Toxonomy &Cell Structure Microbiology Toxonomy &Cell Structure

What is Microbiology Microbiology : Is The branch of biology that deals with microorganisms and their effects on other living organisms. Microorganisms are those organisms that are too small to see with the naked eye and include things like bacteria, fungi, and viruses. Microbiology is Greek word mikros mean small; bios mean life

Eukaryotes (Fugi , protista ,animal, plant and human) Current classification of all forms of life based on the genetic relatedness into 3 domains : Archea ,Bacteria Eucarya Archea and Bacteria called Prokaryotes Eukaryotes (Fugi , protista ,animal, plant and human)

Prokaryotic Cells

Viruses are not included in this classification as they are unique , metabolically inert organisms and therefore replicate only within living cells.

Cell component Prokaryotes Eukaryotes Nucleus no membrane, single circular chromosome membrane bound, a number of individual chromosomes. Extra-chromosomal DNA present in form of plasmid Present as mitochondrial DNA Organelles in cytoplasm Non Mitochondria and chloroplast in photosynthetic organisms Cytoplasmic membrane Contain enzyme of respiration, sit of phospholipids and DNA synthesis Semi-permeable layer not possessing function Cell wall Rigid layer of peptidoglycan No peptidoglycan Sterols Absent Present Ribosome 70 S in cytoplasm 80 S in cytoplasmic reticulum

Basis of Classification Phenotypic classification Morphological Anatomical Staining Cultural characteristics Nutrition Environmental factors Biochemical reactions Antigenic structure Genotypic classification DNA-DNA hybridization G+C content

Morphological classification Bacteria can be classified into six major groups on morphological basis. 1. TRUE BACTERIA Cocci – These are spherical or oval cells. On the basis of arrangement of individual organisms they can be described as Monococci (Cocci in singles) – Monococcus spp. Diplococci (Cocci in pairs) – Streptococcus pneumoniae Staphylococci (Cocci in grape-like clusters) – Staphylococcus aureus Streptococci (Cocci in chains) – Streptococcus pyogenes Tetrad (Cocci in group of four) - Micrococcus spp. Sarcina (Cocci in group of eight)

Staphylococcus tetrad Streptococcus

Morphological classification Bacilli – These are rod-shaped bacteria. On the basis of arrangement of organisms, they can be described as Diplobacilli Streptobacilli Palisades Chinese-letter form Coccobacilli Comma-shaped

bacilli bifidobacterium Coryneform bacteria vibrio cholerae

Morphological classification 2. ACTINOMYCETES (actin- ray, mykes-fungus) These are rigid organisms like true bacteria but they resemble fungi in that they exhibit branching and tend to form filaments. They are termed such because of their resemblance to sun rays when seen in tissue sections.

Morphological classification 3. Spirochaetes These are relatively longer, slender, non-branched microorganisms of spiral shape having several coils.

Morphological classification 4. Mycoplasmas These bacteria lack in rigid cell wall (cell wall lacking) and are highly pleomorphic and of indefinite shape. They occur in round or oval bodies and in interlacing filaments. 5. Rickettsiae and Chlamydiae These are very small, obligate parasites, and at one time were considered closely related to the viruses. Now, these are regarded as bacteria.

Capsule Flagella Spore Capsulate– Streptococcus pneumoniae Non-capsulate – Viridans streptococci Flagella Flagellate – Monotrichous Lophotrichous Amphitrichous Peritrichous Aflagellate – Shigella spp. Spore Spore-forming – Bacillus spp. Non-sporing – Escherichia coli

Based on Staining reaction GRAM’S STAIN Gram-positive cocci – Staphylococcus aureus Gram-negative cocci – Neisseria gonorrhoeae Gram-positive rods – Clostridium spp. Gram-negative rods – E. coli ACID FAST STAIN Acid-fast bacilli –Mycobacterium tuberculosis Non-acid-fast bacilli – Staphylococcus aureus

Based on Cultural characteristics Extra growth factors requirements Fastidious – Hemophilus influenzae Non-fastidious – Escherichia coli Hemolysis on Sheep Blood Agar Alpha-hemolysis – Streptococcus pneumoniae Beta-hemolysis – Streptococcus pyogenes Utilization of carbohydrates Oxidative - Micrococcus Fermentative – Escherichia coli

Based on Cultural characteristics Growth rate Rapid growers– Vibrio cholerae Slow growers – Mycobacterium tuberculosis Pigment production Pigment producer – Staphylococcus aureus Pigment non-producer – Escherichia coli

Based on Nutrition Autotrophs Heterotrophs

Based on environmental factors Temperature Oxygen dependence pH Salt concentration Atmospheric pressure

Based on environmental factors Temperature Psychrophiles (15-200C) – Pseudomonas fluorescens Mesophiles (20-400C) – Escherichia coli, Salmonella enterica, Staphylococcus aureus Thermophiles (50-600C)- Bacillus stearothermophilus Extremely thermophiles (as high as 2500C) -Archea

Based on environmental factors 2. Oxygen dependence Aerobe (grow in ambient temperature, which contains 21% O2 and a small amount of CO2, 0.03%) Obligate aerobes – Strictly require O2 for their growth (Pseudomonas aeruginosa) Microaerophilic (grow under reduced O2, 5-10% and increased CO2, 8-10%)- Campylobacter jejuni, Helicobacter pylori

Based on environmental factors 2. Oxygen dependence Facultative anaerobe (capable of growing either in presence or absence of O2)- E. coli Obligate anaerobe – Clostridium spp. Capnophilic (require increased concentration of CO2, i.e., 5-10%) – H. influenzae, N. gonorrhoeae Aerotolerant

Based on environmental factors 3. pH Acidophiles (Lactobacillus acidophilus) Alkaliphiles (Vibrio) Neutralophiles (pH 6-8) Majority of the medically important bacteria grow best at neutral or slightly alkaline reaction (pH 7.2-7.6)

Based on environmental factors 4. Salt concentration Halophiles Non-halophiles

Other ways of classification Motile/Non-motile Pathogenic/Non-pathogenic Sensitive/Resistant (to particular antibiotic/ chemicals) Lactose fermenter/Lactose non-fermenter Bergey’s Manual of Determinative Bacteriology Gram-negative eubacteria that have cell walls Gram-positive eubacteria that have cell walls Cell wall-less eubacteria: Mycoplasma Archaeobacteria

Structure Structures external to the cell wall Flagella Flagella are whip-like filaments that act as propellers and guide the bacteria towards nutritional and other sources. Composed of single protein called Flagellin.

Type of Flagellum Flagella may be located at one end Monotrichous a single flagellum Lophotrichous All over the outer surface Peritrichous Located at the polar ends Amphitrichous

Fimbriae and pili 1-are fine, hair-like filaments, shorter than flagella, that extend from the cell surface. 2- Pili found mainly on Gram-negative organisms 3- Composed of subunits protein, pilin. 4- mediate the adhesion of bacteria to receptors on the human cell surface – a necessary first step in the initiation of infection. .

A specialized type of pilus, the sex pilus, forms the attachment between the male (donor) and the female (recipient) bacteria during conjugation, when genes are transferred from one bacterium to another.

THE STRUCTURES EXTERNAL TO THE CELL WALL AXIAL FILAMENTS Anchored at one end of the spirochete. Have a structure similar to flagella. Filament rotation produces a movement of the outer sheath. Propels the bacteria in a spiral motion (corkscrew motion). E.g. Treponema pallidum – syphilis Borrelia burgdorferi – Lyme disease

Glycocalyx (slime layer) 1- is a polysaccharide 2-coating that covers the outer surfaces of many bacteria 3-allows the bacteria to adhere frmly to various structures, e.g. oral mucosa, teeth,heart valves and catheters. 4-contribute to the formation of bioflms. This is especially true in the case of Streptococcus mutans

Capsule 1-An amorphous, gelatinous layer (usually more substantial than the glycocalyx) surrounds the entire bacterium. 2- it is composed of polysaccharide, and sometimes protein (e.g.anthrax bacillus).

The capsule is important • It mediates the adhesion of bacteria to human tissues or prosthesis such as dentures or implants prerequisite colonization and infection. It hinders or inhibits phagocytosis; hence, the presence of a capsule correlates with virulence.

The capsule is important It helps in laboratory identifcation of organisms (inthe presence of antiserum against the capsular polysaccharide the capsule will swell greatly – a phenomenon called the quelling reaction). Its polysaccharides are used as antigens in certain vaccines because they elicit protective antibodies (e.g. polysaccharide vaccine of S. pneumoniae

THE CELL WALL Cell wall – a complex, semirigid structure Protects cell from adverse changes in the outside environment. Almost all prokaryotes have cell walls. Major function is to prevent bacterial cells from rupturing. Maintain the shape of the bacterium. Serve as point of anchorage for flagella.

THE CELL WALL Contributes to Pathogenecity Site of action of some antibiotics. Cell wall composition used to differentiate major types of bacteria.

Cell Wall In Gram positive bacteria Peptidoglycan layer forms 50% of cell wall material. Peptidoglycan is responsible for cell wall rigidity. Peptidoglycan is formed of N-acetyl glucosamine and N-acetyl muramic acid. Attached to each muramic acid molecule is a tetrapeptide. Then the tetrapeptide chains are cross-linked together by transpeptidase enzyme.

In addition to peptidoglycan, there is teichoic acid which: is highly immunogenic adheres the bacteria to mucosal surfaces. Lipoteichoic acid links peptidoglycan layer to the cell membrane.

Gram-negative organisms Inner peptidoglycan layer forms only 5-10% of the cell wall material. Outer membrane layer formed of lipopolysaccharides: The lipid portion (lipid A) is called endotoxin. It is released when the bacterial cells are lysed. It is highly toxic. The polysaccharide portion is called somatic or O antigen. It is highly immunogenic. The space between the inner and outer layers is called periplasmic space which contains beta lactamase enzyme that degrades beta lactam antibiotics.

Lipoprotein molecules cross-link the peptidoglycan layer and the outer membrane

Grame Negative Cell Gram Positive Cell 3 Layers 1-Inner cytoplasmic membrane 2- Thin peptidoglycan layer (5-10%) 3-Outer membrane with Lipopolysaccharide(LPS) 2 Layers 2-Outer thick peptidoglycan layer (60-100%) High lipid content Low lipid content Endotoxine(LPS). Lipid A No endotoxine (except Listeria monocytogenes) periplasmic space No periplasmic space porin channel No porin channel Resistto Lysozyme and penicillin attack Virulence to Lysozyme and penicillin attack

In acid fast bacteria These bacteria contain high concentration of mycolic acid and wax in their cell wall. These bacteria are not stained by Gram stain but stained by Ziehl-Neelsen stain. Example: Mycobacterium tuberculosis.

Bacteria with defective cell walls Mycoplasma spp Lacks cell wall. Pleomorphic in shape. Not affected by penicillin. Not stained by Gram stain. The only bacteria that contains sterol in its cell membrane.

Protoplast , Spheroplast, L-Form When bacterial cell wall is lost under the effect of certain conditions like penicillin: Gram positive bacteria form protoplasts. Gram negative bacteria form spheroplasts. If protoplasts and spheroplasts grow and divide, they are called L-forms. Unlike mycoplasma, L-forms can revert to the parental form on removal of the cell wall inhibitor.

Cytoplasmic membrane The cytoplasmic membrane lies just inside the peptidoglycan layer of the cell wall and is a ‘unit membrane’ composed of a phospholipid bilayer similar in appearance to that of eukaryotic cells. However, eukaryotic membranes contain sterols, whereas prokaryotes generally do not (the only exception being mycoplasmas.

The membrane has the following major functions active transport and selective diffusion of molecules and solutes in and out of the cell .• electron transport and oxidativephosphorylation in aerobic specie. • synthesis of cell wall precursors • secretion of enzymes and toxins • supporting the receptors and other proteins of The chemotactic and sensory transduction systems

Mesosome This is a convoluted invagination of the cytoplasmic membrane that functions as the origin of the transverse septum that divides the cell in half during cell division. It is also the binding site of the DNA that will become the genetic material of each daughter cel

Cytoplasm The cytoplasm comprises an inner, nucleoid region (composed of DNA), which is surrounded by an amorphous matrix that contains ribosomes, nutrient granules, metabolites and various ions.

Nuclear material or nucleoid Bacterial DNA comprises a single, supercoiled, circular chromosome that contains about 2000 genes(It is analogous to a single, haploid chromosome.) During cell division, it undergoes semiconservative replication bidirectionally from a fixed point. Electron micrograph of a thin section of Neisseria gonorrhoeae showing the organizational features of prokaryotic cells. Note the electron-transparent nuclear region (n) packed with DNA fibrils, the dense distribution of ribosomal particles in the cytoplasm, and the absence of intracellular membranous organelles

Ribosomes Ribosomes are the sites of protein synthesis. Bacterial ribosomes differ from those of eukaryotic cells in both size and chemical composition. They are organized in units of 70S, compared with eukaryotic ribosomes of 80S. These differences are the basis of the selective action of some antibiotics that inhibit bacterial, but not human.

Cytoplasmic inclusion granules The cytoplasm contains different types of inclusions, which serve as sources of stored energy; examples include polymetaphosphate, polysaccharide and β-hydroxybutyrate.

Bacterial spore Spores are formed in response to adverse conditions by the medically important bacteria that belong to the genus Bacillus (which includes the agent of B.anthrax) and Clostridium (which includes the agents of Cl. tetanus and CL.botulism). These bacteria sporulate (form spores) when nutrients, such as sources of carbon and nitrogen, are scarce