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Micro 220
microbiology final
138
Microbiology
Undergraduate 2
04/07/2012

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Term
What methods are there for quantifying viruses?
Definition
Titer: a measurement of the number of infectious units per volume
Plaque Assay: analogous to the bacterial colony; one way to measure virus infectivity.
**Plaques: clear zones that develop on lawns of host cells.
- lawns can be bacterial or tissue culture
- each plaque results from an infection from a single virus particle
Term
Intact animal methods for virus quantification.
Definition
Procedure:
1)serial dilution of virus sample (generally at 10 fold dilutions)
2) inject samples into several sensitive animals
3) after incubation period: fraction of dead and live animals at each dilution is tabulated.
End tabulations are rated in the form of LD_% (lethal dose...% subjects deceased)
Term
Phases of viral replication.
Definition
- Attachment (absorption) of virus to a suitable cell
- entry (penetration) of the virion or its nucleic acid
- Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
- (maturation) -> Assembly of capsids and packaging of viral genomes into new virions
- release of mature virions from host cell
Term
What type of growth curve is characterized for virus replication?
Definition
A one step growth curve
Term
What are the steps in the virus replication growth curve? What occurs in each step
Definition
Latent period:
Eclipse - Early enzymes --> Nucleic acids --> Protein coats
and then maturation - assembly and release.
Term
Explain the features of viral attachment to cells.
Definition
- attachment of virion to host cell is highly specific...Requires complementary receptors on the surface of a susceptible host
- Receptors on host cell carry out normal functions for cell (ie uptake proteins, cell to cell interactions)
- attachment results in changes to both virus and cell surface to facilitate penetration
Term
What is a permissive cell?
Definition
a host cell that allows the complete replication cycle of a virus to occur
Term
Explain the viral attachment and penetration of Bacteriophage T4.
Definition
Bacteriophage T4: Virus of E. Coli bacteria

- attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope
- Tail fibers retract and tail core makes contact with E. coli cell wall
- Lysozyme-like enzymes forms small pore in peptidoglycan
- tail sheath contracts and viral DNA passes into cytoplasm
Term
What DNA destruction system is only effective against double-stranded DNA viruses?
Definition
Bacterial Restriction-modification systems
Term
What are restriction enzymes?
Definition
Restriction endonucleases
- cleaves DNA at specific sequences.
Term
What is the restriction-modification system?
Definition
it is a bacterial defense system against virus penetration.
DNA destruction system that is only effective against double-stranded DNA viruses
Term
What are the viral methods of evading bacterial restriction systems? (like the restriction-modification system)
Definition
- Glycosylation or methylation (IE chemical modification of viral DNA)
- Production of proteins that inhibit host cell restriction enzymes
Term
Explain the baltimore classification scheme. (Class I to class VII)
Definition
Class I - Double Stranded (ds) DNA viruses
Class II - Single Stranded (ss) DNA viruses
Class III - dsRNA
Class IV and V - ssRNA (+ or -)
Class VI are retroviruses
Class VII are dsDNA viruses that replicate thru RNA intermediates
Term
What are the steps in the production of viral nucleic acid and protein.
Definition
- Generation of mRNA occurs first
- Viral genome serves as template for viral mRNA
- in some RNA viruses, viral RNA itself is the mRNA
**in some cases essential transcriptional enzymes are contained in the virion
Term
What is a positive strand RNA virus?
Definition
Single-stranded RNA genome with same orientation as its mRNA
Term
Negative strand RNA Virus:
Definition
single-stranded RNA genome with orientation complementary to its mRNA
Term
What are early proteins and late proteins? What are their functions?
Definition
Early proteins and late proteins are proteins formed during a viral life cycle, after the synthesis of viral mRNA
Early proteins:
-Synthesized soon after infection
-necessary for replication of virus nucleic acid
-typically catalytic functions
-**synthesized in smaller amounts

Late proteins:
- typically structural components, including virus protein coat
- synthesized in larger amounts
Term
Most bacteriophages consist of what type of genome (ss or ds) (RNA or DNA)
Definition
dsDNA genomes.
Term
Are most bacteriophages naked, or do they possess lipid envelopes?
Definition
Most are naked but some do possess lipid envelopes.
Term
What are the different viral life cycles?
Definition
temperate and virulent.
Virulent: viruses lyse host cells after infection.
Temperate: Virus replicates their genome in tandem with host genome and without killing host. IE can undergo a stable genetic relationship within the host --> but can also kill cells during lytic cycle.
Term
What is T4? What is its genome structure?
Definition
T4 is a virulent bacteriophage that is also related to T6 and T2
- Genome is dsDNA that is circularly permuted and terminally redundant
Term
What does the fact that T4's genome is circularly permuted and terminally redundant effect?
Definition
Both factors effect genome packaging.
Term
What is a concatemer?
Definition
A concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequences linked in series.
Term
What is the modified DNA base that T4 contains? What is this the site for?
Definition
5-hydroxymethylcytosine (HOH2C)
**this DNA is resistent to virtually all known restriction enzymes
It is the site for glucosylation (on the hyroxyl group)
Term
The T4 genome can be divided into what parts?
Definition
Early, middle and late proteins.
Early and middle proteins: enzymes needed for DNA replications and transcription
Late proteins: head and tail proteins. Enzymes required to liberate mature phage particles.
Term
Why are the T-. bacteriophages labeled T-?
Definition
because they have tails
Term
Lysogeny
Definition
State where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
Term
Prophage state
Definition
State when bacteriophage genome is integrated into the host genome and sits there passively.
Term
How can a bacteriophage enter into the prophage state? What keeps their genes from being expressed?
Definition
Integrated through site recombination.
Genetic regulation makes it possible.
It is repressed by negative regulation.
Term
Lysogen
Definition
a bacteria containing a prophage.
Term
Lysogenic virus
Definition
A virus with a lytic pathway and a prophage state --> Ie a virus that is able to be integrated into the host chromosome and who's genome will be regulated thru negative regulation.
Term
Describe bacteriophage lambda and its infection methods.
Definition
- Linear, dsDNA genome
- Has complementary, single-stranded regions 12 nucleotides long at the 5' terminus of each strand
- Upon penetration, DNA ends-base pair, forming the (cos) site and the DNA ligates and forms double stranded circle
- when lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site (att(lambda))
- when it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication
Term
How is the regulation of lytic vs. lysogenic events occur in lambda? What are the key repressor proteins?
Definition
Through complex genetic switch
cl protein: (the lambda repressor) causes repression of lambda lytic events
Cro repressor: controls activation of lytic events
Term
What are the consequences of virus infection in animal cells?
Definition
Persistent infections: release of virions from host cell does not result in cell lysis (infected cell remains alive and continues replicating virus)
Latent infections: delay between infection by virus and lytic events
Transformation: conversion of normal cell into TUMOR cell... (loss of control over cell growth)
Cell fusion: two or more cells become one with many nuclei
Term
What are retroviruses? What is unique about their genome?
Definition
Retroviruses are viruses that replicate through a DNA intermediate
- contain reverse transcriptaste (copies information from its RNA genome into DNA)
- virion contains specific tRNA molecules
UNIQUE GENOME: two identical ssRNA molecules of the + orientation
*contains specific genomes:
gag: encodes structural proteins
pol: encodes reverse transcriptase
env: encode envelope proteins
Term
what is a retroviruses process of replication?
Definition
1) entrance into the cell
2) removal of virion envelope @ membrane
3) Reverse transcriptase of one of the two RNA genomes
4) integration of retroviral DNA into host genome
5) transcription of retroviral DNA
6) assembly and packaging of genomic RNA
7) Budding of enveloped virions; release from cell
Term
What are the methods of physical antimicrobial control?
Definition
heat sterilization
radiation sterilization
filter sterilization
*stops acute food poisoning
*reduces damage done to materials in the industrial world
Term
Clostridium
Definition
A gram + bacteria that causes botulism
*only infects host if consumed in infected food (otherwise it pasts right through us)
Term
What are sulphate reducing bacteria?
Definition
Anaerobic bacteria who use sulphate as terminal electrons.
**in cream separater plants creates dipoles across the colony and corrodes the metal in those high-pressure pipes
Term
What are the different forms of heat sterilization?
Definition
Sterilization : killing all viable organisms within a growth medium
Inhibition : effectively limiting microbial growth
Decontamination : the treatment of an object to make it safe to handle
Disinfection : Directly targets the removal of all pathogens, not necessarily all microorganisms
Term
What is the most widely used form of sterilization? Describe it
Definition
heat sterilization
- High temperatures denature molecules
- Amount of time required to reduce viability 10-fold is called decimal reduction time
- ** spore-forming bacteria can survive heat that would rapidly kill vegetative cells
Term
Thermal death time
Definition
the time at which the temperature kills all of the sample organisms.
**depends on what the initial concentration of the organism is
Term
Autoclave
Definition
An autoclave is a sealed device that uses steam under pressure for heat pasteurization.
- allows temps to exceed 100 C
Term
Pasteurization
Definition
Pasteurization is the process of using precisely controlled heat to reduce the microbial load in heat-sensitive liquids... doesn't kill all organisms though!
Term
Radiation Sterilization
Definition
Microwaves, UV, Xrays, Gamma rays can reduce microbial growth
**UV is NON-PENETRATING!!!
Term
Ionizing radiation sterilization
Definition
- electromagnetic radiation that produce ions and other reactive molecules
- generates electrons, hydroxyl radicals, and hydride radicals

**Amount of energy required to reduce viability tenfold is analogous to D value
Term
Filter sterilization: What types are there.
Definition
Pores of filter are too small for organisms to pass through
Pores allow liquid or gas to pass through
- DEPTH FILTERS --> Thick HEPA filters
- MEMBRANE FILTERS -->Very thin: functions more like a sieve --> filtration by syringe, pump or vacuum
Term
How can antimicrobial agents be classified?
Definition
Antimicrobial agents can be classified as either: Bacteriostatic (stop growths), bacteriocidal(kills viability of cells) or bacteriolytic (bursts cells)
Term
What is MIC (minimum inhibitory concentration)
Definition
The smallest amount of agent needed to inhibit growth of a microorganism
--> varies with the organism used, inoculum size, temp, pH, etc.

*the way to do this procedure is by taking many vials and adding different concentrations (2 fold dilutions) of agent in each vial. The one that results in no growth is the MIC.

**gold standard!
Term
What is disk diffusion assay?
Definition
A method of testing chemical growth assay.
- antimicrobial agent added to filter paper disc
- MIC is reached at some distance --> zone of inhibition = area of no growth around disk
Term
What are the types of chemical antimicrobial agents for external use?
Definition
-Industrialized applications
-Products design to reduce human pathogens
--> sterilants (kills everything, whatever it contacts)
--> disinfectants = sanitizers (reducing pathogenic bacteria to a level below which they wont cause disease through contact)
--> antiseptics (inhibit growth of bacteria)
Term
What are the beta-lactam antibiotics?
Definition
Penicillins and Cephalosporins are examples
Term
What are antibiotic drugs classified on the basis of?
Definition
Molecular structure
Mechanism of action
Spectrum of antimicrobial activity
Term
What is selective toxicity?
Definition
-selective toxicity is the ability to inhibit or kill a pathogen without affecting the host.
**Growth factor analogs --> structurally similar to growth factors but do not function in the cell
Term
What are growth factor analogs?
Definition
Structurally similar to growth factors but do not function in the cell. Play a part in selective toxicity
Term
What are the types of synthetic antimicrobial drugs?
Definition
Sulfa drugs - inhibit growth of bact.
Isaniazid - growth analog effective only in Mycobacterium (interferes with synth. of mycolic acid)
Nucleic acid base analogs - formed by the addition of bromine or fluorine
Quinolones - antibacterial compounds that interfere with DNA gyrase
Term
What are antibiotics?
Definition
naturally produced antimicrobial agents
Term
What was the first antibiotic covered? describe it?
Definition
Penicillin
- primarily effective against gram + bact.
- some synth. are effective against gram -

targets cell wall synthesis
Term
What types of antibiotics are produced by bacteria?
Definition
Aminoglycosides - antibiotics containing amino sugars bonded by glycosidic linkage (considered the last-resort antibio)
Macrolides - broad spec. that targets 50S subunit of ribosome
Tetracyclines (contain four rings) - inhibition of protein synth... inhibits functioning of 30S ribosomal subunit ... *can make u sensitive to sun burn
Term
why may microorganisms be resistent to certain antibiotics?
Definition
- organisms lack structure the antibiotic inhibits
- organism is impermeable to a.b.
- organism can inactivate a.b.
- organism may modify the target of the a.b.
- organism may develop a resistent biochem pathway
- organism may be able to pump out the a.b.
Term
What is efflux?
Definition
efflux pump.
Proton motor force dependent ABC cassette. Establishes a high gradient outside the cell.
Pumps are not very specific : can act on several antibiotics at once
Term
how long does it usually take the immune system to build up a response?
Definition
Three weeks
Term
How long does it take for innate defense to kick in?
Definition
immediately
Term
What are three characteristics of the immune system ?
Definition
1) specificity
2) universality
3) inducibility (immune response takes time to develop)
Term
what are three characterstics of innate defense?
Definition
1. less specific than ISR
2. Less universal than ISR
3. Is "constitutive": acts immediately, or very shortly, after inflammation. E.g. accute inflammation
Term
What are the bodies three levels of defense?
Definition
1) The surface of the body
2) innate defense (accute inflammation)
3) Immune system
Term
what are the major innate defense mechanisms?
Definition
i. accute inflammation
ii. phagocytosis
iii. complement
iv. Interferons
Term
Explain the mechanism of Innate Defence
Definition
When a Mast cell gets a signal from an antibody on its surface, small granules that it contains will fuse with the membrane and the cells contents will spill out into the vicinity of the cell.
One of those is histimine which will trigger a whole series of reactions tht result in acute inflammation.
Term
what does histimine do?
Definition
it causes acute inflammation when it is released from mast cells.
Term
Pathogenicity
Definition
Pathogenicity = the ability of a parasite to inflict damage on the host
Term
Virulence
Definition
Virulence = measure of pathogenicity
Term
Opportunistic Pathogen
Definition
Opportunistic pathogen: causes disease only in the absence of normal host resistance
Term
Infection
Definition
Situation in which microorganism is established and growing in a host, whether or not the host is harmed
Term
Disease
Definition
Damage or injury to the host impairs host function
Term
what is cystic fibrosis?
Definition
Genetic disease where there's a permease that takes things into the cell.
A specific permease has a mutation and does not function properly.
It changes environment outside the cells all over the body.
Term
How do normal oral microflora colonize?
Definition
by first attaching to acidic glycoproteins deposited there by saliva
Term
How many microbial cells are found in GI tract?
Definition
10^13 or 10^14 microbial cells
Term
Which part of the respiratory tract has microflora?
Definition
A restricted group of microflora colonizes the upper respiratory tract
Term
Lactobacillus acidophilus
Definition
A resident organism in the vagina, ferments the glycogen, producing lactic acid
Term
How does one measure virulence?
Definition
Estimated from experimental studies of the LD_50 (lethal dose50) **the amount of an agent that kills 50% of animals in test grop
Term
Attenuation
Definition
The decrease or loss of virulence
Term
toxicity
Definition
Organism causes disease by means of a toxin that inhabits host cell function or kills host cells
Term
Invasiveness
Definition
Ability of a pathogen to grow in host tissue at densities that inhibit host function
Term
What is bacterial adherence facilitated by?
Definition
Bacterial adherence is facilitated by extracellular macromolecules that are not covalently attached to the bacterial cell surface (ie slime layer, bio film)
- fimbriae and pili
Term
What are the types of exotoxins? What do they do?
Definition
Cytolytic toxins : Work by degrading cytoplasmic membrane integrity, causing cell lysis and death
AB toxins : consists of two subunits; A and B
works by binding to host cell receptor (B unit) and transferring damaging agent (A subunit) across cell membrane.
Term
Describe Botulinum toxin
Definition
an AB exotoxin. Consists of several related AB toxins tht are the most potent biological toxins known
Term
Endotoxins
Definition
Endotoxin: liposaccharide portion of cell envelope of certain gram - bact. which is a toxin when solubilized
--> generally less toxic than exotoxins
--> presence detected by LAL assay
Term
Morbidity
Definition
Morbidity of a disease refers to the incidence of disease including fatal and nonfatal disease
Term
innase resistance
Definition
Collection of non-immune defense mechanisms.
*Constitutive rather than inducible
Term
What are the steps in phagocytosis?
Definition
1) binding of bacterium to the surface of phagocytic cell.
2) the envelopment of the bacterium by the membrane of the phagocyte
3) the formation of a phagosome --> phagosome usually fuses with lysosome to form phagolysosome (leading to digestion)
Term
Complement
Definition
Mechanism of Innate defense:
Series of interacting proteins that initiate one another (one protein comp. will activate another "down stream ... Complement Cascade)
Term
what are complement components involved as?
Definition
As inflammatory mediators generated during the inflammatory process.
Term
What is C3b? What is its function?
Definition
C3B is an activated component of the third component of complement C3. Binds to surface of many bact.
- aids process of phagocytosis
--> binding of C3b to the surface leads to the formation of the membrane attack complex ... Results in the formation of holes in membranes
Term
What are the different kinds of interferons?
Definition
Alpha, Beta, gamma. Occurs in cells infected by viruses.
Term
What type of interferon does lymphocytes infected by viruses produce?
Definition
Alpha-IFN
Term
What type of interferon does virally infected fibroblasts produce?
Definition
Beta-IFN
Term
what methods can you use to attenuate a virus?
Definition
- passage through other animal species could lower the virulence
- application of heat over time
Term
What is passive transfer of immunity?
Definition
It is when the cell-free yellow liquid called "serum" is administered to normal, unimmunized animals. It confers protection against the toxins defended against in the serum.
**discovery of this led to the discovery of antibodies!
Term
what does immune serum do to bacteria? Why does this happen?
Definition
It aggutinates it (causes them to clump together).
Bacteria produces soluble, filterable molecules and immune serum contains antibodies specific for these soluble antigens. **precipitin reaction!!
Term
What are the antibodies that facilitate phagocytosis called?
Definition
Opsinins
Term
What kind of antibodies are bound to mast cells?
Definition
cytophilic antibodies
leads to discharge by mast cells
Term
What is humoral immunit?
Definition
Humoral immunity are an expression by soluble antibodies.
Its effects can be transferred to unimmunised animals by transfer of serum.
Term
What are the major classes of antibodies?
Definition
IgM, IgG, IgA, IgE
Term
which class of antibodies causes allergic reactions?
Definition
IgE
Term
Describe a unit of antibody
Definition
Unit consists of:
- two identical light chains (220 amino acids, first region = variable region first 110 aa vary between chains, 2nd half = constant region)
2 identical heavy chain ... first domain is highly variable and nature of other domain determines the class to which the anitbody molecule belongs (IgM, IgG, IgE, IgM)
Term
antibody selection theory
Definition
Postulates that antigen selects good fitting antibodies from the vast array that are premade and waiting to be selected
Term
What are the basic elements of clonal selection theory?
Definition
Selection
Cells able to respond to antigen are clonal (from precursor cell)
Term
What are MHC molecules? What are the different types and their functions?
Definition
Major Histocompatibility Complex (MHC) molecules
*perform central role in recognition of antigens
two kinds:
1) Class I MHC molecules - found on the surface of all cells of the body
*hels in self-nonself differentiation
2) Class II MHC molecules are found mainly on phagocytic cells.
Term
T-cells bearing CD4 antigen (CD4+) bind peptides to what ?
Definition
T-cells bearing CD4 antigen bind peptides to MHC Class II molecules
Term
T-cells bearing CD8 antigens bind to peptides bound to what ?
Definition
MHC class I molecules
Term
What generates T-cells?
Definition
the thymus
Term
What is a substance that can induce antibody called?
Definition
immunogenic
Term
What is a hapten?
Definition
A small immunogenic molecule that can bind (chemically conjugate) to non-immunogenic molecules and induce antibody.
Term
Does removing the thymus prevent an immune response?
Definition
Yes. it does remove the immune response
Term
What is immunoincompetent and what causes it?
Definition
What causes it?: malfunction of thymus or malfunction of bone marrow cells

immunoincompetent is an individual who is unable to emit an immune response
Term
Bone marrow cells and Thymus cells
Definition
Both are required in order to create an immune response
Term
Out of bone marrow cells and thymocytes, which is the precurser cell? Why?
Definition
Bone marrow cells have antibody receptors on their surface (thymocytes dont)
Consistent with the possiblity they are the precursor cells
**thermocytes bear on their surface an antigen referred to ask Thy1
Term
where are the cells corresponding to bone marrow and thymus cells found ?
Definition
They are found in the spleen.
Term
What is the function of the thymus cells present in the thymus? where are these same types of cells found?
Definition
found in the thymus and lymphoid organs.
Needed to allow antigen to induce bone marrow prescusor cells to produce progeny that secrete antibody. They are called helper or inducer T cells.
Term
Helper t-cells exist only for what?
Definition
only for foreign antigens
Term
Antigen-bridge model
Definition
Hypothesis for the nature of the interaction between B and helper T cells required to induce antibody formation.
A B cell can be induced by antigen if a second cell, the helper/inducer T cell, also binds to the antigen.
Term
B-cells express what type of antigens on their surface
Definition
B cells express class II MHC antigens on their surface.
Term
What is recognized by helper T-cells ?
Definition
peptide MHC complexes
Term
What is the MHC-restricted B cell/T helper cell interaction model?
Definition
This model states that
-MHC Class II molecules on surface of B cell binds to peptide produced by antigen molecule.
-helper T-cells will recognize and bind to peptide-MHC complex.
Term
What happens when a self-antigen interacts with the receptors of a B cell in the absence of helper T cells.
Definition
It results in the death of the B cell.
This ensures that anti-self B cells are eliminated by a process called antigen-specific inactivation
Term
What is the concept of cross reactivity?
Definition
Some antigens have very similar or identical epitopes.
If two antigens initiate an antibody (precipitate reaction) than they are said to cross react
Term
What is an epitope?
Definition
The area on an antigen molecule complementary to an antibody molecule
Term
what is autoimmunity
Definition
immunity to self antigens. Caused by a cross-reaction of an antigenic molecules and non-antigenic molecules
Term
What type of response results in a limited disease?
Definition
The induction of an exclusive cell-mediated response results in limited disease
Term
What type of response results in a chronic and/or fatal disease course?
Definition
A humoral or mixed cell-mediated/humoral response results in a chronic and/or fatal course
Term
What prompts the cloning of all T cells?
Definition
the presence of a particular growth hormone - IL2 - is a growth factor for all T-cells
When one T-cell, stimulated with antigen in the presence of IL2, will give rise to upwards of a million identical cells.
Term
Cytokines
Definition
Any of a number of substances, such as interferon, secreted by certain cells of the immune system and having an effect on other cells.
Term
What are the two major types of CD4+ T cells? What do they produce?
Definition
Th1 CD4+ T cells produce IL2 and IFNg (among other cytokines)
Th2 CD4+ T cells produce IL4 and IL10 (among other cytokines)
Term
What does IFNg do?
Definition
Can prevent viral multiplication and its delivery to infected macrophages by pathogen-specific CD4 T cells can result in macrophage activation
Term
Macrophage activation
Definition
An increase in metabolic pathways that are toxic for most pathogens inside the cell
Term
What does the administration of IL4 do? Which other growth factor does the same?
Definition
It increases IgG and IgE responses.
IL10 does the same.
The presence of IL4 or IL10 favors the induction of humoral, Th2 responses
Term
What does the presence of IFNg cytokines do?
Definition
favors the development of Th1 responses.
Term
Which antibody class has subclasses? Why is this?
Definition
IgG antibody class has four subclasses, IgG1-IgG4.
They are produced under different circumstances
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