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109 Cards in this Set
- Front
- Back
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Microbial Disease has had a major impact on the health and morale of civilizations, and the strength and number of soldiers during battle.
Some examples: |
Decline of the Roman Empire
Napolean’s Defeat at Waterloo Bubonic Plague |
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How long did it take the Bubonic Plague to spread across Europe?
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From 1347-1350, 3 years
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Aristotle (384–322 BC):
Dark Ages (AD 476–1000): The Renaissance (1250–1550): |
Believed that frogs formed from damp earth and mice from decaying grain.
Disease epidemics were recorded but no scientific writings survive. The beginning of open inquiry into the forces that shaped human lives. |
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what was Developed between 1590 and 1610 by Zacharias and Hans Janssen
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the microscope! Marcello Malpighi (1628–1694) was the first to use the microscope extensively for biological studies.
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Robert Hooke (1635-1703) – first to see/define...
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cells!
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Who developed a solar microscope with high resolving power? The first bacteria were recorded in
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Antony van Leeuwenhoek (1632–1723)
(300x zoom) 1683. |
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Disproving the Theory of Spontaneous Generation
chemist who laid to rest forever the idea of spontaneous generation. Showed that “germs” present in the air were the cause of fermentation and were widely distributed in nature. how? |
Louis Pasteur (1822–1895)
experiments with the swan-necked flasks - sterilized broth and it remained indefinitely - until tilted and exposed to dust and bacteria in neck... bacteria quickly multiplied in broth |
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Disproving the Theory of Spontaneous Generation
Italian biologist and physician Demonstrated worms found on rotting meat came from eggs of flies landing on meat Proved this by placing rotting meat in jars Covered one jar with fine gauze Gauze prevented flies from depositing eggs No eggs – no worms |
Francesco Redi
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Designed a sterilization system similar to modern autoclave (with Chamberland)
Assisted in solving problem of French silkworm sickness Vaccine studies for chicken cholera Determined a way to cure rabies |
Louis Pasteur (1822–1895)
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also opposed spontaneous generation and showed that microbes were present in air, and that sealed sterile infusions exhibited no growth.
He observed two phases for some bacteria— |
John Tyndall (1820–1893)
a thermolabile phase and a thermoresistant phase. |
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An endospore is a
why |
dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
In endospore formation, the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. The endospore consists of the bacterium's DNA and part of its cytoplasm, surrounded by a very tough outer coating. Endospores can survive without nutrients |
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published studies on the immunization of humans against small pox in 1798.
how |
Edward Jenner (1749–1823)
used cow pox... poor boy |
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The Golden Age of Microbiology (1854-1914)
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Time of great interest in the study of microorganisms
Between 1875 and 1918 most disease-causing bacteria were discovered Work on viruses began Lead to the initiation of prevention and treatment of disease |
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Confirmed germ theory of disease
Originator of “pure culture” method What are still used today to prove an organism is the causative agent of a disease |
Robert Koch (1843-1910)
Koch’s Postulates |
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Koch’s Postulates
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A specific microbe must be present in all cases, and not in healthy animals.
2. The organism should be grown in pure culture. 3. When the cultured microbe is injected into a new host, the new host develops the disease. 4. The microbe must be reisolated from the second host. |
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Bacteria
Archaea Algae Fungi Protozoa Multicellular parasites (worms) Which are prokaryotes and which are eukayotes |
Bacteria
Archaea are pro Algae Fungi Protozoa Multicellular parasites (worms) are euk |
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Characteristics of prokaryotes
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Both are single-celled organisms
Contain no membrane bound nucleus Termed prokaryotes = pre nucleus Pro = pre karyote = nucleus Do not contain any other organelles Cytoplasm is surrounded by rigid cell wall circular (rather than linear) genomes Horizomtal gene transfer (not meiosis) Metabolic diversity (found in crazy places) |
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Most common type in human infection
Members widely diverse Most prominent features include: Specific shapes -Rod-shaped, spherical and spiral Rigid cell walls -Responsible for cell shape Multiply by binary fission -One cell divides into two -Each cell is genetically identical to the first Some are motile -Move by means of flagella |
Bacteria!
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No known pathogens
Chemical composition of cell wall differs from organisms in other domains Organisms of this domain found in extreme environments |
Archaea
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Termed eukaryote = true nucleus
Eu = true karyote = nucleus |
Organisms contain membrane bound nucleus
Contains internal organelles Making organism more complex Example = mitochondria May be single and/or multicellular |
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Non-living infectious agents - acellular; require a host cell to replicate
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Viruses
Viroids Prions |
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Sizes of
Most Eukaryotes Most Bacteria Most Viruses |
>10 uM
0.5-10 uM < 0.1 uM |
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Binomial naming system
Two word naming system |
First word is genus name
Always capitalized Escherichia Second word is species name Not capitalized coli When writing full name, genus usually abbreviated E. coli Full name always italicized Or underlined |
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viruses have general same structure but have different
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host cell attachment
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Magnification
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total size increase
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Resolution
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determines how much detail can be seen
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Contrast
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# of visible shades in a specimen
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Limitation of light microscopes:
The illuminating source for light microscopy is ________. What could have a smaller wavelength? |
one cannot observe objects smaller than the wavelengths of the illuminating source.
Light! ions, electrons could! |
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What is the difference between simple and differential stains?
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Increase contrast, simple just does that, differential also gives idea of structure and identity
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transmission electron microscope (TEM)
vs. scanning electron microscope (SEM |
TEM works like light scope but with electrons (so you can see 2nm vs. 200nm on light)
SEM - e- scanned across specimen, see 2-3 dimensional picture |
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Morphology of Prokaryotic Cells
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Coccus
Bacillus Coccobacillus (short/stubby rods) Vibrio (cresent shaped, cholera) Spirillium (wavy) Spirochete - tighter helix than spirillium |
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Planes of division for cocci
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1. perpendicular = chain
2. parallel planes = sheet 3. 3 planes = sarcina 4. random - look like grapes |
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Composed of Phospholipids and Membrane Proteins
Phospholipids arranged as a bilayer in an aqueous environment fluid mosaic model describes the nonrigid structure of the |
cytoplasmic membrane
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What can and cannot pass through the cell membrane by simple diffusion?
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water, certain gases, and small hydrophobic molecules can
sugar can't |
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Major energy sources for active transport:
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ATP
Proton-motive force Molecules are moved against their concentration gradient |
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What types of molecules would need to be transported in or out of a bacterial cell?
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In:
glucose or other sugars/carbon sources ions - electrochemical gradients proteins -food, signalling molecules Out: Ions - proton motive force and protection against bursting Waste antibacterial agents toxins, virulence factors |
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Bacterial cell wall
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Rigid structure
Surrounds cytoplasmic membrane Determines shape of bacteria Holds cell together Prevents cell from bursting Unique chemical structure Distinguishes Gram- positive from Gram-negative |
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Rigidity of cell wall is due to
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peptidoglycan (PTG)
Compound found only in bacteria Basic structure of peptidoglycan Alternating series of two subunits N-acetylglucosamine(NAG) N-acetylmuramic acid (NAM) Joined subunits form glycan chain Glycan chains held together by string of four amino acids Tetrapeptide chain |
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Gram +
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simplist cell wall structure
up to 50 sheets of ptg in cell wall (no membrane) Techoic and Teichuronic acids provide additional strength and rigidity in G+ cell walls Purple on stain - dehydrated by ethanol to retain crystal violet |
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Gram – cell walls
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are more complex than G+
Have outer membrane and larger periplasm space between outer membrane and cytoplasmic membrane thin layer of peptidoglycan (2-3 layers) Also present in the G- outer membrane: Lipoproteins (interact w/ PTG to outer layer) and porins (size exclusion columns) |
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What's up with the Lipopolysaccharide (LPS)s in the Gram - cell wall?
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On outside: Strain-specific O-polysaccharide interacts with host immmune system, used for bacterial typing, develop antibodies to it
Middle - sugar chain Inside outer membrane: lipid A - endotoxin in part of cell broken open or dying, toxic for host |
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Medical significance of Peptidoglycan
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PTG as a target
Many antimicrobial interfere with the synthesis of PTG Examples include Penicillin Lysozyme |
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Some bacteria naturally lack cell wall
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Mycoplasma
Bacterium causes mild pneumonia Have no cell wall Antimicrobial directed towards cell wall ineffective Sterols in membrane account for strength of membrane Domain Archaea Have a wide variety of cell wall types None contain peptidoglycan but rather pseudopeptidoglycan |
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Capsules and Slime layers: what are their purposes? What are they made of? Where is their cellular location?
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Outside for protection and attachment. Capsule made of sugar layers or polysacchride, slimy coating can cover things immune system would normally see
–Capsule is a distinct gelatinous layer –Slime layer is irregular diffuse layer –Chemical composition of capsules and slime layers varies depending on bacterial species •Most are made of polysaccharide –Referred to as glycocalyx |
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Some bacteria have protein appendages
Not essential for life Aid in survival in certain environments They include |
Flagella
Pili |
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Flagella
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Long protein structure
Responsible for motility Use propeller-like movements to push bacteria Can rotate more than 100,00 revolutions/minute 82 mile/hour Some important in bacterial pathogenesis H. pylori penetration through mucous coat |
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Flagella structure has three basic parts
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Filament -Extends to exterior
-Made of proteins called flagellin Hook-Connects filament to cell Basal body-Anchors flagellum into cell wall |
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Pili
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Considerably shorter and thinner than flagella
Similar in structure Protein subunits Function Attachment These pili called fimbre Movement Conjugation Mechanism of DNA transfer |
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Resides in cytoplasm
In nucleoid space Typically single chromosome Circular double-stranded molecule Contains all genetic information |
Chromosome
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Plasmid
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Circular DNA molecule
Generally 0.1% to 10% size of chromosome Extrachromosomal Independently replicating Encode characteristic Potentially enhances survival Antimicrobial resistance |
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Ribosome
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Involved in protein synthesis
Composed of large and small subunits Units made of riboprotein and ribosomal RNA Prokaryotic ribosomal subunits Large = 30S Small = 50S Total = 70S Different than eukaryotic ribosomes 40S, 60S, 80S Difference often used as target for antimicrobials |
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Storage granules
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Accumulation of polymers
Synthesized from excess nutrient Example = glycogen Excess glucose in cell is stored in glycogen granules |
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Gas vesicles
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Small protein compartments
Provides buoyancy to cell Regulating vesicles allows organisms to reach ideal position in environment |
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Endospores
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Dormant cell types
Produced through sporulation Theoretically remain dormant for 100 years Resistant to damaging conditions Heat, desiccation, chemicals and UV light Vegetative cell produced through germination Germination occurs after exposure to heat or chemicals Germination not a source of reproduction |
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Endospore formation
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Complex, ordered sequence
Bacteria sense starvation and begin sporulation Growth stops DNA duplicated Cell splits Cell splits unevenly Larger component engulfs small component, produces forespore within mother cell Forespore enclosed by two membranes Forespore becomes core PTG between membranes forms core wall and cortex Mother cell proteins produce spore coat Mother cell degrades and releases endospore |
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Growth curve and what is happening at each stage
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Lag – gearing up for growth
Log – exponential growth goes until nutrients run out, making primary metabolites, start making secondary toward the end and continue in stationary Stationary phase – nutrients have run out, equal #s of cells growing and dying death – steep drop as more cells die than grow phase of prolonged decline – conditions deteriorating but some cells survive by other dying cell's nutrients, eventually all die |
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What are primary metabolites and when are they produced?
What are secondary metabolites and when are they produced? |
Primary – during log phase, gas, etc.
Secondary metabolites are produced during late log phase and early stationary phase. The're made when cells sense end of log, may be antibiotic to help with competition |
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How can you calculate how many bacteria you have if you know how many you started with and the rate at which they’re growing?
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Nt = N0 x 2^n (n = doubling times)
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Communities that are protected with polysaccaride film are called
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biofilms! found in nature (and your sink), have plaques
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Effect of temperature on growth: the names for organisms that grow at different temperatures
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Psychrophile
Psychrotroph Mesophiles – 15-45 degrees C thermophile Hyperthermophile Most pathogens are mesophile's like us, our environment is perfect for growth |
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Effect of oxygen on growth – what are the different oxygen requirements and what are those organisms called? Where would you find them in a test tube?
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Obligate aerobe needs oxygen, have catalase and superoxide dismutase enzymes for O2 detoxification
facultative aerobe throughout test tube but better on top – has enzymes Obligate anaerobe – doesn't have enzymes for O2 Microaerophile – likes some oxygen but only has small amounts of enzymes, so partly down in test tube Aerotolerant – don't use oxygen for growth, but can be present, has superoxide dismutase |
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Methods of sterilization
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Heat Sterilization
- Boiling - Moist Heat + Pressure (autoclave) - Dry Heat Pasteurization (for heat-sensitive foods) Irradiation (equipment) Filtration (heat-sensitive reagents) Chemicals (for disinfecting surfaces |
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How does an autoclave work?
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Like giant pressure cooker – 15 psi, 120 C for 15-20 min
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Energy sources for microbes:
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Light (“photo”) – energy from sunlight
Chemicals (“chemo”) – energy from chemical compounds (oxidation of organic or inorganic compounds) |
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Carbon-sources for microbes:
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Autotroph: self-nourishing. Can use entirely inorganic compounds (CO2) as the source of carbon.
Heterotroph: “other”-feeding. Organic chemical compounds serve as the source of carbon |
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Photoautotrophs
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- get energy from the sun and use CO2 as a carbon-source. - algae and some Bacteria
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Chemoheterotrophs
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(Chemoorganotrophs) – energy from oxidation of organic chemical compounds; use carbon substrates other than CO2.
- most common |
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Chemoautotrophs
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(chemolithoautotrophs) – get energy from the oxidation of inorganic chemical compounds (such as NH3 and H2S) and use CO2 as the principle C-source.
- only prokaryotes can do this |
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some Bacteria are Photoheterotrophic
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(energy from sun but need organic compounds as C-source)
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Catabolism=
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degradation processes with release of energy
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Anabolism =
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biosynthetic processes that require energy
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Active Carriers serve as energy shuttles to
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couple energetically unfavorable reactions with energetically favorable ones.
ATP! Has two high-energy bonds and lots of negative charges so it wants to be broken apart. |
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Oxidation and reduction reactions
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Lose electrons - oxidized
Gain electrons = reduced A reduction is occurring if the number of C-H bonds increases An oxidation is occurring if the number of C-H bonds decreases |
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Some electron carriers:
Freely diffusible |
(coenzymes/cofactors) – move electrons from one enzyme to another to take
part in reactions (like batteries or electron taxis) -NAD+/NADH + H+: catabolic, energy-generating reactions, transfers hydride ion (H-, or 2e- + 1H+) -NADP+/NADPH + H: anabolic, biosynthetic reactions (photosynthesis) -FADH/FADH2 : respiration (citric acid cycle) |
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Some electron carriers:
Fixed carriers, |
where carrier is a prosthetic group firmly attached to enzyme in a membrane (electron transport chain)… like a power line or stops on the city bus line
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-catabolic, energy-generating reactions, transfers hydride ion (H-, or 2e- + 1H+)
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NAD+/NADH + H+:
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anabolic, biosynthetic reactions (photosynthesis)
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-NADP+/NADPH + H:
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used for respiration (citric acid cycle)
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-FADH/FADH2 :
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Yield of glycolysis
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2 ATP
reducing power - 2NAD+ converted to 2NADH +2H+ 6 precursor metabolites - amino acids, lipopolysacharides, lipids, peptidoglycan (pyruvate is one) |
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What happens once phosphofructokinase catalyzes the 2nd addition of phosphate
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commited to glycolysis.
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Yield of Pentose phosphate pathway
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Breaks down glucose –> 5-&7-carbon sugars, G3P
makes NADPH + H+, 2 precursor metabolites (amino acids and nucleic acids) |
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Yield of transition step
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2 NADH + 2H+
One precursor metabolite - acetyl- CoA |
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How is the transition step different in prokaryotes
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entire oxidation process takes place in the cytoplasm (instead of entering mitochondria)
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nucleotides contain:
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a pentose sugar
a phosphate group a nitrogenous base. DNA and RNA are polymers made up of nucleotides. |
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What are the DNA nucleotides?
how do they differ from RNA nucleotides? |
(dATP, dCTP, dGTP, dTTP) nucleotides with one of four nitrogenous bases
RNA has OH group (can be quite reactive), DNA is dioxy |
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DNA ligase - enzyme that
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joins two DNA fragments by forming a covalent bond between the sugar phosphate residues of adjacent nucleotides
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DNA polymerases - enzymes that
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synthesize DNA by using one strand as a template, can only add to the 3' end
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Okazaki fragment
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nucleic acid fragment generated during discontinuous replication of the lagging strand of DNA
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Primer
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fragment of nucleic acid (made by primase) to which polymerase can add nucleotides (needs existing fragment)
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In transcription, does the RNA end up looking like the + or - strand of DNA?
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+, because - is the template
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Transcription: key players, mechanism of RNA synthesis
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RNA polymerase has a sigma factor which recognizes and allows it to bond to a promotor sequence of DNA, it then synthesizes mRNA from an exposed strand of DNA. (-) strand of DNA is the template, so RNA looks like (+) strand. Template strand is determined by which direction it's going (always toward 3'!).When it reaches a terminator, a hairpin loop is formed and RNA Polymerase falls off, ending the transcription.
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Primase uses what as a template to make what?
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DNA as a template for RNA primers
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RNA polymerase uses what as a template to make what?
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DNA as a template for RNA
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Anticodon
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sequence of three bases in tRNA that is complementary to a codon in mRNA and allows it to bind
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Ribosomes are composed of
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protein and ribosomal RNA
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What are the three stages of translation?
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Initiation
Elongation Termination |
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What are the three types of base substitution mutation and how are they caused?
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Silent - replaced base at end of codon still codes for the same amino acid
Missense - changes the amino acid Nonsense - creates a stop codon and the whole protein is truncated |
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What are the basic steps of DNA repair?
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Damaged strand–Endonuclease enzyme removes short stretch of nucleotide
–DNA polymerase fills gap –DNA ligase joins ends |
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Positive regulation
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involves activator proteins that stimulate transcription.
Activators interact with sequences usually upstream from the promoter. |
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Positive transcriptional regulation (How does it work? example: maltose operon)
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Example: Positive regulation of the Mal Regulon for uptake and catabolism of maltose. (maltose acts as inducer and lets activator bind so promoters can initiation transcription of genes for dealing with maltose.)
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Negative regulation
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decreases ability of RNA polymerase to transcribe a gene.
Usually involves a repressor protein Repressors bind to specific sites called operators near the promoter and physically block transcription But, when an inducer binds, it prevents the repressor from binding. Alternately, if a repressor cannot bind by itself it may need a corepressor which would then turn of transcription when present. |
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Negative Regulation of the Trp operon
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Tryptophan acts as a co-repressor – make Trp only when it isn’t already available.
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Why does it Need lactose but no glucose in order for Lac operon to make genes for lactose catabolism.
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When glucose is present, there are low levels of cAMP, which acts as an inducer for CAP so it cannot bind to the site and act as an activator.
Without lactose, there is no allolactose to act as an inducer preventing the repressor from binding to the operator, so transcription is blocked from that end too |
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taxonomy
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the branch of microbiology responsible for characterizing and naming organisms and organizing them into groups
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Natural/phylogenetic relationships are based on
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evolutionary relationships (rRNA)
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What is the most commonly used molecule in molecular phylogenetics
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is RNA of the small subunit of ribosomes – 16S rRNA (or 18S rRNA of Eukarya).
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What is the tree of life based on?
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rRNA sequences which show phylogenetic relationships
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Uses principles of DNA replication to make many copies of a discrete segment of DNA
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Polymerase Chain Reaction (PCR)
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What is the first step of the Polymerase Chain Reaciton (PCR)
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Heating to 95C to denature DNA so hydrogen bonds are broken and it's separated
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