Microbiology Flashcards
Viruses are obligate intracellular parasite. what does that mean?
they are only able to reproduce within cells
it relies on host machinery
T/F
Viruses on their own are able to synthesis ATP and other chemical reactions.
False
T/F
Viruses are not cells or living organisms.
True
How can some viruses have ATP stored in their capsid? What can they use it for?
they got it from the last host
they can use it for penetration into the next host
When a virus is not inside a host cell, what does it contain?
only its own genome which could be single stranded or double stranded, linear or circular
If the ratio of adenine to thymine in a DNA virus is not one to one, what can be said about the genome of this virus?
the genome must be single stranded DNA, or RNA which has no T
A disease agent that is isolated from a human cannot reproduce on its own, but it can reproduce when put in a culture of human cells. In its pure form it contains both RNA and DNA, is it a virus? Why?
no because a virus can only have DNA or RNA but not both
What is a bacteriophage?
virus that infects bacteria
What limiting factor affects all viral genomes?
size
What happens if a viral genome triples in size?
it will no longer fit within the normal viral structure and therefore will not be packaged in infectious viral particles
How does the virus adapt to its size constraint?
- carries only a few genes and relies mostly on host encoded proteins for transcription, translation, and replication
- ability to encode more than one protein in a given length of genome by utilizing more than one reading frame within a piece of DNA so that genes overlap
How do ribosomes used to translate viral proteins compare to host ribosomes?
they are the same because viruses use the host ribosomes
What is the protein coat that surrounds the viral nucleic acid genome which is also used to classify viruses?
capsid
Helical capsids?
rod shaped
Polyhedral capsids?
multiple sided geometric figures with regular surfaces
What is the capsid shape of Bacteriophage T4?
Helical and Polyhedral
What is the host for the Bacteriophage T4?
E. coli
Where on the capsid is the genome located?
in the capsid head
What do the tail fibers and the base plate of the capsid do?
attach to the surface of the host cell
What does the sheath of the capsid do?
contracts using energy of stored ATP, injects the genome into the host
Why might a bacteriophage inject its DNA, while animal viruses do not?
a phage must puncture the bacterial cell wall, while animal viruses can be internalized whole because there is no cell wall
The entire viral capsid is composed of _______ while the viral genome is composed of ______.
proteins
nucleic acids
In animal viruses, what surrounds the capsid?
the envelope
What is the envelope?
membrane on the exterior of the animal virus derived from the host membrane
How do animal viruses acquire an envelope?
budding
What are viruses without an envelope?
naked viruses
-plant viruses and phages are all naked because they do not bud through the membrane, they puncture the cell wall
T/F
Viruses are very specific, not random.
True
What is the first step in infection?
virus binds to a specific receptor on the cell surface
-attachment or adsorption
After binding, how does the virus become internalized?
fusion with the plasma membrane or receptor mediated endocytosis
-penetration(animal) or eclipse(plant, bacteria)
If antibodies to a viral capsid protein are ineffective in blocking infection, what might this indicate about the virus?
the virus is enveloped, so the antibody cannot reach its epitope on the capsid surface
In the Lytic cycle, what happens as soon as the phage genome has entered the host cell?
host polymerases and ribosomes begin to rapidly transcribe and translate it
What is one of the first viral gene products made in the lytic cycle?
hydrolase- degrades entire host genome
Early genes?
a group of genes that are expressed immediately after infection and which includes any special enzymes required to express viral genes (ex. hydrolase)
What happens after hydrolase degrades the host genome in lytic cycle?
multiple copies of the phage genome are produced (using dNTPs resulting from degradation) as well as capsid proteins
What happens after copies of the phage genome are produced in the lytic cycle?
each new capsid assembles itself around a new genome
What happens after the new capsids form in the lytic cycle?
enzyme called lysozyme (late gene) is produced which destroys the bacterial cell wall, the host bursts (lyses) releasing hundreds of the new capsids to repeat the cycle
If lysozyme were an early gene, would this be advantageous to the virus?
no the host would burst before the phage had time to replicate and assemble
When phage are first added to a bacterial culture, the number of infective viruses initially decrease before it later increases, why?
many phage have injected their genomes into host cells and are no longer infectious, then the cells lyse and release a bunch of capsids
Bacteria culture in the presence of S-cysteine and P-phosphate are infected with T4, what will be found in the interior of newly infected bacteria?
only P because nucleic acids contain no S and proteins contain no P, when the virus infects bacteria their nucleic acids are injected while the proteins remain on the outside
A bacteriophage with an important capsid gene deleted infects the same cell as another virus (co-infection) with a normal copy of the same gene. What will happen at the time of lysis?
all released viruses will be capable of infecting new hosts, but only some of these new infections will give rise to phage capable of infecting new hosts.
some of the bad genome will be covered by good capsid, which can infect another cell but once in the cell the bad genome will code for bad capsid and its progeny will not be able to infect a host
Advantage and disadvantage of the lytic cycle?
- efficient way for a virus to rapidly increase its numbers
- all host cells are destroyed, eventually all will run out
In the lysogenic cycle, what happens after infection of the host?
the phage genome is incorporated into the bacterial genome and is now referred to as a prophage, host is called a lysogen
What is a prophage in lysogenic cycle?
silent, genes are not expressed, viral progeny not produced
Why is the prophage dormant in lysogenic cycle?
transcription of phage genes is blocked by a phage encoded repressor protein that binds to specific DNA elements in phage promoters (operators)
Why is the lysogenic cycle clever?
every time the host reproduces itself, the prophage is reproduced too
What happens when the prophage becomes activated in the lysogenic cycle?
removes itself from the host genome (excision) and enters the lytic cycle
What is a potential consequence of the lysogenic cycle?
when the viral genome activates, excising itself from the host genome, it may take part of the host genome with it and could integrate that DNA into future infections (transduction)
Why would a bacterial gene, carried with a virus and integrated with viral genes into a new bacterial genome, not be repressed along with the viral genes during lysogeny?
viral repressor proteins bind to a specific sequence on viral DNA, this sequence is not present on the bacterial gene, so the bacterial gene can be expressed while the viral genes are repressed.
What does the virus bind to on animal cells?
animal cells have proteins on the surface of the plasma membrane that serve as specific receptors for viruses
What is one of the first steps in HIV infection?
HIV virus protein gp120 binds to a T cell membrane protein called CD4
Would treatment of an HIV infected person with a soluble form of CD4 protein affect the infectivity of the virus?
yes, the CD4 protein would bind the virus CD4 receptors and block attachment of the virus to the T cells
Mutation of the cell surface receptor that viruses attach to would be a means for an organism to become resistant to viral infections. Why is this mechanism not common?
- the receptor has a specific role in the normal function of the host, which might be compromised
- viruses can evolve rapidly to keep up with the changes of the host
What is the next step in the infection of the animal cell after the virus has been bound to the plasma membrane?
penetration- many animal viruses enter by endocytosis
Endocytosis in animal virus infections?
the host cell engulfs the virus and internalizes it
Once inside the host cell, the viral genome becomes ______.
uncoated (released from capsid)
What are the three possible cycles of an animal virus?
lytic
productive
lysogenic
What is the difference between the productive and lytic cycles?
productive doesnt destroy the cell
How is the cell not destroyed in the productive cycle?
the enveloped virus exits the host by budding through the host’s cell membrane, the cell membrane can reseal itself so the cell doesnt die
What is a provirus in animal cells?
the dormant form of the viral genome in the animal virus lysogenic cycle
What is an example of a provirus in animal cells?
Herpes Simplex I is the virus that causes oral herpes
it can remain dormant until stress reactivates it
What is + RNA?
a piece of single stranded viral RNA which serves as mRNA
What happens when a + RNA virus in injected into the cell?
it acts as mRNA and host ribosomes immediately begin to translate it, creating viral proteins
Infective?
injecting an isolated genome into the host cell will result in virus production (+RNA)
What protein is needed for +RNA virus to replicate itself?
RNA dependent RNA polymerase
What is the role of RNA dependent RNA pol?
to copy the RNA genome for viral replication
What are some examples of +RNA viruses?
common cold, polio, rubella
If a viral genome is + strand RNA, what is used as a template by the RNA dependent RNA pol?
it needs the - strand RNA as a template so it first produces a - strand intermediate before generating new + strand genomes
What happens when a -RNA virus enters the cell?
it codes for and carries the RNA dependent RNA pol, unlike +RNA viruses, so when it enters the cell the enzyme creates a + strand from the - strand, then the cycle can continue
What are some examples of -RNA viruses?
rabies, measles, mumps, flu
What is a retrovirus?
+RNA viruses that undergo lysogeny
How can a retrovirus integrate into double stranded DNA genome if it enters the cell as RNA?
they undergo reverse transcription to make DNA from an RNA template, this is done by RNA dependent DNA polymerase (reverse transcriptase) encoded by the viral genome
Even though retroviruses carry the enzyme, RNA dependent DNA pol, they are theoretically not required to carry it, why?
the viral genome can be translated by host ribosomes so it only needs to encode for the enzyme
What are the three main retroviral genes and what do they code for?
gag- codes for viral capsid proteins
pol- codes for reverse transcriptase
env- codes for viral envelope proteins
After integration of a retrovirus into the cellular genome, a reverse transcriptase inhibitor is added to the cell, will the production of new viruses be blocked?
no because the reverse transcriptase is only required for the copying of the viral RNA genome into DNA, this will have already taken place so it is not needed anymore, so an inhibitor wouldnt block anything
What do double stranded DNA viruses often have?
large genomes that include genes for enzymes involved in dNTP synthesis and DNA replication
Why do double stranded DNA viruses carry around genes for enzymes that are possessed by the host cell?
if the virus wants to reproduce, it doesnt have to wait for the host cell to do it
Why dont RNA viruses carry the genes for dNTP synthesis or replication?
transcription is always occurring in all cells, so NTPs (not dNTPs) are always present
What factor likely limits the size of RNA genomes?
the error rate is much higher in RNA synthesis as opposed to DNA synthesis, so if the RNA genome was too large every copy would suffer too many errors that no infectious virus would be produced
What is the advantage for DNA viruses to induce host cell division?
to produce the ingredients needed for DNA synthesis if it does not already possess them
What is a virus that complements another virus?
helper virus (one virus provides one thing necessary, the other virus provides the other thing necessary, ex. adenoviruses)
What is the primary feature that distinguishes prokaryotes from eukaryotes?
prok do not have membrane bound organelles
What are three examples of prokaryotes?
bacteria
archea (extremophiles)
blue green algae (cyanobacteria)
Taxonomy?
classification of living organisms
What are the three recognized domains of taxonomy?
bacteria
archea
Eukarya
Domains can be subdivided into what?
kingdoms
What are the three Euk kingdoms?
Animalia
Plantae
Fungi
What is the prok genome like?
single double-stranded circular DNA chromosome (not in a nucleus and no nucleosomes)
What is a polyribosome?
many ribosomes translating a single piece of mRNA
Is the free end of mRNA that has already been transcribed 3’ or 5’?
5’ because DNA is transcribed 5’ to 3’
What is the free end of the polypeptide that has already been translated?
N terminus because proteins are made N to C
Why is important that bacterial ribosomes are different than our ribosomes?
the differences allow us to prescribe various antibiotics which interfere with bacterial translation without disrupting ours
What is the plasmid in prok?
circular piece of double stranded DNA which is smaller than the genome, referred to as extrachromosomal genetic elements
Why are plasmids important?
- they encode advantageous gene products, such as antibiotic resistant genes
- they orchestrate bacterial exchange of genetic info (conjugation)
What is the proper name of round shaped bacteria?
cocci (plural)
coccus (singular)
What is the proper name of rod shaped bacteria?
bracilli (plural)
bracillus (singular)
What is the proper name of spiral shaped bacteria?
spirochetes or spirilla (plural)
spirochete, spirillum (singular)
What prevents lysis due to osmotic pressure in bacterial cells?
cell wall
How can animal cells deal with osmotic pressure if they lack a cell wall?
they continuously pump ions across the cell membrane
What is the bacterial cell wall composed of?
peptidoglycan- complex polymer unique to prok
What is peptidogylcan composed of?
cross linked chains made of sugars and amino acids, including D-alanine(not found in animal cells, we have L configuration)
What enzyme is found in tears and saliva which is also made by lytic viruses?
lysozyme
What is target of many antibiotics, including penicillin?
bacterial cell wall
What is a protoplast?
an osmotically fragile structure due to the cell wall (peptidoglycan) being destroyed by lysozyme
Would a protoplast moved from salt water to fresh water shrivel or burst?
burst because concentration inside the cell is higher than outside so fresh water would rush through osmosis (hypotonic)
Gram staining?
method of classification derived from the extent to which bacteria turn color in a procedure
Gram positive?
stain strongly dark purple color
Gram negative?
stain weakly light pink color
What is the difference in cell wall between gram positive and gram negative bacteria?
positive- thick peptidoglycan layer outside the cell membrane and no other layer beyond this
negative- thinner layer of peptidoglycan in the cell wall and an additional outer layer containing lipopolysaccharide
What is the periplasmic space in gram negative bacteria?
intermediate space between the cell membrane and the outer layer which sometimes contain enzymes to degrade antibiotics
Which bacteria would be more susceptible to lysis when treated with lysozyme, positive or negative?
positive because it has a thicker peptidoglycan layer and no other layer, lysozyme hydrolyzes linkages in the peptidoglycan to weaken the cell wall
What are endotoxins in gram negative bacteria?
normal components of the outer membrane that arent poisonous unless when many bacteria die and their outer membranes are released into circulation, the immune system will release chemicals which send the patient into septic shock causing a drop in blood pressure
What are exotoxins found in both gram positive and negative bacteria?
very toxic substances secreted into the surrounding medium, exotoxins help the bacteria compete with other bacteria which could be normal to the body (ex. botulism, tetanus)
What is the capsule that only some bacteria have?
glycocalyx, sticky layer of polysaccharide goo surrounding the bacterial cell wall and often an entire colony of bacteria making it more difficult for the immune system to eradicate them and allows bacteria to stick to smooth surfaces
What are flagella in bacteria?
long whip like filaments involved in motility
Can viruses move via flagella propulsion to find host cells?
no viruses lack any means of energy production or movement on their own, they rely on diffusion into host cells
Monotrichous? Amphitrichous? Peritrichous? (bacteria)
Mono- flagella at only one end
Amphi- flagella at both ends
Peri- multiple flagella
What are the three parts of the flagella?
filament, hook, basal structure
What does the basal structure of flagella do?
anchor flagella to the inner and outer membrane for a gram negative bacteria and serve to rotate the rod and the rest of the attached flagella either clockwise or counterclockwise
How does a bacteria supply the large amount of ATP needed to rotate the rod of a flagella?
supplied by the diffusion of H+ down the proton gradient generated across the inner membrane by electron transport
Chemotaxis?
bacterial motion directed towards attractants, such as food,
or away from toxins, such as acid
What does the connection between chemotaxis and flagellar propulsion depend on?
chemoreceptors on the cell surface that bind attractants or repellants and transmit a signal which influence the direction of flagellar rotation, depends on the change in concentration
What are pili in bacteria?
long projections on the bacterial surface that attach to different surfaces
What is the sex pilus in bacteria?
special pilus attaching F+ male and F- female bacteria which facilitate the formation of conjugate bridges
What are fimbriae in bacteria?
smaller structures involved in adhering to surfaces
What are mesophiles?
bacteria that love moderate temperatures
What are thermophiles?
bacteria that love heat, live in hot springs or geothermal vents in the ocean floor
What are psychrophiles?
bacteria that thrive in cold temps
Autotrophs?
utilize CO2 as their carbon source
Heterotrophs?
rely on organic nutrients created by other organisms (glucose)
Chemotrophs?
get their energy from chemicals
Phototrophs?
get their energy from light
What are the 4 types of bacteria? (trophs)
chemoauto
chemohetero
photoauto
photohetero
Chemoautotroph?
build organic macromolecules from CO2, using the energy of chemicals, obtain energy by oxidizing inorganic molecules like H2S
Chemoheterotrophs?
require organic such as glucose made by other organisms as their carbon source of energy (humans)
Photoautotrophs?
use only CO2 as a carbon source and obtain their energy from the sun (plants)
Photoheterotrophs?
get their energy from the sun but require an organic molecule made by other organisms as their carbon source
A bacteria that causes an infection in the bloostream of humans is most likely to be classified as what? (trophs)
chemoheterotroph because there is no sun involved and most likely uses some of our chemicals
What category best describes an organism that uses sunlight to drive ATP production but cannot incorporate CO2 into sugars?
photoheterotroph
In the lab, what is the most common solid medium that bacteria grow?
agar- firm transparent gel made from seaweed
Plating?
process of putting bacteria on a petri dish
Minimal medium?
contains nothing but glucose and agar
Wild type bacterium?
possesses all the characteristics normal to that particular species
Lawn?
dense growth of bacteria seen in lab petri dish
Plaque?
clear area in the lawn which are the result from death of bacteria and are caused by lytic viruses or toxins
What is the doubling time of E. coli?
20 minutes
Examples of slow growing bacteria?
bacteria in TB or leprosy
What factors determine doubling time?
availability of nutrients and other environmental factors
Auxotroph?
bacteria that cannot survive on minimal medium, needs the certain substance to live (arginine)
Oxygen metabolism is _____ metabolism.
aerobic
Bacteria which require oxygen are called ______.
obligate aerobes
Bacteria which do not require oxygen are called _______.
anaerobes
What are the three subcategories of anaerobes?
Facultative
Tolerant
Obligate
Facultative Anaerobes?
will use oxygen when it is around, but do not need it
How much more ATP can be made if oxygen is around?
16 times more
Tolerant Anaerobes?
can grow in the presence or absence of oxygen but do not use it their metabolism
Obligate Anaerobes?
poisoned by oxygen because they lack enzymes necessary for the detoxification of free radicals which form when oxygen is around
What is the main difference between respiration and fermentation?
respiration uses O2 while fermentation doesnt
What is anaerobic respiration?
glucose metabolism with electron transport and oxidative phosphorylation relying on an external electron acceptor other than O2, such as nitrate
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, how much will the rate of glucose consumption increase or decrease?
increase 16 fold
How do bacteria reproduce?
asexually, there is no meiosis, no gametes
binary fission- bacteria grows in size until it has enough for two and then splits
In prok, does reproduction increase genetic diversity?
no all of the daughter cells are identical
without meiotic recombination, there is no diversity
How is asexual production in Euk different than Prok?
Euk undergo mitosis, Prok do not
Bacterial population growth is ______.
exponential (log phase)
If 10 bacteria in log phase are placed in ideal growth conditions and the doubling time is 20 mins, how many bacteria will there be after 4 hours?
4 hours = 240 mins
240 mins = 12 cycles
answer: 10 * 2^12
Log phase vs Lag phase?
Log- bacteria experiences exponential growth
Lag- prior to log phase where cell division does not occur even if conditions are ideal
If growth conditions are ideal, why wouldnt cell division occur immediately?
during the lag period, bacteria are producing new cellular components so that they can divide, but they are not ready to divide
Will bacteria that are transferred from a culture that is in log phase to a fresh new culture show a lag phase?
no because all the gear necessary for population growth is ready
Stationary phase?
cells cease to divide because of lack of nutrients, cells may die
Carrying capacity?
max population at the stationary phase
If bacteria are grown in a medium with glucose as the main source of energy, when will the glycolytic pathway be more active: during the lag phase or the stationary phase?
the bacteria will use glucose during the lag phase to produce ATP and cell machinery so glucose will be abundant at this time, during the stationary phase the glucose will be depleted and glycolysis rate will have decreased
What are endospores?
Gram positive bacteria form endospores under unfavorable conditions, they have tough outer shells made of peptidoglycan and can survive harsh conditions, it is dormant until germination activates it
What is germination?
reactivation of endospores
When are bacteria most likely to form endospores?
during the stationary phase when times are bad for the bacteria, it is like hibernating, there is no reproducing
What are the three mechanisms of acquiring genetic material in bacteria?
Transduction
Transformation
Conjugation (most common)
What is transformation in bacteria?
pure DNA is added to a bacterial culture, the bacteria internalize the DNA in certain conditions and gain any genetic info in the DNA
What is conjugation in bacteria?
bacteria make physical contact and form a bridge between cells, one cell copies the DNA and transfers it through the bridge to the other cell
A key to bacterial conjugation is the _____ ______.
F(fertility) factor
Bacteria that have the F factor are _____ or _____.
male
F+
males transfer the F factor
Bacteria that do not have the F factor are _____ or _____.
female
F-
females receive the F factor and become male
If all cells in a population are F+, will conjugation occur?
no, it only occurs between male and female
Which cell will produce sex pili in bacteria?
the male cell contains the F factor that encodes the genes for pili
T/F
DNA transfer between F+ and F- occurs in one direction.
True
male to female
High frequency of recombination cell?
a cell with the F factor integrated into its genome
Will an Hfr cell undergo conjugation with an F- cell?
yes it contains the F factor
If bacteria contain only one copy of the bacterial genome, how can recombination occur?
when a Hfr cell conjugates with an F- cell and transfers a portion of the bacterial chromosome, the F- cell will have two copies of some genes
Conjugate mapping?
technique in the lab by allowing Hfr cells to conjugate in time intervals to see what order the genes are in
T/F
Most fungi are nonmotile, multicellular Prokaryotes.
False
Eukaryotes
Yeast are unicellular
Chitin?
rigid cell wall of fungi
also found in the exoskeleton of insects
T/F
All fungi are chemoheterotrophs.
True
Most fungi are either saprophytes or parasites.
Saprophytes?
Parasites?
Mutualists?
Sapro- feed off dead plants and animals
Parasites- feed off living organisms doing harm to the host
Mutualists- live in a symbiotic relationship where both benefit (lichen)
Most fungi are obligative aerobes. Yeast are ______.
facultative anaerobes
The method of nutrition used by fungi is called ______.
absorptive- digestion takes place outside the cell, molecules are absorbed across the cell wall
Can yeast use CO2 as a carbon source?
no they are chemoheterotrophs
Hypha in fungi?
long filament of cells joined end to end
Septate hyphae in fungi?
cells separated by walls called septae
Aseptate hypha in fungi?
cells joined together in a long tube where contents are shared
Haustoria?
hyphae that are specialized to digest and absorb nutrients in parasitic fashion
Mycelium?
meshwork of hyphae
Thallus?
large fungal structure which is visible to the naked eye, meaning body
Vegetative portion of thallus? Fruiting body?
Veg- involved in obtaining nutrients
Fruit- functions in reproduction, makes spores
ex. mushrooms
What is the difference is spores from fungi to bacteria?
fungi- may produce many spores, reproduction
bacteria- produces only one endospore, wait out bad times
T/F
Fungi reproduce both sexually and asexually.
True
Three types of fungal asexual reproduction?
Budding
Fragmentation
Spore formation
Budding in fungi?
new smaller hypha grows outward from an existing one
Fragmentation in fungi?
the mycelium can be broken into smaller pieces and develops into smaller mycelium
Asexual spore formation in fungi?
mitosis to generate many spores from one cell
Sporangia?
specialized structures of spores found elevated in stalk like hypha
Haploid? Diploid?
- cell species with only one copy of each chromosome
- Diploid has two copies (ex. humans)
In humans, _____ gametes are produced from diploid cells through _______. Fusion of two gametes results in ______ _____ which then divides through ______ to produce a diploid adult.
haploid
meiosis
diploid zygote
mitosis
Fungal adults are ______. (hap/dip)
haploid
Summary of life cycle of fungi?
haploid cells derived from haploid adults fuse to produce a diploid zygote which quickly enters meiosis to produce haploid cells again which will divide through mitosis to produce a haploid adult
Gametangia?
part of fungi specialize to reproduce asexually
Dikaryon?
cell with two nuclei occurs when fusion of gamete nuclei does not occur right after the two haploid gametes join together
In a bacterial medium, if a culture is cloudy, what does that mean? Clear?
cloudy- stationary phase
Clear- not growing or in lag phase
What prok process does not introduce new material but creates more?
binary fission
