Chloroplasts: Everything You Need To Know

As many of you may already know from biology class, chloroplasts are plastids in green plant cells. They are responsible for the production of chlorophyll and are necessary for photosynthesis to take place.

Chloroplasts: Everything You Need To Know

But what does this mean exactly? 

Chloroplasts: Etymology & History

The term chloroplast is derived from the Greek words chloros (meaning “green”), and plastes (meaning “the one who forms”). 

Whilst the definitive first discovery of chloroplasts is contested, the first definitive description can be found in 1837 by German botanist Hugo Von Mohl, who described them as chlorophyllkornen, or “grain of chlorophyll. 

In 1883, the term “chloroplastids” was coined by German botanist and phychogeographer Andreas Franz Wilhelm Schimper. 

Similarly, in 1884, the term “chloroplasts” was used by Polish-German professor Eduard Strassburger, becoming the widely agreed upon term. 

Chloroplasts: Key Terminology

When discussing any biological organisms, there are countless words and terminologies which are used to refer to them and classify them within the wider ecosystem. 


A plastid is an organelle, bound in a protective membrane. These are stored in the cytoplasm of a plant cell, and are used to store pigment or food for the plant. 

The term chloroplast is used to describe plastids found in land plants, which contain chlorophyll and are capable of photosynthesis.

They are used to store starch, and can synthesize substances, like fatty acids and terpenes, which are important for the synthesis of other molecules within the plant. 

Plastids occur mainly in land plants, which rely on photosynthesis as their main source of food, energy, and nutrients. 

Underwater plants, such as algae and seaweed use different methods, such as chemosynthesis, to transfer inorganic substances into usable organic compounds for food. 

Cellular Differentiation

Plastids are capable of cellular differentiation, which is a process wherein a stem cell changes from one type to another. This is usually to fulfill a specialized purpose within the plant, and can be done seemingly when the need arises. 

There are several variants that stem cells can differentiate between, and these include: 

  • Chloroplasts – the green plastids which are key to photosynthesis. 
  • Etioplasts – the precursor to the chloroplast. 
  • Chromoplasts – used for synthesizing pigments and storage. 
  • Gerontoplasts – responsible for the dismantling of photosynthesis apparatus. 
  • Leucoplasts – colorless plastids used for synthesizing monoterpene. 
  • Amyloplasts – used for detecting gravity and storing starch. 
  • Elaioplasts – used for the storage of fat. 
  • Proteinoplasts – used for the storage and modification of protein. 
  • Tannosomes – used to synthesize and produce tannins and polyphenols. 

Cellular differentiation is a complex yet fascinating process, and is achieved using the following steps. 

Firstly, each plastid already possesses multiple copies of a 10-250 kilobase plastome, which in essence is a genome within the DNA of chloroplasts. The number of these genomes is variable, and depends on the age of the cell, and the requirements of the differentiation. 

These plastomes contain 100 genes, which are used to encode ribosomal, and transfer ribonucleic acids. They also transport proteins used in photosynthesis, and are used to aid gene transcription and translation. 

Each gene helps to encode almost all plastid proteins, and the plastid and nuclear genes are incredibly tightly regulated in order to properly coordinate plastid development for cellular differentiation. 


Within the biology of a cell, an organelle is a part of a cell reserved for a specialized purpose. 

The name organelle comes from the word “organ”, as the organelles are to the plant cell what the organs are to the human body. This is indeed the perfect analogy for their function, and the way in which they are specialized to fulfill a specific function. 

Whilst most organelles occur within the cell, some are known to protrude outside of the boundaries of the cell, including: cilia, the flagellum, the archaellum, and the trichocyst.

These are all hair-like appendages on the outer surface of cells, and are all used for different kinds of cellular movement and dexterity. 


Plastoglobuli are spherical bubbles of lipids and proteins surrounded by a lipid monolayer. These are found in all chloroplasts, and are more common when the chloroplast is under extreme oxidative stress.

They also occur more in chloroplasts which have transitioned into gerontoplasts. 

It is under these conditions that the most variation in size and mass can be observed. 

Once upon a time, it was thought that the plastoglobuli were floating freely within the stroma, but it is now thought that they are connected to the thylakoid system all the time. 

Chloroplasts: The Functions

Within the plant cells, the chloroplasts have two specific functions. 


Of course, the one most people will associate with chloroplasts is photosynthesis, wherein the light is transferred into chemical energy, and used to produce glucose for food. 

Plants also absorb water and minerals from the ground, using the sunlight absorbed into the chloroplasts to turn them into the above mentioned sugar, glucose, but also to oxygen.

This can both be used by the plant itself, but also expelled and breathed in by other organisms, such as humans. 

Plant Immunity

Whilst plants don’t have specific designed immune systems, or at the very least they don’t have specifically designated immune cells, they do have a generalized immune response. 

The chloroplasts play an important role in ensuring the functionality of this response, and as such are important targets for pathogens that have invaded the intracellular structure of the plant. 

In terms of immune responses, plants generally have two options: the hypersensitive response, and the systemic required assistance. 

The hypersensitive response seals infected cells, where they will then undergo self initiated cell death to protect the rest of the plant. 

The systemic required assistance response is where the affected cells send warning messages to the rest of the cells within the infected plant to alert them to its presence. 

Chloroplasts have also been known to surround the nucleus and the source of the infection during these high alert phases.

Acting as cellular sensors which can transmit signals throughout the plant using salicylic acid, jasmonic acid, nitric oxide, and reactive oxygen species as defensive warning signals. 

Chloroplasts: The Structure

Chloroplasts: The Structure

The structure of chloroplasts differs greatly, depending on whether they are found in land plants, or in algae and seaweed. 

Land Plants

These are generally shapes like lenses, that is to say ovular. 

Algae & Seaweed

Within these plants, there are far more variations in shape and size. 

Most algae cells contain one chloroplast, and these can be shaped like nets, cups, ribboned spirals around the edge of the cell, or bands that are slightly twisted.

Some algae cells contain two chloroplasts, such as the star-shaped zygnema, or the half cell-shaped desmidiales.

In some algae, the chloroplasts can even take up most of the cell itself, and have special pockets for other cell components such as the nucleus and other organelles.

This can be seen in the chlorella, which despite being cup-shaped takes up much of the cell interior. 

Wider Structural Elements

Regardless of the type or shape of chloroplast, they all have a minimum of three membranous systems, consisting of an outer chloroplast membrane, an inner chloroplast membrane, and a system called a thylakoid.

The thylakoid systems are compartments which house the light-dependent reactions of photosynthesis. 

Other chloroplasts may have more than three, but this is generally when they have been subject to secondary endosymbiosis. 

Outer Membrane

Within the outer and inner membranes, there is a thick gel-like fluid called the stroma, which makes up much of the chloroplasts volume. In the stroma, the thylakoid systems float, and are protected in the gel like a fetus in amniotic fluid. 

The outer membrane is porous to allow smaller molecules and ions to pass through.

Larger proteins are too large to permeate through the membrane, so larger molecules are transported across the exterior of the outer membrane using translocons – complexes of proteins designed specifically for this purpose. 

Intermembrane Space

The space between the outer and inner membranes is known as the intermembrane space, and whilst this is not universal to all chloroplasts, it is commonly found, usually approximating 10-20 nanometers in thickness. 

Inner Membrane

The inner membrane touches the stroma, and is used to control how many materials are passed in and out of the chloroplast. 

The inner membrane is also the manufacturing point for fatty acids (carboxylic acid with a hydrocarbon chain), lipids (insoluble organic compounds), and carotenoids (yellow, orange, or red fat soluble pigments). 


This gel-like fluid is rich in proteins, alkalines, and aqueous fluid (water soluble).

The stroma contains chloroplast DNA nucleoids, chloroplast ribosomes (tools for protein synthesis), the thylakoid system with plastoglobuli, granules of starch, and a variety of different proteins. 

One of the proteins stored within the stroma is RuBisCO. This is the most abundant protein on the planet, and is the enzyme that changes carbon dioxide molecules into sugar molecules. RuBisCO stands for ribulose-1, 5-bisphosphate carboxylase-oxygenase

The stroma is also the location for the Calvin cycle, the process during photosynthesis where carbon dioxide is transferred into glucose. 

The Thylakoid System

As mentioned these are small, connected storage sacks that are responsible for storing the membranes that host the light-reactionary stages of photosynthesis. 

These can just be seen using a light microscope, and using an electron microscope the thylakoid system can be seen in more detail. Through this kind of microscope, you can see that the thylakoids are flat, and stacked in a formation known as a grana

Under transmission electron microscopes, you can see that the membranes of the thylakoid are alternating in dark and light bands, which are approximately 8.5 nanometers thick. 

Chloroplasts: Plant-Wide Distribution 

Despite being found in a lot of the different parts of a plant, there are sections which do not possess any chloroplasts. 

In most plants, chloroplasts are generally found in the leaves as one would expect, but in other species of plant, such as cactuses, the chloroplasts are found in the stems. 

Generally speaking, the chloroplasts will position themselves in the part of the cells that are exposed to the most sunlight.

This of course varies depending on the location, plant type, and geographical location, which is why there are so many variations within different ecosystems. 

Chloroplasts: Under The Microscope

Chloroplasts: Under The Microscope

The inner workings of the plant become even more fascinating when under the microscope. To the laymen, plants might seem like inanimate objects with very little going on, but when under intense magnification, the reality couldn’t be further from it.

Chloroplast DNA

Like other types of plastids, chloroplasts have a separate genome from the one contained within their nucleus. 

This genome contains much of the genetic information of the plant, and features ribosomes and synthesized proteins, which proves that, at least to a certain degree, the chloroplast is autonomous. 

This was first sequenced in 1986, and are circular in shape, consisting of a length of 120,000 to 170,000 base pairs. Their contour length is 30 to 60 micrometers, and their mass is generally around 80 to 130 daltons. 

A dalton is a unit of measurement, or unified atomic mass measurement, and is used to calculate the atomic mass of a substance by setting it against its collective mass. 

Most chloroplast DNA has the entire genome combined into one single ring, however certain species of algae, such as members of the dinophyta, have broken genomes split into forty plasmids – which are small extrachromosomal DNA molecules.  

DNA Replication

This has been observed by scientists, but they are not entirely sure how chloroplast DNA replication actually occurs. 

DNA replication has been repeatedly observed using an electron microscope since the 1970s, and it is thought that the process occurs using a double displacement loop. 

As the loop moves through the circular shape of the chloroplast DNA, it takes on an intermediary form. This is known as a Cairns replication intermediate, and this is a temporary moment, before replication is completed. 

However, there are several things they do know for certain. 

For example, it is known that DNA replication always begins from a specific point. This is not a random pattern, and only occurs in parts of the genome where it can be achieved most effectively. 

Multiple replication “forks” are opened, and the DNA is replicated onto these forks.

As the replication process progresses, these forks extend, converging with one another and forming new structures, which then separate and form new chromosomes, referred to as cpDNA chromosomes

Another theory for DNA replication, and one that competes with the former, states that chloroplast DNA is actually linear, not circular, and that the cells replicate using a method of homologous recombination

This is a type of genetic replication which occurs through the exchange of genetic information between similar or even identical molecules. These can be double stranded or single stranded nucleic acids. 

This has been proven in some forms of plants, such as maize, which has been shown to have linear DNA patterns. During some early experiments, it was initially thought that these linear patterns were simply damaged or unfolded circular patterns.

If this is true, then the D-loop theory is perfectly reflective of the processes that chloroplast DNA uses. 

However, if the linear patterns were indeed damaged circular strands of DNA, and there are in fact no linear patterns in plants, then the D-loop theory is not sufficient to assess all DNA replication patterns in plant life. 

This, amongst other inconsistencies, is why linear theory has not been fully appreciated, or indeed adopted, in modern scientific fields. 

However, aside from the circular and linear theories, there are still plant species that deviate, and are too complex for contemporary science to properly observe and understand. 

Inverted Repeats

These feature in most examples of chloroplast DNA, and are used to separate a long single copy section from a short single copy section. 

These have wide variations in their length, and can appear anywhere from 4,000 to 25,000 base pairs long.

Plants tend to possess inverted repeats at the upper end of that spectrum, and can contain anywhere up to 150 different genes, consisting of ribosomal RNA and tRNA genes.  

Inverted repeats occur in pairs, and with any DNA sequence, they are almost always identical to one another. This is a result of evolution. 

Land plants amass the most of these inverted repeats, and have far less mutations than in other species of plant like algae and seaweed. The latter sometimes experience flipping inverted repeats, which then become direct repeats 

Whilst this may sound extremely complex, scientists believe that the purpose of these inverted repeats is to stabilize the genome. 


A nucleoid is an irregularly shaped space within a prokaryotic cell. It is within these that most of the genetic material is stored and protected. 

Young leaves have around 100 copies of its DNA per chloroplast. This changes in older leaves, which have around 15 to 20 copies of their DNA per chloroplast. 

The DNA rings are usually compacted into nucleoids, where several identical copies can be stored and contained. 

Endosymbiotic Gene Transfer

Over time, much of the coding has been transferred from the chloroplasts to the nuclear genome of the host plant. 

As a result of this, the genome of the chloroplasts are drastically reduced compared to other similarly sized organisms.

Such as cyanobacteria, which are known to house over 1500 genes in their genome, in comparison to chloroplasts possessing 60 to 100, depending on the age of the leaves. 

The process of endosymbiotic gene transfer is one of the most important processes we have discovered to help us understand chloroplastic loss and allows us to see the remaining nucleus of the original host, even when the genetic information has been transferred. 

This proves their existence, even if they are no longer present within the former host chloroplast. 

Final Thoughts

And there we have it, everything you need to know about the chloroplast, examining the structural, functional, and distributional circumstances of these amazing organisms. 

Whilst this may seem complex, the most important things to remember are the role chloroplasts play in photosynthesis (where they absorb sunlight to aid chemical transitions into food) and the continued protection of the plant through the regulation of the immune system. 

Jennifer Dawkins

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