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.

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