BIO 225 - Ch. 3 (Bacteria and Archaea)

Flagella arrangement

"-trichous" means flagella (motility tail) Monotrichous = single, polar flagellum. Lophotrichous = tufts (bunches) of flagella at one end or emerging from the same site. Amphitrichous = single flagella at both ends/poles of the cell. Amphilophotrichous = tufts of flagella at both ends. Peritrichous = flagella over entire cell.

Major divisions of bacteria and archaea (based on the nature of cell wall)

*Gracilicutes*: gram-negative with thin cell walls. *Firmicutes*: gram-positive with thick, strong cell walls. (think *firm*) *Tenericutes*: lack a cell wall and are soft. (think *ten*der) *Mendosicutes*: archaea, primitive cells with unusual cell walls and nutritional habits.

What do ALL bacterial cells posses?

-*Cell membrane* (plasma membrane to control the flow of materials in/out of cell. This is the site for most ATP synthesis in bacterial cells is). -*Cytoplasm* (water-based solution filling entire cell). -*Ribosomes* (composed of protein and RNA that are sites of protein synthesis). -*One or a few chromosomes*. ONLY Majority have cell wall and surface coating called glycocalyx.

What do MOST/SOME bacterial cells posses?

-*S layer* (*s*ingle/mono layer of *s*ingle protein linked together used for protection and/or attachment. layer btwn peptidoglycan and glycocalyx, only produced in hostile environments). -*Fimbriae* (hairlike bristles extending from cell surface to help in adhesion to other cells and surfaces) -*Outer membrane* (contains lipopolysaccharide, controls flow of materials). -*Cell wall* (provides structural support, so if bacteria living in salty seawater were displaced to a freshwater environment, this would prevent the cells from rupturing). -*Cytoskeleton* (contributes to shape of cell). -*Pilus* (used for drawing another bacterium close in order to transfer DNA to it). -*Glycocalyx* (coating that serves protection, adhesive, and receptor functions...may have tight fitting shield like *capsule* or very loose shield like *slime layer* that protects cell from loss of water and nutrients). -*Inclusion*/Granule (stored nutrients that can be tapped into when needed). -*Endospores* (dormant body formed within some bacteria that allows for their survival in adverse conditions). -*Flagellum* (long, rotating filament for movement pushing cell forward). -*Plasmid* (double-stranded DNA circle containing extra genes).

Bacterial shapes/arrangements

-Coccus (sphere) -Bacillus (rod) -Vibrio (comma) -Spirillum (spiral wave) -Spirochete (spiral wiggle) -Filamentous (a lot networks of filaments)

How are bacteria and archaea different from eukaryotes?

-The way their DNA is packaged: no nucleus or group proteins. -The makeup of their cell wall: peptidoglycan and other unique chemicals. -Their internal structures: lack of membrane-bound organelles *(some, but not all bacterial cells possess flagella, pili, fimbriae, inclusions, endospores)*.

Bacterial ribosomes

-site of protein synthesis/creation. -composed of rRNA (60%) and proteins (40%). -consist of a large small subunits: small subunit: 30S large subunit: 50S large & small subunits together: 70S Archaeal ribosome: 70S Eukaryotic ribosome: 80S

Correct order of steps in the process of sporogenesis (the process of spore formation)

1. Endospore formation is initiated in response to environmental signals. 2. Vegetative cell becomes a sporangium. 3. A forespore forms, and calcium and dipicolinic acid are deposited around it. 4. Protein spore coats are added. 5. Lysis frees the mature spore which can now remain dormant for thousands of years. Nutrient depletion triggers sporogenesis among endospore-forming bacteria. The vegetative cell is a metabolically active and growing cell. When environmental conditions become challenging, these bacteria will form endospores in a process called sporulation. The endospore exists initially inside the vegetative cell, but eventually the cell disintegrates and the endospore is on its own. Both gram-positive and gram-negative bacteria can form endospores, but the medically relevant ones are all gram-positive. Most bacteria form only one endospore; therefore, this is not a reproductive function for them.

Diplobacilli

A double bacillus, two being linked end to end to each other

Flagella

A long, whip-like filament that helps in cell motility (primary function is motility). Only pocessed by some but not all prokaryotes. *Three distincts parts: filament, hook, basal body*. Attachment points or channels: fimbriae, pili and nanotubes/nanowires.

Endospores

A thick-walled protective spore that forms inside a bacterial cell and resists harsh conditions. Bacillus anthracis: agent of anthrax. Clostridium tetani: cause of tetanus. Clostridium perfringens: cause of gas gangrene. Clostridium botulinum: cause of botulism. Clostridium difficile (C. diff): a serious gastrointensteinal disease. (((Bacterial endospores are *not* produced by Staphylococcus))) Depletion of nutrients like carbon and nitrogen can result in the formation of endospores in some bacteria. Chemical analysis of a bacterial cell structure detects calcium and dipicolinic acid. Endospores are not reproductive structures. One vegetative cell will form one endospore. When the spore is released, the vegetative cell (sporangium) is lysed. When the endospore germinates, it will form one vegetative cell. The vegetative cell is a metabolically active and growing cell. When environmental conditions become challenging, these bacteria will form endospores in a process called sporulation. The endospore exists initially inside the vegetative cell, but eventually the cell disintegrates and the endospore is on its own. Both gram-positive and gram-negative bacteria can form endospores, but the medically relevant ones are all gram-positive. Most bacteria form only one endospore; therefore, this is not a reproductive function for them.

Endotoxin

A toxic component of the outer membrane of certain gram-negative bacteria that is released only when the bacteria die. The lipid portion of the lipopolysaccharide layer on the outer membrane is an endotoxin.

Adaptation

A trait that helps an organism survive and reproduce. Ex: Hyperthermophile - adapted to high temperatures. Psychrophiles - adapted to very low temperatures. Methanogens - convert CO2 and H2 gases into methane. Extreme halophiles - adapted to salty habitats.

Nontypical cell walls

Acid-fast bacteria. mycobacterium and nocardia: contain peptidoglycan and stain gram-positive, but bulk of cell wall is composed of different type of lipids like mycolic acid (causing an acid fast stain to have to be used to stain them).

Pili

Appendages that allow bacteria to attach to each other and to transfer DNA. Used in *conjugation* between bacterial cells. Well characterized in gram-negative bacteria. type IV pilus can transfer genetic material, act like fimbriae and assist in attachment, and act like flagella and make bacterium motile.

Glycocalyx

Coating of repeating polysaccharide or glycoprotein units. The external surface of a plasma membrane that is important for cell-to-cell communication. Extracellular coating that providers protection to the cell. Slime layer: loose, protects against loss of water and nutrients. Capsule: more tightly bound, denser, and thicker; produce a sticky (mucoid) character to colonies on agar. formed by many pathogenic bacteria, have great pathogenicity, protect against phagocytosis.

Sarcina

Cocci arranged in cubes of *eight, sixteen or more* cells as a result of division in three planes

Cell envelope

In a prokaryotic cell, the portion composed of the plasma membrane, the cell wall, and the glycocalyx. All act together as a single protective unit. It is composed of two or three basic layers: the cell wall, the cytoplasmic membrane, and, in some bacteria, the outer membrane. Although each envelope layer performs a distinct function, together they act as a single protective unit.

-taxis

Movement toward or away from a stimulus.

Bacterial arrangement: bacilli

Rod shaped. Single, Diplobacilli (pair of cells with ends attached), Streptobacilli (chains of several cells). Palisades (cells of a chain remain partially attached by a small hinge region at the ends. cells in a chain snap back upon each other forming a row of cells oriented side by side).

Flagella arrangement: monotrichous

Single flagellum on one side

Gram staining

The outcome of the Gram stain is based on differences in the cell's walls. 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 .

Flagella arrangement: amphitrichous

a flagella at *both* poles of the cell.

Periplasmic flagella

also called axial filaments, Internal flagellum enclosed in the space between the cell wall and the cytoplasmic membrane. Internal flagella, enclosed in the space between the outer sheath and the cell wall peptidoglycan Produce cellular motility by contracting and imparting twisting or flexing motion. *Spirochetes*: corkshrew-shaped bacteria that pocesses an unusual, wriggly mode of locomotion due to periplasmic flagella.

Lysozyme

an enzyme found in *saliva and sweat* and tears that destroys the cell walls of certain bacteria. Our bodies themselves contain a powerful antibacterial substance: Lysozyme, an enzyme contained in tears and saliva, hydrolyzes the bonds in the glycan chains and causes the wall to break down.

Flagella part: Basal body

anchors the flagellum

Fimbriae

attachment structures on the surface of some prokaryotes. Small, bristle-like fibers sprouting off the surface of many bacterial cells. Allow tight *adhesion* between fimbriaea and epithelial cells, allowing bacteria to colonize and infect host tissues.

Appendages

cell extensions. can be divided into two major groups: those that provide motility (flagella and axial filaments)... and those that provide attachment points or channels (fimbriae, pili, and nanotubes/nanowires).

Palisades

cells of a chain remain partially attached by a small *hinge* region at the ends

Strepo-

chains

Staph-

clusters

Streptococci

cocci bacteria that form a *chain* pattern after dividing

Staphylococci or micrococci

cocci forms irregular "bunches"; divides irregularly in many planes

Diplococci

cocci growing in *pairs*

Tetrads

cocci that divide in two planes and remain in groups of *four*

Bacterial arrangement: cocci

cocci-single, spherical cells diplococci (pairs). tetrads (4). staphylococcus (grape-like/irregular clusters). streptococci (chains). sarcina (cubical packet of 8, 16, or more cells)

Flagella part: hook (sheath)

connects the filament and the basal body so that the basal body rotates exerts a torque on the filament thus it can spin and propel the cell forward

Lopho-

crest, tuft (bunches)

Diplo-

double/pairs/two

-trichous

flagella

Inclusions bodies

function as metabolic reserves, cell positioners, or as metabolic organelles. Used for food storage. Pack gas into vesicles for bouyancy. Store crystals of iron oxide with magnetic properties. They can store nutrients in inclusion bodies to respond to periods of low food availability. They can pack gas into inclusion vesicles to provide buoyancy in an aquatic environment. They can even store crystals of iron oxide with magnetic properties in inclusion bodies.

Cell wall

helps determine the shape of bacterium. provides strong structural support to keep the bacterium from bursting or collapsing because of changes in osmotic pressure. (Certain drugs target the cell wall, disrupting its integrity and causing cell lysis). *Gains its relative rigidity from peptidoglycan* Peptidoglycan is present in both gram-positive and gram-negative cell wall. Bacteria live and grow in environments that have water in them (water-based environments are termed "aqueous."). Because of this, they are constantly absorbing excess water by osmosis. Were it not for the strength and rigidity of the peptidoglycan in the cell wall, they would burst from internal pressure. Several types of drugs used to treat infection (penicillin, cephalosporins) are effective because they target the peptide cross-links in the peptidoglycan, causing it to disintegrate.

Endotaxin

is a specific cell wall lipid. It can stimulate fever in the human body. It can cause septic shock in the human body. It is involved in typhoid fever and some meningitis cases.

Mycolic acid

long-chained, branched fatty acids characteristic of members of the genus mycobacterium. *Found in cell walls of acid-fast bacteria*. Contributes to pathogenicity of bacteria. Makes bacteria highly resistant to certain chemicals and dyes.

Bacteria

most function as independent single-celled, unicellular organisms (some act as a group in colonies or biofilms. some communicate through nanotubes). have an average size of 1 micron (cocci: circumference 1 micron, rods: length of 2 microns and width of 1 micron). Pleomorphisms: variations in size and shape of cells of a single species due to nutritional and genetic differences.

Negative chemotaxis

movement of a cell away from a repellant or potentially harmful compound

Positive chemotaxis

movement of a cell in the direction of a favorable chemical stimulus

Chemotaxis

movement of bacteria in response to chemical signals. Positive: movement toward favorable chemical stimulus. Negative: movement away from a repellant. Run: rotation of flagellum counterclockwise, resulting in a smooth linear direction. Tumble: reversal of the direction of flagellum, causing the cell to stop and change course. When flagella rotate counterclockwise, the bacterium runs. When flagella rotate clockwise, the bacteria tumbles. A bacterium will experience longer runs toward an attractant, meaning the flagella rotate counterclockwise more often.

Flagella arrangement: peritrichous

multiple flagella *around all* sides

Bacterial plasmids

nonessential pieces of DNA. they are not essential to bacterial growth and metabolism but they do provide protective traits such as resisting drugs and producing toxins and enzymes and antibiotic resistance. often the site of pathogenic genes. During bacterial reproduction, they are duplicated and passed on to offspring. They are not essential to bacterial growth and metabolism, but they do provide protective traits such as resisting drugs and producing toxins and enzymes (see chapter 8). Because they can be readily manipulated in the laboratory and transferred from one bacterial cell to another, plasmids are an important agent in genetic engineering techniques.

Biofilm

organic materials, a surface-coating colony of one or more species of prokaryotes that engage in metabolic cooperation. They complicate the treament of some infections. Ex: plaque on teeth.

Flagella part: Filament

outermost region

Capsules (function of glycocalyx)

prevent phagocytosis. formed by many pathogenic bacteria, have greater pathogenicity. made of polysaccharides, a complex type of carbohydrate. The capsule is usually resistant to dyes. Therefore, most staining methods that show the capsule will stain the cells and the background of the smear, leaving the capsules as clear halos around each cell. Smooth colonies indicate the presence of a capsule. Encapsulated bacteria are usually more pathogenic because they can evade phagocytosis by white blood cells and persist in the host, causing disease. Virulence factors are any features that help a microbe to cause disease in a host. The capsule helps protect the bacteria by helping it evade the immune system.

Gram-negative cell wall

single, thin peptidoglycan layer (1-3 nm thick). Thinness gives these cells greater flexibility and susceptible to lysis. Gram-neg*a*tive contains specialized polysaccharides Lipopolys*a*cch*a*ride: signaling molecules and receptors. Lipopolysaccharide is a major component of gram-negative outer membranes, can stimulate shock and fever, and is also referred to as endotoxin. The outer membrane, cell membrane, periplasmic space and lipopolysaccharide are found in gram-negative cell envelopes. The outer membrane contributes an extra barrier in gram-negative bacteria that makes them resistant to some antimicrobial chemicals such as dyes and disinfectants. For this reason, they are generally more difficult to inhibit or kill than are gram-positive bacteria. Also contains specialized protein *porin* proteins: special membrane channels that only allow certain chemicals to penetrate. During the Gram stain, gram-negative cells decolorize when the alcohol is applied.

Flagella arrangement: lophotrichous

small bunches or tufts of flagella emerging from the *same* side

Bacterial arrangement: Spirilla

spiral wave shaped bacteria, *occasionally found in short chains*.

Bacterial arrangement: Spirochetes

spiral wiggle shaped bacteria, *rarely remain attached after cell division*. have a twisting and flexing locomotion due to appendages called periplasmic flagella (*axial* filaments).

Bacterial chromosomes

the hereditary material in bacteria. Consists of a single ring of circular double stranded DNA. *DNA is aggregated/formed in the nucleoid*. The bacterial chromosome is part of the nucleoid. Nucleoid has hereditary material

Gram-positive cell wall

thick, homogenous sheet of peptidoglycan (20-80 nm thick). They do have a cell membrane. Gram-pos*i*t*i*ve contains te*i*cho*i*d ac*i*d and l*i*pote*i*cho*i*c ac*i*d: function in cell wall maintenance and enlargement. contribute to acidic charge on cell surface. Describing the group of bacteria that have a cell wall that is structurally less complex and contains more peptidoglycan than the cell wall of gram-negative bacteria. Gram-positive bacteria are usually less toxic than gram-negative bacteria. The structures found in a gram-positive cell envelope include the cell membrane, a thick layer of peptidoglycan, and a combination of teichoic acids and lipoteichoic acids. It is the thickness of the peptidoglycan layer that makes gram-positive cell walls stronger than gram-negative cells walls. The teichoic acids in gram-positive cell walls do not significantly contribute to the strength of the cell wall. Gram-positive cells do not have an outer membrane, lipopolysaccharide, or porin proteins.

Pleomorphism

variation in the size and shape of cells of a single species due to nutritional and genetic differences

Nanotubes (nanowires)

very thin, long tubular extensions of the cytoplasmic membrane. Used as channels to transfer amino acids (i.e., food) or to harvest energy by shuttling electrons from an electron-rich surface in the environment to iron-rich substances ("breathing rock instead of oxygen").