Brocks Chapter 1: Terms and Definition

Microbial Culture

a collection of cells that have been grown in or on a nutrient medium

Nutrient Medium

Mixture that contains all nutrients required for a microorganism to grow

Growth

Increase in cell number as a result of cell division

Three structures universal to all cells

Cytoplasm, cytoplasmic membrane, ribosomes

Cell wall

Permeable structure located outside the cytoplasmic membrane

Ribosomes

Makes proteins

Two fundamental cell type based on cellular organization

Prokaryotic and Eukaryotic

Plasmids

Small circular DNA in prokaryotes distinct from chromosomes that confer special property on the cell

Listeria

Soil organisms that can hijack cellular system causing actin to polymerize and propel the cell like a rocket within the host cytoplasm

Genome

Full set of genes in a cell

Gene

Segment of DNA that encodes a protein or RNA molecule

Close circular chromosomes

Bacteria and Archaea Chromosomes

Metabolism

Transforms nutrients from the environment to new cellular structures for survival and reproduction (uses energy during the process)

Enzymes

Proteins with catalytic activity that supplies energy and perform biosynthesis within the cell

All cells carry out these three processes

Transcription, translation, and DNA replication

Motility

Relocation of cell usually by self propulsionas response to environmental conditions

Intercellular communication

Awareness to chemical signals from neighboring cells regardless of species

Horizontal gene transfer

Exchange of genes from neighboring cells regardless of species

Morphology

Cell size and shape

Micrometer

one millionth of a meter

Prokaryotes

Type of cell that relies on diffusion for transport through cytoplasm (which limits their size)

Eukaryotes

Type of cell with complex intracellular structure and can actively transport molecules within the cytoplasm

Epilopiscium fishelsoni

Found in guts of surgeonfish, has 10,000 copies of genome throughout its cytoplasm to overcome diffusional limitations

Thiomargarita

Largest known bacterium. Has a large vacuole in the center of the cell to combat diffusional limitations

Cell size increases

S/V ratio decreases

Coccus/ Cocci

Cell with spherical or ovoid morphology

Rod / Bacillus

cylindrical shaped bacteria

Spirillum

spiral shaped bacteria

Vibrio

a slightly curved rod-shaped prokaryotic cell

Spirochetes

spiral-shaped bacteria that have flexible walls

Diplococci

Cocci in pairs

Streptococci

Long chain of cocci

Tetrads / Sarcinae

Three dimensional cubes or cocci

Staphylococci

grape-like clusters of cocci

Filamentous Bacteria

Long, thin, rod shape bacteria that divide terminally and then form long filaments of cells attached end to end

Electron Micrography

Microscopic technique where specimen are examined at extremely cold temperatures without fixation

Domain

Bacteria, Archaea, Eukarya

Viruses

Group of microorganisms that lack a cellular structure

Five described phyla of Archaea

Euryarchaeota, Crenarchaeota, Thaumarchaeota, Nanoarchaeota, and Korarcheota

Cambrian explosion

Evolutionary burst of eukarya

Kingdoms

Major lineages of Eukarya (instead of phyla)

Nanoflagellates

Microbial eukaryotes which are microbial predator as small as 2um long

Ostreococcus

Genus of green algae smaller than most bacteria

Xenophyophores

Single celled organisms found in deep oceans

Viral genome

DNA or RNA that can be singe or double stranded

Basis of viral classification

Structure, genome composition, and host specificity

Bacteriophage

A virus that infects bacteria

Pandoravirus

Unusually large virus more than 1 micrometer long

Cyanobacteria

Oxygen producing phototrophs that oxygenated Earth’s atmosphere

LUCA

Last Universal Common Ancestor

Extremophiles

Microbes with habitats too harsh for other life forms

Nitrogen Fixation

Process where bacteria convert atmospheric nitrogen (N2) into ammonia (NH3)

pH 2

pH of the stomach

pH 4-5

pH of the small intestine

Lactic acid producing bacteria

Bacteria used to produce sour tasting products like sauerkraut, kimchi, pickles, and etc.

Industrial Microbiology

Focused on the use of microorganisms grown on massive scale in bioreactors to make large amounts of products at relatively low cost

Biotechnology

Employs genetically engineered microorganisms to synthesize products of high commercial value usually on a small scale

Ethanol

Produced by microbial fermentation of glucose obtained from carbon-rich feedstock such as sugarcane, corn, or rapidly growing grasses

Wastewater treatment

Relies on microbes to treat contaminated water so that it can be reused or returned safely to the environment

Bioremediation

Relies on microbes to transform toxic pollutants into non toxic forms

Micrographia by Robert Hooke

First book devoted to microscopic observations

Antoni van Leeuwenhoek

Discovered bacteria while studying pepper-water infusions

Magnification

Capacity of a microscope of enlarge an image

Resolution

ability to distinguish two adjacent objects as distinct and separate

Objective and ocular

Two types of lenses on a modern compound microscope

Total magnification of a compound microscope

Product of the magnification of its objective and ocular lenses

Numerical aperture

Function of the wavelength of light used and the light gathering ability of the objective lens

Dyes

Used to stain cells and increase their contrast

Basic dyes

Positively charged dyes (e.g. methylene blue, crystal violet, safranin)

Differential stains

Stains that render different kind of cells different colors

Purple violet

Color of a gram positive bacteria

Pink

Color of a gram negative bacteria

Phase-contrast and dark-field microscopy

Two forms of light microscopy that improve image contrast of unstained cells

Phase-contrast microscopy

Based on the principle that cells differ in refractive index from their surrounding

refractive index

the ability of a material of alter the speed of light

Phase ring

Device in the objective lens of a phase-contrast microscope that amplifies the difference in phase of light passing through the specimen vs its surroundings

Phase-contrast microscopy (result)

Specimen appear dark on a light background

Dark field microscopy (result)

Specimen appear light on a dark background

Dark field microscopy

Good way to observe microbial motility as it can resolve bundles of flagella

Fluorescence Microscope

Visualizes specimen that fluoresce (emit light)

Fluorescence microscopy

Cells appear to glow in a black background

Differential Interference Contrast Microscopy

Form of light microscopy that employs a polarizer in the condenser to produce polarized light. This passes through a prism that generates two distinct beams that pass through the specimen and into the objective lens where they’re recombined into one.

DIC Microscopy

Produces an optical effect that provides 3D perspective and is used on unstained cells as it can reveal internal cell structures

Confocal Scanning Laser Microscopy

Computer controlled microscope that couples a laser to a fluorescence microscope

Confocal Scanning Laser Microscopy

Generates a high-contrast 3D image and allows access to several planes of focus in the specimen

Confocal Scanning Laser Microscopy

Useful in thick specimen

Electron Microscopes

uses electrons instead of visible light (photons) to image cells and cell structures

Transmission Electron Microscope (TEM)

Used to examine cells at very high resolution and magnification

Negative Staining

Used to observe external features of intact cells

Electron Cryotomography (cryoET)

Imaging technique in which TEM is used to obtain 3D images through rapid freezing so that samples are immobilized in noncrystalline vitreous ice (b&w)

Scanning electron microscope

The specimen are coated with a thin film of heavy metal (usually gold)

Scanning electron microscope (result)

3D surface of the cell (black and white)

Aseptic Technique

Collection of practices that allow for the preparation and maintenance of sterile nutrient media and solutions

Pure cultures

Contains cells from a single type of microorganism

Spontaneous Generation

Life arose spontaneously from non living material

Louis Pasteur

Disproved spontaneous generation using the swan-necked flask experiment

Joseph Lister

Deducted from Pasteur’s discoveries that surgical infections were caused by microorganisms and is credited with aseptic technique for surgeries

Pasteur developed vaccines for

Anthrax, cholera, and rabies

Ignaz Semmelweis

Promoted sanitary methods (e.g. hand washing) to prevent infections but could not prove why these worked

Anthrax

Caused by bacterium Bacillus anthracis