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