Brock Biology of Microorganisms Chapter 1

culture

cells grown in/on nutrient medium

medium

liquid/solid mixture containing all required nutrients

cell

living compartment that interacts with the environment and other cells

cytoplasmic (cell) membrane

barrier that separates the inside of the cell from the outside environment

cytoplasm

aqueous mixture of macromolecules, small organics, ions, and ribosomes inside the cell

ribosomes

protein-synthesizing structures

cell wall

organelle only present in some microbes; provides extra protection and strength

prokaryotes

type of cell: some Bacteria and Archaea, have no membrane-enclosed organelles; no nucleus

organelles

membrane-enclosed structures within a cell

eukaryotes

type of cell: some plants, animals, algae, protozoa, fungi; contains organelles; has DNA-enclosed in a membrane-bound nucleus

genome

a cell's full complement of genes

linear chromosomes (and many more, up to billions of base pairs)

typical eukaryotic DNA shape

circular chromosomes that aggregate in the nucleoid region

typical prokaryotic DNA shape

plasmids

extrachromosomal DNA that confers special properties (like antibiotic resistance) (found in prokaryotes)

metabolism

the chemical transformation of nutrients

enzymes

protein catalysts

transcription

when DNA information is converted into RNA

translation

when RNA is used by ribosome to make protein

motility

when cells move by self-propulsion

differentiation

when microbes modify internal structures to form specialized cells

intercellular communication

when microbes respond to other microbes

activities of microbial cells

-metabolism

-motility

-differentiation

-intercellular communication

-evolution

-live in microbial communities

3.8-4.3 billion y.a.

When did the first cells appear on Earth?

~2.6 billion y.a.

When was O2 introduced to the Earth's atmosphere?

~3.6 billion y.a.

When did the first anoxygenic phototrophs appear?

~0.5 billion y.a.

When did plants and animals appear on Earth?

three domains (distinct lineages of microbial cells

-Bacteria (prok)

-Archaea (prok)

-Eukarya (euk)

LUCA

last universal common ancestor

extremophiles

organisms that live in habitats too harsh for other life forms (ex. hot springs, glaciers, high salt, acidity, alkalinity, pressure)

ecosystem

term that refers to all living organisms plus physical and chemical constituents of their environment

microbial ecology

the study of microbes in their natural environment

microbes as disease agents

microbes that present as bacterial and viral pathogens

gut microbiome

this digests complex carbohydrates in humans and synthesizes vitamins and other nutrients (microbes involved in this)

biofilms

growths on submerged surfaces (ex. pipes storage tanks, implanted medical devices)

industrial microbiology

microbiology involved in the massive growth of naturally-occurring microbes to make low-cost products (ex antibiotics, enzymes, some chemicals)

biotechnology

area of microbe use that genetically engineers microbes, making high-value products in very small amounts

bioremediation

area of microbe use that cleans up pollutants

Robert Hooke

scientist to first describe microbes

Antoni van Leeuwenhoek

scientist to first describe bacteria using his lgiht microscope

magnification

ability to make an object's image larger

resolution

ability to distinguish two adjacent objects as distinct and separate

compound light microscopy

microscopy that uses visible light to illuminate cells

total maginfication

objective magnification x ocular magnification

bright-field scope microscopy

microscopy where specimens are visualized because of differences in contrast between specimen and surroundings; pigmented microbes add contrast

dyes

organic compounds that bind to specific cellular materials

basic dyes

positively charged dyes that bind strongly to negatively-charged cell components (ex. nucleic acids, acidic polysaccharides, etc.) Examples are methylene blue, crystal violet, and safranin

differential stains

stains where different cells become different colors

gram-positive bacteria

appear purple-violet when stained due to a thicker layer of peptidoglycan in cells outside of their cell membranes

gram-negative bacteria

appear pink when stained due to thin layer or peptidoglycan sandwiched between two lipid layers

phase-contrast microscopy

microscopy that improves image contrast of unstained, live cells utilizing a phase ring; appears as dark cells on a light background

phase ring

used in phase-contrast microscopy; amplifies differences in the refractive index of cell and surroundings

dark-field microscopy

microscopy where light reaches the specimen from the sides after being scattered by specimen; image appears light on dark background; good for seeing motility

fluorescence microscopy

microscopy used to see specimens that emit light after illumination with different wavelengths; appear to glow on black background due to filters; used in microbial ecology

differential interference contrast (DIC) microscopy

microscopy that uses a polarizer to create two distinct beams of polarized light; affords a 3D appearance

confocal scanning laser microscopy (CSLM)

microscopy that uses a computerized microscope and a laser source to generate 3D image; computer takes pics of layers and compiles them into 3D images

electron microscopes

microscopes that use electrons instead of visible light to image cells and structures

electron micrograph

image of an e-microscope

transmission electron microscopes (TEM)

e-microscope type:

-specimens are stained with high atomic weight substances that scatter e- well and improve contrast

-negative staining allows direct observation of intact cells/components

scanning electron microscopes (SEM)

e-microscope type:

-specimens coated with heavy metals (ex. gold)

-scattered e- collected to produce image

-only surface can be visualized

aseptic technique

collection of practices that allow preparation and maintenance of sterile chemicals

sterile

no living organisms present

pure cultures

cells from only a single type of microorganism

enrichment culture techniques

ways to isolate microbes using particular metabolic characteristics from nature

Louis Pasteur

chemist and microscopist

-discovered living organisms discriminate between optical isomers

-discovered alcoholic fermentation was a biologically (not just chemically) mediated process (from yeast)

-disproved spontaneous generation

-developed vaccines for anthrax, fowl cholera, and rabies

Robert Koch

physician and microbiologist

-demonstrated link between microbes and infectious diseases

-identified causative agents of anthrax, tuberculosis, and cholera

-proposed postulates for telling if a pathogen was a causative agent

-developed solid media for obtaining pure cultures

-won Nobel Prize for Physiology and Medicine

microbial diversity

study of microbes that focusses on non-medical aspects of microbiology in soil and water

Martinus Beijerinck

scientist who developed enrichment culture technique

enrichment culture technique

technique that says microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions (ex. nitrogen-fixing bacteria)

Sergei Winogradsky

scientist

-demonstrated that specific bacteria are linked to specific biogeochemical transformations

-proposed concept of chemolithography

-showed chemolithographs use carbon from CO2 (autotrophy)

-first to show nitrogen fixations and nitrification

metabolic model chemistry

idea that states that certain macromolecules and reactions are universal

Frederick Griffith

scientist who proved transformation with his mice and R/S strains; first to prove DNA was genetic material

Avery-MacLeoud-McCarty

scientists who proved transformation in vitro

James Watson, Francis Crick, Rosalind Franklin

scientists who first described the structure of DNA

Emile Zuckerland and Linus Pauling

scientists that discovered molecular sequences and evolutionary relationships

Carl Woese

scientist who realized rRNA sequences could be used to infer evolutionary relationships

phylogenetic tree

depicts phylogeny of all cells

Domain: Bacteria

Domain: ???

-prokaryotes

-usually undifferentiated single cells 1-10 micrometers but can vary

-30 major phylogenetic lineages, very diverse

Domain: Archaea

Domain: ???

-prokaryotes

-less morphological diversity

-mostly undifferentiated cells 1-10 micrometers long

-5 well-described phylogenies

-have the most extremophiles, but have non-extremophiles, too

-lack known parasites or pathogens of plants/animals

Domain: Eukarya

Domain: ???

-plants, animals, fungi

-first were unicellular, but now multicellular

-at least six kingdoms

-large diversity

viruses

-obligate parasites that only replicate within a host cell

-do not carry out own metabolism

-small genomes of double or single strand DNA or RNA

-very diverse