Prokaryotes And Eukaryotes

Contents

Life

Living things have three major properties:

Understanding how life began and how life has evolved depends on understanding the origins and importance of these three properties. Ur-life (proto-life/whatever you want to call it) must have developed from simpler abiotic chemistry, by the process termed abiogenesis. Electrical discharge experiments by Miller and Urey showed simple organics could be produced by simulating lightening passing through a mixture of methane, ammonia, carbon dioxide and nitrogen. Comets may have been a major source of water on the early Earth.

Surface chemistry may have been a fore-runner of compartmentalised enzymatic catalysis. Cairns-Smith suggests clays may have been the first replicators, and they are certainly capable of catalysis. Wächtershäuser suggests that hydrogen sulfide reacting to form iron pyrites in black-smoker hydrothermal vents may be the original metabolism (and would explain the thiol groups in coenzyme A). Orgel suggests that an RNA world preceded the DNA/protein/RNA world we see today, with RNA acting as both catalyst and replicator.

Replicators

Replicators are molecules that reproduce themselves. They must possess the following properties to become dominant in a population of other replicators:

Replicators affect their environment by binding other chemicals which aid their replication, leading to the concept of a phenotype. Almost all modern organisms use DNA (some viruses use RNA) as their replicator (or rather, DNA uses bodies to get itself copied). RNA may well have been the first organic replicator, not DNA

ssRNA

The central dogma states that DNA gives rise to RNA by transcription, that RNA is translated to proteins, and that the interactions of proteins produce the phenotype of an organism.

DNA → RNA → protein → phenotype

However, this one way flow of information is now know to be too simplistic.

DNA ⇌ RNA → protein → phenotype

However, "recipe" (as opposed to blueprint) embryology ensures that it is (practically, if not theoretically) impossible to convert phenotype into genetic information. Protein → RNA has never been observed, but is not impossible (we could readily imagine an 'anti-ribosome'), because both are largely digital information.

Catalysts and metabolism

Catalysts increase the rate at which chemical reactions reach equilibrium. Ur-life may have used ribozymes (catalytic RNA). In modern biological systems, proteins (enzymes) perform catalysis, but there are many RNA hangovers (presumably from the 'RNA world'):

Compartments and cells

A cell is a compartment, which increases the local concentration of metabolites and ensures replicators and catalysts are kept together. Modern cells are always bounded by an amphipathic lipid bilayer, usually made of phospholipids, but often with terpenes too.

Similarities and differences

There are many other similarities that are common to all living things:

However, despite these similarities, prokaryotes and eukaryotes have very different cell structures. In general, prokaryotes have a simple cell morphology:

Whilst eukaryotes have a complex system of internal organelles:

However, you shouldn't think of prokaryotes as primitive. Some of their adaptations may be primitive, but a group as a whole cannot be primitive (no matter what your teachers may have told you). Prokaryotes are often biochemically more complex than eukaryotes, and eukaryote molecular biology seems unnecessarily complex. Prokaryotes are quick replicators (r selection); eukaryotes are stress resistors (K selection).

Prokaryotes

The structure of a prokaryote is very much simpler than that of a eukaryote. There are no endomembranes, endosymbionts, nucleus or cytoskeleton. The DNA is carried on the genophore, a circular chromosome, in a ill defined area of the cytosol called the nucleoid. The chromosome is attached to the cell membrane during cell division (fission), frequently at a point called the mesosome.

Prokaryotes are characterised by the lack of a nucleus and membranes bound organelles.

The cytosol contains oil droplets, food reserves and the 70S ribosomes, and is surrounded by a plasmalemma. In Gram negative bacteria, a further outer membrane surrounds the plasmalemma, with a thin cell wall and periplasmic space trapped between them. In Gram positive bacteria, there is no outer membrane, and the cell wall is thicker. The cell wall is composed of peptidoglycan and various organic acids in Eubacteria. Bacteria have flagella, but they are simple proteinaceous strands attached to a rotary motor, completely dissimilar to the complex eukaryotic undulipodium. Membranes may be present in the cell, as in the thylakoids of the Cyanobacteria. The cytosol may also contain various episomes (small circular chromosomes), some called plasmids, and others called (bacterio)phages, which are bacterial viruses.

Prokaryotes are extraordinarily diverse:

Prokaryotic DNA lacks histones (packaging proteins) and molecules have direct access to DNA. They have a junk-free genome, transcribed by just one RNA polymerase. Transcription leads to translation with no intermediate processing, which allows several genes to be encoded in a single transcriptional unit (a polycistron). They have small (70S) ribosomes.

70S ribosome.

Eukaryotes

The structure of eukaryotes is far more complex.

Organelle

% (w/w) in hepatocyte cell

Cytosol

54

Mitochondria

22

RER

9

Nucleus

6

Golgi

3

SER

3

Peroxisomes

1

Lysosomes

1

Endosomes

1

Note that plant cells can be more than 50% chloroplast.

The most characteristic feature of a eukaryotic cell, the nucleus, consists of a nucleoplasm surrounded by a double nuclear membrane pierced by nuclear pores. The nucleoplasm contains the (linear) chromosomes of the cell, which are organised into heterochromatin, which stains only a little, and euchromatin, which stains more densely. The most important euchromatic area is the nucleolus, in which ribosomes are formed.

Animal cell: eukaryotic cells are characterised by the possession of a nucleus and membrane bound organelles.
Animal cell.

The role of the nucleus is three-fold:

DNA storage takes up about 10% of the cell of both prokaryotes (nucleoid area) and eukaryotes (nucleus). However, don't forget that some of the genome resides elsewhere: plasmids, endosymbionts (mitochondria), etc. The nucleus of eukaryotes also protects the genome from the cytoskeleton. Condensation of genome during mitosis is required to withstand these stresses. This is not relevant in prokaryotes, as they lack a cytoskeleton. The existence of the nucleus permits processing of mRNA, and therefore defers translation. Alternative splicing can be performed to generate different proteins from the same RNA primary transcript. mRNA is capped and tailed to permit it to exit the nucleus. rRNA and tRNA are also heavily processed by RNA editing, i.e. base modification (this also occurs to some mRNA in trypanosomes). rRNA modification occurs in the nucleolus, where ribosomes are constructed.

The nucleus is bound by a double-membrane, which is contiguous through the nuclear pores, known as the nuclear envelope. The pores are required to allow RNA out and membrane lipids in (which is needed for growth during S phase).

The inner face of the inner nuclear envelope (INE) is coated by the nuclear lamina, which contains intermediate fibres called lamins A, B and C (at least in mammals). Phosphorylation of lamins by kinases cause nuclear envelope breakdown during prometaphase. Chromosomes occupy definite positions within the nucleus because of the interaction between lamins and telomeres, for example the Rabl conformation in yeast.

Rabl conformation.

In the Rabl conformation, the centromeres are at the pole closest to MTOC; and the telomeres at other, bound to the nuclear lamina. This orientation probably reduces tangling, and is inherited from mitosis. Later in interphase, the chromosomes may lose the Rabl conformation, but chromosomes still occupy discrete territories in the nucleus.

The outer nuclear envelope (ONE) is surrounded by other intermediate fibres, and is essentially just the RER surrounding the nucleus, and continuous with it. The space between the INE and ONE is termed the perinuclear space, and is continuous with the RER cisternae.

The cell wall of eukaryotes (when present) is usually composed of a β-(1→4)-glucan of some sort. In fungi, it is mostly chitin (N-acetylaminoglucan), in plants cellulose, but more exotic ingredients are common. Animal cells lack a wall, but may have a glycocalyx, which is a layer of thickened glycoproteins surrounding them and connecting them to the extracellular matrix.

Almost all eukaryotes have mitochondria, which are the remains of bacteria that became endosymbionts of the eukaryotic cell about a billion years ago. They perform oxidative phosphorylation and generate energy in the form of ATP for the cell. They have their own 70S ribosomes and some of their own DNA. Mitochondria have a double membrane surrounding them, the inner one is highly folded into cristae, surrounding a matrix space.

Photosynthetic eukaryotes also have chloroplasts, which are the remains of cyanobacteria that also became endosymbiotic. They have a triple membrane system. The outer membrane surrounds the inner membrane, which itself surrounds the stroma, in which are embedded a number of thylakoid membranes, some of which occur in stacks called grana. Those that are unstacked are termed intergrana. The thylakoids surround another compartment, termed the lumen. Chloroplasts are one of several different sorts of plastid. Others include proplasts (immature plastids), chromoplasts (full of pigments), etioplasts (formed in the dark) and amyloplasts (full of starch). Plastids carry out photosynthesis, converting light energy into ATP and NADH.

Plant cell.
Plant cell.

Eukaryotes have a cytoskeleton, which is composed of a number of interacting fibre types. The first are the actin microfilaments, which, with the motor protein myosin, form the muscles of the cytoskeleton (and in sarcosomes, form actual muscles too). The actin cytoskeleton forms a cortex beneath the plasmalemma of most eukaryotic cells, which is involved in changes to the external shape of the cell (such as the formation of pseudopodia in amoebae).The second fibre type are intermediate filaments, composed of spectrin, keratin, vimentin, nuclear lamins and other proteins. The intermediate filaments help maintain the relative positions of organelles and give the cell mechanical strength. The third type of cytoskeletal filament are the microtubules, which form the spindle during cell divisions (meiosis and mitosis), and give structure to the cell membrane, forming microvilli. They also form undulipodia, which are waving structures with a typical 9+2 structure, found in cilia (short undulipodia) and flagella (longer ones). The microtubules are composed of tubulin, and are organised by a microtubule organising centre (the centrosome and centrioles in animals), in which the − ends of the microtubules (which grow more slowly than the + ends) are embedded. Vesicles traffic along the microtubules under the influence of motor proteins such as kinesin (which transports items from the −→+ ends, i.e. away from the MTOC) and dynein (which traffics items from +→−). Tubulin is homologous to the FtsZ protein that is involved in bacterial fission.

The body of the cell is composed of a heterogeneous mixture of proteins and solutes called the cytosol. The cytosol contains many 80S ribosomes, on which protein synthesis takes place.

The endomembranes and plasmalemma form a continuous membrane system in the eukaryote cell. The cell contains a rich diversity of membranes, in addition to those found in the endosymbiotic organelles. The outer cell membrane or plasmalemma, controls what gets in and out of the cell by the use of pores, symports, antiports and pumps. It is composed of a fluid mosaic of proteins embedded in a phospholipid bilayer, as are all membranes. The plasmalemma also interacts with the extracellular space through receptors, gap junctions, plasmodesmata, and synapses.

The endomembranes include the nuclear membrane, already mentioned, and the rough and smooth endoplasmic reticula (RER and SER). The lamellae of the rough endoplasmic reticulum are continuous throughout the cell, and also contiguous with the nuclear membrane. They are the site of synthesis for proteins destined for the endomembrane system and the extracellular space, with which its lumen (the cisternal space) is topologically identical. The tubules of the SER are responsible for steroid and lipid synthesis. After translation on ribosomes attached to the RER, proteins are carried in small transport vesicles to the Golgi bodies (dictyosomes), where they go undergo modification to the glycosylation they received as they were imported into the RER. After modification, some proteins are exported from the trans-Golgi network in export vesicles to the extracellular space. The ER is continuous with the nuclear envelope, and probably evolved at the same time, possibly by invaginations of the sort seen in the mesosomes of bacteria.

Endomembranes probably evolved from invaginations of the plasmalemma, as seen in bacterial mesosomes, thylakoids and chromatophores.

The rough ER differs from the smooth ER morphologically. The RER's cytoplasmic surface is studded with ribosomes, and it has flattened cisternae (rather than tubular ones). The RER is denser than SER due to presence of ribosomes. Consequently, disrupted ER 'microsomes' can be separated using density gradient centrifugation.

SER microsomes are less dense than RER microsomes, so can be separated by centrifugation.

Other proteins are destined for the endolysosome system. Material engulfed from outside by phagocytosis (solids) and pinocytosis (liquids) are packaged into phagosomes, and internal organelles destined for destruction are packed into autophagosomes. Endolysosomes containing digestive enzymes fuse with the phagosomes and digest their contents. The fused organelles produced are the cells disposal system, and are called lysosomes. Very large lysosomes are found in plants where they help to bulk the cell with water. Here they are called vacuoles, and are surrounded by a membrane called to tonoplast. Other vacuoles are involved in osmoregulation: for example contractile vacuoles in Amoeba.

Finally, a number of smaller vesicles are found in the cytosol. They are called microsomes, and most seem to be peroxisomes, containing the enzyme catalase, which degrades hydrogen peroxide produced by respiration. In germinating plant seed, many glyoxysomes are present, which perform fat oxidation for growth. Some vesicles also contain food reserves, such as fat droplets.

Eukaryotic DNA is bound by histones, and requires some degree of unpacking for expression. Much of their genome is composed of parasitic DNA and introns. Three RNA polymerases exists, (approximately) one for each sort of major RNA product:

RNA is heavily processed in the nucleus, which allows deferred translation. They possess large 80S ribosomes.

80S ribosome.

Three domains of life

Woese's insight (1976) was that the eukaryotes seem to be monophyletic (i.e. the group contains all of the descendents of a single common ancestor),  but the prokaryotes are not. There are two distinct groups, the Bacteria (Eubacteria) and the Archaea (Archaebacteria). The Archaea seem to be more closely related to the Eukarya than to the (true) Bacteria. It is possible that eukaryotes are archaeons (in the same way that birds are dinosaurs); and it is also possible (in fact, it seems quite likely) that these two groups possess the more ancestral ('primitive') molecular biology.

The Archaea can be thought of as prokaryotic cells (no nucleus, no endosymbionts, no cytoskeleton), with eukaryotic molecular biology (histone-bound DNA, introns in tRNA genes). Many Archaea are extremophiles, growing under conditions of extreme:

Others are more commonplace such as the anaerobic methanogens which perform the reduction of CO2 to CH4, producing marsh gas (in marshes, and also, to everyone's embarrassment, in the human colon too).

It is possible that histones (a DNA-protective packaging protein found only in archaea and eukaryotes) were an adaptation to extreme heat and acidity.

It is also important to note that eukaryotic cells are really colonies of prokaryotes. A plant cell possesses at least three distinct 'ancestors', because eukaryotes possess endosymbiotic bacteria within an archaeal-like substrate.

Lynn Margulis also suggested that the cytoskeleton was endosymbiotic (spirochaete), but evidence here is scant, particularly as tubulin (what the microtubules of the cytoskeleton is made of) are homologous to the bacterial FtsZ protein involved in cell fission. However, it is interesting to note that some eukaryotes genuinely do have symbiotic 'flagella': spirochaetes power the movement of the termite gut symbiont Trichonympha.

Endosymbiosis is still occuring, and various stages in the saga can be seen today:

Almost all eukaryotes possess mitochondria, however a few lineages lack them, such as the Microsporidia, giant amoebae (Pelomyxa) and Giardia. These used to be thought of as 'primitive', but they appear to have lost their mitochondria secondarily: this is evidenced by the fact that many possess either the physical remains of mitochondria (genome-free hydrogenosomes), or have mitochondrial genes in their genomes, taken from mitochondria that no longer exists. This is a salutary lesson to those who dismiss the small and simple as primitive: microsporidia in particular used to be hailed as the missing link between prokaryotes and eukaryotes, but more recent evidence suggests that they are derived from fungi, and are therefore closely (as these things go) related to us!

Eukaryotes are also frequently multicellular.

This requires not just cooperation between genes in a genome, but also cooperation between genomes of different cells in an organism. The cooperation sometimes works (mitochondria and multicellularity), but is always subject to parasitic defection (parasitic DNA, retroviruses and cancer). Genes interact and genomes interact: you shouldn't think of the cell as being 'owned' by any particular gang of genes: the evolutionary strategies of parasites passed through the germ line will become the same as those of the host, which will lead to mutualism. Likewise, genes in the nucleus are selected to cooperate, not because they feel some sense of duty to each other or their cell, but because they share the same route into the next generation.

However, many eukaryotes are unicellular, and these organisms are generically called the 'Protoctista' (or 'Protista' or 'Protozoa', in descending order of modern preference). This group is paraphyletic, i.e. it is defined by exclusion - all eukaryotes except the multicellular ones. This is generally considered bad form these days: most taxonomists are pressing for cladistic phylogenies that only recognise monophyletic groups. As a result, this grouping is being broken into smaller groups as we come to understand their relationships better.

Specialised organelles play similar role to entire organs in multicellular organisms.

Stentor polymorpha and its weird and wonderful organelles
Stentor polymorpha

We can trace evolution over long periods of time by changes in genes, particularly in the small subunit rDNA. The 'tree of life' diagram shows the current best guess as to how things are related.

Tree of life.

This is an unrooted tree: the length of line between any two groups shows how closely related they are. However, there is still argument about where the root of the tree should be, i.e. the point on the diagram where we could 'pick up' the tree and 'shake out' its branches, to yield the branching pattern that evolution has taken. Current favoured points for a possible root are between the Archaea+Eukarya ('Neomura') and the Bacteria, or between the Eobacteria (Chloroflexus, Deinococcus and Thermus) and everything else (with the Neomura being the sister group of the Gram positive bacteria, and the Bacteria being paraphyletic). No-one is yet sure.

This summary table of the differences between the three domains may be useful.

Summary

You may find the domains summary table useful.

Test yourself

  1. Eukaryotes have 80S ribosomes. Why then do eukaryotic cell preparations always contain large numbers of 70S ribosomes too?
  2. If Lynn Margulis is correct, and the cytoskeleton is derived from spirochaetes, what evidence could you try to collect for or against this hypothesis?
  3. Prokaryotes are not a monophyletic group. What does this mean?
  4. Amitochondriate eukaryotes are now thought to have lost their mitochondria secondarily. What evidence can be gathered in favour of this hypothesis?

Answers

Bibliography

Peer Review.
This page has been peer reviewed by 2 people. Thanks to Benjamin Simon for his suggestion.