Microbiology Chapter 9

Transduction

A virus or bacteriophage moves DNA from one bacterial cell to another. When certain viruses are formed within the bacterial cell, they may package bacterial DNA and then transfer that bacterial DNA to other organisms.

When an organism forms a symbiosis with another organism, sometimes certain genes are no longer needed by one of the organisms because it is being provided to them by the shared relationship. Loss of the traits in the absence of selection pressure is called...

degenerative evolution

Phylogenetic trees

depict these evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics

A common strategy of practical identification of a microbial species is through the use of a

dichotomous key

We can use non-sequence based methods to ID microorganisms as well including

dichotomous keys or Probabilistic Indicator tests

A molecular clock is a gene whose sequence can be used to measure

divergence time of a particular gene sequence

In conjugation, one cell act as a _____ & another cell acts as a _____.

donor, recipient

When culturing phages, the period right after infection when phages cannot be detected in growth medium because they have injected their nucleic acid into their host cells is called the...

eclipse period

There are viruses that exist in the world that can infect...

eukaryotes, prokaryotes, plants, and archea

We can use DNA as a tool to determine and predict the ________ using different bioinformatic tools

gene function

Analogous genes

genes that have identical or similar function but don't share a common ancestor and are therefore unrelated as opposed to homologous genes

Conjugation is an exchange of the ________ within two cells that is in direct contact with each other or by forming a temporary bridge-like connection between two cells.

genetic materials

Phylogeny is the evolutionary _____ and _________ of organisms

history, relatedness

In general, __________ are genes that evolved from a common ancestral gene

homologous genes

Drivers of natural selection

include many factors, primarily environmental stressors like nutrient availability, temperature, pH, antibiotic presence, exposure to chemical agents, etc.

Bacteria do not ______ so we can track genetic drift in sequences and see how sequences diverge, or become more dissimilar over time

interbreed

What type of bacteriophage infection results in immediate death of the host cell?

lytic

Generalized transduction events are more associated with the __________ viral lifecycle, whereas specialized transduction events are more associated with the _____________ viral lifecycle.

lytic ; lysogenic

Some genes within a genome have mobility within the chromosome. Some genes can be referred to as ________ and are __________

mobile genetic elements, transposable

We can track genetic changes in a gene using a

molecular clock

Meaningful evolution

occurs when a changed trait (a mutation) affects survival of an organism

Classification

organizing life into groups (taxa)

Two types of homologous genes include

orthologs and paralogs

An organism is more evolutionarily "fit" if it is able to produce more

progeny

As DNA replicates, mutations accumulate at random and we can track the changes in ______ back to their ancestors to see how a gene changes over time

progeny

The new DNA that is added into a bacterial chromosome can incorporated via

recombination

If the newly incorporated DNA is able to survive to a replication event, one of the newly produced cells will ______________ and the other new cell will______________

retain the original genotype prior to the recombination event, have the new genotype from the recombination event

Generalized recombination

The new DNA sequence has to have fairly high sequence homology (similarity) to the host chromosome.

Transduction summarized

The process by which a virus transfers genetic material from one bacterium to another

Transformation summarized

The process of importing free DNA in the environment into bacterial cells

Transposition

The removal and the transfer of a segment of DNA from one site to another of the same or different chromosome

Put the general stages of the lytic lifecycle of a virus in order

Adsorption, penetration, replication, maturation, release

Three domains of Life

Archaea, Bacteria, and Eukarya

Transformation

Bacterial cell takes up foreign DNA from the environment. Transferring the free DNA which is liberated from the donor to the extracellular surrounding results in assimilation and typically an expression of the acquired characteristic in the recipient bacteria (*** For example, the experimental design of Fred Griffith with virulent and aviruelnt strains of Streptococcus pneumoniae)

Double-Stranded DNA Recombination

Both strands of DNA in a particular region that matches sequence homology to the new DNA piece is cut out and both strands of the new incoming DNA are incorporated into the host chromosome

A particular virus can cause disease in a wide variety cell tissues, including skin cells, respiratory cells, and mucosal cells. Because it can infect multiple types of cellular tissue, this virus is said to have ________________.

Broad tissue tropism

Generalized recombination is a huge player in

DNA and gene repair

In conjugation it is termed as sexual reproduction of bacteria as two cells are involved and directly interact with each other for their _________.

DNA exchange

Conjugation

DNA gets transferred between two bacterial cells through a tube.

Conjugation summarized

Direct DNA transfer from one bacterial cell to another through the use of a sex pilus

Comparing the DNA sequences also allow us to see which regions of DNA may have come from a foreign source by tracking things like GC content and analyzing regions of foreign DNA in the form of

Genomic or Pathogenicity Islands

Paralogs

Gene or gene set in a single species undergo a duplication event within that organism's chromosome and eventually, one set of those genes evolves to carry out a completely different function than the original form of that gene

Two main types of Transduction events

Generalized and specialized transduction

Orthologs

Genes that are found in different species, that evolved from the same common ancestor and the gene functions relatively the same in both different species of bacteria

If 100% of the DNA contents inside a viral capsid of a transducing bacteriophage was DNA from the host bacterial chromosome, what would happen when the bacteriophage infected a new bacterial cell?

No more bacteriophage would be synthesized, as there is no bacteriophage genome available to direct synthesis of new viruses

Single-stranded DNA Recombination

Only one section of one strand of DNA is replaced by new DNA

The gene proV codes for an ABC transport protein responsible for bringing proline or glycine betaine into the cell in response to osmotic stress. This gene serves a similar function in both species of Salmonella enterica and Escherichia coli. This is an example of __________ genes.

Orthologous

Shigella dysenteriae undergoes a duplication event of a gene set and now has two copies of that gene set in its chromosome. Over time, one of the gene sets mutates and evolves and takes on a different function independent of the original gene set. This is an example of what type of gene?

Paralogous

Degenerative evolution happens often in

Parasitic or some commensal relationships, when one party is providing that particular component for the symbiont, and so the symbiont gets rid of that particular gene from its chromosome over time as it is no longer needed

which lines up homologous sequences for DNA exchange

RecA (recombinase A)

Defining a species is part of the task of

Taxonomy

Degenerative or reductive evolution

The loss of genes due to lack of selective pressures

Three forms of horizontal gene transfer

Transformation Conjugation Transduction

The use of overlapping reading frames in viral genetics leads to

a shorter genome size

Probabilistic Indicators

can be used for identification - a battery of biochemical tests performed simultaneously on an isolated strain

Nomenclature

standardized system of naming living things

Transposable refers to

the ability of genes to move or jump from one region in a chromosome to a different region

Bioinformatics

the application of computation and analysis tools used to capture and interpret biological data, especially that of DNA sequence analysis

An enveloped virus obtains its envelope from...

the cell membranes of the host cell

Genetic Drift

the change in frequency of an existing gene variant in the population due to random chance

The Baltimore model classification of viral groups is based on all of the following EXCEPT...

the number of progeny that a virus produces from one infected host cell

This newly incorporated DNA can sometimes be seen as replication errors, and may repaired and converted back into

the previous host cell DNA

Specialized transduction

the process by which a restricted or specific set of bacterial genes are transferred to another bacterium. The genes that get transferred (donor genes) depend on where the phage genome is located on the chromosome as an incorporated part of the bacterial host genome

Generalized transduction

the process by which any bacterial gene may be transferred to another bacterium via a bacteriophage, and typically carries only bacterial DNA and no viral DNA. In essence, this is the packaging of bacterial DNA into a viral capsid

Natural selection

the process whereby organisms better adapted to their environment tend to survive and produce more offspring

Phylogeny

the relationship between all the organisms on Earth that have descended from a common ancestor, whether they are extinct or extant

Recombination is...

the transfer and integration of new DNA into the chromosome

Horizontal gene transfer

the transfer of genes from one organism to another coexisting organisms

Why might an organism undergo recombination of DNA that is homologous (the same) to its own?

to repair its own damaged genome

Generational passing of genes from parent to offspring is called

vertical transfer

A molecular clock can only be used to track gene mutations in genes that are inherited _______, not _________

vertically, horizontally

Which of the following is NOT a domain of life?

viruses