of Life, Section 2.11: Nucleotides and Nucleic Acids. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 4: Fundamentals of Molecular Biology, Section 4.1: Heredity, Genes, and DNA. From the textbook The Cell: A Molecular Approach, by Geoffrey M. Cooper, 8th Edn.
  • Part II: BASIC GENETIC MECHANISMS, Chapter 5: DNA Replication, Repair, and Recombination. From the textbook Molecular Biology of the Cell, by Alberts et al., 6th Edn.
  • Me remembering lecture material from school and university

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