4.6: Specialized Internal Structures of Prokaryotes - Biology

4.6: Specialized Internal Structures of Prokaryotes - Biology

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4.6: Specialized Internal Structures of Prokaryotes

All cells on Earth can be classified as either prokaryotic cells or eukaryotic cells. Eukaryotic organisms may be multicellular or unicellular, but prokaryotes are always unicellular organisms.

Eukaryotic cells are larger and more complex than prokaryotes, and usually contain organelles that are absent from prokaryotic cells. This is because eukaryotes contain membrane-bound organelles (like the nucleus, endoplasmic reticulum, Golgi apparatus, and mitochondria), but prokaryotes do not.


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The Cytosol is the part of Cytoplasm that is not occupied by any organelle. It is a gelatinous fluid, where other components of the cytoplasm remain suspended. It mainly consists of cytoskeleton filaments, organic molecules, salt, and water. Cytoskeleton filaments are the protein filaments. The cytoskeleton consists of structures called ‘microfilaments’ and ‘microtubules’ that form a skeletal network, thereby giving shape to the cell and holding the various organelles in place.

Microfilaments are thin fibers made up of actin polymers. They facilitate the movement of substances inside a cell. Microtubules are hollow cylindrical structures made up of tubulin polymers. They assist the movement of different organelles, and play a crucial role in cell division by aiding the movement of chromosomes in the nucleus during mitosis. The cytosol also contains enzymes, fatty acids, sugar, and amino acids. The cytosol accounts for almost 70% of the total cell volume.

4.6: Specialized Internal Structures of Prokaryotes - Biology

School Biology Notes: Introduction to plant & animal cells structure & function

Introduction to plant, animal and bacteria CELL STRUCTURE & FUNCTION

Sub-cellular structures and differences between plant, animal and bacterial cells

Doc Brown's school biology revision notes: GCSE biology, IGCSE biology, O level biology,

US grades 8, 9 and 10 school science courses or equivalent for

14-16 year old students of biology

What features do animal cells and plant cells have in common? In what way do plant cells differ from animal cells? Can you correctly draw and label an animal cell and a plant cell? What are subcellular structures? What is their function in cells?

Sub-index for this page

(a) Introduction to CELLS and types of cells

The majority of living things are made up of cells, the building blocks of life.

Appendix 1. Viruses can be considered a 'non-cellular' form of life.

Why is cell biology important?

Cell biology is very important t understand the structure and function of cells e.g. what do the various sub-cellular structures do? and how does a cell function as a living unit.

Knowledge of cells helps us understand how organisms develop and interact with other organisms e.g. sexual reproduction or our bodies own defences in fighting bacteria.

Knowledge of cell chemistry is also important in the diagnosis of disease and developing drugs to counteract adverse medical conditions e.g. anti-cancer drugs.

A cell is the smallest unit of life able to control its own activities, BUT, it relies on the rest of the organism (if multicellular) or the surroundings (if unicellular) to provide it with raw materials i.e. nutrients and removal of waste material.

The different parts of a cell are referred to as subcellular structures.

The term organelle refers to specialized sub-cellular structure within a cell that perform a specific function (e.g., mitochondria, ribosomes).

Organelles in unicellular organisms are the equivalent of organs in multicellular organisms.

You should know and understand that the structures of different types of cells are related to their functions.

You should know and understand the similarities and differences between animal cells, bacteria and plant cells.

The two main groups of cells

Cells can be either eukaryotic or prokaryotic in character.

Eukaryotes are organisms made of eukaryotic cells, which are complex cells, and all plants and animals are made up of such cells.

Eukaryotes are usually multi-cellular organisms, but can consist of one cell e.g. yeast or algae (unicellular).

Plant and animal cells (eukaryotic cells) all have a cell membrane, cytoplasm and genetic material enclosed in a true nucleus in the cytoplasm (compared to prokaryotic cells described below) and other sub-cellular structures called organelles.

However there are significant differences between eukaryotic plant and animal cells (see later).

Prokaryotes , are smaller and simpler single celled organisms (unicellular prokaryotic) eg bacteria and archaea are prokaryotic cells.

Prokaryotic cells do NOT have a true nucleus in containing the DNA - the DNA is in free floating loops/strands in the cytoplasm.

Archaea are now considered as a separate domain of single celled organisms (see diagram below) even though they are like bacteria

Prokaryotic cells are more primitive than eukaryotic cells and the oldest fossil evidence suggests that bacteria were evolving as much as 3.5 billion years ago.

Planet Earth is reckoned to be about 4.5 billion years old (4.5 x 10 9 years from radiometric data - using the half-lives of elements in rocks - the calculations are VERY complex).

The early bacteria probably existed as thin purple or green coverings on shorelines.

These early bacteria used photosynthesis but produced sulfur instead of oxygen as a waste product.

See also Classification - domain, kingdom, phylum, class, order, family, genus, species, Linnaeus naming of organisms

including the three domain system

Sections (b) and (c) give a detailed comparison of animal cells, plant cells and bacteria cells

All plant and animal cells have similarities in basic structure, BUT, there are important differences between them.

Both eukaryotic and prokaryotic cells contain various subcellular structures, of some are referred to as organelles - a subcellular structure performing a particular function, on a larger scale, rather a like an organ in an animal.

There are also important differences between prokaryotic cells (single celled archaea and bacteria) and (usually) multicellular) eukaryotic cells (plants and animals)

Using diagrams and explanatory notes, their similarities and differences in sub-cellular structures will be described and their functions explained.

(b) ANIMAL CELLS including humans! (eukaryotes, eukaryota)

Most animal cells have the following five parts in these eukaryotic cells - the so called subcellular structures, and, remember, plants cells usually have the same five components too.

The diagram shows the principal subcellular structures of an animal cell.

The cell contents i.e. the sub-cellular structures like cytoplasm, nucleus, (small vacuoles), mitochondria etc. are all held together and enclosed, by the soft cell membrane which controls the passage of substances in and out of the cell.

Because not everything can pass through the membrane, it is described as a semi-permeable or a partially permeable membrane.

The cell membrane allows the free passage of water and gases but may act as a selective barrier to other chemicals.

The cell membrane also contain receptor molecules that are used in cell communication e.g. by hormones.

2. Mitochondria (an example of an organelle - a subcellular structure performing a particular function)

A mitochondria organelle has a double membrane, the inner one is folded in a complex way

Most of the aerobic energy releasing chemistry of respiration occurs in the mitochondria, which is where most energy is released in respiration - eg the aerobic 'burning' of glucose to release energy.

e.g. glucose + oxygen == via enzymes ==> carbon dioxide + water + energy

The equation of aerobic respiration, an exothermic chemical reaction and catalysed by the appropriate enzymes.

glucose + oxygen ===> carbon dioxide + water

C6H12O6(aq) + 6O2(g) ===> 6CO2(g) + 6H2O(l) + energy

RESPIRATION - aerobic and anaerobic in plants, fungi and animals, conditions, substrates etc. gcse biology revision notes

Mitochondria are the power house of the cells and contain all the enzymes needed for the chemical reactions that provide the chemical energy for any of the cells functions.

Liver cells carry out lots of metabolic reactions so lots of energy needed, so they contain a lot more mitochondria.

Similarly, muscle cells need lots of energy eg to contract, so again, they have a lot more mitochondria than other cells to supply the energy for the physical work animals perform.

Cytoplasm is a jelly like fluid (gel-like) in which most of the cells chemical reactions take place and most of these reactions are catalysed by enzymes (biological catalysts) which facilitate and control the rate of these reactions.

Anaerobic respiration (glycoyslis, fermentation) take place in the cytoplasm, but most aerobic respiration takes place in the mitochondria.

The cell nucleus contains all the genetic material, the deoxyribonucleic acid (DNA codes) of the genes in the chromosomes which control the cells functions and the cell division in replication.

The nucleus controls the activities of the cell by sending instructions to the cytoplasm.

The genetic material is organised into chromosomes and the chromosomal DNA contains the instructions for making proteins eg that make up tissue or enzymes.

Ribosomes are involved in the translation of the genetic material from the chromosomes, they can decode the DNA to carry out various chemical synthesis e.g. ribosomes are where protein synthesis takes place - from amino acids in the cytoplasm of the cell - the protein 'factory'!

This organelle is a tiny structure and can just be seen as a dot with a light microscope.

They can be free to move in the cytoplasm or attached to an internal network of channels in the cell.

Glycogen granules

Stored food for respiration.

Small vacuoles - much smaller than in plant cells

Some animal cells may have several small vacuoles of water containing various dissolved substances - might be food or waste products.

7. Some differences between animal, plant and bacteria cells

Animal cells are much larger than bacterial cells, with important differences from plant cells.

Animal cells, unlike plant cells, do not have (i) an outer rigid cell wall, (ii) a permanent vacuole and (iii) chloroplasts.

Note: What is an organelle? An organelle is a specialized part of a cell having some specific function, a sort of cell organ. Organelles are only found in eukaryotes (plant and animal cells). The nucleus, mitochondria, ribosomes and chloroplasts are examples of organelles.

(c) PLANT and algal CELLS (eukaryotes, eukaryota)

Plant cells are much larger than bacterial cells, with important differences from animal cells.

The diagram shows the principal subcellular structures of a plant cell.

Like animal cells, plants cells have (1) a cell membrane, (2) mitochondria, (3) cytoplasm, (4) nucleus and (5) ribosomes, all of which perform the same functions as in the animal cells.

The three extra principal different sub-cellular structures that plant cells have plant, and animal cells do not are: (i) a rigid cell wall, (ii) chloroplasts and (iii) a large permanent vacuole - animal cells do NOT have these three features, but some have small vacuoles.

You need to be able to describe the function of the components of a plant cell including chloroplast, large vacuole, cell wall, cell membrane, mitochondria, cytoplasm and nucleus (see diagram and notes below) and know the differences between plant and animal cells.

(i) Plant and algal cells have a more rigid cell wall made of cellulose, which strengthens the cell, supports it and therefore the plant's structure as a whole.

The plant cell wall is effectively an additional layer outside of the cell's inner membrane.

It is made from cellulose fibres that provide strength to the cell and collectively the strength of a whole multicellular plant.

Unlike the cell membrane, the cell wall does not control what materials can enter or leave the cell.

(ii) Chloroplasts the sites of photosynthesis

Chloroplasts (an organelle) has a complex internal membrane structure.

Chloroplasts can absorb light energy to make food via chlorophyll in photosynthesis

The chloroplasts contain green chlorophyll molecules which are involved in the energy absorbing process of photosynthesis . The chlorophyll molecules absorb the light energy from the sun to promote the endothermic reaction below. The chloroplasts must also contain all the enzymes to catalyse the whole series of complex reactions to make sugars - the equation below is a greatly simplified summary!

sunlight energy + carbon dioxide + water ==> sugars (e.g. glucose) + oxygen

6H2O(l) + 6CO2(g) ====> C6H12O6(aq) + 6O2(g)

Therefore chloroplasts are the site of food production for the plant. The sugars may be used directly as a source of energy or converted to starch grains - the plant's food store (and part of our food store as well!).

Chlorophyll absorbs mainly in the violet-blue and orange-red regions of the visible spectrum, hence it appears green, the light NOT absorbed.

(iii) Large permanent vacuole

Most plant cells have a single large permanent vacuole surrounded by a membrane containing cell sap, a dilute solution of mineral salts and sugars. It maintains the internal pressure to support the cell.

The central vacuole is a cellular organelle found in plant cells. It is often the largest organelle in the plant cell.

The central vacuole's membrane's functions is to hold useful materials and wastes.

It also functions to maintain the proper internal pressure within the plant cells to provide structure and support for the growing plant.

Starch grains

Stored food for respiration from the glucose made by photosynthesis.

(d) BACTERIA (prokaryotes - prokaryotic cells, prokaryota)

The diagram shows the principal subcellular structures of an bacterial cell.

Bacterial cells, single-celled microorganisms, are much smaller than plant or animal cells with some quite distinct and different sub-cellular features.

A prokaryotic bacterial cell consists of cytoplasm within a membrane surrounded by a cell wall.

Bacteria do NOT have a real nucleus, chloroplasts or mitochondria.

Cell wall and inner membrane

The cell contents i.e. the cytoplasm, DNA etc. are all held together within the cell wall by the surface membrane which controls the passage of substances in and out of the cell.

The surrounding outer cell wall gives a bacterium extra structural support.

The cell wall can also be surrounded by a capsule.

The jelly like fluid in which most of the cells chemical reactions take place with the aid of enzyme catalysts. Although they do not have mitochondria, bacterial cells can still respire aerobically in the cytoplasm.

Chromosomal DNA - the genetic material is not confined in a nucleus which doesn't exist in bacteria

The genes are not in a distinct true nucleus, the genetic material is a sort of jumbled cluster comprising of one long circular strand (loop) of DNA floating free in the cytoplasm sometimes accompanied by one or more small rings of DNA called plasmids. As with any other cells the string of DNA controls the cell's activities and cell division for replication.

This single chromosome controls the cells functions and the cell division in replication.

The chromosomal DNA moves freely around in the cytoplasm and is not confined in a distinct nucleus as in plant and animal cells.

Plasmid DNA , not part of the chromosome

Plasmids are small hoops of extra DNA that are separate from the chromosomal DNA.

Plasmids contain genes that help tolerance against drugs and this drug resistance can be passed from one bacteria to another - a problem in dealing with bacterial infectious diseases.

This is how the bacteria MSRA have evolved and become so dangerous because of their antibiotic resistance.

Not all prokaryote cells contain plasmids.

Shape and Flagella (flagella plural, flagellum singular)

Bacteria come in all sorts of shapes e.g. rods, spirals etc. and some have a tail!

The flagellum is a long thin tail, a hair-like structure that projects out of the body of the cell, and can rotate to move the bacteria along.

Some bacterial cells have more than one flagella (flagellum) protruding from the outer layers of the bacterium.

The 'tail' flagellum can be driven by a tiny biochemical electric motor with moving parts, mostly made of proteins!

A rotating flagellum is quite a remarkable piece of biochemical engineering - bioengineering!

The flagellum enables a bacterium away from harmful substances (e.g. toxins) and move towards beneficial materials like nutrients or oxygen.

As with other cells, the place of protein synthesis from decoding genetic material from chromosomes.

Other comments on prokaryotes like bacteria

Unlike eukaryotic cells, prokaryotic cells do not contain a defined nucleus nor do they contain mitochondria or chloroplasts.

(e) FUNGAL CELLS (eukaryotes)

Fungal cells share some similarities with plant and animal cells, but are different to both these groups.

Fungi include yeasts and mushrooms.

In common with plant and animal cells, fungal cells have a nucleus and contain mitochondria and have a cell membrane.

Some differences are:

fungal cells have a cell wall like plant cells,

they have no chloroplasts like animal cells, but unlike plant cells, which do have chloroplasts for photosynthesis.

(f) YEAST CELLS (eukaryotes)

Yeast is used in the production of alcoholic beverages eg beer, wine etc. and in bread making.

A yeast cell has the same organelles as a mature eukaryotic cell.

A yeast cell, a single-cell microorganism, has a nucleus, cytoplasm, mitochondria enclosed in a cell membrane which is surrounded by a cell wall.

Yeast can be regarded as a single celled fungus.

(g) A note on the structure of viruses (which are NOT classified as living organisms)

The basic structure of a virus

Viruses are not considered to be a living organism such as a plant, animal, bacteria or archaea.

Viruses are not considered to alive because they do not fulfil the seven life processes, namely: movement, respiration, sensitivity, nutrition, excretion, reproduction and growth.

Biological science uses the phrase 'strains' of virus and not species.

Viruses are the smallest agents of infectious disease and are exceedingly small (about 20 - 500 nm diameter) and essentially round in shape.

Viruses are consist of a relatively short length of genetic material (DNA or RNA) which is enclosed in a thin protein coat, which is sometimes surrounded by an extra thin fatty coating or envelope.

A typical size of a virus is about 1/50th of a red blood cell, but they can vary in size from 20 to 500 nm).

Within the protein shell the DNA/RNA nucleic acid can be single- or double stranded.

The entire infectious virus particles are unable to grow or reproduce without a host.

They have non of the usual sub-cellular structures seen in most plant or animal cells described above.

Viruses are different from all other infectious microorganisms because they are the only group of microorganisms that cannot replicate outside of a host cell.

Viruses do not consume food, but they obtain materials and energy from host cells by hijacking their host cell's cellular machinery.

Specific types of viruses only infect specific cells and persuades them to reproduce the invading virus.

Some scientists argue that they are more like complex molecules than living creatures.

Viruses are known to infect nearly every type of organism on Earth and some viruses, called bacteriophages, even infect bacteria - nothing is safe from some virus or other!

For more on virus infection mechanism see communicable diseases - pathogen infections

4.6: Specialized Internal Structures of Prokaryotes - Biology

Chapter Name and Number:

Subsections of the Chapter:

1. Biologists use microscopes and the tools of biochemistry to study cells

2. Eukaryotic cells have internal membranes that compartmentalize their functions

3. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

4. The endomembrane system regulates protein traffic and performs metabolic functions in the cell

5. Mitochondria and chloroplasts

6. The cytoskeleton is a network of fibers that organizes structures and activities in the cell

7. Extracellular components and connections between cells help coordinate cellular activities

List All Bolded Vocabulary Terms:

1. light microscope (LM)

3. electron microscope (EM)

4. scanning electron microscope (SEM)

5. transmission electron microscope (TEM)

6. cell fractionation

8. eukaryotic cell

9. prokaryotic cell

12. plasma membrane

14. nuclear envelope

15. nuclear lamina

20. endomembrane system

22. endoplasmic reticulum (ER)

25. glycoproteins

26. transport vesicles

27. Golgi apparatus

29. phagocytosis

31. food vacuoles

32. contractile vacuoles

33. central vacuole

34. mitochondria

35. chloroplasts

36. endosymbiont theory

38. mitochondrial matrix

44. cytoskeleton

45. motor proteins

46. microtubules

53. microfilaments

58. cytoplasmic streaming

59. intermediate filaments

61. primary cell well

62. middle lamella

63. secondary cell wall

64. extracellular matrix (ECM)

66. proteoglycans

69. plasmodesmata

70. tight junctions

72. gap junctions

Subsection 1 Name and Number:

6.1 Biologists use microscopes and the tools of biochemistry to study cells

Pre-reading Questions for Subsection:

1. How do stains used for light microscopy compare with those used for electron microscopy?

The staining used for electron microscopy is more digital and doesn’t involve actual dyes while the light microscopy depends on the way the light bends and reflects the color.

2. Which type of microscope would you use to study…

a. The changes in shape of a living white blood cell?

b. The details of surface texture of a hair?

Subsection 2 Name and Number:

6.2 Eukaryotic cells have internal membranes that compartmentalize their functions

Pre-reading Questions for Subsection:

1. Carefully review Figure 6.8. What are the structure and function of the nucleus, the mitochondrion, the chloroplast, and the endoplasmic reticulum?

Nucleus: Made up of the Nuclear envelope which is a protective double membrane, the nucleolus which is a nonmembranous structure involved in the production of ribosomes, and chromatin which is a material that consists of DNA and proteins.

2. Imagine an elongated cell (such as a nerve cell) that measures 125x1x1 arbitrary units. Predict how its surface-to-volume ratio would compare with those in Figure 6.7. Then calculate the ratio and check your prediction.

I suspect it would be large because it’s quite thin and should have little volume.
Total surface area: (125x1)x4+(1x1)+(1x1)=502
Total volume: 125x1x1x1=125
S-to-V ratio: 502/125=4.016

Subsection 3 Name and Number:

6.3 The eurkaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

Pre-reading Questions for Subsection:

1. What role do ribosomes play in carrying out genetic instructions?

They translate the genetic message that mRNA’s carry out from the nucleus to form specific polypeptides.

2. What is the molecular composition of nucleoli and their function?

A mass of densely stained granules and fibers that join into part of the chromatin. It is where rRNA is synthesized from instructions in the DNA and proteins imported from the cytoplasm are assembled with rRNA into large and small subunits of ribosomes.

3. As a cell begins the process of dividing, its chromatin becomes more and more condensed. Does the number of chromosomes change during this process? Explain.

No the number of chromosomes does not change because the condensed appearance is due to them coiling in preparation to split for cell division. The number is always the same but they are coiled tightly together so they are difficult to distinguish.

Subsection 4 Name and Number:

6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell

Pre-reading Questions for Subsection:

1. What are the structural and functional distinctions between rough and smooth ER?

Rough ER is studded with ribosomes while smooth ER is not. Rough ER aids in synthesis of secretory and other proteins from bound ribosomes adds carbohydrates to proteins to make glycoproteins and produces new membrane. Smooth ER is the site of the synthesis of lipids, metabolism of carbohydrates, Ca 2+ storage, and detoxification of drugs and poisons.

2. How do transport vesicles integrate the endomembrane system?

They transport things between the different parts of the endomembrane system which are not connected.

3. Imagine a protein that functions in the ER but requires modification in the Golgi apparatus before it can achieve that function. What is the protein’s path through the cell, starting with the mRNA molecule that specifies the protein?

The mRNA would be synthesized in the nucleus then pass through a pore complex of nuclear envelope into the rough ER. In the rough ER, the mRNA would combine with a ribosome to build a protein. This protein would then be encased into a transport vesicle which separates from the Rough ER and arrives at the cis face of the Golgi apparatus. The protein travels through the Golgi apparatus, is modified, and leaves in another vesicle from the trans face of the Golgi apparatus to its final destination.

Subsection 5 Name and Number:

6.5 Mitochondria and chloroplasts change energy from one form to another

Pre-reading Questions for Subsection:

1. What are two common characteristics of chloroplasts and mitochondria? Consider both function and membrane structure.

Circular DNA molecules and intermembrane space (double membrane).

2. Do plant cells have mitochondria? Explain.

Yes because the mitochondria in plant cells is what helps convert the sugar into ATP.

3. A classmate proposes that mitochondria and chloroplasts should be classified in the endomembrane system. Argue against the proposal.

The parts of the endomembrane system are related to each other either through direct physical continuity or by the transfer of membrane segments as tiny vesicles. Mitochondria and chloroplasts have their own membrane system, double in fact, and are not related to the other parts of the endomembrane system by means of physical continuity or by transferring components through creating vesicles through its membranes.

Subsection 6 Name and Number:

6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell

Pre-reading Questions for Subsection:

1. What are shared features of microtubule-based motion of flagella and microfilament-based muscle contractions?

Both have a “walking” protein that move against long filaments.

2. How do cilia and flagella bend?

Dyneins “walk” down the microtubule doublets which are bound by cross-linking proteins. The dynein walking bends the structure because the microtubules would otherwise slide against each other.

3. Males afflicted with Kartagener’s syndrome are sterile because of immotile sperm, and they tend to suffer from lung infections. This disorder has a genetic basis. Suggest what the underlying defect might be.

The DNA lacks the instructions for cells to synthesize dynein motor proteins.

Subsection 7 Name and Number:

6.7 Extracellular components and connections between cells help coordinate cellular activities

Pre-reading Questions for Subsection:

1. In what way are the cells of plants and animals structurally different from single-celled eukaryotes?

Tight junctions, desmosomes, and gap junctions connect the cells of animals and plasmodesmata connect plants cells.

2. If the plant cell wall or the animal extracellular matrix were impermeable, what effect would this have on cell function?

The cells couldn’t divide and transfer nutrients between cells and get them to various parts of the multicellular system.

3. The polypeptide chain that makes up a tight junction weaves back and forth through the membrane four times, with two extracellular loops, and one loop plus short C-terminal and N-terminal tails in the cytoplasm. Looking at Figure 5.16 (p. 79) what would you predict about the amino acid sequence of the tight junction protein?

The parts that are in the cell would be polar (hydrophilic) amino acids while the parts while the parts that go through the membrane would be nonpolar (hydrophobic).

6.1 Biologists use microscopes and the tools of biochemistry to study cells

Light microscope (LM): An optical instrument with lenses that refract (bend) visible light to magnify images of specimens.

Organelles: Any of several membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.

Electron microscope (EM): A microscope that uses magnets to focus an electron beam on or through a specimen, resulting in a practical resolution of a hundredfold greater than that of a light microscope using standard techniques.

Scanning electron microscope (SEM): A microscope that uses an electron beam to scan the surface of a sample, coated with metal atoms, to study details of its topography.

Transmission electron microscope (TEM): A microscope that passes an electron beam through very thin sections stained with metal atoms and is primarily used to study the internal ultrastructure of cells.

Cell fractionation: The disruption of a cell and separation of its parts by centrifugation at successively higher speeds.

6.2 Eukaryotic cells have internal membranes that compartmentalize their functions

Comparing Prokaryotic and Eukaryotic Cells

Cytosol: The semifluid portion of the cytoplasm.

Eukaryotic cell: A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with eukaryotic cells (protists, plants, fungi, and animals) are called eukaryotes.

Prokaryotic cell: A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with prokaryotic cells (bacteria and archaea) are called prokaryotes.

Nucleoid: A non-membrane-bounded region in a prokaryotic cell where the DNA is concentrated.

Cytoplasm: The contents of the cell bounded by the plasma membrane in eukaryotes, the portion exclusive of the nucleus.

Plasma membrane: The membrane at the boundary of every cell that acts as a selective barrier, regulating the cell’s chemical composition.

A Panoramic View of the Eukaryotic Cell

6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

The Nucleus: Information Central

Nucleus: The organelle of a eukaryotic cell that contains the genetic material in the form of chromosomes, made up of chromatin.

Nuclear envelope: In a eukaryotic cell, the double membrane that surrounds the nucleus, perforated with pores that regulate traffic with the cytoplasm. The outer membrane is continuous with the endoplasmic reticulum.

Nuclear lamina: A netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleus.

Chromosome: A cellular structure carrying genetic material, found in the nucleus of eukaryotic cells. Each chromosome consists of one very long DNA molecule and associated proteins. A bacterial chromosome usually consists of a single circular DNA molecule and associated proteins. It is found in the nucleoid region, which is not membrane bounded.

Chromatin: The complex DNA and proteins that makes up eukaryotic chromosomes. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.

Nucleolus: (plural, nucleoli) A specialized structure in the nucleus, consisting of chromosomal regions containing ribosomal RNA (rRNA) genes along with ribosomal proteins imported from the cytoplasm site of rRNA synthesis and ribosomal subunit assembly.

Ribosomes: Protein Factories

Ribosome: A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus.

6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell

Endomembrane system: The collection of membranes inside and surrounding a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles includes the plasma membrane, the nuclear envelope, the smooth and rough endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, and vacuoles.

Vesicle: A membranous sac in the cytoplasm of a eukaryotic cell.

The Endoplasmic Reticulum: Biosynthetic Factory

Endoplasmic reticulum (ER): An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions.

Smooth ER: That portion of the endoplasmic reticulum that is free of ribosomes. Smooth ER is the site of the synthesis of lipids, metabolism of carbohydrates, Ca 2+ storage, and detoxification of drugs and poisons.

Rough ER: That portion of the endoplasmic reticulum with ribosomes attached. Rough ER aids in synthesis of secretory and other proteins from bound ribosomes adds carbohydrates to proteins to make glycoproteins and produces new membrane

Functions of Smooth ER

Functions of Rough ER

Glycoprotein: A protein with one or more covalently attached carbohydrates.

Transport vesicle: A small membranous sac in a eukaryotic cell’s cytoplasm carrying molecules produced by the cell.

The Golgi Apparatus: Shipping and Receiving Center

Golgi apparatus: An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably noncellulose carbohydrates.

Lysosomes: Digestive Compartments

Lysosome: A membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protists.

Phagocytosis: A type of endocytosis in which large particulate substances or small organisms are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells).

Vacuoles: Diverse Maintenance

Vacuole: A membrane-bounded vesicle whose specialized function varies in different kinds of cells.

Food vacuole: A membranous sac formed by phagocytosis of microorganisms or particles to be used as food by the cell.

Contractile vacuole: A membranous sac that helps move excess water out of certain freshwater protists.

Central vacuole: In a mature plant cell, a large membranous sac with diverse roles in growth, storage, and sequestration of toxic substances.

The Endomembrane System: A Review

6.5 Mitochondria and chloroplasts change energy from one form to another

Mitochondria: (singular, mitochondrion) Organelles in eukaryotic cells that serve as the site of cellular respiration use oxygen to break down organic molecules and synthesize ATP.

Chloroplast: An organelle found in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water.

The Evolutionary Origins of Mitochondria and Chloroplasts

Endosymbiont theory: The theory that mitochondria and plastids, including chloroplasts, originated as prokaryotic cells engulfed by an ancestral eukaryotic cell. The engulfed cell and its host cell then evolved into a single organism.

Mitochondria: Chemical Energy Conversion

Cristae: (singular, crista) Interfolding of the inner membrane of a mitochondrion. The inner membrane houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP (ATP synthase).

Mitochondrial matrix: The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the citric acid cycle, as well as ribosomes and DNA.

Chloroplasts: Capture of Light Energy

Thylakoid: A flattened, membranous sac inside a chloroplast. Thylakoids often exist in stacks called grana that are interconnected their membranes contain molecular “machinery” used to convert light energy to chemical energy.

Granum: (plural, grana) A stack of membrane-bounded thylakoids in the chloroplast. Grana function in the light reactions of photosynthesis.

Stroma: The dense fluid within the chloroplast surrounding the thylakoid membrane and containing ribosomes and DNA involved in the synthesis of organic molecules from carbon dioxide and water.

Plastid: One of a family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts. Plastids are found in cells of photosynthetic eukaryotes.

Peroxisomes: Oxidation

Peroxisome: An organelle containing enzymes that transfer hydrogen atoms from various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H2O2).

6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell

Cytoskeleton: A network of microtubules, microfilaments, and intermediate filaments that extend throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions.

Roles of the Cytoskeleton: Support and Motility

Motor protein: A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.

Components of the Cytoskeleton

Microtubule: A hollow rod composed of tubulin proteins that makes up p art of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella.

Centrosomes and Centrioles

Centrosome: A structure present in the cytoplasm of animal cells that functions as a microtubule-organizing center and is important during cell division. A centrosome has two centrioles.

Centriole: A structure in the centrosome of an animal cell composed of a cylinder or microtubule triplets arrange in a 9 + 0 pattern. A centrosome has a pair of centrioles.

Flagella: (singular, flagellum) Long cellular appendages specialized for locomotion. Like motile cilia, eukaryotic flagella have a core with nine outer doublet microtubules and two inner single microtubules (the “9+2” arrangement) ensheathed in an extension of the plasma membrane. Prokaryotic flagella have a different structure.

Cilia: (singular, cilium) Short appendages containing microtubules in eukaryotic cells. A motile cilium is specialized for locomotion for moving fluid past the cell it is formed from a core of nine outer doublet microtubules and two inner single microtubules (the “9+2” arrangement) ensheathed in an extension of the plasma membrane. A primary cilium is usually nonmotile and plays a sensory and signaling role it lacks the two inner microtubules (the “9+0” arrangement).

Basal body: A eukaryotic cell structure consisting of a “9+0” arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.

Dynein: In cilia and flagella, a large motor protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella.

Microfilaments (Actin Filaments)

Microfilament: A cable composed of actin proteins in the cytoplasm of almost every eukaryotic cell, making up part of the cytoskeleton and acting alone or with myosin to cause cell contraction also known as an actin filament.

Actin: A globular protein that links into chains, two of which twist helically about each other, forming microfilaments (actin filaments) in muscle and other kinds of cells.

Cortex: The outer region of cytoplasm in a eukaryotic cell, lying just under the plasma membrane, that has a more gel-like consistency than the inner regions due to the presence of multiple microfilaments.

Myosin: A type of motor protein that associates into filaments that interact with actin filaments to cause cell contraction.

Pseudopodia: (singular, pseudopodium) Cellular extensions of amoeboid cells used in moving and feeding.

Cytoplasmic streaming: A circular flow of cytoplasm, involving interactions of myosin and actin filaments, that speeds the distribution of materials within cells.

Intermediate Filaments

Intermediate filament: A component of the cytoskeleton that includes filaments intermediate in size between microtubules and microfilaments.

6.7 Extracellular components and connections between cells help coordinate cellular activities

Cell Walls of Plants

Cell wall: A protective layer external to the plasma membrane in the cells of plants, prokaryotes, fungi, and some protists. Polysaccharides such as cellulose (in plants and some protists), chitin (in fungi), and peptidoglycan (in bacteria) are important structural components of cell walls.

Primary cell well: In plants, a relatively thin and flexible layer that surrounds the plasma membrane of a young cell.

Middle lamella: In plants, a thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young cells.

Secondary cell wall: In plant cells, a strong and durable matrix that is often deposited in several laminated layers around the plasma membrane and provides protection and support.

The Extracellular Matrix (ECM) of Animal Cells

Extracellular matrix (ECM): The meshwork surrounding animal cells, consisting of glycolproteins, polysaccharides, and proteoglycans synthesized and secreted by the cells.

Collagen: A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone the most abundant protein in the animal kingdom.

Proteoglycan: A large molecule consisting of a small core protein with many carbohydrate chains attached, found in the extracellular matrix of animal cells. A proteoglycan may consist of up to 95% carbohydrate.

Fibronectin: An extracellular glycoprotein secreted by animal cells that helps them attach to the extracellular matrix.

Integrin: In animal cells, a transmembrane receptor protein with two subunits that interconnects the extracellular matrix and the cytoskeleton.

Plasmodesmata in Plant Cells

Plasmodesmata: (singular, plasmodesma) Open channels through the cell wall that connect the cytoplasm of adjacent plant cells, allowing water, small solutes, and some larger molecules to pass between the cells.

Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells

Tight junction: A type of intercellular junction between animal cells that prevents the leakage of material through the space between cells.

Desmosome: A type of intercellular junction in animal cells that functions as a rivet, fastening cells together.

Gap junction: A type of intercellular junction in animal cells, consisting of proteins surrounding a pore that allows the passage of materials between cells.

MasteringBiology Quiz results:

Review of Subsection 1:

How do microscopy and biochemistry complement each other to reveal cell structure and function?

Cell fractionation allows biologists to identify enzymes that are not able to be seen under the microscope, while microscopy allows biologists to see what is going on in the cell and correlate biochemistry’s findings to where in the cell the enzymes are.

Review of Subsection 2:

How does the compartmental organization of a eukaryotic cell contribute to its biochemical functioning?

Organelles that interact with each other regularly have located in proximity with each other or have means to reach one another.

Review of Subsection 3:

What is the relationship between the nucleus and ribosomes?

The nucleolus in the nucleus contains DNA which provides instructions for the synthesis of rRNA which combines with proteins imported from the cytoplasm to form into large and small subunits of ribosomes. Once the subunits exit the nucleus to cytoplasm, they are assembled into a ribosome.

Review of Subsection 4:

What is the key role played by transport vesicles in the endomembrane system?

They transport molecules between certain organelles in the cell.

Review of Subsection 5:

What is the endosymbiont theory?

Mitochondria were once oxygen using non-photosynthetic prokaryotes that were engulfed by a eukaryote cell. And later on the chloroplast came about by a eukaryotic cell engulfing a photosynthetic prokaryote. Over evolutionary time, the prokaryotes became organelles of the cell.

Review of Subsection 6:

How many microtubules are in a centrosome?

What is the role of motor proteins inside the eukaryotic cell and in whole-cell movement?

Motor proteins interact with the cytoskeleton to allow organelles to move around the cell. Dyneins, which are a type of motor protein, “walks” along microtubules in flagella and cilia and creates a bend in the microtubule which then turns into the wavelike motion of flagella/cilia.

Review of Subsection 7:

Refer to Figure 6.29. What if in a second experiment, the researchers exposed the plant cells to blue light, previously shown to cause reorientation of microtubules. What events would you predict would follow blue light exposure?

The microtubules would reorient and the cellulose synthase would follow.

Compare the composition and functions of a plant cell wall and the extracellular matrix of an animal cell.

A plant cell wall is composed of microfibrils made of cellulose which are synthesized by an enzyme called cellulose synthase and secreted to the extracellular space, where they become embedded in a matrix of other polysaccharides and proteins. The function of a plan cell wall is to provide structure and hold the plant up[ against the force of gravity. The extracellular matrix of an animal cell is composed of glycoproteins, such as collagen, and other carbohydrate-containing molecules secreted by the cells and its purpose is to regulate a cell’s behavior.


1. Which structure is not part of the endomembrane system?

a. Nuclear envelope

b. Chloroplast

c. Golgi apparatus

d. Plasma membrane

2. Which structure is common to plant and animal cells?

b. Wall made of cellulose

c. Central vacuole

d. Mitochondrion

3. Which of the following is present in a prokaryotic cell?

a. Mitochondrion

b. Ribosome

c. Nuclear envelope

4. Which structure-function pair is mismatched?

a. Nucleolus production of ribosomal subunits

b. Lysosome intracellular digestion

c. Ribosome protein synthesis

d. Golgi protein trafficking

e. Microtubule muscle contraction


5. Cyanide binds to at least one molecule involved in producing ATP. If a cell is exposed to cyanide, most of the cyanide will be found within the…

a. Mitochondria

e. Endoplasmic reticulum

6. What is the most likely pathway taken by a newly synthesized protein that will be secreted by a cell?

a. ER → Golgi → nucleus

b. Golgi → ER → lysosome

c. Nucleus → ER → Golgi

d. ER → Golgi → vesicles that fuse with plasma membrane

e. ER → lysosomes → vesicles that fuse with plasma membrane

7. Which cell would be best for studying lysosomes?

c. Phagocytic white blood cell

d. Leaf cell of a plant

e. Bacterial cell

8. DRAW IT: From memory, draw two eukaryotic cells, labeling the structures listed here and showing any physical connections between the internal structures of each cell: nucleus, rough ER, smooth ER, mitochondrion, centrosome, chloroplast, vacuole, lysosome, microtubule, cell wall, ECM, microfilament, Golgi apparatus, intermediate filament, plasma membrane, peroxisome, ribosome, nucleolus, nuclear pore, vesicle, flagellum, microvilli, plasmodesma.


9. EVOLUTION CONNECTION: Which aspects of cell structure best reveal evolutionary unity? What are some examples of specialized modifications?

10. SCIENTIFIC INQUIRY: Imagine protein X, destined to span the plasma membrane. Assume that the mRNA carrying the genetic message for protein X has already been translated by ribosomes in a cell culture. If you fractionate the cells (see Figure 6.4), in which fraction would you find protein X? Explain by describing its transit through the cell.

1000g because ribosomes that are attached to the nuclear envelope and ER are the ones that translated proteins that are going to be transported to the plasma membrane.

11. WRITE ABOUT A THEME: Emergent Properties. Considering some of the characteristics that define life and drawing on your new knowledge of cellular structures and functions, write a short essay (100-150 words) that discusses this statement: Life is an emergent property that appears at the level of the cell. (Review pp. 3-5 in Chapter 1.)


Our editors will review what you’ve submitted and determine whether to revise the article.

Thermoplasma, (genus Thermoplasma), any of a group of prokaryotic organisms (organisms whose cells lack a defined nucleus) in the domain Archaea that are noted for their ability to thrive in hot, acidic environments. The genus name is derived from the Greek thermē and plasma, meaning “warmth” (or “heat”) and “formative substance,” respectively, which describe the thermophilic (heat-loving) nature of these organisms.

Thermoplasma are members of class Thermoplasmata (subdivision Euryarchaeota) and are characterized as chemoorganotrophs (organisms that derive energy from organic compounds). They are capable of both aerobic and anaerobic metabolism. Their survival in anaerobic habitats is dependent on sulfur respiration, a form of chemolithotrophic metabolism in which carbon and energy are obtained from the reaction of sulfur with organic compounds. Sulfur respiration is an evolutionary adaptation that enables Thermoplasma to thrive in hot sulfur-producing environments, specifically naturally occurring solfataras (sulfur-releasing volcanic steam vents). The organisms also occur in heat-generating coal refuse sites, which produce sulfuric acid via oxidation of pyrite wastes from coal-mining operations. Thermoplasma growth typically requires a pH range of 0.8 to 4.0 and a temperature range of approximately 45 to 60 °C (113 to 140 °F) optimal growth has been reported at pH 1–2 and 59 °C (about 138 °F).

Two species of Thermoplasma have been described: T. acidophilum, discovered in coal refuse and first reported in 1970, and T. volcanium, initially discovered in solfataric fields on Vulcano Island, Italy, and reported in 1988. Similar to other archaea, these organisms lack a cell wall and instead possess a specialized cell membrane made up of ether-linked molecules of glycerol and fatty acids. In Thermoplasma this structure is uniquely adapted to the stress of living in acidic, hot, high-salt habitats.

Chromosomes, Prokaryotic

The genetic material of microorganisms , be they prokaryotic or eukaryotic, is arranged in an organized fashion. The arrangement in both cases is referred to as a chromosome.

The chromosomes of prokaryotic microorganisms are different from that of eukaryotic microorganisms, such as yeast , in terms of the organization and arrangement of the genetic material. Prokaryotic DNA tends to be more closely packed together, in terms of the stretches that actually code for something, than is the DNA of eukaryotic cells. Also, the shape of the chromosome differs between many prokaryotes and eukaryotes . For example, the deoxyribonucleic acid of yeast (a eukaryotic microorganism) is arranged in a number of linear arms, which are known as chromosomes. In contrast, bacteria (the prototypical prokaryotic microorganism) lack chromosomes. Rather, in many bacteria the DNA is arranged in a circle.

The chromosomal material of viruses is can adopt different structures. Viral nucleic acid, whether DNA or ribonucleic acid (RNA ) tends to adopt the circular arrangement when packaged inside the virus particle. Different types of virus can have different arrangements of the nucleic acid. However, viral DNA can behave differently inside the host, where it might remain autonomous or integrating into the host's nucleic acid. The changing behavior of the viral chromosome makes it more suitable to a separate discussion.

The circular arrangement of DNA was the first form discovered in bacteria. Indeed, for many years after this discovery the idea of any other arrangement of bacterial DNA was not seriously entertained. In bacteria, the circular bacterial chromosome consists of the double helix of DNA. Thus, the two strands of DNA are intertwined while at the same time being oriented in a circle. The circular arrangement of the DNA allows for the replication of the genetic material. Typically, the copying of both strands of DNA begins at a certain point, which is called the origin of replication. From this point, the replication of one strand of DNA proceeds in one direction, while the replication of the other strand proceeds in the opposite direction. Each newly made strand also helically coils around the template strand. The effect is to generate two new circles, each consisting of the intertwined double helix.

The circular arrangement of the so-called chromosomal DNA is mimicked by plasmids . Plasmids exist in the cytoplasm and are not part of the chromosome. The DNA of plasmids tends to be coiled extremely tightly, much more so than the chromosomal DNA. This feature of plasmid DNA is often described as supercoiling. Depending of the type of plasmid, replication may involve integration into the bacterial chromosome or can be independent. Those that replicate independently are considered to be minichromosomes.

Plasmids allow the genes they harbor to be transferred from bacterium to bacterium quickly. Often, such genes encode proteins that are involved in resistance to antibacterial agents or other compounds that are a threat to bacterial survival, or proteins that aid the bacteria in establishing an infection (such as a toxin).

The circular arrangement of bacterial DNA was first demonstrated by electron microscopy of Escherichia coli and Bacillus subtilus bacteria in which the DNA had been delicately released from the bacteria. The microscopic images clearly established the circular nature of the released DNA. In the aftermath of these experiments, the assumption was that the bacterial chromosome consisted of one large circle of DNA. However, since these experiments, some bacteria have been found to have a number of circular pieces of DNA, and even to have linear chromosomes and sometimes even linear plasmids. Examples of bacteria with more than one circular piece of DNA include Brucella species, Deinococcus radiodurans, Leptospira interrogans, Paracoccus denitrificans, Rhodobacter sphaerodes, and Vibrio species. Examples of bacteria with linear forms of chromosomal DNA are Agrobacterium tumefaciens, Streptomyces species, and Borrelia species.

The linear arrangement of the bacterial chromosome was not discovered until the late 1970s, and was not definitively proven until the advent of the technique of pulsed field gel electrophoresis a decade later. The first bacterium shown to possess a linear chromosome was Borrelia burgdorferi.

The linear chromosomes of bacteria are similar to those of eukaryotes such as yeast in that they have specialized regions of DNA at the end of each double strand of DNA. These regions are known as telomeres, and serve as boundaries to bracket the coding stretches of DNA. Telomeres also retard the double strands of DNA from uncoiling by essentially pinning the ends of each strand together with the complimentary strand.

There are two types of telomeres in bacteria. One type is called a hairpin telomere. As its name implies, the telomers bends around from the end of one DNA strand to the end of the complimentary strand. The other type of telomere is known as an invertron telomere. This type acts to allow an overlap between the ends of the complimentary DNA strands.

Replication of a linear bacterial chromosome proceeds from one end, much like the operation of a zipper. As replication moves down the double helix, two tails of the daughter double helices form behind the point of replication.

Research on bacterial chromosome structure and function has tended to focus on Escherichia coli as the model microorganism. This bacterium is an excellent system for such studies. However, as the diversity of bacterial life has become more apparent in beginning in the 1970s, the limitations of extrapolating the findings from the Escherichia coli chromosome to bacteria in general has also more apparent. Very little is known, for example, of the chromosome structure of the Archae, the primitive life forms that share features with prokaryotes and eukaryotes, and of those bacteria that can live in environments previously thought to be completely inhospitable for bacterial growth .

See also Genetic identification of microorganisms Genetic regulation of prokaryotic cells Microbial genetics Viral genetics Yeast genetics

A New Catalog

“Historically, people have known about compartments in bacterial cells that carry out specific functions for a long, long time, going back to the 1800s,” said Arash Komeili, a microbiologist at the University of California, Berkeley. Yet, while eukaryotic organelles have been studied in great detail for many decades, it has only recently become possible to do so in prokaryotes. Bacteria are tiny: orders of magnitude smaller than typical eukaryotic cells, and sometimes even smaller than eukaryotes’ organelles. That made it extremely difficult to isolate and analyze bacterial compartments to get a sense of what they were — and what they were doing. (Archaea, which were only recognized as a distinct prokaryotic kingdom in the 1970s, have received even less scrutiny than bacteria.) Better imaging techniques eventually started to make such research easier.

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An electron micrograph of the bacterium Magnetospirillum magneticum (top) reveals the chain of magnetosomes it uses to navigate. A lipid membrane surrounds each magnetic particle (closeups at bottom). These structures, which are among the best-studied prokaryotic organelles, allow the bacterium to navigate through its aquatic environment.

Among the best studied of the bacterial organelles are the magnetosomes, round structures that build magnetic particles within their lipid bilayer membranes. The organelles allow aquatic “magnetotactic” bacteria to navigate vertically along the Earth’s magnetic fields toward the low-oxygen depths in which they thrive. Komeili and his colleagues have been identifying the genes and proteins involved in how magnetosomes are built, maintained and later divided among cellular offspring.

“On a superficial level,” Komeili said, “a lot of those activities, and even the way they look, are reminiscent of the ways that eukaryotic cells build organelles.” At the very least, their function parallels the ability of some animals, including salmon and homing pigeons, to detect magnetic fields — and in a paper published in April, researchers reported that one species of protist achieved this through a symbiotic relationship with magnetotactic bacteria.

But magnetosomes are not alone. Scientists have stumbled on a plethora of other bizarre bacterial compartments, often while searching for something else. Although many of these might not be considered organelles by the strictest definitions — organelles have to be lipid-bound structures completely separated from the cell membrane — some of them do fit the bill.

Tantalizing examples appear in a group of oval-shaped aquatic bacteria known as planctomycetes. Some species of planctomycetes contain a membrane-bound organelle called an anammoxosome, which sequesters a chemical reaction that produces nitrogen along with toxic intermediaries. Anammoxosomes act like energy factories for the bacteria, much as mitochondria do in eukaryotes, though anammoxosomes do not seem to be remnants of symbionts as mitochondria are.

Another kind of planctomycete has been a source of controversy for years. A couple of decades ago, two-dimensional imaging by Fuerst and others seemed to indicate that the DNA of the bacterium Gemmata obscuriglobus was surrounded by a membrane, instantly raising comparisons to the eukaryotic nucleus. Those results have been called into question — imaging seems to indicate that the compartment isn’t entirely closed, meaning it does not satisfy the definition of an organelle — but experts remain excited about these bacteria. They have the most complex internal membrane system seen in prokaryotes to date, and they contain proteins that structurally resemble those that shape and maintain eukaryotic membranes. They also seem capable of processes that were thought to be unique to eukaryotes, such as digesting nutrients inside their cells and synthesizing molecules called sterols.

“The problem is, we basically don’t know anything about [this membrane system],” said Damien Devos, a microbiologist at the Andalusian Center for Developmental Biology in Spain who studies planctomycetes. “We still have a very, very limited view on what it does, how it does it, and what are the molecules involved.”

Bacteria also seem to have a wide variety of enclosed structures that are bound not by a lipid membrane but by a protein coat. Take carboxysomes, which evolved in bacteria twice, independently, to fix carbon. They and smaller, self-assembling nanocompartments have a polyhedral structure that looks shockingly like a viral capsid, the protein shell that encloses viral genomic material.

The catalog keeps getting longer: Komeili and his colleagues recently discovered a new lipid-bound organelle that accumulates iron, which they’ve dubbed the ferrosome. Bacteria seem to have a cornucopia of such organelles, with more waiting to be discovered. Scientists are now starting to explore what that means in the context of eukaryotic evolution. They hope either to establish direct evolutionary relationships among the growing list of structures, or to pinpoint factors that are unique and necessary for compartmentalization and complexity.


Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure 1) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.

Figure 1 This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the inner and outer membranes, the cristae, and the mitochondrial matrix. (credit: modification of work by Matthew Britton scale-bar data from Matt Russell)

Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. Carbon dioxide (CO2), water, and light energy are used to make glucose and oxygen in photosynthesis. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure 2). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

Figure 2 This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and stroma.

The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.

Theory of Endosymbiosis

We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.

How did complex life evolve? The answer could be inside out

A new idea about the origin of complex life turns current theories inside out. In the open access journal BMC Biology, cousins Buzz and David Baum explain their ‘inside-out’ theory of how eukaryotic cells, which all multicellular life - including us - are formed of, might have evolved.

Scientists have long pondered the question of how simple “prokaryotic” cells, like bacteria, which are little more than a membrane-bound sack, evolved into more complex eukaryotic cells, which contain numerous internal membrane compartments. These compartments include the nucleus, which holds genetic information in the form of DNA the endoplasmic reticulum, which shunts proteins and lipids around the cell and mitochondria which act as the cell’s powerhouse. The mitochondria also contain their own distinct DNA, which is one good indicator of their once having been separate organisms. The trouble is that no one has identified eukaryotic cells that are intermediate in complexity, making it much harder to know how they evolved.

At present, the most widely accepted theory is that mitochondria derive from a bacterium that was engulfed by an archaeon (plural = archaea), a kind of prokaryote that looks similar to a bacterium but has many molecular differences. The eukaryotic membrane systems, including the nuclear envelope, then formed within the boundaries of this archaeal cell through the invagination of the outer membrane. This fits with much current data, but a few problems remain. Most significantly, no archaeal cells are known that invaginate membranes.

Furthermore, it seems unlikely that mitochondria were engulfed since engulfing food requires a lot of energy, which in eukaryotes is provided by mitochondria, and engulfment likely also requires mitochondrial-derived lipids.

David Baum, University of Wisconsin, says: “All agree that eukaryotes arose from a symbiotic relationship between two cell types: bacteria that became mitochondria and a host cell, archaea, or a close relative of archaea that became the cytoplasm and nucleus. This symbiosis explains the origin of mitochondria, but what about other eukaryotic structures, most notably the nucleus?”

The Baums’ inside-out theory provides a gradual path by which eukaryotic cells could have evolved. The first stage began with a bacterial cell whose outer membrane forms protrusions, which the Baums call ‘blebs’ that reached out from the cell. These protrusions trapped free-living mitochondria-like bacteria between them. Using the energy gained from being in close contact with bacteria (and using bacterial-derived lipids), cells were able to get bigger and expand the size of their blebs.

The sides of the blebs formed the endoplasmic reticulum and their inner surfaces formed the outer membrane of the nucleus, with the original outer membrane of the archaeon becoming what we now call the inner nuclear membrane. Finally, the fusion of blebs with one another led to the formation of the plasma membrane. The result was the eukaryotic cell as we now know it. This inside-out theory is explained in more detail using a diagram in the research article (see Figure 1).

David Baum explains the differences between the outside-in and inside-out theories using a metaphor: “A prokaryotic cell can be thought of as a factory composed of one large, open building in which managers, machinists, mail clerks, janitors, etc. all work side by side. In contrast, a eukaryotic cell is like a factory complex, composed of a several connected work spaces: a single control room and specialize rooms for receiving, manufacturing, shipping, waste disposal, etc. The traditional theories propose that the factory complex arose when partitions were built within a single hangar-like building. The inside-out theory, in contrast, imagines that a series of extensions were added around an original core building - now the control room - while others functions moved out into new, specialized quarters.”

The inside-out theory is radically different from all existing theories because the action in building the eukaryotic cell is outside the boundaries of the ancestral cell. As David Baum, who came up with an outline of the model 30 years ago, when still an undergraduate, noted: “The inside-out model ought to be an obvious alternative to the outside-in models, but maybe you have to be a naive undergraduate to consider such an inverted perspective.”

We can’t know how these very early evolutionary steps occurred, but we can look at current processes for inspiration. The Baums use some examples of modern archaea that produce bleb-like protrusions to support the credibility of their ideas, and draw on many common features of eukaryotes that are easily explained by the inside-out model.

Like any good scientific theory, the inside-out model leads to predictions that can be tested in modern cells. The Baums hope, therefore, that their theory will stimulate empirical research, since there is still a lot that it not known about the biology of prokaryotic and eukaryotic cells.

Commenting on the inside-out theory Miranda Robertson, Editor of BMC Biology, says: “Not everyone is going to be convinced by this theory – any reconstruction of events in a past as far distant as the origin of eukaryotes is going to have areas of uncertainty which it would be futile to try and fill in. But a theory doesn’t have to be right to be useful, if it provokes people to think. And to test it.”

Buzz Baum, University College London, says: “Even if the hypothesis or parts of it are refuted, we are optimistic that the effort to evaluate it will spawn new cell biological discoveries and, in so doing, will improve our understanding of biology of eukaryotic cells as they grow and divide. Although students studying cell biology may come to think that it’s too late for them to contribute to a field where almost everything is known, this simply isn’t the case. As the model helps to make clear, there is still much to be discovered about the basic logic of eukaryotic cell organisation."

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Notes to Editor

1. Research
An inside-out origin for the eukaryotic cell
David A Baum and Buzz Baum
BMC Biology 2014, 12:76

A copy of the article is available at journal website here

Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.

2. BMC Biology is the flagship biology journal of the BMC series, publishing peer-reviewed research and methodology articles of special importance and broad interest in any area of biology, as well as commissioned reviews, opinion pieces, comment and Q&As on topics of special or topical interest.

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