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Microbiology - Viruses


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What is Attenuation?
A mechanism for controlling gene expression; typically transcription is terminated after initiation but before a full-length mRNA is produced.
How is attenuation different from other transcriptional regulation?
Attenuation is a mechanism whereby gene expression (typically at the level of transcription) is controlled after initiation of RNA synthesis. Most attenuation mechanisms involve a coupling of transcription and can therefore occur only in prokaryotes.
Where does two-component sensory transduction occur?
Cell Membrane
What protein modifications are important for chemotaxis sensory transduction?
Sensory proteins or methyl accepting chemotaxis proteins (MCP's)or receptor-transducer proteins or transducder. 5 MCP's have been identified; CheA, CheB, CheW, CheY, and CheZ.
What kind of genome do viruses have?
Any form of nucleic acid you can think of.
How are bacteriaphages/Viruses quantified?
1)Direct electron microscope counts
2)Indirect counts which measure a property of the viruses effect on the host they infect (Plaque Assays, Titer dilutions)
Describe the life cycle of phage T4.
1)The tail binds to the lipopolysaccharide (LPS) outer membrane of host cell
2)Penetration - contact of cell wall by tail pins (spikes), contraction of the tail sheath, injection of DNA
What is a temperate phage?
It is a virus whose genome is able to replicate along with that of its host and not cause damage to cell health, in a state called lysogeny
Why are host cell proteases important in lambda infection?
Proteases such as lambda's RecA are changed from their normal state when the DNA of the host cell is damaged as a result of Lambda invasion. It destroys the Lambda repressor and new transcriptional events can be initiated.
What is transformation in the context of viral infection of animal cells?
A change in the state of the cell so that it is no longer growth inhibited (growth becomes uncontrolled).
What is the difference between point mutations and frame shift mutations?
- A single nucleotide change (point mutation) is usually silent and has no effect
- A frame shift mutation (reading frame change)and the translation of the gene is completely upset
What are missense mutation?
Is when the chemical "sense" (sequence of amino acids) in the ensuing polypeptide has changed
What is a nonsense mutation?
Is the result of a base pair substitution which results in a stop condon, which leads to an incomplete protein that would not be functional.
What are silent mutations?
A change in the RNA which has no effect on the protein (silent).
What are revertants?
Is a strain in which the actual (original) type phenotype that was lost in the mutation is restored.
Two types - 1)Same-site revertants,2)same-site revertants
What are suppressor mutations?
Suppressor mutations are second site mutations that are new mutations that compensate for the original mutation. Usually given a color name.
What are some important mutagens?
1)UV Radiation
3)Ionizing Radiation
5)Nitrous Acid (HNO2)
What is the Ames test?
Uses histidine auxotroph to see how many revertants arise.
What are the three main genetic exchange mechanisms in prokaryotes?
Which organisms show natural competence?
1)Bacillus subtilis
How are generalized and specialized transduction different?
1)Specialized-only certain genes are transferred

2)Generalized-any gene can be transferred
What is conjugation?
Transfer of DNA mediated by conjugation plasmids, through a mechanism called "sex pilus"
What does F+ mean?
Cells possessing an unintegrated F plasmid. Normally known as the donor male
What does F- mean?
Cells without on F plasmid are called F- and are recipients (female).
What does F mean?
F plasmid is is a circular DNA molecule of 99,159 base pairs.
What are transposons?
A type of transposable element that carries genes in addition to those involved in transposition
When did life originate on earth?
First evidence of life 3.8 billion years ago.
When did photosynthesis originate on earth?
~2.0 billion years ago
When did Eukaryotes originate on Earth
~2.0 billion years ago?
What is the evidence for the endosymbiotic theory?
-Chloroplasts/mitochondria - divide independently of host eukaryotes
-Ribosomes are "bacterial"-like
-Enclosed double lipid bilayer
-Mitochondria/chloroplasts - own - DNA, Ribosomes, RNA polymers, and tRNA
-Sequence of 16s rRNA are bacterial
-- mito= alpha proteobacteria
-- chloroplasts= cyanobacteria
Why is 16s rRNA a good molecule for phylogenitic reconstruction?
-use of molecular sequences
-molecule used 16s is the same for all organisms classified
-16s is functionally homologous
-gene/molecule align in sequence
-the rate of change is proportional
How are bacteriaphages/virus cultured in the lab?
By promoting growth of a cell culture in a bottle or Petri dish which contains the appropriate nutrients, blood serum and on occasion antibiotics to control bacterial contamination. Then it is incubated.
How do cells "sense" their environment for chemotaxis?
By responding to a change in the temporal gradients(the change in concentration of a chemical outside the cell over time).
What are some important animal viruses?
1)Pox virus - smallpox
2)Herpes - genital & mouth
3)Parovirus - Infects dogs
4)Arenavirus - Hanta virus
What are the two most important components of SOS repair?
1)Lex A - a repressor, which represses expression of SOS genes
2)Rec A - recombination repair protease for Lex A (can clive Lex A)
What are the important parameters of the phage one-step growth curve?
1)Early-Early enzymes are the first proteins produced, involved in taking over the cell
2)Middle-Replication of genes and protein production of the virion (latent period)
3)late-genes involved in assembly packaging and lysis
What are true revertants?
A true revertant reverses the original mutation at the same site and in the same sequence as the original.
What does it mean to say a lysogen?
A lysogen can spontaneously produce virions of the temperate virus along with those of the host and pass them from one generation to the next. (Lambda is a Lysogen)
What is SOS repair?
It is induced DNA repair in a complex cellular mechanism. It is activated as a result of DNA damage. However, some DNA repair occurs in the absence of template instruction, which results in many errors/mutations.
What is competence?
Recognizing DNA repeats and acquiring only DNA that has these repeats.
How do cro and cI determine whether the lytic or lysogenic pathway is used upon infection by lambda?
cro is cI competitor for operator binding sites. If cro is greater than cI the Pr(promoter right) transcripts lytic genes.
If cI is greater than cro the Pl(promoter left) transcripts lysogenic genes.›
What is mutation?
An inheritable genetic change in the base sequence of the genome of an organism.
How can you use conjugation to map the order of genes?
Conjugation results in the transference of chromosomal genes always in the same order from a fixed site in a given Hfr strain. Mapping of genes is accomplished using this constant by timing the recombinants containing different genes after mixing Hfr and F- bacteria by the process known as interrupted mating.
How is taxonomy different from phylogeny?
Taxonomy - based on similarities

Phylogeny - evolution only
How is the replication of retroviruses and hepadnaviruses fundamentally different from replication of other viruses?
The reverse transcription in their replication processes encapsulate DNA genome, rather than RNA genome as do the other viruses.
How is the species concept different for prokaryotes?
Combination of taxonomy & phylogeny which is inconsistent. Usually taxonomy is used, DNA/DNA hybridization
In the clinical setting serology (use of antibodies to distinguish strains is used.
What are insertion sequences?
Specific sites on the host chromosomes where the F plasmid can integrate. These site are regions of homology between the chromosome and F plasmid DNA
What are the general stages of bacteriophage (lytic) infection?
1)Attachment (absorption)-virion binds to a receptor on host cell
2)Penetration (Injection)-of the virion or its nucleic acid into the cell
3)Replication-of nucleic acid and production of viral protein
4)Assembly & Packaging-new nucleic acid is packaged info proteins and new nucleocapsids
5)Release-of mature virions usually by lysis of the cell host or by budding
What are the two most common viral protein conformations?
1) Helical (filamentous) example-TMV
2)Icosahedral (almost spherical) 20 facets
3) Combination of Helical/Icosahedral -example T4
What are viruses?
Non-cellular obligate parasites that can replicate independently of a cells chromosomes but not independently of the cells themselves.
What does Hfr mean?
High frequency of recombination, cells that have chromosome integrated F plasmid
What is MOI?
Multiplicity of Infection - the ratio of infectious virions in a host cell

Infectious virions/# host cells
What is the endosymbiotic theory for the origin of eukaryotes?
That chloroplasts and mitochondria arose from intracellular bacterial symbionts. Proposed by Darnier, Margulis, Sogin)
What is transduction?
Acquisistion of foreign DNA (non-viral) mediated by viruses. There are two types - specialized and generalized
What is transformation?
Acquisition of free DNA from the environment
What is two-component sensory transduction?
Characteristically, such systems include two different proteins: 1) a specific sensor protein located in the cell membrane.
2)A partner response regulator protein.

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