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Eukaryotic and prokaryotic cell structure and function

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I once rescued my biology grade back in secondary school in Romania by knowing the definition of a cell.
“The cell is the structural and functional unit of living things” I wrote. I wasn’t far off was I?
So yes, the cell is the unit of life. It’s a delimited volume where the chemistry of life can happen. In unicellular organisms, the cell is themselves, the body, the whole, the organism.



In complex, multicellular organisms cells organise themselves in such a way that enables a greater structure and function. Cells differentiate into specific structures and functions, and organise themselves as such into tissues. The different tissues can then form organs with yet a higher level of structure and function, and organs can work together in certain broad areas of the organism’s structure and function by taking part in organ systems.


Isn’t that grand? Let me tell you a little secret. For anyone who’s seen the film Life starring our first Martian life form called Calvin, there is way that cells can associate the way Calvin does. In this case, cells aren’t at all differentiated to do different things in tissues, organs, etc. but instead maintain their single cell status among equal single cells. They associate at a higher level to produce certain greater effects, and can even look as if the structure were multicellular or complex, but it isn’t really, or at least it isn’t in the same way it is for true multicellular organisms.


This is the case for algae as you can already see in the green algal cells pic, as well as for fungi and creepy Martian creatures.

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.


Eukaryotic cells


The core components of cells are the outer membrane, the cytoplasm (substance inside which contains all other stuff) and the nucleus (contains DNA). All the other stuff is made up of various components with specific functions – these are called organelles.



The ones you must know about are:

1. Centriole
2. Nucleus
3. Mitochondria
4. Chloroplasts (plants and algae)
5. Golgi apparatus and Golgi vesicles
6. Lysosomes
7. Ribosomes
8. Rough endoplasmic reticulum and smooth endoplasmic reticulum
9. Cell wall (plants, algae, fungi)
10. Cell vacuole (plants)


In complex multicellular organisms, eukaryotic cells are specialised and therefore organised accordingly into tissues, organs and systems. For example, a small intestine epithelial cell which absorbs nutrients from food is part of the epithelium tissue of the small intestine organ of the digestive system.
So, what are we waiting for? Let’s delve right into these organelles.


1. Centriole


The centriole is a tubey spaghetti thing that aids in cell division when the duplicated chromosomes need to move into their subsequent new offspring cells from the parent cell (during mitosis).



They’re made of a special protein called tubulin because they’re tubeeeeeeeeeeeees. Why didn’t they call it spaghettulin? I guess spaghetti aren’t hollow but…

2. Nucleus

Usually it is the large rounded organelle in a cell. It has a double membrane with many pores through which materials can pass. Each cell normally has one nucleus. The main functions are cell division, replication and protein synthesis. These can be achieved due to the presence of chromosomes in the nucleus, which are made of linear DNA tightly wound up with the help of special proteins such as histones, as well as one or more nucleoli.

DNA and chromosomes may seem like completely separate things. Well, they’re not. In fact, all chromosomes are individual DNA molecules coiled and twisted around, because DNA is huge. At least in eukaryotes it is. That’s one of the first differences between eukaryotes and prokaryotes in their DNA – prokaryotes have less DNA.

Eukaryotic DNA is stored within the nucleus of each cell (apart from cells without one, e.g. red blood cells). Because of its sheer size, it must be organised well. Proteins called histones help do just that:



The nucleolus is a part of the nucleus that has many special functions including creating ribosomes.



3. Mitochondria (mitochondrion, singular)


This is basically the easily identifiable sausage-like organelle with the cool inner membrane that forms the cristae. It is the site of aerobic respiration, where most ATP is made. Look:

Mitochondria has its own DNA because back in ancient times it used to be its own simple organism before it got engulfed and started chilling with a bigger cell and then all the multicellular business happened (or was that before?) and then BAM! complex beings and stuff. ATP synthase is the enzyme that catalyses the formation of ATP, while the cristae ensure a large surface area for all these energy-producing reactions to occur.


It’s the powerhouse of the cell and mutations in its DNA can cause severe illness. So much so, that for the inheritable variety, a genetic engineering intervention has been introduced. It was covered in the news as the “three-parent” affair and involves replacing the biological mother’s faulty egg mitochondria with a donor egg with healthy mitochondria.


The main chromosomal DNA in the child’s nucleus is of the biological parents, but because the mitochondrial DNA is sourced elsewhere, it became exaggeratedly dubbed the three-parent technique. The first child to be born of this technique was a boy. As it happens, mitochondrial DNA is passed on the maternal line (that’s how genetic connections can be traced back to “mitochondrial Eve”) so the boy won’t have children with the “foreign” DNA, just in case anything might’ve gone wrong.


4. Chloroplasts (plants and algae)


Chloroplasts contain all the substances and machinery necessary for photosynthesis. Without photosynthesis, you and I would not be here right now. Impressive. Take a closer look at this intricate organelle, the chloroplast, to whom we owe our lives:



This gooey mess whose constituent components have slightly uncommon and incredibly hard to memorise names is a chloroplast. Let’s crunch them one by one.

Thylakoid, a disc-shaped organelle which contains chlorophyll (the lovely green pigment) rhymes with Kayla+Droid. Trust me, once you get the hang of this little word you will love it. Chlorophyll is involved in capturing sunlight (and the light dependent reaction). Multiple thylakoids stack together like towers within the chloroplast. A tower is called a granum, pl. grana. This arrangement enhances the surface area available.


The stroma is the fluid-filled space which is the site of the light-independent reaction.


The outer membrane and inner membrane are selectively permeable to allow O2, CO2, glucose and certain ions through.


Features which make chloroplasts well adapted to serve their function:


1. Chloroplasts are relatively flat and so ease the diffusion of molecules coming in and going out. This is achieved by a shorter diffusion pathway.

2. Plenty of available surface area for the reaction between chlorophyll and light to take place.
Now that wasn’t so bad!


5. Golgi apparatus and Golgi vesicles

The apparatus is a stack of flattened membrane discs which receives packages of protein from the rough ER, and is involved in synthesising chemicals before they are secreted from the cell. There are 3 types of vesicle the Golgi apparatus produces:



a) exocytotic vesicles which are routed to leave the cell; upon packaging their content, they bud off and approach the plasma membrane where they fuse and release the content into the extracellular space; an example of this is antibody release

b) secretory vesicles also head out of the cell; the difference here is that they stand by until a signal arrives for them to move towards the membrane and release their content e.g. neurones secreting neurotransmitters

c) lysosomal vesicles contain proteins and ribosomes headed for lysosomes which degrade them; read on to learn more about the lysosome


6. Lysosomes


These are small vesicles of membrane that contain enzymes which take part in digestion. They look like tiny balls. Its enzymes are thus called lysozymes for example acid hydrolases or proteases which break down its waste products. The cargo includes both digestive enzymes and membrane proteins.



7. Ribosomes


My personal favourite 🙂 Ribosomes are made of a small subunit (30S) and a large subunit (50S). Together, they form the whole ribosome which in eukaryotes is 80S. They are found on the rough ER and free within the cytoplasm, and they are the site of translation where the genetic code is used to build protein. Under the microscope within a cell, they appear as mere dots. But remember, awesome comes in small packages!



8. Rough endoplasmic reticulum and smooth endoplasmic reticulum


There are two different kinds of endoplasmic reticulum – rough and smooth endoplasmic reticulum, hence their short names rough ER and smooth ER. The roughness and smoothness business is down to ribosomes attached to the rough ER, but not to smooth ER.

Rough ERtransport system: collects, stores, packages and transports the proteins made on the ribosomes

Smooth ER – synthesis of lipids and some steroids; detoxification e.g. alcohol breakdown.

What does it look like? Well, imagine this is a bit like the inner membrane of the mitochondria, but more tightly packed.


9. Cell wall (plants, algae, fungi)


A leaf cell is surrounded by its cell wall which is made of cellulose.

The role of the cell wall is multi-fold:

1. Provides the plant with strength

2. Prevents the cell from bursting due to water flooding in by exerting pressure against the water flow

3. Gives tissues mechanical strength e.g. plants that rise high above the ground

4. Maintains the cell’s specific shape.



Fungi are actually more closely related to us than plants. However, they also sport a cell wall, indeed so do bacteria and they’re not even eukaryotic! Generally, cell walls provide structural support, act as defence, and can have varied other functions depending on species.



10. Cell vacuole (plants)


The vacuole is a very large vesicle which contains a solution of various organic and inorganic compounds. The size of the vacuole changes upon cell requirements, as the compounds within are used up or stored. Some of the functions of the vacuole, depending on cell type, include:

-storing small molecules and water
-isolating waste products or harmful substances
-maintaining cell rigidity by keeping in check hydrostatic pressure



The membrane surrounding the vacuole is called tonoplast. It controls the transport of things across it between the vacuole and the rest of the cell, via many transporter proteins. These also determine the reshaping of the vacuole as needed.




You will need to know about the difference between light, transmission electron and scanning electron microscopes – LM, TEM and SEM. Both the latter (as the name suggests) use a beam of electrons, rather than light, to produce an image of the sample.


TEM uses electrons which pass through the sample, so the resulting micrograph (image) shows everything within the sample in black and white, for example organelles in a cell. SEM uses electrons which scan the sample in 3D, resulting in a coloured micrograph with 3D detail, but no components from within the sample.


In light microscopy, light does go through the sample, but the outcome depends on the thickness of the sample. For example, the plant root slice in the diagram (LM) is thin enough to be able to see through the thickness of the sample. Light would also travel freely through air but not various materials of high opacity.



When talking about microscopes, differentiating between resolution and magnification is important. In principle, it’s not hard to understand. Imagine zooming in a photo to try to see a detail. That is magnification. Now imagine the photo has a low resolution, and if you magnify it, you can only see annoying pixels. If the image had a high resolution, you would be able to see the detail clearly after zooming in. So magnifying is zooming in, while resolution is the focus power. You will need to be able to calculate actual sizes and magnifications of various drawings. The equation for that is Image size on paper = Magnification x Actual size. This gives magnification = image size on paper / actual size. “I AM” summarises it nicely in a triangle.



Staining is a key precursor to microscopy. Most samples would not register well under a microscope without some form of staining. This can also be critical to the experiment carried out. For example, we might need a stain for the cell nucleus as well as a stain for the cell fibres.

For microscopes with fluorescent wavelength filters, fluorescent stains are used. These can be bound to very specific antibodies to target specific cell types or cell organelles.



Muscle cells can be stained for their nuclei (blue) or one of the constituent proteins like actin (red). Stains of different colours and hence wavelengths are used to differentiate the various parts that we want to visualise. Advanced microscopes such as confocal microscopes that use lasers can focus on multiple points in the sample, and relay multiple wavelengths at the same time to create an impression of a section through the sample, add together the data through the multiple layers in the sample, and create complex images of specimens.


Ok byeeeeee





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