Last Minute Flashcards
A bacterial strain lacking the RecA protein will be
unable to perform generalized recombination
RecA is involved in generalized recombination. Phase variation is an example of site-specific recombination, which does not require RecA.
A mutation always results in
change in genotype
Any change to the DNA sequence results in a change in the genome. Mutations may be beneficial or neutral. A neutral or silent mutation may not affect the phenotype.
An insertion sequence contains a gene for this enzyme
Transposase
An insertion sequence (IS) is a simple transposable element that consists of a transposase gene flanked by short, inverted repeats that are the target of transposase.
Avery, MacLeod, and MacCarthy performed landmark experiments showing transformation in which bacterium?
Streptococcus pneumoniae
Studies identifying transformation were performed in the 1940s using Streptococcus pneumoniae.
Bacteria may donate DNA to
other bacteria of the same or of a different species, some eukaryotic cells, and bacteriophages.
Bacteria can donate DNA to a wide variety of other cells and also viruses. For example, the bacterium Agrobacterium tumefaciens can transfer DNA into plants and phages can acquire bacterial DNA during infection.
Based on gel electrophoresis, a nonfunctional protein is found to have a smaller molecular weight than its wild-type counterpart. A likely explanation for this observation is a
nonsense mutation in the DNA coding for the
protein
A nonsense mutation causes a premature stop codon, shortening the protein and lowering its molecular weight. A silent mutation does not change sthe amino acid sequence of the protein. A missense mutation, which replaces one amino acid with another, is unlikely to have a large effect on protein molecular weight. A duplication of the DNA may change the amount of protein being produced, but not its molecular weight.
DNA encoding for which capability is part of the flexible gene pool?
Antibiotic resistance
Not all organisms need to contain the genes encoding resistance to specific antibiotics. Genes encoding enzymes involved in DNA replication, ribosome synthesis, and cell membrane synthesis are part of the core gene pool, which consists of genes needed by organisms for independent growth and replication.
During DNA synthesis, if DNA polymerase incorporates a wrong nucleotide,
methyl mismatch repair will correct the unmethylated daughter strand to match the methylated template strand.
DNA polymerase is very accurate, but not 100% accurate. Methyl mismatch repair may catch and fix mistakes. The parent strand is methylated and the newly synthesized daughter strand is at first unmethylated, so the unmethylated strand gets repaired.
Horizontal gene transfer can occur via
Conjugation, transformation, and transduction can all lead to horizontal gene transfer.
If a bacterial cell is competent, it means that
the bacterium can import free DNA fragments and incorporate them into its genome
Competence refers to the ability to perform transformation.
If a bacterial cell is missing AP endonuclease genes, which of the following could NOT occur
Base excision repair
AP endonucleases are used during base excision repair, after a glycosylase removes a damaged base, forming an AP site.
If a cytosine deaminates and becomes a uracil, which enzyme will cleave the uracil from the DNA backbone in the first step of a repair process?
Glycosylase
Glycosylases remove damaged or wrong bases from the phosphodiester backbone in an early step of base excision repair.
In generalized recombination, which protein complex is responsible for homology searching?
RecA
During generalized recombination, the RecA protein complex finds homology and mediates strand invasion.
In the basic Ames test for mutagenesis, a mutagen is tested to see if it can
produce colonies on basic medium that lacks
histidine, starting with a hisG mutant strain of bacteria
The Ames test is a reversion test, meaning that the mutagen is tested to see if it can restore the ability to synthesize histidine to hisG mutant bacteria.
One sign of horizontal gene transfer is
GC base ratio different from flanking chromosomal DNA
Each type of microorganism has particular GC ratios. Regions of the genome with highly different ratios may be example of genes acquired via horizontal transfer. Uniform codon usage argues against horizontal gene transfer. Gene duplication may occur during replication, but this is not a form of horizontal gene transfer. Gene loss may lead to pathogenicity, but gene loss is not horizontal gene transfer.
Over time, the genome of a species
may change due to mutation or gene swapping
Over time, genomes change due to a variety of different mechanisms. Harmful mutations will not persist in a population and although whole genomes may double, this is a rare event.
Pathogenicity islands (PAIs) are often found integrated near
tRNA genes
The tRNA genes often serve as sites of PAI integration.
Replicative transposition differs from nonreplicative transposition in that
only replicative transposition results in the insertion sequence appearing in new host DNA, while still remaining in the original DNA site
The term “replicative” refers to whether the DNA element is replicated (replicative) or excised and moved (non replicative).
Site-specific recombination
needs very little sequence homology between the donor and recipient DNA
Unlike generalized recombination, which requires RecA and large regions of sequence homology, site-specific recombination requires only minimal regions of homology.
The enzyme photolyase repairs DNA damage caused by
UV radiation
The mutation rate in a wild-type E. coli cell is on the order
of
10^–9 per base pair replicated
The mutation rate in a cell is approximately 10^–9 to 10^–10 per base pair replicated.
The process of importing free DNA from the environment into cells is called
transformation
Transformation is the uptake of DNA from the environment. Conjugation requires cell-cell contact, transduction is mediated through a bacteriophage, and transcription is the production of an RNA complementary to a DNA template.
The relaxase enzyme, used during conjugation, has which enzymatic activity?
Endonuclease
Relaxase nicks the phosphodiester backbone at oriT site on the fertility factor prior to transfer of a single strand into the recipient cell.
Transduction is an example of
horizontal gene transfer
Transduction, the acquisition of a gene from a bacteriophage, is an example of horizontal gene transfer. It does not imply gene duplication, although this may occur. Vertical gene transfer occurs during cellular DNA replication and cell division.
Transposable elements differ from plasmids in that only plasmids
may exist autonomously, not integrated into host DNA
Transposable elements may “jump” from one DNA molecule to another, but they do not replicate independently as plasmids can. Both plasmids and transposable elements are comprised of dsDNA and both may code for antibiotic resistance. Conjugative transposons may be transmitted horizontally.
Uptake of foreign DNA into a bacterium
may help or harm the bacterium
Bacteria can take up foreign DNA via transformation, conjugation, or transduction. Uptake of foreign DNA may be harmful or helpful depending on what the DNA codes for. For example, uptake of genes that encode useless products drain energy from the bacterium, whereas some plasmids can confer antibiotic resistance, which can be helpful if the bacterium is exposed to that particular antibiotic.
Purines such as guanine are susceptible to spontaneous hydrolysis of the glycosidic bond connecting the base to the sugar backbone. This leads to an apurinic site in a process known as
depurination
Which function do bacterial pheromones promote?
Conjugation
Pheromones are signaling molecules that help facilitate “bacterial sex,” also known as conjugation.
Which of the following can cause mutations?
Chemical mutagens, UV radiation and spontaneous mutations during DNA replication
Which of the following DNA repair mechanisms is error prone?
SOS repair
SOS repair, which is error prone, only occurs during extreme DNA damage. Methyl mismatch repair, nucleotide excision repair, and photoreactivation are error proof.
Which of the following enzymes is used in methyl mismatch repair, nucleotide excision repair, and base excision repair?
DNA polymerase I
DNA polymerase I is used to synthesize new, correct DNA in all of the repair mechanisms listed. The other enzymes are specific to certain types of repair mechanisms.
Which of the following is a laboratory technique for inducing transformation?
Electroporation
Electroporation makes the membrane temporarily permeable to DNA so researcher-supplied DNA can be taken into bacterial cells. The translocasome is involved in natural transformation. Conjugation via sex pili is not a lab technique.
Which of the following is a mutation?
A harmful deletion of part of an organism’s DNA
A single base change that enhances fitness
A change in the DNA that does not change protein
structure
Which type of DNA uptake is dependent on transferable plasmids?
Conjugation
A transferable plasmid is needed when one cell directly transfers DNA to another cell as occurs in conjugation. Transformation, the uptake of DNA from the environment, and transduction, the acquisition of a gene from a bacteriophage, do not
require a transferable plasmid.
Which type of DNA uptake is dependent on viruses?
Transduction
Transduction requires bacteriophages, viruses that infect bacteria, to transfer DNA. Conjugation, the direct transfer of DNA from one bacterial cell to another, and transformation, the uptake of DNA from the environment, do not rely on viruses.
A DNA microchip, scanned with cDNAs, can give information about
the transcription of specific genes
Scanning a DNA microchip with cDNAs prepared from mRNAs can give information about which mRNAs were present in the cell.
Accumulation of the heat-shock sigma factor, sigma H, increases at high temperatures because
at high temperatures sigma H mRNA adopts an unfolded secondary structure
At normal temperatures the sigma H mRNA adopts a folded secondary structure that hides the ribosome binding site limiting translation. At higher temperatures this secondary structure is lost and the ribosome binding site becomes available.
Acyl homoserine lactone produced by luxI of Allivibrio fisherii is an example of
an autoinducer
Acyl homoserine lactone is an autoinducer. High environmental concentrations of the autoinducer lead to transcription of the lux operon, production of luciferase, and bioluminescence.
An inducer causes gene expression by binding
a repressor protein to remove it from the DNA
Inducers activate gene transcription by binding a repressor protein and removing the inhibitory repressor from DNA.
Anti-anti-sigma factors
bind anti-sigma factors, releasing sigma factors to activate transcription
Anti-anti-sigma factors allow sigma factors to work by binding and inhibiting anti-sigma factors.
AraC is one of a large family of AraC-like proteins. What do all these proteins have in common?
They all contain a high degree of homology to AraC and XylS
The AraC-like proteins all contain two helix-turn-helix DNA-binding motifs, although these recognize different consensus sequences. They are not homologous in the ligand-binding domain.