Exam 1: chapter 1 + 2
Naming microbes
- An organism's scientific name consists of its genus name and its specific epithet - Species names can be personalized or describe some aspect of its appearance / habitat - Example: Escherichia coli Rules for naming: 1. Genus name is always capitalized 2. Epithlet is always lower case 3. If it is hand written, it must be underlined if it is hyped it needs to be in italics 4. The first time it appears in any scientific paper, it must be spelled out completely After the first time it can be abbreviated (E. coli)
size of things
- Animal cell = 10 micrometers - Bacteria cells = 1 micrometers - Viruses can be 10 times smaller
frequency
- describes the rate of vibration of the wave, or the number of wavelengths within a specified time period
Archaea
- a single-celled prokaryotes - Cell walls lack peptidoglycan and instead are composed of other polymers - Some archaea live in extreme environments, such as the Morning Glory pool, a hot spring in Yellowstone National Park
binomial nomenclature
- a two-word naming system for identifying organisms by genus and species - The genus part of the name is always capitalized; it is followed by the species name, which is not capitalized (both are italicized)
Parasitic worms (helminths)
- eukaryotes that range in size from microscopic forms to adult tapeworms several meters in length
Fungus
- eukaryotic organisms - Include multicellular molds and single-celled yeasts - Also macroscopic mushrooms - Obtain their food from other organisms and have cell walls - Large colonies of microscopic fungi can often be observed with the naked eye, as seen on the surface of these moldy oranges
Phylogenies
- evolutionary relationships - In these diagrams, groups of organisms are arranged by how closely related they are thought to be
transmission electron microscopes (TEM)
- generates a beam of electrons that passes through a thinly sliced dehydrated specimen - Instead of using glass lenses, electrons are focused through magnetic fields - The image is then beamed onto a fluorescent screen that changes the electrons energy into visible light - TEM produces a flattened extremely high resolution picture of the specimen
Robert Koch
- identified the specific microbes that cause anthrax, cholera, and tuberculosis
The Cloaca Maxima
- Also known as Greatest Sewer, ran through ancient Rome - It was an engineering marvel that carried waste away from the city and into the river - These ancient latrines emptied into the Cloaca Maxima
candida albicans
- is a unicellular fungus, or yeast - It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants - Has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism
Leeuwenhoek
- made some of the first simple microscope in order to examine the quality of loth - Reported the existence of protozoa in 1674 and of bacteria in 1676 - called them wee beasties - By the end of the 19th century, Leeuwenhoek's beasties were called microorganisms - Today they are also known as microbes - Leeuwenhoek was able to observe single-celled organisms, which he described as "animalcules" or "we little beasties," swimming in a drop of rain water - We now know he was looking at bacteria and protists
refraction
- occurs when light waves change direction as they enter a new medium
Eukaryotes
- organisms whose cell contain a nucleus - Nucleus: central structure / composed of genetic material surrounded by a distinct membrane - The domain eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as protists, fungi, plants, and animals
Algae
- plantlike eukaryotes that are photosynthetic - They make their own food from carbon dioxide and water using energy from sunlight - Include multicellular and unicellular organisms
Marcus Terentius Varro
- proposed that disease could be caused by "certain minute creatures... which cannot be seen by the eye"
Protozoa
- single-celled eukaryotes - Similar to animals in their nutritional needs and cellular structure - Most are capable of locomotion (movement) - Some cause disease (example: malaria)
Hippocrates
- the "father of Western medicine," believed that diseases had natural, not supernatural causes - He dismissed the idea that disease was caused by supernatural forces - Instead, he posited that diseases had natural causes from within patients or their environments
focal length
- the distance to the focal point
refractive index
- the extent to which a material slows transmission speed relative to empty space - Large differences between the refractive indices of two material will result in a large amount of refraction when light passes from one material to the other - For example, light moves much more slowly through water than through air, so light entering water from air can change direction greatly We say that the water has a higher refractive index than air When light crosses a boundary into a material with a higher refractive index, its direction turns to be closer to perpendicular to the boundary (i.e., more toward a normal to that boundary) - this is the principle behind lenses
focal point
- the image point when light entering the lens is parallel
Scanning Electron microscopes (SEM)
- the surface of the specimen is first coated with a metal such as platinum or gold - The SEM then focuses the beam of electrons back and forth across the surface of the coated specimen, scanning it rather than penetrating it - Electrons scattered off the surface of the specimen pass through a detector this produces a signal displayed on a mirror - SEM produces a high resolution 3D image of the specimen - not quite as high resolution as TEM
Prokaryotes
- unicellular microbes that lack a true nucleus - Microbes within the domains Bacteria and Archaea are all prokaryotes
Bacteria
- unicellular prokaryotes - Cell walls are composed of a polymer called peptidoglycan - Though some bacteria lack cell walls - Most are beneficial, but some cause disease
Horizontal gene transfer
- when a gene of one species is absorbed into another organism's genome - Especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related - Consequently, some scientists now think in terms of "webs of life" rather than "trees of life"
Staining
After the bacteria is fixed to the slide, we can add stains without the bacteria falling off Stain: dye that colors an organism so that the shape and structures of the organism can be distinguished - Provides contrast between organisms and background (increases resolution) - Staining allows us to see morphology (shape) and arrangement (goruping) - Some staining techniques help identify organisms further (differential stains!) Bacteria are negatively charged, stain take advantage of this property Basic dyes: the colored ion (chromophore) is positively charged
morphology
the shape of cells - Most cells are monomorphic (one shape only) - A few cells are pleomorphic (variety of shapes) - Some common morphologies - Coccus - round (or sometimes oval) - Bacillus - rod shaped - Spira - corkscrew shaped - Vibria - curved - Spirillia - helical and flexible - Spirochetes - helical and flexible - Use axial filaments for movement
Biofilms
- A biofilm forms when planktonic (free-floating) bacteria of one or more species adhere to a surface, produce slime, and form a colony
Basics of preparing a slide
- Bacteria are not (usually) colored, so we have to stain (color) them - Before we stain we have to fix a smear of the bacteria to the slide Fix: stick the bacteria to the slide Smear: a thin film of specimen Here's how to do it! 1. Get a slide and sterilize it by passing it over a flame 2. Apply a small drop of distilled water to the middle of the slide 3. O brain an inoculation loop and sterilize it 4. Gently take some of the bacteria from the provided agar with your loop 5. Mix the bacteria with the drop of water 6. Re-sterilize your loop and sterilize another slide 7. Dip your loop in your waterbacteria mixture and then spread it on your new slide - don't add too much! Only need a little! It is ok if you don't see any bacteria right now! 8. Let your new slide air dry 9. Pass it over a flame 2 times to "fix" the bacteria onto the slide. Done!
Woese and Fox's phylogenetic tree contains three domains
- Bacteria, Archaea, and Eukarya - Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms
capsule staining
- Certain bacteria and yeasts have a protective outer structure called a capsule - Since the presence of a capsule is directly related to a microbe's virulence (its ability to cause disease), the ability to determine whether cells in a sample have capsules is an important diagnostic tool - A negative staining technique (staining around the cells) is typically used for capsule staining - The dye stains the background but does not penetrate the capsules, which appear like halos around the borders of the cell
confocal microscopes
- Confocal microscopes use fluorescent dyes in conjunction with UV lasers to illuminate the fluorescent chemicals - The lasers can target only one thin plane of a specimen at a time - Several images are taken and digitized - Computers construct three-dimensional images of the entire specimen - Confocal microscopy can be used to visualize structures such as this roof-dwelling cyanobacterial biofilm
Carolus Linneaus / Classification
- Developed a taxonomic system for naming plants and animals and grouping similar organisms together - Biologists still use a modification of Linnaeus's taxonomy today - All living organisms can be classified as either eukaryotic or prokaryotic
Bright and Dark Field Microscopy
- Different types of microscopy are used to visualize different structures - Brightfield microscopy renders a darker image on a lighter background, - Darkfield microscopy increases contrast, rendering a brighter image on a darker background
Endospore Staining
- Endospore staining: dormant structure formed by few bacteria during adverse conditions - Must be seen with "malachite green" dye that is heated to promote penetration - Counterstained with safranin to see other parts of the bacteria
fluorescent microscopes
- Fluorescent microscopes use an ultraviolet (UV) light source to make objects fluorescent - Because UV light has a shorter wavelength than visible light, resolution is increased - Also contrast is improved because fluorescing structures are visible against a black background
the role of genetics in Modern Taxonomy
- Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective - Modern taxonomy relies heavily on comparing the nucleic acids or proteins from different organisms - The more similar the nucleic acids and proteins are between two organisms, the mroe closely related they are considered to be
The extent of microbial life
- Global estimate is 5 x 10^30 cells - Most microbial cells are found in oceanic and terrestrial sub surfaces - Microbial biomass is significant, and cells are key reservoirs of essential nutrients
Overview of Microbes
- Have existed for a majority of earth's history (3.8 billion years) - Present virtually everywhere and highly adaptable - very small organisms - Microorganisms can be multicellular, unicellular, and even acellular (not composed of cells) - Microorganisms are found in each of the three domains of life: Archaea, Bacteria, and Eukarya - Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus) - Microbes in the domain Eukarya are eukaryotes (their cells have a nucleus) - Some microorganisms, such as viruses, do not fall within any of the three domains of life
Linneaus Taxonomy
- In his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned) - Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities - The names of the levels in Linnaeus's original taxonomy were kingdom, class, order, family, genus, and species
Prions
- Just a protein! (definitely acellular) - destroy brain tissue - BSE (bovine spongiform encephalopathy) → mad cow disease
Viroids
- Just a single short piece of RNA!! (acellular to the max) - No protein coat - Typically is about 100 nm in length - 10 times smaller than a typical bacterium - Known to cause disease in plants - Could potentially cause other diseases we haven't detected yet?
Interactions of Light (reflection absorbance)
- Light waves interact with materials by being reflected, absorbed, or transmitted - Reflection - occurs when a wave bounces off of a material - Absorbance - occurs when a material captures the energy of a light wave - Transmission - occurs when a wave travels through a material, like light through glass (the process of transmission is called transmittance)
Units of Measurement
- Lipids = 1 nm - Protein = 5 nm - Flu virus = 100 nm - Bacteria = 1 microm - Red blood cell = around 6 microm - Plant cell / animal cell = 50 microm - Human egg = 125 microm
Viruses
- Microbes so small that they were hidden from microbiologists until the invention of the electron microscope in 1932. - All are acellular obligatory parasites - They are neither prokaryotes nor eukaryotes
Dark-field microscopes
- Pale objects are best observed with dark-field microscopes - Utilize a dark-field stop in the condenser that prevents light from directly entering the objective lens - Light passes into the slide at an angle - Only light rays scattered by the specimen enter the objective lens and are seen - The specimen appears light against a dark background
phase microscopes
- Phase microscopes use a phase plate to retard light rays passing through the specimen - The waves are ½ wavelength out of phase with neighboring light waves - This produces contrast - Phase-contrast microscopes produce sharply defined images in which fine structures can be seen
Carl Woese
- Pioneered the use of rRNA (ribosomal RNA) for phylogenetic studies in the 1970s - Established the presence of three domains of life: Bacteria, Archaea, and Eukarya - Provided a unified phylogenetic framework for Bacteria
Why is there a difference in color between gram positive and gram negative?
- The different colors are due to structural differences in cell walls - In general, gram (+) bacteria have thicker cells walls and gram (-) bacteria have thinner cell walls - So the gram (+) bacteria can hold the purple dye during the decolorization step - Because the gram (-) cell walls have an outer wall made of lipids, the alcohol decolorizer dissolves this layer and the purple drain away - The gram (-) are now clear, they an take up the counterstain - Some gram (+) bacteria: Bacillus, Streptococcus, - Some gram (-) bacteria: Escherichia coli, Salmonella
Electron Microscopy
- The shortest wavelength of visible light is about 400 nm - Structures closer together than about 200 nm cannot be distinguished using light microscopy - Electrons traveling as waves have wavelengths between 0.01 nm and 0.001 nm Their resolving power is much greater, and they typically magnify objects 10,000x to 100,000x - Electron microscopes use magnets to focus electron beams similarly to the way that light microscopes use lenses to focus light
Otis the Iceman
- a 5300 year old mummy found frozen in the ice of the Otzal Alps - Some researchers think Otzi may have been trying to treat his infections
Thucydides (460-395)
- a historian, observed that survivors of the Athenian plague were subsequently immune to the infection - considered the father of scientific history because he advocated for evidence-based analysis of cause-and-effect reasoning - made the important observation that survivors did not get re-infected with the disease, even when taking care of actively sick people - Shows an early understanding of the concept of immunity
Taxonomists use one or more of five procedures to identify and classify microorganisms:
1) Physical characteristics are used to identify microorganisms a) Example: scientists can usually identify protozoa, fungi, algae, and parasitic worms based solely on their morphology b) The appearance of bacterial colonies also gives clues to help identify microorganisms 2) Biochemical tests: a) Noting a particular microbe's ability to utilize or produce certain chemicals can distinguish one organism from another 3) Serological tests a) Antibodies can bind to features on the outside of the organisms you are trying to identify b) Clumping caused by antibodies (agglutination) indicates the presence of the target cells c) Allows scientists to distinguish between cell types 4) Bacteriophages (or simply phages) a) Viruses that infect and usually destroy bacterial cells b) Whenever a specific phage is able to infect and kill bacteria, the resulting lack of bacterial growth produces within the bacterial lawn a clear area called a plaque c) Phage typing may thus reveal that one bacterial strain si susceptible to a particular phage, whereas another is not i) Allows scientists to distinguish between bacteria types 5) Nucleic acids a) The DNA and RNA an organism can be used to distinguish between species
Principle of microscopy is that resolution distance is dependent on:
1) the wavelength of the electromagnetic radiation - The shorter the wavelength, the better the resolution 2) the numerical aperture of the lens (its ability to gather light) - Immersion oil is used to fill the space between the specimen and a lens to reduce light refraction and thus increase the numerical aperture and resolution Contrast - Contrast refers to differences in intensity between two objects, or between an object and its background - Since most microorganisms are colorless, they are stained to increase contrast - Polarized light may also be used to enhance contrast
Light Microscopy
Bright-Field, Dark-field, phase, fluorescent microscopes, confocal microscope
arrangement
how cells are grouped - Some common arrangements: - Strepta - chains; staphly lococci - clusters - Dipla - pairs; tetrads - groups of 4; sarcinae - groups of 8
flagella staining
Flagella: thin whip like tails bacteria use for mobility - Very small so mordant is often used to enhance color
simple direct staining
The chromophore sticks to the bacteria giving it color Sometimes during simple staining, the use of a mordant is required Mordants are often used to visualize structures like flagella Iodine is a common mordant Acidic dyes: the chromophore is negatively charged
negative (indirect) staining
The dye colors the background, not the specimen
Bright-Field Microscopy
The most common microscopes The background (or field) is illuminated There are two basic types: Simple microscopes contain a single magnifying lens - these are similar to a magnifying glass Compound microscopes use a series of lenses for magnification
acid fast staining
Used to identify bacteria belonging to genus Mycobacterium - a group of bacteria that can cause diseases like tuberculosis and leprosy - they have a waxy cell wall that does not easily take stain Two different methods for acid-fast staining are the Ziehl-Neelsen Technique and the Kinyoun technique
General Principles of microscopy
Wavelength of Radiation: - Various forms of radiation differ in wavelength, which is the distance between two corresponding parts of a wave - The human eye distinguishes different wavelengths of light as different colors Moving elections also act as waves: - Wavelengths dependent on the voltage of an electron beam - Electron wavelengths are much smaller than those of visible light, and so they can give images with better resolution - The amplitude is the height of a wave, whereas the wavelength is the distance between one peak and the next -Magnification: making an object look larger - Resolution: the ability to distinguish between objects that are close together
image point (focus)
We can think of a lens as an object with a curved boundary (or a collection of prisms) that collects all of the light that strikes it and refracts it so that it all meets at a single point called the image point (focus)
scanning probe microscope
does not use light or electrons, but rather very sharp probes that are passed over the surface of the specimen and interact with it directly This produces information that can be assembled into images with magnifications up to 100,000,000x Such large magnifications can be used to observe individual atoms on surfaces To date, these techniques have been used primarily for research rather than for diagnostics There are two types of scanning probe microscope: the scanning tunneling microscope (STM) and the atomic force microscope (AFM)