EK Microbiology COPY Flashcards
“cocci”
circular bacteria, sphere
ex. streptococcus refers to round like shape to it!
“bacilli”
rod shaped bacteria
ex. e.coli famous rod shape but exception not with last name bacilli, but does have this apperance thats an important exception* very often tested
** think bascillus in Harry Potter, killed with a rod through the head- so rod shaped bacteria**
spirilli
spiral shaped bacteria. tells us spiral like spagetti, squiggle line.
ex. Syphilis an std has this cork screw shape, uses cork screw shape to its advantage once it happens to pass by if there is some nic in the skin, will take that cork screw and screw into tissue make that infection. Imagine in mind says has to be doing that, three different shapes expected to know
flagella
“______” trichous, this ending refers to fact bacteria does have a flagella! a couple of different ways to describe flagella, so if you were to see monotrichous means only has one flagella
can be: monotrichous, amphi trichous, peritrichous
mono- means one flagella
amphi- arrangement of flagella either end of bacteria
peri - many many flagella all over the place, all over bacteria
prokaryotic cells
Unicellular
Lack a nucleus & membrane bound organelles
Two classes of prokaryotes: archaea and eubacteria
archaea
Ancient prokaryotes, distinct from bacteria
Some biochemical mechanisms are eukaryotic-like (transcription, translation)
Some but not all live in extreme environments
Thermophiles – grow and thrive in very hot environments (e.g., boiling ocean vent)
Halophiles – can grow in saturated salt
Methanogens – generate methane during their growth
Less is known than about eubacteria
eubacteria (bacteria)
DNA is double stranded circular chromosome
Transcription and translation occur in the cytoplasm
Peptidoglycan cell wall: sugar and peptide polymer
Ribosomes similar to eukaryotic ribosomes but smaller
One or more plasmids – circular DNA molecules, often confer antibiotic resistance
Roughly 1/10 size of eukaryotic cells; 10× bigger than virus
Observable with light microscope
Targets of antibiotics are ribosome and cell wall synthesis
Basal unit connected to hook, hook connects basal unit to filament, reverse spin of filament to go counterclock wise in opposite direction*
two diff arrangements for cell wall and membrane gram positive or gram negative
bacterial shapes
Bacteria can be classified by shape, gram-staining, and metabolism
Shapes are rod (bacillus), sphere (coccus), or helical (spirilla, spirochete)
gram staining
Gram stain is retained by peptidoglycan wall
Gram positive bacteria are stained purple
Gram positive bacteria: thick peptidoglycan wall
Gram negative bacteria: very thin peptidoglycan wall, outer membrane
Gram positive bacteria are vulnerable to antibiotics that target cell wall synthesis
gram negative bacteria
Very thin peptidoglycan wall, outer membrane
LIGHT PINK COLOR b/c cell wall a lot thinner, because a lot thinner cannot retain as much as hte stain as gram positive would be able to so its lighter in color as a result
Gram positive bacteria are vulnerable to antibiotics that target cell wall synthesis
cell wall is btw two membranes outer membrane and inner membrane, so one thing that happens with gram negative bacterium tend to be more antibiotic resistant*** a lot harder for antibiotic to make it through two membranes we have shown here* so if you are readin a passage tells you particular pateint has bacteria infection given antibiotics not working what is the reason for this?….. describe scenario with gram negative or gram positive situation, it will be gram negative that most likely causes that particular infection because tends to be more antibitoic resistant*-
to remember=think did the antbotics works “NEGATIVE” so gram negative thin wall pink
space in btw membranes calld periplasmic space contains enzymes that say an antibiotic happens to get in well those enzymes happen to break down that antiobitc so no effect on particular bacteria- so a couple raesons why can fight off antibiotics!
gram positive
Gram positive bacteria are stained dark purple
Gram positive bacteria: thick peptidoglycan wall
Thick cell wall keeps dye stuck in cell, within cell wall molecule peptidoglycan is found in cell wall to rpovide it with strength and stability
Cell wall surrpounds cell membrane, helps prevent cell from taking on too much water and what lysozyme will punch holes into to make sure can’t regulate osmosis take on too much water and break open
aerobes and anaerobes
Aerobic growth uses oxygen for metabolism
Anaerobic growth occurs in the absence of oxygen
Obligate aerobe (bacteria) requires oxygen and cellular respiration for growth, use it and survive bound to lifestyle of living with oxygen, if oxygen not there will die off
Obligate anaerobe utilizes anaerobic fermentation, does not grow in oxygen; in this case they prefer to live with oxygen absent and can only live with oxygen absent, if oxygen is prsent they will die off! ex bacteria in gut mainly obligate anaerobe, they are living in lumen where food passing through** not physically living in cells that make up lining so yes oxygen in cells supply with oxygen they need but in lumen by time food gets down to gut that is why they are obligate anerobes****
Facultative anaerobe can grow in aerobic or anaerobic conditions; in case oxygen is there can actually use it!!! and still survive! so use it and still survive, but prefer to ferment adn survive without oxygen! much rather be fermenting “think faculty make it work”
tolerant anaerobe- oxygen doesnt kill them but not using it; so doesn’t use it doesnt kill them
heterotrophs and autotrophs
Heterotroph – consumes organic matter for food
Most bacteria are heterotrophs
Autotroph – synthesizes its own food from inorganic substances (e.g., CO2, H2S, NH3)
Photosynthetic autotrophs use light to generate energy
Chemosynthetic autotrophs use chemical nutrients for energy
Some bacteria are photosynthetic autotrophs (e.g., cyanobacteria)
symbiosis and parasitism
Symbiotic relationship: bacteria (symbiont) lives together with host
Three types of symbiotic relationships
- Mutualism: both organisms benefit (e.g., bacteria in our gut synthesize vitamins B, K)
- Parasitism: one organism benefits at the other’s expense (e.g., tuberculosis)
- Commensalism: benefits bacterium, neutral for host
Opportunistic infections: normally harmless bacteria cause disease in certain situations
• Example: intestine penetrated, mutualistic bacteria enter and infect abdominal cavity
bacterial toxins
Exotoxins – secreted proteins can cause pathology in absence of bacteria
Endotoxins – toxins that are integral part of bacterial membrane
*some bacteria cause symptoms because they secrete proteins becuase they are toxic, they are secreted by bacteria and then cause all kinds of symptoms like coughin in the host*
other bacteria that have endotoxins meaning proteins that cause symptoms are actually part of the bacterial membrane, not released from host, certainly aggregavate host part of host cell; if bacteria causing symptoms becuase of endotoxin attached to bacteria, if kill bacteria symptoms end, if having bacteria releasing some exotoxin you cna kill the bacteria and the person will still be very sick for a while*** ex of that is whooping cough, bacteria causes whoopign cough releases toxin that causes ppl to cough for months and months can get rid of bacteria completley done and person will still have horribel cough for months becuase of exotoxin, thsi is why if traeated with antibitoics immediately before they even have symptosm then antibitoics will ehlp, but realisatically until ppl do not cough heavily because they do not know they are infected- why this vaccine is so so improtant***
bacteria reproduction
Bacteria reproduce asexually by binary fission, forms a colony; basically like mitosis
Can undergo fission each ~20 min under optimal conditions
Chromosome replicates, septum forms between cells
Growth kinetics have (1) lag phase, (2) exponential growth, (3) saturation, and (4) death
- Lag phase: bacteria acclimate to nutrients in surroundings, adapt gene expression
- Exponential phase: bacteria double robustly
- Saturation phase: growth subsides as bacteria compete for limiting nutrients
- Death phase: bacteria die from lack of nutrients and accumulated toxic waste products, waste products start killing cells*
ALL ASEXUAL could be sponatenous mutaiton but no genetic change built in! in contrast with the processes with dna transfer and sexual reproduction: 3 processes that alter dna of bacterial cells: transformaton, transduction and confirmation
bacteria genetic diversity
Bacteria can mutate spontaneously
Rapid growth affords significant genetic diversity
Can incorporate DNA by recombination (see below)
bacteria can exchange DNA by 3 mechanisms:
Bacteria can exchange DNA by three mechanisms:
Transformation: uptake of DNA from external environment
Transduction: phage transfers bacterial genes from one cell to another
Conjugation: transfer of DNA via mating
- transformation
Transformation: uptake of DNA from external environment
In nature, DNA released from lysed bacterial cells or elsewhere can be taken up
In the laboratory, can force bacteria to take up plasmids
- transduction
Transduction: phage transfers bacterial genes from one cell to another
Bacterial DNA can be incorporated during imprecise prophage excision (specialized)
Bacterial DNA can be mistakenly encapsulated by phage (generalized)
- conjugation
how bacteria does want to gain any genetic variability!!!
Conjugation: transfer of DNA via mating
Conjugation is sexual reproduction
Requires a conjugative plasmid that carries a gene producing a pillus
F and R plasmids: F = Fertility, R = Resistance
F+ bacteria (male) mates with F– bacteria (female)
F+ makes pillus and transfers plasmid DNA to recipient
Integration of F plasmid to chromosome allows transfer of chromosomal genes
F plasmid integrant = Hfr strain (High frequency recombination)
R plasmids can spread antibiotic resistance
one where there is a bridge! where dna gets passed over the bridge from one cell to another*
the plasmid has the genes required to build the mating bridg,e but there can also be other genes on F plasmid, most common example is gene for antiobitoic resistance, so if ever get question or passage abotu soemone who is becomign resistant to a certain antibtoic answer will be= conjugation, main mechnaism for antiobiotic resistance spreading in patients**
endospores
When growth conditions are unfavorable, bacteria can form an endospore
Endospore forms within bacterium and is released by breakdown of the cell wall
Endospore is tough and can survive adverse conditions (e.g., poor nutrients, heat, UV)
Dormant endospore can persist for long periods of time
Endospore will germinate when conditions for growth are good
Examples of bacteria that form endospores: anthrax, tetanus
bacterial flagellar movement
Bacteria often use a flagellum for movement
Flagellum has three components: filament, hook, basal body
Filament is hollow tube made up of flagellin protein subunits
Hook is a curved structure that connects the filament to the basal body
Basal body is composed of rings that anchor the flagellum to the cell wall and membrane
Basal body contains a motor protein that is driven by protons
Chemotaxis = movement of cell toward or away from a chemical cue (like food or toxin)
general characteristics of fungi
Fungi are eukaryotes VERY VERY DIVERSE
Share properties of complex eukaryotes (organelles, introns, linear chromosomes)
Cell wall made of chitin (nitrogen-containing sugar)
Most fungi are multicellular (e.g., molds and mushrooms)
Some fungi are unicellular (i.e., yeast)
Fungi are heterotrophs: require carbon energy from outside sources
Fungi are typically saprophytes: consume dead organic material, so they have asked before fungi are X….. they are saprophytes becuase they consume dead organic material
Most are aerobic, some are facultative anerobes (e.g., yeast)
Can form filamentous stalks called hyphae
Mycelium is a bunch of hyphae
Fungi can be helpful (antibiotics, alcohol) or pathogenic (athlete’s foot)
very varied category- can reproduce asexually or sexually
fungi life cycle
Fungi have two life forms: haploid and diploid
Typically grow as haploids
Haploid = 1 copy of each chromosome (1n)
Haploid fungi reproduce asexually by budding or binary fission
Budding is the formation of a smaller daughter cell from a mother cell
In adverse conditions, fungi undergo sexual reproduction and become diploids
During sexual reproduction, two haploid cells fuse to form a diploid
Diploid = 2 copies of each chromosome (2n)
Diploid cells undergo meiosis and yield 4 haploid spores
Spores can survive adverse conditions before germination
viruses
Viruses are acellular
Need host cells for reproduction = are obligate intracellular parasites: means they can only reproduce inside of a host* can’t complete their life cycle* in a nutrient broth vs why bacteria*
NOT TECHNICALLY ALIVE, but everything else is alive*
Smaller than bacteria (need an electron microscope to visualize virus)
Can pass through filters that catch bacteria, because so tiny
Contains DNA or RNA, not both
DNA or RNA can be single-stranded or double-stranded- very diverse, usually DNA or RNA surrounded by protein coat claled a capsid* the protein coat around the virus
Capsid is the external protein coat
Some viruses also have an outer membrane envelope
Envelope is derived from host cell membrane and contains viral proteins
Single virus particle is called a virion
viral vs bacterial distinctions
Bacteria can grow in purified nutrient broth, virus cannot
Virus requires host cells to infect and propagate itself
Bacteria is susceptible to antibiotics (ribosomes, cell wall)
Virus not affected by antibiotics (no ribosomes, no cell wall)
Virus can pass through filters that trap bacteria (virus is smaller)
bacterial viruses
BACTERIOPHAGES
Bacteriophages (phages) are viruses that infect bacteria
Capsid coat has a head and tail
Head contains nucleic acid
Tail attaches to bacterium and injects nucleic acid
After injection of DNA, capsid remains outside of cell
If protein is labeled with radioactive sulfur and DNA is labeled with radioactive phosphorus, the signal for phosphorus will end up inside the bacterial cell and the signal for sulfur will remain outside (Hershey-Chase experiment).
After entering bacterium, 2 alternative pathways for growth: lytic and lysogenic
lytic growth
In lytic growth, phage enters cells and replicates
Uses host machinery to synthesize viral components
Viral components self-assemble and form mature virions
Lytic enzymes cause bacterium to burst, releasing phages
Burst can release hundreds or thousands of phages
Phages that only reproduce via lytic growth are called virulent
Punches a hole (plaque) on a bacterial lawn
lysogenic growth
In lysogenic growth, phage DNA integrates in bacterial chromosome
Integrated phage DNA is called prophage
Prophage replicates along with host chromosome
In adverse conditions (poor nutrients, stress) prophage will enter lytic cycle
Occasionally, prophage will spontaneously enter lytic cycle
Phages that reproduce by lysogenic cycles are called temperate
receptors + virus entry
Coat proteins of the virus determine which cells can be infected
Coat proteins bind to a cell surface receptor to enable viral entry
Tissue- and species-specificity of infection depends on host receptor expression
Can use different receptors in different tissues
viral life cycle
Virus binds and gains entry to cell via a receptor
Some viruses bind to receptor and fuse with membrane directly
Some viruses bind to receptor, are endocytosed → into endosome
Then must escape endosome
Within cell, capsid opens and releases nucleic acid and proteins
Nucleic acid enters nucleus and is replicated
Viral mRNAs are synthesized
Viral proteins are produced on host ribosomes
Virus assembles and is released from cell by lysis or budding
Virus infection may inhibit host DNA, RNA, protein synthesis and damage the cell
retroviruses
Retrovirus is class of RNA virus (e.g., HIV)
Contains an RNA to DNA polymerase = reverse transcriptase
RNA is reverse-transcribed to ssDNA and then dsDNA
DNA is stably integrated to host chromosome
Integrase is enzyme for integration
Virus can remain dormant for a long time
Ability to integrate into DNA makes retroviruses possible route for gene therapy
REMEMBER WE DO NOT HAVE REVERSE TRANSCRIPTASE, HIV so hip brings its own
anti-HIV and antiviral drugs
Virus growth not affected by antibiotics
Anti-viral drugs target certain steps of life cycle
Some antiviral drugs often block nucleic acid synthesis (e.g., AZT for HIV)
Other antiviral drugs affect viral entry or assembly
viroids
Smaller than viruses, another subviral particle
Contain circular RNA (circular genome) but no protein coat, no capsid meaning must be coinfected with something else to have an effect, if take hep D virus a type of viroid by itself doesnt do anythign but if coinfected with Hep B virus causes it to have silencing effect on liver cells****
Known to cause disease in plants
virus like particles!
DO NOT CODE FOR PROTEINS do not effect humans
prions
Misfolded, infectious proteins- ppl really questioned whether proteins could be infectious, very mysterious do not carry dna or rna so how are they making ppl sick, the answer is sometimes if have misfolded protein its like interlocking one really mishapen protein can cause another one to misfold cause anothe rone…. get big clump or tangle of proteins, prions diseases are associated with neurodegenreation clumps of proteins or tangles of proteins in neurons, hallmark of disease*
Convert other proteins to misfolded form
Contain no DNA or RNA
Can cause neurodegenerative disease (e.g., Creutzfeldt-Jakob disease)
no organelles, no membrane, very small***
dangerous b/c = extremely stable****
very easy to misfold protein, if change temperature, pH salt concentration enough to alter protein folding, a prion can withstand those high temperatures, extreme pHs, and strong salt solutions so very hard to treat, no cure if happen to get one of these bad prions here!
is a virus living?
A VIRUS IS NOT LIVING! the reason we do not consider it living is to reproduce it has to rely on something else to reproduce and gets its energy from some other thing!
when does relying on a particular host to carry out reproduction and energy source= ends up harming a the host, therefore they are obligate intracellular parasites
obligate= bound to paritcular life style having to always rely on someone else to reproduce to get its energy, in the process harms that particular host!
virus only made of two things
- protein
- nucleic acid inside protein
bacteriophage is the most common virus, not a bacteria, virus that infects bacteria!!!
one of the most commonly studied virus out there bacteria is pretty cheap do not take up a lot of room so great source to do a whle bunch or research experiments on, if capsid what are the building blocks whole bunch of amino acids strung to gether to form that particular capsid there, within capsid where we find genome where nucelic acid is found, viruses are intersting used to see genome being RNA or DNA, CANNOT BE BOTH AT HTE SAME TIME THOUGH**
viral life cycle
2 basic steps
- attachment, adsorption- HIGHLY specific process, ppl can be immune to certain viruses because they do not have hte receptor there** like some ppl have no receptor for HIV so can enver have it
- not yet infected
- virus then squats down and injects genome into particular host- can call it injection or penetration
- once genome is in there IT IS INFECTED! be careful, mcat can give you thsi whole question stem about injection process but then ask you if during adsorption is the particular bacteira infected- answer no*
- if says adsorption one little word can make the question wrong, not infected during attachment or adsorption, you are infected with penetration!
- all viruses follow these steps, depending on life cycle there will be some differences frm this point onward*
lytic life cycle 2
- transcribe and translate the viral genome
- early genes: hydrolase, capsid protein
- hydrolase: destroys host cell genome= if get rid of host genome no host genome to transcribe or translate, all energy will be directed toward viral transcription or transaltion, so viral dna cannot be included, so is not htat it will not be included but the reason why you want ot also destroy it besides want to direct all energy toward production of virus is that in order to be able to replicate, what the virus wants to do, wants to be able to make more viruses to g out and infect ven more cells, in order to replicate you have to take a template and after that template create new genome, problem if this aprticular bacteiral not going through reproduciton won’t have particular nuceltides just hanging out so instead of having to wait days, weeks months or years, chop up bacteria genome becuase genome ocmposed of whole bunch of nuceltoides*
rason #1= all cellular energy is directed toward hte production of viral proteins
reason #2= create a pool of free dNTPs that can now be used to replicate viral genome
reasons why want ot use that hydrolase!
lytic life cycle 3
STEP 2= replicate the viral genome
already been makign capsin proteins, now will immediately assemble with those capsid proteins so that nucelci acid will be housed safely behind capsid, automatic second finish replication you will assemble with capsid proteins its automatic*
step 3- last step, lysis of host and release of new viral particles (what you created) can then go and infect another host there*
virus will get out of particualr bacteria by producing lysozyme, which PUTS HOLES IN BACTERIAL CELL WALLS* cell wall v rigid structure, so besides providign with support it actually prevents the cell from taking on too much water through osmosis, so if you now punch these holes in cell then that particular bacteria takes on more and more water until point it ruptures when it ruptures all those viral cells created go to new bacteria and new host*
lysozyme
do not want to do this step one, its the very last thing to produce once did all that replication then want to lyse host
enzyme that puts holes in bacteiral cell wall
we find it in our tears or saliva, if get any bacteria into eye or mouth from food eating that enzyme puts holes in that bacteira cell wall and can kill off bacteria*
why when drop sandwich you are totally ok because of that lysozyme
lysogenic cycle 2
Issue: lyse host so if that is yoru last host can be in troubel if virus nothing lef tot replicate, so another cycle can enter into is lysogenic
once particular genome in bacteira, viral genome will intrgrate itself into host genome so steps:
- integrate viral genome with host genome, could call this a provirus or prophage, means virus integrated itself into host genome** currently in lysogenic cycle***
- normal host activity, including reproduction- we want to remain silent within host genome, so one thing they will want to produce early on in transcription/translation they will code for repressor proteins!!! which wil block transcription adn translatioN! taht way will not make that lysozme and will not lyse host, so repressor viral protein*** whole purpose of this so can remain silent, once bacteria undergoes reproduction it will also get reproduced as well*
- excision and lytic cycle, so removes viral genome frm particular host and enters lytic cycle, meaning we now have to have access to that enzyme lysozome, will require the removal of that particular repressor**- requires the removal of resspor- triggered by stress!!
if say provirus/ prophage….
means virus integrated itself into host genome** currently in lysogenic cycle***viral genome
ex cold sore
repressor just a protein, talked about protein folding and how you can misfold a protein, if repressor protein will be subject to all those things that can misfold it- light, different chemicals, anytime this particular host will be stressed out**
cold sores appear around lips, when not feeling good they usually appear, temperature will be slightly elevated to fight a particular infecton, as that temperature rises within the body we don’t liek to be at different temperatures want to matain human body temp, misfolds protein, removes repressor and ltyic cycle takes place!
excision in lysogenic cycle (step 3 of cycle)
step 3- sometimes takes not only viral genome but bacterial genome as well, when that happens replicate that viral genome meaning some of that bacterial genome will also get replicated and passed on in that particular virus, when it does this takes bacteria genome with it, one of the ways how bacteria gains genetic variability asexual reproduction is just making an identical copy, no differences in genome which is usualy just a genetic copy way to gain additional informaiton such as antibiotic resistance which is a great thing!!
whole process of lysogenic virus, integrating itself into host, removing not only own viral genome but also part of host genome and passing it on is called transduction** so transfer of host genome ot new host via a lysogenic virus
transduction 2
how bacteria can gain some additional information there
transfer of host cell genome to a new host via a lysogenic virus
productive cycle
ANIMAL CELLS ONLY so if talk abotu it only talking about animal cells**
like lytic cycle, but one difference= no lysis of host*
budding virus acquires a coating of the lipid bilayer= envelope*
advantages:
def some protection coated yourself in lipid bilayer of this animal cell, looks like just another animal cell offering it some protection
- get a lot more virus
- envelope- a. provides us with some immune protection, like wolf in sheep clothing, can walk amogn sheep and not get recognized so can jsut wait for the right moment and make his attack, hidden from immune system which tries to get rid of anythign foreign
b. also find in this case easier infection, all you essentially have to do is fuse with another lipid bilayer memebrane, easy to do since already have lipid bilayer around you then just dumped into cell allows for easier infection will not have to bind and recognize that paritcular receptor we have previously talked about
different RNA genomes a virus can have:
+RNA strand
- RNA virus also efered to as positive sense RNA strand** same thing, covid positive sense rna virus*
- +RNA= mRNA, translated it and created proteins from that particular strand what we read to strign together all those amino acids to create our desired peptide, just like mrna, can immediately start transalting it and will start to form viral proteins, just looks like another mRNA strand to particular cell, oh this must just be some mRNA and I will translate this- what the host tries to do, host ribosomes will start to ranslate it and form all those viral proteins talked about previously, capsid etc will be formed here
- Do we have anything in our cells that takes RNA and replicates RNA?= NO DNA replication, and take that to make rna but no machinery to take rna and replicate meaning make more RNA*** so thats what we need to do in this case becuase rna genome what we need to be replicating, so need to form RNA complimentary strand to it, so this is complimentary to red but not identical* so in process of doing this we form the negative strand!
RNA dependent RNA polymerase
- so to replicate our RNA need to use fancy enzyme RNA dependent RNA polyermase*** so this name tells us it READS RNA= RNA DEPENDENT
- RNA polymerase= tells you what it makes!!! so RNA polymerase makes RNA**
- so its reading rna and making RNA, for viral rna genomes, use negative strand as a template to create another complimetnary strand to form a positive strand** so that is wht it does after forms negative strand can produce tons adn tons of complimetnary positive strand here, this is the type of virus we are so package that up adn infect new hosts here* package up as new virus***
- for this rna dependent rna polymerase do we need to be carrying this ith us or can we just get into host, start to make that particular protein adn then use it? do we need to carry or can we just code for it= we do not have to carry it with us can just make it because mRNA can immediately start to translate strand and form proteins, enzymes are proteins so as its translating and makign all these viral proteins soem of these proteins can be this enzyme*
do you need to carry RNA d RNA polymerase?
NO can just make it, we said enzymes are proteins so as its translating making all these viral proteins those can be this viral enzyme here, can just wait and get into host translaton takes place and start to use nezyme to do replication, must code for it must have it within code but do not need to be carrying it!
SO MUST CODE For rna depdent rna polymerase, you do not need to carry!
this is positive rna genome, how covid works!!!
-RNA viral genome
- NOT LIKE rna, treat as template for mRNA
- meaning if create complimentary strand for this then the complimentary strand is mRNA, can then form all the differnt viral proteins we want, means will have to take this strand and form the positve RNA strand
- so think= TEMPLATE FOR mRNA, cannot immediately translate it!
- when looking at negative strand did not have start codon there didn’t form anything, but when form complimetnary strand with rna dependent rna pol we are forming a protein from this, so cant’ read -rna strand but if use as template for rna we can then read it!
- why we cannto immediately start to form proteins off of this, once form positive strand cna start to translate it and form viral proteins using host ribosomes to do that but remember we are a negative sense virus and that is what we are ultimately going to be packaging up and spreading for new hosts here, so ned to replicate strand one more time, use RNA depdent and rna polymerase to produce tons adn tons of that negative strand as we have shown here*
- in this case can we code for the enzyme RNA dep RNA pol or carry?= now in this paritcular case we have to be carrying it! bacuase if not carrying the enzyme no way to form that paricular enzyme no way to translate that particular strand, need to carry enzyme with us, transfer over to create positive strand then can replicate MUST CARRY AND CODE rna depednet rna polymerase
- then those new strands get packaged up with the enzyme as new virus, so packaged up with enzyme as new virus* and that will be oru new virus
-rna viral genome 2
actually see its pretty common, flu virus adn common cold
why does it want to do this with evolutionary purposes?
when she says must be carried, means puts particular enzyme of rna dependent rna polymerase inside capsid** that is the green enzyme packaged up in there so once gets into new host have that enzyme to use will all get injected into host here
+Rna lysogenic virus
Common name= retrovirus, ex HIV
third kind of RNA viral genome
how they infect:
- start off as positive RNA virus, an instead of makign more RNA as we have seen previously they will actually make DNA, so take rna as we have shown here and make single stranded DNA (ssDNA)
- name of enzyme that converts RNA to ssDNA= RNA dependent (meanign reading RNA) DNA polymerase (DNA polymerase because making DNA) also refered to as reverse transcriptase** so doing opposite reverse of transcription, going in backward direction from RNA back over to DNA** reverse transcriptase*
- now that we have formed single stranded DNA- now replicate DNA here, replicate usign host DNA polymerase to becoem double stranded dna here
- now inserts itself into host cell genome- where it gets bad man! once inserted into host cell genome it is permanently within hsot cell genome, used to taking DNA transcribing/translating it, making more RNA meaning just take this strand and make positive RNA from it and produce tons adn tons of more virus here, make all those viral proteins and produce more of that strand and get packaged up adn be able to infect another cell here, why these retroviruses can be so bad because once in genome you are permanently within genome**
why + RNA lysogenic viruses are so bad:
our problems with this virus
- permanently in genome
- pretty prone to mutations, very rapid mutations
see this first point of mutations gets introduced by reverse transcriptase, dna polymerase not very error prone proof reading ability if puts in wrong nucleotide cna back up and remve it with good nucletoide, in case of reverse transcriptase doesn’t have tha tability if wrong nuceltoide will just leave it, first form of mutation gets introdcued
the other is with our own rna polymerase if noticed last time didn’t talk about rna polymerase and how error prone it is; does make msitakes unlike DNA doesnt have proofreading ability can make an error, make and RNA strand with differnt nucleotide there, as saw in the case of our genetic code if add in wrong nucleotide get same amino acid becuse ton of codons code for same amino acid
also find rna doesnt stay around for very long, we have in the case of eukaryotic cell need to put on AAA cap and 5’ end becuase will immediately get chopped up once in cytosol, bad in case of reotrovirus becuase new virus that gets packaged up so why its so hard to get vaccine for HIV virus, mutations occuring anytime * can’t come up with vaccine, anytime come up with it virus alreayd mtuted nad vaccine no longer working very very tricky little suckers haven’t quite come up with a vaccine to stop this**
two categories of prions
- normal prions found in membranes of our neurons, don’t know what they are doing ther ebut jsut found there- have nice little alpha helices, mostly alpha helical shapes* problem is once you start to form a mutant prion or bad prion, what happens is alpha helices get converted to beta sheet, once in beta sheet start to accumulate in neuron adn start to trigger apoptosis for tha tneuron, we need neurons so if going to kill off can’t constantly do new cell division to create more of them so why it happens ot be so deadly!!
- go around msifolding even more proteins we have, discovered this in what is known as madcow’s disease, ranchers a while back thought how can I get more money off my cows? wanted to produce more milk, get more money for that cow, grind up and feed back to cows rich in all these proteins can get them to inc in size and produce more milk, so fed them all these animal byproducts not knowing within those animal byprodcuts was sheep that had mad cows disease
- two cateogires of prions: normal prions (good) and mutant prions (bad) ex. mad cow disease spongiform encephalopathies- human version
- so once you ingest infected prion or mutant prion you get it, cliam they got rid of mad cows diease prions but do not just know with 100% certainty so with netflix documentary convince you to give up meat maybe thnk abot this
mutant “bad” prion can happen 3 ways:
- arise from a mutation in hte prion gene, can go around misfolding all your other proteins
- can also be inherted-gene code for bad prion, means all offpsring cna end up with bad protein as well
- be ingested- eat cow brains, also couple of tribes with canna bilism how they ended up with it by eating infected flesh, once get bad prion converts good prions to beta sheet shape and converts good protiens
as start to accumulate, ends up with apoptosis or if inget it misfolds proteins and how you also end up with apoptosis taking palce!
How viroids work
viroids are = virus like particles, circular genome
- act as miRNAs or siRNAs to block translation! so they will bind to rna and block translation, meaning will not be able to get any of those proteins off of RNA strand, so when happens in case of liver liver cannot get all proteins it needs and why there is a silencing effect!
Researchers from another lab confirmed that hte Hantavirus respondible for kidney disease caused errors in the syntehsis of methionyl-tRNA shortly before cellular lysis is observed in infected cells. how would this affect protein syntehsi sin the late stge infected cells?
A. proein syntehsis would be truncated by an inc in number of stop codons
B. protein synthesis would proceed
C. nio proteins would be translated
D. since primary and not secondary structure of met-tRNA was altered, protein syntehsis would proceed normally
what does Met- TRNA do that is the start codon translating start codon! which if do not have start codon error, cant get protein trasnlated what kicks this whole thing off here, so looking for answer choice in lien with that rational:
A- no proteins synthesized wrong
B. nope no protein synthesis would proceed, no first amino acid
C. yes no proteins would be translted
D. …… protein syntehsis would proceed normally- NOPE
how big is a virus
100x smaller than eukaryotic cell
10x smaller than bacteria
not likely can have viral particle build up caused blockages in lympathic vessels…. no would have to have an INSANE amount of virus to do this
cDNA probe is….
has to be single stranded and complimentary to whatever you were using to create it
when have complimentary cDNA have to be complimentary what makes it unique, not going to hybridize to whatever size its more is it complimetnary or not!!! so size doesnt really matter will hybridize
bacteria 2
- may have plasmid may not, can also pick up from environment, additional genetic information besides what they have in genome
- no membrane bound organelles, dna floating around in cytoplasm vs eu cell nice and safe in nucelus*
- flagella helps bacteria get around, hair like projections are called pilli what will help us have conjugation take place : two bacteria come together to share enetic infromation
- capsule helps it do adhesion, stick to different surfaces because it is a rather sugary component that makes it up
- know different shapes!
mesophiles 2
bacteria that can live at medium temp
this is the bacteria on door handle, on desk, on toilet, cell phone will all be mesophiles
thermophiles 2
bacteria can live at high temperatures
ex bacteria that lives in hot spring Yellowstone
psychrophiles
bacteria exist at cold temperatures
pneumonic: anyone who likes the cold is a psycho
says girl from texas
auxotrophs
”-“ means cannot do something!!!!
ex arg- cant make arginine amino acid on their own, so have to supply plate of bacteria with amino acid arginien or will die off! same thing if had leu- means can’t make leucine
leu+= can make leucine!
lac- can’t metabolize lactose, only sugar supply gave bacteria than those bacteria will die off have to give htem something such as glucose or will die off! so a lot of students get this confused because means can’t do something lac- can’t make lactose, NOO means dont have machinery to break down lactose*** anytime see amino acid with minus sign that means they cannot make it vs. antime see sugar with minus sign, means can’t metbaolize sugar**** so if lac- means can’t metbaolize lactose and if that is the only sugar source they will not be able to survive***
binary fission
HUGE inc in population size, reproduction for bacteria
but NO genetic variability
- lag phase- plating bacteria onto plates so have to adjust to new environment placed htem on, need to see if they are going to be able to survive or not, do they have the sugars and can they break down sugars do they have amino acids, producing nucletoides, new cellular components so can do binary fission over adn over again
- log phase- huge jump in population size have already produced nuceltoides need in order to split in half over and over again
- staitonary phase- plateu, hit this becaue all metabolites had on tht plate become depleted so if you do not add anythign enw to those plates and just continue to let them exist on that one plate, results in death because used up all the nutrients and cannot survive; once hit stationary phase known as carrying capcaity, max populatuon can hold on that carrying palte
- death
not gaining any genetic variability just huge inc in population size !
conjugation 2
F plasmid contains conjguation genes** so can do conjuation with neighboring bacteria
F+ bacterium “male” has the plasmid, no plasmid F- or female bacterium
F+ has genes for conjugation bridge, will extend and form conjugation bridge from hair like projections form that conjugation bridge, extend so can connect the two
also refered to as sex pillius, referring to fact you have physically joined these two here; once form bridge F+ bacterium starts to replicate plasmid* and then send it on over to the F- bacterium, so tht when it does so that means that bacteirum will now also contain a plasmid, can no longer refr to this as F- bacteirum it does have an F+ plasmid, so now call it male not female bacterium and F+ not F-
if instead of keeping plasmid separate….
one thing that can happen is plasmid becomes integrated, plasmid can integrate itself into bacterium genome, once the plasmid gets integrated into this particular bacterium, we refer to this as hfr bacterium, if passage talking about hfr bacterium refers to fact plasmid no longer separate its integrated into the baceria here!!
hfr stands for= high frequency recombination
so one thing that can happen in this situation- have cobjugation genes within bacterium genome so can still form conjugation bridge becuase have conjugation genes; still replicating plasmid as have prviously done, only going to be replicating and sending over plasmid* if noticed we didn’t replicate adn send over bacetria genome with conjugation just replicate dand sent over plasmid!! BUT NOW plasmid within bacteira genome, so still going to replicate and send over that portion of the plasmid!! sometimes that is all you send over, the actual plasmid part over into neighboring cell here, but sometimes if conjuaton bridge remains intact can send over plasmid adn dna polymerase continue on, doesn’t stop perfectly at plasmid starts to replicate a portion of bacteria genome, so all of this will then get sent over* and now that paritcular bacterium has porton of plasmid and bacteria genome** (drawn here in blue) one way to distinguish order of genes are on this paritcular bacteria genome, say keep cojugation bridge intact for 3 minutes, in that 3 minutes dna has only tiem to replicat eprotion of plasmid so thats what gets sent over, but say conjugation bridge intact for 6 minutes, so not only replicate plasmid but also in this protion contains genes to replicate arginine, so now bacteirum over here that couldnt reproduce argine on its own now has informaton pushed over can syntehsis amino acid arginine, so can survive withotu adding argine to palte! or maybe keep conjugation bridge intact for 9 minutes maybe some antibitoic resistance can track how long keep conjuation bridge intact what new information showing up like to tract gene order! NOT ONLY CAN YOU SEND OVER PLASMDI ALSO SEND OVER SOME BACTERIA GENOEM ONLY FOR hfr genome*** if plasmid separate only sending over plasmid not sending any bacteria genome over*** but in hfr sending some plasmid and some bacteria genome as well***
so if bacteria will gain any new genetic information
- will be through transduction-when a lysogenic virus integrates itself into bacteria and takes some information out
or 2. through conjugation, form conjugation bridge and send over some information*** because how they reproduce binary fission, asexual reproduction only get genetic copy! so these are the two ways how you get genetic variation!
photo is ex of conjuation with hfr**
ex. e.coli
prokaryotes so no nucleus! or internal organelles
or which of the followign could researchers not study in this experimetnal system: somethign about elcoli no nuclear membrane** characteristics of these different cells(=* important to know that fungi are eukaryotes* so if given something about eukartotes you can study nulcear membrane, mitochondrial membrane any organelle
bacteria details
DNA concentrated in one part of the cell, referred to as nuceloid region but not a true nucelus becuase not surrounded by membrane
double stranded!!! vs viruses can be double stranded or single strande,d but bacteria are ALWAYS DOUBLE STRANDED
ex. e. coli
bacteria have a cell wall, peptidoglycan cell wall this sugar peptide polymer and some bacterial cells have a thick and some have a thin peptidigclan layer gives you difference btw gram positive and gram negative; if testing bacteria if use gram stain appling it to the slide if thick peptidoglycan layer will really soak up staina dn see a very purple looking clel what ahppens when stain is really well absorbed, called gram positive; pale pink washed out looking result with gram stain called gram negative; important ofr antiobtioics, gram psoitive many more options that can work for it, can use an antiobitoic that disrupts the peptidoglycan layer* how pencillin works! causes cells to lyse by messing with peptidoglycan layer of the cell wall, once that layer is disrupted that cell will becoem unstable nad cell will lyse*
CLUES
if can grow and survive just on nutrient broth, it has to be bacteria
if take infectious serum and pass through filter, inject in mouse and mouse gets sick then its not bacteira its virus because it is small enough to go through a filter
antiobiotics- if kill it bacteria, if antiobiotics don’t kill it do not know if virus or resistant antibacteria
ex image of virus
ex influenza has also a membrane envelope surroudning everything, so capsid is not the outer most membrane for influenza but it is for a bacteriophage, protein surrounding DNA is called capsid
lysogenic verus lytic image
viral particles in lytic cycle- cause cell to lyse and then bacteriphages can go out and infect other cells, very destructive for host clel; phage gets in, uses cell’s machinery to make more of itself and then causes cell to lyse*
vs
lysogenic cycle- alternative see blue DNA that came from phage, the viral DNA integrates itself into bacteria host chromosome, where says prophage blue part of brown circle; viral DNA is joining up with bacterial DNA, and then what happens virus can lie dormant for a bunch of generations, bcateria divides everytime bactera of dna replicates viral dna replicates then have a situation where a whole colony of bacteria cells all have hidden viral dna in their chormosomes and then can have mass destruction if those viral dna comes back out and then goes back into lytic cycle all the cells can burst*
can cause this in lab by altering environmenta conditions; if itmes are good and a lot of nutreitns virus will stay, bacteria thriving making lots of copies me virus will hang out there, but if virus under stress other harsh environmental conditions will trigger lytic cycle; “oh its bad here I am getting out of here I am bursting my way out”
HIV
we do not carry reverse transcriptase at all, brings reverse transcriptase
rna-dna hydrbid, double stranded DNA, has code viral dna, goes into nucleus and gets integrated into host dna
Enzyme inetgrates** helps entrage viral dna into host genome* not seen in pic
host cell’s machinery is hijacked to make more viral RNA nad viral proteins, all those viral particles that get packed up and exit cell and can then go and infect another cell*
itnegrase asked about- antiviral drug integrase inhibitor, have to really know life cycle nad try to target it at some very specific point** so an integrase inhibitor would help to treat HIV infections to prevent it from geting put into host genome
proteases- come in at hte end when viral particles are packaging themselves up and ready to leave use a bunch of protesases, if protease inhibitiors can prevent HIV from elaving cell adn going to infect other cells*
called class of drugs- retroviruses, RNA genome, reverse transcriptase* and then the virus can be integrated into the host’s genome and can then lie dormant for a long long time* characteristic of HIV infections*
Q3 . when a virus transfers genetic mateirial to bacteria that it is infecting, the process is known as:
a. transformation
b. binary fission
c. conjugation
d. transduction
d. transduction
the definition of transduction is A VIRUS infects one bacteria cell as its leaving takes some bacteria from cell then when bacteria infects another drops off bacteria
so virus becomes carrier**
vs. conjugation two bacterial cells are in physical direct contact with each other conneced by mating bridge; transduction you are sending dna from one bacteria cell to another but two cells never in contact, virus carries it from cell A to cell B; bacteria destroyed little phages have to lyse cell to go escape and infect another cell
so then the virus say we are following hte little guy now goes over; phage goes to infect next bacterial cell
so when the phage like sits down and squeezes its dna in that is the viral DNA which you also have this DNA from first bacterial cell, that is viral DNA and then of course you have hte bacteria cell’s genome in blue for bacterial cell number 2
sometimes that fragment of viral dna/green gets destroyed transduction isn’t always successful but sometimes if that green snippet can become integrated* sometimes you get lsat image: not guarantee that will become integrated and persist into the future, but it can happen and where you get recomibnant dna and sexual process change in second bacterial cell
if dna form first bacterial cell is integrated into new host, host becomes recombinant see next card image, fragments get destroyd very quickly, noncircular fragments get destroyed pretty quickly in bacterial cells, what is also possible new dna comes into cell and it doesnt get destroyed nothing happens; circular dna does not get destroyed why plasmids can be inherited or passed on they do not destroy plasmids recognize circular loops as being ok; if cell lyses obviously get destroyed, restriction enzymes in the bacteira are what destroy these fragments of DNA that the cell perceives as virus** we have harnessed restriciton enzymes to cut plasmids and DNA
Q19- population A is most likely infected with what:
a. a virus, b/c healthy mice can be re-infected with filtered pathogen cultures
b. a virus, because healthy nice cannot be re-infected with filtered pathogen cultures
c. a bacterium, because healthy mice can be re-infected with filtered pathogen cultures
d. a bacterium, because healthy mice cannot be re-infected with filterd pathogen cultures.
Answer= d
ex 1- so we are culturing in broth, so that means that only bacteria should survive if cultured in broth, virus needs to be cultured in cells** reinject mice get new infection, THAT MEANS pathogen was able to survive just on nutrient broth very very good pieces of evidene it is bacterial; pass broth through filter big things iwll get filtered out smaller goes through, virus would be hte smaller thing that goes through bacteria would fitler out; so after passing the broth through the filter, when we inject hte mice mice do not get sick suggests filter got rid of pathogen , suggests pathogen was bigger! two differnt pieces of evidence dealing with bacteria here
ex 2- infected mice with noninfected mice cualifies as positive control group!!! becuase just showing that yeah there is somthing infectious here, there is an infectious agent here, this is an improtant baseline to establish there is a contageious disease we wil ldo other experiments and find out nature of it
population C exacty the same as A, both have to be bacteria becuase they are indetical
population B turns out ot be a virus, b/c we cultured tissue in broth and then inject the healthy mice and they do not get sick so that is consistent with a virus becuase viruses wouldnt be able to persist just on broth they need cells to complete their life cycles
second part- when pas broth through a filter and then reinject healthy mice the broth passing through fitler already didn’t have any virus in it, so filter step is totally irrelevant there** no virus in it because cant be there in broth not there anymore filter step doesnt do anything
Q24 When influenza virus is endocytosed by a respiratory epithelial clel, it si at first contained in a vesicle-like structure that becomes progressively more acidic, eventually allowing the virus to escaape into the cytoplasm. This structure is known as a(n):
a. capsid
b. endosome
c. peroxisome
d. invagination
b. endosome
endosome is a fancy word for vesicle, so it is just another word special vesicle that contains a virus* becomes more and more acidic which allows virus to escape from endosome into cell cytoplasm to complete it’s life cycle; lots of examples of virus in endosome have mechanisms to get out of endosome into the rest of the clel to replicate and keep going, one interesting virus that works this way is ebola, aimed at trapping virus in endosome, if virus gets into endosome and can never get out, stuck in there forever degraded could never get degraded and make more copie sof itself or make more cells, person should not have a severe set of symptoms
if want to make an antiviral drug you have to really really know the life cycle of virus and find some targeted point to attack it out; for viruses that go through endosomes trappign virus in endosome is a cool option, all tehse things are hard ot do but another drugable target* whatever allows virus out of endosome for researches to jam that up*
Q20- based on the results of the two experiments, populations B and C are likely to be infected with:
B. virus and bacteria respectively
what is a bacteriophage?
aka a phage
this is a virus!!! It infects and replicates within bacteria and archaea.
bacteriophage literally means bacteria eater* because bacteriophages destroy their host cells.
All bacteriophages are composed of a nucleic acid molecule that is surrounded by a protein structure. A bacteriophage attaches itself to a susceptible bacterium and infects the host cell. Following infection, the bacteriophage hijacks the bacterium’s cellular machinery to prevent it from producing bacterial components and instead forces the cell to produce viral components. Eventually, new bacteriophages assemble and burst out of the bacterium in a process called lysis. Bacteriophages occasionally remove a portion of their host cells’ bacterial DNA during the infection process and then transfer this DNA into the genome of new host cells. This process is known as transduction.
endosome 2
Many cells that get into cells via endocytosis, can get to a point where it buds off this is the virus, still the bigger host cell, bubble like a vesicle called an endosome
Vocabulary word comes up a bunch on mcat
The problem here is that virus then has to escape from endosome in order to replicate, in the rest of the host cell all this machinery so virus has to get out of the endoscope to be replicated by the cell, different mechanisms for this, question dealing with enfluenza how it gets into cell, endoscytosed, flu particle in endoscope triggers endoscope to get more and more acidic and how endoscope escapes into cytoplasm of host cell, for viruses that get endocytose and end up in endocytose always some mechanism to get them out of it. to try to jam up that mechanism is a strategy for antiviral drugs**
famous examples of viruses (image)
conjugation image
Fungi lifecycle
Chemotaxis =
= movement of cell toward or away from a chemical cue (like food or toxin)
