Microbial Genetics Flashcards
Most complex microbial genome is a ____ genome. My can be single or double stranded ____ and ___
Viral
DNA
RNA
____ sense RNA genome means it is not translatable at that time
Minus
Eukaryotic cells can have ____ similar to bacteria
Plasmids
Chloroplast DNA, mitochondrial DNA, and nucleus DNA can all replicate ____ of each other
Independently
Prokaryotic DNA is ____ and they usually have plasmids as well
Circular
Prokaryotic cells have a ____ genome than eukaryotes but still too large to fit in the cell
Smaller
Bacterial chromosome replication:
____ ____ __ synthesizes the DNA.
DNA polymerase III
The enzymes involved in bacterial DNA replication are just different enough to eukaryotic enzymes, that you can ___ them with antibiotics. Especially the ______ enzymes in bacterial
Target
Topoisomerase I
_____ unzips the DNA helix
_____ synthesizes the RNA primer
____ ____ synthesizes the DNA
___ _____ removes the primer, repaired mismatches
Helicase
Primase
DNA Polymerase III
DNA Polymerase I
Bacterial chromosome replication takes place across two ____ ____ that move it opposite directions until they get all the way across the circular structure
Replication forks
Diagram of bacterial chromosome replication:
The ____ ____ is when the bacterial chromosome is midway through replicating. The ___ must be resolved to detach the two chromosomes and ____ repairs the nick
Theta phase
Nick
Ligase
Flow of generic information in microbes:
DNA is transcribed into _____ which is translated into ____
RNA
protein
Microbes have
tRNA, mRNA, rRNA, micro RNA, interfering RNA, riboswitches, antisense RNA, similar to eukaryotes. Microbes also have ____ over the gene expression
Control
Compare and contrast gene expression strategies in bacteria and eukaryotes:
DNA dependent RNA polymerase (DdRp) is and enzyme that polymerizes ___ and uses ___ as a template
RNA
DNA
RNA polymerase ___ makes the messenger RNA in eukaryotes. There is ___ RNA polymerase in prokaryotic cells
II
One
In prokaryotes, transcripts that encode for protein are ____ meaning you can have one long RNA that can be translated into multiple types of proteins
Polycistronic
In prokaryotes the transcription is controlled by variants of the ____ ___
In eukaryotes, there are ___ different types of transcription factors
Sigma factor
Many
Translation is the same in prokaryotes and eukaryotes but the ___ of the ribosome is different.
Prokaryotes: ___ + ___ = 70S
Eukaryotes: ___ + ___= 80S
Structure
30S 50S
40S 60S
Viral gene expression strategies:
All viruses have the ability to be able to express viral protein is completely dependent on the ___ ____.
Host cell
Bacterial gene expression control:
Most ___ ____ ___ interact with DNA in a sequence specific manner. They manly bind to the ___ ___ of DNA. ____ ____ frequently are binding sites for regulatory protein, allows for better affinity
DNA-binding proteins
Major groove
Inverted repeats
Outcomes of DNA binding proteins:
1. It may _____ a specific reaction on the DNA
2. They can block transcription called ___ ___
3. They can activate transcription called ___ ___
Catalyze
Negative regulation
Positive regulation
_____ is a cluster of genes arranged in a linear fashion whose expression is under the control of the single operator. The operator is located downstream of the _____. Transcription is ___ blocked when a repressor binds to an operator, which is called __ ___
Operon
Promoter
Physically
Negative control
Diagram of operon:
____ ____ binds to the promoter region in the operon
RNA polymerase
A repressor protein needs a _____ molecule to become active. The _____ is usually what the gene is transcribing, creating a ___ ___ loop.
Corepressor
Corepressor
Negative feedback
Diagram of operon off:
Another form of negative control:
The lac operon is normally off because the repressor protein is already in the correct ___ to bind. When ____ is added it pulls the repressor out of the way, which is called an ____. Ensure that the operon is only being utilized when ____ is present
Shape
Lactose
Inducer
Lactose
When lactose is ____, further enzyme synthesis is not necessary so the repressor binds to the operator again
Depleted
The ____ sits inbetween the promoter and the genes that need to be expressed
Operator
Positive control is implemented by regulators called ___ ____. They bind to the activator binding sites on the DNA and ___ transcription. Activator protein activity is modified by ____.
Activator proteins
Stimulate
Effectors
Promoters of positively controlled operons only ___ bind RNA polymerase. An ___ ___ helps RNA polymerase recognize the promoter by either causing a change in ___ ____ or by interacting directly with ___ ___. The activator binding site may be close to the promotor or several hundred bases away
Weakly
Activator protein
DNA structure
RNA polymerase
In positive control, the ____ is right next to the genes and the activator binding site is upstream from the promoter
Promotor
The maltose activator protein binds to ___ ___ to help it find the promoter. This only occurs when ___ is present which acts as an inducer.
RNA polymerase
Maltose
Diagram of when the activator binding site is farther away from the promoter:
Transcription is ____ to translation in bacteria. While transcription is still occurring, ribosomes bind and start translating. This is because there are no ____ ___ ____, allowing ribosomes to have excess to the newly transcribed RNA
Coupled
Membrane bound organelles
___ ___ is a mechanism by which bacteria assess their population density. Prokaryotes can respond to the presence of other cells of the same ____. Each species produces a specific ____ that diffuses freely and binds to activator protein that triggers ____ of specific genes
Quorum sensing
Species
Autoinducer
Transcription
Autoinducer will reach ____ concentrations inside of the cell only if ___ cells are near
High
Many
Quorum sensing was first discovered as mechanism, regulating light production in bacteria, including ____. The ___ operon encodes bioluminescence
V. Fischeri
Lux
Quorum sensing is used to create _____
Biofilms
____ ___ ___ is the ability of bacteria to transfer genetic information to another bacteria. 3 different modes:
Horizontal gene transfer
Conjugation , transform, transduction
____ is direct transfer that takes place between two living cells using a ____
Conjugation
Pilus
____ is indirect transfer using free donor DNA fragments. The recipient cell is alive
Transformation
____ is indirect transfer where the donor cell is lysed bacteria. Defective bacteriophage is the carrier of donor DNA to a live recipient of the same species
Transduction
Horizontal gene transfer diagram:
Genetic exchange:
____ is an important evolutionary process and cells have specific mechanisms for ensuring that recombination takes place. It involves DNA transfer during the process of transformation transduction
Recombination
____ ___ uses donor DNA that is transferred into another cell. The donor DNA gets nicked and a single strand of that DNA finds a spot somewhere on the recipient DNA where there is a ____ sequence
Homologous recombination
Homologous
Diagram of genetic exchange:
Transformation occurs when the donor cell ____ and DNA is ___. If this fragmented DNA bumps into a cell of the same species it can be taken into the recipient cell and perform ___ ____ for genetic exchange
Dies
Fragmented
Homologous recombination
Transformation:
____ cells are capable of taking up DNA and being transformed. Only certain strains of bacteria are competent. Procedures are necessary to make cells competent and electricity can be used to force cells to take up DNA called _____.
Competent
Electroporation
Free DNA is taken up into a cell in a ____ ____ form. Only the very ____ of the strand has to have a homologous sequence with the ____ ___. It’s only looking for a place to start and then it can swap in this transformed DNA segment.
Single strand
Beginning
Bacteria DNA
Transduction of DNA from one cell to another mediated by a ____ (virus). Two modes:
_____ transduction: DNA derived from virtually any portion of the host genome is packaged inside the mature virion.
_____ transduction: DNA from a specific region of the host chromosome is integrated directly in the virus genome
Bacteriophage
Generalized
Specialized
There are two ways a bacteriophage can infect a host cell: ___ and ___ . The pathway that is takes is dependent on the species of ____ that is infecting the host.
Lysis
Lysogeny
Bacteriophage
All bacterial phages have the ability to go through the ____ pathway. Only some bacterial phages can go through the ___ pathway. A ____ virus has the ability to perform both pathways
Lytic
Lysogenic
Temperate
The lysogenic pathway involved the ____ of viral DNA into the host DNA. The host cell then undergoes cell division.
Integration
The lytic pathway involves the viral DNA being ____ inside the host cell. Then ___ ___ are synthesized and virus particles assemble. The host cell then undergoes ___ and releases these particles
Replicated
Coat proteins
Lysis
Diagram of lysis and lysogeny:
Bacteriophage can determine the ____ of the host cell. If the host cell is ___ the virus will go the lytic pathway. If the host cell is ____ it will take the lysogenic pathway.
Fitness
Stressed
Healthy
If a bacteriophage is in the lysogenic pathway and senses stress it will perform ____ and switch to the lytic pathway
Induction
When a virus goes straight to the lytic cycle, once and awhile a segment of the ___ DNA is packaged by a virus particle. This mistake turns into a ____ particle. This is called ____ transduction
Host
Transducing
Generalized
When a bacteriophage goes the lysogenic pathway, the virus is integrated into the host cell. If the host cell gets stressed, the virus will ___ itself out of the host genome and start to package into ___ ___. Sometimes a portion of the ___ DNA is exchanged for phage DNA and gets packed into viral particles. These can then undergo _____ transduction
Loop
Viral particles
Host
Specialized
Generalized transduction is when a bacteriophage accidentally carries ____ host DNA
Only
Specialized transduction if when bacteriophages accidentally carry ____ host DNA and viral DNA after lysogenic pathway.
Both
____ is a mechanism of DNA transfer in prokaryotes that requires cell to cell contact. Genes carried by the ___ ____ control conjugation. The information that the cell needs to perform conjugation is embedded in the __ ___. F stand for ___.
Conjugation
F plasmid
F plasmid
Fertility
Plasmid DNA transfer involves replication via the ___ ___ mechanism, meaning only 1 replication fork instead of 2.
Rolling circle
The F plasmid is a circular DNA molecule that contains genes that regulate ___ ___. It contains several transposable elements that allow the plasmid to ___ into the host chromosome using ___ ____ (IS). It contains the ___ gene that encodes transfer functions.
DNA Replication
Integrate
Insertion sequences
tra
And __ ___ cell is a donor cell that has received the F plasmid
F+
If the F plasmid is integrated into the donor cell, those cells are called ___ ____ of ____ cells.
High frequency of recombination (HFR)
If a cell does not have the F plasmid it is called __ __ cell.
F minus
F+ cells can make a ____ when it finds an F- cell. This allows for transfer of the F plasmid
Pilus
Picture of conjugation
F+ cells do not bind to another ___ cell
F+
What happens if the F plasmid is integrated into the bacterial chromosome rather than sitting as a plasmid? The host chromosome becomes an ___ cell
Hfr
Diagram of Hfr strains and chromosome mobilization:
The integrated F plasmid still thinks it is a plasmid, when the Hfr cells function as a donor to an F- cells, it will go through the process of ____ ___ replication as if it was still a plasmid. It will be transferring genes from the ___ chromosome to an F- recipient. The plasmid will never be able to transfer everything before the host cell aborts the process. The F- cell gets what it gets, does not get the full sequence of the ___ ___.
Rolling circle
Host
F plasmid
The F- strain will remain F- because it did not pick up all the ___ ___. But the F- cell will still pick up new properties
F plasmid
When Hfr cells conjugate with F- cells, the F- cells remain ____
F-
___ ___ are mobile DNA segments that move from one location to another.
_____: when a transposon is excised from one location and reinserted at a second location, the number of transposons stays constant.
_____: when a new copy of transposon is produced and inserted at a second location, the number of transposons present doubles.
Transposable elements
Conservative
Replicative
Diagram of conservative and replicative transposable element:
Diagram of Hfr to an F- cell. The yellow portion is the F plasmid
