# Structural Biochemistry/Cellular Basis/Eukaryotic Cell

This page discusses the properties of eukaryotic cells. Eukaryotic cells are one of two types of cells that an individual organism may be classified. Both cells have a cytoplasm and nuclear membrane, and the use of DNA for its genetic information. The main distinguishing factor of a Eukaryotic Cell from the Prokaryotic Cell is the presence of nuclear envelope. Prokaryotic cells are generally smaller than Eukaryotic cells. In addition, their DNA is not packed inside a nucleus, instead it can be found in the cytoplasm.
Eukaryotic cells contain many other membrane-bound organelles such as the mitochondria, endoplasmic reticulum, or golgi body which are contained in the cytoplasm. Examples of Eukaryotic cells include animals, fungi, plants and proti. Organisms containing eukaryotic cells may be either multi-cellular organisms, such as mammals and plants, or unicellular microorganisms, such as yeast. These organisms are classified under the domain called Eukarya, one of the three fundamental domains that make up the possible evolutionary path of life (See 'Evolutionary Background' below.)

## Comparison

Fundamental Properties of Cells
All organisms are comprised of cells. All cells of the simplest and most complex organisms share some basic fundamental properties that can be seen at the biochemical level. These basic fundamental properties include plasma membrane, cytoplasm (cytosol), and nucleus/nucleoid.
All cells are enclosed by plasma membrane that separates the cell's contents from its surrounding. The inner environment of the cell enclosed by the plasma membrane is called cytoplasm which is composed of aqueous solution called cytosol.
Cytosol consist of variety of suspended organelles/particles each with their corresponding functions. Ribosomes (the site of protein synthesis) and Proteasomes (degrade proteins that are no longer needed by the cell) are examples of some organelles that are suspended in cytosol.
The third item that all cells are composed of is nucleus/nucleoid. The genetic information is stored in the nucleus. All prokaryotes (Bacteria and Archaea)have nucleoid which is not separated from the cytoplasm by a nuclear envelope. Therefore a defining feature of a eukaryotic cell is the presence of the nuclear envelope.
Another remarkable thing worth noting is that the distinguishing features that define "life" is displayed even at the cellular level. All cells display high degree of chemical complexity and organization. Cells are able to extract, transform and use energy from their environment. The organelles composed the cell each have their defined functions and the interactions among organelles are highly regulated. Cells can sense and respond to changes in their surrounding environment. Cells can precisely replicate and assemble themselves. Furthermore they have potential to change over time by gradual evolution.
Eukaryote vs Prokaryote
Regular Sizes;
While most bacteria (or prokaryotes) are approximately 1-10 µm in diameter, Eukaryotes range from 10-100 µm in diameter.

### Genome

Prokaryotic cells are known to be much less complex than eukaryotic cells since eukaryotic cells are usually considered to be present at a later time of evolution. It is likely that Eukaryotic cells have evolved from Prokaryotic cells. These differences in complexity can be seen at the cellular level. The DNA of prokaryotes is circular and attached to the plasma membrane, while eukaryotic DNA is packed into chromosome bundles. Prokaryote's DNA is contained in nucleoid which is not surrounded by nuclear membrane. Eukaryotic DNA is more complex where it has histone (protein that winds the DNA into a more compact form), and nonhistone proteins in chromosomes. Chromosomes are contained in the nucleus with a nuclear envelope (a defining feature of eukaryotic cells).

### Membrane Bounded Organelles

Membrane bound organelles are absent in prokaryotic cells. Eukaryotic cells are known to be multicellular organism that have membrane enclosed organelles. A variety of membrane bound organelles can be found in a eukaryotic cells, each with their corresponding function. For example ATP (cellular currency) synthesis happens in mitochondria (for animals), and chloroplasts (for plants and some algae), endoplasmic reticulum assist in glycosylation of proteins while Golgi complexes is the main transport system for the cell.

### Cell Division

Prokaryotes simply divide by fission, which the more complex eukaryotes go through mitosis which include mitotic spindle which hold the chromosomes during cell division. Mitosis is a more orchestrated version of cell division where all genetic info,and membrane bound organelles are precisely identical in the daughter cells as it is in the mother cell.

### Nutrition

The majority of prokaryotes simply absorb nutrients from their surrounding, but some photosynthesize. The eukaryotes on the other hand have elaborate digestive systems which allow ingestion of nutrients, and excretion of nitrogenous waste. Some eukaryotes (plants) go through photosynthesis with the help of chloroplasts.

### Energy Metabolism

Prokaryotes have no membrane bound organelles, hence no mitochondria. Instead they have oxidative enzymes bound to their plasma membrane for energy metabolism. Various species of prokaryotes display a great variation in their metabolic pattern.
In contrast, eukaryotes have these oxidative enzymes packed into their mitochondria, and they display a more unified pattern of oxidative metabolism which include the krebs cycle and the electron transport chain. The electron transport systems for eukaryotic cells are located in the inner membrane of the mitochondria while in prokaryotic cells, they are located in the cytoplasmic membrane.

### Cytoskeleton

Prokaryotes have none of this sort. The Eukaryotes have complex array of cytoskeleton which composed of microtubules, intermediate filaments and actin filaments. This protein-developed cytoskeleton reinforces the cell's outer structure to help with the rigidity of cell and intracellular transport.

### Intracellular Movement

Intracellular movement is absent in prokaryotic cells. Due to the presence of cytoskeleton, intracellucar movement is possible in eukaryotic cells.
Plant Cells
Plant cells have a rectangular structure, which is enclosed by a cell wall made of cellulose. The plant cell also contains plastids, a main vacuole, glyoxysomes, and chloroplasts, apart from a nucleus and other common organelles with the animal cell. The main vacuole of the plant can take up to 90% of the volume of the cell and is used to store water.
Animal Cells
Animal cells are enclosed by a plasma membrane made of a phospholipid bilayer and proteins. Unlike a plant cell, an animal cell have centrioles, lysosomes, and flagella. The flagella is needed for cell movement. Examples of animal cells include muscle cells, neurons, and skin cells.
Fungus Cells
Fungi are eukaryotes that are mostly multicellular with cell structures that mimic both plants and animals. Fungi contain cell walls, like plants, but unlike plants they are composed of chitin. Fungi do not create their own food however and, like animals, store their food as glycogen. Fungus cells are unique in that they are composed of hyphae, filaments that contain internal crosswalls known as septa.
Single Celled Eukaryotes
Eukaryotes also exist in the single celled variety. Some examples include: brown algae, microsporidia, and dinoflagellata. Single celled eukaryotes are quite varied and can be found with numerous different structures.

## Mitosis/Meiosis

Multicellular eukaryotes undergo cell division processes called mitosis and meiosis.
Mitosis The process of mitosis is divided up into four parts called: prophase, metaphase, anaphase, telophase. During prophase, the genetic material inside the nucleus known as chromatin begins to condense into a more structured form called a chromosome. Chromosomes consist of two sister chromatids which separate upon complete cell division. The sister chromatids are bound by a centrosome. Centromeres also begin to form during prophase, which are used to separate the sister chromatids on opposite ends of the cell. During metaphase, the chromosomes align at the center and spindles connect to each chromosom's centromere forming a kinetochore complex. Each centromere has two spindles connect to it, one on each side. Before the cell can move onto anaphase, all the centromeres must be attach to the spindles. During anaphase, the sister chromatids begin to separate creating two distinct sister chromosomes and are then pulled to opposite ends of the cells by having the kinetochore microtubules shorten in length. Telophase marks the last stage of mitosis in which the cell begins to elongate and separate and the sister chromosomes form into a nucleus and unfold back into chromatin.
Meiosis Meiosis(needed for sexual reproduction) is a type of cell division that produces haploid gametes in diploid organisms. Many of the stage of meiosis closely resemble corresponding stages in mitosis.For both mitosis and meiosis, the chromosomes replicate only once, in the preceding interphase. Meiosis is preceded by the replication of chromosomes followed by 2 successive cell division: Meiosis I and Meiosis II which result in 4 daughter cells (each with single haploid set of chromosome). It means meiosis makes daughter cells with only half as many chromosome as the original (parent) cell

## Organelles

Centriole
A pair of centrioles are found within a centrosome of an animal cell and each composed of 9 sets of triple microtubules arranged in a ring.Centrioles are short, cylinder shaped organelles composed of nine triplet microtubules. It is found in most eukaryotes except for high plants and fungi. It organizes proteins that form flagella and cilia.Centrioles may help organize microtubule assembly, they are not essential for those function in all eukaryotes.
Chloroplasts
Chloroplasts are typically found in the mesophyll cells on the inside of plant cells only. Their function is to produce glucose and oxygen, by receiving carbon dioxide and water. In order for this to happen, there has to be the presence of light in order to drive the reaction forward. Chloroplasts are members of the plastid family. Through photosynthesis, the chloroplasts turn light energy into sugar. Inside a chloroplasts are disk like structures known as thylakoids and when several thylakoids are stack on top of each other, the form a granum. The chloroplasts, like the mitochondria, has a dual membrane system with an inter membrane space. The space between the granum and the inner membrane is known as the stroma which is where the Calvin cycle occurs. The Calvin cycle is known as the dark reaction because it does not need light and its purpose is to make sugar out of CO$_2$. The light reaction occurs in the thylakoids and its purpose is to draw energy from water by splitting the oxygen from the hydrogen forming O$_2$.
Chromosomes
Chromosomes is an organized structure of the genes the comprise themselves into DNA. Because of Eukaryotes have a nucleus, the chromosomes must compact itself into chromatin(complex of DNA and protein), which would then securely fit inside the cell. Chromatin usually has two identical strands of chromatid "tied" together by a centromere. Chromosomes are responsible for carrying the genetic information.
Cytoplasm
The cytoplasm is the space between the plasma membrane, or cell wall, and the nucleus.Cytoplasm means the interior of prokaryotic cell. In eukaryotes, this is where most of the membrane-bound organelles are located. This space is where glycolysis occurs which is important in the production of ATP for the cell. The final net product of glycolysis is 2 ATP, 2 pyruvate, and 2 NADH.
Cytoskeleton
Made up of three kinds of protein filaments: actin filaments (microfilaments), intermediate filament, and microtubules. Its functions are establishing cell shape, providing mechanical strength, locomotion, chromosome separation, and intracellular transport of organelles
Endoplasmic Reticulum
The interconnected network of tubules, vesicles, and sacs. It specializes in protein synthesis, sequestration of calcium, production of steroids, storage of production of glycogen, and insertion of membrane proteins. There are two kinds: smooth ER that lacks ribosomes and rough ER that is bounded by ribosomes. Muscle cells have a different form of endoplasmic reticulum known as the sarcoplasmic reticulum which is needed for the regulations of calcium secretion that is used for muscle contractions.
Golgi apparatus
Consists of a stack of membrane-bounded cisternae that located between the endoplasmic reticulum and the cell membrane. Its functions are to sort out the processed proteins and send them to the destination, also, it can reclaim processing proteins for reuse. The Golgi apparatus sorts its protein by inserting a oligosaccharide into the protein which acts as a signal showing telling the vesicles where the target destination is.
Lysosomes
Lysosomes are found in many eukaryotic cells. They are created by the Golgi complex. Lysosomes contain enzymes that help them digest other cells. These enzymes were first developed by the rough endoplasmic reticulum, then transferred to the Golgi apparatus where small vesicles are made. These vesicles are the lysosomes. The functions of a lysosome is to recycle the cell's worn out organic material and to digest macromolecules such as lipids, carbohydrates, nucleic acids, and proteins.
Membranes Along with the plasma membrane (which selectively filters out substances), there is the membrane that hold the organelles neatly in the cell. Eukaryotes have an extensive internal membrane that provides a barrier between organelles as well as ea storage space for them as well. These membranes consist of phospholipids and lipids (of which are composed by various proteins. Each membrane has various enzymes that help the organelle function.
Mitochondria
The mitochondria is also known as the cell's powerhouse. It produces Adenosine Triphosphate (ATP), the energy currency of the cell. ATP is produced through the Krebs cycle and oxidative phosphorylation. There are two plasma membranes for a mitochondria, inner and outer. Both of the plasma membranes of the mitochondria is a bilayer that has pores in it so that substances like pyruvate can be transported into the mitochondrial matrix. Here the pyruvate will be modified and then is sent through the Krebs cycle. The products of the Krebs cycle, NADH and FADH$_2$, then undergoes oxidative phosphorylation which occurs along the inner membrane region of the mitochondria. The inner membrane of the mitochondria has many folds to increase the surface area to increase energy output because there is more space for oxidative phosphorylation to occur. Each NADH yields about 2.5 ATP and each FADH$_2$ gives about 1.5 ATP. The mitochondria also has its own DNA and Ribosomes that came from the organism's mother. It is important to note that before entering the Krebs cycle, pyruvate was made into Acetyl CoA and releach 1 NADH. The final product of glycolysis, Acetyl CoA production, and Krebs cycle is 10 NADH, 2 FADH$_2$, and 4 ATP (note 2 pyruvate were used).
Nucleus
The nucleus is comprised of small chromatin units bundled into chromosome, which make up deoxyribonucleic acid (DNA). The nucleus is surrounded by a nuclear envelope structurally composed of two lipid, porous layers. The holes in the envelope permit the nucleus to pass information with the rest of the cell. Another important structure contained within is the nucleolus, which produces the ribosomes essential for protein production.
Peroxisomes
Peroxisomes are similar to lysosomes in the way that they both contain digestive enzymes. A key difference is the type of enzymes they carry. The enzymes peroxisomes contain are oxidative enzymes which are responsible for breaking down hydrogen peroxide produced by white blood cells.
Ribosomes
These organelles are the protein synthesizers of the cell. They either float freely in a cell's cytoplasm or attach themselves to the endoplasmic reticulum. Ribosomes are responsible for connecting each amino acid to develop long chains. Protein synthesis involves the two subunits of the ribosomes locking into a strand of mRNA created by the nucleus. Another nuclei acid, tRNA, helps protein synthesis by binding into free amino acids in the cell and transferring them to the ribosomes. Ribosomes are comprised of ribosomal RNA and are produced in the nucleolus.
Vacuoles
The vacuole in a plant cell is used in order to store water as well as maintain the shape of the cell, however, the vacuole in an animal cell is used to store water, as well as ions and waste. The vacuole in the animal cell is nowhere near as big as the vacuole in the plant cell

## Metabolic Requirements

Though Eukaryotic cells are generally larger than Prokaryotic cells, there is a metabolic limit on the practical size for a cell. The smallest, lowest limit of a cell (of which is practical to have functional DNA and sustain itself) has a diameter of approximately 0.1-1.0 µm.
Metabolic activity requires a selective plasma membrane that allows enough oxygen, nutrients, and wastes in and out of the cell. In addition, each µm$^2$ of the membrane can only allow a certain number of substances to cross at a time. So, as the size of a cell increases, the volume increases proportionally larger than the cell's surface area. Smaller objects therefore, have a greater ratio of surface area to volume and an easier time of allowing nutrients in and out of the plasma membrane. Similarly, the surface area of the plasma membrane has a limit to efficiently sustain the volume inside a cell. Larger organisms in turn, sustain themselves by having more cells rather than larger cells.

## Evolutionary Background

It is believed that Eukaryotic cells were formed when a prokaryote absorbed another prokaryote that acts like a mitochondria or chloroplasts. This theory is known as endosymbiosis. The exact mechanism of how the mitochondria cell entered the host cell is not known. The DNA of the mitochondrial prokaryote and the host prokaryote then mix to create a new genome for the new cell. The other membrane bound organelles were formed by the infolding of the plasma membrane of the prokaryote. This evolutionary process occurred over 2 billion years ago. The origins of other organelles of the eukaryotic cells are still being researched by scientists.

## References

* Campbell, Neil A., Jane B. Reece. Biology. Seventh Edition. 2005. ISBN 0-8053-7146-X
* Berg, Jeremy M., John L. Tymoczko, Lubert Stryer. Biochemistry. Sixth Edition. 2007.