micro exam 2

1. List the two bacterial appendages that are responsible for motility: Flagella and axial filament 2. List the two bacterial appendages that are responsible for attachment or channels: Fimbria and Pilus

1. Flagella and axial filament 2. Fimbria and Pilus

True or false: 1. Protozoan are always unicellular. 2. All eukaryotes have a cell wall.

1. True 2. False

1. Cellular vesicles that contain digestive enzymes and hydrolytic components and are used for intracellular digestion and protection against pathogens are called: 2. Cellular vesicles that contain contents engulfed by a cell and are mainly in storage are called:

1. lysozomes 2. vacuoles

What is the highest resolution distance of light microscopy?

100-2 micrometers 0.2 μm

What is the magnification of the oil immersion objective lens on the classroom microscopes?

100X

What is the main component of cytoplasm?

70-80% water

A eukaryotic flagella is __ times longer and __ times thicker than a prokaryotic flagella.

A eukaryotic flagella is 10 times longer and 10 times thicker than a prokaryotic flagella.

Define the term mycelium:

A woven intertwining mass of hyphae that make up a mold colony

Which type of differential stain is used to detect Mycobacteria (TB) species?

Acid-fast stain

An internal flagellum enclosed between the cell wall and the cytoplasmic membrane is called an ___. Organisms with such an internal flagellum have a shape referred to as ___ and move in a ___ motion.

An internal flagellum enclosed between the cell wall and the cytoplasmic membrane is called an axial filament. Organisms with such an internal flagellum have a shape referred to as spirochete and move in a spiral motion.

List the four medically significant Clostridium sp. discussed in class.

C. botulinum, C. tetani, C. difficile, C. perfringens (Bacilli sp. are also spore forming bacteria discussed in class - such as B. anthracis and B. cereus)

Specialized Functions of the Glycocalyx (in Bacteria) Capsules: formed by ___ bacteria - Protect bacteria against __ so they are free to __ Other types of glycocalyces can be important in the formation of biofilms: - Example: The Cell Envelope= Composed of two or three basic layers:

Capsules: formed by pathogenic bacteria - Protect bacteria against phagocytic white blood cells so they are free to multiply Other types of glycocalyces can be important in the formation of biofilms: - Example: Plaque on teeth protect bacteria; infect long-term indwelling artificial devices (community of microbes) The Cell Envelope=chemically complex external covering that lies outside the cytoplasm Composed of two or three basic layers: - Cell wall, cytoplasmic membrane, and outer membrane (in some bacteria) - The layers are stacked and tightly bonded (each layer performs a distinct function) Act as a single protective unit

List the three general shapes of bacteria:

cocci, bacilli, curved/spiral

The process of DNA transfer from one cell to another is called:

conjugation

The Gram-Negative Outer Membrane= Lipopolysaccharide: - Endotoxin: Lipoproteins: Porin proteins: - Can alter ___ to block the entrance of harmful chemicals - Act as a defense against certain ___

contains specialized types of polysaccharides and proteins Lipopolysaccharide: polysaccharide chains function as cell markers and receptors; in uppermost layer - Endotoxin: stimulates fever and shock reactions (lipid portion) Lipoproteins: anchor the outer membrane to peptidoglycan; innermost layer (phospholipid layer) Porin proteins: completely span the outer membrane; only allow small molecules to penetrate - Can alter size to block the entrance of harmful chemicals - Act as a defense against certain antibiotics

Archaea that: convert CO2 and H2 into methane gas are known as ___ grow in very high NaCl concentrations (36%) are known as ___ grow at very low temperatures are known as ___ grow at very high temperatures are known as ___

convert CO2 and H2 into methane gas are known as methanogens. grow in very high NaCl concentrations (36%) are known as extreme halophiles. grow at very low temperatures are known as psychrophiles. grow at very high temperatures are known as hyperthermophiles.

Select the type of microscope that allows for the visualization of intracellular organelles and viruses in thinly sliced specimen preparations. a) Compound light microscopy b) Scanning electron microscopy c) Dark-field microscopy d) Transmission electron microscopy

d) Transmission electron microscopy

Ringworm (tinea corporis), tinea capitis, onychomycosis, tinea versicolor, cutaneous and oropharyngeal candidiasis are all examples of ___ diseases.

fungal

Fungi that obtain nutrients from dead plants or animals are termed:

saprobes

Define the term organelle:

small compartment in eukaryotic cells that is bounded by membrane and specialized in function

Considerable variety in size, shape, and colonial arrangement - Average size of bacteria: - Thiomargarita namibiensis: - Mycoplasma pneumoniae: - Nanobacteria:

• Average size of bacteria: 1-2 μm • Thiomargarita namibiensis: 100 to 750 μm (largest bacteria ever discovered) • Mycoplasma pneumoniae: 0.15 to 0.30 μm (limit of resolution for most microscopes) • Nanobacteria: 0.05-0.2 μm (living or crystallization of minerals?)

List the three cytoskeleton types found in eukaryotic cells:

(1) Actin filaments (2) Intermediate filaments (3) Microtubules

What three characteristics of mitochondria and chloroplast that provide supportive evidence of the endosymbiotic theory?

(1) Divide independently (2) Contain their own circular DNA (3) Have bacterial sized 70 S ribosomes

Where are ribosomes found within a eukaryotic cell?

(1) Free in the cytoplasm (2) Attached to the surface membrane of the rough endoplasmic reticulum.

What two methods of specimen preparation as discussed in class are used to prepare live cultures for viewing under a microscope?

(1) Wet mount and (2) Hanging drop

Individual bacterial cells are capable of carrying out all necessary life activities:

- Reproduction - Metabolism - Nutrient processing

Appendages for Attachment and Mating for Bacteria Attachment can enhance ___ - ___ factors (still bacterial flagella) -->bacterial surface appendages Fimbriae: - Composition varies, but most contain ___ - Have the inherent tendency to ___ - May be responsible for the formation of __ - __ and ___ use fimbriae to ___ to epithelial cells Pili (sex pilus): - Only found in gram-___ bacteria - Used in ___: • - Production of pili is controlled ____ - There is a special type of structure in some bacteria called a ___=it can act like fimbriae and assist in attachment, and act like flagella and make a bacterium motile

Attachment can enhance pathogenicity in some bacteria - Virulence factors (still bacterial flagella) -->bacterial surface appendages Fimbriae: small, bristle-like fibers sprouting off the surface of certain species of bacteria - Composition varies, but most contain protein - Have the inherent tendency to stick to each other and to surfaces - May be responsible for the formation of biofilms - Escherichia coli and the gonococcus use fimbriae to adhere to epithelial cells Pili (sex pilus): long, rigid tubular structure made of pilin protein - Only found in gram-negative bacteria - Used in conjugation, the partial transfer of DNA from one cell to another (mating process) • Conjugation in gram-positive bacteria does occur but involves aggregation proteins rather than pili. - Production of pili is controlled genetically - There is a special type of structure in some bacteria called a Type IV pilus=it can act like fimbriae and assist in attachment, and act like flagella and make a bacterium motile

What shape are bacterial chromosomes? Define the term nucleoid.

Bacterial chromosomes are circular Nucleoid - Aggregated/dense DNA (not to be confused with nucleus of a eukaryote)

Bacterial ribosomes are composed of a large __ S and a small __ S subunit and are referred to as __ S ribosomes. Eukaryotic ribosomes are composes of a large __ S and a small __ S subunit and are referred to as __ S ribosomes.

Bacterial ribosomes are composed of a large 50 S and a small 30 S subunit and are referred to as 70 S ribosomes. Eukaryotic ribosomes are composes of a large 60 S and a small 40 S subunit and are referred to as 80 S ribosomes.

What are the three defining features of a bacterial flagella as discussed in class:

Basal body, hook, filament

What is the difference between a slime layer and a capsule? What is their similarity?

Both are composed of glycoproteins and glycolipids and surrounds the cell membrane of some bacteria Slime layer: Forms loosely around the cell Protects the cell from loss of water and nutrients Helps initiate and maintain biofilms Capsule: More tightly bound to a cell than a slime layer Denser and thicker than a slime layer Protects against phagocytosis

Find Points of Flagellar Function in Bacteria Chemotaxis: - Positive chemotaxis: - Negative chemotaxis: Phototaxis: Run: Tumble: - Random walk=

Chemotaxis: movement in response to chemical signals - Positive chemotaxis: movement of a cell in the direction of a favorable chemical stimulus - Negative chemotaxis: movement of a cell away from a repellant or potentially harmful compound Phototaxis: movement toward light Run: counterclockwise movement of the flagella; cell swims in a smooth, linear direction toward a stimulus (STRAIGHT) Tumble: flagellum reverses direction, causing the cell to stop and change course; repellants cause numerous tumbles (RANDOM) - Random walk=alternation between runs and tumbles o In response to a concentration gradient of an attractant molecule, the bacterium will begin to inhibit tumbles, permitting longer runs and overall progress toward the stimulus (movement becomes a biased random walk in which movement is favored (biased) in the direction of the attractant)

Chloroplasts: Photosynthesis Machines Capable of converting the energy of sunlight into chemical energy through photosynthesis Photosynthetic role of chloroplasts: Thylakoids= · Stroma=

Chloroplasts: Photosynthesis Machines Capable of converting the energy of sunlight into chemical energy through photosynthesis (in algae and plant cells) Photosynthetic role of chloroplasts: • Primary producers of all organic nutrients • Primary producers of oxygen gas Larger than mitochondria and contain special pigments (more varied in shape) Most are composed of 2 membranes (one enclosing the other), smooth outer membrane in addition to an inner membrane Thylakoids=vesicles of chloroplast formed by elaborate folding of the inner membrane to for discs stacked in grana; carry the green pigment chlorophyll · Stroma=surrounds the thylakoid; site of dark reactions

Three general shapes of bacteria: Can also be categorized according to arrangement/style of grouping - influenced by pattern of division Coccus= - Diplococci= - Tetrads= - Staphylococci= - Streptococci= - Sarcina= Bacillus= - Coccobacillus= - Diplobacilli= - Streptobacilli= - Spirillum= • Spirilla -Spirochete= •Spirochetes - Branching filaments • Streptomyces Curved= Pleomorphism:

Coccus=spheres, oval, bean-shaped, pointed (greatest variety of arrangements) - Diplococci=pairs - Tetrads: groups of four - Staphylococci=(irregular) clusters - Streptococci=chains of a few to hundreds of cells (irregular clusters) - Sarcina=cubical packet of 8, 16, or more cells These are the result of division of a coccus in a single plane, 2 perpendicular planes, or several intersecting planes (daughter cells remain attached) Bacillus=cylindrical rod, filamentous, club-shaped (less varied in arrangement, only divide in the transverse plane) - Coccobacillus=rod is short and plump - Diplobacilli=pairs of cells with their ends attached - Streptobacilli=chains of cells - Palisades: cells of a chain remain partially attached and fold back, creating a side-by-side row of cells (Example: Corynebacterium diptheriae) - Spirillum=curled/spiral shaped cylinder, rigid helix, and a twisted axis • Spirilla occasionally found in short chains -Spirochete=spiral, more flexible (spring) •Spirochetes rarely remain attached • moves in a screw-like manner that is mediated by axial fibrils located in the cell's periplasmic space - Branching filaments • Streptomyces form Curved=vibrio, spiral Pleomorphism: variations in size and shape among cells of a single species (have nutritional or slight genetic diff), extreme in micro plasms (no cell wall) - Example: Rickettsia rickettsia Rickettsia rickettsia (Rocky Mountain Spotted Fever) - Coccoid cells, rod-shaped cells, and hybrid forms

Bacteria can also act as a group: Communicate w/ each other through ___ that cause them to behave differently Examples: - -

Communicate w/ each other through chemicals that cause them to behave differently Examples: - Colonies - Biofilms (universal and found almost everywhere): Biofilms are universal and found almost everywhere • tend to accumulate on damaged tissues • Artificial heart valves, Teeth, Catheters • often impervious to antibiotics - can lead to systemic infections

Bacterial Internal Structure Cytoplasm: • Prominent site for the cell's ___ and ___ activities • __ to __% water (solvent for cell pool) • Cell pool: • Also contains Bacterial Chromosome: • Aggregated in a dense area called the ___ (instead of a nucleus) • DNA is tightly coiled around ___ to fit into the cell compartment Plasmids: • Separate, double-stranded circles of ___ (can become integrated into chromosome) • Duplicated and passed on to offspring during ___ (during ___) • Confer ___ traits • Important agent in ___ engineering Ribosomes: Svedberg (S) units: - Bacterial ribosomes: - Eukaryotic ribosomes: Inclusion Bodies: Unique inclusions: **In the early 2000s, new compartments inside bacterial cells were discovered · Bacterial microcompartments, or BMCs · Outer shells are made of protein, arranged geometrically, and are packed full of enzymes that are designed to work together in pathways, thereby ensuring that they are in close proximity to one another. The Cytoskeleton: • Arranged in ___ ___ around the cell just under the ___ ___ • Contribute to ___ and ___

Cytoplasm: gelatinous solution contained by the cytoplasmic membrane • Prominent site for the cell's biochemical and synthetic activities • 70 to 80% water (solvent for cell pool) • Cell pool: complex mixture of sugars, amino acids, and salts->building block for cell synthesis or energy • Also contains chromatin, ribosomes, granules, and fibers that act as the cytoskeleton Bacterial Chromosome: single circular strand of DNA (some bacteria have multiple) • Aggregated in a dense area called the nucleoid (instead of a nucleus) • DNA is tightly coiled around basic protein molecules to fit into the cell compartment Plasmids: nonessential pieces of DNA • Separate, double-stranded circles of DNA (can become integrated into chromosome) • Duplicated and passed on to offspring during replication (during conjugation) • Confer protective traits • Important agent in genetic engineering Ribosomes: made of RNA (rRNA 60%) and protein (40%) - fine, spherical specks - dispersed throughout the cytoplasm, often found in chains (polysomes) Svedberg (S) units: measurement of the relative size of cell parts through sedimentation during centrifugation - Bacterial ribosomes: 70S o (50S + 30S) - Eukaryotic ribosomes: 80S o (60S + 40S) Inclusion Bodies: storage sites for nutrients during periods of abundance • Single-layered membranes - can carry glycogen and PHB (energy rich, organic) Unique inclusions: • Gas vesicles (buoyancy) • Granules (crystal inorganic compounds not enclosed in membranes) ->granules of Corynebacterium and Mycobacterium (metachromatic=important source of building blocks) • Crystalline particles of iron oxide (magnetosomes) - have magnetic properties (involved in cell orientation) • Vary in size, number, and content The Cytoskeleton: long polymers of proteins similar to eukaryotic actin (have also been identified in archaea) • Arranged in helical ribbons around the cell just under the cytoplasmic membrane • Contribute to cell shape and function in cell division

Cytoplasmic Membrane Structure of Bacteria: Lipid bilayer embedded with proteins: - - Special cytoplasmic membranes: - Mycoplasmas contain high amounts of ___ - ___ contain unique branched hydrocarbons rather than fatty acids - Some ___ bacteria (dense stacks of internal membranes w/ enzymes/pigments) Functions of the Cytoplasmic Membrane - Selective permeability: - Secretion - • ___ (help synthesize structural macromolecules to be incorporated into the cell envelope and appendages) • ___ processing • ___ reactions

Cytoplasmic Membrane Structure: 5 to 10 nm thin flexible sheet molded completely around the cytoplasm; just beneath the cell wall Lipid bilayer embedded with proteins: - 30 to 40% phospholipids - 60 to 70% proteins Special cytoplasmic membranes: - Mycoplasmas contain high amounts of sterols - Archaea contain unique branched hydrocarbons rather than fatty acids - Some environmental bacteria (dense stacks of internal membranes w/ enzymes/pigments) Functions of the Cytoplasmic Membrane: because bacteria have no organelles the membrane provides a site for functions - Selective permeability: • Water and small uncharged molecules diffuse freely • Transport regulation • Special carrier mechanisms exist for passage of most molecules • Passage of nutrients into the cell - Secretion - discharge of metabolic products into the extracellular environment (i.e. waste, toxins, exoenzymes, etc.) • Synthesis reactions (help synthesize structural macromolecules to be incorporated into the cell envelope and appendages) • Nutrient processing • Energy reactions

Cytoplasmic Membrane= The Cytoskeleton= Functions: Three main types:

Cytoplasmic Membrane=typical bilayer of phospholipids embedded with embedded protein molecules - contain sterols: stabilize eukaryotic membranes Selectively permeable barriers=sophisticated mechanisms for transporting nutrients in and waste and other products out The Cytoskeleton=crisscrossed flexible framework of molecules in the cytoplasm Functions: - Anchoring organelles - Moving RNA and vesicles - Permitting shape changes and movement Three main types: - Actin filaments=long, thin, protein strands found throughout a eukaryotic cell (mainly concentrated inside the cell membrane), responsible for cellular movements and formation of cellular extensions - Intermediate filaments=ropelike structures (10nm) - proteinaceous fibers in eukaryotic cells that help provide support to the cells and their organelles - Microtubules=long hollow tubes; maintain the shape of the cell and transport substances, involved in separating chromosomes in mitosis and movement

Dimensions of macroscopic organisms are given in terms of ___ and ___ Dimensions of microscopic organisms are measured from ___ to ___ to ___ • Smallest bacteria: ___ • Protozoa and algae: ___ • Viruses: ___

Dimensions of macroscopic organisms are given in terms of meters (m) and centimeters (cm) Dimensions of microscopic organisms are measured from millimeters (mm) to micrometers (μm) to nanometers (nm) • Smallest bacteria: 200 nm • Protozoa and algae: 3 to 4 mm • Viruses: 20 to 800 nm

Who proposed the theory of endosymbiosis and what does the theory describe?

Dr. Lynn Margulis described a revolutionary theory that organelles such as mitochondria and chloroplasts were at one time independent prokaryotic bacteria which were endocytosed (meaning brought inside of) by a larger "pre-eukaryotic" (or aka precursor) cell. Dr. Margulis described how the large precursor cell and early prokaryote mutually benefitted each other for survival. Eventually each independent organism lost its ability to survive on its own, and developed a true endosymbiotic relationship, meaning one organism resides within, and provides a benefit to, a host cell.

Germination of Endospores begins when favorable conditions arise:

Germination begins when favorable conditions arise: pH, Osmotic pressure, Temperature - (breaking of dormancy) exposure to water and a germination agent (organic molecule or inorganic salt) which stimulates the formation of hydrolytic (digestive) enzymes that break down the cortex and exposes the core to water - Core rehydrates and takes up nutrients and bacterium grow out of the endospore coat - Once initiated, proceeds to completion in 1.5 hours (becomes a vegetative cell again)

Endoplasmic Reticulum: • Rough endoplasmic reticulum: • Smooth endoplasmic reticulum: Golgi Apparatus: Where it is close to the Golgi apparatus, the ER forms __ that are picked up by the Golgi apparatus Golgi apparatus adds ___ to the proteins in the transitional vesicles and pinches off ___ • Conveyed to lysosomes or transported as secretory vesicles

Endoplasmic Reticulum: microscopic series of tunnels used in transport and storage • Rough endoplasmic reticulum: • Originated from the outer membrane of the nuclear envelope and extends through the cytoplasm (even to the membrane) - cisternae transports materials from the nucleus to the cytoplasm (then surface) • Ribosomes attached to its surface • Proteins held for packaging (cisternae) and transport (synthesize proteins) • Originated from the outer membrane of the nuclear envelope and extends through the cytoplasm (even to the membrane) • Smooth endoplasmic reticulum: • Closed tubular network without ribosomes • Functions in nutrient processing and synthesis and storage of nonprotein molecules (ex: lipids) Golgi Apparatus: site of protein modification and transport • Consists of a stack of flattened, disc-shaped sacs • Closely connected to the endoplasmic reticulum Where it is close to the Golgi apparatus, the ER forms transitional vesicles that are picked up by the Golgi apparatus Golgi apparatus adds polysaccharides and lipids to the proteins (modifying them) in the transitional vesicles and pinches off condensing vesicles • Conveyed to lysosomes or transported as secretory vesicles

Bacterial Endospores Endospores: Two-phase life cycle: 1) Vegetative cell: - Sporulation: 2) Endospore: Endospores can resist:

Endospores: withstand hostile conditions and facilitate survival (bacillus, clostridium, sporosacrina) - produced by most bacteria (gram-positive most medically relevant) **only form one - not reproductive** - Bacillus anthracis, Clostridium tetani, and Clostridium botulinum are all members of spore-forming genera Two-phase life cycle: 1) Vegetative cell: metabolically active and growing - Sporulation: spore formation induced by environmental conditions 2) Endospore: inert, resting condition Endospores can resist: - Heating, drying, freezing, radiation, chemicals - The heat resistance=linked to their high content of calcium and dipicolinic acid (removes water and leaves it dehydrated so it's less vulnerable) - Metabolically inactive and highly resistant to dying - The thick, impervious cortex and endospore coats protect against radiation and chemicals The longevity of bacterial endospores verges on immortality

What are two other structural differences of eukaryotic flagella discussed in class? And how does the movement of a eukaryotic flagella differ from that of a prokaryotic flagella?

Eukaryotic flagella are composed of a 9+2 arrangement of microtubules which are covered by an extension of the cell membrane. Bacterial flagella rotate, whereas eukaryotic flagella wave in a whip like motion.

Eukaryotic vs Bacterial Flagella Eukaryotic flagella= • __xthicker • __x longer and structurally more complex • Covered by an extension of the cell membrane ->___ • Sheathed cylinder containing regularly spaced hollow microtubules that extend the ___ ___ • 9+2 arrangement (flagella and cilia) Cilia= • Similar in overall structure to ___ • ___ and more ___—up to several thousand in some cells • Found only in a single group of ___ and certain ___ cells (examples: Stentor, Paramecium) • Ciliated in ___ on over the cell surface (beat back and forth) • Function as ___ Cell Wall=found in ___ and ___ - rigid and provide ___ and ___ • Different chemical composition than chemical cell walls Eukaryotic: ___ in fungi or ___ in plants + outer layer of ___ Bacterial: ___ Glycocalyx= · Usually composed of ___, appears as a network of fibers, a slime layer, or a capsule (like bacteria) · Provides ___ and ___ · What lies beneath varies: fungi= protozoa/animal cells=

Eukaryotic flagella: • 10x thicker • 10X longer and structurally more complex • Covered by an extension of the cell membrane -->membrane sheath • Sheathed cylinder containing regularly spaced hollow microtubules that extend the entire length • 9+2 arrangement (flagella and cilia) Cilia • Similar in overall structure to flagella • Shorter and more numerous—up to several thousand in some cells • Found only in a single group of protozoa and certain animal cells (examples: Stentor, Paramecium) • Ciliated in rows on over the cell surface (beat back and forth) • Function as feeding and filtering structures on some cells Cell Wall=found in fungi and algae - rigid and provide structural support and shape • Different chemical composition than bacterial cell walls Eukaryotic: chitin in fungi or cellulose in plants + outer layer of glycans Bacterial: Peptydoglycan Glycocalyx=outermost boundary found in most eukaryotic cells that come into direct contact w/ environment (ECM) · Usually composed of polysaccharides, appears as a network of fibers, a slime layer, or a capsule (like bacteria) · Provides protection and adherence · What lies beneath varies: fungi=thick, rigid cell wall protozoa/animal cells=lack cell wall

What are the advantages of heat fixing a specimen onto a glass slide?

Kills the cells Secures the specimen to the slide Preserves cellular components in a natural state with minimal distortion

True/False: Fungal spores are as resilient as bacterial endospores.

False

External Structures Bacteria Different types of accessory structures sprout from the surface of bacteria (appendages) Two major groups of Appendages: ___ and ___, ___ and ___

Flagella and axial filaments (motility) and Fimbriae and pili (attachment or channels)

Appendages for Motility Bacteria Flagellum: · Filament= · Hook= · Basal body= 1. Polar: - Monotrichous: - Lophotrichous: - Amphitrichous: 2. Peritrichous: **assessed using ___ or ___** Axial filament: **Archaea flagella may also have flagella but they differ structurally and are called ___**

Flagellum:used to propel the organisms through the fluid enviro - Filament=helical structure composed of proteins (20nm diameter, 1-70 micros in length) that extends out of the cell - Hook=filament is inserted in, anchored to the cell by the basal body, a stack or rings anchored through the cell wall to the cytoplasmic membrane and outer membrane (360 degree movement) - Basal body=anchors the hook to the cell, stack of rings anchored through the cell wall to the cytoplasmic membrane and outer membrane o Filament inserted into a curved tubular hook anchored to the cell by the basal body **assessed using semisolid media or through the hanging drop technique** 1. Polar: flagella attached at one or both ends of the cell - Monotrichous: single flagellum - Lophotrichous: small bunches or tufts - Amphitrichous: flagella at both poles of the cell 2. Peritrichous: flagella are dispersed randomly over the surface of the cell Axial filament: two or more long coiled threads found in spirochetes (corkscrew) - Internal flagellum enclosed between the cell wall and the cytoplasmic membrane=periplasmic flagellum - Impart a twisting or flexing motion to the cell **Archaea flagella may also have flagella but they differ structurally and are called archaellum**

Features of Eukaryotic Cells Found in ALL eukaryotic cells: Found in some eukaryotic cells:

Found in ALL eukaryotic cells: • Cytoplasmic membrane - supports the structure and shape of the cell • Nucleus - DNA • Mitochondria - site of ATP synthesis (through cell respiration) • Endoplasmic reticulum - protein synthesis • Golgi apparatus - packages and secretes molecules • Vacuoles - membrane sacs containing fluids or solids to be digested or stored • Cytoskeleton - microtubules, actin filaments, and intermediate filaments - shape and help organize the cell's parts • Glycocalyx - carbohydrate coating Found in some eukaryotic cells: • Cell wall - Fungi and algae • Appendages - flagella • Chloroplasts - photosynthesis

Which eukaryote have a cell wall and what is it composed of?

Fungi: Chitin Plants and algae: Cellulose

Gram Stain • Developed a century ago by ___, it remains the ___ technique for bacteria • Permits ready differentiation of major categories based on the color reaction of cells: 1. 2. Acid-Fast Stain • Differentiates ___ from ___: • Some bacteria have very impervious outer walls that ___ to the dye ___ even when washed w/ acidic solution, these bacteria are called ___ • Acid-fast bacteria stain ___ • Nonacid-fast bacteria stain ___ • Detects the agents of Mycobacteria species -> ___ Endospore Stain • Used to distinguish ___ and the cells they become (___ cells) • Detects endospore-forming members of the genera ___ and ___

Gram Stain • Developed a century ago by Hans Christian Gram, it remains the universal diagnostic staining technique for bacteria • Permits ready differentiation of major categories based on the color reaction of cells: 1. Gram-positive bacteria stain purple 2. Gram-negative bacteria stain pink Acid-Fast Stain • Differentiates acid-fast bacteria from nonacid-fast bacteria: • Some bacteria have very impervious outer walls that holds "fast" (tight) to the dye carbol fuchsin even when washed w/ acidic solution, these bacteria are called "acid-fast" • Acid-fast bacteria stain pink • Nonacid-fast bacteria stain blue • Detects the agents of Mycobacteria species (originated as specific method to detect mycobacterium TB) Endospore Stain • Used to distinguish endospores and the cells they become (vegetative cells) • Detects endospore-forming members of the genera Bacillus and Clostridium

Gram Stain: developed in ___ by ___; delineates two major groups of bacteria - differences lie in the structure of ___ - Used to make bacteria in ___ more visible - __ of cell to charged dye - Timed, sequential applications of: - after Gram's ___ is added, all cells appear purple - when ethanol is applied correctly, gram-positive cells appear __ and gram-negative cells appear __ - must use ____when performing a Gram stain Gram-positive shows: - stain ___ - example: Gram-negative shows: - stain ___ - example:

Gram Stain: developed in 1884 by Hans Christian Gram; delineates two major groups of bacteria - differences lie in the structure of the cell envelope - Used to make bacteria in infectious specimens more visible - attraction of cell to charged dye - Timed, sequential applications of crystal violet (primary dye), gram's iodine (mordant), an alcohol rinse (decolorizer), and contrasting counterstain - must use fresh cells when performing a Gram stain - after Gram's iodine is added, all cells appear purple - when ethanol is applied correctly, gram-positive cells appear purple and gram-negative cells appear colorless Gram-positive shows: - Thick cell wall composed of peptidoglycan and cytoplasmic membrane, inner cytoplasmic membrane (no outer membrane) - stain purple - example: Staphylococcus aureus Gram-negative shows: - Outer membrane, thin cell wall, inner cytoplasmic membrane - stain red - example: Pseudomonas aeruginosa

Gram-positive organisms have a __ layer of peptidoglycan in their cell wall. This differs from gram-negative organisms which have a relatively __ layer of peptidoglycan in comparison, covered by a hydrophobic LPS layer. This difference forms the basis of the Gram staining procedure. Since alcohol dissolves the ___ layer in __ organisms, the primary stain washes out, leaving the cells __. Counterstaining with __ turns the cells __. Conversely, gram-__ cells, with their __ layer of peptidoglycan, retain the primary stain because the large dye complexes are inaccessible, and the cells remain __.

Gram-positive organisms have a thick layer of peptidoglycan in their cell wall. This differs from gram-negative organisms which have a relatively thinner layer of peptidoglycan in comparison, covered by a hydrophobic LPS layer. This difference forms the basis of the Gram staining procedure. Since alcohol dissolves the outer membrane layer in gram-negative organisms, the primary stain washes out, leaving the cells colorless. Counterstaining with safranin turns the cells red/pink. Conversely, gram- positive cells, with their thick layer of peptidoglycan, retain the primary stain because the large dye complexes are inaccessible, and the cells remain purple

History of non-eukaryotic cells extends back ___ billion yrs - Bacteria are viewed best w/ ___

History of non-eukaryotic cells extends back 2.9 billion yrs - Bacteria are viewed best w/ a scanning electron microscope (shows them as 3D)->can be viewed w/ a light microscope

How long does it take most sporulating species to complete sporulation? How long does it typically take an endospore to germinate?

How long does it take most sporulating species to complete sporulation? 6-8 hrs How long does it typically take an endospore to germinate? 1-2 hrs

List and define the three properties of light microscopy:

I. Magnification: Increase in size II. Resolution: Ability to distinguish fine details III. Contrast: Ability to distinguish on the basis of color or luminance.

Bacterial Cell Structure In All Bacteria - ___ In Some Bacteria - ___ - Nanowires=___

In All Bacteria - Cytoplasmic membrane, bacterial chromosome, ribosome, cytoplasm In Some Bacteria - S layer, fimbriae, outer membrane, cell-wall, actin cytoskeleton, pilus, capsule, inclusion granule, microcompartments, plasmid, flagellum - Nanowires=structures which are appendages that can be many micrometers long and used for transferring electrons or other substances outside the cell onto metals (intertwine w/ neighboring bacteria for exchange)

The Transport Process Cellular Vesicles Lysosomes: • Involved in: • Synthesized by ___-->___ and then derived from ___ Vacuoles: • Main function is • Not derived from Golgi - formed in ___ cells in response to food (phagosome) ->vacuole merges w/ lysosome=phagosome to digest

Lysosomes: originate from the Golgi apparatus and contain a variety of enzymes • Involved in intracellular digestion of food and protection against invading microorganisms (also help w/ digestion/removal of cell debris+damaged tissue) • Synthesized by RER->SER and then derived from Golgi Vacuoles: membrane-bound sacs - contain fluids or solid particles to be digested, excreted, or stored • Main function is storage (water, pigments, waste) + also osmotic regulation in protozoa • Not derived from Golgi - formed in phagocytic cells in response to food (phagosome) ->vacuole merges w/ lysosome=phagosome to digest

Methanogens: Extreme Halophiles: Psychrophiles: Hyperthermophiles:

Methanogens: convert and into methane gas - Common inhabitants of anaerobic swamp mud, bottom sediments of lakes and oceans, and the digestive systems of animals - Gas produced in swamps may become a source of fuel - May contribute to greenhouse gases and global warming Extreme Halophiles: require salt to grow - Can multiply in 36% NaCl that would destroy most cells - Exist in inland seas, salt lakes, salt mines, and in salted fish - Use a red pigment to synthesize ATP in the presence of light (halobacteria) Psychrophiles: grow at very low temperatures Hyperthermophiles: grow at very high temperatures - Flourish at temperatures between 80°C and 113°C and cannot grow below 50°C - Live in volcanic waters and soils and submarine vents - Often salt and acid tolerant as well as heat tolerant Archaea are not just environmental microbes - have been isolated from human tissue (colon, mouth, and vagina) and may be capable of causing human disease

Movement of a bacteria in the direction of a favorable chemical stimulus is called ___, while movement of a cell away from a repellant or potentially harmful compound is called ___. Direction of movement is dependent on alternating the rotation of flagella, wherein a counterclockwise movement results in a ___, versus a clockwise rotation which results in a ___.

Movement of a bacteria in the direction of a favorable chemical stimulus is called positive chemotaxis, while movement of a cell away from a repellant or potentially harmful compound is called negative chemotaxis. Direction of movement is dependent on alternating the rotation of flagella, wherein a counterclockwise movement results in a run, versus a clockwise rotation which results in a tumble.

What differentiating feature is found in the cell wall of Mycobacterium sp. that is not present in Gram-positive or Gram-negative bacteria? What staining procedure is used to detect Mycobacteria?

Mycolic acid Acid-fast stain

Do parasitic fungi require a host to complete their life cycle?

No

Nontypical Cell Wall: - Bulk of the cell walls of ___ and ___ is composed of unique lipids (but stain positive) Mycolic acid or ___ ____: - Makes them ___to certain chemicals and dyes - ___ used to diagnose tuberculosis and leprosy - since resistant to dyes Mycoplasmas: - May be unaffected by ___ that target ___ - Membrane is stabilized by ___ and is resistant to ___ - ___ shape (ability to ___ ____) - filamentous to coccus or doughnut shaped - Range from___ (limit of light microscope!) - Often associated with in ___ tissue culture contamination - Causes "___ ___" - don't depend on host

Nontypical Cell Wall: lack cell wall structure of gram-positive or gram-negative bacteria - Bulk of the cell walls of Mycobacterium and Nocardia is composed of unique lipids (but stain positive) Mycolic acid or cord factor: very-long-chain fatty acid; contributes to pathogenicity of these organisms - thick/waxy nature - Makes them resistant to certain chemicals and dyes - Acid-fast stain used to diagnose tuberculosis and leprosy - since resistant to dyes Mycoplasmas: naturally lack a cell wall - May be unaffected by common antibiotics that target cell wall - Membrane is stabilized by sterols and is resistant to lysis - Pleomorphic shape (ability to change shape) - filamentous to coccus or doughnut shaped - Range from 0.1 to 0.5 μm (limit of light microscope!) - Often associated with in vitro tissue culture contamination - Causes "walking pneumoniae" - don't depend on host

Nucleus: • Contains the ___ - compact sphere, most ___ organelle • Separated from the cytoplasm by the ___ - composed of 2 parallel membranes separated by a narrow space and perforated w/ pores) Nucleolus: Chromatin=

Nucleus: single rounded structure bounded by a double membrane • Contains the genetic material Compact sphere, most prominent organelle • Separated from the cytoplasm by the nuclear envelope • (composed of 2 parallel membranes separated by a narrow space and perforated w/ pores) Nucleolus: site for ribosomal RNA synthesis, collection area for ribosomal subunits (stains more intensely due to its RNA content) Chromatin=dark fibers that are the genetic material of the nucleus->makes chromosomes (w/ histone)

Differences in Cell Envelope Structure Outer membrane in gram-negative bacteria - Infections with gram-positive bacteria are treated ___ ___ infections with gram-negative bacteria (especially ____) The cell envelope can interact with human tissues and cause disease: - ___ in the outer cell wall of gram-positive bacteria can be toxic - ___ in the cell wall of Mycobacterium can be harmful to human cells - ___in the cell wall are seen as foreign and can stimulate antibody production by the immune system

Outer membrane in gram-negative bacteria makes them more impervious to antimicrobial chemicals - more difficult to kill than gram-positive bacteria (except for alcohol-based compounds: dissolve the lipids in the outer membrane and break it down) - Infections with gram-positive bacteria are treated differently than infections with gram-negative bacteria (especially drugs that can cross the outer membrane) The cell envelope can interact with human tissues and cause disease: - Proteins in the outer cell wall of gram-positive bacteria can be toxic - Lipids in the cell wall of Mycobacterium can be harmful to human cells - Macromolecules in the cell wall are seen as foreign and can stimulate antibody production by the immune system

Bacterial Form and Function: Bacteria and Archaea vs. Eukaryotes Packaging of DNA: - Eukaryotes have ___ - Bacteria and archaea have ___ Cell wall makeup: - Eukaryotes: - Bacteria: - Archaea: Internal structures: - Eukaryotes: have ___ - Bacteria and archaea: ___

Packaging of DNA: - Eukaryotes have a nucleus - Bacteria and archaea have nuclear material that is free in the cytoplasm Cell wall makeup: - Eukaryotes: Cellulose or chitin - Bacteria: cell wall made of peptidoglycan - Archaea: cell wall distinct from bacteria and eukaryotes Internal structures: - Eukaryotes: have membrane bound organelles - Bacteria and archaea: no membrane-bound organelles

Define the term pleomorphic and give two example of an organism that exhibits pleomorphism:

Pleopmorphic - ability of a single species to vary in size and shape. Examples: Mycoplasma and Rickettsia

What quality of microscopy is enhanced by the use of shorter wavelength of electron beams in electron microscopy versus the longer wavelength of visible light utilized by microscopy?

Resolution

Describe the difference between the Rough Endoplasmic Reticulum (RER) and the Smooth Endoplasmic Reticulum (SER).

Ribosomes are attached to the surface of the RER which functions in protein synthesis of proteins directed for packaging and transport. The SER does not contain ribosomes and is the site of synthesis and storage of non-protein molecules (ex. lipid synthesis).

Ribosomes: • Large and small subunits of ___ • Eukaryotic size of ribosome is ___S • Distributed throughout the cell: • Scattered freely in the ___ and ___ • Attached to ___ • Inside ___ and ___ • Polyribosomes:

Ribosomes: site of protein synthesis • Large and small subunits of ribonucleoprotein • Eukaryotic size of ribosome is 80S (combination of 60S and 40S subunits) • Distributed throughout the cell: • Scattered freely in the cytoplasm and cytoskeleton • Attached to RER • Inside mitochondria and chloroplasts • Polyribosomes: short chains of ribosomes

Surface Coatings: S Layer and Glycocalyx (help to protect Bacteria) S layer: Glycocalyx: - Slime layer: - Capsule:

S layer: thousands of copies of a single protein linked together - Provides protection from environmental conditions ("armor") - Only produced in hostile environments - Clostridium difficile and Bacillus anthracis Glycocalyx: glycoprotein and glycolipid covering that surrounds the cell membranes of some bacteria (repeating polysaccharide units, can include proteins) - Protects the cell and can help it adhere to surfaces in it enviro - Slime layer: • Forms loosely around the cell • Protects the cell from loss of water and nutrients • Helps initiate and maintain biofilms - Capsule: (can be viewed after special staining or agar) • More tightly bound to a cell than a slime layer and also denser and thicker than a slime layer • Protects against phagocytosis

What is a plasmid and what purpose may it have within an organism?

Separate circular DNA found in some bacteria. Contains genes that are nonessential but may confer protective traits such as resistance factors or virulence factors.

Describe the difference between Simple and Differential stains and give an example of each.

Simple stains require a single dye and are uncomplicated to perform. For example, staining with only crystal violet or methylene blue and no other counterstain. Differential staining uses two differently colored stains to clearly contrast cell types or cell parts and is a more complex staining technique. Examples include Gram stain, Acid-fast stain, endospore stain, capsule stain, flagella stain.

Medical Significance of Endospores Some diseases are related to the persistence and resistance of their spores: Endospores are constant intruders where sterility and cleanliness are important:

Some diseases are related to the persistence and resistance of their spores: - Bacillus anthracis: Anthrax - B. cereus: food poisoning - Clostridium tetani: Tetanus (lockjaw) - C. botulinum: botulism - deadly form of food poisoning - C. difficile: pseudomembranous coli - C. perfringens: gas gangrene Endospores are constant intruders where sterility and cleanliness are important: - Resist ordinary cleaning methods: boiling water, soaps, and disinfectants - Frequently contaminate cultures and media - Hospitals must protect against endospores in wounds (prevent C. diff) - Destruction of endospores important in the food-canning industry (120degrees for 20-30m)

Special Stains • Some staining techniques (___ and ___) which are differential are also in the "special" category as they pinpoint a ___, such as the presence of an ___ • Used to ___ that may not be revealed by conventional staining methods Examples: Capsule Stain • Method of observing the ___ • Capsule=tightly bound ___ • Visualized through ___ staining with ___ or special ___ stains • Useful in identifying pathogens such as ___ Flagellar Staining • Tiny, slender filaments used by bacteria for movement • Flagella must be ___ in order to be seen • A coating is deposited on the ___ of the filament and then ___

Special Stains • Some staining techniques (endospore, capsule) which are differential are also in the "special" category as they pinpoint a particular characteristic, such as the presence of an endospore • Used to emphasize certain cell parts that may not be revealed by conventional staining methods Examples: Capsule Stain • Method of observing the microbial capsule (unstructured protective layer surrounds the cell) • Capsule=tightly bound glycocalyx • Visualized through negative staining with India ink or special positive stains • Useful in identifying pathogens such as Cryptococcus (soil fungus) Flagellar Staining • Tiny, slender filaments used by bacteria for movement • Flagella must be enlarged in order to be seen • A coating is deposited on the outside of the filament and then stained

Endospore Formation and Resistance The stimulus for endospore formation: - Transformation takes ___ (time)

Stimulus for endospore formation: depletion of nutrients, especially carbon and nitrogen sources which causes it to undergo sporangium to become a sporulating cell - Transformation takes 6 to 8 hours in most species

Structure of the Cell Wall Characteristics of the cell wall: Peptidoglycan: - Unique macromolecule composed of ___ - Provides: ~This function of the cell wall has been a tremendous boon to the drug industry. Several types of drugs used to treat infection (penicillin, cephalosporins) are effective because they target the peptide cross-links in the peptidoglycan, thereby disrupting its integrity. With their cell walls incomplete or missing, such cells have very little protection from lysis, which is the disintegration or rupture of the cell. Lysozyme, an enzyme contained in tears and saliva, provides a natural defense against certain bacteria by hydrolyzing the bonds in the glycan chains and causing the wall to break down~

Structure of the Cell Wall Characteristics of the cell wall: - Helps determine the shape of a bacterium - Provides strong structural support to keep the cell from bursting or collapsing due to osmotic pressure Peptidoglycan: found in the cell walls of most bacteria (provide relatively rigid quality) - Unique macromolecule composed of glycan (sugar) chains cross-linked with short peptide (protein) fragments - Provides a strong but flexible support framework

Mitochondria: Energy Generators of the Cell Supply the bulk of the energy of a cell Structure: Unique Characteristics of Mitochondria

Structure: • Cristae: folds on the inner membrane that hold the enzymes and electron carriers of aerobic respiration (ATP Synthesis) • Matrix: holds ribosomes, DNA, and enzymes and other compounds used in metabolism Unique Characteristics of Mitochondria Divide independently of the cell Contain circular strands of DNA Have bacteria-size 70S ribosomes • These characteristics provide evidence that mitochondria were cells engulfed by other cells and became organelles

The Archaea: - Share ribosomal RNA sequences not found in __ w/ ___ - Protein synthesis and ribosomal subunit structures are similar to ___ Differences from other cell types:

The Archaea: more closely related to Domain Eukarya than to Bacteria (but share bacterial characteristics) - Share ribosomal RNA sequences not found in bacteria - Protein synthesis and ribosomal subunit structures are similar to eukarya Differences from other cell types: - Certain genetic sequences are only found in their rRNA - Unique method of DNA compaction - Unique membrane lipids, cell wall composition, and pilin proteins • Exhibit unusual and chemically distinct cell walls - in some the wall can be entirely composed of polysaccharides or pure protein (all lack true peptidoglycan structure) ~ Lack true peptidoglycan structure - some completely lack cell wall (membrane serve dual functions) - The most primitive of all life forms - most closely related to cells that originated 4 billion years ago; live in habitats that are similar to the extremes found anciently—heat, salt, acid, pH, pressure, atmosphere - Methane producers, hyperthermophiles, extreme halophiles, and sulfur reducers

Describe the function of the Golgi Apparatus.

The Golgi apparatus is the site of protein modification (ex. lipid modification).

The Gram-Positive Cell Wall: The Gram-Negative Cell Wall:

The Gram-Positive Cell Wall: thick, homogenous sheath of peptidoglycan, 20 to 80 nm thick Functions of teichoic (polymer of ribitol/glycerol and phosphate) and lipoteichoic acid (similar but attached to lipids in membrane): - Cell wall maintenance - Enlargement during cell division - Acidic charge on cell surface The Gram-Negative Cell Wall: single thin sheet of peptidoglycan (1-3 nm); somewhat rigid structure - Thinness gives Gram-negative bacteria greater flexibility and sensitivity to lysis - Contains specialized polysaccharides and proteins

The Kingdom Fungi (Myceteae) Mycology= - best conditions: Approximately 5 million species of fungi can be divided into two groups: • Macroscopic fungi: • Microscopic fungi: • Forms:

The Kingdom Fungi Mycology=the study of Fungi - Best conditions: slightly acidic conditions (pH 4 - 6) Approximately 5 million species of fungi can be divided into two groups: • Macroscopic fungi: mushrooms, puffballs, gill fungi • Microscopic fungi: molds (multicellular), yeasts (unicellular) • Forms: - Unicellular - Colonial - Complex/multicellular (mushrooms, puffballs)

The actual "fuel" for the flagellum to turn is a ___ that are generated by the ___ of the bacterium and that bind to and detach from parts of the flagellar motor within the cytoplasmic membrane, causing the filament to rotate Archaea flagella may also have flagella but they differ structurally and are called ___

The actual "fuel" for the flagellum to turn is a gradient of protons (hydrogen ions) that are generated by the metabolism of the bacterium and that bind to and detach from parts of the flagellar motor within the cytoplasmic membrane, causing the filament to rotate Archaea flagella may also have flagella but they differ structurally and are called archaellum

How do the following features in Mycoplasmas compare to those of Gram-positive and Gram-negative bacteria? What common disease condition is associated with a Mycoplasma infection? (do not confuse Mycoplasma with Mycobacteria). a. Cell wall: b. Shape: c. Size:

a. Cell wall: NO CELL WALL (membrane is stabilized by sterols) b. Shape: Pleomorphic c. Size: 0.1-0.5 μm

The History of Eukaryotes The first eukaryotic cells appeared on the earth ____ years ago Bacteria and eukaryotes evolved from a precursor called the ___ - Neither prokaryotic nor eukaryotic - Gave rise to: - Organelles: - Organelle:

The first eukaryotic cells appeared on the earth 2 to 3 billion years ago Bacteria and eukaryotes evolved from a precursor called the last universal common ancestor (LUCA) - Neither prokaryotic or eukaryotic - Gave rise to bacteria, archaea, and eukarya separately - Organelles: originated from more primitive cells that became trapped in eukaryotic cells - Organelle: small compartment in eukaryotic cells that is bounded by membrane and specialized in function

1. The size of a eukaryotic ribosome is __ S and is composed of a combination of __ S and __ S subunits.

The size of a eukaryotic ribosome is 80 S and is composed of a combination of 60 S and 40 S subunits.

What is the name of the organism that is commonly associated with causing athlete's foot?

Trichophyton rubrum (causes tinea pedis)

What is the difference between a vegetative cell and an endospore?

Vegetative cell: metabolically active Endospore: inert, resting condition

Describe the difference between the morphology of yeast and hyphae?

Yeast are round and reproduce asexually via budding which may appear as pseudohyphae. Hyphae are long thread like structures found in filamentous fungi.

A human squamous cell measures 75 micrometers (μm) in diameter. What is the size of this cell in millimeters (mm)? a) 75,000 mm b) 0.75 mm c) 0.075 mm d) 75 mm

c) 0.075 mm

Storage sites for nutrients within a bacterial cell are called

inclusion bodies

Fungal infections are referred to as

mycoses

Endosymbiosis: • Organelles of modern eukaryotes similar to ___ • Example:

over 2 billion years ago eukaryotic cells arose when a very large precursor cell engulfed small bacterial cells that began to live and reproduce inside the large cell rather than be destroyed - Dr. Lynn Margulis • Organelles of modern eukaryotes similar to bacteria • Example: Mitochondria - Independent division - Circular chromosome s - 70S ribosome

From Single-Celled to Multicellular First primitive eukaryotes were single-celled and independent: • Became ___ to perform a particular function in a colony • ___, ___ organisms evolved when cells lost the ability to survive apart from the colony • Tissues=

• Became specialized to perform a particular function in a colony • Complex, multicellular organisms evolved when cells lost the ability to survive apart from the colony • Tissues=cell groupings w/ a specific function (groups of tissues make organs)

Nucleus, ER, and Golgi Apparatus: Nature's Assembly Line

• Genetic information originates from the nucleus->directs cell activities • Segment of DNA (w/ instructions) is segmented into RNA which is then passed through nuclear pores to ribosomes on the RER • Proteins are synthesized on ribosomes and deposited into the ER • Proteins are then transported to the Golgi apparatus to be chemically modified and packaged into vesicles for transport