Simplifying Microbiology One Post Every Saturday + Helpful Glossary

#3- The Noodles with a Twist: Genome

A massive recipe book with specific instructions to keep you going and making you, you

Hopefully having read my first two posts, you are now armed with the basic knowledge of what a cell and its organelles are!

In this post, I shall talk about the genome, what they are made of, and introduce you to what chromatin and chromosomes are. It will be brief, but I will elaborate on that more in other posts within the category called the macromolecules of life.

It’s time to leave the cytoplasm and head straight into the nucleus!

What’s a Genome?

For starters, the genome is the genetic information found in every organism. Be it a mouse, a fly, your cat, yourself, the virus causing this pandemic, the mould ruining your bread, and so on. It is passed down from parents to their offspring through different forms of reproduction. Not to forget it also includes mitochondrial DNA, and in plants, chloroplast DNA as well.

The genome in all living things is in the form of DNA or deoxyribonucleic acid. In some cases, RNA genomes exist in nature, like, in some viruses. For example, SARS-CoV2, the one causing the COVID-19 pandemic, has an RNA genome. Viruses (my area of interest!) are interesting and shall be a topic for another time once you know enough and can handle the ✨real microbiology

In the genome, there is a mix of 2 types of regions — coding and non-coding. Coding regions have instructions required to make proteins, while on the other hand, non-coding regions code for RNA molecules instead of proteins which play a different role in cells.

Observing the DNA

You all may have noticed this rather famous molecule with a twisted ladder-like shape, right? Good! Because we are going to see its building blocks, or in other words, monomers/monomeric units and how they keep it together.

A rotating DNA molecule, looking like a twisted staircase with nucleotides interacting with each other, appearing like ladder rungs, rotating in an anti-clockwise direction. The bases lay flat and interact with the ones on the opposite strand. Source in caption.
Figure 1- The DNA molecule. The bases are lying flat and are interacting by hydrogen bonds. Source- By Zephyris, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=2118354

A good ol’ DNA molecule is composed of four bases (nucleobases or nitrogenous bases are fine too):

  • Adenine (A)
  • Thymine (T)
  • Guanine (G)
  • Cytosine (C)

When any nitrogenous base combines with a phosphate group and a deoxyribose sugar, it forms a nucleotide (Fun Fact: the DNA actually gets its name from this deoxyribose sugar!). One nucleotide’s sugar connects to the next one’s phosphate in a polymer chain by phospho-diester linkages (school students! Remember this bit of info!).

These nucleotides can line up, looking like some kind of gibberish, but it is a code which the proteins in our cells know how to read quite well.

Looking at Figure 1, you may have seen that there are two polynucleotide strands intertwined with each other to form a complete DNA molecule. Thing is, the strands run antiparallel and the nucleotides interact with their opposite neighbours, complementing each other via hydrogen bonds (or H-bonds, in short).

Remember! The two polynucleotide strands in a DNA molecule are named forward (5'-3'- read as ‘5 prime to 3 prime’) and reverse (3'-5') strands (See Fig. 2).

The chemical structure of the DNA and a closer look at the 4 nucleotides. Adenine and thymine share a double hydrogen bond, and guanine and cytosine have a triple hydrogen bond. The phosphate group is yellow and deoxyribose sugar is orange and is connected by phospho-diester links. Source in caption.
Figure 2- Chemical structure of DNA showing the four bases, complete with deoxyribose sugar and phosphate groups. Source- By Madprime (talk · contribs)— Own workiThe source code of this SVG is valid. This vector image was created with Inkscape. CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=1848174

Adenine and guanine have five- and six-membered rings on the complex chemistry side of things, making them purines. Whereas, cytosine and thymine possess a single six-membered ring, hence, belonging to the pyrimidine group.

Pnemonic time!: All Gold is Pure’ refers to Adenine and Guanine as Purines to remember them easily.

By base pairing rules, adenine always bonds with thymine via double hydrogen bonds, and guanine bonds with cytosine via triple hydrogen bonds in DNA molecules (See Fig. 2). And ta-da! You have the familiar, double-stranded DNA.

One more important point! When a nucleotide forms a hydrogen bond with the other, it is called a basepair or 1 bp.

The major bonds keeping the whole DNA structure as it is are, hydrogen bonds and phospho-diester linkages.

Summary of the DNA structure basics. (A) Nucleotide structure. (B) Single polynucleotide strand. (C) Addition of nucleotides to base-pair with the ones in the template strand and form a complete DNA molecule. Source in caption.
Figure 3- Simplified summary of DNA structure. (A) Structure of a single nucleotide. (B) The appearance of a single DNA strand. (C) Addition of nucleotide monomers to a template DNA strand to complete the DNA molecule. Source- The Molecular Biology of the Cell, by Alberts et al., 6th Edn.

Chromatin and Chromosomes: The Art of Packing Up

Formation of the 30-nanometer fibre with histones and a DNA molecule. The histone octamer core contains histones H2A, H2B, H3 and H4, two of each. A 147 bp of DNA molecule wraps around the octamer to look like a ‘bead-on-a-string’ or nucelosome, and many nucleosomes get coiled tightly to form a 30 nanometer fibre. Source in caption.
Figure 4- Formation of the 30-nanometer fibre with histones and a DNA molecule. Source- By David O Morgan — The Cell Cycle. Principles of Control., Attribution, https://commons.wikimedia.org/w/index.php?curid=89674546

Strands of DNA can’t be found sitting around in the nucleus, completely opened, left to get tangled up like the wired earphones in your pocket and get seriously damaged. And honestly, there is around 2 meter-worth of DNA present in one cell, that is why it needs to be packed up real tight to occupy way less space in the nucleus.

Cue the histone proteins, the ones that take part in packing the DNA up. There are four types of histones — H2A, H2B, H3 and H4. Two of each gives an octamer (8 histone protein units) around which a DNA molecule will wrap around, forming something called the nucleosome which resembles a bead-on-a-string (See Fig. 4). Multiple ‘beads-on-a-string’, known as chromatin, get coiled further to give a 30-nanometer thick fibre.

Now, this very 30 nm fibre gets coiled up even further with more proteins to finally produce the most condensed form of DNA called the chromosome. This whole amazing feat of packing is known as DNA supercoiling (See Fig. 5).

The chromosome stage only happens when the cell wants to undergo cell division. While the cell is just sitting around and doing other interesting biological processes, some parts of the DNA will be loosened for protein expression, and parts that are not frequently needed, are turned into 30 nm fibres. In other words, the DNA either exists looking like ‘beads-on-a-string’ or a 30 nm fibre in the nucleus.

The DNA supercoiling process. It starts as a molecule of DNA wrapping around an octamer of histones, later forming a cluster of nucleosomes that get coiled up to form a 30-nanometer thick fibre, and finally turning into a highly condensed, yet neatly organised mass of DNA with many proteins termed the chromosome. Source in caption.
Figure 5- Summarising DNA supercoiling process. It starts as a strand of DNA wrapping around an octamer of histones, eventually forming a cluster of nucleosomes that get coiled up to form a 30-nanometer thick fibre, and finally turning into a highly condensed, yet neatly organised mass of DNA and many proteins termed the chromosome. Source- By Original uploader was Richard Wheeler at en.wikipedia — Transferred from en.wikipedia to Commons by sevela.p., CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=4017531

Easy to Remember!: Supercoiling is more like holding a string at one end, twisting it continuously till it gets all rumpled and compact, having a multitude of coils.

What’s a Karyotype?

The term karyotype refers to the full collection of chromosomes, and also the process of viewing a set of chromosomes to check whether an organism has a normal set or has any abnormalities associated with the number and appearance of the chromosome. The chromosomes are arranged from largest to smallest so it looks organised and is easy to look at.

In a typical healthy human karyotype, there are 23 pairs of chromosomes or 46 individual chromosomes (See Fig. 6). They usually occur in pairs and the largest pair is number 1. The 23rd pair is always the sex chromosome. In the image below (See Fig. 6), a man has a healthy karyotype and XY chromosomes as his sex chromosomes. On the other hand, a woman has XX chromosomes (not shown here).

A healthy human male karyotype containing 23 pairs of chromosomes, starting with the largest named as ‘1’ and ending with the sex chromosomes XY as the 23rd pair.  Y is the smallest chromosome. Source in caption.
Figure 6- A healthy human male karyotype containing 23 pairs of chromosomes. Source- https://www.genome.gov/genetics-glossary/Karyotype

Imagine This!: Since a single cell of ours has about 2-meter worth of DNA, then taking all the DNA from ALL our cells from one person would be equal to twice the diameter of the solar system!!

Good work! You made it through the twists and turns of this post (pun intended). I may have answered some of your questions from my previous posts only to leave you with more unanswered questions at the end of this; all the better for you to look forward to more simplified microbiology and for me, since I need to brush up on some of the fascinating concepts of this subject 😄

Do send in comments and feedback for me and look out for more posts every Saturday! 😊

Glossary

Chloroplast- A fancy type of plastid found in green plants which carry out photosynthesis

RNA- Ribonucleic Acid; has ribose sugar instead of deoxyribose

SARS-CoV2- Severe Acute Respiratory Syndrome Coronavirus 2; the coronavirus responsible for the pandemic in 2020 and cause of COVID-19 disease

COVID-19- Coronavirus Disease 2019; disease with serious symptoms caused by the SARS-CoV2 virus

Polynucleotide- Several nucleotides joining together via phospho-diester links to form a long nucleotide chain

Transcription- Process of ‘reading’ DNA to produce a messenger RNA for protein production

Basepair or bp- A measurement of sorts to indicate the length of a double-stranded genome, for example, this piece of DNA is 1500 bp long

Sources

  • Part I: Introduction to the cell, Chapter 1: Cells and Genomes. From the textbook Molecular Biology of the Cell, by Alberts et al., 6th Edn.
  • Me remembering my school and university lecture material

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Treveni Mukherjee

Treveni Mukherjee

A University of Leeds alumna with an Integrated Masters degree in Microbiology taking a break from science 😄