Unit 1 Flash Cards (Lecture + Book)
What are the 3 common traits shared between most bacteria?
1) Thick, complex outer envelope
2) Compact genome - not a lot of non-coding genes/DNA
3) Tightly coordinated functions - parts of the cells work together very closely and mechanistically.
What is a main similarity of archaea and bacteria?
They are both prokaryotes (cells do not contain a membrane-bound nucleus.)
What is a main trait of eukaryotic cells?
Extensive membrane-bound organelles
What is a trait of the plasma membrane of most bacteria like E.coli?
It has two membranes: inner and outer
What is between the inner and outer cell membranes?
the cell wall, which has a chain of sugars and peptides: peptidoglycan
What is a gram-negative bacterium?
A type of bacteria that is not stained by the crystal violet stain.
What is the peri plasm?
the space surrounding gram-negative bacteria’s cell wall that . it contains water, nutrient-binding molecules, and secretion machinery
What constitutes the outer wall of a gram-negative bacteria?
Phospholipids and lipopolysaccharides
What are lipopolysaccharides?
A type of lipids attached to long sugar chains. This layer maybe surrounded by thick capsules.
What is a benefit to the capsules that may surround LPS layers?
The layer is slippery and prevents phagocytosis by macrophages.
What are flagella?
external helical proteins used to propel bacteria around.
What do the chromosomes attach to in bacteria?
the cell membrane/envelope
What is a nucleoid?
the circular, coiled formation of chromosomes. not contained in a membrane.
What are the common chemical components shared between all cells?
1) water
2) essential ions
3) small organic molecules
4) large macromolecular structures
What is the point of microbes having a high content of nucleic acids?
to maximize reproduction of its chromosomes and minimized cell resources
Why can’t humans digest bacteria?
because we do not have the enzymes to digest the uric acid from the breakdown of the high content of nucleic acids.
What is the proteome?
proteins expressed in a cell under certain conditions.
What is cell fractionation?
The separation of cellular components.
What has microscopy revealed?
1) humans consist and are covered in microbes
2) we live in a world that is filled with microbes and their usefulness
3) bacteria are beautiful
What is the smallest resolution of our eyes?
~0.1mm
What is resolution?
The smallest distance by which two objects can be separated and still be distinguished.
What is detection?
ability to determine the presence of an object. Different from resolution.
What is magnification?
increase in the size of an image to resolve smaller separations between objects
T/F: not all bacteria are microscopic.
true
What are examples of eukaryotic microbes?
1) protozoa
2) algae
3) fungi
T/F: eukaryotic microbes are typically smaller than bacteria.
False
What is the typical size range of eukaryotic microbes?
10-100um (can be seen under a light microscope)
What is the typical size range of prokaryotes (bacteria and archaea)?
0.4-10um (cannot be seen under a light microscope)
T/F: prokaryotic cells are simpler shapes than eukaryotic cells.
True
What are common shapes of bacteria?
1) cocci - spheres
2) Bacilli - rods
3) spirilli - rigid spiral
4) Spirochetes - flexible spiral
5) Appendaged - protrusions
What is the size range for the resolution of microbes by the human eye?
1-0.1mm
What is the size range for the resolution of microbes by light microscopy?
1mm - 200nm
What is the size range for the resolution of microbes by scanning electron microscopy?
1mm - 5nm
What is the size range for the resolution of microbes by transmission electron microscopy?
25um-5nm
What is the size range for the resolution of microbes by atomic force microscopy?
5um - 1 angstrom
What is the size range for the resolution of microbes by X-ray crystallography?
10nm - 1 angstrom
What is the wavelength range of visible light?
400-750nm
What are the 3 conditions for light to resolve an object?
1) contrast between the object and its medium
2) the wavelength needs to be significantly smaller than the object
3) magnification
T/F: Microscopy takes advantage of how light interacts with matter because light has both wave and particle properties.
True
What are the ways that light can interact with matter?
1) absorption: object blocks part of the light
2) reflection: light bounces off the surface at an equal angle from where it was received
3) refraction: light will bend when it enters a substance that changes its speed
4) scattering: small fraction of the light is scattered in all directions.
When does light scattering occur/
When the size of the object is similar to the wavelength size.
What type of light-object interaction does magnification require?
refraction
How does refraction work in magnification?
- light shift direction as they enter a substance of a higher refractive index.
What is a focal point?
- when parallel rays enter through a parabolic glass and the rays that pass through all meet at this certain point.
What limits the ability of what we see with a microscope?
resolution.
What is the resolution limit from wavelength of light/
200nm or 0.2um
What is empty magnification ?
Magnification without increasing detail/resolution.
What is bright-field microscopy?
generates a dark image of an object over a light background.
How do you increase resolution with bright-field microscopy?
1) use shorter wavelength light
2) have balanced light and contrast
3) use immersion oil
4) use wider lens closer to specimen
5) higher numerical aperture
What is the refractive index/
the ratio of the speed of light in a vacuum to its speed in another medium
What is the refractive index of water, air, immersion oil, and glass?
1) 1.3
2) 1.0
3) 1.5
4) 1.5
How does immersion oil help in microscopy/
- minimizes the loss of light rays by refracting them
- makes 100x magnification possible with minimal distortion
How does increasing the cone of light filling the object change the numerical aperture and lens width?
- increasing = an increase in NA
- increase = a wider lense
What is a compound microscope?
system of multiple lenses to correct for aberration
contains: ocular and objective lens
What is total magnification with a compound microscope?
magnification of the ocular lens multiplied by that of the objective lens
What is we mount preparation?
Observes microbes by placing them in a drop of water on a slide with a coverslip
What are the advantages to wet mount?
- observe cells in natural state
- fast and easy
What are the disadvantages to wet mount prep?
-little contrast between cell and background
- some microbes move fast
-sample dries out quickly
What does a sample look like when it is too far away?
beyond focal point looks empty with interference rings
What does a sample look like when it is too close?
image is blurred
what are some examples of how to fix cells?
methanol or flaming
What charges do stain have?
Positive charge to react with the negatively charged groups of the bacterial cell envelope.
T/F: both staining and fixation kills the cell.
True
What is a simple stain?
adds a dark color to cells but not the external medium or surrounding tissue
- methylene blue is a common example of this
What is a differential stain?
stains one kind of cell but not another
- ex: Gram stain
what is the step procedure for staining with methylene blue?
1) loopfuls of culture on clean slide
2) spread thinly over film
3) air-dry
4) fix cells
5) stain with a certain time period
6) wash off slide with water
7) blot off excess water
What is the procedure for differential staining with gram stain?
1) fix cells to surface
2) add crystal violet stain
3) add iodine, binds to stain in gram positive cells
4) wash with ethanol
5) add safranin (counterstain)
what are gram-positive bacteria?
Bacteria that retain the crystal violet stain because of their thicker cell wall
What are gram-negative bacteria?
bacteria that do not retain crystal violet stain
What is acid-fast stain?
carbolfuchsin stains mycobacterium
What are spore stains?
malachite green detects spores of bacillus and clostridium
What is a negative stain?
stains the background, making the capsules more visible
Why are some structure too difficult to image with BF microscopy?
1) too small: size is below the limit of resolution of light
2) too clear: cytoplasm is transparent`
What light technique does dark field take advantage of?
light scattering, visualized as halos of bright light against darkness
- detects very narrow cells (0.1um)
- resolves flagella
what light technique does phase contrast take advantage of?
refraction, which light passes through the cytoplasm it slows down more
- differences in refractive indexes between cytoplasm and surrounding medium
- superimposes image of specimen onto a second beam of light that generates interference fringes
What is fluorescence microscopy?
specimen absorbs light of a defined wavelength, then emits light of lower energy = lower wavelength (allows specimen to fluoresce)
- view cellular processes in various cell types
Process of fluorescence microscopy?
1) light passes through color filter that selects excitation wavelength
2) excitation light is reflected by dichroic mirror (reflects light below a wavelength, transmits light above that wavelength)
3) reflected light passes objective lens and excites fluorophroes in specimen
4) emitted light of longer wavelength passes through objective and dichroic
5) ocular lens focuses light onto camera
What is a fluorophore?
a fluorescent chemical compound
What are the ways to label/add fluorescence to cell parts/
1) chemical affinity (membrane dyes)
2) labeled antibodies (immunofluorescence)
3) DNA hybridization
4) Gene fusions (adding GFP to a POI)
T/F: super-resolution imaging beats the diffraction limit of light/
True
What is total internal reflection fluorescence microscopy (TIRFM)?
use of an angled laser illumination to resolve sub cellular details at the membrane surface of the cell
What does atomic force microscopy (AFM) do?
images the contours of live bacteria in water or exposed air.
- measures VDWFs between electron shells of adjacent atoms of the cell surface and a sharp tip.
T/F: electron microscopy uses high frequency of waves.
true
T/F: sample doesn’t need to absorb electrons in electron microscopy?
false
T/F: electron beam and sample are in a vacuum where lenses are magnetic fields.
true
What is TEM?
- electrons pass through specimen
- reveals internal structures
- cell requires slicing, then stain
-images dead cells
What is SEM?
- electrons scan the specimen surface
- reveals external 3D structures
- does NOT require slicing
- images dead cells
What is the order of bacterial cytoplasm and cell parts?
Ordered, but flexible and adaptable structure. cytoplasm is very dense and well-organized.
What is the purpose of the LPS layer in bacteria?
To evade immune systems
What is the order of layers that make up the envelope of a gram-negative bacteria?
1) LPS
2) outer membrane
3) cell wall
4) Periplasm
5) Inner Membrane
What are some of the functions of membrane proteins?
- structural support for the cell
- detection of environmental signals
- secretion of virulence factors and communication signals
- ion transport and energy storage
What are the 2 ways that active transport can acquire energy?
1) cotransport of another substance down its gradient
2) coupling transport to energy-yielding chemical reaction
Do kinks (double bonds) increase or decrease fluidity in phospholipid membranes?
increase
Do cyclic structures in unsaturated fatty acids decrease or increase fluidity of cell membranes?
decrease
What happens if cell membranes become too fluid?
Membrane will not be stable and fall apart.
What is a main reason why archaea are stable in extreme conditions?
- extreme variations in phospholipid side-chains keep stability
What are ether linkages?
Links between glycerol and FAs
What are terpenoids?
structures where every 4th carbon has a methyl branch attached
What are the benefits to having methyl branches on FAs of phospholipids?
limits movements of hydrocarbon chains = strengthens the membrane
T/F: bilayers in archaea can fuse into monolayers
True
What are cyclopentane rings?
Terpenoids that have had their methyl groups cyclize into pentagons, stiffening the membrane.
In prokaryotes, what is the layer that protects the cell membrane?
Exoskeleton
T/F: All prokaryotes have outer layers in their cell membrane.
False, mycoplasmas do not (just 1 cell membrane barrier + peptidoglycan layer)
What is the point of a cell wall/sacculus?
- helps with shape and rigidity
- withstands tutor pressure from taking in water
-porous, cage-like structure is open to many ions and organic molecules
What are some of the linkages in the cell wall?
1) G bonds of N-acetylGlucosamine
2) M bonds of N-acetylMuramic acid
3) peptide (4-6AA) linkages between M-M, forming cross bridges between parallel glycan strands
T/F: the cell wall is the most common target of anti-bacterial drugs
True
How can we visualize Peptidoglycan growth?
-Use fluorescent D-AAs instead of regular L-AAs in fluorescence microscopy to monitor growth
- watch D-AAs be taken up during PG in real-time
- Sequential addition to one side of organism during PG
How thick is the cell wall in gram-positive bacteria?
thick, 3-20 layers to compensate for no outer membrane
How thick is the cell wall in gram-negative bacteria?
thin, 1-2 layers, has outer membrane
What is special about mycobacteria’s cell wall?
they are complex and multilayered
What threads together the peptidoglycan layers in gram-positive bacteria?
teichoic acids - negatively charged threads that help retain gram stain
What is the capsule portion of gram-positive and some gram-negative bacterias’ cell envelope?
- protects cell from phagocytosis
- sticky and helps the cell to not dry out, doesn’t let water escape
- seen using DF microscopy or with a negative stain
- made of polysaccharide and glycoprotein
What is a benefit to outer membranes in gram-negative bacteria?
has defensive abilities and toxigenic properties on many pathogens
What consists of the outward-facing leaflet of the outer membrane in GN (Gram-negative) bacteria?
1) LPS cross-linked by Mg2+
2) porins
What consists of the inward-facing leaflet of the outer membrane in GN bacteria?
lipoproteins (associates with the cell wall)
What is the S-layer?
- extra protective layer in bacteria and archaea
- crystalline layers of thick units of proteins
- contributes to cell shape and protection from osmotic stress
T/F: the nucleiod is not organized into domains.
False, form chromosome loops called domains, radiate from the center
Does transcription and translation occur at the same time in prokaryotes?
yes: DNA to ssmRNA bound by ribosomes to be translated to peptide chain
T/F: Bacteria coordinate DNA replication and gene expression
True
What is transertion?
the coupling of transcription, translation, and membrane insertion
What is SRPs role in transertion?
binds to growing peptides and targets it for insertion into the membrane.
T/F: prokaryotes synthesizes RNA and proteins continually while the cell’s DNA undergoes replication.
True
What is a replisome?
the DNA replication fork, DNA polymerase, accessory proteins, and newly synthesized DNA
T/F: Prokaryotes can continue to divide before the previous round of replication and division has been completed.
True
What is FtsZ?
Tubulin-like GTPase that polymerizes into z-ring, allowing the cell to split apart.
T/F: bacteria have chemical and physical asymmetry in age.
True
What is polar aging?
Two cell poles differ in their origin and age
What is the old pole in polar aging?
the pole where division did not occur
What is the new pole in polar aging?
the pole where division occurred
T/F: with each cell division, the old pole degrades slightly.
True, this raises the chance of lysis
What are Thylakoids in bacteria?
extensively folded intracellular membranes in photosynthetic bacteria
What are carboxysomes?
Polyheral bodies packed with the enzyme Rubisco to fix CO2 (only found in bacteria)
- fixes CO2 into sugar for cells to grow
What are gas vesicles?
Organelle that helps traps hydrogen and CO2 gases to increase buoyancy
- done by phototropes at the top of water to collect sunlight
What are sulfur globules?
holds granules of elemental sulfur to be used as antioxidant and to avoid predation
What are pili/fimbrae?
straight filaments of piling PROTEIN used in attachment
What are sex pili used for?
conjugation
What is conjugation?
extend pili into another cell to transfer DNA
What are stalks?
MEMBRANE-embeded extensions of the cytoplasm that attached to surfaces
What are holdfasts?
adhesion factors secreted by the tips of stalks.
- allows mother cells to hold on to sediment while daughter cell pinches off and swims away with a flagellum
What are nanotubes?
intercellular connections that pass big material from one cell to the next
What is monotrichous flagella?
1 flagella on the backend of the bacteria
What is amphitrichous flagella?
1 flagellum on the front and back ends of the bacteria
what is lophotrichous flagella?
bacteria that have many flagella in the back end
What is pertrichous flagella?
flagella is randomly distributed around the cell.
-flagella rotate together in a bundle behind the swimming cell
What is the magnetosome?
a MEMBRANE-bound organelle that allows bacteria to navigate the Earth’s magnetic field
What are characteristics of magneto tactic bacteria?
- align and navigate magnetic fields
- ubiquitous in aquatic environments
- stays in low oxygen environments
- Magnetite is biomineralized in membrane-bound organelles
-magnetosomes are organized by a filament to form an intracellular compass needle.
What is cell fractionation?
separates cellular components such as membranes, ribosomes, and flagella
What are 4 lysis methods?
1) sonication (physical)
2) French Press (Physical)
3) Glass beads (physical)
4) lysozyme (chemical)
What is sonication?
sound waves at high frequencies pop cells
What is French press lysing?
high pressure environments pop the cells
What is glass-bead lysing?
shake tiny glass beads to crush open cells
What does lysozyme do?
a chemical that degrades cell walls
What are macronutrients?
nutrients that are needed in large quantities.
Ex:
- major elements: S, C, H, P, O, N
- Cations for protein function: Mg, Ca, Fe, K
What are micronutrients?
need trace amounts of these nutrients for enzyme function
- Co, Cu, Mn, Zn
what are lithotrophs?
organisms that use inorganic molecules as a source of electrons.
What are Organotrophs?
organisms that use organic molecules
T/F: most heterotrophs organisms are lithotrophs.
False, most are heterotrophs are organotrophs
What are nitrogen fixers?
organisms that use nitrognase to convert gaseous N2 to ammonium ions
What are nitrifires?
oxidize ammonium ions to generate energy = production of NO3-
What are denitrifiers?
use oxidized forms of nitrogen as alternative forms of electron acceptors (NO3 to N2)
What is a symbiont?
An organism that lives in intimate association with another organism.
Ex: Rhizobium
What are permeases?
substrate-specific carrier proteins
What are nutrient-binding proteins?
proteins that patrol the periplasmic space and binds to the nutrients present there
What are ABC transporters?
ATP-Binding Cassettes (family of energy-driven transport systems), found in all three domains of life
What are Uptake ABC transporters?
critical for transporting nutrients
What are efflux ABC transporters?
generally used as multi drug efflux pumps
What is group translocation?
uses energy to chemically alter a substrate during transport.
What is the phosphotransferase system?
PTS uses energy from PEP to attache phosphates to specific sugars
- present in all bacteria
What are the 2 types of culture media that bacteria are grown in?
1) Liquid/broth
2) solid
What is liquid/ broth media good for studying?
studying the growth characteristics of a pure culture
What is solid culture media best for?
best for trying to separate mixed cultures from clinical specimens or natural environments
What are the 2 main techniques that allow for pure colony isolation?
1) Dilution streaking
2) spread plate
What is dilution streaking?
a loop with your sample is dragged across the agar plate, thinning the sample more and more as you drag it across and make different passes
What is spread plating?
perform serial dilutions in liquid culture, then spread a small amount of each dilution is plated to see what will give you isolated colonies.
What are the 5 types of experimental media?
1) Complex media
2) Minimal Media
3) Enriched Media
4) Selective media
5) Differential media
What is complex media?
nutrient rich but poorly defined (has a bunch of unknown properties in it)
What is minimal media?
contains only nutrients that are essential for growth of a given microbe
What is enriched media?
complex media to which specific components are added
What is selective media?
favors growth of one organism over another
What is differential media?
exploits differences between two species that grow equally well.
what are growth factors?
specific nutrients not required by other species
- needed to grow in lab media
What are the 5 techniques for counting organisms?
1) spread plating
2) opitical density using a spectrometer
3) Hemocytometer
4) Fluorescence microscopy
5) Flow cytometry
How does Optical density work?
Bacteria in liquid can be detected by how cloudy the medium is as more cells scatter light more.
-quick and easy approximation of cell density
-cell volume, length, and morphology can alter the OD value mistakenly
- dead cells scatter light too, so not a live count
How does a hemocytometer work?
place a dilution of organisms sample on a special microscope slide called a hemocytometer/Petroff-Hausser chamber = gets counted by a machine
How does fluorescence microscopy work?
easy to distinguish living from dead cells based on differential staining
- stain live cells with Syto-9 dye (enter all cells)
- dead cells fluoresce red with propidium dye (only enters dead cells)
How does flow cytometry work?
Cells are sorted based on characteristics:
1) fluorescence (live vs dead)
2) side scatter correlates to cell size
What is binary fission?
the process how most bacteria divide
- one parent cell splits into two equal daughter cells
- some divide asymmetrically by budding
If the cell divides by binary fission, what is the number of cells proportional to?
2raised to the power of n = exponential growth
- n = number of generations
What is a batch culture?
a liquid medium within a closed system where nutrient consumption and toxic products eventually slow growth rate
What influences the length of the lag phase?
changes in growth conditions like temp, pH, and nutrient richness
What is the lag phase in bacterial growth?
bacteria are preparing cell machinery for growth
What is a chemostat used for?
a system that continuously removes used/bad media/products from the microbes’ environments and replaces it with fresh, nutrient-rich media.
What are homotypic aggregations?
organisms groups together to survive environmental stressors
What is quorum sensing?
A group of bacteria collectively respond to environmental changes
What is swarming?
A group of bacteria move across a surface
What are biofilms?
a group of bacteria adheres to each other and to a surface.
- can be formed by one or multiple species
- form when nutrients are plentiful
- if nutrients become scarce, individuals detach to find more food
What are biofilms protected by?
an extracellular matrix composed of curly and cellulose
What is Curli?
CsgA protein fibers that are resistant to denaturants that form in sheets of amyloid
- found in biofilm ECM
What is cellulose?
- glucose fibers that are resistant to denaturants
- highly wettable
What are the 5 stages in biofilm development?
1) initiation - attached to monolayer by flagella
2) maturation - forms micro colonies
3) Maintenance
4) dissolution
What are endospores?
a formation induced by starvation/stressors in gram-positive bacteria
- asymmetric division that produces foreshores and ultimately an endospore
- forming these spores takes a lot of energy and is the last option
- spores are heat resistant and do not need nutrients until the germinate
What is sporulation?
the process where bacteria turn into spores, uses a lot of energy
What are heterocyst?
-present in cyanobacteria
- make nitrogenase to fix gaseous nitrogen
- produce 3 additional cell walls
- form a specialized O2 barrier
- degrades photosynthetic machinery
- present in every 10th cell to allow for both photosynthesis to occur in other cells and fix nitrogen in heterocysts
- fix nitrogen anaerobically at night
What are fruiting bodies?
Found in myxococcus xanthus
- starvation triggers the aggregation of 100,000 cells, which form a larger “fruiting” body
What are considered “normal growth conditions”?
-Pressure: sea level
- Temperature: 20-40oC
-pH: near neutral
- salt concentration: ~0.9%
- ample nutrients
- anything outside these conditions is considered extreme
What temps do psychrophiles live in?
0-20oC
What temps do mesophiles live in?
~15-45oC
What temps do Thermophiles live in?
~ 40-70oC
What temps do Hyperthermophiles live in?
~65-121oC
What type of extremophiles are typically human pathogens?
mesophiles
What are psychroptrophs?
cold-resistant mesophiles that grow between 0-35oC
What is osmolarity?
a measure of the number of solute molecules in a solution.
What are compatible solutes
molecules that accumulate in cells and balance the osmotic difference between the cells surroundings and the cytosol- especially in hypertonic solution
What are mechxnosensitive channels?
channels used to leak solutes out of the cell - especially in hypotonic solutions.
What is a prophage?
the viral genome stabilized in the host cell
What are some forms of prophage DNA?
- plasmid
- integrated into the host genome
What are the 3 different life cycles that bacteriophages can under go?
1) Lytic cycle: kill
2) Lysogenic cycle: sleeper cell
3) slow-release cycle: Persistent Phage
What are the steps of the lytic replication cycle?
1) phage recognizes the host cell and attaches to it
2) phages gains access/inserts its DNA into the host genome
3) Using the host machinery, the phage components are expressed and assembled into progeny phages
4) many progeny phage kills and exits host cell in search of new host cells
What is a temperate phage?
a phage that infects and lyses the cell but maintains the genome as a prophage without complete destructions of the cell
What is lysogeny?
- phages are quiescent as prophage
- prophage presence prevents superinfection and a lot of cell death
- prophage is replicated and inherited along with host chromosome each generation.
- can become reactive/lytic again
What decides whether a cell/phage enter the lytic or lysogenic cycles?
- dictated by environmental cues/triggers
- events that threaten host cell trigger a lytic burst
What is the slow-release cycle of a persistent phage?
-phage produce phage particles without lysing the host cell
- host will reproduce, but more slowly than uninfected cells
What happens when a new type of phage enters GI tract?
1) transduction: horizontal gene transfer
2) lysogeny
3) Lysis: to depopulate bacterial species
What can lysogenic cells use to detect cell density and trigger lysis for population control?
quorum sensing
How do phage monitor immune system?
suppresses t-cell activation and tumor formation
What is something unusual that phage infections can erode?
biofilms of pathogens
What are some defenses that bacteria have evolved against phage infection?
1) genetic resistance: alter/block receptor proteins
2) Restriction/Modification: cleave phage DNA lacking methylations
3) CRISPR
What does CRISPR in bacteria do against phages.
