Microbiology Midterm 1 (Week 1/2 Stuff)

Paramecium

An example of a fungi

Incubation Period

The length of time it takes between being exposed to a disease and showing the symptoms

Yeast

The most common microbe used in food production

Units in which microorganisms are often measured

micrometers µm (10^-6 m)

“W” Shaped Mortality Curve

Caused by certain generations have immune protection from previous exposures that other generations didn’t have (Black Death/Bubonic Plague)

Microorganism

Organism too small to be seen with the naked eye

Prokaryote/Prokaryotic (he hates this word)

Cells lacking a membrane-bound nucleus

Eukaryote/Eukaryotic

Cells with a membrane-bound nucleus and other organelles

Old 5-Kingdom Tree of Life

Plants, Animals, Fungi, Protists, Monera

Bacteria Characteristics

Nucleiod, Free-Floating Circular DNA, No organelles, 0.02 to 2 µm in diameter, Binary Fission, 70s ribosome

Eukaryotes Characteristics

Nucleus, Linear DNA, Membrane-Bound organelles, 10 to 100 µm in diameter, Mitosis and Meiosis, 80s ribosomes

Species

Individuals that are able to reproduce and produce fertile offspring

Phenotype

Physical Characteristics of the organism

Genotype

Genetics/DNA

Phylogenetics

Evolutionary relationships, sequence-based, 16s rRNA

Polyphasic Taxonomy

Using phenotype, genotype, and phylogenetics to classify organisms

Dr. Claire Fraiser

First to sequence the complete genome of a free-living organism

16s rRNA

universally conserved in all bacterial life, used in molecular-based classification

Restriction Fragment Length Polymorphism (RFLP)

Amplify fragments by PCR and digest with restriction enzymes. Pattern is characteristic in certain groups of microbes.

Multi-Locus Sequence Typing (MLST)

Expansion of the rRNA sequencing. Instead of comparing the sequences of one gene, compare the sequences of five to seven genes. Identical sequences in multiple different genes is more stringent criteria and can distinguish between strains within a given species.

Single Nucleotide Polymorphism (SNP)

Similar concept to MLST, but instead searching for SNPs that are characteristic indicators of a given microbe

G/C Content

Higher G/C content = higher melting temps

Varies 25 to 80%

Related microbes have similar G/C content

Molecular ID Tools

Genome Sequencing, 16s rRNA sequencing, Mol% G/C, DNA-DNA Hybridization, MLST, SNP, Genomic Fingerprinting

Carl Woese

Divided prokaryotes into bacteria and archaea and replaced five-kingdoms system with three domain system: eukaryotes, bacteria, and archaea

Eukaryotes Examples

Protists: Algae, Protozoa, Slime molds, Water molds

Fungi: yeasts, molds, mushroom

Microbes not in 3 Domains

Viruses and Prions

Virus

Not alive, acellular, cannot replication without a host cell, include viroids, satellites, and bateri0phages

Dr. Jillian Banfield

Leveraged genomics to describe microbial diversity and build microbe tree of life

Archaeal Membranes

Ether Linkages, Isoprene-derived hydrocarbon

More resistant to chemical/heat stress

Bacterial Membranes

Ester Linkages, Fatty Acid

Glycerol Diether Lipids

Archaeal Lipid: Two hydrocarbons (~20 C long) attached to glycerol

Diglycerol Tetraether Lipids

Archaeal Lipid: Two glycerol molecules linked by 2 hydrocarbons (~40 C long)

Archaea Cell Walls

Highly Variable sometimes with protein s-layer, peptidoglycan-like layer, gram positive-like structure, no cell wall

Archaea Ribosomes

Have some similarities to both eukaryotic and bacterial ribosomes, but most bacterial-targeted antibiotics don’t work against it (intermediate between bacteria and eukaryotes)

Archaea DNA Packaging

Have histone proteins that form nucleosomes homologous to eukaryotic nucleosomes, except, only 4 histones vs. 8 in eukaryotes with less DNA

Purpose of Microscopy

Our eyes can only seem up to 0.1 mm (10^-1 m) and bacteria are usually in μm range (10^-6 m)

Magnification

Making an object bigger

Resolution

Making two adjacent objects appear distinct and separate

Defines smallest object that can clearly be seen

Limiting Factor for Resolution

The wavelength of the light used for detection (nothing smaller than the wavelength of light used can be seen)

Types of Light Microscopy

Bright Field, Dark Field, Phase Contrast, DI-M, Fluorescence

Total Magnification

ocular magnification * objective magnification

Oil Immersion Objection

A technique in light microscopy where immersion oil is used to match the refractive index of glass to prevent refraction of light rays

Dark Field Microscopy

Inversion of the image so cells appear bright on a dark background, using a dark field stop that creates a hollow cone of light that only magnifies the sample

Best For: Small/Thin cells at limit of resolution of light microscopes (~0.2 μm)

Phase Contrast Microscopy

Boosts contrast between sample and surrounding medium via destructive interference which exploits differences in refractive index

Best For: Not having to stain cells (stain can kill cells) and seeing internal structures

Differential Interference Microscopy (DI-M)

Uses prisms to make 3D-like image with enhanced contrast

Simple Stains

Provide coloration to cells indiscriminately for easy viewing. Usually charged molecules

Differential Stains

Provide coloration to some cells but not others

Examples: Gram Stain, Acid-Fast Stain, Endospore Stains

Gram Stain

Gram Positive-like turn purple and Gram Negative-like turn pink

Fluorescence Microscopy

Fluorescent molecules detect cells/cellular structures (specific targeting utilizes proteins and antibodies)

Super Resolution Microscopy

Computers predict peak location to allow resolution beyond wavelength threshold

Electron Microscopy

Electrons detect instead of light which leads to much higher resolution (0.2 nm limit vs. light’s μm limit). However, cells must be dead since it is done in a vacuum

Atomic Force Microscopy

0.2 nm resolution like electron microscopy but done on alive cells using topographical (surface) map