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Prokaryotic cells and viruses

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Prokaryotic cells

Prokaryotes do not have a nucleus like eukaryotes do. Their DNA is not membrane-bound, just free in the cytoplasm. The extra features of prokaryotic cells vs. eukaryotic cells you must learn are:

-the cytoplasm overall does not contain membrane-bound organelles such as mitochondria and endoplasmic reticulum

-prokaryotic ribosomes are smaller than their eukaryotic counterparts; due to their size (and the centrifugation level they separate from the cell at) they are termed 70S ribosomes; the bigger eukaryotic ribosomes are 80S

-as previously covered, and their primary defining element, they lack a nucleus; instead, their DNA is a single circular molecule freely present in the cytoplasm and not associated with any proteins such as histones in eukaryotes; however, the general area where the genetic material hangs out is termed a nucleoid

-they have a cell wall which contains a special glycoprotein called murein (also known as peptidoglycan)


Some prokaryotes also go further to have some specialised parts, some seen in the diagram:

-one or more plasmids which are also circular DNA loops but much smaller; these can be exchanged between cells or even between different species as they can carry genes for antibiotic resistance

-a capsule made of polysaccharides as their outermost layer (on top of the cell wall on top of the plasma membrane)

-one or more flagella which aid in locomotion

Amongst bacteria, the cell wall composition is a key determinant of what type they belong to. This is important in terms of predicting their response to various antibiotics. Based on different bacteria species' response to crystal violet stain, Gram positive bacteria are able to take up the stain and appear violet under a microscope, while Gram negative bacteria do not take the stain up and will appear pink if a counterstain is added after washing off the crystal violet stain (this will persist in the Gram positive bacteria).

The difference arises because different bacteria have different cell walls. The bacterial cell wall is one of the main targets of antibiotics.



Notice the difference in thickness of the murein layer in gram positive versus gram negative cells. This layer is what absorbs the violet stain. Hence gram positive bacteria turn violet, while gram negative bacteria lose the stain upon washing.

Penicillin is an antibiotic used against gram positive bacteria. It doesn't work on gram negative bacteria because their outer membrane (cell envelope) protects against it. Penicillin works by interfering with the production of the cell wall component murein, and as gram positive bacteria have so much of it and at the outer surface, losing it kills them off. Gram negative bacteria have much less murein and an outer membrane, so penicillin doesn't interfere with their function.

There are many different classes of antibiotics, some of which do work against both types of bacteria, for example by interfering with DNA synthesis.


Viruses

Viruses are a special little topic indeed. Here we are talking about life in one of its most bizarre, misunderstood and disturbing expressions. Viruses are the stuff of horror movies.

They are tiny microscopic entities that have absolutely no activity whatsoever. In the presence of a larger organism of their specific fit (and there are viruses to target anything), they come alive by hijacking its life tools: nutrients, energy, ribosomes, you name it.

They only carry the genetic information they need to invade and replicate. Invade and replicate. A bit of a glitch of life, or the perfect expression of it?



Both DNA and RNA viruses make use of their host's transcription and translation machinery such as ribosomes and enzymes to enable protein synthesis. Retroviruses on the other hand bring their own reverse transcriptase enzyme to enable the production of DNA using their RNA template once inside the host cell. Once the RNA is reverse transcribed into DNA (DNA->RNA is transcription, hence RNA->DNA is reverse transcription), the normal protein synthesis pathway can take place.


Lytic cycle and latency

As if the horror movie wasn't bad enough as it is, it now has a truly creepy plot twist. Not only does the viruses invade, replicate and kill the host cell, making it burst (lyse) hence the lytic cycle, but it can invade and just lie quietly inside the host cell's genetic material until a later time. This is latency also known as the lysogenic cycle.

Instead of expressing the virus genes to create more viruses, the genetic material of the virus simply incorporates itself into the host DNA. With it, it replicates with each cell division and spreads until a later time when a genetic separation event (such as a recombination event resulting in excision of the viral DNA) allows the viral DNA, termed prophage because it precedes the virus (phages are viruses that target bacteria) to split from the main host genetic material and activate its lytic cycle all over again.

This results in the synthesis of viral components including viral proteins and viral genetic material, and their assembly (which can be spontaneous) into new viruses. The host cell is compromised and the viruses are free to spread again.





Fighting viruses

So far we've learnt that viruses aren't cells. They aren't alive. They're just biological elements that interact with preexisting life forms that are actually capable of carrying out life chemistry on their behalf. In some ways viruses are biological entities like seeds. They are biological in nature but not alive except in special circumstances where the environmental input is greater than for living organisms.

How do you fight something that's not even living? At the point of infection, it becomes alive by virtue of its replication activity. Therefore the only way to directly target viruses is by interfering with the replication event. Antivirals work this way by targeting one of the many stages of infection and replication:

1. virus attachment
2. release of its contents into host cell
3. synthesis of virus components
4. assembly of new viruses
5. release to infect more cells

There are many types of drugs available that aim to target DNA synthesis by binding the enzyme responsible for its synthesis, so no further nucleic acids can attach and replicate. Others prevent the attachment of the virus onto the surface of host cells by blocking their attachment proteins.

Overall, the efficiency of antivirals at fighting viral disease once infection has already taken hold is poor. Therefore, the focus is on prevention  of further spread of the virus in the affected population.

In 2014, an Ebola outbreak occurred in West Africa. The mortality rate was very high, over 50% and higher for those not hospitalised. A cure did not exist so most efforts went into prevention of spread. This involved three broad areas:

Firstly, contact tracing was implemented. This involved keeping track of all diagnosed cases and anyone who'd come into contact with the patient. They would be monitored for 21 days to see if they, too, became infected as a result of the contact.

Secondly, raising awareness in the affected communities was key to making sure residents knew of Ebola, the risks, symptoms and spread, and encourage stricter hygiene practices such as hand washing where possible (in many place a lack of clean drinking water made hand washing an unpractised habit as it would be wasteful).

Thirdly, implementing travel quarantine attempted to prevent spread by isolating any travellers who showed key symptoms such as high temperature, between affected countries at checkpoints such as airports.

Efforts to develop vaccines were underway, but this takes a long time, and when an outbreak is sudden and progresses rapidly, it might not be developed in time. Additionally, there are several ethical concerns regarding administering new drugs that are yet to be tested fully.

Some of these questions include:

Is it ok to administer a drug that could work, but could also make the disease worse and kill a patient who might otherwise have a chance of surviving?

Is it ok to administer a drug to a person who cannot consent because they are too young, cannot understand the situation, are unconscious, etc.?

Is it ok to administer a drug to some patients simply to test it where there would be no other people you could test it on?

Ok byeeeeeeeeeeee

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