**Bio: Microbiology (Bacteria, Viruses) Flashcards
Obligate intracellular parasite
Only able (obligated) to reproduce within (intra) cells Virus
Are viruses alive?
Not alive
Describe viral genome
A given type of virus only contains one type of nucleic acid (in contrast to a true cell which contains not only its genome but mRNA, rRNA, tRNA)
Varies a lot!
DNA or RNA, single or double stranded, linear or circular
Viruses carry very few genes and so it has adaptations to take this into account:
How can virus encode more than 1 protein in a given length of genome?
Rely on host-encoded proteins for transcription, translation, and replication
Virus can encode more than 1 protein by having multiple reading frames
*Where is virus genome? What is the genome made of?
In capsid (protein) head The genome is made of DNA or RNA (nucleic acid)
What is an envelope? Naked virus
What can enveloped viruses infect?
If antibodies to a viral capsid protein are ineffective in blocking infection, what might this indicate about the virus?
Some animal viruses also possess an envelope that surrounds the capsid.
Enveloped viruses can ONLY infect animals not humans
This is a membrane on the exterior of the virus derived from the membrane of the host cell. It contains phospholipids, proteins, and carbs from host membrane and proteins encoded by the viral genome
Enveloped viruses acquire this through budding through the host cell membrane
Naked virus = Virus without envelope
This may indicate the virus is enveloped, so the Ab cannot reach its epitope on the capsid surface in infectious virus
Is viral infection specific?
Yes! A virus binds to a specific receptor on the cell surface as the first in infection
Attachment or adsorption
Eclipse
Attachment or adsorption - binding to exterior of a bacterial cell wall
Eclipse or penetration - injection of the viral genome into the host cell in a process
*Lytic cycle
What genes transcribed and translated (early vs late genes)? Disadvantage?
- Transcribe and translate the viral genome
a) all cellular energy goes toward replication of viral genome
b) Free pool of dNTPs
Early genes -> hydrolase (destroy host cell genome), capsid proteins - Replicate the viral genome
a) assembly with capsid - Lysis of host and release of new viral particles
a) Late gene: lysozyme
enzyme poke holes in the bacterial cell wall
releasing 100 progeny viruses, which can begin another round of the cycle
Disadvantage -> kill host that you need to divide
Tissue tropism
Viruses have specific affinities for certain issues
Attachment/adsorption is tissue specific
Lysogenic Cycle
Prophage? Lysogen?
What is a consequence that happens during excision?
What is transduction?
- Integrate viral genome and host genome and is now referred to as prophage and the host is now called a lysogen
- The prophage is silent and phage genes blocked by phage protein due to phage-encoded repressor protein (repressor gene from virus) that binds to specific DNA elements in phage promoters (operators) - Normal host activity, including reproduction - every time the host cell reproduces itself, the prophage is reproduced too
- Excision and lytic cycle - eventually the prophage becomes activated (stressed by heat, pH, salt, detergent, lack of sleep, upcoming exams) and it now removes itself from the host genome (called excision) and enters the lytic cycle
*When viral genome activates, excising itself from the host genome, it may take part of the host genome along with it so in subsequent infections, the virus will integrate “stolen” host DNA -The presence of new DNA will become evident if it codes for a trait that the newly infected host did not previously have, such as the ability to metabolize glucose
This process = transduction
What are two ways virus can enter cell?
Bacteria have cell wall so virus inject genetic material inside
Other cells endocytose virus
Productive Cycle
Productive Cycle similar to lytic cycle but does not destroy the host cell bc the enveloped viruses exit cell by budding through the host’s cell membrane, becoming coated with this membrane
Positive sense RNA
What does it code/carry/both? How does that protein work?
Viruses (dont memorize, just understand what enzymes it makes and needs)
What does it code for - 2 things ?
Only RNA goes into host
Codes for RNA dep - RNA polymerase but doesn’t need to carry it
Can make proteins directly from (+) RNA unlike (-) RNA
A (+) RNA virus, with a single-stranded RNA genome -> A piece of single stranded viral RNA which serves as mRNA
The viral genome acts like mRNA and host ribosomes begin to translate it
*Makes viral proteins (enzymes, caspids) including RNA replicase = RNA dependent - RNA polymerase (which makes complementary RNA strand by using a (-) strand intermediate as a template)
This RNA replicase replicates the RNA and makes complementary (-) RNA strand then RNA replicase can be used again to make more (+) RNA which can be packaged up as new virus
Negative sense mRNA
What does is carry/code/both?
Must encode AND carry RNA dep RNA polymerase (RNA replicase)
Must have both: RNA (which codes for RNA dep RNA polymerase) and the enzyme RNA dep RNA pol (RNA replicase) itself so that it can pass on genetic material for RNA dep RNA polymerase
Retroviruses
What does it encode?
examples
Why this virus is problematic for us
Do retroviruses have to carry, code or both for reverse transcriptase?
What happens to viral genome once integrated into host DNA?
Positive sense (+) RNA lysogenic Must encode reverse transcriptase
RNA dep DNA polymerase/reverse transcriptase to turn pos sense RNA into ssDNA, then replicate using host DNA pol to make dsDNA, then integrase to insert into host genome (make provirus) then two things happen
a) transcribe and translate using host enzymes to make viral proteins
b) transcribe only using host RNA polymerases to make more (+) RNA ]
Problems with this virus:
- permanently inside host genome
- Rapid mutation (error rate in RNA synthesis is much higher than DNA synthesis bc mxn to proofread and correct errors in DNA synthesis
AIDS, HTLV
There are (+) viruses that undergo lysogeny, so they integrate into host genome as proviruses
In order to integrate into our double stranded DNA genome, a viral genome must also be composed of double-stranded DNA
Since these viral genomes enter the cell in an RNA form, they must undergo reverse transcription to make DNA from an RNA template
(lower yield) Double-Stranded DNA viruses
What do they encode? (more in textbook biochem pg 144)
often encode enzymes required for dNTP synthesis and DNA replication
This is because host cells will only make dNTPs in preparation for replication. If 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
Prions Characteristics, what are the two categories?
Misfolded version of protein that already exists
No DNA or RNA, no membranes, no organelles, very small, extremely stable
Two categories = Normal prions (good) and mutant prions (bad like made cow disease - Spongiform encephalopathies)
Bad prions can also be inherited if mutation in sperm or egg (genetically linked), bad prions lead to degeneration of nervous system
Infectious proteins -> when normally folded protein comes into contact with prion, the prion acts as a template; the shape of the normal protein is altered and it too becomes infectious
How do mutant “Bad” prions come about?
What do they do to proteins?
Mutant prions accumulate and lead to cell death
They have high affinity for central nervous system and change good prions into bad prions, leads to cell death, no cure
a) spontaneous mutation in gene which ends up coding for mutant “bad” prion
b) can be inherited
c) transmission by consumption
What are viroids? What does it lack? How does it spread? What does it do?
virus-like, circular single stranded positive sense RNA, lack capsids
Spread through mouths of bugs and most diseases caused by viroids are found in plants, The only human disease linked to viroids is Hepatitis D but it can only enter hepatocytes if it is contained in a capsid with a binding protein and since viroids do not have capsids, successful Hepatitis D infection required coinfection with Hepatitis B, from with derives its capsid.
*Can hijack cell’s DNA dep RNA polymerase and direct it to read RNA templates
What is the main difference between eukaryotes and prokaryotes?
Who has ribosomes?
Prokaryotes lack membrane bound organelles (since ribosomes don’t have membranes, prokaryotes do have these)
What kind of genetic material do prokaryotes have (single/ double stranded? shape?)? And that one (you know what I’m talking about) important?
Prokaryotes have genome which is a single double stranded circular DNA chromosome
They also have a plasmid which is a circular piece of double-stranded DNA which is much smaller than the genome
Plasmid important bc they encode advantageous gene products and orchestrate bacterial exchange of genetic information, or conjugation
Conjugation done by using the prokaryote’s _____
Plasmid
Bacterial shape:
Cocci
Bacilli
Spirochetes or spirilla
Cocci -> circular
Bacilli -> rectangle
Spirochetes or spirilla -> spiral
What structural features/membranes do bacteria have? What is the outer one made of?
Have lipid bilayer (like us) and outside of that a cell wall made of peptidoglycan and provides support for cell so that it does not lyse due to osmotic pressure
Explain gram neg and gram pos, how do they stain? Which is more antibiotic resistant? Which would be more susceptible to lysozyme? What do they secrete?
What is the difference between endotoxins and exotoxins?
Gram-positive stain strongly (dark purple) and Gram-negative bacteria stain weakly (a light pink)
Gram-pos -> have thick peptidoglycan layer outside of the cell membrane and no other layer
Gram-neg -> have thinner layer of peptidoglycan in the cell wall but have an additional outer layer containing lipopolysaccharide, the space between the two layers is called the periplasmic space which can hold enzymes which degrade antibiotics
Lysozyme hydrolyzes linkages in peptidoglycan to weaken the cell wall and the peptidoglycan in gram-pos cells is more accessible, since these cells do not process an additional outer layer so gram pos lyse more easily
Both gram pos and neg secrete exotoxins (very toxic) to help the bacterium compete with other bacterial species
Also, endotoxins are normal components of the lipopolysaccharide layer (the unique outer membrane) of Gram-negative bacteria. Endotoxins aren’t inherently poisonous but can cause septic shock when too many bacteria die and it is released
Gram neg more antibiotic resistant bc periplasmic space that allows bacteria to load with digestive enzymes that can attack antibiotics before they get inside
Endotoxin exclusive to gram neg bc outer lipopolysacharide membrane
Is Flagella for prokaryotes same as Eukaryotes?
Monotrichous
Ampitrichous
Peritrichous
What is basal unit, hook, filament? *But the most important thing to remember is the difference between this prokaryotic flagellum and the eukaryotic one
Flagella for Prokaryotes different than that of Eukaryotes
Monotrichous - flagellum located at only one end
Ampitrichous - flagellum at both ends
Peritrichous - multiple flagella
The basal unit, hook, filament are aspects of the flagella
*The prokaryotic flagellum is different from the eukaryotic flagellum because the eukaryotic one has 9+2 arrangement of microtubules
Chemotaxis, how does it work/ what is it?
What does it detect?
Bacteria motion can be directed toward attractants, such as food
Chemoreceptors on the cell surface that bind attractants or repellents and transmit a signal that influences the direction of flagellar rotation
The response of flagellar rotation to chemical attractants is not dependent on absolute concentration but to a change in concentration over time, thus as the bacterium moves through the solution it is able to detect whether moving toward or away (like hot and cold game)
Sex pili
special pili attaching F+ (male) and F- (female) bacteria which facilitates the formation of conjugation bridge
Mesophile
Love Medium temp
Thermophile
Love Hot temp
Pyschrophile
Love Cold temp
Bacteria can be characterized by their \_\_\_\_ source and \_\_\_\_\_ source Photo Chemo Auto Hetero
carbon source and energy source
Photo and chem is where get ultimate energy from and auto vs hetero is where get carbon chains from
Photo -> energy source sun
Chemo -> energy source rxns to get ATP, E from chemicals
Auto -> make own carbon chains from CO2
Hetero -> eat other critters
Chemoautotroph
Chemoheterotroph
Photoautotroph
Photoheretotroph
Chemoautotroph -> Deep sea vent bacteria
Chemoheterotroph-> animals
Photoautotroph -> plants, photosynthetic bacteria
Photoheretotroph -> carniverous plants
What is a plaque in a petri dish?
Plaque is where there is clear area in lawn, so basically bacteria death
*Auxotroph
What does arg- mean? What does lac- mean?
A bacterium which cannot survive on minimal medium because it can’t synthesize a molecule it needs to live
ex. a bacterium which is auxotrophic for arginine means it won’t form a colony when plated onto minimal medium and if the medium is supplemented with arginine a colony will form, this type of bacterium is denoted
arg-
lac- means can’t metabolize it
amino acids - = can’t make it
sugar - = can’t metabolize it
What happens to Obligate anaerobe when O2 present? When O2 absent?
O2 absent:
Survive
O2 present:
die
Flash card said before: (error?)
O2 Present
-use it
-survive
O2 Absent
-die (only one out of others that does this)
What happens to Facultative anaerobe when O2 present? When O2 absent?
O2 Present
- use it
-survive
PREFERS WHEN O2 PRESENT (duh bc cell resp gives you more ATP than 2 ATP from fermentation) There are cases where have anaerobic resp and still do ETC, PDC, krebs, but have diff final e- acceptor
O2 Absent
- ferment
- survive
What happens to Tolerant anaerobe when O2 present? When O2 absent?
O2 present:
- doesn’t use it
- doesn’t die
O2 absent:
- ferment
- survive
What happens to Obligate anaerobe
when O2 present? When O2 absent?
O2 present:
die bc lack enzymes to detoxify of free radicals cause by O2
O2 Absent
- ferment
- survive
What is conjugation?
Bacteria do not reproduce sexually, they do possess a mxn termed conjugation for exchanging genetic information
What is lag, log, stationary, and dearth phase of bacteria reproduction?
Lag phase is prior to exponential growth
so if put bacteria in medium it won’t start growing right away bc during this time biosynthetic pathways are very actively producing new cellular components so that cells can begin to divide
They need to make the components needed for cell division like dNTPs
If 10 bacteria in log phase are placed in ideal growth conditions and the doubling time is 20 minutes, how many bacteria will there be in four hours?
Will bacteria that are transferred from a culture that is in log phase to a fresh new culture show a lag phase?
4 hours = 240 min so the bacteia will divide 12 times so one bacterium will produce
2^n
2^12
These bacteria will not show a lag phase as they already made gear necessary to divide
endospore
What forms it? Why are they formed? Is this a method of reproduction?
Gram pos bacteria can form endospores (have thick external shells comprised of peptidoglycan)
bacteria responsible for Botulism
Endospores can survive temps above 100ºC
They are formed during stationary phase to live through the bad times
only one bacteria can make one endospore so this is not a method of reproduction
Transduction
It is transfer of genomic DNA from one bacterium to another by lysogenic phage (virus)
Transformation
Transformation refers to if pure DNA is added to a bacterial culture, the bacteria internalize the DNA in certain conditions and gain any genetic information in the DNA
Have source of DNA, can come from dead bacteria, and force a bacteria to take it up by electrocuting it, any form of stress etc, basically force bacteria to take up random nearby DNA
Conjugation
Where does the genetic material go (from where to where? ) What does it transfer? There are 2 things that can happen, what are they?
Allows bacteria to exchange genetic information
Bacteria make physical contact and form a bridge to other cell
F+ bacterial are male and transfer the F plasmid (extrachromosomal element) to female F-
The F factor is a single circular DNA molecule
2 things can happen in conjugation:
a) plasmid from F+ goes to F-
b) Or F plasmid joins the OG bacterial genome which makes Hfr (high frequency recombination) and then that part of bacterial genome is replicated (could also take some of OG genome with it) and brought to F- female bacterium w/ use of pili
Male produces sex pili and pili contact the female to make a conjugation bridge
The F factor is replicated and transferred from the F+ to F- cell
Even though the F factor is a extrachromosomal element, it does sometimes become integrated into the OG F+ bacterial chromosome through recombination and then called Hfr and this F factor DNA that is now in the chromosome can be replicated and do conjugation (some of the OG DNA can also be transferred to female bacteria)
When the F- gets the portion of the bacterial DNA, it will have 2 copies of some genes, and recombination can occur b/w the 2 copies
Parasitic bacteria can be obligate or facultative
Obligate -> need host cell to replicate
Facultative -> can live and replicate inside or outside of a host cell
Obligate intracellular parasite
Virus
*Obligate intracellular parasite
Virus
Anaerobic Respiration
what can it do? What is different??
-Still do ETC, krebs, PDC
but has a different final e- receptor
What happens to bacteria when add more nutrients during stationary phase? What happens when put bacteria in stationary phase in new medium (diff that OG medium)?
Bacteria reproduce by binary fission:
You can rescue bacteria in stationary phase by giving it more nutrients, and if tale bacteria from stationary phase and put in new medium (ex. Has glucose now which it hasn’t seen in while) then start with lag phase again, but if put in plate with same medium then it continues log phase
Transfection
Make a eukaryotic cell to take up DNA but same process as transformation
*IMPORTANT
How does penicillin bind to enzyme active site
What is a irreversible inhibitor?
Penicillin COVALENTLY (IRREVERIBLY, PERMENANT) binds to enzyme active site (no matter where binds = suicide inhibitor Permanently off
