These lecture notes will provide an outline of information from the lectures. They are not complete. They should be used to help follow the lecture and as a guideline for information I think is important. You will need to fill in the gaps.


Chapters 3 and 4

I    Prokaryotes A   No membrane-bound organelles
B   DNA is one circular chromosome and is not enclosed within a membrane (nuclear membrane)
C   DNA is not associated with histone proteins (almost completely naked)
D   Usually have cell walls, and their cell walls usually contain peptidoglycan (a complex polysaccharide)
E   Reproduce by binary fission
F   Simple flagella having a rotating movement; no cilia
G   Glycocalyx present either as a capsule or slime layer
H   Plasma membrane lacks carbohydrates and sterols, as a rule, but otherwise is similar to eukaryotic membrane that is a bilayer of lipids and floating proteins ("fluid mosaic structure")
I    No cytoskeleton and no cytoplasmic streaming; no centriole
J   Ribosomes are small, 70S
K   No meiosis occurs; there may be transfer of DNA fragments
 II    Eukaryotes A    DNA is contained within chromosomes that are found within the cell's nucleus, which is separated from the cytoplasm by a nuclear membrane (true nucleus)
B    DNA is associated with histone proteins
C    Membrane-bound organelles, such as lysosomes, Golgi complex, ER, mitochondria
D    Flagella are complex, consisting of multiple microtubules, and have a whipping motion; cilia may be present
E    Glycocalyx may be present in some cells that lack a cell wall
F    Cell wall is present in algae, fungi and plants; there is no peptidoglycan (fungi's polysaccharide is called chitin; plants and algae contain cellulose)
G    Plasma membrane has sterols and carbohydrates that serve as receptorsand is a bilayer of lipids and floating proteins ("fluid mosaic structure")
H    Cytoskeleton is present and cytoplasmic streaming occurs; centriole is present
I    Two sizes of ribosomes: larger, 80S, and smaller, 70S (in organelles)
J    Cell division is through mitosis
K    Sexual reproduction involves meiosis
 III    Anatomy of the Bacterium A    Shape
1.    Spherical coccus (.5-1.0 microns)
2.    Rod-shaped bacillus (0.5-20 microns)
3.    Spiral B    Arrangement
1.    Cocci
a)    Single
b)    Pairs
c)    Tetrads
d)    Sarcinae
e)    Chains
f)    Clusters 2.    Bacilli
a)    Single
b)    Pairs
c)    Chains
d)    Palisade C    Structures
1.    The Cell Wall
2.    Everything Outside of the Cell Wall
3.    Everything Inside of the Cell Wall
 IV    The Cell Wall A    With a few exceptions, all prokaryotes have a cell wall
1.    No cell wall at all is found within the Genus Mycoplasma
2.    No cell wall or an unusual cell wall having very little cell wall material is found within the Class Archaeobacteria
3.    Lysozyme damage forms protoplasts (Gram positive) and spheroplasts (Gram negative)
4.    Some strains of bacteria lose the ability to form walls and are called L-forms of the bacteria B    Completely surrounds the plasma membrane
C    Functions
1.    Maintains shape of bacterium
2.    Protective
a)    Barrier against some toxic chemical and biological agents
b)    Prevents bacterial cell from rupturing in hypotonic solutions (inside of bacteria is HYPERTONIC to the outside: therefore, water from the outside would rush in, causing cell to swell and burst if not for the wall)
c)   Both penicillin and human lysozyme found in tears and saliva prevent peptidoglycan formation, ultimately making the cell vulnerable to lysis (most dramatic in the Gram positive cell) D    Structure 1.    Composed of molecules of peptidoglycan a)    Lattice-work of repeating disaccharides (NAG and NAM in your book, p. 100) attached to each other by polypeptides (the amino acids)
b)    The polypeptides always include tetrapeptide (4 amino acids) side chains which are either directly bonded to each other or linked by a peptide cross-bridge 2.    This lattice surrounds and protects the cell
a)    The lattice can be very thick and composed of many layers of peptidoglycan (these cells are "Gram positive" cells) and containing an additional polysaccharide called teichoic acid
b)    Or, the lattice is very thin and composed of a very thin layer of peptidoglycan (these cells are "Gram negative" cells) and NO teichoic acid; these walls will be surrounded by an OUTER MEMBRANE that is never found in Gram positive bacteria
c)    This difference is the basis for a very important test, the Gram stain, that differentiates bacteria into two broad groups, Gram positive and Gram negative bacteria E    Clinical significance
1.    Contributes to virulence of the organism
2.    Is the site of action for some antimicrobials
3.    Is used to differentiate the major types of medically important bacteria V    Everything Outside of the Cell Wall A    Glycocalyx
1.    Takes the form of a capsule or a slime layer
2.    Is composed of either polysachharides, polypeptides, or protein (polysachharide is most commonly found)
3.    Never found in spiral bacteria; various rods and cocci can form this
4.   Important in the formation of biofilms, which exist wherever a fluid meets a solid surface and contain small colonies of bacteria ("bio") attached to a variety of surfaces by their glycocalyx
5.   Bacteria that have a glycocalyx are more virulent than those that do not
a)    Capsules
(1)    Capsules are very organized in structure and firmly attached to the cell wall
(2)    Capsules protect the cell from drying out.
(3)    Capsules protect pathogenic bacteria from phagocytosis by the host cells
(4)    Capsules may facilitate the attachment of the organism to host tissue
(5)    Capsules contribute to bacterial virulence
(6)    Capsules can be observed microscopically through the use of a negative stain, such as India ink
(7)    Capsules contain the 'capsular' or 'K' antigens, which are polysachharides that can be used to serologically identify a bacterium
(8)    Encapsulated bacteria, when cultured on solid media, have a colony morphology that is smooth and mucoid in appearance
(9)    The unencapsulated form of a bacteria capable of forming a capsule has a colony morphology on solid media that is rough and non-mucoid in appearance
(10)    Not all bacteria produce capsules, and often, certain nutrients must be present in the environment before the capsule will appear in those bacteria capable of forming them b)    Slime layer
(1)    Slime layers are unorganized in structure and loosely attached to the cell wall; contain dextran, which helps the bacterium to ATTACH to tissue surfaces (great example is Streptococcus mutans, the cause of tooth decay)
(2)    Aids in trapping nutrients, slowing dehydration, and binding cells together
(3)    May also help in attachment of microbe to host tissue B    Outer Membrane
1.    Found ONLY in Gram negative bacteria
2.    Consists of lipoproteins, lipopolysaccharides (LPS), that are unique to Gram negative bacteria and phospholipids
a)    LPS contains O polysaccharides that are antigenic and useful for identifying members of the species (for example, E. coli O157:H7 is a very virulent strain of the normally placid E. coli that are normal intestinal flora)
b)    LPS also contains a lipid portion, lipid A, that is an endotoxin and is toxic when in the host's blood stream or GI tract
c)    Lipid A causes fever and shock
d)    It is released if the organism is destroyed through lysis 3.    Functions
a)    Contributes to virulence of bacterium
b)    Helps organism evade phagocytosis
c)    Helps organism evade the action of complement
d)    Provides a barrier to certain antibiotics
e)    Provides a barrier to digestive enzymes such as lysozyme, detergents, heavy metals, bile salts, and certain dyes
(1)    Porins are proteins in this membrane that permit the passage of important molecules into the cell
(2)    They are also the Achille's heel of the microbe because they provide attachment sites for viruses and harmful substances C    Flagella
1.    Not found in all bacteria (many rods and spiralla will have flagella; very few cocci will)
2.    Composed of a protein subunit called flagellin that allows the flagellum to rotate (the protein 'H' is useful for distinguishing among serovars, members of the same species that are not identical to each other; serological tests can demonstrate their non-identity by the identification of different types of H proteins)
3.    Four arrangements
a)    Monotrichous (single polar flagellum)
b)    Amphitrichous (tuft of flagella at each end)
c)    Lophotrichous (two or more flagella at one pole)
d)    Peritrichous (flagella distributed over entire cell) 4.    Basal body of the flagellum serves to anchor it to the cell wall and plasma membrane
5.    Function is to provide motility to bacteria
6.   CHEMOTAXIS is the stimulation of the flagella by certain chemicals; either the organism will move TOWARDS the chemical stimulant ("attraction") or AWAY from it ("repulsion")
7.   These contribute to virulence because they allow the bacteria to evade phagocytosis and to move through the tissues
 D    Axial filaments
1.    Found in Spirochetes, a type of spiral-shaped bacteria
2.    These are bundles of fibrils, also called endoflagella, that arise at the ends of the cell beneath the outer sheath and spiral around the cell
3.    Anchored at one end of the spirochete
4.    Are structurally similar to flagella, but not the same
5.    Allow for a cork-screw type of boring motion E    Fimbriae (pili that are used for attachment only)
1.    1. Composed primarily of protein subunits called pilin and are found in many, but not all, Gram negative bacteria
2.    May occur at the poles or be evenly distributed over the entire surface of the cell
3.    Function is to enable a cell to adhere to surfaces (contribute to virulence of bacterium) through proteins called ADHESINS that stick to tissue surfaces
4.    Some microbiologists refer to these as 'common pili' to distinguish them from 'sex pili' (below) F    Pili
1.    Usually longer than fimbriae and only 1-2 per cell
2.    Join 2 bacterial cells in preparation for the transfer of DNA from one cell to another
3.    Sometimes called sex pili VI    Everything Inside of the Cell Wall A Plasma or cytoplasmic membrane
1.    Thin structure, composed of double-layered membrane of phospholipids and proteins, lying inside the cell wall and enclosing the cytoplasm of the cell
2.    Fluid mosaic model refers to dynamic arrangement of phospholipid and protein molecules
a)    Phospholipid layers parallel each other and enclose the protein layer
b)    Membrane proteins move freely performing their functions, but without destroying integrity of the membrane 3.    Functions
a)    Selectively permeable through which materials enter and exit
b)    Breakdown of nutrients
c)    Production of energy 4.    Clinical Significance
a)    Is the site of action for some antimicrobials
b)    These compounds include certain alcohols, quaternary ammonium compounds, and polymyxin antibiotics
c)    All cause leakage of intracellular contents, leading to cell death B    Cytoplasm
1.    Substance of the cell that is inside the plasma membrane
2.    Composed of 80% water and various solutes and structures
a)    Solutes include proteins (enzymes), carbohydrates, lipids, inorganic ions, and low molecular weight compounds
b)    Structures include DNA, ribosomes, and inclusions, none of which is surrounded by any membrane 3.    No cytoplasmic cytoskeleton or cytoplasmic streaming are present C    Ribosomes
1.    The sites of protein synthesis
2.    These are composed of two subunits
a)    Each subunit consists of protein and ribosomal RNA (rRNA)
b)    Together, the two subunits make up a 70S ribosome (the S indicates the relative rate of sedimentation during ultr-high-speed centrifugation) 3.    Clinical significance
a)    Are the site of action for some antimicrobials
b)    These inhibit protein synthesis
(1)    By attaching to 30S subunit (streptomycin and gentamycin)
(2)    By attaching to 50S subunit (erythromycin and chloramphenicol) D    Inclusions
1.    Reserve deposits within the cytoplasm, whose contents vary
2.    Those that are not commonly found, but limited to a few groups, may be used as a means to identify the organism E    Nuclear area
1.    Also called the nucleoid
2.    Contains one long circular molecule of double-stranded DNA, the bacterial chromosome
a)    Cell's genetic information found here
b)    Carries all the information required for the cell's structures and functions
c)    Does not include histones
d)    Is not surrounded by a nuclear membrane
e)    Is attached to the plasma membrane F    Plasmids
1.    Often found in bacteria
2.    Small circular, double-stranded DNA molecules
3.    Are extrachromosomal genetic elements
4.    Are not connected to the main chromosome
5.    Replicate independently of the main chromosome
6.    Are associated with the plasma membrane proteins
7.    Usually contain 5-100 genes that are not critical to bacterial growth
a)    They are significant, however, because they may provide a survival advantage
b)    Carry genes for antibiotic resistance ("R factors"), tolerance to toxic metals, the production of toxins, and the synthesis of enzymes
c)  Plasmids may be transferred between cells during GENETIC RECOMBINATION and replicate during binary fission 8.    May be gained or lost without harm coming to the cell
9.    Usually transferred from one bacterium to another during binary fission
10.    Conjugative plasmids are able to transfer a copy of themselves to another (non-daughter) bacterial cell
a)    This transfer occurs during conjugation G    Endospores
1.    Only found among certain Gram positive bacteria
2.    These are specialized "resting" cells
3.    They are formed internal to the bacterial cell membrane
a)    The process is called sporulation or sporogenesis
b)    The vegetative cell (that is, the growing, maturing, and reproductive bacterium) takes a few hours to complete sporulation
c)    A newly replicated bacterial chromosome and a small amount of cytoplasm are isolated by an ingrowth of the plasma membrane, the spore septum
d)    Spore septum becomes a double-layered membrane surrounding the new chromosome and cytoplasm
e)    Thick layers of peptidoglycan are laid down between the two membrane layers
f)    Thick spore coat of protein forms around the outside membrane
g)    This coat is responsible for the resistance of endospores to many harsh chemicals 4.    Spores are either terminal, subterminal or central to the vegetative cell
5.    When the endospore matures, the vegetative cell wall ruptures, killing the cell and releasing the endospore
6.    Endospores do not carry out metabolic reactions
7.    They can remain dormant for thousands of years, surviving environmental extremes
a)    Germination occurs when environmental conditions improve
b)    This is not a means of reproduction, as it does not increase the number of cells 8.    Clinical significance
a)    Highly resistant to processes that kill vegetative cells
b)    When present in food, if conditions for growth occur, some produce toxins and disease
c)   Examples of clinically significant endospore forming bacteria include Bacillus anthracis, Bacillus cereus, Clostridium botulinum, Clostrium perfringens, and Clostridium tetani (causative agents of anthrax, gastroenteritis, botulism, gas gangrene, and tetanus, respectively) VII    The Gram Stain (pages 77-80) A    Very useful because it classifies bacteria into two large groups, Gram positive and Gram negative
1.    The Gram stain reaction is based on the bacteria's cell wall composition
2.    Some bacterial cells stain poorly or not at all
3.    This is a differential stain because it is used to differentiate two groups of bacteria, based on their reaction B    Four chemicals used in the stain
1.    Crystal violet, the primary stain
2.    Iodine, the mordant
3.    Alcohol, the decolorizer
4.    Safranin, the counterstain C    Why the difference?
1.    Gram positive bacteria's cell surface structures are different from Gram negative bacteria's.
a)    Gram positive bacteria's cell walls are very thick
b)    Gram positive bacteria's cell walls are composed of many layers of peptidoglycan (murein).
c)    Gram negative bacteria's cell walls are very thin and only have one or a very few layers of peptidoglycan.
d)    Gram negative bacteria have an outer membrane composed of lipids that sits on top of the cell wall. 2.    When crystal violet is applied, it stains both cell types.
3.    The iodine forms large crystals with the crystal violet, which are deposited in the peptidoglycan layers.
a)    Gram positive cells have more of these layers than Gram negative cells, and thus, take up much more of the crystal violet-iodine crystal combination. 4.    The alcohol is a decolorizer that removes the purple stain of crystal violet from any cells in which the primary stain did not anchor well
a)    Because Gram positive cell walls are so much thicker, and because there is no outer membrane that is damaged by the alcohol, the crystal violet-iodine crystals remain.
b)    HOWEVER, IF DECOLORIZATION CONTINUES LONG ENOUGH, EVENTUALLY EVEN THE GRAM POSITIVE CELL WALL WILL SUCCUMB TO THE EFFECTS OF THE ALCOHOL!
c)    In Gram negative cells, the alcohol dissolves the lipids in their outer membrane, thus allowing the crystal violet-iodine crystals to eke out of the thinner cell wall. 5.    When safranin is added, any cells that are colorless after the addition of the alcohol will be available for staining by this counterstain
a)    Gram negative cells are thus able to be stained by the counterstain, because they have been rendered colorless by the actions of the alcohol.
 VIII Bacterial Reproduction and Requirements for Growth
A    Binary fission
1.    Asexual reproduction
2.    Bacterial chromosome duplicates, cell elongates, plasma membrane pinches inward at center of cell
3.    Once nuclear material is evenly distributed, cell wall thickens and expands to separate dividing cell
B    Generation time
1.    Generation time is the time required for a population of bacteria to double in number; also known as doubling time: interval of time between binary fissions (from one bacterium to two; from 1000 bacteria to 2000)
2.    May be as short as 20 minutes or as long as 18 hours
C    Bacterial Growth Curve
1.    Bacterial growth refers to an increase in numbers of bacteria, not in size of bacterium (through binary fission)
2.    The growth curve is a graph that depicts growth of bacterial cells (y axis) over time (x axis)
3.    Four distince phases: lag, logarithmic, stationary, decline or death phase
4.    Lag: first few hours of curve when bacteria are adapting to their new environment
5.    Logarithmic: active stage of growth when the mass of each cell increases rapidly and doubling of bacteria results in an exponential explosion of growth
6.    Stationary: reproductive and death rates equalize; if these conditions continue, then next (and final) phase is imminent
7.    Decline or death phase: the number of dying cells exceeds the number of new cells formed; sporulation will occur here, if the organism is capable of this process
D    Bacterial Requirements for Optimal Growth
1.    Temperature Requirements
a)    Psychrophiles have their shortest generation time (most optimal growth) from 0o -20 o C. These live in the ocean depths and in the Arctic and Antarctic regions.
b)    Mesophiles have their shortest generation time at ranges from 20o -40 o C. Most bacteria are mesophiles; all pathogenic bacteria are mesophiles and grow well at 37o C. (98.6 o F)
c)    Thermophiles have their shortest generation time at ranges from 40o -90 o C. and higher. Hyperthermophiles grow in hot water vents, compost heaps, and hot springs and can tolerate temperatures above boiling.
d)    Some of the above bacteria may be able to tolerate temperatures outside of their ideal temperature ranges. Growth may occur, although it will not be optimal (shortest generation time). Mesophiles that can tolerate cold temperatures are called PSYCHROTROPHIC or PSYCHROTOLERANT to distinguish them from the true Psychrophiles that thrive at cold temperatures. These are important to know about, because they can grow at refrigerated temperatures.
2.    Oxygen Requirements
a)    Obligate aerobes are those bacteria that cannot grow (undergo binary fission) unless oxygen is present.
b)    Obligate anaerobes are those bacteria that cannot grow in the presence of oxygen, requiring an oxygen-free environment. Some use sulfur in place of oxygen for their metabolic activities. Thus, instead of producing H2O as a waste product, they produce H2S! Special anaerobic jars are used to encourage their growth in the lab.
c)    Facultative organisms can grow in either oxygen-rich or oxygen-free environments; generally generation times are shortest under aerobic conditions. These organisms are called facultative anaerobes, and most bacteria are facultative anaerobes.
d)    Microaerophiles require small amounts of oxygen; large amounts of oxygen are destructive to them. Some microaerophiles are also CAPNOPHILIC, which means they require an atmosphere low in oxygen but rich in carbon dioxide. Special carbon dioxide-generating units are used to encourage their growth in the lab.
e)    Aerotolerant anaerobes, unlike obligate anaerobes, can tolerate and grow in the presence of oxygen; however, they are anaerobic because they do not consume the oxygen.
3.    pH (acidity/alkalinity)
a)    pH refers to the acidity of alkalinity of a solution
b)    There is a wide range of pH tolerance among bacteria, from as low as pH 2.0 to as high as 9.5
c)    Most bacteria grow best, however, under neutral conditions (7.0), which is close to human blood pH (7.4) and human tissue pH (7.2)
d)    Acidophilic bacteria are those unusual bacteria that thrive under acidic conditions and are important in the food industries. Extreme acidophiles are found among the archaeabacteria (which will not be studied in this course)
 4.    Nutrition Requirements
a)    The two questions to be answered when considering nutrition requirements are, 'what is the source of energy?' and 'what is the source of carbon?'
b)    If light is the source of energy, the organism is a phototroph; if oxidation-reduction of inorganic/organic compounds is the source of energy, the organism is a chemotroph.
c)    If carbon dioxide or carbonate is the source of carbon, the organism is an autotroph; if organic molecules are the source of carbon, the organism is a heterotroph
d)    Photoautotroph: bacteria deriving energy from the sun and carbon from carbon dioxide (plants are also photoautotrophs). Examples are the blue-green algae known as the cyanobacteria.
e)    Photochemotroph: bacteria deriving energy from the sun and carbon from organic compounds
f)    Chemoautotroph: bacteria deriving energy from reactions that occur in their cytoplasm (oxidation-reduction) and carbon from carbon dioxide
g)    Chemoheterotrophs: bacteria deriving energy from reactions that occur in their cytoplasm (oxidation-reduction) and carbon from organic compounds. THESE ARE THE PARASITIC bacteria, the pathogens of humans, because they require living organic matter (human tissues) to survive.
h)    The biologic relationship of one organism to another or one population to another is called "symbiosis."
(1)    Mutualism occurs when the relationship is of benefit to both populations.
(2)    Commensalism occurs when one population receives a benefit, while the other is neither benefited nor harmed.
(3)    Parasitism occurs when one population receives a benefit at the expense (detriment) of the other.
(4)    Synergism occurs when two populations live together and accomplish what neither population could accomplish alone. Synergistic populations may be parasitic in humans (see page 120 for explanation of trench mouth).
 5.    Osmotic pressures
a)    Osmotic pressure is the force with which water moves from a solution of lower solute concentration (hypotonic) to a solution of higher solute concentration (hypertonic)
b)    Hypertonic solutions cause most bacteria to undergo plasmolysis, as water rushes from within bacteria to the outside environment, and an inhibition of growth
c)    Halophiles are the exception and are able to withstand high osmotic pressures. Environments that contain high osmotic pressures would have large concentrations of dissolved solutes (such as salt or sugar) within the solvent (water)
 IX    Bacterial Cultivation
A    In clinical microbiology situations, it is desirable to grow and identify the pathogenic organism so that appropriate medical intervention can occur.
B    Bacterial cultivation will be the focus of the labs.
C    For now, it is important to recognize that not all bacteria can be cultivated. Important exceptions (important because they are pathogens of humans) include the bacterial rickettsieae and the bacterial chlamydiae. These require living cells in order to multiply (similar to viral requirements for growth).






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