Microbiology: Bacteria and Viruses Flashcards
Describe the lytic cycles of bacteriophages
A lytic life cycle always end up destroying it the host cell that the virus infected: the virus produces the early gene of hydrolase, which degrades the entire host’s genome. The dNTP’s from this genome are then used to create multiple copies of the phage genome. New proteins are also synthesized for the capsid for each new genome. After that, the virus will express the late gene of lysozyme, which degrades the bacteria’s cell wall, causing it to lyse and release ~100 viral progeny
Describe the lysogenic cycle of bacteriophages
When the virus injects its genome into the host cell, it incorporates this genome into the host cell’s genome. This virus is now considered a prophage, and the host is now referred to as a lysogen. The prophage is silent thanks to its repressor proteins that bind to specific DNA elements in the phage promoters (operators). Therefore, the viral genes are not expressed and viral progeny are not produced; however, when the host reproduces itself, the prophage is also reproduced. The prophage has the ability to remove itself from the genome (process called excision) and become activated, which means it’ll undergo the lytic cycle; however, excision and followed by the lytic cycle will only occur if the host cell itself experiences stress (i.e. high temps, change in pH, or change in salt concentration of surrounding solution)
The first step of viral infection is the binding to the exterior wall of the bacteria in a process called ______
attachment or adsorption
After the virus has undergone attachment/adsorption, it injects its genome into the host cell in a process called _____
penetration or eclipse (called eclipse because the capsid remains on the outer surface of the bacterium while the genome disappears into the cell, removing the infectious virus from the media)
What is transduction?
Refers to transfer of host cell DNA to another host via a bacteriphage. This occurs when the lysogenic virus undergoes excision, and will excise some host cell genome in addition to its own genome.
What is an envelope on a virus? How does the virus obtain this?
Refers to an outer covering on the capsid, which is obtained by budding though the host cell’s membrane. Thus, this envelope is comprised of phospholipids, proteins, and carbohydrates from the host membrane.
To infect a new host, some enveloped viruses fuse their envelope with the host’s plasma membrane, which leaves the de-enveloped capsid inside the host cell.
What is a naked virus?
refers to a virus that doesn’t contain an envelope.
all viruses that infect bacteria and plants are naked viruses.
*Side note: all envelope viruses are animal viruses, but not all animal viruses must contain an envelope to infect animal cells.
All phages and plant viruses are naked. Why?
phages and plant viruses infect hosts that possess cell walls; therefore budding is not possible. When the virus exits the cell, the cell wall is destroyed and the host membranes rupture, so there is no membrane left in which to bud with.
Describe the productive life cycle
- Like the lytic cycle, but without lysis. Viral copies leave via the process of budding, which results in an enveloped virus.
- This life cycle is only found in viruses that infect animal cells
Only _____ cell viruses undergo the productive cycle
animal
What are the advantages of an envelop on a virus
It allows the virus to be less detectable to the immune system (although the immune system will eventually recognize the enveloped virus)
It allows for easier infection because the enveloped virus will be able to attach to a cell specific receptor on the host cell. The cell will swallow the enveloped virus as a whole, allowing the whole virus genome to enter the host cell and allows the capsid to be recycled.
Briefly describe the process of how positive sense RNA replicates via a lytic cycle
positive sense RNA can be picked up by host ribosomes and directly be translated. Hydrolase and viral proteins will first be translated and synthesized. The translated positive sense RNA will be translated and synthesized into a new strand of negative sense RNA (complementary to the positive sense RNA). RNA dependent RNA polymerase will use that negative sense RNA strand to synthesize multiple new positive sense RNA strands. Each strand will become a new viral genome.
Briefly describe the process of how negative sense RNA replicates via a lytic cycle
once -RNA is injected into host cell, the RNA dependent RNA polymerase must first create a positive sense strand of RNA. That +RNA can then be translated by a ribosome, which will be translated into a -RNA.
Is RNA dependent RNA polymerase carried by the virus, or is the code incorporated into the viral genome
+ RNA viruses: incorporated into the viral genome only
- RNA: actual enzyme is carried with the virus in addition to also must carry the code in the genome
What enzyme is responsible for converting viral RNA into ssDNA?
RNA dependent DNA Polymerase (aka reverse transcriptase)
What is a retrovirus?
refers to the +RNA virus that contains an encoding for reverse transcriptase (aka RNA dependent DNA Polymerase), which is necessary for the +RNA to be translated into DNA, which can then be incorporated into the host’s genome as a provirus.
After integration of the retrovirus into the cellular genome, a reverse transcriptase inhibitor is added to the cell. Will the production of the new viruses be blocked?
No. the +RNA genome can still be translated by host ribosomes
Are retroviruses required to carry the enzyme reverse transcriptase?
No. Although some retroviruses do carry the enzyme, it is not required, as the + RNA already encodes for reverse transcriptase and can directly be translated by ribosomes
dsDNA viruses often have large genomes that include genes for enzymes involved in deoxyribonucleotide synthesis and DNA replication. Given the limited information that viruses may contain in their genomes, why carry around genes for an enzyme possessed by the host?
The host cell will only make dNTPs in preparation for replication. If the virus wants to reproduce without waiting for the host to do so, it must encode its own enzymes for the synthesis of DNA building blocks.
Why do dsDNA viruses, but not RNA viruses, carry enzymes for (d)NTP synthesis?
the host cell is always performing transcription and therefore always has NTPs present in the cell that the virus can use.
the host cell will only produce dNTP during times of replication and, therefore, the virus must carry these enzymes if they want to reproduce without waiting for the host to do so. it must encode its own enzymes for the DNA building blocks
What is a prion?
an infectious protein that has an ability to self replicate
these proteins do not have any RNA or DNA, any membrane structures, or any organelles
What are transmissible spongiform encephalopathies?
Refers to prion diseases in mammals that cause degeneration of nervous tissues, ultimately leading to loss of coordination, dementia, and death. These are usually passed by consumption of prion diseased meat.
-side note: incubation period for prion diseases can be several months to several years in animals and humans
What are viriods?
- short circular pieces of RNA that are virus like, but do not have capsids. Therefore, in order for viroids to infect host cells, they must be coinfected (uses other viruses’ capsids).
- Viroids also don’t code for proteins; rather they act like miRNAs and siRNAs to block translation. Viroids hijack the cell’s enzymes for their own replication.
- viroids are mostly associated with infecting plants
what is the classification of bacteria that has: 1) one flagella, 2) 2 flagellas on opposite sides, and 3) bacteria that are just generally covered in flagellas?
1) monotrichous
2) amphitrichous
3) peritrichous
What’s the difference between gram + and gram - bacteria
gram + bacteria have a very thick cell wall, which means they have a lot of peptidoglycan
gram - bacteria have a very thin cell wall, and thus have little amounts of peptidoglycan
Which types of bacteria can create endospores?
gram +
This is because the spores cell walls are made of a thick peptidoglycan layer, which is only produced in gram + bacteria
Which type of bacteria has an inner membrane, a thin cell wall, and an outer membrane?
gram - bacteria
What is the space found between the inner and outermembrane of gram- bacteria?
periplasmic space
this space contains digestive enzymes that help the bacteria become more resistant to harsh environments i.e. amy carry a digestive enzyme that degrades a certain abx, thus making it more resistant to abx
Which type of bacteria produces and releases endotoxins?
gram -
It’s the outer lipopolysaccharide membrane that helps produce these endotoxins (these endotoxins can cause septic shock in infected individuals)
Differentiate between mesophiles, thermophiles, and psychrophiles
mesophiles: live in medium temps (~30 degrees celsius)
thermophiles: live in hot temps (i.e. ~100 degress celsius)
psychrophiles: live in cold temps (~0 degrees celsius)
Differentiate between obligate aerobes, facultative anaerobes, tolerant anaerobes, and obligate anaerobes
obligate aerobes: requires oxygen to survive (uses O2 for cellular respiration)
facultative anaerobes: they prefer oxygen for cellular respiration, but are able to undergo fermentation and thus live in an environment that lacks oxygen
tolerant anaerobes: don’t use oxygen for cellular respiration, but can survive in an environment where oxygen is present
obligate anaerobes: don’t require oxygen for cellular respiration, but will die in presence of oxygen in environment
Differentiate between phototrophs, chemotrops, autotrophs, and heterotrophs
phototrophs: get their energy from sun i.e. plants and cyanobacteria
chemotrophs: get their energy from ATP i.e. animals
autotrophs: makes their own carbon chains from CO2 i.e. carnivorous plants
heterotrophs: eat other organisms to obtain carbon chains i.e. deep sea/cave bacteria
When referring to auxotrophy, what does a - sign indicate?
The - sign means that that organism cannot do something.
When there is a - sign after an amino acid, this means that the organism cannot make that AA
When there is a - sign after a sugar, this means that organism cannot metabolize that sugar
Briefly explain the process of binary fission
simply just asexual replication of a bacteria
advantage: this reproduction is exponential and therefore produces a huge increase in population size
disadvantage: no change in genetic diversity
Differentiate between the lag phase, log phase, stationary phase, and death phase
lag phase: there is no bacterial growth (bacteria are becoming used to the medium they are in)
log phase: represents massive exponential growth in a bacteria population
stationary phase: population size has hit its max. there is no active increase in population size because carrying capacity of medium has been reached
death phase: population starts to die off because there is toxic accumulation of waste products
How can the death phase in binary fission be avoided?
it can be avoided if the carrying capacity of the medium is increased (nutrients are added to and waste products are washed off in the medium
What is bacterial conjugation?
allows exchange of genetic material from one bacteria to another with the use of a fertility factor
allows for a huge increase in genetic diversity (will not produce a change in population size)
A bacteria that has an F plasmid can be referred to as a ____ bacterium
F+
whereas one that doesn’t have the F plasmid is referred to as a F- bacterium
What is responsible for producing the sex pilus and thus conjugation bridge during conjugation?
fertility factor (whether that’s from a F plasmid or a fertility factor incorporated into its genome)
After the F plasmid is replicated in the F+ bacterium and gets transferred into the F- bacterium via the conjugation bridge, that F- bacterium is now classified as a ____ bacterium
F+ bacterium
Differentiate between a F+ bacterium and Hfr bacterium
F+ has a fertility factor as a plasmid that is separate from the bacterium’s genome
Hfr has a fertility factor that is incorporated into its genome
When an Hfr bacterium conjugates with a F- bacterium, the F- bacterium becomes a ________ bacterium
F- recombinant
Differentiate between endo and exotoxins
endotoxins are normal components of the outer membrane of gram- bacteria that aren’t inherently poisonous, but can still cause our immune system to have such an extreme rxn that we may die as a result. When the bacteria die and their endotoxins are disintegrated into our bloodstream, there are so many chemicals released that it can cause us to go into septic shock.
exotoxins can be produced and secreted by both gram- and gram+ bacteria into the surrounding medium; these toxins can cause disease i.e. botulism, diptheria, tetanus, and toxic shock syndrome
What is the function of the capsule/glycocalyx found in some bacteria?
this is a sticky layer of polysaccharide “goo” surrounding the bacterial cell and often surrounding the entire bacteria colony.
this layer can make it harder for immune cells to eradicate the bacteria; and this layer can also help the bacteria stick better to smooth surfaces
What are the 3 main components of the bacterium flagella and which component is responsible for rotation?
filament, hook, and basal structure
the basal structure contains a number of rings that anchor the flagellum to the inner an outer membrane (for a gram- bacterium) and serve to rotate the rod and the rest of the attached flagellum in either a clockwise or counterclockwise manner
How do eukaryotic flagellum differ from prokaryotic flagellum?
the eukaryotic flagellum is composed of dynein and protein filaments called microtubules, which have a 9 + 2 arrangement.
prokaryotic flagella is composed of a single globular protein called flagellin, which is wrapped around in a helical fashion to create a rigid, hollow cylinder.
What is chemotaxis?
refers to the movements that bacteria will undergo to propel them towards food or away from toxins
What are fimbriae?
smaller projectile structures on the bacteria surface that are involved in adhering the bacteria to surfaces
Differentiate between aerobic respiration, anaerobic respiration, and fermentation
aerobic respiration catabolizes glucose with the use of oxygen as a final e- acceptor
anaerobic respiration catabolizes glucose with the use of a final e- acceptor besides for oxygen. note that this type of catabolism still utilizes an electron transport chain and oxidative phosphorylation
fermentation is glucose catabolism which does not use an inorganic e- acceptor, but rather a reduced by-product of glucose catabolism (i.e. lactate and ethanol are given off as waste)
In an experiment, facultative anaerobic bacteria that are growing on glucose in air are shifted to anaerobic conditions. If they continue to grow at the same rate while producing lactic acid, then the rate of glucose consumption will: A) increase by 16 fold B) decrease by 16 fold C) decrease by 2 fold D) no change
A) increase by 16 fold
Bacteria are using fermentation, which only produces 2 net ATP molecules per 1 glucose, compared to the 32 ATP they were producing before in presence of O. However, there is no decrease in growth rate. Therefore, glucose catabolism and consumption must increase in order to keep up with no change in population growth.
The metabolic reactivation of an endospore is termed _____
germination
How can lab chemists determine the order sequence of genes on Hfr bacteria?
They analyze recipient cells (F- bacterium) during conjugation to see what genes were transferred.
Furthermore, they can allow the Hfr bacteria to conjugate and then stop the conjugation process after different time intervals. After each time interval, they will assess to see which genes the F- recombinant bacteria now possess.
What is transformation?
When bacterium takes up free floating DNA (perhaps from a close by bacterium that just died) and then can start expressing that DNA
What is a prophage?
a dormant bacteriophage incorporated into a bacteria’s genome
What is a lysogen?
refers to the infected bacteria with a bacteriophage
What is a provirus?
a dormant animal virus that is incorporated into the host cell’s genome
the bacteria wall protects them from ____ pressure, preventing lysis and preventing bacteria from consistently having to export/import ions likes animal cells do
osmotic
rotation of bacterial flagellum is performed by the _____ on the inner membrane
e- transport
**bacteria need energy from ATP to move their flagella, as movement costs energy. bacteria get this energy from the e- transport chain
what are bacterial pili?
long projections of bacterial surface i.e. sex pilus forms the conjugation bridge
*note this is different from fimbriae (short projections that help the bacteria adhere to surfaces) and flagellum (used for motion)
minimal growth media has only _____
glucose
a ____ is a clear area on the lawn of a petri dish
plaque
what is an auxotroph?
a bacterium that cannot survive on minimal media because it cannot synthesize one or more molecules it needs to live
i.e. an arginine auxotroph is denoted arg- because it cannot make arginine on its own; it must collect it from it’s environment
bacteria that can digest lactose are lac_ whereas bacteria that cannot digest lactose are lac_
can digest = lac+
cannot digest = lac-
the glycolytic pathway is most active during which stage of bacteria life cycles: lag, log, stationary, or death
lag: the bacteria are actively using glucose as energy so they can produce the machinery needed (i.e. dNTPs and proteins) to divide
If the bacteria is the log phase are transferred to a fresh new culture medium, will they show a lag phase or continue the log phase? Why?
they will not show a lag phase and will continue the log phase because they already have all the machinery needed to divide/continue cell division
What are the similarities of archea between prok and euk.
archea are single celled and divide via binary fission like prok
archea have introns and use many similar mRNA sequences like euk.
archea cell walls lack peptidoglycan (like bacteria) and are able to live in extreme environments.
parasitic bacteria may be facultative or obligate. distinguish between the two
facultative parasitic bacteria can survive and reproduce outside of the host cell.
obligate bacteria must be inside a host cell to replicate
*both, being parasites, ultimately damage the host cell
Does binary fission increase genetic diversity?
no
what is phage typing?
refers to identifying the type of bacteriophage.
*note that this does not identify the type of bacteria (i.e. gram staining helps identify the type of bacteria)
