Chapter 9 review Flashcards
Mutations
Heritable change in genome
Spontaneous mutations
Occur without
external intervention
most mutations occur by
Most result from occasional errors by D N A polymerase
during replication
Induced mutations are caused
environmentally or deliberately
what Can result from exposure to natural radiation or chemicals
that chemically modify D N A
induced mutations
Types of Mutations
Base pair substitutions
Frameshift mutations
Reversions
Silent mutations
Missense mutations
Nonsense mutations
What type of mutation does the Ames test detect?
Revertant mutations that restore the ability to synthesize histidine.
What type of organism is used in the Ames test?
A strain of Salmonella with a mutation in the his gene (histidine auxotroph).
Why can’t the test strain grow on minimal media?
It cannot synthesize histidine due to a his gene mutation.
What does growth on minimal media without histidine indicate?
A mutation (reversion) restored the ability to produce histidine.
What is the role of minimal medium in the Ames test?
It selects for revertants that can grow without added histidine.
Why is the test strain more sensitive to mutagens?
It has mutations that inactivate nucleotide excision repair (NER) and increase cell wall permeability.
What does a high number of colonies on minimal media suggest?
The chemical being tested is likely mutagenic
Why is the Ames test considered simple and sensitive?
It detects rare revertants using a straightforward growth assay.
What are two genetic modifications in the Ames strain (besides his mutation)?
1) Defective NER system
2) More permeable cell wall
What is the purpose of the NER-deficient mutation in the test strain?
To prevent repair of induced mutations, increasing test sensitivity.
What do genomic islands provide evidence for?
Horizontal gene transfer.
What are genomic islands?
Segments of DNA in a genome that have been acquired through horizontal gene transfer
Name three types of genomic islands.
Pathogenicity islands, symbiosis islands, and fitness islands.
What are pathogenicity islands?
Genomic islands that carry genes contributing to a microorganism’s ability to cause disease.
What are symbiosis islands?
Genomic islands that contain genes involved in establishing beneficial relationships with hosts.
What are fitness islands?
Genomic islands that provide advantages for survival in specific environments.
What protein is essential for homologous recombination in Bacteria, Archaea, and most Eukarya?
RecA
What is the first molecular event in homologous recombination?
An endonuclease nicks one strand of the donor DNA molecule.
What enzyme separates the nicked strand from the other strand in homologous recombination?
Helicase
After helicase action, what binds to the single-stranded DNA?
Single-strand binding protein and RecA
What is strand invasion in homologous recombination?
The single-stranded donor DNA base pairs with the recipient DNA, displacing one of its strands.
What forms when the donor and recipient DNA strands pair?
A recombination intermediate with heteroduplex regions.
What are heteroduplex regions?
DNA regions where each strand comes from a different chromosome.
What are the possible outcomes of homologous recombination
“Patches” or “splices” of DNA.
What is horizontal gene transfer?
The movement of genetic material between organisms other than by descent from parent to offspring.
What is transformation in bacteria?
The uptake and incorporation of free DNA from the environment into a bacterial genome.
What type of DNA is taken up during transformation?
Free/naked DNA from lysed cells.
What makes a bacterial cell “competent”?
Its ability to take up foreign DNA from the environment.
What is transduction in bacteria?
Transfer of DNA from one bacterium to another via a bacteriophage (virus).
What are the two types of transduction?
Generalized and specialized transduction.
What happens during generalized transduction?
A random piece of host DNA is packaged into a phage and transferred to another cell.
What happens during specialized transduction?
Only specific bacterial genes near the prophage are transferred by the virus.
What is bacterial conjugation?
The direct transfer of DNA between two bacteria via cell-to-cell contact.
What structure is required for conjugation?
A sex pilus (produced by the donor cell).
What is the F plasmid?
A fertility plasmid that carries genes for pilus formation and DNA transfer in conjugation.
What is an Hfr cell?
A bacterium with the F plasmid integrated into its chromosome, allowing chromosomal gene transfer.
Can bacteria transfer genes across biological domains?
Yes, some bacteria can transfer genes to organisms in other domains of life.
What bacterium causes crown gall disease in plants?
Agrobacterium tumefaciens
What special plasmid does Agrobacterium tumefaciens carry?
The tumor-inducing plasmid (Ti plasmid)
How does Agrobacterium tumefaciens transfer the Ti plasmid to plants?
Via conjugation
What happens to plant cells when they receive the Ti plasmid?
They form tumors (crown galls)
What surprising discovery was made about gene transfer from humans?
DNA transfer from humans to bacteria has been observed.
Which bacterium was found to acquire human DNA?
Neisseria gonorrhoeae (strain L1)
What are mobile genetic elements?
DNA sequences that can move from one location to another within a genome.
What are transposable elements?
Segments of DNA that can move between or within chromosomes.
Where are transposable elements found?
In virtually all life-forms.
What is an insertion sequence (IS)?
A simple transposable element containing only a transposase gene and flanking inverted repeats.
What enzyme do insertion sequences use to move?
transposase
What are the short DNA sequences flanking an IS element called?
Inverted repeat sequences
What is the function of the transposase enzyme?
It recognizes the inverted repeats and cuts the DNA to move the IS element.
What are the two mechanisms by which IS elements can transpose?
Replicative transposition and nonreplicative transposition.
What happens in replicative transposition?
The IS element is copied, and the copy is inserted at a new site while the original stays in place.
What happens in nonreplicative transposition?
The IS element is cut out of its original location and inserted into a new site (also called “cut and paste”).
What are transposons?
Complex transposable elements that carry additional genes, such as antibiotic resistance genes.
How are transposons different from insertion sequences (IS)?
Transposons carry extra genes (e.g., drug resistance), while IS elements only contain transposase
Name three types of transposons.
Composite transposons, complex transposons, and conjugative transposons.
What is a composite transposon?
A transposon consisting of two IS elements flanking additional genes (like antibiotic resistance).
What is a conjugative transposon?
A transposon that can transfer between cells via conjugation.
What is the significance of transposons in medicine?
They can spread antibiotic resistance genes between bacteria.
how can bacteria protect themselves
successdul infection
modification of virus receptor
restriction endonucleases degrade dforeign dna
phage exclusion- enzyme modifies viral dna preventing replication
absortive infection- host cell committs suicude to avoid infection
crispr- cas system specifically recognizes foregn dna and degreades it.
What is the restriction-modification system?
A bacterial defense mechanism involving the cleavage of foreign DNA (restriction) and the protection of host DNA (modification).
What is the role of restriction endonucleases in the restriction-modification system?
They enzymatically cleave foreign (alien) DNA to protect the host from invaders.
What is the protective modification that occurs in the restriction-modification system?
Methylation of host DNA to protect it from being cleaved by restriction endonucleases.
What is the function of methylation in the restriction-modification system?
Methylation marks the host’s DNA as “self,” preventing it from being cut by its own restriction endonucleases.
Why is restriction-modification important for bacteria?
It protects bacteria from viral (bacteriophage) infections by cleaving foreign DNA while preserving the integrity of their own genome.
What does CRISPR stand for?
Clustered Regularly Interspaced Short Palindromic Repeats.
What is the function of the CRISPR system?
It seeks and destroys foreign nucleic acids, such as viral DNA.
What are the repeating sequences in CRISPR made of?
Short repeats of host DNA sequences alternating with short variable DNA sequences called spacers.
What is the purpose of the spacers in the CRISPR system?
The spacers act as a “memory bank” storing sequences of DNA that have previously invaded the cell.
What are CRISPR-associated (Cas) proteins?
Proteins that work with CRISPR to perform endonuclease activity, cutting foreign DNA
What are the two main functions of the CRISPR system?
Defense – Destroy foreign DNA.
Incorporate new spacers – Add new spacer sequences to the CRISPR region for future defense.
How do Cas proteins recognize viral DNA?
Cas proteins recognize specific PAMs (protospacer adjacent motifs) in the viral DNA.
What happens when Cas proteins recognize a viral DNA with a PAM?
Cas proteins cleave the viral DNA near the PAM and insert a short segment of the viral DNA into the host chromosome as a spacer, providing genetic memory.
What happens when the cell encounters the same virus again?
The CRISPR system recognizes the viral DNA and destroys it through an RNA-dependent process.
What is pre-CRISPR RNA (pre-crRNA)?
Pre-crRNA is a long RNA transcript processed into smaller spacer RNAs (crRNAs).
What is the role of crRNA in the CRISPR system?
crRNA associates with Cas proteins and guides them to complementary viral DNA to direct cleavage.
How does CRISPR interfere with viral DNA?
The viral DNA:crRNA complexes are cleaved and degraded, effectively interfering with the viral DNA.
How widespread is the CRISPR system in nature?
CRISPR is found in 90% of Archaea and 70% of Bacteria.
What are some ways viruses have evolved to avoid CRISPR defense?
Mutating PAM regions
Producing Cas protein inhibitors
Phage-encoded CRISPR (found in some bacteriophages)
How do mutations in the PAM region help viruses avoid CRISPR?
Mutating the PAM region prevents Cas proteins from recognizing and cleaving the viral DNA.
What is the role of Cas protein inhibitors in viral defense against CRISPR?
Viruses may produce inhibitors that block the action of Cas proteins, preventing DNA cleavage.
Where is phage-encoded CRISPR found, and what does it do?
In the Vibrio cholerae bacteriophage, phage-encoded CRISPR targets and interferes with the host Vibrio defense system.
