Glossary of Bio 181: Genetics of Viruses and Prokaryotes

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What is a varion?
It consists of a DNA or RNA genome and a few proteins (virus).
What are some of the advantages of studying gene expression in viruses and bacteria?
-Contain much less DNA
-Grow and reproduce rapidly
-Haploid genomes
-Readily exchange DNA, allowing genetic analysis
-Mechanisms are models for regulating gene expression in Eukaryotes
What's one definition of virus?
Obligate Intracellular Parasites
What are bacteriophages?
Viruses that infect bacteria.
Describe the Lytic Cycle of a bacteriophage.
-Phage DNA is injected into host bacteria
-Bacteria is converted to factory to replicate phage DNA and translate phage proteins
-New virions are assembled
-Host cell bursts releasing new particles to infect other bacteria
Describe the Lysogenic Cycle of a bacteriophage.
-Viral DNA is inserted into the bacterial chromosome
-Further infection of the host bacteria is blocked
-Virus remains quiescent for many generations
-When conditions are appropriate, virus enters lytic cycle.
What is decieving about a bacteria cell in the Lysogenic Cycle?
The cells genetic information contains the DNA of a virus. This virus remains "dormant" within the cell, and may enter the Lytic Cycle with conditions are right.
What is a retrovirus? Give an example.
A retro virus is a virus in which RNA genomes are replicated through a complementary DNA intermediate.
Example: HIV
Most of the important principles for control of gene expression were first discovered in bacteria. Why?
-Ease of handling
-Short generation time
-Large numbers
-Molecular mechanisms are universal
-Prokaryotic Genes Mutate
-Mechanisms for exchange of DNA between prokaryotic cells exist
What is bacterial congugation?
genetic recombination in bacteria; the direct transfer of DNA from one bacterium to another
Describe the mechanism of DNA transfer between bacteria during conjugation.
-"Male" bacteria have genes termed "F-factor" for formation of a sex pilus
-Sex pilus brings two cells together
-Transfer of DNA occurs in the conjugation tube inside sex pilus
-Normally only a portion of the donor chromosome is transferred
-"Female" become "Male" following conjugation
Describe how recombination occurs following DNA transfer.
-DNA from a donor cell can be incorporated into the chromosome of the recipient cell
-Homologous segments of chromosome can recombine
-The resulting recombinant chromosome is the explanation for the Lederberg-Tatum experiment
Describe bacterial transformation
-Some bacteria can spontaneously absorb DNA from their environment. DNA may have come from dead bacterial cells.
-Following DNA uptake, recipient bacteria can incorporate the DNA into their genomes by recombination
Describe transduction. What are the two types of transduction.
Transduction is the genetic transfer by a virus carying baterial DNA.
-Specialized transduction: Specific bacterial gene(s)
-Generalized transduction: Bacterial DNA replaces virus DNA
What are plasmids?
Extra chromosomes in bacteria.
What is a bacterial Fertility Factor (F-factor)?
An extra chromosomal DNA element in the cell (carried in a plasmid) that codes for the synthesis of proteins necessary for recombination and conjugation.
-Cells with F-factors are called F-plus or "male"
-Transfer of a copy of the F-factor to a recipient F-minus ("female") cell causes the recipient cell to become male (F-plus)
F-factor plasmids can be created that carry other genes into cells in addition to the fertility factor. What is one of the results, and how is it important?
-The result can be a partial diploid cell line, containing different alleles of the same gene
-Such lines are important in genetic analysis of gene regulation
What are R-Factors?
Plasmids with antibiotic resistance genes.
Describe R-Factors.
• Carry genes coding for enzymes that inactivate or destroy antibiotics
• Many have multiple antibiotic resistance genes
What are some other plasmids?
• Metabolic enzymes, i.e. special pathways
• Pathogenic factors
What happens in the absence of the inducer lactose (during absence of lactose)?
The repressor protein binds to the operator, preventing transcription of the operon.
The Lac Operon DNA Sequence Consists of 4 Elements. What are there?
1. The promoter and structural gene for the repressor protein, lac I
2. The operator region (o) to which the repressor binds
3. The promoter for the lac structural genes, Plac
4. The structural genes for the three enzymes lac Z (b-galactosidase), lac Y (beta-galactoside permease) and lac A (thiogalactoside transacetylase.
What is a promoter?
A Promoter is a binding site for start of RNA synthesis (on DNA).
What is an operator?
An Operator is a binding site for protein that blocks transcription.
What do promoter-operator interactions regulater?
The transcription of mRNA for enzymes.
What is an inducer?
The compound that stimulates the synthesis of inducible enzymes
What type of proteins are those required for utilization of lactose in E. coli?
Inducible proteins
There is a lag period before the metabolism of lactose begins. Why?
The enzymes required for lactose metabolism must be synthesized, i.e. Transcription and Translation (Gene Expression) occurs.
What are constitutive genes?
Genes that are expressed at all times under all conditions of growth, i.e. transfer RNA, ribosomal RNA, ribosomal proteins, RNA polymerase, glycolysis enzymes (glucose metabolism).
What are inducible genes?
Genes that are expressed at a high level only at certain times or only under certain defined conditions; at other times they are expressed at a very low level, i.e. enzymes for amino acid biosynthesis, enzymes for metabolism of specific energy sources (i.e. lactose metabolism).
What are transposable elements?
-DNA elements that guide their insertion at new chromosomal locations
-Gene movement within an individual cell
What is one result from transposon insertion?
new phenotypes
What are transpons? and how do transpons on plasmids function?
-Transpons are genes flanked by two transposable elements that are copied and inserted as a unit.
-Transpons on plasmids can transfer genes to recipient cells.
What happens when lactose is present?
In the presence of lactose, the repressor is allosterically altered such that it does not bind to the operator. In this case, mRNA is synthesized. Proteins are translated from this polycistronic mRNA.
Is the repressor gene (lacI) constitutive or inducible?
What is the repressor? and what happens when it is allosterically altered by the inducer?
-The repressor is the regulatory protein that blocks transcription
-The inducer causes the repressor to change shape, and not bind the operator
An example of a repressible system is the trp operon, which contains genes for five enzymes that convert precursor to tryptophan. How is this system different from that of the lac operon?
The lac operon is INDUCED when enzymes are needed. On the other hand, the trp operon is always active unless REPRESSED by corepressors in the presence of trp (trp itself is a repressor).
Describe the example of catabolite expression in E. Coli.
If glucose and lactose are both present in the growth media (or the human intestine), E. coli will preferentially use glucose for growth until it is all consumed. Only then will the cells express enzymes for the metabolism of lactose.
In E. Coli, what is the intracellular signal for low glucose?
What happens when glucose levels fall?
-when glucose levels fall, cAMP levels rise.
When glucose levels are low in E. coli, cAMP binds to cAMP receptor protein and forms the cAMP-CRP complex. Instead of preventing the synthesis of enzymes, the complex...?
...enhances the binding of RNA polymerase to the promoter.
What happens when cAMP is absent in E. coli?
RNA polymerases "bounce off" the promoter, and transcription is reduced.
In studies of Mycobacterium genitalium,
what Categories of Genes were not Dispensable for cells grown in the laboratory in a nutrient-medium?
1. Ribosomal protein and ribosomal RNA genes
2. Transcription machinery
3. Translation apparatus
4. DNA metabolism
5. 111 genes of unknown function
6. 10 genes for glycolysis enzymes
7. 8 genes for ATP-proton-motive force interconversion
8. 12 ATP-binding proteins, possibly transporters
What is the Minimal Genome Required for Life (smallest known genome to date)?
Mycobacterium genitalium
What is genomics?
DNA Sequence Analysis of chromosomes
How does an inducer function?
The inducer binds to the repressor protein and induces a conformational change so that the repressor does not bind to the operator DNA sequence.
An E. coli strain is lac Z. The structural gene for ß-galactosidase is encoded at the lac Z locus. How would you describe the regulation of lactose metabolism in these cells?
-Inability to synthesize the lac Z gene product, ß-galactosidase.
-Cells mutated in the structural gene lac Z which encodes the enzyme ß-galactosidase cannot synthesize the enzyme.
Cells of an E. coli strain that are trp- lac Z- met+ bio+ were mixed with cells of an E. coli strain that are trp+ lac Z+ met- bio- and cultured for several hours. How did these few cells become trp+ lac Z+ met+ bio+?
Who first decribed conjugation between bacteria?
Lederberg and Tatum
What is sexduction?
-a special type of conjugation
-The process by which autonomous pieces of DNA are carried into an F bacterium by an F factor DNA is called sexduction.
Describe why the following Z genes were able to grow on minimal medium: the lac Z allele on the bacterial chromosome and the lac Z allele on the F' episome.
E. coli cells with an F' episome may have more than one allele of a particular gene. In this case the lac Z allele of the F' episome is dominant to the lac Z allele of the bacterial chromosome. When cells are partially diploid for one or a few genes, dominance among the various alleles can be experimentally studied.
Describe the normal regulation of lactose metabolism.
Plac O lac Z DNA sequence on the episome is regulated by the repressor and CRP protein encoded on the bacterial chromosome.
What would happen to the expression of lac Z+, if an Oc mutation prevents binding of the repressor?
Expression of lac Z+ would be constitutive, and Lac Z mRNA is synthesized even in the absence of the inducer.

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