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BIO 223 First Half > Viruses > Flashcards

Viruses Flashcards

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1
Q

Lysogenic Cycle of Phage Lambda Begins

A

when a phage binds to the surface of a host bacterium

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2
Q

Second Stage of Lysogenic Cycle

A

the phage injects its DNA into the host cell (leaving the empty protein coat outside)

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3
Q

Lysogenic Cycle (Prophage)

A

the viral DNA is incorporated into the host cell DNA (called a prophage)

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4
Q

Prophage

A
  • 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)
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5
Q

Lytic Cycle

A
  • 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
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6
Q

What is the difference between the Lytic Cycle and the Lysogenic Cycle

A
  • lytic cycle concludes with rupture of the host cell
  • lysogenic cycle involves replication of viral DNA along with replication of the host
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7
Q

CRISPR

A
  • a recently developed technology
  • discovered by scientists studying immune responses in bacteria
  • stand for Clustered Regularly Interspaced Short Palindromic Repeats
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8
Q

CRISPR-Cas

A
  • 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
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9
Q

Bacteriophages

A
  • viruses that infect bacteria
  • called phages for short
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10
Q

TYPE ll CRISPR systems

A

have been widely adapted for the development of CRISPR-based (genome-editing technology)

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11
Q

Immunity

A
  • is defined as a host’s ability to resist pathogenic insults
  • via defense mechanisms that differentiate self from non self
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12
Q

Bacterial Defense Mechanisms

A

include both innate immunity and adaptive (or acquired immunity

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13
Q

Adaptive Immunity

A

is defined by more refined feature of specificity + diversity + memory

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14
Q

Repeats (CRISPR)

A

are multiple short sequences that all have the same sequence

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15
Q

Spacers (CRISPR)

A
  • are variable sequences derived from invading phage DNA
  • are the molecular memory of previous phage attacks
  • enabling the immune system to be adaptive
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16
Q

Cas Genes (CRISPR)

A
  • 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
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17
Q

Steps of Type ll CRISPER-Cas System

A

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

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18
Q

Space Acquisition Steps

A

1) phage infects the bacterial cell with its DNA
2) phase DNA incorporated as a new spacer into CRISPR array

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19
Q

crRNA Biogenesis Steps

A

3) transcription of CRISPR locus (yielding pre-crRNA)
4) pre-crRNA processed into mature crRNA

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20
Q

Interference CRISPR Steps

A

5) mature crRNA forms complex with Cas nuclease
6) crRNA-Cas machinery cuts complementary target DNA of invading phage

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21
Q

crRNA

A
  • is transcribed and processed to help direct the Cas protein to target DNA
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22
Q

Cas9

A
  • 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
23
Q

Cas9 two signature nuclease domains

A

DNA HNH (cleaves the strand that is complementary to the crRNA)
RuvC (cleaves the strand that is not)

24
Q

PAM sequence

A

is critical to this adaptive immune system’s ability to distinguish self from non self (invasive) DNA sequences

25
Q

What are the situations where the phage could potentially infect the bacteria?

A
  • 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
26
Q

What are situations where the bacterium could potentially destroy phage DNA?

A
  • 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
27
Q

Viruses

A
  • 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
28
Q

What distinguished a host cell from a viruses?

A

only host cells have ribosomes

29
Q

What does the Lytic Cycle and Lysogenic Cycle have in common?

A

viral genes are replicated

30
Q

Lysogenic Cycle

A
  • the viral DNA incorporates into the bacterial DNA
  • is passed on to the daughter bacterial cells when infected
  • bacteria infected reproduce normally
31
Q

Nonenveloped Viruses

A

typically exit host cell by bursting through the plasma membrane

32
Q

Enveloped Viruses

A
  • generally escape from the host cell by budding
  • the viral envelope is often derived from the host cell’s plasma membrane
33
Q

HIV

A
  • 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
34
Q

A Backed UP

A
  • article has undergone the process of peer review
  • must also be relevant
35
Q

Intent (BIAS test)

A
  • 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
36
Q

The Authority

A
  • 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
37
Q

The Source

A
  • 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)
38
Q

Peer Review

A
  • 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
39
Q

Objective Intent

A

intended to educate

40
Q

Partial Intent

A

intended to entice or for entertainment purposes

41
Q

Genetic Variation (Bacteria)

A
  • 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
42
Q

Binary Fission Reproduction Steps

A

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

43
Q

Binary Fission

A
  • is a form of asexual reproduction
  • where a single individual is the sole parent and passes copies of all its genes to its offspring
44
Q

Binary Fission DNA replication beings

A

at the origin of replication

45
Q

When the DNA Replication is Complete

A

the plasma membrane grows inward (dividing the parent cell into two daughter cells

46
Q

Two Daughter Cells of Binary Fission

A

theoretically are genetically identical

47
Q

Mutations in Binary Fission

A
  • 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
48
Q

F Factor

A
  • 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
49
Q

Mating Bridge

A
  • links two bacterial cells during conjugation
  • allowing for DNA transfer
50
Q

Steps of Conjugation & Transfer of an F Plasmid

A

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

51
Q

Steps of Conjugation & Transfer of an Hfr Bacterial Chromosome

A

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

52
Q

F+ cell

A
  • carries the F factor in a plasmid
  • may donate a plasmid to another cell
53
Q

Hfr cell

A
  • carries the F factor in its circular chromosome
  • may donate genes from its chromosome to another cell
54
Q

F- cell

A
  • 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

BIO 223 First Half (8 decks)

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