Bacteria and vocab

Genus Staphylococcus

These are commonly known as “Staph” by many people. Relatively large, more or less round cells, said to be cocci. Found in various environments including in association with the human body.

Staphylococcus epidermis

Is on the skin on everyone. It’s normally harmless but will turn up sometimes in surgical wound infections and in infection with in-dwelling devices (catheters, pacemakers, etc.). This kind of organism, that causes diseases only under unusual circumstances of exposure, like surgery, or only makes people sick if they are in weakened state of some kind, is said to be an opportunistic pathogen.

Staph. aureus.

the first primary pathogen that we are introducing in our course. These creatures are organisms that can cause disease in otherwise normal healthy people under ordinary circumstances. You can still find primary pathogens living on and within the human body. For example, this pathogen is commonly found living in association with about 30% of people.

Genus Streptococcus

Not related to Staph. Very large genus, many recognized species. Relatively small coccoidal cells, sometimes in chains.

Strep. pyogens

Also called “Group A strep”. An important human pathogen causes among other things “strep throat”. “Group A” is a reference to a type of carbohydrate present on the surface of many types of streptococcal cells called the group carbohydrate that is useful in classifying these organisms. The presence of the “A” group carbohydrate on the cell surface actually defines this species.

Step. Pnuemoniae.

Most important bacterial cause of community acquired ________.

Community acquired

acquired while going about one’s ordinary life

nosocomially acquired

acquired in the hospital

Genus Bacillus

Gram positive rods, very large genus, very common in soil. Many recognized species, form endospores.

Bacillus subtilis

Other than E. coli it is probably the most important bacterial model system from a historical standpoint

Model system

an organism that we study in the lab because it’s safe to work with, easy and/or cheap to work with and closely similar to lots of other organisms so that we learn about the ____ ____ we can apply to many other creatures

B. megaterium

After subtilis probably the main model system in the genus

genus

a taxonomic tank in biology used to group closely related species that share common physical or genetic characteristics.

B. anthracis

causes anthrax, probably the only real major pathogen in the genus

B. cereus

an important cause of mild food poisoning (vomiting and/or diarrhea, sometimes encountered in connection with rice).

Clostridium

This genus resembles Bacillus in many ways, especially in morphology, spore, formation and habitat (soil etc.), but all are ANEROBIC, they are poisoned by oxygen and cannot live in its presence. They are also much more common in the human gut than is Bacillus.

Cl. tentani

cause of tetanus

Cl. botulinum

cause of botulism

Cl. perfringens

cause of gangrene (a very dangerous tissue destructive condition)

Cl. difficile

cause of gastrointestinal distress in people who have taken broad-spectrum antibiotics.

Steptomyces

an important example of a large group of bacteria that live in the soil and have a morphology that is sort of like that of fungi (growing in long strands, making spores, etc.). One member of this genus makes the antibiotic streptomycin. NOT RELATED TO STREPTOCOCCUS.

Corynebacterium

Kind of oddly shaped rods (sometimes described as “club shaped”). Also found in soil. One species, C. diphtheriae, can cause a serious potentially life-threatening disease especially in children call diphtheria.

Escherichia coli.

Up until recently this was only species in this genus. ____ is arguably the most important cellular model in history and probably the best understood cellular organism in the world. Strains of ___ can vary from harmless to rather dangerous pathogens.

Salmonella

includes causes of food-borne illness and the cause of a very dangerous multi-organ system infection now called enteric fever (historically typhoid fever)

Shigella

includes organism responsible for a very dangerous food/water borne infection called bacillary dysentery

Klebsiella

includes some organisms responsible for a very dangerous nosocomial pneumonia

Proteus and serratia

mainly seen if at all in hospital infections

Genus Vibrio

Curved rod, “comma shaped”. Frequently found in marine and brackish (partly saline partly freshwater) environments. Several diarrheal disease called cholera.

Rhizobium

Rod-shaped. Nitrogen fixer. fixes nitrogen in association with leguminous plants (beans, peas, etc.) and so is hugely important in agriculture.

Azotobacter

Rod-shaped. Nitrogen fixer. Fixes it in the free-living state.

Nitrogen-fixer

taking nitrogen gas and incorporate it into living matter

Genus Pseudomonas

Everywhere, like bacillus its in the soil. Slender Gram (-) rods. Large genus with many species; these are common in soild and variety of other environments, including “domestic” environments (where people tend to hang out). The only one that we will name right now is Pseu. aerugionosa, which is a hugely important cause of nosocomial infections. Usually in hospitals or dorms.

Cytophaga

Gram (-) and in common in the soil. Important decomposer, it breaks down cellulose and thus helps rid environments of dead plant matter.

Myxococcus

Gram (-) and in common in the soil. Has a unique life cycle: the actively metabolizing cells are rod shaped, but it makes so-called “spores” (don’t confuse with bacillus) that are coccoidal.

Beggiatoa and Thiothrix

Gram (-) and in common in the soil. Interesting physiologies that enable them to derive energy from hydrogen sulfide, a very toxic sulfur compound common in flooded soils. The action of organisms like these enables us, for instance, to grow rice in flooded soils

Microscope

An instrument that produces a visible, magnified image of an object that is too small to see with the naked eye.

Microscopy

The use of ________ to observe and study objects too small to be seen directly

Compound light microscope

A microscope that uses visible light and two lens systems, the objective and ocular, to magnify a specimen

Objective lens

The lens closest to the specimen that provides most of the microscopes magnification

Ocular lens/ Eyepiece

The lens closest to your eye that you look through to view the magnified image.

Condenser

A lens system that focuses light into a sharp beam and directs it onto the specimen

Light path

The route light travels through a microscope: Light source → condenser → specimen → objective → ocular → eye.

Bright-field microscopy

A type of microscopy in which the background is bright, and the specimen appears darker because it absorbs or scatters some of the light.

Dark-field microscopy

A type of microscopy in which the specimen appears bright against a dark background because reflected/scattered light is observed.

Electron microscope

A microscope that uses a beam of electrons instead of visible light to produce an image

Electron beam

A stream of electrons used as the source of illumination in an electron microscope

TEM (Transmission Electron Microscope)

An electron microscope that passes electrons through a thin specimen to examine internal structures.

SEM (Scanning Electron Microscope)

An electron microscope that examines the surface of a specimen by scanning/reflection of an electron beam

Image recording system

A system, often a digital camera, that records the image produced by a microscope

Image inhancement system

Software or another system used to improve the clarity or quality of a microscope image.

Classification

the process of organizing organisms into meaningful categories

Taxonomy

The science/process of naming and classifying organisms

Systematics

The study/classification of organisms, particularly their relationships to one another.

Linnaeus

Swedish scientist who developed the hierarchical classification system and binomial naming system commonly used for organisms.

Taxonomic hierarchy

A system that organizes organisms into increasingly specific catergories.

Hierarchy

Kingdom → Phylum → Class → Order → Family → Genus → Species

Kingdom

The broadest classification category in the traditional Linnaean system discussed in your handout

Genus

A group of closely related species; the first part of an organism’s scientific name

Species

A specific category of organisms; in the classical species concept, organisms that can mate and produce fertile offspring

Binomial/ Binomial nomenclature

A scientific naming system using two names: genus + species

Linnaean binomial

the two-part scientific name developed as part of Linnaeus’s naming system.

Genome

The total set of genetic information/genus in an organism

DNA sequence

The specific order of nucleotides in DNA; comparing DNA sequences can help determine evolutionary relationships.

Evolutionary relationship

The relationship between organisms based on their common ancestry.

Asexual

Reproduction that does not involve mating between two organisms.

Coccus

A spherical or round bacterial cell

Rod

A bacterial cell that is elongated or cylindrical in shape

Spirilllum/ spirilla

A spiral-shaped bacterium/bacteria

Comma-shaped

A curved rod shape characteristic of bacteria such as Vibrio

Gram-positive (Gram +)

Bacteria with a thick peptidoglycan cell wall that generally stain purple during a Gram stain

Gram-negative (Gram -)

Bacteria with a thin peptidoglycan layer and an outer membrane that generally stain pink/red during a Gram stain.

Gram stain

A differential staining method that separates bacteria into Gram-positive and Gram-negative groups based largely on differences in their cell envelopes.

Family

A taxonomic group containing related genera

Pathogen

An organism of causing disease

Primary pathogen

An organism capable of causing disease in an otherwise healthy person under ordinary circumstances

Opportunistic pathogen

An organism that normally does not cause disease but can cause disease when conditions provide an opportunity, such as weakened defenses or a medical procedure.

Nosocomial infecrtion

an infection acquired in a healthcare/ hospital setting

Community-acquired infection

An infection acquired while living normally in the community rather than in a healthcare setting.

Ribosome

A cellular structure responsible for protein synthesis

Protein synthesis

The process of producing proteins using genetic information

Bacterial ribosome

found in bacteria; its structure and composition differ from those of eukaryotic _______. __________ are molecular machines that synthesize proteins by translating messenger RNA (mRNA) into polypeptides, which are essential for bacterial growth and survival.

Ribosome subunit

One of the structural components that combine to form a functional ribosome.

Plasma membrane

The selectively permeable membrane surrounding the bacterial cytoplasm that controls interactions between the cell and its environment

Selective permeability

The ability of a membrane to allow some substances to cross while restricting others.

Phospholipid

A major type of lipid that forms the basic structure of biological membranes.

Phospholipid bilayer

A double layer of phospholipids forming the basic framework of the plasma membrane

Cell wall

A rigid structure outside the plasma membrane that provides protection, strength, and helps maintain cell shape

Cell envelope

The layers surrounding the bacterial cell, including the plasma membrane and cell wall and, in Gram-negative bacteria, the outer membrane.

Peptidoglycan

A strong mesh-like material made of sugars and peptides that forms an important part of bacterial cell walls

N-acetylglucosamine (NAG)

a sugar component of peptidoglycan

N-acetylmuramic acid (NAM)

a sugar component of peptidoglycan

Teichoic acid

a negatively charged polymer associated with the cell wall of Gram-positive bacteria.

Lipoteichoic acid

A type of teichoic acid associated with the bacterial membrane and extending through the Gram-positive cell wall.

Thick peptidoglycan layer

The major structural feature of the Gram-positive cell wall

Outer membrane

An additional membrane found outside the thin peptidoglycan layer of gram-negative bacteria

Periplasm/ periplasmic space

The region between the inner plasma membrane and outer membrane of Gram-negative bacteria where the thin peptidoglycan layer is located

LPS (Lipopolysaccharide)

a major component of the Gram-negative outer membrane consisting of lipid and polysaccharide portions.

Lipid A

The lipid potion of LPS that anchors LPS in the outer membrane.

Core Polysaccharide

The middle portion of LPS connecting Lipid A to the O antigen

O antigen

The outer polysaccharide portion of LPS that extends outwards from the bacterial surface.