Chapter 3 Prokaryotic Profiles: The Bacteria and Archaea

Prokaryotes are unicellular organisms without a cell nucleus, or indeed any other membrane-bound organelles, which are of micro individual, plain morphology and low evolution status, and which include eubacteria and archaea. In this chapter, morphologies, chemical composition and cytoarchitecture of bacteria, Gram staining, cytoplasm and inclusion, forming and heat resisting mechanism of spores, and the structures and function of accessory organelles of bacterial cells, such as flagellum, capsule and pilus etc., are introduced firstly. Then, based on those, morphologies, structures and biological characteristics of several special eubacteria, such as actinomycete, cyanobacteria, mycoplasma, nickettsia, chalamydia and spirochete, are also recommended. Having special gene structures or phylogenies biomacromolecule order, archaea are briefly presented from three aspects of their characteristics, major groups and life biogenesis. At last, basic knowledge of bacterial taxonomy is introduced.    

prokaryotic cells

The chief distinguishing characteristics of procaryotic cells are：

1. genetic material （DNA） is not enclosed within a membrane.

2. They lack other membrane bounded organelles.

3. Their DNA is not associated with histone proteins （special chromosomal proteins found in eucaryotes）.

4. Their cell walls almost always contain the complex polysaccharide peptidoglycan（肽聚糖）。Bacteria（细菌） and archaeobacteria（古细菌）

Bacteria are small, single-celled, microorganisms that belong to a group called prokaryotes. Bacteria are ubiquitous. They are a highly successful and diverse group of organisms that can obtain energy and carbon from a wide range of sources and therefore can colonize every niche on our planet from deep ocean trenches to volcanic craters. In the 1970s， using DNA sequencing information， it was found that the group we know as the bacteria could be split into two， the eubacteria and the archaeobacteria and it appears that these two groups evolved away from each other very early in the history of living things at about the same time that the first group of eukaryotic cells evolved. Members of the eubacteria include some of the more familiar bacteria such as Escherichia coli（大肠埃希氏菌）and Staphylococcus aureus（金黄色葡萄球菌） and are the prokaryotes that are best studied and understood. The archaebacteria are a very diverse group of organisms， which differ from the eubacteria（真细菌） in a number of features having， in particular， very different cell walls and membranes. This group includes bacteria that are capable of existing in extreme environments.

Size， Shape， and Arrangement of Bacterial Cells

1 Most bacteria are from 0.20 to 2.0 /μm in diameter and from 2 to 8μm in length.

2 The three basic bacterial shapes are coccus（spheres）， bacillus（rods），and spiral （twisted）。

3 In addition to the three basic shapes， there are star-shaped cells （genus Stella） and recently discovered square， flat cells （halophilic（嗜盐的） archaeobacteria） and triangular cells （Haloarcula）

4 the shape of a bacterium is determined by heredity.However， a number of environmental conditions can alter that shape.Pleomorphic（多型性的） bacteria can assume several shapes.

Gram Stain：

The eubacteria are frequently divided into two groups on the basis of their reaction to a stain devised by Christian Cram in 1884. The differential reaction to the staining procedure is because of the structure of the cell wall in these two groups of bacteria. Gram-positive bacteria have a single membrane called the cytoplasmic （or plasma） membrane， surrounded by a thick layer of peptidoglycan （20-80 nm）。 The Gram-negative bacteria have only a thin layer of peptidoglycan （1-3 nm） but on the outside of this there is a further outer membrane which acts as an additional barrier.

The procedure for the Gram stain is as follows. Fixed cells are stained with a dark stain such as crystal violet， followed by iodine which complexes with the stain in the cell wall of the bacteria. Alcohol is added， which washes the dark stain of crystal violet-iodine out of ceils that have thin cell walls but not from those that have thick cell walls. Finally， a paler stain such as carbol fuschin， called a counter stain， is added which stains the decolorized cells pink but is not seen on the dark staining cells that retained the first stain. The cells that retain the stain （with thick cell walls） are called Gram-positive and appear dark purple under light microscopy. The ones that lose the stain （with thin cell walls and an outer membrane） are called Gram-negative and stain pink or pale purple.

一、The Cell Wall

1. The cell wall surrounds the plasma membrane and protects the cell from changes in osmotic pressure（渗透压）and provides rigidity and strength.

2. The bacterial cell wall consists of peptidoglycan（肽聚糖）, a polymer consisting of NAG and NAM and short chains of amino acids.

3. Gram-positive（革兰氏阳性） cell walls consist of many layers of peptidoglycan and also contain teichoic acids（垣酸）.

4. Gram-negative（革兰氏阴性）bacteria have a lipidprotein-lipopolysaccharide-phospholipid outer membrane surrounding a thin peptidoglycan layer.

5. The outer membrane protects the cell from phagocytosis and penicillin（青霉素）， lysozyme（溶菌酶）, and other chemicals.

6. Porins（孔蛋白）are proteins that permit small molecules to pass through the outer membrane; specific channel proteins allow other molecules to move through the outer membrane.

7. The lipopolysaccharide（脂多糖，LPS） component of the outer membrane consists of sugars that function as antigens and lipid A， which is an endotoxin（内毒素）。

teichoic acid：

Gram-positive cell walls also contain large amounts of another polymer， called teichoic acid， made up of glycerol or ribitol joined by phosphate groups. D-Ala， glucose or sugars may be attached to the glycerol or ribitol and the poly-mers are attached either directly to the NAM in the peptidoglycan or to lipids in the membrane （in this case they are called lipoteichoic acids）。 The function of these molecules is unclear but they may have a role in maintaining the structure of the cell wall and in the control of autolysis.

periplasmic space（周质空间）

The outer membrane of Gram-negative bacteria acts as an additional barrier protecting the peptidoglycan from toxic compounds such as lysozyme which act on the cell wall. It creates an aqueous space between the two membranes called the periplasmic space which is thought to have a gel-like structure with a loose network of peptidoglycan running through it. Estimates as to the width of the peptidoglycan vary from 1-71 nm but it has proved to be difficult to obtain a real definitive value. The periplasmic space contains a range of proteins associated with：

(1) transport of nutrients into the cell；

(2) enzymes that are involved in nutrient acquisition such as proteases；

(3) enzymes that defend the cell against toxic chemicals such as в-lactamases that destroy penicillin.

outer membrane

The outer membrane of Gram-negative bacteria is made up of phospholipids membrane，but it also contains some unique features

1. Pores formed by proteins called porins such as OmpF and OmpC that allow the passive diffusion of small molecules into the periplasmic space.

2. An abundant small lipoprotein called Braun's lipoprotein that is covalentlybound to the peptidoglycan and is embedded in the outer membrane by it shydrophobic lipid， therefore holding the peptidoglycan and outer membraneclose together.

3. LPS molecules are found in the outer leaflet of the outer membrane projecting into the surrounding medium.

Atypical（缺陷的） cell walls

Atypical（缺陷的） cell walls

1. Mycoplasma（支原体） is a bacterial genus that naturally lacks cell walls.

2. Archaeobacteria have pseudomurein（假肽聚糖）； they lack peptidoglycan.

3. .l forms are mutant bacteria with defective cell walls.

Archaeobacterial cell walls

One of the distinctive features of archaebacteria is the nature of the lipids in the plasma membrane which， unlike the ester-linked lipids of eubacteria and eukaryotes are ether-linked to glycerol. They are also long chained and branched. Archaebacterial cell walls and envelopes show great diversity and complexity in structure. They do not contain peptidoglycan although some do have a similar compound called pseudomurein which contains N-acetyl-alosaminuronic acid in place of muramic acid. Another common type of cell wall is the S-layer， a two-dimensional， paracrystalline， array of protein or glycoprotein on the cell surface. Others have thick polysaccharide walls outside their plasma membrane.

一、DAMAGE TO THE CELL WALL

peptidoglycan used to be a target for antimicrobial agents that destroy prokaryotic cells specifically， but do not harm eukaryotic cells； an example of this is the antibiotic penicillin （Topic F7）。 Lysozyme， a natural antibacterial agent found in tears and natural secretions， breaks down the linkage between NAM and NAG. Removal of the cell wall under conditions where the osmolarity of the medium is the same as the inside of the cell （isotonic solution） results in the formation of round protoplasts（原生质体）（Gram-positives）or spheroplasts（球形体） （Gram-negatives） which survive as long as the isotonicity is maintained. These structures lyse， however， if placed in a dilute medium， illustrating the importance of peptidoglycan to the cells' survival.

1. In the presence of lysozyme， gram-positive cell walls are destroyed and the remaining cellular contents are referred to as a protoplast.

2. In the presence of lysozyme， gram-negative cell walls are not completely destroyed and the remaining cellular contents are referred to as a spheroplast.

3. Protoplasts and spheroplasts are subject to osmotic lysis.

4. Antibiotics such as penicillin interfere with cell wall synthesis.

二、PLASMA （CYTOPLASMIC） MEMBRANE

1 The plasma membrane encloses the cytoplasm and is a phospholipid bilayer with protein （fluid mosaic）

2 most of bacteria lack of steriol（固醇）

3 The plasma membrane is selectively permeable.

4 Plasma membranes carry enzymes for metabolic reactions， such as nutrient breakdown， energy production， and photosynthesis.

5 Mesosomes—irregular infoldings of the plasma membrane—are now considered artifacts

6 .Plasma membranes can be destroyed by alcohols and polymyxin.

三、CYTOPLASM（细胞质）

1 Cytoplasm is the fluid component inside the plasma membrane.

2 The cytoplasm is mostly water， with inorganic and organic molecules， DNA， ribosomes， and inclusions.

四、RIBOSOMES

1 The cytoplasm of a procaryote contains numerous 70S ribosomes； ribosomes consist of rRNA and protein.

2 Protein synthesis occurs at ribosomes； this can be inhibited by certain antibiotics.

五、INCLUSIONS

1 Inclusions（内含物） are reserve deposits found in procaryotic and eucaryotic cells.

2 Among the inclusions found in bacteria are metachromatic granules（异染粒） （inorganic phosphate）， polysaccharide granules （，多糖，usually glycogen or starch）， lipid inclusions（脂滴），sulfur granules（硫粒）， carboxysomes （，羧酶体，ribulose 1，5-diphosphate carboxylase）， and gas vacuoles（气泡）。

六、NUCLEAR AREA

The nuclear area contains the DNA of the bacterial chromosome. Bacteria can also contain plasmids， which are extrachromosomal DNA circles.

FLAGELLA

1. Flagella（鞭毛） are relatively long filamentous appendages consisting of a filament， hook， and basal body.

2. Procaryotic flagella rotate to push the cell.Motile（运动）。

3. bacteria exhibit taxis（趋性）—positive taxis is movement toward an attractant and negative taxis is movementaway from a repellent.

FIMBRIAE AND PILIF

1. fimbriae（菌毛） and pili（性毛） are short， thin appendages.

2. Fimbriae help cells adhere to surfaces.

3. Pili join cells for the transfer of DNA from one cell to another.

ENDOSPORES（芽孢）

1. Endospores are resting structures formed by some bacteria for survival during adverse environmental conditions.

2. The process of endospore formation is called sporulation； the return of an endospore to its vegetative state iscalled germination.

Endospores are a method as survival， not one of reproduction. Certain bacteria will form a spore within their cell membrane （an endospore） that allows them to wait out deteriorating environmental conditions. Certain disease causing bacteria （such as the one that causes the disease Anthrax） can be virulent （capable of causing an infection） 1300 years after forming their endospore！

BACTERIAL DIVISION

1. The normal reproductive method of bacteria is binary fission， in which a single cell divides into two identical cells.

2. Some bacteria reproduce by budding.， aerial spore formation， or fragmentation.

binary fission（二分裂）

The method by which bacteria reproduce. The circular DNA molecule is replicated； then the cell splits into two identical cells， each containing an exact copy of the original cell's DNA.

Rickttsias ， chlamydias and mycoplasmas

The rickttsias（立克次氏体） and chlamydias（衣原体） are gram-negative obligate intracellular parasites that key metabolic enzymes.

The rickettsias are extremely small， pleomorphic rods or coccobacilli that cannot synthessiz their own ATP. Most have a complex life-style that cyces between arthropod vectors and vertebrate hosts.

The rickettsias are ususlly transmitted by tickor tick feces.

The chlamydias are small， gram-negative， pleomorphic， intracellular parasites that have no catabolic pathways. They exist in two forms： the elementary body， which is the form transmitted between human hosts through direct contact and body secretions， and the reticulate body， which multiplies intracellularly.

Chlamydia trachomatis（沙眼衣原体） is the agent of several STDs： NGU （nongonococcal urethritis），pelvic inflammatory disease， and lymphogranuloma venereum. It also causes ocular trachoma， a serious eye infection.

Chlamydia pneumoniae（肺炎衣原体） is the agent of respiratory infections in young adults and asthmatics.

Chlamydia psittaci（鹦鹉热衣原体） is the agent of ornithosis， an influenza-like disease carried by birds that has serious systemic complications if untreated. Antibiotic therapy is usually successful.

Mycoplasmas（支原体） are tiny pleomorphic bacteria that lack a cell wall. Although most species are parasitic， mycoplasmas can be cultured on complex artificial media. They are considered membrane parasites because they bind tightly to epithelial linings of the respiratory and urogenital tracts.

Mycoplasma pneumoniae（肺炎支原体） is the agent of primary atypical pneumonia （walking pneumonia）。

M. hominis（人型支原体） and M. urealyticum（脲支原体） are agents of sexually transmitted infections of the reproductive tract and kidneys， and more recently， of fetal infections.

M. incognitos is a recently identified pathogen that causes systemic infection by suppressing the immune system.

Review questions:

1. List three differences between procaryotic and eucaryotic cells.

2. Match the structures to their functions.

Cell wall; Endospore; Fimbriae; Flagella; caupsle; Plasma membrane; Ribosome  

A：Protection from osmotic lysis; B： Attachment; C： Protection from phagocytes; D： Resting; E： Protein synthesis; F： Selectively permeable; G： Transfer of genetic material material

3. Why is an endospore called a resting structure？ Of what advantage is an endospore to a bacterial cell？

4. Why can procaryotic cells be smaller than eucaryotic cells and still carry on all the functions for life？

5. Two types of procaryotic cells have been distinguished： eubacterial and archaeobacterial. How do these cells differ from each other？ How are they similar？

6. What is the evolutionary advantage of the monolayer often found in Archaeal membranes？

7. The endospore is a highly resistant differentiated bacterial cell produced by certain types of Gram-positive Bacteria. Spore formation leads to a nearly dehydrated spore core that contains essential macromolecules and a variety of substances， such as calcium dipicolinate and small acid-soluble proteins， absent from vegetative cells. Spores can remain dormant indefinitely but germinate quickly when the appropriate trigger is applied.

●What is dipicolinic acid, and where is it found？

●What are SASPs, and what are their functions？

●What happens when an endospore germinates？

8. In addition to peptidoglycan, Gram-negative Bacteria contain an outer membrane consisting of lipopolysacchaaride, a protein, and lipoprotein. Proteins called porins allow for permeability across the outer membrane, and a space called the periplasm is present, which contains various proteins involved in important cellular functions? What components constitute the LPS layer of Gram-negative Bacteria？