Knowing The ‘Virus’ To Understand The Ongoing Pandemic Better (technique used- diagrams)

Viruses have always been the focal point of concern for man because of their great infectivity, great numbers in which they exist, ultramicroscopic size, ever-changing genetic nature due to mutations etc and their status /existence (living or nonliving).

In this blog, we will try to shed some light on various aspects of virus viz. structure, infectivity, virulency, genetic changes or mutations, and nature of Coronavirus.

Structure of virus

Structure Of A DNA Virus(Icosahedral) & A Bacteriophage(Icosahedral head & Helical tail) (Photo credit- Pinterest)

All viruses contain two components

1) A nucleic acid genome – DNA or RNA and not both

2) A protein coat or capsid – that covers the genome

Together they are called Nucleocapsid.

3) In addition, many animal viruses contain a lipid envelope

The entire intact infectious virus particle is called VIRION. So, a Virion consists of an RNA or DNA core, with a protein coat, sometimes with external envelopes.

The core confers infectivity and the capsid provides specificity to the virus.

The Protein capsid is 2 types

1) ICOSAHEDRAL– (a) Identical protein subunits form an icosahedron (made up of equilateral triangles fused together in a spherical shape) coat or capsid.

(b) Such viruses are released into the environment when the host cell dies, breaks down or lyses, thus releasing the virion.

(c) Ex- polio rhinovirus

2) HELICAL– (a) The proteins are arranged in a circular fashion, creating a disc like shape. The disc shapes are attached helically creating a tube, with room for nucleic acid in the middle.

(b) Ex- tobacco mosaic virus

Two types of virus based on structure

1) ENVELOPED Virus- (a) in these viruses, the nucleocapsid is surrounded by a lipid bilayer called envelope, which is derived from the host cell membrane during replication after infection.

(b) The envelope is formed when the virus is exiting the host cell via budding. (Non-enveloped viruses kill the host cell in order to escape).

(c) Ex- herpes simplex, chickenpox, influenza virus, hepatitis C virus

(d) Some viruses have projections from the envelope known as ‘SPIKES’ which help in attachment of virus to the host cell. Ex- HIV, coronavirus

2) COMPLEX Virus – (a) These virus structures have a combination of icosahedral and helical shape and may have head- tail morphology.

(b) This head- tail morphology is unique to viruses that only infect bacteria and are known as bacteriophages.

(c) Here, the head is icosahedral with the helical tail. The tail is used to attach to the bacterium.

(d) Ex – poxvirus

Different Types Of Viruses (Photo credit- Pinterest)

Classification of Viruses

The virus may contain RNA ( so called RNA viruses)or DNA (so called DNA viruses) in their genome. RNA viruses comprise about 70% of all viruses on earth.

The RNA single strand may be –

(1) a sense strand ( plus strand) which can function as a mRNA or

(2) an anti-sense strand (minus strand) which cannot function as mRNA for protein translation.

So, RNA & DNA viruses can be classified as –

1)Plus strand RNA viruses
2) Minus strand RNA viruses
3) Double- stranded RNA viruses
4) Single-stranded DNA viruses
5) double-stranded DNA viruses

Genetic changes in viruses (Mutations)

Viruses are continuously changing as a result of genetic selection. They undergo subtle genetic changes through Mutation and major genetic changes through Recombination.

Mutation occurs when an ERROR is incorporated in the viral genome. Recombination occurs when two related viruses exchange genetic material during co-infection of a host cell creating a NOVEL virus.

Alterations in the genetic material of a virus may lead to change in the function of viral proteins. Such changes may result in the creation of new viral serotypes or viruses of altered virulence.

Mutations arise when the virus replicates inside host cells and mistakes are made in copying its genetic code.

Mutations in virus happen by chance all the time. Most have little effect, and some hamper the virus, but over time, single or multiple mutations can potentially buildup, that make the virus more successful by enabling it to spread more easily.

Mutations can also make the virus more dangerous, for example, by making it more efficient at infecting cells.

Mutations can make a virus either more or less virulent.

A virus that is less virulent could infect far more hosts because the hosts are well enough to come in contact with many other potential hosts.

Seasonal influenza virus mutates so rapidly that we need a different vaccine each year.

The faster a virus mutates, the quicker it changes its behaviour.

Mutations may cause the virus’s outer surface to appear different to a host previously infected with the ancestor viral strain. So, antibodies produced by previous infection cannot effectively fight the mutated virus and disease results.

Significance Of Proteins –

Proteins are large molecules made up by 20 small molecules called amino acids. All living organisms have the same 20 amino acids ( as described in the previous blog), but they are arranged in different ways and this determines the different function for each protein.

7 types of proteins are:-

• antibodies

• contractile proteins

• enzymes

• hormonal proteins

• structural proteins

• storage proteins

• transport proteins

Characteristics of Coronavirus

Structure Of Coronavirus (Photo credit- Pinterest)

• family of Plus strand RNA viruses

• encode a complex RNA- dependent RNA polymerase

• coronavirus is a non-reverse transcribing RNA virus

• coronavirus is an ENVELOPED Virus

• coronavirus has large genomes

• coronavirus is a plus strand single-stranded RNA virus with helical nucleocapsid

• coronavirus is a recombinant virus

• it causes diseases in mammals and birds

RNA virus versus DNA virus –

DNA viruses are able to attack both human cellular and metabolic processes simultaneously.

RNA viruses interact with human PROTEINS functioning in specific cellular processes and intra cellular transport.

Single Nucleotide Variation (Substitution) in human gene/DNAcaused by viral infection (Photo credit- Pinterest)
How do viruses multiply?

Viruses multiply in the host cell, where they find the machinery, the PROTEINS with which they can copy their genetic material before infecting other cells.

Which Viruses show higher mutation rate?

• RNA viruses mutate faster than the DNA viruses as RNA nucleotides are more unstable than DNA nucleotides.

• Single-stranded viruses mutate faster than double- stranded viruses.

• The lesser the genome size, the higher is the mutation rate.

Decoding the Genetic code and viewing Gene Expression (protein synthesis) through its lens (using Flow Chart technique)

This early morning, when I took the Morning Daily in my hand, I was awestruck and pained by the most haunted news about the pandemic – the steeply rising global tally of Covid-19 cases and death toll. This aching health issue anguished me and urged me to take a call, and share with readers, the biology of this one entity- the VIRUS,which is playing havoc in the lives of a great chunk of world’s populations. In my last blog, I had given a fair idea about the different types of WBCs which fight against the foreign invaders – bacteria and viruses, which are the causative agents of so many diseases/ infections in our body. As we all know that these foreign intruders viz. virus and bacteria cannot be seen with naked eye. Viruses are ultramicroscopic, even smaller than bacteria, ranging in size from 30 nm to 300 nm.

To know the structure & functioning of virus, we must first broadly understand the set of rules (Genetic code) by which information encoded in the genetic material viz. Nucleic acid (DNA or RNA) is translated into proteins (amino acid sequences). Biological decoding is accomplished by the ribosome using tRNA to read mRNA three nucleotides at a time. Most viruses have either RNA or DNA as genetic material (or genome). The nucleic acid may be single or double stranded. The simplest viruses contain only enough RNA or DNA to encode 4 proteins. Most complex can encode 100- 200 proteins. The portion of the genome that codes for a protein or an RNA is referred to as a GENE. (Significance of Proteins – Autism is linked to egg cells’ difficulty creating large proteins.) The Genetic code is highly similar among all organisms with the exception of some RNA viruses. They all use the same 4 bases ie. Guanine(G), Adenine(A), Cytosine(C) & Thymine(T) – or Uracil(U) in case of RNA and make the same amino acids.Because of Genetic code, many different species have same genes.

What is Genetic code ?

RNA or DNA is a long polymer made from repeating units called nucleotides. A Nucleotide has three components viz. (1) a nitrogenous base, which are two types- Purines (A,G) and Pyrimidines (C,T). Purines pair with Pyrimidines. So, Adenine(A) pairs with Thymine (T) (in RNA, Thymine is replaced with Uracil (U) ) & Guanine (G) pairs with Cytosine (C). This is called Complementary Base Pairing. (2) a pentose sugar (5-carbon sugar)– ribose in case of RNA and 2-deoxyribose for DNA. (3) a phosphate group The Genetic code is the sequence of the nucleotide bases in nucleic acids (RNA & DNA), that code for 20 different amino acids, by triplets formed from combinations of the above 4 nucleotide bases. A triplet is called a CODON. The Genetic code is the set of rules by which information encoded within DNA or (mRNA sequences) is translated into Proteins by living cells. The Genetic code can be expressed in 64 entries. Of the 64 codons, 61 codons specify 20 different amino acids and 3 codons (UAA, UAG, UGA) serve as Stop Codons to end Protein Synthesis. The codon AUG (codes for amino acid – Methionine) serve as Start Codon for beginning of Protein Synthesis (Translation).

Multiple codons may specify the same amino acid. For example – the codons UCU, UCC, UCA, UCG, AGU, and AGC all specify the amino acid – Serine. See the table below :-

Amino Acid Sequencing Table (Photo credit- Shutterstock)

The Genetic code has redundancy but no ambiguity.

Types of RNA – 3 types:-

(1) messenger RNA (mRNA):

mRNA plays important roles in Transcription process. Transcription is the first step of Gene Expression. It is the process that involves copying the genetic information contained in DNA into an RNA message. During transcription, the DNA strand unwinds and allows the enzyme RNA polymerase to transcribe only a single strand of DNA. When RNA polymerase transcribes the DNA into a mRNA molecule, Adenine pairs with Uracil and Cytosine pairs with Guanine.

(2) transfer RNA (tRNA):

The job of tRNA is to translate the nucleotide sequences of mRNA into specific amino acid sequences. The amino acid sequences are joined together to form a Protein.

(3) ribosomal RNA (rRNA):

The cell organelle called Ribosome consists of ribosomal proteins and rRNA. A ribosome consists of 2 subunits – a large subunit and a small subunit.

Process of Protein Synthesis (Translation):

During translation, a small ribosomal subunit attaches to a mRNA molecule. At the same time an initiator tRNA molecule recognises and binds to a specific codon sequence on the same mRNA. A large ribosomal subunit then joins the newly formed complex. Both ribosomal subunits travel along the mRNA translating the codons on mRNA into a polypeptide chain as they go. When a termination codon is reached on mRNA, the translation process ends. The polypeptide chain is released from the tRNA and the ribosome splits back into large and small sub units. The new formed polypeptide chain undergoes several modifications before becoming a fully functional protein. These proteins are used in the membrane of the cell, others remain in cytoplasm or transported out of the cell.

Process of Protein Synthesis (Translation) (Photo credit- Shutterstock)

Tips for following’Flow Chart’ methodology:

(1) Divide the matter into brief, small, all- inclusive key points .
(2) Step-wise/ sequential jotting down of these points.
(3) Separating each step by a downward arrow.

Quick Recap of Transcription & Translation through FLOW CHART teaching methodology:

TRANSCRIPTION PROCESS :

Enzyme RNA polymerase binds to ⬇️ DNA transcription unit at PROMOTOR Site ⬇️ Sigma unit of RNA polymerase target START site to align polymerase onto Promotor ⬇️ Unwinding of one helix turn of DNA ⬇️ Tight binding of Polymerase with initiation of RNA Synthesis (first base added is usually a Purine) ⬇️ RNA polymerases use nucleoside triphosphate as substrate & polymerises in a template dependent fashion following the rule of Base Complementarity ⬇️ Elongation continues at a rate between 30 & 50 nucleotides per second ⬇️ Cessation of Elongation ⬇️ Release of Transcript ⬇️ Dissociation of Polymerase & mRNA chain from Template ⬇️ Post- transcriptional modifications of mRNAs (removal of INTRONS etc) ⬇️ Poly-A tail (Adenine bases) added to one end & a Guanosine triphosphate Cap added to the other end of mRNA for its protection

TRANSLATION PROCESS :

mRNA binds to smaller subunit of Ribosome ⬇️ Anticodon arm of tRNA binds to a specific codon sequence on same mRNA ⬇️ A large ribosomal subunit joins this complex ⬇️ Initiator tRNA in the P site of ribosome is released & tRNA in A site of ribosome is translocated to P site ⬇️ ‘A’ binding site becomes vacant ⬇️ Another tRNA recognising new mRNA codon attaches to this site ⬇️ Pattern continues ie. old tRNAs are released from the complex, new tRNAs attach and amino acid chain grows ⬇️ Ribosome reaches a termination codon on mRNA ⬇️ Polypeptide chain formed and released from tRNA ⬇️ Ribosome splits back into large and small subunits ⬇️ Newly formed polypeptide chain undergoes modifications ⬇️ Fully functional PROTEIN is formed

About next blog:

In the wake of the knowledge on Genetic code and Protein Synthesis shared in this blog, we’ll apply this information to know the ‘Genetic change in Viruses’ causing serious diseases, Structure of Virus, with a mention of Coronavirus also, in my next blog.

Till then, Happy Reading…

Teaching/Learning Science Concepts Through Storytelling Coupled With Analogy

Here, in this blog I’ll throw some light on an innovative teaching technology/ method of learning Science concepts(which I’ll also be taking up in next few of my upcoming blogs).

Science learning seems difficult, boring and scary, if done through textbook reading. One of the methods, which I found very interesting and effective during the course of my profound teaching, is learning science concepts through Storytelling coupled with Analogy.

As is a worldwide established fact that stories always are welcomed and listened with great enthusiasm. Stories arouse immense interest in students and so, can be used as an effective tool for teaching-learning process.The concepts learned through this method will remain etched in the minds of students forever.

Another objective of this blog is to touch simple methods of learning difficult scientific terms with ease.

Our Storytelling Tool. Let’s practice it with the science concept –Knowing the types of white blood cells(WBCs).

Let’s begin our story – The title of the story is the “WBC Brigades”. Once there was a country called ‘Human body’. It was a very peaceful country until it was once invaded by some foreign intruders called bacteria. (The foreign intruders can be virus, bacteria, fungi or parasites). The intruders soon captured the entire country ( body). The country‘s peace was disrupted (infection/bacteria spread all through the body). Immediately, the country‘s head (brain) sent a message to the country’s Army

(body’s immune system/ body’s defence mechanism comprising of WBCs) (via lymphoid organs) to fight against the intruders and defuse the situation (get rid of infection/ bacteria). The Country’s Army had 5 Brigades (5 types of WBCs). They are – 1. Eosinophils 2. Basophils 3. Neutrophils. 4. Lymphocytes 5. Monocytes.

5 Types Of WBCs (Photo credit- Shutterstock)

Comparative analysis of the 5 Brigades (5 types of WBCs):- Brigade 1(Eosinophils):-Uniform (structure)- granular cytoplasm ; lobed nucleus Duty (function) – to bring about destruction of toxins of protein origin Strength (number)-2 to 3% of TLC. Brigade 2 (Basophils):- Uniform (structure)- cytoplasm contain coarse granules ; lobed nucleus Duty (function)- fight allergens by releasing Histamine Strength (number)- 0 to 4% of TLC Brigade 3 (Neutrophils):-Uniform (structure)- cytoplasm contains fine granules ; many shaped nucleus (polymorphonuclear) Duty (function)- engulf the bacteria and digest Strength (number)- 65 to 70% of TLC Brigade 4 (Lymphocytes):- Uniform (structure)- agranular cytoplasm which is much less ; large spherical nucleus Duty (function)- to produce antibodies Strength (number)- 20 to 30% of TLC Brigade 5 (Monocytes):- Uniform (structure)- agranular cytoplasm which is more ; bean shaped or oval nucleus Duty (function)- motile in nature and engulf the bacteria. Strength (number)- 4 to 8% of TLC

Simple methods to spell & pronounce the difficult Scientific terms/ names correctly:-

1. Break the word and then spell and pronounce Eosinophils = eo- si- no- phils Lymphocytes = lym- pho- cytes

2. Memorising the endings (-phils, -cytes) which are common to the terms/names

Some ideas to get you going with storytelling & analogy technique:-

1. Germination of Seed- using development of an egg into an adult analogy…… 2. Monocot & Dicot seeds- using objects like sun ☀️,moon 🌔(Monocots); sandwich 🥪, burger 🍔 (Dicots) for analogy…… 3. Cycles in nature (water, nitrogen etc)- using cyclic movement in a clock analogy……

A Holistic module for science learning

Science, invariably called as the systematised knowledge, has always fascinated people because of its multitude inventions and applications.What incites me to write this blog is the craving to share and capture a few Takeaways of Science, which make it a fun way to learn.

Over the long long years of my study and teaching, my greatest Takeaway from Science is that, a keen observer comprehends rules fuller and faster. So, the keyword to learning/getting insight into Science is OBSERVATION. The more you observe (your surroundings-be them the man-made wonders like home, park, shopping mall, airport, seaport, factory on the one hand or the mother nature on the other hand) the better learning unfolds.

Let’s extrapolate it further. Will simply observing things- living or non-living, help you understand Science concepts or extract the laws of Science? The answer is’NO’. As introduced earlier that science is a systematised knowledge, so one needs to arrange/organise his/her observations.

I have devised a Six-Step Module, which I call ‘TOPPIC’ to understand any Science concept by experiencing.

T – Task that fascinates you

O – Observation

P– Point wise Penning down

P – see the Patterns like similarities, differences etc

I – Interpretation

C – Conclusion

Seed Dispersal By Wind (Photo credit- WordPress photo library)

Let’s show up with an example:-

Task– I see fluffy clusters flying freely in the air in front of my house all the time.

Observation – The fluffy clusters are breaking off from Alstonia tree in front of my house and flying everywhere.

Point wise penning down– 1.The fluffy clusters are seen in my backyard, driveway, on road in front of my house, under the tree, near the Colony Main Gate (which is about 30 metres away).

2. I took them in my hand and found them to be soft, light and hairy.

3. When I opened the cluster, they all separated out into individual units, each having a bead-like thing in the centre with hair all around.

Patterns– 1. The hairy clusters are all coming out of pod-like structures hanging from the tree.

2. All hairy units are alike.

3. They are moving to far and near places.

Interpretation– 1. Since, the hairy units are coming out of a pod-like structure (which is tree’s fruit),so these hairy units should be seeds.

2. Because these seeds are light and hairy, they are able to move to far off distances.
3. Seeds, when grown in soil, give rise to a new plant.

ConclusionSeeds are dispersed by wind.