Viruses Flashcards
Lysogenic Cycle of Phage Lambda Begins
when a phage binds to the surface of a host bacterium
Second Stage of Lysogenic Cycle
the phage injects its DNA into the host cell (leaving the empty protein coat outside)
Lysogenic Cycle (Prophage)
the viral DNA is incorporated into the host cell DNA (called a prophage)
Prophage
- viral DNA is incorporated into the host cell DNA
- every time the host bacterium reproduces (it replicated the phage DNA along with its own DNA and passes the copies on to daughter cells)
Lytic Cycle
- the phage DNA exits the bacterial chromosome (imitating the cycle)
- the viral DNA takes over the metabolic machinery of the host cell to make phage DNA and proteins
- host cell lyses (releasing phages) which can infect other cells
- virus parts are made
- new viruses are assembled & releasing newly assembled viruses
What is the difference between the Lytic Cycle and the Lysogenic Cycle
- lytic cycle concludes with rupture of the host cell
- lysogenic cycle involves replication of viral DNA along with replication of the host
CRISPR
- a recently developed technology
- discovered by scientists studying immune responses in bacteria
- stand for Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Cas
- is described as a DNA-encoded + RNA-mediated and DNA-targeted immune system
- upon exposure to pathogenic insult or viral challenge (ex. bacteriophages)
- ability to target specific phage DNA sequences for destruction and empowers the bacteria (with molecular memory) of previous viral attacks
Bacteriophages
- viruses that infect bacteria
- called phages for short
TYPE ll CRISPR systems
have been widely adapted for the development of CRISPR-based (genome-editing technology)
Immunity
- is defined as a host’s ability to resist pathogenic insults
- via defense mechanisms that differentiate self from non self
Bacterial Defense Mechanisms
include both innate immunity and adaptive (or acquired immunity
Adaptive Immunity
is defined by more refined feature of specificity + diversity + memory
Repeats (CRISPR)
are multiple short sequences that all have the same sequence
Spacers (CRISPR)
- are variable sequences derived from invading phage DNA
- are the molecular memory of previous phage attacks
- enabling the immune system to be adaptive
Cas Genes (CRISPR)
- encode proteins involved in several functional roles (ex. spacer acquisition + crRNA biogenesis + interference)
- new spaces derived from invading phage DNA are inserted in the CRISPR array by these genes
Steps of Type ll CRISPER-Cas System
1) phage infects the bacterial cell with its DNA
2) phase DNA incorporated as a new spacer into CRISPR array
3) transcription of CRISPR locus (yielding pre-crRNA)
4) pre-crRNA processed into mature crRNA
5) mature crRNA forms complex with Cas nuclease
6) crRNA-Cas machinery cuts complementary target DNA of invading phage
Space Acquisition Steps
1) phage infects the bacterial cell with its DNA
2) phase DNA incorporated as a new spacer into CRISPR array
crRNA Biogenesis Steps
3) transcription of CRISPR locus (yielding pre-crRNA)
4) pre-crRNA processed into mature crRNA
Interference CRISPR Steps
5) mature crRNA forms complex with Cas nuclease
6) crRNA-Cas machinery cuts complementary target DNA of invading phage
crRNA
- is transcribed and processed to help direct the Cas protein to target DNA
Cas9
- is an endonuclease
- encoded by cat genes in the bacterial genome
- that cleaves invasive viral DNA
- associates with crRNA and tracrRNA (forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence)
- employs a strategy to distinguish the bacterium’s own DNA from invasive viral DNA
- will not cleave DNA lacking a PAM sequence
Cas9 two signature nuclease domains
DNA HNH (cleaves the strand that is complementary to the crRNA)
RuvC (cleaves the strand that is not)
PAM sequence
is critical to this adaptive immune system’s ability to distinguish self from non self (invasive) DNA sequences
What are the situations where the phage could potentially infect the bacteria?
- the phage’s DNA has been engineered to remove all its PAM sequences
- the phage has undergone a mutation near a PAM sequence since the bacterium encountered it last
What are situations where the bacterium could potentially destroy phage DNA?
- the phage attacks a bacterial cell whose parent cell encountered the phage before it divided
- the phage has undergone a mutation far away from a PAM sequence since the bacterium encountered it last
Viruses
- are infectious particles that contain genetic material (either DNA or RNA)
- surrounded by a capsid (protein shell)
- can also have a membrane envelope that contain glycoproteins
- the capsid enters the host cell if the virus is enveloped
- a retrovirus contains RNA
- HIV contains reverse transcriptase
- contain either single stranded DNA or double-stranded DNA or single-stranded RNA or double-stranded DNA
What distinguished a host cell from a viruses?
only host cells have ribosomes
What does the Lytic Cycle and Lysogenic Cycle have in common?
viral genes are replicated
Lysogenic Cycle
- the viral DNA incorporates into the bacterial DNA
- is passed on to the daughter bacterial cells when infected
- bacteria infected reproduce normally
Nonenveloped Viruses
typically exit host cell by bursting through the plasma membrane
Enveloped Viruses
- generally escape from the host cell by budding
- the viral envelope is often derived from the host cell’s plasma membrane
HIV
- human immunodeficiency virus
- is a retrovirus
- contains two copies of its RNA genome and two copies of reverse transcriptase
- viral envelope facilitates binding to a white blood cell
- after entry the reverse transcriptase synthesizes viral DNA and viral RNA
A Backed UP
- article has undergone the process of peer review
- must also be relevant
Intent (BIAS test)
- of the article is the reason the article was written and the audience it was written for
- authors and publishers often have their own agendas when writing and publishing an article
- written (to educate + entertain + entice)
- the reader must decide whether the purpose of the article is objective or partial
The Authority
- of the article is the qualification the author and reputation of the publisher
- the author of the article should have the qualifications to be considered an expert in the field in which they’re writing
- an article should be found in a reputable peer-reviewed journal that is relevant to the subject area of the article
The Source
- of the article describes the articles appropriateness for your research and the type (primary or secondary)
- scientific articles are typically more detailed and contain (terms + statistics + vocabulary the general population may not understand)
Peer Review
- occurs when peers in the same scientific field examine the work and evaluate the claims made from the study design and methodology
- provides accuracy and quality assurance of the readers of the article
- articles must be less than 10 years old
- are more relevant articles
Objective Intent
intended to educate
Partial Intent
intended to entice or for entertainment purposes
Genetic Variation (Bacteria)
- is crucial to natural selection and evolution
- the great success of bacteria due to the extensive variation found in the population
- exists despite the fact that bacterial reproduction is asexual
Binary Fission Reproduction Steps
1) chromosomes replication begins
- one copy of the origin moves rapidly toward the other end of the cell by a mechanism not yet fully understood
2) replication continues
- one copy of the origin is now at each end of the cell
- the cell elongates
3) replication finishes
- the plasma membrane grows inward
- a new cell wall is deposited
4) two daughter cells result
Binary Fission
- is a form of asexual reproduction
- where a single individual is the sole parent and passes copies of all its genes to its offspring
Binary Fission DNA replication beings
at the origin of replication
When the DNA Replication is Complete
the plasma membrane grows inward (dividing the parent cell into two daughter cells
Two Daughter Cells of Binary Fission
theoretically are genetically identical
Mutations in Binary Fission
- where mistakes during DNA replication are made
- resulting in changes to the nucleotide sequences of the DNA
- leading the small mutation to create genetic variation
F Factor
- is a piece of DNA that contains about 25 genes
- most genes in this factor are related to the production of a structure called a mating bridge
- may be found on a separate piece of DNA called a F plasmid
- may be found with a main bacterial chromosome
Mating Bridge
- links two bacterial cells during conjugation
- allowing for DNA transfer
Steps of Conjugation & Transfer of an F Plasmid
1) a cell carrying an F plasmid (an F+ cell) forms a mating bridge with and F- cell
- one strand of the plasmid’s DNA breaks
2) using the unbroken strand as a template
- the cell synthesizes a new strand
- the broken strand peels off and one end enters the F- cell
- synthesis of its complementary strand begins
3) DNA replication continues in both donor and recipient cells
- the transferred plasmid strand moves farther into the recipient cell
4) once DNA transfer and synthesis are completed
- the plasmid in the recipient cell circularizes
- both cells are F+ cells
Steps of Conjugation & Transfer of an Hfr Bacterial Chromosome
1) the f-factor is integrated into the bacterial chromosome
- an Hfr cell has all of the F factor genes
- the cell can form a mating bridge with an F- cell and transfer DNA
2) a single strand of the F factor breaks and begins to move through the bridge
- DNA replication occurs in both donor and recipients cells
- resulting in double-stranded DNA
3) the mating bridge usually breaks before the entire chromosome is transferred
- DNA recombination can result in the exchange of homologous genes between the transferred DNA and the recipient’s chromosomes
4) cellular enzymes degrade any linear DNA not incorporated into the chromosome
- the recipient cell (with a new combination of genes but no F factor) is now a recombinant F- cell
F+ cell
- carries the F factor in a plasmid
- may donate a plasmid to another cell
Hfr cell
- carries the F factor in its circular chromosome
- may donate genes from its chromosome to another cell
F- cell
- may become recombinant after conjugation with an Hfr cell
- may receive genetic materials
- cannot donate genetic material
- may become F+ after conjugation with an F+ cell
