Microbiology Test # 3
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- Viruses pass through filters meant for bacterial thus they are often called
- filterable agents
- Viruses are really small (how many microns?) and reproduce, how?
-
30-200 nano meters
using the hosts' machinery - What are the two characteristics REQUIRED to be classified as a virus?
-
Genomes (ss/ds DNA/RNA)
Capsids (made of protein coat) - Although viruses use the host cell's machinery to replicate, they do have their own genomes and often use their own....
- enzymes
- Viral capsids are one of two shapes (which is unique to viruses)?
- Helical or icosahedral (icosahedral)
- Viruses are
- Obligate intracellular parasites, some of which cannot carryout metabolic pathways or reproduce on their own.
- Only some viruses have envelopes and ____________ ussually used for...
- spikes; attachment to host cells
- The 2 most important viral enzymes
- Reverse transcriptase and RNA-dependent RNA polymerase
- Function: Reverse transcriptase
- enzyme that snthesized DNA from an RNA template (RETROVIRUSES)
- Function: RNA dependent RNA polymerase
- enzyme that synthesize RNA from an RNA template.
- What is the sequence of events for reproduction of a phage. (7 steps)
-
1.) Attachment
2.) Penetration (uncoating)
3.) Expression of viral genes
4.) Genome replication
5.) Capsid formation
6.) Packaging (Maturation)
7.) Release
APE G CPR - During the attachment phase of reproduction, a capsid binds to... which is usually...
- a host receptor (a SPECIFIC protein lipid or polysaccharide); HIGHLY SPECIFIC.
- Some typical viral proteins include those which...
-
code for capsid proteins
block host gene expression
block restriction systems
block apoptosis
aid in their genome replication (enzymes)
proteins for assembly of viral particles - Genome replication in viruses is highly dependent (in other words is very different) according to....
- the varying genetic material of the virus (ss/ds RNA/DNA)
- In cell lysis, the virus lyses the cell and exits a process called... and creating a ....
- Budding and creates an enveloped virus with the hosts lipids from membrane.
- Differences between lytic and lysogenic
-
Lytic- Kills the host
Lysogenic- incorporates its DNA into the hosts'.
Lytic- more common - Lysogen
- a cell with integrated virus. process is called integration.
- In the lysogenic cycle prophages excise themselves and lyse the cell when "things are bad"... called...
- Prophage INDUCTION
- In animal viruses, by what process does receptor binding occur?
- Endocytosis (cell "engulf"ing)
- In order to reproduce viruses need to get to where...
- the nucleus of the host.
- The process by which viruses enter the cell is _________ while the process of the virus exiting the cell is called___________.
- Endocytosis; Exocytosis
-
Polio virus:
-genome type
-structure of capsid
-infects _____________ -
ssRNA (+)
icosahedral/nonenveloped
nerve cells - Polio virus must be in ___________ form to penetrate (mRNA)
- Positive (?)
- Proteolysis is.... carried out by...
- The breaking of a long polyprotein to smaller proteins... proteases
- Polio and post transcriptional modifications. this allows what?
-
Polio can be translated without a 5' Guanine cap.
this fact allows it to inactivate host mRNA's ability to produce Guanine caps- limiting its own translation. -
Flu virus
-genetic material
-capsid structure
- infects -
ssRNA
segmented genome (8 segments)
enveloped
helical capsid
infects mucus membrane cells - 2 Structural proteins that allow the flu virus to attach to the hosts respiratory epithelial cells.
- Hemagglutin and Neuraminidase
- Specifically Hemagglutinin
- mediates fusion of the viral envelope to the host cell membrane. (mediates the virus' getting in to the host)
- Specifically neuraminidase
- Breaks down aialic acid and assists budding. It helps the virus get out out of the cell.
- Antigenic shift is the
- mixing of genome segments from different values. this occurs when 2 different viruses effect the same host.
-
HIV attacks...
AIDS is diagnosed when... -
CD4 cells (T cells)
CD4 T cell count is < 200 - HIV is a _____________ meaning that is an RNA virus that replicates through a DNA intermediate
- retrovirus
- 2 important enzymes in HIV virus.
-
Reverse Transcriptase- makes
DNA from RNA
Protease- processes proteins after translation. - genetic material of HIV
- + ssRNA
- HIV treatment includes
-
two inhibitors of the two important enzymes.
Reverse transcriptase inhibitors. (2)
Protease inhibior (1) - what makes HIV so difficult to treat?
- reverse transcriptase is not very accurate (makes alot of mistakes) and is therefore constantly changing.
- Prions are
- Infectious proteins. the wrong conformation causes the problems.
- Prion disesases include
-
Spongiform encephalopathies
Scrapie (sheep and goats)
Creutzfeldt-Jacob (humans)
Kuru (humans)
Mad cow (cows) - Why are prions so dangerous
- extreme heat does not kill these infectious proteins
- If a protein transmits the disease where is its gene?
- The prion gene (Prp) mutant forms of the gene that cause disease.
-
Cell culture methods-
cultures that grow indefinitely - immortilized cell lines made from whole organ cultures
- How do we quantify the number of viruses
- Plaque assays- dilutions are made and then plated the number of plaques allows us to estimate the number of viruses originally.
- 2 types of anti-viral defenses and examples
-
1.) Non-specific defense- fever, interferon
2.) specific mechanisms- antibodies (identify and tag viruses) and phagocytosis (cell eating- attack viruses) - Why are there so few antiviral dugs?
- Since viruses incorporate into the hosts cell, any drugs that stop its production hinders the hosts productions.
- Successful Antiviral drugs
-
Amantadine- treats influenza A infections.
Acyclovir- prevents herpes infections (only when growing NOT DORMANT) - 5 effects viruses cause to the host cell
-
1.) cell lysis- rupture of the cell.
2.) production of toxic substances
3.) cell transformations (can be carcinogenic effects)
4.) production of foreign substances
5.) Sturctural alterations in either the cytoplasm or nucleus -
Nonspecific host defenses
1.) Nucleases
2.) Proteases
3.) Interferon -
1.) Nucleases- kill DNA or RNA of the virus.
2.) Proteases- Kill viral proteins.
3.) Interferon- interferes w/ viral replication - _________ action allows the virus to grow in the host before immune response can build.
- FAST
- What is the job of compliment?
- The hosts compliment attacks its own infected cells. (like autoimmune)
- Evading immune response: Inhibition of MHC class I restricted antigen
- This is the antigen that tags cells as "self" and "non-self". Viruses inhibit its function.
- Evading immune response: Inhibition of NK cells
- Virus cause lysis in natural killer cells who defend the host against viruses.
- evading immune response: interference with apoptosis
- The infected cell attempts to undergo apoptosis (cell-programmed death). Viruses interfere with apoptosis.
- Evading immune responses: inhibition of cytokine activity
- Viruses hinder Communication of death messages and immune system interaction.
- Routes of viral entry
-
Respiratory tract- most common
Skin
Genital tract
ALL ARE EPITHELIAL CELLS - Mechanisms of virus spread
-
1.) local spread across epithelial surfaces
2.) Viremia- spread by the bloodstream - Virus-Host interactions (3)
-
Permissive (or productive) Get in, replicate, get out.
Persistant- incorporation virus does not kill host.
Latent- no virus reproduction (herpes) - Cytopathic effects (visible effects of viruses)
-
lysis of cells
Nuclear or cytoplasmic enlargement
SYNCYTIA FORMATION- cells fuse to become a "mega cell" - how do viruses affect cilia.
- Viruses do not allow cilia to work properly to prevent the spread of virus into the body.
- What is different of a ONE STEP GROWTH CURVE relative to normal bacterial growth curve.
- after innoculation the number of infections first goes down because the genome is being incorporated into the hosts genome.
- The reduction in number or growth inhibition of microorganisms
- Sterilization
- KILLING ALL MICROORGANISMS
- Sterilization
- How does the autoclave work? Sterilization? temperature?
- The autoclave works by steam under pressure and is a form of sterilization. it works at 121 degrees Celsius.
-
Radiation is effective
2 forms of radiation used -
1.) UV- poor pentrating power. Safe disinfectant.
2.) Gamma and X-rays- used for perservation and sterilization of surgical tools. - Disinfectants-
- Chemicals used to kill microbes on INANIMATE OBJECTS.
- Antiseptics
- chemicals used to kill microbes on living tissue. (alcohol~ purell)
- Common food spoilage organisms
-
E.coli and Salmonella- meats
Erwina, Aspergillus, Psuedomonas- fruits - Pastuerization
-
Heat treatment to REDUCE microbes
1.) High heat short time
2.) mild heat long time - Chemical perservatives that increase "shelf life"
-
Sodium Benzoate
Sodium Propionate - Measuring ANTImicrobial acticity... MIC
- A series of dilutions are made of an antibiotic. THE LOWEST CONCENTRATION OF ANTIBIOTIC THAT INHIBITS GROWTH is the recommended dose.
- Another method to test for antibiotic effects is to...
- Agar diffusion assay- where organism is grown and disks of antibiotics are placed on agar. as they diffuse a zone of clearing forms (inhibiting growth)
- Growth factor analogs
- A substance that is structurally related to a growth factor that blocks its use.
- Sulfanilamides inhibit growth by
- inhibiting folate synthesis necesssary for bacteria and not for humans (we get folate from food).
- substances produced by microbes (fungi and bacteria) NATURALLY that inhibit growth in microbes.
- Antibiotics.
- Antifungals- AZOLES
- target ergosterol, the main componene in bacterial cell membrane. It does not harm cholesterol in our membranes.
- Antibiotic resistance is commonly passed through __________ by what process?
- R plasmids by conjugation
-
Proteins that confer antibiotic resistance-
Cloramphenicol acetyltransferase - acetylates chloramphenicol rendering it useless.
-
Proteins that confer antibiotic resistance-
B-lactamase - Cleaves B-lactam rings
- Proteins that confer antibiotic resistance- Tetracycline pump
- Punps out tetracycline.
- 3 forms of penicilin
-
1.)Natural- grown and crystalized
2.) Semi-synthetic- removal of R group and replaced with other groups.
3.) Add excess R-group precursors to the fermentor - Commercial Microbial Prducts
- Vitamins, A.A, Cortisone, Enzymes, Vinegar, Citric Acid, Yeast, Beer and Wine, Distilled beverages, commodity ethanol, Food
- Cortisone (steroid)
- produced by bioconversion (where bacteria involved in final conversion only).
- 1 enzyme produced by microorganisms is Glucose isomerase which....
- increases fructose production (sweeter)
- Citric acid used to acidify foods and soft drinks made by _____________ fungus. How?
- Aspergillus niger. uses citrate to obtain iron.
- the process of forming all alcohols is called (not fermentation)
- distillation
- Gasohol
-
90% gasoline
10% ethanol
it is made by Saccromyces Cerevisiae who use either 5C or 6C sugar to alchol - In the fermentation of beer and wine. One has had all sugar broken down and one doesnt.
-
In wine all of the sugar has been broken down.
In beer there is a fermented malt step (more difficult) - In water treatment plants, primary treatment includes
- Physical removal of debris by filters and the removal of sediment in ANAEROBIC sludge digestor.
- The final product for the primary treatment of water are
- CH4 and CO2... Methane produced by Methanogens (Archea) and is used for fuel.
-
In secondary treatment of water, there are two methods
-trickle filter -
Here the purpose is to remove organics and reduce BOD (oxygen using bacteria).
here water are passed over rocks with microbes that consume organics. (OPEN/AEROBIC) -
The other secondary treatment method
-activated sludge treatment - Here BOD and organics are removed only it takes place in an open, AERATED tank for a short time.
- Phototrophs vs Chemotrophs
-
Energy from light
Engery from chemicals -
Chemotrophs can further be divided into
Organotrophs
Lithotrophs -
Use organics as energy source
Use inorganics as energy - Heterotrophs vs. Autotrophs
-
Use organics as Carbon source
Use CO2 as Carbon source - the synthesis of chemical compounds usinf energy from light.
- Photosynthesis
- the main pigment for harvesting light energy for photosynthesis
- Chlorophyll
- What is the center atom in a cholrophyll molecule that activates it...?
- Mg
- Anoxogenic photosynthesis (MICROBES ONLY... not plants)
- Light yields ATP + PMF
- The anoxygenic photosynthesis (dark reactions) produce
-
NADH and ATP.
Electrons flow from Bacteriopheophytin to Quinones to Cytochromes. - Oxygenic photosynthesis overall
-
Light + H20 + NAD yields
ATP + PMF + NADH + O2 - Electron sources in oxygenic vs anoxygenic
-
In oxygenic electrons come from water
In anoxygenic electrons come from inorganics (N, S, H) - Calvan cycle
-
the reverse of glycolysis.
It is CO2 fixation - Calvan cycle overall
-
5 Carbon + CO2 (1 carbon)
with enzyme RUBISCO
yield
2- 3C phosphoglycerates - Rubisco is the most abundant enzyme on earth!
- :op
- The calvan cycle is a ________________ process
- Reductive... reducing CO2 to glucose
- In the Calvin cycle Rubisco is...
- regereated
- What enzyme is critical to the regeneration of rubisco
- Phosphoribulokinase
- Chemolithotrophs use inorganics as energy source. Name 5 bacteria and there inorganic source.
-
Psuedomonas- Hydrogen
Thiobacillus- sulfur
THIOBACILLUS FERROXIDANS- iron
Nitrosomonas- Ammonia
Nitrobacter- Nitrate - Thiobacillus ferroxidans is used in... for...
- in the copper mining industry to fish out copper from iron ore.
- How is NADPH produced in chemolithotrophs?
- it may be produced directly or through reverse electron transfer.
- Direct production of NAD(P)H overall (realize this makes photosynthesis not necessary)
-
H2 + NAD(P)
in the presence of HYDROGENASE
NAD(P)H - Nitrogenase enzyme
- catalyzes the reduction of N2 to NH3 (useful and beneficial)
- Methanogenic Archea produce methane from 5 sources
- H2 + CO2, formate, methanol, methylamines, acetate
- the process of making methane
- Methanogenesis
- Methanogenesis is a complete reduction of _______ to _______.
- CO2 to CH4
- What are the unusual conezymes of methanogenesis
-
Methanofuran
Methanopterin
Coenzyme B - Archea are actually very similar to
- Eunkaryotes
- Thermophiles
- Heat loving microbes (optima > 45 degrees
- hyperthermophile
- Extreme heat loving microbes (optima 80 degrees C)
- An example of a Hyperthermophiles are .... who use.... as their energy source.
- Black smokers; inorganic sulfur
- Psychrophiles
- Cold loving microbes (optima 4 degrees C)
- Acidophiles
- Organisms that thrive below pH 5. These organisms keep their cytoplasms neutral
- Alkaliphiles
- microbes who thrive in alkaline pH. They keep their cytoplasms neutral.
- Halophiles
- SALT LOVING ORGANSISMS. Halophiles tolerate high Na+ content by accumulating excess K+ in the cytoplasm.
- Bacteriorhodopsin
- pigment that functions as chlrophyll by absorbig light and exciting electrons. (retinal)
- what is humus?
- a complex mixture of organic materials.
- Syntrophy
- When two organisms produce metabollic products which cannot be produced by either independently.
- Rumen microbiology- what product is broken down that normally cannot be broken down
-
Cellulose.
Microbes in the rumen of cow can break down Betta 1,4 glycosidic bonds of cellulose) - Nitrogen fixation
- N2 to NH3
- Denitrification
- NH3 to N2
- Ammonia Flux
- Use of NH3 (metabolization)
- Nitrification
- NH3 to NO2 to NO3
- The most usable source of sulfur is
- H2S- hydrogen sulfide
- Assimilation
- Direct use of C, H, N, S into Amino acids.