Micro Bio Test 1 Flashcards
What is microbiology?
The study of microorganisms
What is a prokaryote?
unicellular organism that lacks a defined nucleus; bacteria and archaea
What is a eukaryote?
Cell with a nucleus and membrane bound organelles
What is bacteria?
Bacteria are one-celled living organisms so small that they can be seen only with a microscope
What is archaea?
a domain of single-celled microorganisms that are prokaryotes; different ribosomes than bacteria
What are viruses?
Viruses are non-cellular entities that are parasites of cells, NOT LIVING
Thermophiles
Archaea that thrive in very hot environments, such as volcanic springs.
Cyanobacteria
Bacteria that can carry out photosynthesis
Central Dogma
DNA-transcription-RNA-translation-protein
Escherichia coli
gram negative, fast growth, 1x3 um in diameter
Robert Hooke
Late 1600s, first to observe “small chambers” in cork and call them cells (30x magnification).
Antoni Van Leeuwenhoek
Late 1600s, “Father of microbiology”, first to observe motility of bacteria (300x magnification)
spontaneous generation
the mistaken idea that living things arise from nonliving sources, “vital force”
Francesco Redi
Mid 1600s, challenged spontaneous generation with maggots experiment
John Needham
Late 1700s, SG advocate, Heated broth in sealed flasks.When the broth became cloudy with microrganisms, he mistakenly concluded that they developed spontaneously from the broth
Felix Pouchet
Late 1800s, SG theory advocate
Louis Joblot
Late 1600s, believed microbes arose from microbes, found microbes in hay infusions; described protozoa
Spallanzani
Late 1700s, Boiled two jars of gravy, sealing one jar immediately while leaving the other open to the air. The sealed jar remained free of microorganisms.
Endospore
A thick-walled protective spore that forms inside a bacterial cell and resists harsh conditions…lack of endospores caused differing results for spontaneous generation scientists, spores = growth!!
Louis Pasteur
Mid 1800s, disproved spontaneous generation, swan-necked flask
Pasteurization
treating a substance with heat to kill or slow the growth of pathogens, flash/batch method
Sterilization
The process that completely destroys all microbial life, including spores.
Tyndall
Late 1800s, showed evidence that some microbes have very high heat resistance and are difficult to destroy, Intermittent sterilization
Cohn
Late 1800s, discovered endospores, father of microbiology
Attenuation
the decrease or loss of virulence, Pasteur
Robert Koch
Late 1800s, Father of medical microbiology, a sequence of experimental steps for directly relating a specific microbe to a specific disease
Koch’s Postulates
- The organism must be observed in every case of the disease.
- It must be isolated and grown in pure culture.
- The pure culture must, when inoculated into a susceptible animal, reproduce the disease.
- The organism must be observed in, and recovered from, the experimental animal.
Chemolithotrophs
organisms that obtain energy from the oxidation of inorganic compounds, use inorganic electron donors
Parts of a microscope
Ocular, objective, stage, condenser, focusing knobs, light
Magnification
the ratio of an object’s image size to its real size, Ex: 10x ocular and 100x objective = 1000x mag
resolving power (resolution)
-the ability to show detail
-to get the best resolution you want SHORT wavelengths
-lower the power, the better the detail
R = 0.5*wavelength/numerical aperture
immersion oil
oil placed on a slide to minimize refraction of the light entering the lens, increases the numerical aperture
brightfield microscope
a microscope that allows light rays to pass directly to the eye without being deflected by an intervening opaque plate in the condenser, straining generally required, 1000x magn.
simple stain
a method of staining microorganisms with a single basic dye, heat kills cells, only dead cells allow stain penetration
Basic (cationic) stains
have a positive charge, attracted to acidic, negatively charged components on bacterial cell walls
-cell surfaces are negative so basic stains most common (crystal violet, methylene blue, etc)
Acidic (anionic) dyes
have a negative charge, repelled by acidic, negatively charged components on bacterial cell walls (India ink)
differential stain
a stain that distinguishes between 2 cell types/cell parts
gram positive stain
purple, decolorized with alcohol
gram negative stain
pink, decolorized with alcohol
acid fast stain
a differential stain used to identify bacteria that are not decolorized by acid-alcohol
mycobacteria = Red
other bacteria = Blue
endospore stain
Spore = green
mother cell = red
flagellular stain
Very thin, thicken flagella
capsule stain
negative stain, zone of clearing
darkfield microscopy
Has “stop” barrier
-The specimen appears light on a dark background, unstained cells are bright
-can’t see color and size distorted
-VIEW LIVE CELLS
-no stain required
phase contrast microscope
-living organisms
-no stain required
-differences in refractive indices among different subcellular structures
hanging drop preparation
-Prepared with concave (depression) slide, Vaseline adhesive or sealant, and a coverslip
-Overcomes the disadvantages of wet mounts
wet mount preparation
-a simple way to observe microbes by placing them in a drop of water on a slide with a coverslip
-Disadvantages: which plane/ moving too fast?
fluorescence microscopy
-uses a fluorescent dye that emits fluorescence when illuminated with ultraviolet radiation
-cellular auto fluorescence = chlorophyll live cells
-DAPI stains DNA
-FISH
differential interference contrast
Accentuates diffraction of the light that passes through a specimen; uses two beams of light, polarized light
-unstained live cells
confocal laser scanning microscope
a microscope using a laser as the light source and producing images of very high resolution, layer by layer to compile image,
biofilms + mushrooms
atomic force microscope
-can produce images of individual atoms on a surface
-challenging with sticky/live/flexible samples
Electron microscope
-microscope that forms an image by focusing beams of electrons onto a specimen
-vacuum and magnets
-live microscopy NOT possible
-very small resolution, fine details
-Transmission: 2D cells, special stains
-Scanning: 3D image with heavy metals, surface image
-used to see protein structure
All living cells
- Are surrounded by plasma membrane
- Can yield energy through metabolism
- Use DNA as genetic material
growth, replication, evolution
Ways to classify cells/organisms?
-microscopy (phenotypes, size/shape)
-molecular based approaches (16S/18S rRNA)
-physiological parameters (metabolism)
Cell size
-yeast cell = ~8um
-eukaryotic celol = 2 - 600um
-E.Coli = 1x3 um
-Bacteria = ~0.2 - 700 um
-being small is good, but there is a limit
-surface:volume ratio inversely proportional to size
Nucleoid
Prokaryotes
-non membrane enclosed
-1-2 circular chromosomes + plasmids
-haploid
-no sex, horizontal gene transfer
-more efficient
Nucleus
Eukaryotes
-membrane enclosed
->1 chromosome
- diploid
- sexual + asexual
- less efficient
Virology
-no cytoplasm
-no ribosomes
-no metabolic activity
-NOT LIVING
-must infect a pro or eukaryotic cell
Morphology
Corkscrew, rod, sphere, vibrio
Haeckel (1865)
3 kingdoms
-Animalia
-Plantae
-Protista
-invented “phylogeny” = evolutionary history of organisms
Whittaker (1969)
5 kingdoms
-plants
-animals
-fungi
-Protista
-bacteria
Carl Woese
Modern Tree of Life: 3 domains
-bacteria = cell wall (peptidoglycan), 70s, ester-linked lipids, f-Met (mod. Methionine)
-archaea = ether-linked lipids, 70S, Met
-eukarya = has nucleus, ester-linked lipids, 80S ribosome, Met
LUCA = last universal common ancestor
Endosymbiotic theory
Mitochondria and chloroplasts were once independent beings but now are organelles in eukaryotes
Archaea
-no known pathogens
-thermophile = high temp
- halophile = high salt
- methanogens = anaerobes, produce methane
Heterotrophs
Require organic compounds as carbon source (sugars, proteins, lipids)
Autotroph
Utilize CO2
Chemolithoautotroph
Inorganic energy source, CO2 carbon source
Chemoheterotroph
Organic energy source, reduced carbon source
Photoautotroph
Light energy source, CO2 carbon source
Photoheterotroph
Light energy source, reduced carbon
Carbohydrates (CH2O)n
glycosidic bonds (dehydration rxn between 2 hydroxyl groups), monosaccharides
Lipids
Energy storage, cell membrane, signaling
-single lipid = ester bonds
-complex = amphipathic, + and - sides
-glycolipid - cell signaling, communication
saturated vs unsaturated fats
Saturated: trans double bond, straight, stiff
Unsaturated: cis double bond, bent, membrane fluidity
Nitrogeneous Bases
Adenine, Thymine, Guanine, Cytosine
uracil for RNA
Nucleotide
monomer of nucleic acids made up of a 5-carbon sugar (ribose) , a phosphate group, and a nitrogenous base
Nucleoside
nitrogenous base + sugar
-lacks phosphate group
phosphodiester bond
the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide
-forms between 3’OH and 5’ phosphate groups
-5’P to 3’OH
Amino acids/proteins
-cell structure, transport, cell signaling, function as enzymes
-polar (hydrophilic), nonpolar (hydrophobic), acidic (-), basic (+), sulfhydryl group (methionine and cysteine)
peptide bond
-covalent bond formed between amino acids to form proteins
-between amino group and carbonyl group
-N terminus to carboxy terminus
Enzymes
-proteins that act as biological catalysts
-increase rate of rxn
-not consumed
-do not determine direction
metabolic energy
Change in Gibbs free energy
-determines direction of rxn
- neg G = exergonic
- pos G = endergonic
nuclease
DNA cutting enzyme, cleaves phophodiester bond
Protease
enzyme that digests protein, cleaves peptide bond
synthase
condenses two molecules together during anabolic reaction
Isomerase
rearranges bonds within a molecule to form an isomer
Polymerase
catalyzes polymerization reactions such as the synthesis of DNA and RNA
Kinase
adds phosphate
Phosphatase
removes phosphate group
Oxidoreductase
oxidation-reduction reactions
prosthetic group
A cofactor or coenzyme that is covalently bonded to a protein to permit its function
-heme
-Fe S cluster
coenzyme
-moves between enzymes
-recycled
-NAD+
-FAD
catabolic pathways
release energy by breaking down complex molecules into simpler compounds
- neg g
anabolic pathways
consume energy to build complex molecules from simpler ones
- pos g
OILRIG
oxidation is loss, reduction is gain
-OX = e acceptor (NAD+)
-RED = e donor (NADH)
redox tower
- Represents the range of possible reduction potentials
- The reduced substance at the top of the tower donates electrons
- The oxidized substance at the bottom of the tower accepts electrons
- The farther the electrons “drop” the greater the amount of energy released
Glycolysis (Emden‐Meyerhof‐
Parnas pathway)
-6 essential precursors + ATP (from substrate level phosphorylation) + NADH + H+
-no oxygen required
- 70% glucose flow
Pentose Phosphate Pathway
- 2 essential precursors + NADPH + H+ (no ATP)
- 30% glucose flow
Citric acid/Krebs/TCA cycle
- 4 essential precursors + ATP + NADH +H + FADH2 + H
Fermentation
A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.
- recycles NADH+H from glycolysis or TCA
-re oxidize coenzyme
substrate-level phosphorylation
The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.
oxidative phosphorylation
The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.
Electron Transport Chain (ETC)
series of electron carrier proteins that shuttle high-energy electrons during ATP-generating reactions
Aerobic vs. Anaerobic Metabolism
Aerobic= with oxygen (oxidase)
Anaerobic= without oxygen (reductase)
