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Virology > Virology - general, replication > Flashcards

Virology - general, replication Flashcards

1
Q

Virus size range from

A

10 to 1000 nm in size

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2
Q

Genome size range

A

from 3000 nucleotides to >1,000,000 base pairs

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3
Q

viral Replication cycle time frame

A

from minutes to days

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4
Q

Explain Retrograde evolution theory

A

Intracellular parasites lost the ability for independent metabolism keeping only those genes necessary for replication

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5
Q

Explain this viral evolution theory: Origin from cellular DNA and RNA components

A

Some DNA genomes resemble plasmids or episomes.
Maybe this DNA acquired protein coats and the ability to be transferred from cell to cell efficiently

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6
Q

Explain viral evolution theory:
Descendants of primitive precellular life forms

A

Viruses originated and evolved along with primitive, self-replicating molecules

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7
Q

Name the 3 viral evolution theories.

A

retrograde evolution
origin from DNA/RNA components
descendents of primitive life forms

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8
Q

define variolation

A

obsolete method of immunizing patients against smallpox by infecting them with substance from the pustules of patients with a mild form of the disease

aka inoculation

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9
Q

Who was Edward Jenner?

A

was an English physician who observed that dairymaids who had had cowpox did not get small pox.

and pioneered the concept of vaccines

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10
Q

what is a Chamberland filter

A

also known as a Pasteur–Chamberland filter, is a porcelain water filter invented by Charles Chamberland in 1884.

Pasteur found that rabies passed through it

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11
Q

what is an eclipse period

A

The time between infection by (or induction of) a bacteriophage, or other virus, and the appearance of mature virus within the cell.

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12
Q

What is the baltimore system?

A

Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis.

By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group.

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13
Q

Virion

A

a complete virus with all the components needed for host cell infection

Virion is different from a virus. It is a virus in an extracellular phase.

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14
Q

Capsid

A

the protein shell of a virus particle surrounding its nucleic acid

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15
Q

Capsid + genome =

A

nucleocapsid

By definition, nucleocapsid is a viral protein coat that surrounds the genome (either DNA or RNA). N

Ø NB! Only as a substructure!

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16
Q

viral envelope

A

A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells.

surrounds the nucleocapsid

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17
Q

Protein spikes

A

a spike protein is a protein that forms a large structure known as a spike projecting from the surface of an enveloped virus. The proteins are usually glycoproteins.

helps to attach to the host cell

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18
Q

icosahedral definition

A

is a polyhedron with 20 faces

Icosahedron = polygon
with 20 faces, each an
equilateral triangle

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19
Q

how many types of viral genome?

A

7 types of viral genome

  1. ds DNA
  2. ss (+) sense DNA
  3. ds RNA
  4. ss (+) sense RNA
  5. ss (-) sense RNA
  6. ss (+) sense RNA with DNA intermediate in lifecycle
  7. ds DNA with RNA intermediate
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20
Q

define capsomere

A

is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus. Capsomeres self-assemble to form the capsid.

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21
Q

What is the difference between a viral envelope and a capsid?

A

Envelope and capsid are two structural parts in viruses. Capsid is the protein shell which surrounds the viral genome.

Envelope is the lipid membrane acquired by the viruses from the host cells. It covers the nucleocapsid.

not all viruses have envelopes but essentailly all have capsids

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22
Q

in which direction do positive sense strands code?

A

5’-3’

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23
Q

in which direction do negative sense strands code?

A

3’-5’

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24
Q

another name for sense strand

A

coding strand

carries the translatable code in the 5′ to 3′ direction

The main difference between sense and antisense strand is that sense strand is incapable of being transcribed into mRNA whereas antisense strand serves as the template for the transcription.

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25
Q

another name for antisense strand

A

template strand

is directed in the 5’ to 3’ direction.

The main difference between sense and antisense strand is that sense strand is incapable of being transcribed into mRNA whereas antisense strand serves as the template for the transcription.

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26
Q

describe the lytic viral lifecycle

A

In a lytic cycle, the virus introduces its genome into a host cell and initiates replication by hijacking the host’s cellular machinery to make new copies of the virus.

Once infection is complete, the newly replicated and assembled virus particles are released through lysis of the host cell into the surrounding waters.

is also commonly referred to as the “reproductive cycle” of the bacteriophage, is a six-stage cycle. The six stages are: attachment, penetration, transcription, biosynthesis, maturation, and lysis.

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27
Q

describe the lysogenic viral lifecycle

A

lysogenic cycle: The phage infects a bacterium and inserts its DNA into the bacterial chromosome, allowing the phage DNA (now called a prophage) to be copied and passed on along with the cell’s own DNA.

instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host.

Viral DNA multiplies as the host cell multiplies. Each new daughter cell created is infected with the virus’ DNA.

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28
Q

define non-covalent

A

a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule.

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29
Q

define Quasi-equivalence

A

quasiequivalent = Very similar, but different.

can be defined as the extent of similarity between these structurally unique environments occupied by the chemically identical subunits in the virus capsid.

Quasi-equivalent capsids should contain 60T subunits, however, there are exceptions.

The conceptual basis for viral quasi-equivalence is the interchangeable formation of hexamers and pentamers by the same protein molecule

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30
Q

define pentamer & hexamer

A

A pentamer is an entity composed of five sub-unit

hexamer is an oligomer having six subunits; A subunit of a viral capsid.

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31
Q

What are the 5 steps of the virus replication cycle?

A
  1. Attachment
  2. Penetration or viral entry
  3. Synthesis (replication)
  4. Assembly
  5. Release
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32
Q

cellualr receptors are needed for all viruses except for what 2 exceptions and why?

A

except for fungi and plant viruses because they enter the cells by mechanical damage so no receptors needed.

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33
Q

How many receptors does a virus need to bind in order to enter a cell?

A

2-3 receptors
but some require up to 5 like the polio virus

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34
Q

what was the first cell receptor to be discovered?

A

sialic acid receptor for the influenza virus

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35
Q

What are the 2 methods of viral entry?

A
  1. fusion with the membrane (only enveloped viruses)
  2. endocytosis of various kinds (both enveloped and non-enveloped)
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36
Q

what type of viruses use membrane fusion for cell entry

A

only enveloped viruses e.g. herpes virus

37
Q

what type of viruses use endocytosis of various kinds for cell entry

A

both enveloped and non-enveloped

e.g. adeno virus

38
Q

Name 3 types of viral entry endocytosis

A

clathrin-dependent
clathrin-and-claveolin-independent
caveolin-dependent

39
Q

What is unique about calveolin-dependent viral entry?

A

The calveolin coated vesicle/endosome with virus is carried to the endoplasmic reticulum instead of the cell nucleus. The viral genome is then deposited into the endoplasmic reticulum instead of the cytosol or nucleus.

e.g. SV40 (simian virus 40)

40
Q

What regulates viral fusion-entry?

A

location
pH

41
Q

viral entry (fusion) at neutral pH at the plasma membrane requires what to complete entry?

A

needs second protein receptor interaction

42
Q

viral entry (fusion) at low pH at the plasma membrane requires what to complete entry? (2)

A

▫ proteolytic cleavage for the fusion proteinactivation or
▫ Endosome fusion receptor

43
Q

what are the 4 modes of nuclear entry?

A
  1. released segmented viral ribonucleoprotein (RNP) fit through the nuclear pores
  2. viral portal docks onto a nuclear pore
  3. Also involves portal docking to nuclear pore but in this case the virus is pulled apart on the outside of the nucleus
  4. Binding to nuclear pore causes disruption in the nuclear membrane through which virus passes
44
Q

What does non-enveloped adeno virus require for entry via endocytosis? (2)

A

bind to cell surface receptor
and then also requires second binding to an integrin protein
so that it may be incorporated into an endosome

45
Q

name 2 intracellular motor proteins

A

kinesin
dynein

46
Q

genome type for class 3 of the baltimore system

A

Double stranded RNA (dsRNA) viruses

Have:
RdRp
& Naked RNA

47
Q

genome type class 5 of the baltimore system

A

negative sense Single stranded RNA (ssRNA) viruses

meaning they must be transcribed by a viral polymerase to produce a readable strand of mRNA. The genomes of Class V viruses may be segmented or non-segmented.

Have:
RdRp
RNA coated with protein (nucleocapsid)

48
Q

genome type class 4 of the baltimore system

A

positive sense Single stranded RNA (ssRNA) viruses

meaning they can be directly read by ribosomes to translate into proteins.
Have:
No RdRp
Naked RNA

Exceptons:
Retrovirus,
Coronavirus

49
Q

explain RdRp

A

RNA dependent RNA polymerase
Viral enzymes that copy viral RNA from DNA.
catalyzes the replication of RNA from an RNA template.

note: diff sources claim either RNA or DNA as template

Builds new RNA strand in the 5’ to 3’ direction

50
Q

what are The two modes of initiation of RNA synthesis

A

De novo initiation (de novo = anew)
&
Primer-dependent initiation

51
Q

De novo initiation of RNA synthesis begins with?

A

the 3’ end of the template strand

52
Q

Primer-dependent initiation of RNA synthesis begins with?

A

a terminal protein or a capped primer, and then goes from the 3’ end of the template strand

53
Q

How many types of polymerase are there?

A

4 kinds:
RNA dependent RNA polymerase
RNA dependent DNA polymerase
DNA dependent DNA polymerase
DNA dependent RNA polymerase

54
Q

the viral genome of polio virus is?

A

mRNA

this means it doesn’t need to visit the host cell’s nucleus at all, it just goes directly to the cell’s ribosomes

55
Q

viral RNA synthesis always occurs on what type of “platform”?

A

on membranous vesicles induced by the virus

these don’t exist in cells not infected by viruses

56
Q

what is the correct term for describing RNA virus replication?

A

mRNA synthesis

it is incorrect to call it transcription (only applies to dsDNA)

57
Q

genome type for class 1 of the baltimore system

A

double-stranded DNA viruses

e.g. HSV, adeno- & papillomaviruses

It makes use of the host polymerases to replicate its genome, and is therefore highly dependent on the host cell cycle.

58
Q

genome type for class 7 of the baltimore system

A

gapped double-stranded DNA viruses

e.g. hepatitis B virus

they replicate via a ssRNA intermediate. The dsDNA genome is gapped, and subsequently filled in to form a closed circle serving as a template for production of viral mRNA. To reproduce the genome, RNA is reverse transcribed back to DNA.

59
Q

genome type for class 2 of the baltimore system

A

single-stranded DNA viruses

e.g. parvo virus

Most ssDNA viruses have circular genomes and replicate mostly within the nucleus by a rolling circle mechanism.

60
Q

genome type for class 6 of the baltimore system

A

positive-strand RNA viruses with reverse trasnscriptase

e.g. retroviruses

they replicate through a DNA intermediate which is later incorporated into the cell genome.

61
Q

What is the first biosynthetic event that must take place after viral DNA enters the cell?

A

The first biosynthetic event for viral dsDNA is mRNA synthesis (transcription).

62
Q

what type of viral genome is the only type that you can make mRNA straight from

A

dsDNA is the only DNA that you can make mRNA straight from

63
Q

DdRp

A

DNA-dependent RNA polymerase

Found in all Eukaryotic cells – we make them too in the nucleus!
◦ Three kinds of polymerase enzymes
All initiate RNA synthesis de novo (= no primer needed)

64
Q

how many types of DdRp are there

A

RNA pol I
RNA pol II
RNA pol III

65
Q

What type of viruses encode an RNA polymerase?

A

Only DNA viruses that replicate in cytoplasm
(e.g. Poxvirus, giant viruses) encode an RNA pol

66
Q

Polyadenylation

A

is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA).

this happens to viral pre-mRNA just before it exits the nucleus on the road to becoming finished mRNA

67
Q

tata sequence

A

also known as the TATA box

is a sequence of DNA found in the core promoter region of genes
The TATA box is considered a non-coding DNA sequence
it contains a consensus sequence characterized by repeating T and A base pairs.
is the site of preinitiation complex formation, which is the first step in transcription initiation in eukaryotes.

68
Q

the core promoter region is

A

the DNA segment of 50–100 bp within which transcription initiates

69
Q

what is Modular organization

A

DNA binding proteins have a modular organization

the proteins function is to control of transcription and translation, DNA repair, splicing etc.

modular organization means that these various proteins are organized together but in distinct modules of their own
“regions with specialized functions”

70
Q

what is a promoter in relation to transcription

A

is a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene.

The resulting transcription produces an RNA molecule (such as mRNA).

71
Q

Origin of transcriptional components for retroviruses with simple genomes?

A

Host only

72
Q

Origin of transcriptional components for Bacteriophages T3, T7?

A

Host + 1 viral protein

73
Q

Origin of transcriptional components for Hepadnaviruses, parvoviruses,
papillomaviruses, polyomaviruses, retroviruses with complex genomes?

A

Host + 1 viral protein

74
Q

Origin of transcriptional components for Adenoviruses, herpesviruses?

A

Host + >1 viral protein that stimulate transcription

75
Q

Origin of transcriptional components for Mimiviruses, Poxviruses?

A

Viral

76
Q

what is Cascade regulation

A

a type of Regulation of transcription by viral proteins

a la You make one thing to will also effect something else downstream

77
Q

what is Positive (or negative) autoregulatory loop

A

a type of Regulation of transcription by viral proteins

E.g. Protein X stimulates its own promoter, you make many more transcripts

78
Q

Histone

A

A type of protein found in chromosomes. Histones bind to DNA, help give chromosomes their shape, and help control the activity of genes.

They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin.

79
Q

what are the 2 types of splicing called?
what is the difference between them?

A

Constitutive splicing is the process of intron removal and exon ligation of the majority of the exons in the order in which they appear in a gene.

Alternative splicing is a deviation from this preferred sequence where certain exons are skipped resulting in various forms of mature mRNA.

80
Q

Why is viral DNA replication always delayed after infection?

A

The transcription phase of replication is required first. Viral DNA replication always requires synthesis of at least one viral protein before replication can begin.

81
Q

semi conservative and conservative replication

A

In semi-conservative replication each strand makes its own daughter strand.

In conservative replication only one daughter strand is produced. produces one helix made entirely of old DNA and one helix made entirely of new DNA.

82
Q

which way is dna read and which way is it built

A

the template strand is read in the 3’ to 5’ direction
so
the new strand is synthesized in the 5’ to 3’ direction

83
Q

exonuclease function

A

DNA replication enzyme that acts as a proofreaders during DNA polymerisation in DNA replication, to remove unusual DNA structures

84
Q

What are the two main mechanisms of dsDNA synthesis called?

A

Replication fork-method & strand displacement method.

85
Q

On what strand is DNA synthesis continuous?

A

on the leading strand

86
Q

On what strand is DNA synthesis interrupted?

A

on the lagging strand

87
Q

topoisomerase function

A

removes helical twists by cutting a DNA strand and then resealing the cut thus they unwind supercoiled molecules.

88
Q

what is ori

A

is the origin of replication

They have binding sites for transcriptional regulators. Viruses have 1-3 Ori’s depending on the virus.

89
Q

why do viruses not replicate well in quiescent(dormant/nonreplicating) cells?

A

Most of our cells do not divide or do so rarely.
Viruses do not replicate well in quiescent cells because they need the host’s replication machinery to replicate themselves.
So viruses must induce host replication proteins, done by the virus encoded early gene products.

Virology (5 decks)

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