Exam 2 Flashcards
What is a virus?
Small sub cellular particles that can replicate only within living host cells. Obligate intracellular parasite
Basic structure of a virus
RNA or DNA genome enclosed in a protein shell (capsid) which together are called the nucleocapsid. Some contain viral envelop, a membrane that surrounds the capsid
Who first found a virus?
Dimitri ivanovski in tobacco plants
Who found the cause of yellow fever?
Walter reed. Transmitted by mosquitos
What is the size of a virus?
10-100 nanometers
Range of nucleotides in viruses
Few thousand to 200,000
What are the four largest viruses and their size
Mimivirus- 400 nm
Megavirus chilensis- genome of 1.2 Mbp
Pandoravirus salinus- 2.47 Mbp
Pithovirus sibericum- 1.5 micrometers long and 500 nm wide
What are capsomeres?
Subunits of the capsid that are made of 1 or more polypeptides
Common shapes of the capsid and their structure
Helical morphology- capsomeres form a helix and the capsid resembles a hollow tube
Icosahedral morphology- capsomeres form a 20 sided polygon and each capsomeres makes up a face of the icosahedron
What do bacteriophages infect
Only bacteria, no plants or animals
What do enveloped bacteria infect
Animals, very few for plants or bacteria
Who discovered and coiled the term bacteriophages?
Felix d’Herelle
Host, structure, size, genome size, and genetic material of poliovirus
Humans Non-enveloped, icosahedral 30nm 7,700bp ssRNA
Host, structure, size, genome size, and genetic material of tobacco mosaic virus (TMV)
Tobacco and related plants Non-enveloped, helical 300x18 nm 6,400 bp ssRNA
Host, structure, size, genome size, and genetic material of T4
E. coli Non-enveloped 200x90 nm 170,000bp dsDNA
Host, structure, size, genome size, and genetic material of variola virus
Humans Enveloped, complex 300x250 nm 186,000bp dsDNA
Host, structure, size, genome size, and genetic material of mimivirus
Amoeba Enveloped, complex 400nm 1,200,000bp dsDNA
What is an viral enveloped made of?
Plasma membrane
How do viruses bind to a host cell?
Through the viral attachment protein on the surface of a virus and the receptor with which the attachment protein interacts. (spike like structure)
3 methods a virus enters a cell
- virus attaches to cell receptor –> endocytosis is initiated –> endosome forms with the virus inside –> nucleocapsid escapes to the cytoplasm and uncoats to release the genome
- virus attaches to the cell receptor –> conformational change in the attachment protein and bound receptor initiates membrane fusion –> viral envelop fuses with plasma membrane –> nucleocapsid enters the cytoplasm and uncoats to release the genome
- virus attaches to the cell receptor–> endocytosis is initiated –> endosome forms with virus inside –> low pH of endosome initiates fusion of the viral envelop with the endosome membrane and the nucleocapsids are released
Steps from viral entry into the cell to exiting the cell
- attaches to the cell
- entry and uncoating of the viral genome
- gene expression and protein production
- genome replication
- assembly and exit from the host cell
what are the 3 hypotheses about the origin of the virus?
- coevolution hypothesis- viruses may have originated prior to or at the same time as the primordial cell and have continued to coevolve with these hosts
- regressive hypothesis- viruses may represent a form of “life” that has lost some of its essential features and has become dependant on a host
- progressive hypothesis- viruses may have originated when genetic material in a cell gained functions that allowed the DNA or RNA to replicate and be transmitted in a semi-autonomous fashion
Types of bacteriophage replication
- lytic cycle- virus enters, replicates, and lyse host cell
- lysogenic cycle (temperature phage)- phage integrates their genome into host genome (prophage), prophage genome is replicated until stress occurs and then enters the lytic phase
general process of bacteriophage cultivation
Inoculate appropriate cells with virus, as the viruses are replicated the bacterial cells die (due to lysing), and the culture starts to turn from turbid to clear as the cells die. Afterwards the culture can be filtered to get rid of cell remains
what is plaque?
when host cells and viruses are plated on agar, small circles called plaque appear. these circles are dead cells
how are viruses purified?
- low speed centrifugation gets rid of whole and broken host cells
- transfer the supernatant (which contains the virus) into a new tube to be ultracentrifuged (differential centrifugation)
- viruses are collected at the bottom in a concentrated state
explain gradient centrifugation
it depends on the different densities of viral components. first a tube is filled with layers of decreasing concentration of sucrose, then viruses are added on top, this is centrifuged and the cell debris and intact viruses should be in different densities
what are the 4 types of viral quantification?
- direct count
- hemagglutination assay
- plaque assay
- endpoint assay
how does direct count of viruses work?
electron microscope is used to look at a known concentration and then scaled up to determine titer. this method doesn’t differentiate between infections and non-infectious
how does hemagglutination work?
some viruses stick to red blood cells and forms a gel mat. button shape means fewer viral particles are present. shield means theres a high number of viral particles. not all viruses do this and it doesn’t differentiate between viable/non-viable and doesn’t give an exact number
how does a plaque assay work?
virus is placed on target cell, plaques are counted and scaled to get original titer. can be used or phage and plant viruses
how does an endpoint assay work?
- tissue culture infectious dose 50 (TCID50): amount of virus needed to produce a cytopathic effect in 50% of cultured cells
- lethan dose 50 (LD50): amount of virus needed to kill 50% of test animal subjects
examples of how viruses were named
- letter number combo
- organism they infect
- location discovered
- appearance of virus
- disease caused by virus
what is ICTV?
international committee on taxonomy of viruses. classify viruses in order, family, subfamily, genus, and species based on morphology, genome structure, biological features, disease caused, envelope, and genomes
what is the Baltimore classification system?
based on the mRNA production methods and separated into 7 classes:
- dsDNA genome
- ssDNA genome
- dsRNA genome
- ssRNA genome, positive sense
- ssRNA genome, negative sense
- ssRNA genome, DNA intermediate
- dsDNA genome, RNA intermediate
how are viruses identified?
first through electron microscopy, then nucleic acid analysis (PCR and reverse-transcriptase PCR)
name two virus like particles
viroids and prions
describe viroids
- consist of only RNA
- very small (less than 400 nucleotides)
- lots of internal complementation (bases link together to form loops)
- resistant to ribonuclease
- only causes disease in plants so far
describe prions
- proteinaceous infectious particles
- no nucleic acids, no genes, just protein
- responsible for transmissible spongiform encephalopathies (mad cow)
prion replication
- still unclear
- idea: revolves around conversion of protein conformations from normal to abnormal (fibrils)
explain how CRISPR works
- transcription and translation of cas genes forming cas proteins
- transcription of CRISPR locus, forming the pre-crRNA transcript
- cas proteins cleave the pre-crRNA forming mature crRNA subunits
- other cas proteins interact with mature crRNA subunits, forming CRISPR-cas surveillance complexes (clusters of regularly interspaced short palindromic repeats)
- CRISPR-cas surveillance complex surveys calls for complementary phage DNA. once detected, the complementary sequences are aligned and the phage DNA is targeted for destruction
what are the 2 types of metabolism
- catabolism (releases energy)
- anabolism (consumes energy)
what are the nutritional requirements of cells
- macronutrients required by all cells: C,N,P,S,O
- micronutrients required by some cells: Fe, Cu, Na, Mg, Mn, and others
what are the fundamentals of nutrition?
- energy source- photo (photosynthetic) or chemo (organic or inorganic)
- electrons- organo or litho
- carbon source- heterotroph (fixed organic) or autotroph (CO2)
types of aerobic growth
obligate aerobes- require 02
microaerophiles- grow best in low levels of o2
types of anaerobic growth
aerotolerant anaerobes- aren’t harmed by o2 but dont use it
obligate anaerobes- cannot grow when o2 is present
faculative anaerobes- can grow in the absence od o2 but grow better when it is present
toxic oxygen species
- siglet oxygen- comes from photochemical reaction; product of peroxidase enzymes, defence is antioxidant such as caroenoid pigments
- superoxide anion- comes from one electron reduction of molecular oxygen, defence is superoxide dismutaase or superoxide reductase enzymes
- hydroxyl radical- comes from reduction of o2 during respiration, defence is antioxidant such as glutathione
- hydrogen peroxide- comes from reduction reactions, defence is catalase and peroxide enzymes
how does temperature affect cells?
affects macromolecular structure, membrane fluidity, an enzyme function
what is the temperature range for eukarya?
Psychrophiles (-15°-10), mesophiles (10-55), some thermophiles (55-~70)
what is the temperature range for archaea?
psychrophiles, mesophiles, thermophiles, hyperthermophiles (-15-130+)
what is the temperature range for bacteria
psychrophiles, mesophiles, thermophiles and some hyperthermophiles (~100)
how to psychrophiles live?
higher proportion of unsaturated fatty acids in membrane phospholipids. enzymes denature at higher temperatures)
what is psychrotolerance?
able to grow ~0-4 but optimal at 20-40
what is selective media?
allows for isolation of microbes with specific properties
what is differential media?
allows certain microbes to be recognized based on visual reactions in the medium
what is enriched media?
used to increase the population of microbes with a specific property
3 methods to obtain a pure culture
- streak plate method
- spread plate method
- pour plate method
3 methods to quantify microbes
- direct count (known volume counted on microscope)
- viable cell count (serial dilutions and CFU counted)
- turbidity measurements (spectrophotometer)
4 phases of mirobe’s growth curve
- lag phase- preparing for stead growth
- exponential phase- replicating at a constant and steady exponential rate
- stationary phase- replication has halted or equal to the death rate
- death phase- nutrients are depleted and waste levels are high, cells die at steady exponential rate
what is continuous culture?
used to keep microbes in exponential growth in a limited but continuous flow of nutrients
calculations from a growth curve
generation time- time to double the population in the exponential phase
growth rate- number of generations/unit of time (inverse of generation time)
growth yield- maximum population density and/or amount of cellular material produced by the culture
what is filtration and possible problems that can result
filtration os the physical removal of microbes (0.2-0.45 micrometer pore size). problems can be that large particles clog the filter, viscous fluids don’t filter well, and unltafiltration (for viruses) require high pressure
what is the common pore size for sterilization
0.2 micrometers and it is ideal when the material is heat or radiation sensitive
what is varying pore size used for
to separate or distinguish organisms and to retrieve small cells from a mixture of large cells
what is a depth filter
randomly overlapping fibers and is used as a “pre-filter”
what is a conventional membrane filter?
polymer filter (0.45-0.22 micrometers): cellulose acetate or cellulose nitrate and the pore diameter is variable during production
what are nucleopore filters?
thin polycarbonate film (~10 micrometers thick): radiation damage, cracks enlarged by chemical etching and has a consistent pore size. it is useful for microscopy as the filtered material is on a single surface plane
describe what temperature manipulation does and some problems associated with it
it denatures proteins and nucleic acids and 100° kills most microbes while an autoclave adds pressure so that the liquid doesn’t evaporate. some problems are that it doesn’t kill hyperthermophiles, endospores can be created, and some materials can’t be heated
describe an autoclave
creates steam under pressure (121°C and 15psi). efficiency is determined by destruction of endospores and vegetative cells
what does pasteurization do?
- destroys pathogens
- kills 90-99% of other microbes but does not sterilize
- increases shelf life
- keeps flavour
3 different pasteurization methods
- High temp short time (HTST): 72°C for 15 seconds
- ultrahigh temp (UHT): 135°C for less than 1 second
- extended shelf life: filtration hen lower temp treatment
explain freezing
- damages cells by forming ice crystals
- stops biochemical reactions
- long-term preservation
what is bacteriostatic?
growth inhibitory
what is bacteriocidal?
kills cells
what is bacteriolyic?
causes cell lysis
disinfectant vs antiseptic
disinfectant- used on non-living surfaces to kill potentially infectious microbes
antiseptic- used on living tissue to kill potentially infectious microbes (usually topical)
5 types of disinfectants/antiseptics
- alcohols: ethanol is an example and used in lab setting and hand sanitizer. targets membranes
- phenolic compounds: triclosan is an example and is added to cosmetics + soap. targets membranes
- oxidizing agents: sodium hypochlorite is an example and is added to pools
- benzalkonium chlorate: major ingredient in Lysol and targets membranes
- Glutaraldehyde: used to prepare biological specimens. targets crosslink proteins
what are antimicrobics/antibiotics and how do they work?
antibiotics are antimicrobal agents produced by microbes. static, cidal, or lytic. work by disrupting essential functions that are necessary for growth and survival.
who found the first antibiotic?
alexander fleming
how do we measure effectiveness of killing microbes?
decimal reduction time: ime required to kill 90% of the target organism under specific conditions
give example of broad-spectrum and narrow spectrum antibiotics and what they target
Broad-spectrum: -tetracyline, targets inhibition of protein synthesis
narrow-spectrum: -polymyxin B, disruption of cell outer membrane
-penecillin, inhibition of cell wall synthesis
generally describe proteobacteria
- very encountered bacteria
- related to mitochondria
- metabolically diverse (chemolithotrophs, chemoorganotrophs, phototrophs)
- morphologically diverse
- 5 phylogenic groups (alphs, beta, gamma, delta, epsilon)
describe proteobacteria tree
- all descend from 1 ancestor
- epislon and delta lost photosynthetic ability and are chemoorganotrophs
- alpha, beta, and gamma are from one common phototroph ancestor and are both chemolitho and chemoorgano
what is anoxygenic photosynthesis?
- photosynthesis is inhibited by o2
- colours determined by bacteriochlorophylls and carotenoids
what are purple sulfur bacterial blooms?
- photoautotrophs of gamma proteobacteria
- oxidize H2S to S0 during photosynthetic CO2 reduction in anoxic lake water
- stored in the periplasm and disappears when oxidized to sulfate
what are methylotrophs?
-oxidize inorganic carbon compounds (1 carbon)
what are mathanotrophs?
- methylotrophs capable of oxidizing ethane into methanol
- intracytoplasmic membranes
- obligate c1 users
- obligate aerobes, often microerophilic
- found in soil and water and cattle rumen and swamps
what are nitrifiers?
-use reduced nitrogen compounds as energy source (chemolithoautotrophs)
subdivisions of nitrifiers
- nitrosocossus and nitrosomonas: ammonia oxidizer and ammonia monooxygenase
- nitrobacter and nitrospira: nitrite oxidizers and nitrite oxidase
what are pseudomonas?
- heterogenous group with evolving taxonomy
- aerobic chemoorganoheterotrophs
- nutritionally and ecologically versatile
- some are fluorescent
describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of fungi
heterotrophic, usually non-motile, chitin cell wall, nucleus and mitochondria present
describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of protozoa
heterotrophic, cilia, flagella or pseudopods, no cell wall, nucleus and mitochondria present
describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of slime molds
heterotrophic, pseudopods, no cell wall, nucleus and mitochondria present
describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of algae
phototrophic, non-motile or flagella, cellulose cell wall, nucleus, mitochondria, and chloroplasts present
what are saccharomyces ceerevisiae?
fungi used to make bread, beer, wine (yeast)
name the 5 fungal categories
- chytridiomycota: early branching water molds
- zygomycota: bread mold (branch with black dot)
- glomeromycota: mycorrhizal fungi; important for plants
- ascomycota: spore shooters; cup/sac fungi, yeast
- basidiomycota: spore droppers, club fungi, typical mushrooom
what are slime molds and 2 examples
- individual cells that communicate and come together
- Dictyostelium discodeum: model for studying ecology and cell-cell communication
- physarum: fuses many cells into a continuous giant cell
example of a algae species
chlamydomonas: has two flagella which are good for studying
describe the saccharomyes life cycle (fungus)
- can undergo meiosis to form an ascus
- haploid mating types can fuse to reproduce sexually or be maintained asexually by mitosis
- not limited to ascus form
- budding off of smaller cells can occur or fission of identically sized cells
describe the chlamydomonas life cycle (algae)
- maintains a motile haploid state
- haploids can differentiate and fuse into diploids in bad conditions (spore formation)
describe the dictyostelium life cycle
- exists in a haploid unicellular form unless bad conditions which turns into a “slug” with a stalk and a fruiting body
- spores form in the fruiting body
- haploid cells can fuse into diploid macrocyst form
- macrocyst form undergoes meiosis to generate more haploid cells
evidence of the endosymbiotic theory
- mitochondria and chloroplasts resemble bacteria in size and shape
- double membranes
- cell division with FtsZ
- each has its own DNA and rRNA
- circular chromosome
what is rhytisma?
an ascomycete fungus that infects sycamores and maples (tar spots)
what is phytophthora infestans?
causes potato blight
what are cordyceps?
fungus that grows out of insects
what are some benefits of eukaryal microbes?
- primary producers provide energy (produce oxygen)
- biodegraders recycle nutrients
- come can degrade cellulose which recycles plant matter much better than animals
