microbio exam 1 condensed

Miasma theory

Disease arose from bad air created by decaying matter.

Genotypic characterization

G+ C content

Genotypic characterization

Hybridization

Spontaneous generation theory

Life could arise from nonliving matter if the material contained pneuma.

Robert Hooke

Coined the term cell and was one of the first to observe microbes through a microscope.

Francesco Redi

Life comes from life; maggots grew on meat exposed to flies, while covered meat did not develop maggots in the meat.

Independent vs dependent variable

Independent = manipulated by researcher; dependent = measured/observed response.

Positive vs negative control

Positive = known to produce expected effect; negative = expected not to produce effect and provides comparison.

Louis Pasteur

Father of germ theory; swan-neck flask experiment disproved spontaneous generation by showing airborne microorganisms, not air itself, cause microbial growth.

Miasma theory challenged by

Cholera linked to contaminated water and reduced infections from hand disinfection/antiseptic procedures.

Koch's postulates

Criteria used to establish a microorganism as the cause of a particular disease.

Microbiology as a field

Includes bacteriology, protozoology, parasitology, and immunology.

Prokaryotes

Unicellular; no nucleus; DNA in nucleoid; no membrane-bound organelles; usually single circular DNA molecule; binary fission.

Eukaryotes

Nucleus; unicellular or multicellular; membrane-bound organelles; multiple linear chromosomes; mitosis/meiosis.

Viruses

Acellular; DNA or RNA; replicate using host-cell machinery; no independent metabolism.

Metabolism/energy — eukaryotes

Cellular respiration or photosynthesis; energy production in mitochondria or chloroplasts.

Metabolism/energy — prokaryotes

Diverse metabolic pathways including aerobic, anaerobic, and photosynthetic; energy-generating processes at cell membrane.

Metabolism/energy — viruses

No metabolism; rely on host for energy.

Coccus

One spherical cell.

Diplococci

Two spherical cells.

Streptococci

Chain of spherical cells.

Staphylococci

Cluster of spherical cells.

Bacillus

One rod-shaped cell.

Diplobacilli

Two rod-shaped cells.

Streptobacilli

Chain of rod-shaped cells.

Spirillum

Spiral/wavy shape.

Resolution

Ability to distinguish two objects as separate.

Numerical aperture

Ability of a lens to gather light and resolve an image.

Immersion oil

Helps direct light into the objective and improves resolution.

Light microscopes

Brightfield, darkfield, phase contrast, fluorescence, TIRF, and DIC; generally cannot visualize viruses.

Brightfield

Usually used for stained/fixed bacteria.

Darkfield

Live, unstained organisms; specimen appears bright against dark background because only scattered/reflected light enters objective.

Phase contrast

Living, unstained, transparent cells; enhances contrast, allows cell movement/internal structures to be seen, and produces halos.

Fluorescence

Uses fluorophores excited by specific wavelengths; useful for locating particular molecules/proteins; can be used with live or fixed cells.

TIRF

Fluorescence technique used to visualize molecules/proteins near the cell membrane.

TEM

Electron microscopy used for internal structures and viruses; thin specimen; cannot view living cells.

SEM

Electron microscopy used for detailed 3D-like surface features; cannot view living cells.

DIC

3D-like contrast of living specimens; can visualize eukaryotic organelles.

Compound microscope

Uses multiple lenses to magnify small objects.

Simple stain

Uses one dye to increase contrast and view morphology/arrangement.

Differential stains

Gram = distinguishes Gram+/Gram−; acid-fast = detects mycolic-acid/waxy cells; endospore = detects endospores.

Gram stain

Crystal violet → iodine → alcohol/ethanol → safranin; Gram+ = purple; Gram− = pink/red; too much alcohol can make Gram+ falsely appear pink.

Acid-fast stain

Detects mycolic-acid/waxy cells; positive = red/pink; negative = blue.

Endospore stain

Detects bacterial endospores; positive = green endospores with red/pink vegetative cells; negative = only red/pink vegetative cells.

Heat in staining

Acid-fast and endospore staining use heat to help stain penetrate.

Fixation

Preserves morphology and attaches cells to slide; without heat fixation, cells may wash off.

Basic vs acidic dyes

Basic dyes bind negatively charged bacterial surfaces; acidic dyes are repelled and often stain the background.

General bacterial characteristics

Unicellular; circular DNA; no nucleus; grow in diverse environments; typically have peptidoglycan cell walls.

Capsule

Protects cell, helps adherence to surfaces, and helps evade immune cells.

Membrane reinforcement

Bacteria = hopanoids/hopanes; eukaryotes = cholesterol.

Bacterial membrane

Selectively permeable; involved in transport, signaling, secretion, and energy processes.

Channels vs carriers

Channels = passive/facilitated diffusion; carriers can perform active or passive transport.

Bacterial cell wall

Provides shape/rigidity and osmotic protection; contains peptidoglycan.

Peptidoglycan

Polymer of NAG and NAM disaccharide subunits; unique to bacteria and a useful antibiotic target.

Efflux pumps

Pump toxins or harmful compounds out of cells.

Gram-positive bacteria

Thick peptidoglycan with teichoic acids; stains purple.

Gram-negative bacteria

Thin peptidoglycan plus outer membrane containing LPS; stains pink/red.

LPS

Lipopolysaccharide in Gram-negative outer membrane; Lipid A is endotoxin and can trigger severe inflammation.

Archaea

May contain pseudopeptidoglycan or no peptidoglycan.

Mycolic acids

Waxy cell-envelope components responsible for acid-fast properties.

Pili

Sex pili allow DNA transfer; some pili contribute to motility.

Fimbriae

Primarily used for attachment to surfaces.

Nucleoid

Non-membrane-bound region containing bacterial DNA; DNA is supercoiled by nucleoid-associated proteins.

Bacterial ribosomes

Site of protein synthesis; 70S = 30S + 50S.

Plasmids

Extrachromosomal DNA that replicates independently and may carry antibiotic-resistance or toxin genes.

Inclusions

Store excess nutrients and chemicals.

Endospores

Dormant, dehydrated, metabolically inactive structures highly resistant to harsh conditions.

Vegetative cells

Metabolically active growing cells that are more sensitive to harsh conditions.

Flagellum

External filament used for bacterial motility.

Flagellar arrangements

Monotrichous = one; amphitrichous = opposite ends; lophotrichous = many at one end; peritrichous = distributed over surface.

Chemotaxis

Movement in response to chemical gradient; attractant = CCW/bundle/run; repellent = CW/tumble.

Phagocytosis vs pinocytosis

Phagocytosis = large particles; pinocytosis = extracellular fluid/small particles.

Exocytosis

Vesicles fuse with membrane to secrete material.

Prokaryotic vs eukaryotic transport

Prokaryotes use active/passive transport but not typical endo/exocytosis; eukaryotes use active/passive transport plus endo/exocytosis.

Cytoskeleton

Structural support and intracellular transportation.

Mitochondria

Eukaryotic organelles involved in cellular respiration; have two membranes and bacterial-like ribosomes.

Nucleolus

rRNA synthesis and ribosome assembly.

Eukaryotic ribosomes

80S = 40S + 60S.

Peroxisome

Hydrogen peroxide and lipid metabolism.

Rough vs smooth ER

Rough ER = protein synthesis/bound ribosomes; smooth ER = lipid synthesis, detoxification, carbohydrate metabolism/no bound ribosomes.

Golgi

Cis = incoming/receiving; trans = outgoing/shipping.

Lysosome

Breakdown and recycling of cellular material.

Endosymbiotic theory

Mitochondria and chloroplasts originated from free-living prokaryotes; supported by their own DNA and bacterial-like features.

Actinobacteria

Gram-positive bacteria with high G+C DNA content.

Actinomycetes

Gram-positive bacteria; characteristic snapping division.

Cyanobacteria

Gram-negative photosynthetic bacteria.

Firmicutes

Gram-positive bacteria with low G+C DNA content (<40%).

Alphaproteobacteria

Gram-negative; many are intracellular.

Chloroflexi

Green non-sulfur bacteria; generally do not metabolize sulfur for photosynthesis.

Mycoplasma

Gram-positive lineage identified by 16S rRNA; lacks a cell wall and has unusual motility.

Dichotomous key

Used to identify organisms based on a series of characteristic choices.

GC content

Higher organisms 30-50%

Prokaryotes vary widely in GC content

10% difference/ not closely related

ANI

Threshold of 95%

MLST and MLSA (compare small sections of DNA)

97%

Actinomyocetes

High G+C, soil, fungal like growth

Firmicutes

Low G+C content

Streptomycetes

Antibiotics/ secondary metabolites

Arthrobacter

Snapping division

Mycoplasma

No cell wall, pleomorphic