GSU Microbiology Exam 2 Chapter 5-7

*Septation is divided into several steps:* (Cytokinesis - Septation)

(1) *selection of the site* where the *septum* will be *formed*; (2) *assembly of the Z ring*, which is composed of the cytoskeletal protein FtsZ; (3) *assembly of the cell wall-synthesizing machinery* (i.e., for synthesis of peptidoglycan and other cell wall constituents); and (4) *constriction of the cell and septum formation*; (5) *linkage of Z ring to plasma membrane* (cell wall).

*programmed cell death* (glossary)

(1) In eukaryotes, apoptosis. (2) In some bacteria, a mechanism proposed to account for the decline in cell numbers during the death phase of a growth curve.

*Eukaryotic ribosomes* (Text)

(i.e., those not found in mitochondria and chloroplasts) are larger than bacterial and archaeal 70S ribosomes. Each ribosome is a dimer of a 60S and a 40S subunit. The 60S subunit is composed of three rRNA molecules (5S, 28S, and 5.8S rRNAs) and about 50 proteins. The 40S subunit is composed of an 18S rRNA and about 30 proteins. Each ribosome is about 22 nm in diameter and has a sedimentation coefficient of 80S and a molecular weight of 4 million (figure 5.14). Eukaryotic ribosomes are either associated with the endoplasmic reticulum or free in the cytoplasm. When bound to the endoplasmic reticulum to form rough ER, they are attached through their 60S subunits.

• Developed porcelain bacterial filters used later in the discovery of viruses

*Charles Chamberland* (1884) (Discovery of Viruses)

*macroautophagy* (glossary)

*Digestion of cytoplasmic components* that involves enclosing the material (e.g., an organelle) in a double-membrane structure called an *autophagosome*. The autophagosome *delivers the material to a lysosome for digestion*.

• demonstrated that causative agent of tobacco mosaic disease passed through bacterial filters • thought agent was a toxin

*Dimitri Ivanovski* (1892) (Discovery of Viruses)

• published case reports of successful attempts to prevent smallpox by exposure to cowpox.

*Edward Jenner* (1798) (Early Attempts to Prevent Viral Disease)

• showed that leukemia in chickens were caused by a virus

*Ellerman* and *Bang* (1908) (Discovery of Viruses) (Ellerman pictured)

• separated TMV particles into protein and nucleic acid components

*F.C. Bawden* and *N.W. Pirie* (1935) (Discovery of Chemical Nature of Viruses) (Pirie pictured)

• firmly established the existence of bacteriophages • devised method for enumerating them • demonstrated that bacteriophages only reproduce in live bacteria

*Felix d'Herelle* (1917) (Discovery of Bacterial Viruses)

• first to isolate viruses that infect bacteria (bacteriophages or phages)

*Frederick Twort* (1915) (Discovery of Bacterial Viruses)

• proponent of inoculation of children with material for the smallpox lesions (brother had died of smallpox in 1713) • observed this practice among Turkish women

*Lady Wortley Montagu* (early 1700s) (Early Attempts to Prevent Viral Disease)

• showed that *hoof and mouth disease* in cattle was caused by filterable virus

*Loeffler* and *Frosch* (1898-1900) (Discovery of Viruses)

• Bacterial Ecologists • Showed the causative agent of tobacco mosaic disease was still infectious after filtration • referred to agent as filterable agent

*Martinus Beijerinck* (1898-1900) (Discovery of Viruses)

• showed that muscle tumors in chickens were caused by a virus (can cause cancer)

*Peyton Rous* (1911) (Discovery of Viruses)

• crystallized tobacco mosaic virus • showed that TMV was composed mostly of protein

*W.M. Stanley* (1935) (Discovery of Chemical Nature of Viruses)

• showed that yellow fever in humans was caused by filterable virus transmitted by mosquitoes

*Walter Reed* (1900) (Discovery of Viruses)

*Virions Having Envelopes =* (The Structure of Viruses)

*enveloped* viruses

*Reduce osmotic concentration of cytoplasm in hypotonic solutions* (Microbes Adapt to Changes in Osmotic Concentrations)

*mechanosensitive* (MS) channels in plasma membrane allow solutes to leave

*In biofilms interactions occur among the attached organisms and exchanges take place ... *

*metabolically*, *DNA* (plasmids: new gene) *uptake* and *communication*.

*Virions Lacking Envelopes =* (The Structure of Viruses)

*naked* viruses

*Viruses* (Acellular Agents)

*proteins* and *nucleic acid*

*Continuous Culture of Microorganisms* (text)

... it is possible to grow microorganisms in a system with constant environmental conditions maintained through continual provision of nutrients and removal of wastes. Such a system is called a continuous culture system. These systems can maintain a microbial population in exponential growth, growing at a known rate and at a constant biomass concentration for extended periods. Continuous culture systems make possible the study of microbial growth at very low nutrient levels, concentrations close to those present in natural environments. These systems are essential for research in many areas, particularly microbial ecology. For example, interactions between microbial species in environmental conditions resembling those in a freshwater lake or pond can be modeled. Continuous culture systems also are used in food and industrial microbiology. Two major types of continuous culture systems commonly are used: chemostats and turbidostats.

*psychrophiles* (Temperature Ranges for Microbial Growth)

0°C - 20°C (ground and ocean water)

*psychrotrophs* (Temperature Ranges for Microbial Growth)

0°C - 35°C (some found on us)

*Microbes that live on land and water surface live at ______ (atm).* (Pressure)

1 atmosphere

*The Growth Curves 4 Phases*

1) lag 2) exponential 3) stationary 4) senescence and death

*The *E. coli* R1 plasmid Proteins Essential for its Inheritance*

1.) *ParM*: similar to MreB, *actin* homolog forms long filaments 2.) *ParR* (repressor) and *ParC* (centromere-like): both bind to origins and link ParM 3.) *ParM* filaments elongate and separate plasmids to opposite ends of the cell

*Three methods used for viral entry and uncoating*

1.) fusion of the viral envelope with the host membrane; nucleocapsid enters 2.) endocytosis in vesicle; endosome aids in viral uncoating 3.) *injection* of nucleic acid

*mesophiles* (Temperature Ranges for Microbial Growth)

20°C - 45°C (some found on us)

*thermophiles* (Temperature Ranges for Microbial Growth)

55°C - 85°C (hot springs)

*Ribosome Size and Structure in Domain Bacteria* (table 5.2)

70S; 3 rRNAs; ∼55 ribosomal proteins

*Ribosome Size and Structure in Domain Archaea* (table 5.2)

70S; 3 rRNAs; ∼68 ribosomal proteins

*Ribosome Size and Structure in Domain Eukarya* (table 5.2)

80S; 4 rRNAs; ∼80 ribosomal proteins

*hyperthermophiles* (Temperature Ranges for Microbial Growth)

85°C - 113°C (not boiling liquid because pressure is so high.)

*virion* (glossary)

A *complete virus particle*; at the simplest, it consists of a *protein capsid surrounding a single nucleic acid molecule*.

*phagosome* (glossary)

A *membrane-enclosed vacuole* formed by the invagination of the cell membrane during endocytosis.

*lysosome* (glossary)

A *spherical membranous* eukaryotic *organelle* that *contains hydrolytic enzymes* and is *responsible for the intracellular digestion* of *substances*.

*Endoplasmic Reticulum (ER)* (glossary)

A *system of membranous tubules and flattened sacs (cisternae)* in the cytoplasm of eukaryotic cells. Rough endoplasmic reticulum *(RER) bears ribosomes* on its surface; smooth endoplasmic reticulum *(SER) lacks them*.

*pour plate* (glossary)

A Petri dish of solid culture medium with isolated microbial colonies growing both on its surface and within the medium that has been prepared by mixing microorganisms with cooled, still-liquid medium and then allowing the medium to harden.

*spread plate* (glossary)

A Petri dish of solid culture medium with isolated microbial colonies growing on its surface that has been prepared by *spreading a dilute microbial suspension evenly over the agar surface*.

*streak plate* (glossary)

A Petri dish of solid culture medium with isolated microbial colonies growing on its surface that has been prepared by *spreading a microbial mixture over the agar surface, using an inoculating loop*.

*divisome*

A collection of proteins that aggregate at the region in a dividing microbial cell where a septum will form.

*Media Component: Agar*

A complex sulfated polysaccharide, usually from red algae, that is used as a solidifying agent; most microorganisms cannot degrade it.

*turbidostat* (glossary)

A continuous culture system equipped with a photocell that adjusts the flow of medium through the culture vessel to maintain a constant cell density or turbidity.

*batch culture* (glossary)

A culture of microorganisms produced by inoculating a closed culture vessel containing a single batch of medium.

*continuous culture system* (glossary)

A culture system with constant environmental conditions maintained through continual provision of nutrients and removal of wastes. See also chemostat and turbidostat.

*chloroplast* (glossary)

A eukaryotic plastid that contains chlorophyll and is the site of photosynthesis.

*thylakoid* (glossary)

A flattened sac in the chloroplast stroma that contains photosynthetic pigments and the photosynthetic electron transport chain. Similar structures are observed in the cytoplasm of cyanobacteria.

*penicillins* (glossary)

A group of antibiotics containing a β-lactam ring.

*adenosine 5′-triphosphate (ATP)* (glossary)

A high energy molecule that serves as the *cell's major form of energy currency*.

*murein*

A large polymer composed of long chains of alternating N-acetylglucosamine and N-acetylmuramic acid residues. The polysaccharide chains are linked to each other through connections between tetrapeptide chains attached to the N-acetylmuramic acids. It provides much of the strength and rigidity possessed by bacterial cell walls; also called Peptidoglycan.

*replisome* (glossary)

A large protein complex that copies the DNA double helix to form two daughter chromosomes.

*proteasome* (glossary)

A large, *cylindrical protein complex that degrades ubiquitin-labeled proteins* to peptides in an ATP-dependent process. Also called 26S ______ .

*residual body* (glossary)

A lysosome after digestion of its contents has occurred. It contains undigested material.

*endosome* (glossary)

A membranous *vesicle formed by endocytosis*. It *undergoes a maturational process* that starts with *early endosomes* and *proceeds to late endosomes* and *finally lysosomes*.

*Golgi apparatus* (glossary)

A membranous eukaryotic *organelle* composed of stacks (*dictyosomes*) of flattened sacs (*cisternae*) that is involved in *packaging* and *modifying materials* for *secretion* and many other processes.

*halophile* (glossary)

A microorganism that requires high levels of sodium chloride for growth.

*Halophile* (Solute and Water Activity: Microbial Responses to Environmental Factors) (T. 7.2)

A microorganism that requires high levels of sodium chloride, usually above about 0.2 M, to grow (ex: Halobacterium)

*reverse transcriptase (RT)*

A multifunctional enzyme used by retroviruses and ______ ______ DNA viruses during their life cycles. It has RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and RNAase activity. Its function in these viruses is to synthesize double-stranded DNA from single-stranded RNA; this is a reverse of the flow of genetic information in cells, which proceeds from DNA to RNA.

*Cytoskeleton* (glossary)

A network of structures made from filamentous proteins (e.g., actin and tubulin) and other components in the cytoplasm of cells.

*lag phase* (glossary)

A period following the introduction of microorganisms into fresh culture medium when there is no increase in cell numbers or mass during batch culture.

*water activity (a↓w)* (glossary)

A quantitative measure of water availability in the habitat; the water activity of a solution is one-hundredth its relative humidity.

*electron transport chain (ETC)* (glossary)

A series of electron carriers that operate together to *transfer electrons from donors to acceptors such as oxygen*. Molecules involved in electron transport include nicotinamide adenine dinucleotide (*NAD+*), NAD phosphate (*NADP+*), *cytochromes, heme proteins, nonheme proteins* (e.g., iron-sulfur proteins and ferredoxin), *coenzyme Q*, flavin adenine dinucleotide (*FAD*), and flavin mononucleotide (*FMN*).

*origin of replication* (glossary)

A site on a chromosome or plasmid where DNA replication is initiated.

*organelle*

A structure within or on a cell that performs specific functions and is related to the cell in a way similar to that of an organ to the body of a multicellular organism. (size of bacteria)

*chitin* (glossary)

A tough, resistant, *nitrogen-containing polysaccharide* found in the walls of certain *fungi*, the *exoskeleton* of *arthropods*, and the *epidermal cuticle* of other *surface structures* of certain protists and animals.

*What are Viruses?*

Acellular *infectious* agents

*Cytoplasm* (glossary)

All material in the cell enclosed by the plasma membrane, with the exception of the nucleus in eukaryotic cells.

*Chromosome Partitioning* (text)

Although the process of DNA synthesis and movement seems rather straightforward, the mechanism by which *chromosomes are partitioned to each daughter cell* has not been fully elucidated. Evidence suggests that the mechanism varies with bacterial species. The models include *daughter chromosomes being pushed to opposite sides of the cell by the replisome*. Other models propose that *condensation of daughter chromosomes by structural maintenance of chromosomes (SMC) proteins pulls the DNA molecules to each end*. Evidence also exists for involvement of *the cytoskeletal protein MreB (murein cluster B) present in rod-shaped microorganisms. MreB is similar to eukaryotic actin and is important in generating rod-shaped cells*. How it might contribute to chromosome segregation is unclear. However, *cells with mutations in the gene encoding MreB fail to segregate chromosomes properly*. Finally, proteins related to those in a plasmid partitioning system called ParABS have been shown to be involved in chromosome segregation in C.

*prion* (glossary)

An *infectious agent consisting only of protein*; they cause a variety of spongiform encephalopathies such as scrapie in sheep and goats.

*virus* (glossary)

An *infectious agent* having a simple *acellular* organization with a *protein coat* and a *nucleic acid* genome, *lacking independent metabolism*, and *multiplying only* within living *host* cells.

*viroid* (glossary)

An *infectious agent* that is a *single-stranded RNA not associated with any protein*; the *RNA does not code for any proteins and is not translated*.

*hydrogenosome* (glossary)

An *organelle* found in some *anaerobic protists* that *produce ATP by fermentation*.

*Acylhomoserine Lactone (AHL)* (Quorum Sensing)

An autoinducer molecule produced by many gram-negative organisms: • diffuses across the plasma membrane • once inside the cell, it induces *expression* of target genes that regulate a variety of functions • many microbes produce effect (Text: It is now known that many Gram-negative bacteria make AHL molecular signals that vary in length and substitution at the third position of the acyl side chain (figure 7.18). In many of these species, AHL is freely diffusible across the plasma membrane. Thus at a low cell density, the diffusion gradient favors movement of AHL from the cytoplasm to the outside of the cell. However, when the cell population increases, the diffusion gradient is reversed so that movement of AHL into the cell is favored. Because the influx of AHL is cell density dependent, it enables individual cells to assess population density. When AHL reaches a threshold level inside the cell, it induces the expression of target genes that regulate a number of functions, depending on the microbe. These functions are most effective only if a large number of microbes are present.)

*neuraminidase*

An enzyme that cleaves the chemical bond linking -their- acids to the sugars present on the surface of animal cells; in virology, one type of envelope spike on *influenza viruses* has ______ activity and is used to identify different strains.

*guanosine 5'-triphosphate (GTP)* (web)

An immediate precursor of guanine nucleotides in RNA; *similar to ATP*; has a *crucial role in microtubule formation*.

*FtsA, ZipA* (Divisome Proteins and Their Functions) (T 7.1)

Anchor Z ring to plasma membrane

*autophagocytosis (or autophagy)* (glossary)

Ancient means of homeostasis whereby *intracellular components are recycled*.

*Binary Fission* (glossary)

Asexual reproduction in which a cell or an organism separates into two identical daughter cells. (cloning process)

*Is NaOH acid or base?*

Base

*The Spread Plate and Pour Plate*

Both may be used to determine the *number* or *viable* microorganisms in an original sample.

*Psychrotroph* (Temperature: Microbial Responses to Environmental Factors) (T. 7.2)

Can grow at 0-7°C; has an optimum between 20 and 30°C and a maximum around 35°C (ex: Listeria monocytogenes, Pseudomonas fluorescens)

*Thermophile* (Temperature: Microbial Responses to Environmental Factors) (T. 7.2)

Can grow at 55°C or higher; optimum often between 55 and 65°C (ex: Geobacillus stearothermophilus, Thermus aquaticus, Cyanidium caldarium, Chaetomium thermophile)

*Cilia and flagella* (table 5.1)

Cell movement

*Senescence and Death* (Text)

Cells growing in batch culture cannot remain in stationary phase indefinitely. Eventually they enter a phase that for many years was described simply as the "death phase" (figure 7.27). During this phase, the number of viable cells often declines exponentially, with cells dying at a constant rate. It was assumed that detrimental environmental changes such as nutrient deprivation and the buildup of toxic wastes caused irreparable harm to the cells. That is, even when bacterial cells were transferred to fresh medium, no cellular growth was observed. Because loss of viability was often not accompanied by a loss in total cell number, it was assumed that cells died but did not lyse. This view is currently being debated. There are two alternative hypotheses. Some microbiologists think the cells are only temporarily unable to grow, at least under the laboratory conditions used. This phenomenon, in which the cells are called viable but nonculturable (VBNC), is thought to be the result of a genetic response triggered in starving, stationary phase cells. Once the appropriate conditions are available (e.g., a change in temperature or passage through an animal), VBNC microbes resume growth. VBNC microorganisms could pose a public health threat, as many assays that test for food and drinking water safety are culture based. The second alternative to a simple death phase is programmed cell death. In contrast to the VBNC hypothesis whereby cells are genetically programmed to survive, programmed cell death predicts that a fraction of the microbial population is genetically programmed to die after growth ceases. In this case, some cells die and the nutrients they leak enable the eventual growth of those cells in the population that did not initiate cell death. The dying cells are thus "altruistic"—they sacrifice themselves for the benefit of the larger population. The view that the death phase is best described as an exponential decline in viability is also being questioned. Long-term growth experiments reveal that some microbes have a very gradual decline in the number of culturable cells. This decline can last months to years (figure 7.29). During this time, the bacterial population continually evolves so that actively reproducing cells are those best able to use the nutrients released by their dying brethren and best able to tolerate the accumulated toxins. This dynamic process is marked by successive waves of genetically distinct variants. Thus natural selection can be witnessed within a single culture vessel.

*During log phase cells exhibit balanced growth:* (Balanced Growth - log phase)

Cellular *constituents* manufactured at *constant* rates relative to each other.

*Rates of synthesis of cell components vary relative to each other and occurs under a variety of conditions:* (Unbalanced Growth - NOT exponential)

Change in *nutrient* levels: • shift-up (poor medium to rich medium) • shift-down (rich medium to poor medium) Change in *environmental* conditions

*FtsK* (Divisome Proteins and Their Functions) (T 7.1)

Chromosome segregation and separation of chromosome dimers

*Plasmids are very common in what Domains?* (table 5.2)

Common in Domains *Bacteria* and *Archaea*

*Obligate aerobe* (Oxygen Concentration: Microbial Responses to Environmental Factors) (T. 7.2)

Completely dependent on atmospheric O₂ for growth (ex: Micrococcus luteus, most protists and fungi)

*Cytoskeleton* (table 5.1)

Composed of actin filaments, intermediate filaments, and microtubules; provides cell structure and movements

*Cytoplasm* (table 5.1)

Composed of cytosol (liquid portion) and organelles; location of many metabolic processes

*Filaments that Form the Cytoskeleton* (The Cytoplasm of Eukaryotes)

Create and Perform Shape and Movement • *microfilaments* (actin); • *microtubules* (like flagellum); • *intermediate filaments*; • *motor proteins* (myosin, kinesin, and dynein)

*differential media* (glossary)

Culture media that *distinguish* between groups of microorganisms *based on differences in their growth* and *metabolic products*. (ex: blood agar-hemolytic vs. nonhemolytic; ex: MacConkey agar-lactose vs. nonlactose fermenters)

*selective media* (glossary)

Culture media that *favor* the *growth of specific microorganisms*; this may be accomplished by *inhibiting* the *growth* of *undesired microorganisms*. (ex: *MacConkey agar: selects for gram-negative bacteria*)

*supportive media* (glossary)

Culture media that are able to *sustain the growth* of many different kinds of microorganisms. (ex: tryptic soy agar)

*defined (synthetic) medium* (glossary)

Culture medium made with components of *known composition*.

*complex medium* (glossary)

Culture medium that contains some ingredients of *unknown chemical composition*.

*histone-like proteins stabilize ______ .* *Adaptations of Thermophiles*

DNA (may have evolved from heat shock proteins)

Basis for Classification: *Chemical composition; type* (T. 7.4)

Defined (synthetic), complex

*Facultative anaerobe* (Oxygen Concentration: Microbial Responses to Environmental Factors) (T. 7.2)

Does not require O₂ for growth but grows better in its presence (ex: Escherichia, Enterococcus, Saccharomyces cerevisiae)

*Obligate anaerobe* (Oxygen Concentration: Microbial Responses to Environmental Factors) (T. 7.2)

Does not tolerate O2 and dies in its presence (ex: Clostridium, Bacteroides, Methanobacterium)

*What Domain are plasmids rare in?* (table 5.2)

Domain *Archaea*

*Which Domain has a true membrane-bound nucleus?* (table 5.2)

Domain *Eukarya*

*What Domain/s have Gas Vesicles?* (table 5.2)

Domains *Bacteria* and *Archaea* not *Eukarya*

*Mitochondria* (table 5.1)

Energy production through use of the tricarboxylic acid cycle, electron transport, oxidative phosphorylation, and other pathways. (string-like very long tubes)

*Blood agar*

Enriched and differential media distinguish between hemolytic verses nonhemolytic Enriched and differential: supports the growth of many fastidious bacteria. These can be differentiated based on their ability to produce hemolysins—proteins that lyse red blood cells. Hemolysis appears as a clear zone (β-hemolysis) or greenish halo around the colony (α-hemolysis) (e.g., Streptococcus pyogenes, a β-hemolytic streptococcus).

*Stationary Phase and Starvation Response*

Entry into stationary phase due to *starvation* and other *stressful* conditions activates survival strategy: • morphological changes: *endospore* formation • decrease in *size*, protoplast shrinkage, and *nucleoid* condensation • RpoS protein assists *RNA polymerase* in transcribing genes for starvation proteins

*autolysins* (glossary)

Enzymes that partially digest peptidoglycan in growing bacteria so that the cell wall can be enlarged. (In general terms, any molecule that increases its own level of production.)

*Plasma Membrane Lipids in Domain Bacteria* (table 5.2)

Ester-linked phospholipids and hopanoids; some have sterols

*Plasma Membrane Lipids in Domain Eukarya* (table 5.2)

Ester-linked phospholipids and sterols

*Stationary Phase* (Text)

Final population size depends on nutrient availability and other factors, as well as the type of micro-organism. In stationary phase, the total number of viable microorganisms remains constant. This may result from a balance between cell division and cell death, or the population may simply cease to divide but remain metabolically active. One obvious reason microorganisms enter the stationary phase is nutrient limitation; if an essential nutrient is severely depleted, population growth will slow and eventually stop. Thus the stationary phase is similar to growth in oligotrophic environments. Interestingly, many of the survival strategies used in oligotrophic environments are also used by populations in the stationary phase of the growth cycle. Microbes enter the stationary phase for other reasons besides nutrient limitation. Aerobic organisms often are limited by O₂ availability. Oxygen is not very soluble and may be depleted so quickly that only the surface of a culture will have an O₂ concentration adequate for growth. Population growth also may cease due to the accumulation of toxic waste products. This seems to limit the growth of many cultures growing in the absence of O₂. For example, streptococci can produce so much lactic acid and other organic acids from sugar fermentation that their medium becomes acidic and growth is inhibited. Finally, some evidence exists that growth may cease when a critical population level is reached. Thus entrance into the stationary phase may result from several factors operating in concert.

*FtsZ* (Divisome Proteins and Their Functions) (T 7.1)

Forms Z ring

*Psychrophile* (Temperature: Microbial Responses to Environmental Factors) (T. 7.2)

Grows at 0°C and has an optimum growth temperature of 15°C or lower (ex: Bacillus psychrophilus, Chlamydomonas nivalis)

*Aerotolerant anaerobe* (Oxygen Concentration: Microbial Responses to Environmental Factors) (T. 7.2)

Grows equally well in presence or absence of O₂ (ex: Streptococcus pyogenes)

*Piezophile (barophile)* (Pressure: Microbial Responses to Environmental Factors) (T. 7.2)

Growth more rapid at high hydrostatic pressures (ex: Photobacterium profundum, Shewanella benthica)

*Acidophile* (pH: Microbial Responses to Environmental Factors) (T. 7.2)

Growth optimum between pH 0 and 5.5 (ex: Sulfolobus, Ferroplasma)

*Neutrophile* (pH: Microbial Responses to Environmental Factors) (T. 7.2)

Growth optimum between pH 5.5 and 8.0 (ex: Escherichia, Euglena, Paramecium)

*Alkaliphile* (pH: Microbial Responses to Environmental Factors) (T. 7.2)

Growth optimum between pH 8.0 and 11.5 (ex: Bacillus alcalophilus)

*Hyperthermophile* (Temperature: Microbial Responses to Environmental Factors) (T. 7.2)

Has an optimum between 85 - 113°C (ex: Sulfolobus, Pyrococcus, Pyrodictium)

*Stationary Phase* (notes)

In a closed system population growth eventually ceases, total number of *viable* cells remain constant: • active cells stop reproducing or reproductive rate is balanced by death rate

*Ciliary Movement and Coordination in Ciliates* (Copyright © 1967 Academic Press Inc. Published by Elsevier Inc. All rights reserved.)

In certain ciliates and especially in metazoan epithelia, ciliary activity produces a displacement not of the cells themselves but of particles in the environment. Activity under these circumstances becomes progressively more stereotyped and restrictively adapted to special needs. The autonomous movement of the individual cilium is not rotatory but simply pendular. Thus in a given ciliated field, movement occurs in the same plane during all phases of the beat. In an intact epithelium, ciliary movement is metachronal, but it seems to be synchronous in isolated ciliated cells. Ciliated epithelia of many metatoa operate under the secondary control of the nervous system, and this control is usually of an inhibitory nature. In the activity of metazoan ciliated epithelia another tendency, encountered in rudimentary form in some ciliates, seems to accompany the stabilization of the beating plane: the role of elastic elements as antagonists of contractile forces becomes more significant in the beating cycle in some epithelia. The chapter discusses some of the fragmentary and scattered data on the mechanism of ciliary activity. Two principal types of ciliary movement must be recognized: in one the planes of the effective and recovery phases of beat are identical; in the other these planes are different. Both types comprise several varieties, among which some may differ even as to the physical basis of the effective stroke.

*cristae* (glossary)

Infoldings of the inner mitochondrial membrane.

*Lysosomes* (table 5.1)

Intracellular digestion

*Cellular Growth and Determination of Cell Shape*

Is determined by *peptidoglycan* synthesis in bacteria (Text: As we have seen, bacterial and archaeal cells have defined shapes that are species specific. These shapes are neither accidental nor random, as demonstrated by the faithful propagation of shape from one generation to the next. In addition, some microbes change their shape under certain circumstances. For instance, Sinorhizobium meliloti switches from rod-shaped to Y-shaped cells when living symbiotically with plants. Likewise, Helicobacter pylori, the causative agent of gastric ulcers and stomach cancer, changes from its characteristic helical shape to a sphere in stomach infections and in prolonged culture. To consider the shape of a cell, we must consider the function of the cell wall. The cell wall constrains the turgor pressure exerted by the cytoplasm, thereby preventing the cell from swelling and bursting. Turgor pressure is a term used to describe the force pushing against the cell wall as determined by the osmolarity of the cytoplasmic contents. The component of the bacterial cell wall that is responsible for protecting the cell from lysis is peptidoglycan. The problem faced by bacterial cells is that the strength of the existing peptidoglycan in the cell wall must be maintained as new peptidoglycan subunits are added. Thus understanding peptidoglycan synthesis is critical to understanding the determination of cell shape. also review Peptidoglycan structure (section 3.4) Peptidoglycan synthesis involves many proteins, including a group of enzymes called penicillin-binding proteins (PBPs). They bear this name because they were first noted for their capacity to bind penicillin. While this property is important, their function is to link strands of peptidoglycan together and catalyze controlled degradation so that new units can be inserted during cell growth. The PBP enzymes that degrade peptidoglycan are called autolysins. Figure 7.6 illustrates some of the components of the peptidoglycan-synthesizing machinery and outlines a general scheme of peptidoglycan synthesis (see figure 12.10 for a more detailed diagram). After the NAG-NAM-pentapeptide building block is constructed, it is ferried across the plasma membrane by a lipid soluble carrier called bactoprenol. Upon release into the periplasmic space, the NAG-NAM-pentapeptide units are inserted into a peptidoglycan strand. The cellular location of autolysin activity and peptidoglycan export is not random and plays an important role in determining cell shape.)

*Mathematics of Growth* (text)

Knowledge of microbial growth rates during the exponential phase is indispensable to microbiologists. Growth rate studies contribute to basic physiological and ecological research, and are applied in industry. The quantitative aspects of exponential phase growth discussed here apply to microorganisms that divide by binary fission. During the exponential phase, each microorganism is dividing at constant intervals. Thus the population doubles in number during a specific length of time called the generation (doubling) time (g). This can be illustrated with a simple example. Suppose that a culture tube is inoculated with one cell that divides every 20 minutes (table 7.8). The population will be 2 cells after 20 minutes, 4 cells after 40 minutes, and so forth. Because the population is doubling every generation, the increase in population is always 2n where n is the number of generations. The resulting population increase is exponential; that is, logarithmic (figure 7.30).

*MacConkey (MAC) agar*

Lactose verses nonlactose fermenters. First test for gram-negative rod. Selective and differential: The selective components in MAC are bile salts and crystal violet, which inhibit the growth of Gram-positive bacteria. The presence of lactose and neutral red, a pH indicator, allows the differentiation of Gram-negative bacteria based on the products released when they use lactose as a carbon and energy source. The colonies of those that release acidic products are red (e.g., E. coli).

Basis for Classification: *Physical nature; type* (T. 7.4)

Liquid, semisolid, solid

*FtsQLB* (Divisome Proteins and Their Functions) (T 7.1)

May provide a scaffold for assembly of proteins involved in peptidoglycan synthesis

*enriched media* (glossary)

Media that *contain blood* or other *nutrients* to encourage *growth of fastidious microbes*. (ex: blood agar)

*viable but nonculturable (VBNC) microorganisms* (glossary)

Microbes that have been determined to be living in a specific environment but are not actively growing and cannot be cultured under standard laboratory conditions.

*osmophiles* (glossary)

Microorganisms that grow best in or on media of high solute concentration.

*Extremophiles* (The Influence of Environmental Factors on Growth)

Microorganisms that grow in extreme environments.

*Flagella in Domain Eukarya* (table 5.2)

Microscopic in size; membrane bound; usually 20 microtubules in 9 + 2 pattern

*What is the chromosome organization in Domain Eukarya?* (table 5.2)

More than one; chromosomes are linear

*Chromosome Replication and Partitioning* (text)

Most bacteria have a single circular chromosome. Each circular chromosome has a single site at which replication starts called the origin of replication, or simply the origin (figure 7.3). Replication is completed at the terminus, which is located directly opposite the origin. In a newly formed E. coli cell, the chromosome is compacted and organized so that the origin and terminus are in opposite halves of the cell. Early in the cell cycle, the origin and terminus move to midcell, and a group of proteins needed for DNA synthesis assemble at the origin to form the replisome. DNA replication proceeds in both directions from the origin. As progeny chromosomes are synthesized, the two newly formed origins move toward opposite ends of the cell, and the rest of the chromosome follows in an orderly fashion.

*Some media components* (TEXT)

Most complex media contain undefined components such as peptones, meat extract, and yeast extract. Peptones are protein hydrolysates prepared by partial proteolytic digestion of meat, casein, soya meal, gelatin, and other protein sources. They serve as sources of carbon, energy, and nitrogen. Beef extract and yeast extract are aqueous extracts of lean beef and brewer's yeast, respectively. Beef extract contains amino acids, peptides, nucleotides, organic acids, vitamins, and minerals. Yeast extract is an excellent source of B vitamins as well as nitrogen and carbon compounds. Three commonly used complex media are *nutrient broth, tryptic soy broth, and MacConkey agar* (table 7.6).

*Is a basic environment good for most bacteria?*

No, it's generally kills them.

*Mitochondria, Chloroplasts, Endoplasmic Reticulum, Golgi, and Lysosomes are observed in which Domain?* (table 5.2)

Observed only in Domain *Eukarya*

*What is the chromosome organization in Domain Archaea?* (table 5.2)

One circular chromosome

*intermediate filaments* (glossary)

One of the proteinaceous components of the cytoskeleton.

*microtubules* (glossary)

One of the proteinaceous components of the cytoskeleton. They are composed of tubulin proteins and are also found in the flagella and cilia of eukaryotic cells.

*Actin filaments* (glossary)

One of the proteinaceous components of the cytoskeleton; also called *microfilaments*.

*Of the 3 Domains which one has a nucleolus?* (table 5.2)

Only Domain *Eukarya*

*Peptidoglycan in the cell wall is only found in which Domain?* (table 5.2)

Only in Domain *Bacteria*

*Osmotolerant* (Solute and Water Activity: Microbial Responses to Environmental Factors) (T. 7.2)

Organisms that are able grow over wide ranges of water activity, solute, or osmotic concentration (ex: Staphylococcus aureus, Saccharomyces rouxii)

*osmotolerant* (glossary)

Organisms that grow over a fairly wide range of water activity or solute concentration.

*Golgi apparatus* (table 5.1)

Packaging and secretion of materials for various purposes; lysosome formation

*FtsI, FtsW* (Divisome Proteins and Their Functions) (T 7.1)

Peptidoglycan synthesis

*Chloroplasts* (table 5.1)

Photosynthesis—trapping light energy and forming carbohydrate from CO₂ and water

*Chloroplasts* (text)

Plastids are cytoplasmic organelles of photosynthetic protists and plants. They often possess pigments such as chlorophylls and carotenoids, and are the sites of synthesis and storage of food reserves. The most important type of plastid is the chloroplast. Chloroplasts contain chlorophyll and use light energy to convert CO₂ and water to carbohydrates and O₂; that is, they are the site of photosynthesis. Two major types of chloroplasts have been identified: those that evolved from a primary endosymbiotic event and those that evolved from a secondary (or tertiary) event (Microbial Diversity & Ecology 5.1). The chloroplasts of plants and some photosynthetic protists are primary plastids and are the focus of this discussion. Chloroplasts are quite variable in size and shape, but they share many structural features. Most are oval with dimensions of 2 to 4 μm by 5 to 10 μm, but some photosynthetic protists possess one huge chloroplast that fills much of the cell. Like mitochondria, chloroplasts are encompassed by two membranes (figure 5.17). A matrix called the stroma is enclosed by the inner membrane. The stroma contains DNA, ribosomes, lipid droplets, starch granules, and a complex internal membrane system whose most prominent components are flattened, membrane delimited sacs called thylakoids. Clusters of two or more thylakoids are dispersed within the stroma of most algal chloroplasts (figure 5.17b). In some photosynthetic protists, several disklike thylakoids are stacked on each other like coins to form grana (s., granum). Photosynthetic reactions are separated structurally in the chloroplast just as electron transport and the tricarboxylic acid cycle are in the mitochondrion. The trapping of light energy to generate ATP, NADPH, and O₂ is referred to as the light reactions. These reactions are located in the thylakoid membranes, where chlorophyll and electron transport components are also found. The ATP and NADPH formed by the light reactions are used to form carbohydrates from CO₂ and water in the dark reactions. The dark reactions take place in the stroma.

*cytokinesis* (glossary)

Processes that apportion the cytoplasm and organelles, synthesize a septum, and divide a cell into two daughter cells during cell division.

*apoptosis* (glossary)

Programmed cell death. A physiological suicide mechanism that results in fragmentation of a cell into membrane-bound particles that are eliminated by phagocytosis.

*Ribosomes* (table 5.1)

Protein synthesis

*receptors* (glossary)

Proteins that bind signaling molecules (ligands), thereby initiating cellular responses. Many viruses use host receptors to gain access to the cell.

*Aw =*

Psoln/Pwater

*What Domain are introns in genes rare in?* (table 5.2)

Rare in Domains *Bacteria* and *Archaea*

*Nucleus* (table 5.1)

Repository for genetic information

*Microaerophile* (Oxygen Concentration: Microbial Responses to Environmental Factors) (T. 7.2)

Requires O2 levels between 2-10% for growth and is damaged by atmospheric O2 levels (20%) (ex: Campylobacter, Spirillum volutans, Treponema pallidum)

*Nucleolus* (table 5.1)

Ribosomal RNA synthesis; ribosome construction

*In Domains Bacteria and Archaea their cytoskeleton is... * (table 5.2)

Rudimentary and primitive

*Mannitol salt agar*

Selective and differential: A concentration of 7.5% NaCl selects for the growth of staphylococci. Pathogenic staphylococci can be differentiated based on the release of acidic products when they use mannitol as a carbon and energy source. The acidic products cause a pH indicator (phenol red) in the medium to turn yellow (e.g., Staphylococcus aureus).

*Eosin methylene blue (EMB) agar*

Selective and differential: Two dyes, eosin Y and methylene blue, inhibit the growth of Gram-positive bacteria. They also react with acidic products released by certain Gram-negative bacteria when they use lactose or sucrose as carbon and energy sources. Colonies of Gram-negative bacteria that produce large amounts of acidic products have a green, metallic sheen (e.g., fecal bacteria such as E. coli).

*Which Domain has DNA complexed with histones?* (table 5.2)

Some *Archaea* and all *Eukaryotes*

*Cell wall and pellicle* (table 5.1)

Strengthen and give shape to the cell

*Flagella in Domain Archaea* (table 5.2)

Submicroscopic in size; filament composed of multiple different flagellins

*Flagella in Domain Bacteria* (table 5.2)

Submicroscopic in size; filament composed of single type of flagellin

Basis for Classification: *Function; type* (T. 7.4)

Supportive (general purpose), enriched, selective, differential

*Temperature Ranges and Microbial Growth* (see T. 7.3 for more info)

TEXT: The cardinal temperatures vary greatly among microorganisms (table 7.3). Optima usually range from 0°C to 75°C, whereas microbial growth occurs at temperatures extending from less than −20°C to over 120°C. Some archaea even grow at 121°C (250°F), the temperature normally used in autoclaves. A major factor determining growth range seems to be the availability of water. Even at the most extreme temperatures, microorganisms need liquid water to grow. The growth temperature range for a particular microorganism usually spans about 30 degrees. Some species (e.g., Neisseria gonorrhoeae) have a small range; others, such as Enterococcus faecalis, grow over a wide range of temperatures. The major microbial groups differ from one another regarding their maximum growth temperatures. The upper limit for protists is around 50°C. Some fungi grow at temperatures as high as 55 to 60°C. Bacteria and archaea can grow at much higher temperatures than eukaryotes. It has been suggested that eukaryotes are not able to manufacture stable and functional organellar membranes at temperatures above 60°C.

*Measurement of Cell Mass* (text)

Techniques for measuring changes in cell mass also can be used to determine population size. One approach is the determination of microbial dry weight. Cells growing in liquid medium are collected by centrifugation, washed, dried in an oven, and weighed. This is an especially useful technique for measuring the growth of filamentous fungi. However, it is time-consuming and not very sensitive. Because bacteria weigh so little, it may be necessary to centrifuge several hundred milliliters of culture to collect a sufficient quantity. A more rapid and sensitive method for measuring cell mass is spectrophotometry (figure 7.37). Spectrophotometry depends on the fact that microbial cells scatter light that strikes them. Because microbial cells in a population are of roughly constant size, the amount of scattering is directly proportional to the biomass of cells present and indirectly related to cell number. When the concentration of bacteria reaches about a million (106) cells per milliliter, the medium appears slightly cloudy or turbid. Further increases in concentration result in greater turbidity, and less light is transmitted through the medium. The extent of light scattering (i.e., decrease in transmitted light) can be measured by a spectrophotometer and is called the absorbance (optical density) of the medium. Absorbance is almost linearly related to cell concentration at absorbance levels less than about 0.5. If the sample exceeds this value, it must first be diluted and then absorbance measured. Thus population size can be easily measured as long as the population is high enough to give detectable turbidity. Cell mass can also be estimated by measuring the concentration of some cellular substance, as long as its concentration is constant in each cell. For example, a sample of cells can be analyzed for total protein or nitrogen. An increase in the microbial population will be reflected in higher total protein levels. Similarly, chlorophyll determinations can be used to measure phototrophic protist and cyanobacterial populations, and the quantity of ATP can be used to estimate the amount of living microbial mass.

*Vacuole* (table 5.1)

Temporary storage and transport; digestion (food vacuoles); water balance (contractile vacuole)

*Flagella Types* (External Cell Covering)

Text: In certain ciliates and especially in metazoan epithelia, ciliary activity produces a displacement not of the cells themselves but of particles in the environment. Activity under these circumstances becomes progressively more stereotyped and restrictively adapted to special needs. The autonomous movement of the individual cilium is not rotatory but simply pendular. Thus in a given ciliated field, movement occurs in the same plane during all phases of the beat. In an intact epithelium, ciliary movement is metachronal, but it seems to be synchronous in isolated ciliated cells. Ciliated epithelia of many metatoa operate under the secondary control of the nervous system, and this control is usually of an inhibitory nature. In the activity of metazoan ciliated epithelia another tendency, encountered in rudimentary form in some ciliates, seems to accompany the stabilization of the beating plane: the role of elastic elements as antagonists of contractile forces becomes more significant in the beating cycle in some epithelia. The chapter discusses some of the fragmentary and scattered data on the mechanism of ciliary activity. Two principal types of ciliary movement must be recognized: in one the planes of the effective and recovery phases of beat are identical; in the other these planes are different. Both types comprise several varieties, among which some may differ even as to the physical basis of the effective stroke.tinsel - tip pulls cell along (covered with hairs and thus appears thicker in light microscopy. Usually, are anteriorally-directed.)

*The Streak-Plate*

Text: In this technique, cells are transferred to the edge of an agar plate with an *inoculating loop* or swab and then *streaked out over the surface in one of several patterns*. After the first sector is streaked, the *inoculating loop is sterilized and an inoculum for the second sector is obtained from the first sector*. A similar process is followed for streaking the *third sector*, except that the *inoculum is from the second sector*. Thus *this is essentially a dilution process*. Eventually very few cells will be on the loop, and *single cells will drop from it* as it is rubbed along the agar surface. *These develop into separate colonies*.

*catabolism* (glossary)

That part of metabolism in which larger, more complex molecules are *broken down* into smaller, *simpler molecules* with the *release of energy*.

*vesicular transport* (endocytic and secretory pathway) (glossary)

The *movement of materials* in small *membrane-bound vesicles* between the *endoplasmic reticulum, Golgi apparatus, lysosomes, plasma membrane*, and other *organelles* of the *endocytic and secretory pathways* in eukaryotic cells.

*nucleolus* (glossary)

The *organelle*, located within the nucleus and *not bounded by a membrane*, that is the *location of ribosomal RNA synthesis* and the *assembly of ribosomal subunits*.

*Cis and Trans Face Functions* (The Golgi Apparatus)

The *sacs* on the *cis or forming face* are closest to the *ER (nucleus)* and often associated with it. The *sacs* on the *trans or maturing face* are farthest from the *ER*. The two faces of the Golgi *differ in thickness, enzyme content, and degree of vesicle formation*. *Cis Face → Trans Face → vesicle*

*chromosomes* (glossary)

The bodies that have most or all of the cell's DNA and contain most of its genetic information (mitochondria and chloroplasts also contain DNA).

*Virology*

The branch of microbiology that is concerned with study of viruses and viral diseases.

*stroma* (glossary)

The chloroplast matrix that is the location of the photosynthetic carbon dioxide fixation reactions.

*nuclear envelope* (glossary)

The complex *double-membrane structure* forming the outer boundary of the eukaryotic nucleus. It is covered by nuclear pores through which substances enter and leave the nucleus.

*tricarboxylic acid (TCA) cycle* (glossary)

The cycle that *oxidizes acetyl coenzyme A to CO₂* and *generates NADH and FADH₂* for *oxidation* in an *electron transport chain (ETC)*; the cycle also supplies precursor metabolites for biosynthesis. AKA: *citric acid cycle* and *Krebs cycle*.

*pyrenoid* (glossary)

The differentiated region of the chloroplast that is a center of starch formation in some photosynthetic protists.

*phagocytosis* (glossary)

The endocytotic process in which a *cell encloses large particles* in a *phagocytic vacuole* and *engulfs them*.

*Nucleus* (glossary)

The eukaryotic organelle enclosed by a *double-membrane* envelope (with pores) that *contains* the cell's *chromosomes*.

*mitochondrion* (glossary)

The eukaryotic organelle that is the *site of electron transport, oxidative phosphorylation*, and *pathways* such as the *Krebs cycle*; it *provides* most of a *nonphotosynthetic cell's energy under aerobic conditions*. *"Frequently are called the "powerhouses" of the cell because it's the place where the energy is made! Big deal with oxygen!"*

*nuclear pore complex* (glossary)

The nuclear pore plus about 30 proteins that form the pore and are involved in moving materials across the nuclear envelope.

*adenosine diphosphate (ADP)* (glossary)

The nucleoside diphosphate usually *formed upon the breakdown of ATP* when it provides energy for work.

*stationary phase* (glossary)

The phase of microbial growth in a batch culture when population growth ceases and the growth curve levels off.

*exponential (log) phase* (glossary)

The phase of the growth curve during which the microbial population is growing at a constant and maximum rate, dividing and doubling at regular intervals.

*quorum sensing* (glossary)

The process in which *bacteria monitor their own population density by sensing the levels of signal molecules* (e.g., N-acylhomoserine lactone) that are released by the microorganisms. When these signal molecules reach a *threshold concentration, quorum-dependent genes are expressed*.

*endocytosis* (glossary)

The process in which a cell takes up solutes or particles by enclosing them in vesicles pinched off from its plasma membrane. It often occurs at regions of the plasma membrane coated by proteins such as clathrin and caveolin. ______ involving these proteins is called clathrin-dependent ______ and caveolin-dependent ______, respectively. When the substance _____ed first binds to a receptor, the process is called receptor-mediated ______ .

*Plasmolysis* (glossary)

The process in which water osmotically leaves a cell, which causes the cytoplasm to shrivel up and pull the plasma membrane away from the cell wall.

*septation* (glossary)

The process of forming a *cross wall* between two daughter cells during cell division.

*septation* (glossary)

The process of forming a cross wall between two daughter cells during cell division.

*Secretory Pathway*

The process used by eukaryotic cells to *synthesize proteins and lipids*, followed by *secretion* or *delivery* to *organelles* or the *plasma membrane*.

*secretory pathway* (glossary)

The process used by eukaryotic cells to *synthesize proteins* and *lipids*, followed by *secretion or delivery* to *organelles* or the *plasma membrane*.

*The Turbidostat* (text)

The second type of continuous culture system, the turbidostat, has a photocell that measures the turbidity (defined as the amount of light scattered) of the culture in the growth vessel. The flow rate of media through the vessel is automatically regulated to maintain a predetermined turbidity. Because turbidity is related to cell density, the turbidostat maintains a desired cell density. Turbidostats differ from chemostats in several ways. The dilution rate in a turbidostat varies, rather than remaining constant, and a turbidostat's culture medium contains all nutrients in excess. That is, none of the nutrients is limiting. A turbidostat operates best at high dilution rates; a chemostat is most stable and effective at lower dilution rates.

*cell cycle* (bacterial) (glossary)

The sequence of events in a cell's growth-division cycle between the end of one division and the end of the next.

*basal body* (glossary)

The structure at the base of flagella that attaches them to the cell.

*anabolism* (glossary)

The synthesis of *complex molecules from simpler molecules* with the *input of energy and reducing power*.

*Senescence and Death Phase* (text)

There are 2 alternative hypotheses: *1)* Some microbiologists think the cells are only temporarily unable to grow, at least under the laboratory conditions used. This phenomenon, in which the cells are called viable but nonculturable (VBNC), is thought to be the result of a genetic response triggered in starving, stationary phase cells. Once the appropriate conditions are available (e.g., a change in temperature or passage through an animal), VBNC microbes resume growth. VBNC microorganisms could pose a public health threat, as many assays that test for food and drinking water safety are culture based. *2)* programmed cell death. In contrast to the VBNC hypothesis whereby cells are genetically programmed to survive, programmed cell death predicts that a fraction of the microbial population is genetically programmed to die after growth ceases. In this case, some cells die and the nutrients they leak enable the eventual growth of those cells in the population that did not initiate cell death. The dying cells are thus "altruistic"—they sacrifice themselves for the benefit of the larger population.

*Senescence and Death Phase* (notes)

There are 2 alternative hypotheses: 1) cells are *viable* But Not *culturable* (VBNC); cells alive, but dormant, capable of new growth when conditions are right 2) *programmed cell death*; fraction of the population genetically programmed to die (commit suicide)

*FtsN* (Divisome Proteins and Their Functions) (T 7.1)

Thought to trigger constriction initiation

*Endoplasmic reticulum (ER)* (table 5.1)

Transport of materials; lipid synthesis

*What is the chromosome organization in Domain Bacteria?* (table 5.2)

Usually one circular chromosome

*Does Domain Archaea have introns in their genes?* (table 5.2)

Yes, they do

*In Domain Eukarya their cytoskeleton is... * (table 5.2)

a network of structures made from filamentous proteins and other components in the cytoplasm of cells.

*Barotolerant* (Pressure)

are adversely affected by *increased pressure*, but not as severely as *nontolerant* organisms.

*Facultative Anaerobes* *Oxygen and Bacterial Growth*

are fermenters that do NOT require O₂ but grow better in its presence

*pH is critical in ______. *

bacteria identification

*Media Component: Extracts*

beef and yeast extract are aqueous extracts of lean beef and brewer's yeast and brain

*Cyanobacteria =*

blue from oxidized copper (copper oxide)

*Dilution Rate and Microbial Growth*

cell density maintenance at wide range of dilution rates chemostat works best at low dilution rate

*Biofilms can be formed on any ______ surface.*

conditioned

*Glycolysis is done in the ______ .*

cytoplasm

*Disrupts chemical structure of many molecules, including DNA* (Ionizing Radiation)

damage may be repaired by DNA *repair mechanisms* if small dose

*The higher the temperature and pH the more _____ it can be for many mibrobes.*

deadly

*Deinococcus raiodurans* (Ionizing Radiation)

extremely resistant to *DNA* damage (oldest organisms on earth and are still around!)

*Halophiles* (Effects of NaCl on Microbial Growth)

grow optimally a > 0.2 M

*Aerotolerant Anaerobes* (Oxygen and Bacterial Growth)

grow with or without O₂

*Anaerobe* (Oxygen and Bacterial Growth)

grows best in the absence of O₂ but will not die in the presence of O₂

*Aerobe* (Oxygen and Bacterial Growth)

grows in presence of atmospheric oxygen (O₂) which is 20% O₂

*Oxygen Concentration*

growth in oxygen correlates with microbes energy conserving metabolic processes and the *electron transport chain* (ETC) and natural terminal *electron* acceptor

*neutrophile pH*

growth optimum between 5.5 - 8.0

*alkaliphiles alkalophiles*

growth optimum between 8.5 - 11.5

*acidophile pH*

growth optimum between between 0 - 5.5

*Some Bacteria and Archaea live in deep sea with very high ______ pressures.* (Pressure)

hydrostatic

*Viruses are... *

important model systems in *molecular* biology

*Aw = Psoln/Pwater*

low water activity means most water is bound

*Bacterial Cell Cycle:*

most bacteria divide by *binary fission*

*Important Members of Aquatic World* (Viruses)

move organic matter from particulate to dissolved

*Prions* (Acellular Agents)

only *Proteins*

*Viroids* and *Virusoids* (Acellular Agents)

only *RNA*

*Changes in ______ concentrations in the environment may affect microbial cells* (Solutes and Water Activity)

osmotic (hyper/hypotonic)

*Media Component: Peptone*

protein hydrolysates prepared by partial digestion of various protein sources

*Cisterna (plural cisternae)* (The Golgi Apparatus)

refers to a *flattened membrane disk that makes up the endoplasmic reticulum and Golgi apparatus*. A Golgi stack may contain anywhere from three to twenty of them but most contain about six. Golgi _______ can be separated into *four classes; cis, medial, trans, and TGN (trans-Golgi network)*. Each _______ class *contain different enzymes* working within it.

*A group of proteins needed for DNA synthesis assemble at the origin to form the ______ .* (Chromosome Replication and Partitioning)

replisome

*Extreme Halophiles* (Effects of NaCl on Microbial Growth)

require > 2 M

*Halophiles* (Extremely Adapted Microbes)

require the presence of NaCl at a concentration above about 0.2 M

*Microaerophiles* (Oxygen and Bacterial Growth)

requires 2 - 10% O₂

*Obligate Aerobe* (Oxygen and Bacterial Growth)

requires oxygen or it will die

*Virologists*

scientists that study viruses

*Most bacteria have a ______ chromosome.* (Chromosome Replication and Partitioning)

single circular

*Increase internal solute concentration with compatible solutes in increase their internal osmotic concentration in hypotonic solutions* (Microbes Adapt to Changes in Osmotic Concentrations)

solutes compatible with *metabolism* and *growth*

*It is now known a variety of virions have enzymes.* (Virion Enzymes

some are associated with the envelope or capsid but most are within the capsid

*Cytoplasmic Microtubules* Electron micrograph of a transverse section through the axopodium of a protist known as a heliozoan (×48,000). Note the parallel array of microtubules organized in a spiral pattern. (5.7)

strings of doublets that form this spiral and has little connections keeping it all together

*Virion Size* (The Structure of Viruses)

their range is ~ *10-400* nm in diameter and most must be viewed with an electron microscope

*These microbes cannot ______ O₂ (Strict Anaerobic Microbes)

tolerate

*Biofilms are ______ in nature in water.*

ubiquitous

*Obligate Anerobe* (Oxygen and Bacterial Growth)

usually killed in the presence of O₂

*Many microorganisms change the pH of their habitat by producing acidic or basic ______ products.* (pH)

waste

*Flagella (s., flagellum)* (External Cell Covering)

• *100 - 200µm* long (∼ 2mm) *Move in undulating fashion* *tinsel*: tip pulls cell along *whiplash*: naked flagellum

*Cilia (s., cilium)* (External Cell Covering)

• *5 - 20µm* long (bacteria ∼ 1µm) • beat with 2 phases, working like oars (bacteria like propellers)

*Endocytosis*

• *Clathrin-coated* and some *caveolin-coated vesicles* deliver their contents to *endosomes* (organelles containing hydrolytic enzymes). • *Early* endosomes mature into late endosomes, which fuse with *lysosomes*. • caveosome then fuse with early endosomes (to become a lysosome) (Text: Clathrin-coated vesicles and some caveolin-coated vesicles deliver their contents to small organelles containing hydrolytic enzymes. These organelles are called early endosomes (figure 5.10). Early endosomes mature into late endosomes, which fuse with lysosomes. The development of early endosomes into late endosomes is not well understood. It is thought that maturation involves the selective retrieval of membrane proteins. Phagosomes and some caveolin-coated vesicles take a different route to lysosomes. Phagosomes fuse directly with lysosomes (figure 5.10) to form a phagolysosome. The caveolin-coated vesicles deliver their contents to an organelle termed a caveosome. The caveosome then fuses with an early endosome.)

*Bacterial Cell Cycle:* *Two Pathways Function During Cycle*

• *DNA* replication and partition • *cytokinesis*

*Mitochondrial Matrix Inner Membrane Structure*

• *Is* a *Good* (tight) Barrier • highly folded to form *cristae* (s., crista) • location of *enzymes* and *electron* carriers for the *electron transport chain (ETC)* and *oxidative phosphorylation* • matrix enclosed by inner membrane (text: the inner membrane has infoldings called cristae (s., crista), which greatly increase its surface area. The shape of cristae differs in mitochondria from various species. Platelike (laminar) cristae, cristae shaped like disks, tubular cristae, and cristae in the shape of vesicles have all been observed.)

*Mitochondrial Outer Membrane Structure*

• *NOT* a *good* (loose) Barrier • contains *porins* and thus is similar to the outer membrane of *Gram-negative* bacteria (text: The mitochondrion is bounded by two membranes: an outer mitochondrial membrane separated from an inner mitochondrial membrane by a 6 to 8 nm intermembrane space (figure 5.15). The outer mitochondrial membrane contains porins and thus is similar to the outer membrane of Gram-negative bacteria.)

*Eukaryotic Ribosome Proteins*

• *Proteins* made on the *ribosomes of the RER* are often *secreted* or are *inserted* into the *ER membrane* as *integral membrane proteins* • *Free ribosomes* are the sites of *synthesis* for *nonsecretory* and *nonmembrane proteins* • Some proteins synthesized by free ribosomes are inserted into organelles (Text: Both free and ER-bound ribosomes synthesize proteins. Proteins made on the ribosomes of the RER are often secreted or are inserted into the ER membrane as integral membrane proteins. Free ribosomes are the sites of synthesis for nonsecretory and nonmembrane proteins. Some proteins synthesized by free ribosomes are inserted into organelles such as the nucleus, mitochondrion, and chloroplast. Proteins called molecular chaperones aid the proper folding of proteins after synthesis. They also assist the transport of proteins into eukaryotic organelles such as mitochondria.)

*Eukaryotic Microbe Reproductive Strategies*

• *asexual* (mitosis) and *sexual* (meiosis; same species) • haploid or diploid

*Virions* (General Properties of Viruses )

• *complete virus particle* • consists of *≥1 modelcule of DNA or RNA enclosed in a coat of protein* • may have additional layers • *cannot reproduce* independent of living cells nor carry out cell division • but can exist extracellularly

*infection in eukaryotic cells *

• *cytocidal* infections results in cell death through lysis • persistent infections may last years • *cytopathic* effects (CPEs) -degenerative changes -abnormalities • transformation to *malignant* cell

*After a Lysosome is Formed... *

• *digestion occurs* without release of lysosome enzymes into the cytoplasmic matrix • as contents are digested, *products leave the lysosome* and can be *used as nutrients* • resulting lysosome called a *residual body* which can *release its contents to the cells exterior* by a process called *lysosome secretion*

*Viable Counting Methods: Spread and Pour Plate Techniques*

• *diluted* sample of bacteria is spread over solid agar surface or mixed with agar and poured into a Petri plate • after incubation the number of organisms are determined by counting the number of *colonies* multiplied by dilution factor • results expressed as *colony forming unit* (CFU) CFU = single cell in count

*Quantification of Virus*

• *direct* counting - count viral particles • indirect counting by an observable of the virus - *hemagglutination* assay - plaque assays

*The Nuclear Envelope* (The Nucleus)

• *double-membrane structure* that *delimits* the *nucleus* • continuous with *ER* • penetrated by *nuclear pores*

*Bacteria and Archaea Reproduction*

• *haploid* only • asexual - *binary fission* • budding • filamentous (string end-end; eg.: actinomycetes) • all must replicate and segregate the genome prior to division

*Intermediate Filaments*

• *heterogeneous* elements of the cytoskeleton: *∼ 10 nm in diameter* • *keratin* (hair) and *vimentin*

*Measuring Biological Effects *

• *infectious dose* and lethal dose assays - determine smallest amount of virus needed to cause infection (ID) or death (LD) of *50%* of exposed host cells or organisms - resulted expressed as LD₅₀ or LD₅₀

*Smooth ER*

• *membrane synthesis* • devoid of ribosomes (*detoxification* function) • *synthesis* of *lipids* by *ER-associated enzymes*

*Possible Reason for Stationary Phase*

• *nutrient* limitation • limited *oxygen* availability • *toxic waste* accumulation • critical *population density* reached

*Chromosome Partitioning*

• *replisome* pushes, or condensation of, daughter chromosomes to opposite sides of the cell • *MreB* (*murein cluster B*): an actin homolog; plays a role in determination of cell shape as spiral inside cell periphery, and chromosome segregate

*Rough ER*

• *ribosome* attached (studded) • *synthesis* of secreted *proteins* by ER-associated ribosomes

*Capsomers* (Icosahedral Capsids)

• *ring or knob-shaped* units made uo of 5-6 protomers • *pentamers* (pentons) - 5 subunits ______ • *hexamers* (hexons) - 6 subunits ______

*Important in Evolution* (Viruses)

• *transfer genes* between bacteria and others (inject gene from old host to new and may be an off-shoot of host itself!)

*Functions of ER*

• *transport proteins*, *lipids*, and other materials within the cell • major site of cell *membrane synthesis*

*virus and cancer *

• *tumor* -growth or lump tissue; -benign tumors remain in place • *neoplasia* -abnoraml new cell growth and reproduction due to loss of regulation • *anaplasia* -reversion to a more primitive or less differentiated state • *metastasis* -spread of cancerous cells throughout body

*Quality Assurance Mechanism* (The Secretory Pathway)

• *unfolded* or *misfolded proteins* are secreted into cytosol, *targeted* for *destruction* by *ubiquitin polypeptides* • *proteasomes* destroy targeted proteins

*The Nucleolus*

• *≥ 1* nucleolus/nucleus • *organelle* but *not membrane enclosed* • important in *ribosome synthesis*

*MinCDE system in E. coli:* *3 Proteins Compose the System*

• 1) MinC, 2) MinD, and 3) MinE: these proteins oscillate from one end of the cell to the other; • link Z-ring to cell membrane • Z ring *constricts* and cell wall synthesis of septal wall (Text: limits Z-ring formation to the center of the cell. Three proteins compose the system (MinC, MinD, and MinE). These proteins oscillate from one end of the cell to the other (figure 7.4). This oscillation creates high concentrations of MinC at the poles, where it prevents formation of the Z ring; thus Z-ring formation can occur only at midcell, which lacks MinCDE.

*Chloroplast Structure... What are they made of?*

• A matrix called the *stroma* is enclosed by the inner membrane. • The *stroma contains DNA, ribosomes, lipid droplets, starch granules*, and *thylakoids*. (text: A matrix called the stroma is enclosed by the inner membrane. The stroma contains DNA, ribosomes, lipid droplets, starch granules, and a complex internal membrane system whose most prominent components are flattened, membrane delimited sacs called thylakoids.)

*Virions Infect All Cell Types *

• Bacterial viruses called bacteriophages (*phages*) • Few *archaeal* viruses • Most are eukaryotic viruses (plants, animals, protists, and fungi) • Classified into families based on *genome structure*, life cycle, morphology, genetic relatedness

*External Cell Covering*

• Cilia • Flagella

*Microbial Growth on Solid Media*

• Colony *characteristics* that develop when microorganisms are grown on agar surfaces aid in identification • Microbial growth in *biofilms* is similar Differences in growth rate from edges to center is due to: -oxygen, nutrients, and *toxic* products -cells may be dead in some areas (Text: Colony development on agar surfaces aids microbiologists in identifying microorganisms because individual species often form colonies of characteristic size and appearance (figure 7.26). When a mixed population has been plated properly, it sometimes is possible to identify the desired colony based on its overall appearance and use it to obtain a pure culture.)

*Neural Loss*

• Evidence suggests that must be present for neural degeneration to occur • Interaction of PrP(↑Sc) with PrP(↑c) may cause PrP(↑c) to crosslink and trigger apoptosis • PrP(↑c) conversion form through unknown mechanism

*synthesis stage *

• Genome dictates the events • *dsRNA* typical flow: - virus must carries in or synthesizing the proteins necessary to complete synthesis • stages may occur (ex. early or late)

*Plasma Membrane Lipids in Domain Archaea* (table 5.2)

• Glycerol diethers • Diglycerol tetraethers

*Assembly *

• Late proteins are important to assembly • Assembly is complicated but varies: -*bacteriophages* - stages -some are assembled in nucleus -some are assembled in cytoplasm -may be seen as *paracrystalline* structures in cell

*Early Development of Virology*

• Many epidemics of viral diseases occurred before anyone understood the nature of their causative agents (prions, etc...) • Historical evidence suggests that epidemics caused by *measles* and *smallpox* viruses were among the causes for the decline of the Roman Empire.

*Organelles Involved in Energy Conservation* (nothing happens without this energy currency)

• Mitochondria • Hydrogenosomes • Chloroplasts (All designed to make energy by making enough gradient to make ATP)

*Organelles Involved in a Genetic Control of the Cell*

• Nucleus • Ribosomes

*Current Model of Disease Production by Prions *

• PrP(↑c) (prion protein) is present in "normal" form in host and abnormal form of prion protein is PrP(↑Sc) • Entry of PrP(↑Sc) into animal brain causes PrP(↑c) protein to change its *conformation* to abnormal form, PrP(↑Sc) • The newly produced PrP(↑Sc) molecules then convert more normal molecules to the abnormal form through unknown mechanism

*attachment (adsorption) *

• Specific receptor attachment • Receptor determines host preferences

*chromatin* (glossary)

• The complex of *DNA and proteins*, including histones, from which *chromosomes* are made. • Has more protein than (about 55%) than DNA.

*water activity (a↓w)*

• The water activity of a solution is 1/100 the relative humidity of the solution (when expressed as a percent). • It is also equivalent to the ratio of the solution's vapor pressure (Psoln) to that of pure water (Pwater). • Aw = Psoln/Pwater (low water activity means most water is bound) • *osmotolerant* microbes can grow over wide ranges of water activity

*Thylakoid Function in Chloroplasts*

• a flattened membrane-delimited sacs • grana (s., granum) - stacks of thylakoids • site of *light* reactions (trapping of light energy to generate *ATP*, NADPH, and oxygen) (text: Clusters of two or more thylakoids are dispersed within the stroma of most algal chloroplasts (figure 5.17b). In some photosynthetic protists, several disklike thylakoids are stacked on each other like coins to form grana (s., granum).)

*Peptidoglycan Determines Synthesis in Bacteria* (Cellular Growth and Determination of Cell Shape)

• a group of enzymes called *penicillin-binding proteins (PBPs)* link strands of peptidoglycan together and catalyze controlled degradation so that new units can be inserted during cell growth. • *autolysins* are PBP enzymes that degrade peptidoglycan and site new units added • The cellular location of autolysin activity and peptidoglycan export is not random and plays an important role in determining cell shape.

*Biofilms*

• a mature biofilm is a complex, *dynamic community*, of microorganisms • *heterogeneity* is the differences in metabolic activity and locations of microbes • interactions occur among the attached organisms

*Isolation of Pure Cultures*

• a population of cells arising from a single cell developed by *Robert Koch* • allows for the study of a single type of microorganism in a mixed culture • spread plate, streak plate and pour plate are techniques used to isolate *pure cultures*

*Spread Plate*

• a small volume of a diluted mixture containing around 30-300 cells is transferred to the center of an agar plate and... • spread evenly over the surface with a sterile bent rod. • The dispersed cells develop into isolated colonies.

*Chloroplasts... What are they?*

• a type of *plastid* • same pigment organelles observed in plants and algae • site of *photosynthetic* reactions, (thylakoid sacs for proton gradient) • surrounded by *double* membrane (like cyanobacteria) (test: Plastids are cytoplasmic organelles of photosynthetic protists and plants. They often possess pigments such as chlorophylls and carotenoids, and are the sites of synthesis and storage of food reserves. The most important type of plastid is the chloroplast.)

*Phagocytic Endocytosis*

• a type of endocytosis that *involves the use of cell surface protrusions to surround and engulf particulates*. • *fuses with lysosomes* and resulting in *vesicles* called *phagosomes*.

*Icosahedral Capsids *

• a viral capsid that has the shape of a regular polyhedron having 20 equilateral triangular faces and 12 corners (vertices). • it is one of natures favorite shapes

*The Two Types of Vesicle Transport* (The Secretory Pathway)

• after release some vesicles deliver their contents to *endosomes and lysosomes* *2 types of vesicles transport materials to the plasma membrane*: • 1st type: *constitutive delivery to membrane*. (never stops; always on) (text: 1 type constitutively delivers proteins in an unregulated manner, releasing them to the outside of the cell as the ______ fuses with the plasma membrane) • 2nd type: *Secretory vesicles* in multicellular eukaryotes *store the proteins* until the cell receives an appropriate *signal to release*

*Virion Composition* (The Structure of Viruses)

• all contain a nucleocapsid which is composed of nucleic acid (DNA and RNA) and a protein coat (*capsid*) • some viruses only consist of a nucleocapsid, others have additional components

*Exponential Phase*

• also called *log* phase • rate of growth and division is *constant* and *maximal* • population is most uniform in terms of chemical and physical properties during this phase *"magic phase"* FULL OUT DIVISION: every cell is *happy and dividing!*

*Major Cause of Disease* (Viruses)

• also important as a new source of therapy • new viruses are emerging

*water activity (a↓w)* (Solutes and Water Activity)

• amount of water available to organism • reduced by interaction with *solute* molecules (osmotic effect) higher [solute] → lower a↓w • reduced by absorption to surfaces (matric effect)

*MreB (murein cluster B)* (Chromosome Partitioning)

• an actin homolog • plays a role in determination of cell shape as spiral inside cell periphery, and chromosome segregation • new origins associate with their tracks • if mutated chromosomes do not segregate

*The Secretory Pathway: Overview & RER*

• are used to move materials to various sites *within the cell*, as well as, to either the *plasma membrane* or the *cell exterior* • *proteins destined* for the *plasma membrane*, *endosomes*, and *lysosomes* or *secretion* are synthesized by *ribosomes* on the RER. • targeted to the RER lumen and are released in small *budding vesicles* from the RER

*Nuclear Pore* (The Nucleus)

• associated proteins make up the *nuclear pore complex* • pores allow *materials (protein, mRNA, tRNA, transcriptase*, etc...) to be *transported into* or *out* of the *nucleus* • "more of a trap to keep DNA in!" the *nuclear pore complex*

*basal body*

• at base of flagellum or cilium • directs synthesis of flagella and cilia

*Steps for Viral Multiplication*

• attachment to host cell • *entry* • uncoating of genome • synthesis • *assembly* • release

*Viable Counting Methods: Membrane Filter Techniques*

• bacteria from aquatic samples are trapped on membranes of known *pore size* • membrane soaked in culture media • colonies grow on membrane • colony count determines number of bacteria in *original* sample

*Cell to Cell Communication Within the Microbial Populations*

• bacterial cells in biofilms communicate in a *density-dependent* manner called *quorum sensing* • produce small proteins that increase in concentration as microbes replicate and convert a microbe to a competent state and... • *DNA uptake* occurs, *bacteriocins* are released

*Clathrin-dependent Endocytosis*

• begins with *coated pits*, which are specialized membrane regions *coated* on the *cytoplasmic side* with the *protein clathrin*. • *coated pits* have external *receptors* that specifically *bind with macromolecules* • *pinching off* of *coated pits forms coated vesicles* • called *receptor-mediated endocytosis* (Text: begins with coated pits, which are specialized membrane regions coated on the cytoplasmic side with the protein_____m. The endocytic vesicles formed when these regions invaginate are called coated vesicles. ______ is used to internalize hormones, growth factors, iron, and cholesterol.)

*Molecular Unity in Eukaryotic, Bacterial and Archaeal Cells*

• biochemical processes, metabolic pathways • *genetic code, double strand, same bases*

*Measurement of Microbial Growth*

• can measure changes in *number of cells* in a population • can measure changes in *mass* of population

*Prions - Proteinaceous Infectious Particles*

• cause variety of degenerative diseases in humans and animals - *scrapie* in sheep - bovine spongiform encephalopathy (BSE) or mad cow disease - *Creutzfeldt- Jakob* disease (CJD) and variant CJD (vCJD) - Kuru

*Lag Phase*

• cell synthesizing new components (to *replenish* spent materials and to *adapt* to new medium or other conditions) • varies in length (in some cases can be very short or absent)

*Direct Counts on Membrane Filters*

• cells filtered through special membrane that provides *dark* background for observing cells • cells are stained with *fluorescent* dyes • useful for counting bacteria; NOT eukaryotes as they don't pick up dye • with certain dyes, can distinguish *living* from *dead* cells

*Culture Media Classification*

• chemical constituents from which they are made • physical nature • function

*Vibrio* (Cell Wall Growth and Cell Shape Determination)

• comma-shaped bacteria (curved) • FtsZ: forms Z ring • MreB: *helical* polymerization throughout cell • Crescentin (Text: The last cell shape we consider is that of comma-shaped cells, as studied in the aquatic bacterium Caulobacter crescentus. In addition to the actin homologue MreB and the tubulin-like protein FtsZ, these cells (and other vibrioid-shaped cells) produce a cytoskeletal protein called crescentin, a homologue of eukaryotic intermediate filaments (see figure 3.32). This protein localizes to one side of the cell, where it slows the insertion of new peptidoglycan units into the peptidoglycan sacculus (figure 7.8). The resulting asymmetric cell wall growth gives rise to the inner curvature that characterizes this cell shape. also review Caulobacteraceae and Hyphomicrobiaceae (section 22.1))

*Chromatin* (The Nucleus)

• complex of DNA, *histones*, and other *proteins* • *5 types of histones in cells*: H1, H2A, H2B, H3, and H4 (all come together to spool DNA) • chromatin *condenses* into chromosomes during division

*carcinogenesis *

• complex, mulitstep process • often involved oncogenes -cancer causing genes -may come from the virus -may be transformed host *protoncogenes* which are involved in normal regulation of cell growth and *differentiation*

*The Cytoplasm of Eukaryotes*

• consists of a liquid component, the *cytosol*, in which many *organelles are located*. • is a vast, dynamic *network of interconnected filaments* within the cytoplasmic matrix • filaments form the cytoskeleton • plays a role in both cell *shape* and *movement*

*Membranes Structure* (Eukaryotic Cell Envelopes)

• consists of the plasma membrane and all coverings external to it ("everything happens here!")

*Importance Continuous Culture Methods*

• constant supply of cells in exponential phase growing at a known rate • study of microbial growth at very low nutrient concentrations, close to those present in the natural environment • study of *interactions* of microbes under conditions resembling those in aquatic environments • food and industrial microbiology

*Microbial environments are complex, ______, often contain low nutrient concentrations ( ______ ) and may expose a microorganism to overlapping ______ and environmental factors.* (Microbial Growth in Natural Environments)

• constantly changing • oligotrophic environment • gradients of nutrients

*growth in an open system*

• continual provision of nutrients • continual removal of wastes

*Counting Chamber*

• counting known volume of liquid • easy, inexpensive, and quick • useful for counting both eukaryotes and prokaryotes • cannot distinguish living from dead cells; stain kills anyway, but can backstain metabolic activity

*"If your function is in the cytoplasm you're probably going to get made in the ______ . If function is in the organelle or a lysosome you're going to go to the ______ to get made."*

• cytoplasm • ER

*Autophagy*

• delivery of materials to be digested by route that *does not involve endocytosis* • *macroautophagy* involves *digestion* and *recycling* of cytoplasmic components • *double membrane* surrounds cell component forming an *autophagosome* • *autophagosome fuses* with a *lysosome*

*FtsZ Role in Cocci Divisome* (Cell Wall Growth and Cell Shape Determination)

• determines site of cell wall growth • may recruit PBPs for synthesis of septum

*Nucleolus Role in Ribosome Synthesis*

• directs *synthesis* and *processing* of *rRNA* • directs assembly of *rRNA* and *ribosomal proteins* to form partially completed *ribosomal subunits* (self-assemble) • *ribosomes mature* in *cytoplasm* (You are not making proteins in the nucleus you are making them in the cytoplasm)

*viral genomes *

• diverse nature of genomes • a virus may have a single or double stranded *DNA* or *RNA* • the size of the nucleic acid also varies form virus to virus • genomes can be segmented or *circular*

*Evidence Hydrogenosomes Descended From a Common Mitochondrial Ancestor*

• double membrane, no cristae, usually lack DNA • ATP is generated by *fermentation* process rather than respiration • CO₂, H₂, and *acetate* are products

*Variant Creutzfeldt-Jakob (vCJD) v. CJD:* *Difference in Disease is the Origin*

• eating meat from BSE infected cattle can cause variant Creutzfeldt-Jakob (vCJD) in humans • CJC is caused by spontaneous mutation of the gene that codes the prion protein

*Caveolin (Caveole)-dependent Endocytosis*

• enriched in *cholesterol* and the *membrane protein ______ * • when ______ pinch off are called *______ -coated vesicles* • they *do not deliver their contents to lysosomes* • may play a role in *signal transduction, transport of small molecules and macromolecules* (Text: involves caveolae ("little caves"), tiny, flask-shaped invaginations of the plasma membrane (about 50 to 80 nm in diameter) that are enriched in cholesterol and the membrane protein ______ . The vesicles formed when ______ pinch off are called ______ -coated vesicles. ______ has been implicated in signal transduction, transport of small molecules such as folic acid, as well as transport of macromolecules. Evidence exists that toxins such as cholera toxin enter their target cells via ______ . ______ also are used by many viruses, bacteria, and protozoa to enter host cells.)

*viral entry and uncoating *

• entire genome or nucleocapsid • varies between naked or enveloped virus • three methods used

*Prions Cause Bovine: Spongiform Encephalopathy* (BSE or *mad cow disease*) (Other Prion Diseases)

• epidemic proportions in England 1900s • initially spread because cows were fed meal made from all parts (including brain tissue) or infected cattle

*Virusoids*

• formally called *satellite* RNAs • covalently closed, circular infectious ssRNAs • encode one or more gene products • require a *helper virus* for replication - human hepatitis D virus is virusoid - required human hepatitis B virus

*Continuous Culture of Microorganisms*

• growth in an *open* system • maintains cells in *log* at a constant biomass concentration for extended periods • achieved using a continuous culture system (spectrometer reading)

*Variant Creutzfeldt-Jakob (vCJD) v. CJD:* *All Prion Caused Disease*

• have *no effective* treatment • result in progressive *degeneration of the brain* and *eventual death*

*Extreme Halophiles* (Extremely Adapted Microbes)

• have adapted so completely to hypertonic, saline conditions that they require NaCl concentrations between about 2 M and saturation (about 6.2 M). • extremely high concentrations of *potassium* • cell wall, proteins, and plasma membrane require high salt to maintain *stability* and activity

*Hypertonic Solutions* (Solutes and Water Activity)

• higher osmotic concentration (H₂O) • water leaves the cell • membrane shrinks from the cell wall (plasmolysis) may occur; most cells have a cell wall.

*Viable Counting Methods are used when... *

• if microbe cannot be cultured on plate media • dilutions are made and added to suitable media • *turbidity* determined to yield the *most probable number (MPN)*

*production of starvation proteins* (Starvation Responses)

• increase *cross-linking* in cell wall • Dps proteins protect *DNA* • *chaperone* proteins prevent protein damage

*Increase in cellular constituents that may result in:* (Growth)

• increase in cell *number* • increase in cell *size*

*Viroids*

• infectious agents only composed of closed, circular ssRNAs • do not encode *gene* products • requires host cell DNA-dependent *RNA polymerase* to replicate • cause *plant* diseases -some found in infected host cell nucleolus, others found in chloroplast -may cause disease by triggering RNA silencing

*Crescentin in Vibrio* (Cell Wall Growth and Cell Shape Determination)

• intermediate homologue cytoskeleton protein • localizes to short, curved side • asymmetric cell wall synthesis forms curves

*Secretory Endocytic Pathway*

• intricate *complex of membraneous organelles* and *vesicles* that *move materials* into the cell *from outside*, and *from inside to the outside*, and *within* the cell • *Endoplasmic reticulum* (ER) • *Golgi apparatus* • *lysosomes* ("like your stomach")

*Endoplasmic Reticulum (ER)*

• irregular *network* of branching and fusing *membranous tubules* and *flattened sacs* called *cisternae (s., cisterna)*.

*Mitochondrial Matrix Structure*

• is *enclosed by inner membrane* • *contains ribosomes* (same size as bacteria), *DNA* (may be circular like bacterial DNA), and large *calcium phosphate granules* • *contains enzymes* of the *tricarboxylic acid cycle* (where *most of ATP made*) and *enzymes involved in catabolism of fatty acids* *"THIS IS ALL ABOUT ATP PRODUCTION!"* (text: The inner membrane encloses the *mitochondrial matrix, a dense material containing ribosomes, DNA, and often large calcium phosphate granules. In many organisms, mitochondrial DNA is a closed circle*, like most bacterial DNA. However, in some protists, mitochondrial DNA is linear.... (figure 5.15). *Metabolic processes such as the tricarboxylic acid cycle and the generation of ATP, the major energy currency of all life forms, take place here*. ... They are about the *same size as bacterial cells*. Some cells possess *1,000 or more mitochondria*; others (some yeasts, unicellular algae, and trypanosome protists) have a *single, giant, tubular mitochondrion twisted into a continuous network* permeating the cytoplasm.)

*Plasma Membrane* (Eukaryotic Cell Envelopes)

• is a *lipid bilayer* • major membrane lipids include *phosphoglycerides*, *sphingolipids* and *cholesterols*, all of which contribute to the *strength* of the plasma *membrane* • *microdomains* participate in a variety of cellular processes (e.g., signal transduction, assembly and release of virus particles, and endocytosis)

*The Growth Curve*

• is observed when microorganisms are cultivated in batch culture • usually plotted as a *logarithm* of cell number verses time • has 4 distinct phases:

*Stroma Function in Chloroplasts*

• it is the site of dark reactions of photosynthesis (formation of carbohydrates from *water* and *carbon dioxide*) • algal chloroplasts many contain a *pyrenoid* which participate in polysaccharide synthesis.

*virion enzymes *

• it was first erroneously thought that all virions lacked enzymes • now known a variety of virions have enzymes

*capsid *

• large macromolecular structures which serve as a protein coat of virus • protect viral genetic material and aids in its transfer between host cells • made of protein subunits called *protomers* • capsids are helical, *icosahedral*, or complex

*Eukaryotic Ribosomes Density*

• larger that *70S* (density not weight) bacterial • *80S* in size: *60S + 40S subunits = 80S* in size (*not 100*; it's the time of sedimentation) • may be *attached to ER* or *free in cytoplasmic matrix* *60S* is *bound* to *subunit ER*

*cells are called persister cells (subset of the species)* (Starvation Responses)

• long-term survival • increased virulence (making antibiotic, acid waste, combat other cell types)

*Hypotonic Solutions* (Solutes and Water Activity)

• lower osmotic concentration (H₂O) • water enters the cell • cell swells and may burst

*Viral Envelopes and Enzymes *

• many viruses are bound by an outer, flexible, membranous layer called the envelope • animal virus envelope (lipids and carbohydrates) usually rise from host cell plasma or nuclear membranes

*archaeal viruses *

• may be lytic or temperate • most discovered so far are temperate by unknown mechanisms

*Receptor determines host preferences* (attachment/adsorption)

• may be specific tissue (tropism) • may be more than one *host* • may be more than one receptor • may be in *lipid rafts* providing entry of virus

*pH*

• measure of the relative acidity of a solution • negative logarithm of the *hydrogen ion [H+]*

*Plasma membrane* (table 5.1)

• mechanical cell boundary; • *selectively permeable barrier* with transport systems; • *mediates cell-cell interactions* and adhesion to surfaces; • secretion; • signal transduction

*viral multiplication*

• mechanism used depends on viral structure and genome • steps are similar

*The Nucleus*

• membrane-bound *spherical* structure that *houses genetic material* of eukaryotic cells • contains dense fibrous material called *chromatin*

*Lysosomes*

• membrane-bound *vesicles* found in most eukaryotes • involved in *intracellular digestion* • contain *hydrolases* enzymes which *hydrolyze molecules* and *function* best under *slightly acidic* conditions (usually around *pH 3.5 - 5.0*) • maintain an *acidic environment* by *pumping protons* into their *interior*.

*Ultrastructure of Flagella and Cilia*

• membrane-bound cylinders ∼2µm in diameter • *axoneme* • basal body

*Common Features of Eukaryotic Cells*

• membrane-delimited *nuclei* • membrane-bound *organelles* that perform functions • *intracytoplasmic membrane complex* serves as a *transport system* (not common in bacteria) • more structurally complex and generally larger than bacterial or *Archaea* cells.

*The Golgi Apparatus*

• membranous organelle made of *cisternae* stacked on each other • *cis* and *trans faces* • *dictyosomes* • involved in *modification, packaging*, and *secretion* of *material*

*Biofilm Formation*

• microbes *reversibly* attach to a *conditioned surface* (can leave if conditions not right) and *release* *polysaccharides*, proteins, and DNA to form the *extracellular polymeric substance (EPS)* • additional *polymers* are *produced* as *microbes reproduce* and the biofilms *matures*

*Temperature*

• microbes cannot regulate their internal temperature • enzymes have optimal temperature at which they function optimally • high temperatures may inhibit *enzyme* functioning and can be lethal

*Flow Cytometry*

• microbial suspension forced through small orifice with a laser beam of light • movement of microbe through orifice impacts electric current that flows through orifice • instances of *disruption* of current are counted • specific *antibodies* can be used to determine size and internal complexity

*Organisms exhibit distinct cardinal growth temperatures* (Temperature)

• minimal • maximal • optimal

*Microfilaments* (within cytoplasm)

• minute *protein filaments 4-7 nm in diameter* • *scattered* within *cytoplasmic matrix* or *organized* into *networks* and *parallel arrays* • composed of *actin protein* (move things around in the cell) • involved in *cell motion and shape changes*

*Protein structure stabilized by a variety of means:* *Adaptations of Thermophiles*

• more *H* bonds • more *proline* (genetic) • more chaperones (heat shock proteins)

*membrane stabilized by a variety of means* *Adaptations of Thermophiles*

• more saturated, more branched, and higher molecular weight lipids (that stay together at higher temperatures • ether linkages (archael membranes) (monolayer; no Van der Waals)

*Chromosome Replication and Partitioning* (notes)

• most bacteria have a single *circular* chromosome. • single *origin of replication*: site at which replication begins. • *terminus*: site at which replication is terminated, located opposite the origin. • replication is completed at the *terminus*, which is located directly opposite the origin. (semi-conservative) • *replisome*: group of proteins needed for DNA synthesis • DNA replication proceeds in both directions from the origin. • origins move to opposite ends of the cell

*The Influence of Environmental Factors on Growth*

• most organisms grow in fairly moderate environmental conditions • Extremophiles: grow under harsh conditions that would kill *other* organisms (pH, temp., salt: extremely high or low)

*Direct Measurement of Cell Numbers* (direct cell count)

• must be seen under microscope • counting *chambers* • electronic counters - flow *cytometry*, count with current • on *membrane* filters (John's stream paper)

*Culture Media*

• needed to grow, transport, and store microorganisms in the laboratory • is *solid or liquid* in preparation • must contain all the nutrients required by the organism for growth (Text: A culture medium is a solid or liquid preparation used to grow, transport, and store microorganisms. To be effective, the medium must contain all the nutrients the microorganism requires for growth. Specialized media are essential in the isolation and identification of microorganisms, the testing of antibiotic sensitivities, water and food analysis, industrial microbiology, and other activities. Although all microorganisms need sources of energy and macro- and micro- nutrients, the precise composition of a satisfactory medium depends on the species being cultivated due to the great variety of nutritional requirements. Knowledge of a microorganism's normal habitat often is useful in selecting an appropriate culture medium because its nutrient requirements reflect its natural surroundings. Frequently a medium is used to select and grow specific microorganisms or to help identify a particular species. Media can also be specifically designed to facilitate the growth of one type of microbe present in a sample from nature.)

*Cocci Divisome* (Cell Wall Growth and Cell Shape Determination)

• new peptidoglycan forms only at the central septum

*Virion release *

• nonenveloped viruses lyse the host cell -viral proteins may attack *peptidoglycan* or membrane • enveloped viruses use budding -viral proteins are first incorporated into host membrane -mucleocapsid may bind to viral proteins -envelop derived from host cell membrane, but may be *ER, golgi* or other -virus may use host actin tails to propel through host membrane

*The Endocytic Pathway* (Endocytosis)

• observed in all eukaryotic cells • used to *bring materials into the cell* • *solutes* or *particles* taken up and enclosed in *vesicles* pinched from *plasma membrane* • in most cases materials are then delivered to a *lysosome* and *destroyed* (then recycled)

*Each circular chromosome has a single site at which replication starts called the ______ or simply the ______.* (Chromosome Replication and Partitioning)

• origin of replication • origin

*"Eukaryotic ______ target us because they are ______ because they _______ ."*

• pathogens or parasites • like us • match us closely

*Host for plant viruses *

• plant tissue culture • plant *protoplast* culture • suitable whole plants - may cause localized necrotic lesions or generalized symptoms of infection

*Measuring Concentration of Infections Units *

• plaque assays - *dilutions* of virus preparation made and plated on lawn of host cells - number of plaques counted - resulted expressed as plaque-forming units (PFU) - *plaque forming units* - PFU/ml = number of plaques/sample dilution

*Plasmid Segregation*

• plasmids *replicate independently* and carry proteins necessary for segregation • *E. coli* R1 plasmid produces 3 proteins essential for its inheritance

*Intermediate Filaments Role in Cell (unclear)*

• play *structural* role • some shown to form *nuclear lamina* (nuclear membrane protein) • other help *link cells together* to *form tissues*

*Growth refers to ______ rather than growth of ______ .* (Growth)

• population growth • individual cells

*Visible Light at high intensities generates singlet oxygen (¹O₂)* (Radiation Damage)

• powerful oxidizing agent (takes e- away) • *carotenoid* pigments (fat loving w/ chlorophyll a & b) • protect many light-exposed microorganisms from *photooxidation *

*Eukaryotic microorganisms are... *

• prominent members of the *ecosystems* • useful as *model systems* and in *industry* • some are major human *pathogens* • two groups include *protists* and fungi

*lysogeny *

• prophage (bacteriophage) -intergrated phage *genome* • lysogens (lysogenic bacteria) -appwar *normal* -can switch from lysogenic (dormancy period) to lytic (bursting phase) cycle

*Z Ring Formations Role in Septation*

• protein FtsZ • MinCDE system in *E. coli* limits Z ring to the center of the cell

*Acid Tolerance Response* (pH)

• pump *protons* out of the cell • some synthesize acid and *heat shock proteins* that protect their proteins

*The Chemostat*

• rate of incoming medium = rate of removal of medium from vessel • an essential nutrient is in limiting quantities

*Golgi apparatus Involvement* (The Secretory Pathway)

• released in *small vesicles → cis face → trans face of Golgi apparatus* • *modifications of proteins* occurs in the Golgi; *targets protein* for their *final destination* • *transport vesicles* released from the *trans face* of the Golgi • exceptions to the rule of vesicle transport

*Barophilic (peizophilic) organisms* (Pressure)

• require or grow more rapidly in the presence of *increased pressure* • change membrane *fatty acids* to adapt to high pressures.

*the cultivation of viruses *

• requires inoculation of appropriate living host

*Pour Plate*

• sample is *serially* diluted • diluted samples are mixed with liquid agar • mixture of cells and agar are poured into sterile culture dishes (text: is particularly useful when sampling a heterogeneous population of microbes, some of which might produce colonies that spread over an agar surface if isolated by the streak-plate or spread-plate methods. In the pour-plate method, the original sample is diluted several times to reduce the microbial population sufficiently to obtain separate colonies when plating (figure 7.25). Then small volumes of several diluted samples are mixed with liquid agar that has been cooled to about 45°C, and the mixtures are poured immediately into sterile culture dishes. Most microbes survive a brief exposure to the warm agar. Each cell becomes fixed in place to form an individual colony after the agar hardens.)

*Most microbes grow attached ( ______ ) rather than free floating ( ______ ).* (Biofilms)

• sessile • planktonic

*Helical capsids *

• shaped like hollow tubes with protein walls • protomers *self assemble* • size of capsid is a function of *nucleic acid*

*Microtubules*

• shaped like thin cylinders *∼ 25 nm in diameter* (largest of the group) • help *maintain cell shape* • involved with *microfilaments (actin) in cell movements* • participate in *intracellular transport* processes

*Rods* (Cell Wall Growth and Cell Shape Determination)

• similar to cocci but elongate prior to septation • MreB determines cell diameter and elongation as Z ring forms in the center (Text: Most rod-shaped cells undergo a similar process; however, prior to cell division, they elongate (figure 7.7b). In these cells, proteins in the actin homologue MreB family play an essential role. MreB proteins polymerize, creating patches of filaments along the cytoplasmic face of the plasma membrane. Although it is not clear how MreB controls elongation, much information has been gained by studying Bacillus subtilis, which has three MreB proteins—MreB, Mbl, and MreBH. Prior to division, cell wall growth occurs in numerous bands around the circumference of the cell. The bands occur along the length of the cell but not at the poles. It has been suggested that MreB functions much like a scaffold inside the cytoplasm upon which the cell wall synthesizing machinery assembles. As the time for commencement of cytokinesis approaches, the FtsZ ring forms at the midcell, specifying peptidoglycan synthesis in this region. In some cells, MreB proteins have been shown to redeploy from the sidewalls to the midcell, so MreB may also contribute to cell wall synthesis during cytokinesis. In any event, cell wall growth switches from the side wall to the septum at this time. Despite the uncertain mechanisms by which MreB proteins function, their importance in determining cell shape is demonstrated by two observations. First, rod-shaped cells in which MreB has been chemically depleted assume a spherical shape. In addition, while almost all rod-shaped bacteria and archaea synthesize at least one MreB homologue, coccoid-shaped cells lack proteins in the MreB family.)

*These attached microbes are members of a complex, ______ enclosed community called a ______ .

• slime • biofilms

*Hydrogenosomes*

• small energy conservation organelles in some *anaerobic protists* (Text: are *small organelles involved in energy-conservation processes in some anaerobic protists* (figure 5.16). Like mitochondria, hydrogenosomes are bound by a *double membrane. However, they often lack cristae and usually lack DNA*. They also differ from mitochondria in terms of the method used to generate ATP. Within hydrogenosomes, pyruvate is catabolized by a fermentative process rather than respiration, and *CO₂, H₂, and acetate are formed*. In some hydrogenosome-bearing protists, these metabolic products are consumed by symbiotic bacteria and archaea living within the protist. The symbiotic archaea include methanogens that consume the CO₂ and H₂ and generate methane (CH₄).)

*Capsids of Complex Symmetry *

• some viruses do not fit into the category of having helical or icosahedral capsids *Examples*: • *proxviruses* - largest animal virus • *large bacteriophages* - binal symmetry (head resembles icosahedral, tail is helical)

*Dictyosomes* (The Golgi Apparatus)

• stacks of *cisternae* web: each individual subunit of the Golgi body

*Processes regulated by quorum sensing involve host-microbe interactions*

• such as symbioses and pathogenicity • *symbiosis*: *Vibrio fischeri and bioluminescence in squid • *pathogenicity* and increased *virulence* production • DNA uptake for *antibiotic* resistance genes

*All strict anaerobic microorganisms lack or have very low quantities of:* (Strict Anaerobic Microbes)

• superoxide dismutase • catalase

*Aerobes Produce Protective Enzymes* (Basis of Different Oxygen Sensitivities)

• superoxide dismutase (SOD) • *catalase* • peroxidase

*Oxygen easily reduced to toxic reactive oxygen species (ROS)* (Basis of Different Oxygen Sensitivities)

• superoxide radical • *hydrogen peroxide* • hydroxyl radical

*Functional Types of Media*

• supportive • enriched • selective • differential

*lysogenic conversion *

• temperate phages changes phenotype to its host -bacteria becomes *immune* to superinfection • two advantages to lysogeny for virus -phage remains viable but may not replicate -multiplicity of infection ensures survival of host cell • under appropriate conditions they will *lyse* and release phage particles -phage particles, a process called *induction*

*Bacterial replication is completed at the ______ , which is located directly opposite the ______ .* (Chromosome Replication and Partitioning)

• terminus • origin

*Biofilm Microorganisms*

• the *EPS* and *change* in attached organisms' *physiology protects microbes* from *harmful agents* (UV light, *antibiotics*, antimicrobials, • when formed on medical devices, such as implants, often lead to illness • sloughing off of organisms can result in contamination of water phase above the biofilm such as in a drinking water system (text: While in the biofilm, microbes are protected from numerous harmful agents such as UV light and antibiotics. This is due in part to the EPS in which they are embedded (figure 7.17), but it also is due to physiological changes. Indeed, numerous proteins found in biofilm cells are not observed when these cells are free-living, planktonic cells, and vice versa. The resistance of biofilm cells to antimicrobial agents has important consequences. When biofilms form on a medical device such as a hip implant (figure 7.15b), treatment with antibiotics often fails, which can lead to serious systemic infections. The treatment failure is in part due to the presence of persisters in the biofilm. The persisters survive antibiotic treatment and then repopulate the biofilm once treatment ceases. Often the only way to manage patients in this situation is by removing the implant. Another problem with biofilms is that cells are regularly sloughed off (figure 7.16). This can have many consequences. For instance, biofilms in a city's water distribution pipes can serve as a source of contamination after the water leaves a water treatment facility.)

*axoneme*

• the central strand (cytoskeleton structure), or inner core, of a cilium or flagellum • it is composed of an array of microtubules in 9 + 2 arrangement

*Most Microbes Maintain an Internal pH Near Neutrality* (pH)

• the plasma membrane is impermeable to a *proton* • exchange *potassium* for protons

*Differences in Eukaryotic Cells From Bacterial and Archaeal Cells*

• they have a nucleus • larger and more complex • *meiosis* (sexual reproduction) and mitosis (similar to binary fission) • complex processes much different from the other Domains • each organelle is about the size of a bacterial cell

*Generation (doubling) Time* (Mathematics of Growth) (notes)

• time *required* for the population to double in size • varies depending on species of microorganism and environmental conditions • range is from *10 minutes* for some bacteria to veral *days* for some eukaryotic organisms

*hosts for animal viruses *

• tissues (cell) culture -cells are infected with virus (phage) -viral plaques -localized area of cellular destruction and lysis that enlarge as the virus • cytopathic effects • *embryonated* for animal viruses -microscopic or macroscopic degenerative changes or *abnormalities* in host cells and tissues • *embryonated* for animal viruses (incubate virus)

*Domains Bacterial and Archaea* (Eukaryotic Cell Envelopes)

• unlike the *peptidoglycan* in the cell wall of *Bacteria* and *Archaea*, many eukaryotes lack or have a chemically distinct cell wall • cell walls of *photosynthetic algae* have *cellulose*, *pectin* and *silica* (in diatoms) • cell walls of *fungi* consist of *cellulose*, *chitin*, or *glucan*

*hosts for bacterial and archaeal viruses *

• usually cultivated in broth or agar cultures of suitable, young, actively growing bacteria • broth cultures lose *turbidity* as viruses reproduce • *plaques* observed on agar cultures

*possible mechanisms by which viruses cause cancer *

• viral proteins bind host cells tumor suppressor proteins • carry oncogene into cell and insert it into host genome • altered cell *regulation* • insertion of *promotor or enhancer* next to celluar oncogene

*Ultraviolet (UV) Radiation* (Radiation Damage)

• wavelength most effectively absorbed by DNA is *260 nm* • mutation → death • causes formation of thymine *dimers* in DNA • requires direct exposure on microbial surface • DNA damage can be repaired by several repair mechanisms

*Viral Envelope Proteins *

• which are viral encoded, may project from the envelope surface as *spikes* or *peplomers* • involved in viral *attachment* to host cell (ex. Hemagglutin of influenza virus) • used for identification of virus (ex. neuraminidase of influenza virus) • may play a role in nucleic acid replication

*These anaerobes must be grown without O₂* (Strict Anaerobic Microbes)

• work station with incubator • *GasPak* anaerobic system

*Ionizing Radiation* (Radiation Damage)

• x-rays and gamma rays • mutations→ death (sterilization) • disrupts chemical structure of many molecules, including DNA • *Deinococcus raiodurans*

*bacterial and archaeal viral infections *

•*virulent* phage - one reproductive choice -mulitplies immediately upon entry -lyses bacterial host cell • *temperate* phages have two reproductive options -reproduce *lytically* as virulent phages do -remain within host cell without destroying it -many temperate phages integrate their genomes into host genome in a relationship called lysogeny