MMG 2010 Exam 1

Describe how microorganisms are classified and distinguished as unique species

Microorganisms are classified with a taxonomic binomial/nomenclature system.

Taxa: Domain -> kingdom -> phylum -> class -> order -> family -> genus -> species

Compare historical and current systems of taxonomy used to classify microorganisms

Used to be classified by anatomical or behavioral differences, or traits. Groups could often be groups wrong (especially with convergent traits etc.)

Modern taxonomy is now based off of genetic data: 16S rRNA sequencing for bacteria and archaea and 18S rRNA sequencing for microbial eukaryotes.

List the various types of microorganisms and describe their defining characteristics

Prokaryotes: only unicellular, lack a nucleus, 2 domains, divide by binary fission, no organelles. Bacteria have peptidoglycan cell wall, archaea have pseudomurein cell wall

-Bacteria and Archaea

Eukaryotes: unicellular or multicellular, distinct nucleus, divide by mitosis, polysaccharide cell wall

-Animals, Plants, fungi, protists

Viruses: Not a cell - an agent that invades a host cell

Identify and define the characteristics of electromagnetic radiation (EMR) used in microscopy

EMR includes the light spectra, X rays, gamma ray, radio waves, and more. This can be utilized with certain fluorescent dyes to get them to emit photons at a higher energy wavelength that we can then see.

Describe historical developments and individual contributions that led to the invention and development of the microscope

Van Leeuwenhoek - simple microscope where light passed through one lens

Galileo - compound microscope where light passes through 2 lenses

Describe the distinguishing features and typical uses for various types of light microscopes, electron microscopes, and scanning probe microscopes

Brightfield microscopy is very standard, image on bright background

Darkfield increases contrast without staining, bright image on dark background. Useful for live specimens

Phase contrast - Makes high contrast images, high resolution useful for observing structures like endospores and organelles.

Fluorescence - can be used for various stains, living/dead, gram, autofluorescence, etc.

Electron Microscopy uses electron beams focused with magnets to produce an image rather than light. It is very detailed and can be useful to observe the 3D structure of a surface or small thin sections.

Scanning probe microscopes - Uses a probe passes horizontally at a constant distance above specimen, can map the structure of surfaces at an atomic level. Works best with conducting materials.

Contrast vs resolution vs magnification

magnification - how zoomed in

Contrast - how distinguished structures are from each other

Resolution - how focused/blurry

Differentiate between simple and differential stains

Simple stain - a single dye is used to emphasize a particular structure in specimen

Differential staining - 2 or more dyes distinguish organisms based on interactions with different stains.

Explain the procedures and name clinical applications for Gram stain

Gram Stain - Uses crystal violet, grams iodine, decolorizer, and safranin on heat or chemical fixed cells. (+ purple and - pink) outcomes used to distinguish cells by cell-wall type. A positive stain demonstrates a thick PG layer with no outer membrane. A gram negative tells us its a thin PG layer with an outer membrane.

Endospore stain

Endospore stain - heat stains with malachite green, washed and counterstained with safranin. Used to distinguish organisms with endospores (green) from those without.

Acid-fast stain

Acid-Fast stain - Stained with basic fuchsin, rinsed with alcohol, counterstain methylene blue. Used to distinguish acid-fast bacteria from non acid fast bacteria. Acid fast bacteria have mycolic acid in their cell wall which makes them resistant to decolorization and will appear pink, while the decolorized ones will take the counterstain blue.

Negative Capsule stain

Negative capsule stain - Background stained with india ink, leaving clear area of the cell and capsule. Used to distinguish cells with capsules from those without, capsules will appear clear or as halos if present.

Flagella stain

Flagella stain - Coated with a tannic acid then stained with fuchsin or pararosaline. Used to view and study flagella, makes them visibly present.

Explain the key points of endosymbiotic theory and cite the evidence that supports this concept

Mitochondria and chloroplasts arose as a result of prokaryotic cells engulfing them. Evidence that supports this is the structural similarities in ribosomes, mitochondrial and chloroplast DNA. Also binary fission of these organelles is similar to binary fission in bacteria. DNA sequencing supports this as well.

Explain the contributions of Semmelweis, Snow, Pasteur, Lister, and Koch to the development of germ theory

Germ theory states that diseases may result from microbial infection.

Shows hand washing reduces illness, cholera bacteria, disproves spontaneous generation, microbial fermentation, surgery disinfectent, determine causative agents for bacterial infections.

Explain the distinguishing characteristics of prokaryotic cells

-Unicellular

Bacteria and Archaea

Lack a Nucleus

Asexual reproduction - binary fission

Cell wall of peptidoglycan for bacteria, peptidomurein for archae

No membrane bound organelles

Describe common cell morphologies typical of prokaryotic cells and explain how cells maintain their morphology

Cells maintain morphology with a cytoskeleton

Describe common cellular arrangements typical of prokaryotic cells

Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function

Flagella

Pilus

Fimbriae

Nucleoid

Ribosome

Compare the distinguishing characteristics of bacterial and archaeal cells

Archaeal cells are more closely related to eukarya

They have different cell walls made of pseudomurein, more complex RNA, typically reside in extreme environments

Explain the distinguishing characteristics of eukaryotic cells

Circular, far more complex DNA, nuclear membrane, membrane bound organelles, cell wall made of cellulose or chitin

Describe internal and external structures of eukaryotic cells in terms of their physical structure, chemical structure, and function

Nucleus - stores DNA and site of transcription and replication

ER (rough and smooth) - Produces and folds proteins and lipids

Golgi complex - The mail center, modifies, packages, and sorts proteins and lipids for transport to different locations

Ribosomes - Make proteins that are inside the cell

Mitochondria - ATP production

Identify and describe symbiotic relationships

a close, long-term biological interaction between two different species.

Mutualism, parasitism, commensalism

Compare normal/commensal/resident microbiota to transient microbiota

Long term/life long residents of host

Transient microbiota only reside for so long.

Explain how prokaryotes are classified

16S RNA sequencing

Used to be more based on morphology, behavior, motility, etc.

Describe the unique features of each class within the phylum Proteobacteria: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria

Alphaproteobacteria: Nutrient poor environments, Unusual cellular lifestyle, important symbiotic relationships

Betaproteobacteria: found in soil and water, metabolically diverse, some pathogenic

Gammeproteobacteria: very metabolically diverse, environmental organisms, normal microbiota, major pathogens

Epsilonproteobacteria: Found on animals and GI environments. Microaerophilic conditions

Deltaproteobacteria, zetaproteobacteria irrelevant

Describe the unique features of nonproteobacteria gram-negative bacteria

Includes Spirochetes, Chlamydiae, Bacteriodes

Chlamydiae does not have peptidoglycan, distinct life cycle

Bacteriodes includes fusobacteria. Important in decomposition and nutrient cycling

Several associated with human/animal microbiomes. Some can be opportunistic pathogens

Describe the unique features of phototrophic bacteria

Phototrophic bacteria capture energy from sunlight through photosynthesis or photophosphorylation.

ex. cyanobacteria

Describe the unique features of each category of high G+C and low G+C gram-positive bacteria

Actinobacteria: High GC content. Acid fast, partially acid fast, and filamentous branching bacteria.

Includes streptomyces and actinomycetota → Mycobacterium and Nocardia.

Firmicutes: Low GC content. Includes GPC, GPB, some endospore formers. Common human pathogens

Describe the unique features of deeply branching bacteria

Extremophiles, thermophiles, hyperthermophiles

First non-LUCA to be produced by evolution

Describe the unique features of each category of Archaea

Crenarchaeota - very diverse, all aquatice, mostly hyperthemophiles. Some alkaliphiles and acidophiles (pH).

Euryarchaeota - includes many methanogens, halophiles (salt)

Summarize the general characteristics of unicellular eukaryotic parasites

Some protozoa. Many many species, classified by motility: Amoeba (pseudopodia), Flagellates, ciliates, apicomplexans (apical complex; gliding motility)

No cell walls, chemotrophs and phototrophs, sexual or asexual reproduction, complex life cycles.

Describe the general life cycles and modes of reproduction in unicellular eukaryotic parasites

They are all very different but generally follow the same pattern

Somehow they get enveloped into the host (whether that be blood stream, ingestion, absorption, etc).

They multiply and divide into many different unicellular organisms

Find a way to infect another host and spread (sporulated oocyst, other things eat infected host, etc.)

Explain why we include the study of parasitic worms within the discipline of microbiology

Because where else would it go…

they cause diseases that are diagnosed by finding microscopic eggs and larvae in clinical specimens

Compare the basic morphology of the major groups of parasitic helminthes

Nematodes - round cross section

Cestodes - flat cross section, ribbon like tapeworms. Many segments.

Trematodes - flat cross section, one segment

Describe the characteristics of parasitic nematodes

Unsegmented. Have a complete digestive system. Most are dioecious.

Describe the characteristics of parasitic trematodes and cestodes, and give examples of each

Cestodes (tapeworms) - No mouth, digestive system, or vascular tracts. absorbs what it needs. Monoecious in each segment (proglottid). Scolex is the head region contains hooks/suckers to attach to wall of small intestine.

Trematodes (flukes) - have a ventral and oral sucker. most are monoecious. have complex lifestyles with intermediate hosts. Attach to inner walls of intestines, lungs, blood vessels, or liver.

Identify examples of the primary causes of infections due to nematodes, trematodes, and cestodes

Nematodes - ingestion or skin absorption of eggs. Pinworms

Cestodes - ingestion. Beef tapeworm

Trematodes - ingestion, skin penetration. Blood flukes.

Explain why the study of fungi such as yeast and molds is within the discipline of microbiology

Because the fungi domain includes mold, mushrooms,(multicellular) or yeast (unicellular). They are all eukaryotes

Describe the unique characteristics of fungi

Eukaryotes, multicellular or unicellular. Cell walls made of chitin. Asexual and sexual reproduction

Chemotrophs

Nonmotile

Potentially pathogenic

Grow in high sugar/ high salt concentrations, can grow in low moisture content, require less nitrogen than bacteria

Describe examples of asexual and sexual reproduction of fungi

A spore is how fungi reproduce asexually or sexually that detach from parent and grow.

Asexual reproduction - cell division and mitosis

-Conidiospore - not enclosed in a sac

-Arthroconidia - Fragmentation of septate hyphae

-Blastoconidia - Buds of the parent cell (budding yeast)

-Chlamydoconidia - Spore with a hyphal segment

-sporangiospore - enclosed in a sac

Sexual reproduction - fusion of nuclei from 2 opposite mating strains. 3 phases of sexual reproduction.

-Plasmogamy: + penetrates cytoplasm of -

-Karyogamy: + and - nuclei fuse to form a diploid zygote

-Meiosis: diploid nucleus produces haploid nuclei

Compare and classify the major groups of fungi

Classified by morphology: colonies, hyphae, and spores

Ascomycota, Basidiomycota, microsporidia, zygomycota

Explain why algae are included within the discipline of microbiology and describe unique characteristics of algae

Algae are multicellular or unicellular autotrophic protists

Chloroplasts contain pyrenoids that synthesize and store starches, boosting photosynthesis. Can be motile or non motile

Explain why lichens are included in the study of microbiology and describe the unique characteristics of lichen and the role of each partner in the symbiotic relationship of a lichen

A lichen is a combination of two organisms, a green alga or cyanobacterium and fungus, living in a symbiotic relationship.

They have large effects on the chemical composition of their environments.

Describe the general characteristics of viruses as pathogens

Infectious, acellular pathogens. Obligate intracellular parasites w/ host and cell type specificity

Describe viral genomes

Can have:

DNA or RNA

single stranded or double stranded

Envelope (some studded with glycoproteins) or naked

Lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce.

Describe the general characteristics of viral life cycles

Entry, replication, exit

Differentiate among bacteriophages, plant viruses, and animal viruses

Bacteriophages (phages) - infect bacteria. Attach to bacterium and usually only inject nucleic acid. Complex head and tail structure. Move from one bacterium to another after virions are released, often lyse the bacterial cell.

Plant viruses - Infect Plant cells. Usually enter through damaged tissue or transmitted by vectors like insects. Move between cells through plasmodesmata and throughout the plant vasculature tissue. Often spread without immediately lysing the plant cell. Commonly helical or icosahedral and usually lack an envelope

Animal Viruses - Enter through membrane fusion, endocytosis, or direct penetration. Commonly icosahedral, both naked and enveloped. Spread between cells through body fluids, nerves, blood, or respiratory secretions. Released through cell lysis, exocytosis, or budding.

Describe the characteristics used to identify viruses as obligate intracellular parasites

Acellular, no cell wall. No independent reproduction or metabolism, require a host cell to do that.

Describe the replication process of animal viruses

1. attachment - The phage attaches to the surface of the host

2. Penetration - the viral DNA enters the host cell

3. Biosynthesis - Phage DNA replicates and phage proteins are mage

4. Maturation - New phage particles are assembled

5. Lysis - The cell lyses, releasing the newly made phages

Describe unique characteristics of retroviruses and latent viruses

Latent viruses happens when a viral genome exists in a host genome as a provirus but virions are not produced within the cell: it is inactive. Proviruses insert themselves within the genome, so as the cell divides, the prophage DNA is passed onto daughter cells. Under stressful conditions, the prophage DNA is excised from the bacterial chromosome and enters the lytic cycle, replicating as normal. (ex. herpes)

Retroviruses are +ssRNA viruses that carry a reverse transcriptase within a capsid that synthesize a complementary ssDNA from the ssRNA template. This is made into dsDNA, and can integrate into the host chromosome and become a permanent part of the host (now a provirus). Then is now a latent virus until stressed into the lytic cycle (but doesn’t excise self from chromosome).

Discuss human viruses and their virus-host cell interactions

4 types:

Acute Infection - Replication of virions, host cell lysis. Acute signs/symptoms for host; often quick resolution

Chronic Infection - Slow/limited release of virions from host cell by budding (no lysis). Infected cell remains alive and continues to produce virus

Latent infection - Viral genome exists in host genome as a provirus, virions not produced. Infection asymptomatic until virus begins to replicate again

Transformation - Persistent/chronic infection that causes conversion of normal cell into tumor cell

Discuss why viruses were originally described as filterable agents

To isolate viruses, infected host cells can be obtained/grown. Virions can be separated from host cells by filtration: filters will remove anything above a certain size such as the host cell leaving the virions present in the medium to be collected below.

Describe the cultivation of viruses and specimen collection and handling (compare techniques)

Can be grown in vivo or in vitro (outside.)

In vivo could infect animals or egg embryos

In vitro can use many different type of cells, but cells are extracted and grown on a petri dish

Describe prions and their unique characteristics

PRIONS are misfolded, rogue forms of a normal protein in the cell. This misfolding can be due to many things like a genetic mutation, spontaneous. It can be infectious, stimulating other endogenous normal proteins to become misfolded leading to a whole clump of misfolded proteins. This is bad and can lead to cell death or whatever (ex. encephalopathy)