Module 1 Practice Questions Flashcards
When humans manipulate microorganisms to make products in an industrial setting.
Ex: Some specialized bacteria have unique capacities to mine precious metals or clean up human-created contamination.
Biotechnology
What are required for proper isolation of micros?
Inoculation tools
Agar in a petri dish
An area of biotechnology that manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms (GMOs)
Ex: Recombinant DNA Tech: makes it possible to transfer genetic material from one organism to another and deliberately alter DNA.
Genetic Engineering
Refers to the ability of microorganisms–ones already present or those introduced intentionally–to restore the stability of an ecosystem or to clean up toxic pollutants.
Bioremediation
Bacteria invented photosynthesis long before the first plants appeared, first as a process that did not produce oxygen
Anoxygenic Photosynthesis
Name four disease processes where microbial infection has been implicated.
Gastric ulcers
DM1
Schizophrenia
Obesity
In general, bacterial and archaeal cells are about 10x smaller than _______ cells.
eukaryotic cells
The belief that invisible vital forces present in matter led to the creation of life.
Spontaneous Generation
The belief in spontaneous generation as a source of life.
Abiogenesis
a= without
bio= life
genesis= beginning
The belief that living arise only from others of their same kind.
Biogenesis
Demonstrated using swan flasks that dust were a source of microbes
Louis Pasteur
Probably the earliest record of microbes is in the works of
Robert Hooke
Eventually became interested in more than just thread count and used his finest lens to find “animalcules” in rainwater; he also looked at plaque on teeth.
Antonie van Leeuwenhoek
What microbes does “animalcules” refer to?
Protozoa and bacteria
Three scientists discovered little molecular “scissors” inside bacteria. The scissors chop up DNA in specific ways, and enabled scientists to cut DNA in tailored ways. Opened up floodgates for genetic engineering.
Discovery of restriction enzymes 1970s
A breakthrough in our ability to detect tiny amounts of DNA and then amplify it into quantities sufficient for studying.
Polymerase Chain Reaction technique 1980s
The discovery that perhaps only 2% of DNA codes for a protein, so much RNA doesn’t end up with a protein counterpart–thus they have critical roles in regulating what happens in the cell.
The importance of small RNAs 2000s
The discovery that even though the exact types of microbes found in and on different people are highly diverse, the overall set of metabolic capabilities the bacterial communities possess is remarkably similar among people.
Genetic Identification of the Human Microbe 2010s and beyond
Formulate a question Do background research Construct hypothesis Test hypothesis Analyze data and reject or accept hypothesis Communicate results
Scientific Method
The discovery and detailed description of heat-resistant bacterial endospores was by
Ferdinand Cohn
First to introduce aseptic technique
English surgeon Joseph Lister
A theory originating in the 1800s that proposed that microorganisms can be the cause of diseases; so well established that it is considered a fact.
The Germ Theory of Disease
Bacterium that causes anthrax
Bacillus anthracis
Four main families of macromolecules
Lipids, nucleic acids, carbohydrates, proteins
All macromolecules are formed by polymerization, a process in which repeating subunits termed monomers are bound into chains of various lengths called ______.
polymers
Nucleic acids
Nitrogen base Purines
adenine (A) and guanine (G)
Nucleic acids
Nitrogen base Pyrimidines
thymine (T)
cytosine (C)
uracil (U)
Cell walls in plants and many microscopic algae derive their strength and rigidity from ______, a long, fibrous, polysaccharide.
Cellulose
A polysaccharide found in seaweed and commonly used to prepare SOLID culture media.
Agar
A network of polysaccharide chains cross-linked by short peptides that forms the rigid BACTERIAL cell walls.
Gram neg bacteria have smaller amounts of this rigid structure than gram pos
(think closed sandwich cell wall with gram pos)
Peptidoglycan
A molecular complex of lipid and carbos found in bacterial cell walls.
The portion of this complex in a gram neg bacteria is an ENDOTOXIN with generalized pathologic effects just as fever.
Lipopolysaccharide
A filamentous network or carbohydrate-rich molecules that coats cells.
Serves as a protective outer layer, and can also play a role in attachment of the cells to other cells or surfaces.
Glycocalyx
Water-loving region of a phospholipid in a membrane
hydrophilic
Water-fearing region of phospholipid in membrane.
Hydrophobic
Best known member of a group of lipids called steroids.
Commonly found in cell membranes and animal hormones.
Reinforces the structure of the cell membrane in animal cells and in mycoplasms (cell wall deficient unusual bacteria)
Cholesterol
Building blocks of proteins
amino acids
Initial protein organization described by type, number, and amino acids in the chain.
Primary Structure (of proteins)
A protein biocatalyst that facilitates metabolic reactions
enzyme
RNA that is a copy of a gene that provides the order and type of amino acids in a protein
Messenger RNA
Type of RNA that is a carrier that delivers the correct amino acids for protein assembly
transfer RNA (tRNA)
Type of RNA that is a major component of ribosomes
ribosomal RNA (rRNA)
A nucleotide that is the primary source of energy to cells.
Adenosine Triphosphate (ATP)
Animals, plants, fungi, and protozoa are all made up of ________ cells.
eukaryotic
The science of classifying living beings
Taxonomy
The assignment of scientific names to the various taxonomic categories and to individual organisms.
Nomenclature
Always a combination of the genus name followed by the species name.
Ex: Escherichia coli
Genus species
Binomial system of nomenclature
What is the genus of:
Staphylococcus aureus
Staphylococcus
Method of organizing organisms into several descending ranks, beginning with the most general all-inclusive taxonomic category and ending with the smallest most specific category.
Classification
What are the taxonomic categories from top to bottom
DKPCOFGS
Domain, kingdom, phylum, class, order, family, genus, species.
Compare humans to protozoa in terms of classification
Both nucleated cells (eukaryotes) so they are in the same domain: Eukarya.
But they are in different kingdoms b/c humans are multicellular (Kingdom Animalia) and protozoa are single-cellular organisms that, together with algae, belong to kingdom Protista
The scheme that represents the natural relatedness between groups of living things
Phylogeny
Classification tree description
The trunk of the tree represents the origin of ancestral lines
taxonomic groups with less divergence from the common ancestor closer to the root of the tree
taxa with lots of divergence closer to the top
Five Major Taxonomic Kingdoms
FAMPP: Fungi Animals Monera Protists Plants
Three Domain System
Bae:
Bacteria
Archaea
Eukaryotes
Sample is introduced into a container of growth medium to culture microorganisms.
Medium can be solid, liquid, or a live animal.
Inoculation
Body fluids (blood, cerebrospinal fluid, peritoneal fluid), discharges (sputum, urine, feces), anatomical sites (nose, throat, genital tract, ear, eye), or diseased tissue (such as an abscess or wound)
Other: soil, water, foods, air, sewage, other inanimate objects.
Clinical specimens
Once a container of medium has been inoculated, it is placed in a temperature-controlled chamber to encourage multiplication.
Incubation
A growth medium that contains one a single known species or type of microorganism.
Pure Culture
A container that holds two or more identified, easily differentiated species of microorganisms.
Mixed culture
Was once a pure or mixed (with known species) culture but has since has contaminants (unwanted microbes of uncertain identity introduced).
Contaminated culture
Three properties of media
- Physical state ie. liquid, soild, solid, semisolid
- Chemical composition ie. complex, defined
- Functional type ie. enriched, selective, assay
Water based solutions that do not solidify at temperatures above freezing.
Growth appears cloudy, or as flakes, or settle at the bottom of the vessel.
Liquid media
Firmer than liquid media but not as firm as solid media.
Do not flow freely, and have a soft, clot-like consistency at room temp.
Used to examine motility of bacteria and to provide a backdrop for visible reactions to occur.
Semisolid Media
Media containing 1%-5% agar are solid enough to remain in place when containers are tilted or inverted.
Can be liquified with heat.
Provide a firm surface on which cells can form discrete colonies.
Solid/Reversible to Liquid Media
What media is essential for the development of discrete, isolated colonies?
Solid media.
Once it is liquefied, agar does not resolidify until it cools to ____ degrees Celsius.
Agar has a boiling temp of ___ degrees Celsius.
42
100
Media whose compositions are precisely chemically defines are termed ______ or ______.
Defined or synthetic
Media whose compositions are not precisely chemically defined are termed ______.
This media can contain extracts of animals, plants, yeasts, ground up tissues or secretions, such as blood, serum, or meat extracts.
Complex
Three examples of complex media.
Nutrient broth
Blood agar
MacConkey agar
There are many more microbes that we ______ cultivate in the lab than those that we ____.
; Cannot
; Can
Media that will allow the growth of as broad a spectrum of microbes as possible.
Ex: brain-heart infusion, trypticase soy agar (TSA), and nutrient and agar broth
General-purpose media
Media that contains complex organic substances such as blood, serum, hemoglobin, or special growth factors (specific vitamins, amino acids) that CERTAIN species MUST have.
Bacteria that require these conditions are termed fastidious.
Enriched media
Bacteria requiring special nutritional or environmental conditions for growth
Fastidious
______media are also useful in the clinical laboratory to encourage growth of pathogens that may be present in very low numbers, such as in urine or blood specimens.
Enriched
Example of enriched media.
Chocolate agar
; blood agar with added hemin and nicotinamide adenine dinucleotide
Contains one or more agents that inhibit the growth of certain types of microbe(s).
Ex: Microbes A, B, C, D are inoculated, but the media inhibits all but microbe D to grow.
Selective Media
List three examples of selective media.
; dyes like methylene blue and crystal violet, as well as antimicrobial drugs can act as selective agents
- MacConkey Agar (contains bile salts as selective agent)
- Tomato juice again (contains tomato juice, acid for selective agent)
- Lowenstein-Jensen (contains Malachite green dye for selective agent)
Media that do not inhibit growth but display visible differences between microorganisms through variations in colony size/color, media color changes, or in formation of gas bubbles and precipitates.
Ex: Blood agar (intact red blood cells) Urea broth (urea, phenol red) Birdseed agar (seeds from thistle plant) Mannitol salt agar (mannitol, phenol red)
Differential media
A single medium can be both _________ and _________.
selective and differential
Dyes are frequently used as differential agents b/c many of then are ____ indicators that change color in response to the production of an ____ or a ____.
; pH
; acid / base
MacConkey agar contains neutral red, a dye that is ______ when neutral and _____ or ____ when acidic.
yellow - neutral
pink or red - acidic
This media contains a substance that absorbs oxygen or slows down the penetration of oxygen in a medium, thus reducing its availability.
; important for growing bacteria that don’t require oxygen or for determining oxygen requirements
Reducing medium
This media contains sugars that can fermented (converted to acids) and a pH indicator to show the reaction.
Carbohydrate fermentation media
Media used to maintain and preserve specimens that have to be held for a period of time before clinical analysis or to sustain delicate species that die rapidly.
Transport media
Media used by technologists to test the effectiveness of antimicrobial drugs and by drug manufacturers to assess the effect of disinfectants, antiseptics, cosmetics, and preservatives on the growth of micros.
Assay media
Trick: “Assess media”
Media used by industrial and environmental microbiologists to count the numbers of organisms in milk, water, food, soil, and other samples.
Enumeration media
Once the cultures have grown, they may need to be re-inoculated (and incubated) in such a way that SEPARATE SPECIES are obtained.
This is called:
Isolation
Proper isolation requires that a ______ number of cells be inoculated into a relatively large volume or over a large area of medium.
Requires: a ____ surfaced medium, a petri dish and cover, and inoculating tools
; small
; firm
Three main ways to accomplish isolation
- Streak plate method - small droplet of culture is spread over the surface of a medium with loop in a pattern that thins out the sample and separates the cells spatially over several sections
- Pour plate method - sample is inoculated into a series of cooled but still liquid agar tubes to dilute the # of cells in each successful tube; then is poured into petri dishes and allowed to harden (usually the third plate has few enough cells that there is ample space to grow colonies)
- Spread plate method - small volume of of liquid sample if pipetted onto the surface of the medium and spread around evenly by a sterile spreading tool “hockey stick”, and cells are pushed into separate areas to form individual colonies
Methods that can determine fundamental chemical characteristics such as nutrient requirements, products given off during growth, presence of enzymes, and mechanisms for deriving energy.
; part of inspection and identification
Biochemical tests
Genetic and immunologic characteristics are also used for _________.
Identification
The smallest bacteria are around _____ nm
200
___________ occurs in two phases (images)
Magnification
The objective lens forms the forms the initial image of the specimen called the _____ ______.
real image
When the image is projected up through the microscopic body to the plane of the eyepiece, the ocular lens forms the second image (phase of magnification)
The virtual image (received by the eye and converted to a retinal and visual image)
What is the magnifying power of the objective lens?
What is the power of the ocular lens?
- Ranges from 4x to 100x
2. Usually 10x
Total magnification of the 100x oil immersion objective
1000x
The capacity of the optical system to distinguish two adjacent objects or points from one another.
Ex: the human eye can resolve two objects that are not closer than 0.2mm apart.
Resolution/Resolving Power
Lens that uses oil to capture some of the light that would otherwise be scattered
; reducing scatter increased resolution
Oil Immersion Lens
Refers to the degree of bending that light undergoes as it passes from one medium, such as water or glass, to another medium, such as bacterial cells.
Measured in refractive index
-> the higher the difference in refractive indexes (the more bending of light) the sharper the contrast that is registered
Contrast
Most widely used microscope.
Forms its image when light is transmitted THROUGH the specimen.
Specimen absorbs more light (more dense than surroundings).
Specimen will be darker than the surrounding brightly illuminated field.
Used for live, unstained, preserved, stained material
Bright-Field Microscope 2000x
Adapted from a bright-field microscope by adding a special disc called a STOP to the condenser.
The STOP blocks all light from entering the objective lens expect the peripheral light that is reflected off of the sides of the specimen itself.
Causes specimen to be lit up brightly, and surroundings to be dark.
Most effective with living cells that would be distorted by drying or heat or that cannot be stained
Dark Field Microscope 2000x
Contains devices that transform the subtle changes in light waves passing through the specimen into differences in light density.
ex: denser cell parts such as organelles alter the pathway of light more than less dense regions like the cytoplasm
Most useful for observing intracellular structures such as bacterial endospores, granules, and organelles, as well as locomotor structures of eukaryotic structures such as cilia.
Phase-Contrast 2000x
Used UV rays as source of illumination.
Dyes are used and emit visible (florescent) light when bombarded by short UV rays.
For an image to be formed, the specimen must first be coated or placed in contact with a source of florescence.
Usually emits an intense red, blue, or green against a black field.
Useful for diagnosing infections and pinpointing particular cellular structures.
Fluorescence Microscope
method of choice for viewing the detailed structure of cells and viruses.
produces image by TRANSMITTING electrons through the specimen.
Specimen must be sectioned extremely thinly.
Darker areas suggest denser areas of specimen.
Transmission Electron Microscope (TEM) 100,000,000x
Provides some of the most dramatic and realistic images in existence.
three dimensional image.
to produce images: bombards the surface of the metal-coated specimen with electrons while scanning back and forth over it.
displays like a TV
canning electron microscope SEM
100,000,000x
Uses laser beam of light to scan various depths in the specimen and deliver a sharp image focusing on just a single plane.
Confocal microscope
The manner in which a slide specimen is prepared depends on:
- The condition of the specimen (living or preserved)
- The aims of the examiner (whether to observe overall structure, identify the organism, or see movement
- The type of microscopy available, whether it is bright-field, dark-field, phase-contrast, or fluorescence
Examined using wet mounts or in hanging drop mounts so they can be as close to their natural state as possible.
cells are suspended in water, broth, or saline, which provides space for locomotion
overlaid with a coverslip
Fresh, living preparations
Specimen is dried and attached to the glass “smear technique”
air dried smear is usually heated and kills the specimen while securing it to slide
Fixed, stained smears
The dye sticks to the specimen and gives it color
Positive stain
Dye does not stick to specimen but settles some distance from its outer boundary, forming a silhouette
b/c cells are neg charged and repel stain
Negative stain
Common stains used for neg stain
Nigrosin (blue-black)
India ink
Acidic dyes are used for ______ staining
Negative
Basic dyes are used for ______ staining.
Positive
Examples of positive (basic) dyes
Crystal violet
Methylene blue
Safranin Malachite green
Type of pos staining technique that used a single dye to ass color to cells
Simple stain
a technique that utilizes two dyes to distinguish between different microbial groups or cell parts by color reaction
Differential stain
Gram Stain
-Differential stain
Steps:
1. Primary dye (crystal violet) + & - are purple
2. Gram’s iodine (the mordant)
3. Alcohol rinse (decolorizer for gram neg=clear gram neg cell wall)
4. Counterstain (safranin) makes gram neg red
An important diagnostic stain that distinguishes between acid-fast (acid resistant) bacteria from non-acid-fast (non acid resistant) bacteria.
originated as use for detecting Mycobacterium tuberculosis
Acid-fast stain
similar to acid-fast method in that the dye is forced by heat into resistant bodies called endospores.
used to distinguish between endospores and the cells that they came from (vegetative cells)
Endospore stain
method of observing the microbial capsule, an unstructured protective layer surrounding the cells of some bacteria and fungi
; often stained with India ink or may be demonstrated with some pos stains
Capsular staining
method of revealing flagella
flagellar staining
_________ and _________ have nuclear material that is free inside the cell (no nucleus is encasing it)
Bacteria and archaea
Bacteria have a unique wall structure compared to eukaryotes, it is made of a chemical called __________
peptidoglycan
Archaeal walls are tough and distinct from ________ and _______.
bacteria and eukaryotes
A few bacteria and archaea have internal membranes, but they do not surround ________.
organelles
Discuss the external structure of a bacterial cell
may have appendages like flagella, pili, fimbriae, nanowires/nanotubules
may have surface layers like s layer and glycocalyx
Specific structures that are found in some but not all bacteria are:
flagella, and outer membrane, pili, fimbriae, nanowires, plasmids, inclusions, endospores, and microcompartments
All bacterial cells invariably have:
cytoplasmic membrane, cytoplasm, ribosomes, and one or a few chromosomes
Majority have a cell wall and glycocalyx
An appendage used for drawing another bacterium close in order to transfer DNA to it
Pilus
A coating or layer of molecules external to the cell wall. It serves protective, adhesive, and receptor functions.
It may fit tightly (capsule) or be very loose (slime layer)
Glycocalyx
Stored nutrients such as fat, phosphate, or glycogen deposited in dense crystals or particles that can be tapped into when needed
Inclusion/Granule
relating to chap 3
Double-stranded DNA circle containing extra genes
Plasmid
dormant body found within some bacteria that allows for their survival in adverse conditions
-also very infectious
Endospores
membrane extensions that allow bacteria to transmit electrons to other bacteria or onto environmental surfaces
Nanotubes/Nanowire
Protein coated packets used to localize enzymes and other proteins in the cytoplasm
Bacterial microcompartments
fine, hair-like bristles extending from the cell surface that help in adhesion to other cells and surfaces
Fimbriae
extra membrane similar to cytoplasmic membrane but also containing lipopolysaccharide
controls flow of materials
portions of it are toxic to mammals when released
outer membrane
monolayer of protein used for protection and/or attachment
S layer
although bacteria are single celled they are capable of carrying out:
reproduction, metabolism, nutrient processing, and all necessary life activities
Some bacteria communicate with each other using ______ as well for exchanging nutrients
nanotubes
spherical or ball shaped bacteria “grape bunches”
can be oval, bean-shaped, or even pointed variants
Coccus
cylindrical, spindle-shaped, round-ended bacteria
bacillus or rod
When a rod bacteria is short and plump it is called
coccobacillus
singly occurring rods that are gently curved
vibrio
bacteria that is slightly curled or spiral-shaped
spirillum
bacteria that resembles a spring
spirochete
a few bacteria produce multiple branches off of a basic rod structure
filaments
normal variability of cell shapes in a single species
Pleomorphism
Diplococci
pair of cocci
tetrad of cocci
four cocci
staphylococci or micrococci
irregular clusters
streptococci
chains to hundreds of cocci
a cubical packet of 8, 16, or more cells; coccus
Sarcina
Pair of rod cells with end attached
Diplobacilli
chain of rod shaped bacterial cells
streptobacilli
arrangement formed when the cells of a chain remain partially attached by a small hinge at the ends
Palisades
appendages that provide motility
flagella and axial filaments
Appendages that provide attachment points or channels
Fimbriae, pili, nanotubes/nanowires
Three distinct parts of the flagella
the filament, the hook (sheath), and the basal body
filament= helical structure composed of proteins
All spirilla are ________
flagellated
With a single flagellum
monotrichous
with small bunches or tufts of flagella emerging from the same site
lophotrichous
with flagella at both poles of the cell
amphitrichous
flagella are dispersed randomly over the surface of the cell
peritrichous
One way to detect motility using a medium.
Stab a tiny mass of cells into a soft (semisolid) medium in test tube.
OR
use a hanging drop slide
Flagellar bacteria can move in response to chemical signals, this is called
Chemotaxis
Movement of a cell in the direction of a favorable stimulus
Positive chemotaxis
movement away from a potentially harmful compound is called
negative chemotaxis
What is the fuel that allows flagellum to turn?
a gradient of protons- hydrogen ions
When the flagellum rotates counter clockwise and swims itself in a smooth linear direction toward a stimulus
a run
Runs are interrupted by ________, which is when the flagellum reverses direction and causes the cell to stop and change direction
tumbles
Type of internal flagellum that is enclosed in the space between the cell wall and cytoplasmic membrane
; found on spirochetes (spring like/cork screw)
Periplasmic Flagella/Axial Filaments
Structures that are partially responsible for the sticking of cells that leads to biofilms
Fimbriae
Process which involves partial transfer of DNA from one cell to another
;only occurs between compatible gram neg cells
Conjugation (done by special conjugation pili)
Only produced by bacteria when they are in hostile environments
S layers
A glycocalyx is called a ______ when it is more tightly bound to the cell than a slime layer is and it is denser and thicker.
capsule
List three bacteria that form capsules
Streptococcus pneumoniae Haemophilus influenzae (one cause of meningitis) Bacillus anthracis (anthrax)
Glycocalyces can be important in the formation of _______.
Biofilms
The streak plate technique works by using an inoculating loop to spread the bacterial sample in a patter that thins it out but this only works if ______________________________.
The inoculating loop is re-sterilized at each thinning step
Name two functions of the glycocalyx
Protection and adherence
Biofilms are medically significant b/c they can adhere to the surfaces of ___________ and ____________
plastic catheters and teeth
the cell envelope is composed of the ____________ and ____________
cell wall and cell membrane
the glycocalyx is important in the ability of bacteria to cause infection b/c it
allows the bacteria to adhere well to medical devices
allows for formation of biofilms
Functions of the cell wall
maintaining the shape of the bacterium
preventing destruction the changes in osmotic pressure
The cell wall in bacteria is primarily composed of
peptidoglycan
full sandwich cell envelope
gram neg
components of peptidoglycan
sugar chains
short peptides
lysozyme destroys cells by
hydrolyzing peptidoglycan
which staining technique allows for differentiation of mycobacterial cells?
Acid-fast stain
the bacterial chromosome is compacted to fit into the cell by coiling around
basic protein molecules
the bacterial chromosome consists of a single
circular, DS DNA
Plasmids are _______ DNA molecules
DS
bacterial ribosomes are located
in the cytoplasm
attached to the cytoplasmic membrane
which domains are most closely related
archaea and eukarya
archaea that have adapted to very low temps
psychrophilic
why can it be difficult to group bacteria into species
an later their genetic make up
accept genetic material from other, sometimes unrelated cells
do not use typical mode of sexual repro
