Microbiology - Ch. 8

Front 1

Def: Virus

Back 1

Genetic element that cannot replicate independently of a living (host) cell.

A.k.a. - Obligate Intracellular Parasite

Front 2

Def: Virion

Back 2

Extracellular form of a virus. It exists outside host and facilitates transmission from one host cell to another.

Front 3

When do Viruses Replicate?

Back 3

Replication/reproduction occurs only upon infection (entry into host cell).

Front 4

Viral Components and Activities

Back 4

Capsid

Naked Virus

Enveloped Virus

Nucleocapsid

Front 5

Def: Capsid

Back 5

The protein shell that surrounds the genome of a virus particle.

Front 6

Def: Naked Virus

Back 6

(e.g., most bacterial viruses) have no other layers.

Front 7

Def: Enveloped Virus

Back 7

(e.g., many animal viruses) have an outer layer consisting of a phospholipid bilayer (from host cell membrane) and viral proteins.

Front 8

Def: Nucleocapsid

Back 8

Nucleic acid + protein in enveloped viruses.

Front 9

Back 9

Front 10

Def: Virulent (lytic) Infection

Back 10

Replicates and destroys host.

Front 11

Def: Lysogenic Infection

Back 11

Host cell genetically altered because viral genome becomes part of host genome.

Front 12

Viral Genomes

Back 12

Either DNA or RNA genomes.

Single-stranded or double-stranded

Single-stranded may be plus sense (same as mRNA) or minus sense (complementary to mRNA).

Either linear or circular.

Usually smaller than those of cells.

Front 13

Virus Classification

Back 13

Bacterial viruses (bacteriophages; model systems).

Archaeal viruses.

Animal viruses (extensively studied).

Plant viruses (less well studied).

other viruses.

Front 14

Average Size of Virus

Back 14

Most viruses are smaller than prokaryotic cells; range from 0.02 to 0.3 µm.

Front 15

Virion Structure: Capsomere

Back 15

Individual protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid making up the capsid.

Capsids can be put together through self-assembly (spontaneous) or require host cell folding assistance.

Front 16

Virus Symmetry: Helical

Back 16

Rod-shaped viruses (e.g., tobacco mosaic virus or TMV).

Length of virus determined by length of nucleic acid.

Width of virus determined by size and packaging of capsomeres.

Front 17

Virus Symmetry: Icosahedral

Back 17

Spherical viruses (e.g., human papillomavirus).

Most efficient arrangement of subunits in a closed shell.

Requires fewest capsomeres.

Front 18

Enveloped Viruses (Part 1)

Back 18

Have lipoprotein membrane surrounding nucleocapsid.

RNA or DNA genomes.

Envelope proteins attach to and infect animal host cell.

Front 19

Enveloped Viruses (Part 2)

Back 19

Relatively few enveloped plant or bacterial viruses because of cell walls surrounding cell membrane.

Entire virion enters animal cell during infection.

Enveloped viruses exit more easily.

Front 20

Enzymes Inside Virions: Lysozyme

Back 20

Makes hole in cell wall to allow nucleic acid entry.

Also lyses bacterial cell to release new virions.

Front 21

Enzymes Inside Virions: Neuraminidases

Back 21

Destroy glycoproteins and glycolipids.

Allows liberation of viruses from cell.

Front 22

Enzymes Inside Virions: Nucleic Acid Polymerases

Back 22

RNA replicases: RNA-dependent RNA polymerases.

Reverse transcriptase: RNA-dependent DNA polymerase in retroviruses.

Front 23

Prokaryotic Viruses VS. Eukaryotic Viruses

Back 23

Nucleic acid entry in prokaryotes and virion entry in eukaryotes.

Front 24

Phases of Rep. In Permissive (supportive) Host Cell

Back 24

Attachment (adsorption) of the virion.

Penetration (entry, injection) of the virion nucleic acid.

Synthesis of virus nucleic acid and protein by host cell metabolism as redirected by virus.

Assembly of capsids and Packaging of viral genomes into new virions.

Release of mature virions from host cell.

(or, A.P.S.A.P.R.)

Front 25

A.P.S.A.P.R. Visual

Back 25

Front 26

Overview of Virus Life Cycle

Back 26

Eclipse: genome replicated and proteins translated.

Maturation: packaging of nucleic acids in capsids.

Latent Period: eclipse + maturation.

Release: cell lysis, budding, or excretion.

Burst Size: number of virions released.

Front 27

Def: One-Step Growth Curve

Back 27

Increase occurs when cells burst.

Front 28

Culturing Viruses

Back 28

Bacterial viruses are easiest to grow (hosts in liquid medium or spread as “lawns” on agar and inoculated with virus).

Animal viruses (and some plant viruses) can be cultivated in tissue cultures (from animal organ in culture medium).

Front 29

Culturing Viruses: Visual

Back 29

Front 30

What is a Plaque Assay?

Back 30

Used for detecting and counting viruses.

Plaques are clear zones that develop on lawns of host cells where successful viral infection occurs.

Front 31

Def: Titer

Back 31

Number of infectious units per volume of fluid.

Front 32

Attachment (Part 1)

Back 32

Major factor in host specificity

Requires complementary receptors on the surface of a susceptible host for its infecting virus.

Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or other cell structures.

Front 33

Attachment (Part 2)

Back 33

Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell-to-cell interaction, flagella, pili).

Front 34

Attachment Visual

Back 34

Front 35

Penetration (Part 1)

Back 35

Capsid left outside cell.

Viral genome and viral proteins (for some viruses) enter host cell.

Front 36

Penetration of T4 Bacteriophage (Part 1)

Back 36

Virions attach to cells via tail fibers that interact with polysaccharides on E. coli LPS layer.

Tail fibers retract, and tail pins contact cell wall.

Front 37

Penetration of T4 Bacteriophage (Part 2)

Back 37

T4 lysozyme forms small pore in peptidoglycan.

Tail sheath contracts, and viral DNA passes into cytoplasm.

Capsid stays outside.

Front 38

Penetration Visual

Back 38

Front 39

How long does Virion synthesis take?

Back 39

About 30 minutes and ends in release of new virions from lysed cell.

Front 40

How many parts of T4 Genome are there?

Back 40

3...

(1) Early proteins

(2) Middle proteins

(3) Late proteins

Front 41

T4 Early Proteins

Back 41

Enzymes needed for DNA replication and transcription.

Enzyme for the synthesis and glucosylation of the T4 base Hydroxymethylcytosine.

Enzymes that function in T4 replisome.

Proteins that modify host RNA polymerase.

Front 42

T4 Middle and Late Proteins

Back 42

Head and tail proteins and enzymes required to liberate mature phage particles.

Additional RNA polymerase-modifying proteins.

Viral head and tail proteins.

Enzymes for liberating new virions from cell.

Front 43

Replication Chart

Back 43

Front 44

Effect of T4 proteins on Host

Back 44

T4-specific proteins modify host RNA polymerase specificity to recognize only phage promoters.

Host transcription shut down.

Front 45

T4 Genome Packaging

Back 45

Genome is pumped into head under pressure using ATP.

Packaging in three stages...

- Proheads (bacteriophage head

precursors) assembled.

- Packaging motor assembled at

opening.

- Double-stranded linear genome

pumped into prohead using ATP.

Front 46

T4 Genome Assembly

Back 46

After head is filled with DNA, T4 tail, tail fibers, and other components are self-assembled late enzymes break membrane and peptidoglycan.

Lysis occurs, virions released.

Front 47

Virus Replication Visual

Back 47

Front 48

Basic Viral Replication Visual

Back 48

Front 49

Def: Virulent Life Cycle

Back 49

A virus that always lyses, kills, their host after infection.

Front 50

Def: Temperate Life Cycle

Back 50

Viruses that replicate their genomes in tandem with host genome and without killing host, establishing long-term, stable relationship.

Can be lytic/virulent.

Can enter lysogeny: most viral genes are not transcribed, viral genome is replicated with host chromosome and passed to daughter cells.

Front 51

Def: Lysogen

Back 51

lysogen: host cell that harbors temperate virus.

Can result in lysogenic conversion with new properties (e.g., virulence in pathogens).

Front 52

Replication Cycle of Temperate Phage

Back 52

In lysogeny, genome is either integrated into bacterial chromosome (lambda) or exists as a plasmid (P1).

Prophage: viral DNA.

Lysogeny maintained by phage-encoded repressor protein.

Inactivation of repressor induces lytic stage.

Cell stress (e.g., DNA damage) induces lytic pathway.

Front 53

Temperate Phage Chart

Back 53

Front 54

Bacteriophage Lambda (Part 1)

Back 54

Linear, dsDNA virus with head and tail.

Complementary, single-stranded “cohesive” regions 12 nucleotides long at the 5′ terminus of each strand.

Upon penetration, DNA ends base pair, forming the cos site, and the DNA ligates and forms double-stranded circle.

Front 55

Bacteriophage Lambda (Part 2)

Back 55

When it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication.

Genome-sized lengths cut at cos sites; genomes packaged into phage heads.

After tails added, lysis occurs.

Front 56

Bacteriophage Lambda (Part 3)

Back 56

Transduction (packaging of host chromosomal genes and transfer to new host) can also occur.

When lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site (attλ) using lambda integrase.

Front 57

What is regulates Lambda lysis/lysogeny

Back 57

Regulates the lambda lifestyle.

Key elements are two repressor proteins.

CI protein (the lambda repressor):

causes repression of lambda lytic

events.

Cro repressor: controls activation of

lytic events.

First repressor to accumulate controls infection outcome.

Front 58

Temperate Bacteriophage Viral Replication Visual

Back 58

Front 59

An Overview of Animal Virus Infection (Part 1)

Back 59

Major tenets (capsid and DNA/RNA genome, infection and takeover of host, assembly and release) universal.

Classified by genomes.

Front 60

An Overview of Animal Virus Infection (Part 2)

Back 60

Most human viral diseases are caused by RNA viruses.

Two key differences.

Entire virion enters the animal cell.

Eukaryotic cells contain a nucleus,

the site of replication for many

animal viruses.

Front 61

Back 61

Front 62

An Overview of Animal Virus Infection (Part 3)

Back 62

Bind specific host cell receptors, typically used for cell-cell contact or immune function.

Different tissues and organs express different cell surface proteins.

Often viruses only infect certain tissues.

Entry usually occurs by fusion with cytoplasmic membrane or endocytosis.

Front 63

An Overview of Animal Virus Infection (Part 4)

Back 63

Uncoating occurs at cytoplasmic membrane or cytoplasm.

Viral DNA genomes enter nucleus, most viral RNA is converted to DNA within nucleocapsid.

Bind specific host cell receptors, typically used for cell-cell contact or immune function.

Front 64

Def: Latent Infection

Back 64

Viral DNA exists in host genome and virions are not produced; host cell is unharmed unless/until virulence is triggered.

Front 65

Def: Persistent infections

Back 65

Release of virions from host cell by budding, does not result in cell lysis.

Infected cell remains alive and continues to produce virus.

Front 66

Def: Transformation

Back 66

Conversion of normal cell into tumor cell.

Front 67

Animal Virus Life Cycle Visual

Back 67

Front 68

Animal Virus Developmental Chart

Back 68

Front 69

Retrovirus

Back 69

RNA viruses that replicate through a DNA intermediate (e.g., human immunodeficiency virus [HIV]).

Contain a reverse transcriptase (copies information from RNA to DNA), integrase, and protease.

Enveloped.

Front 70

Enveloped Animal Virus Visual

Back 70

Front 71

Uniqueness of Retrovirus Genome

Back 71

Two identical ss(+)RNA molecules.

Contains specific genes.

gag: encode structural proteins.

pol: encode reverse transcriptase

and integrase.

env: encode envelope proteins.

Front 72

Retrovirus Replication (Part 1)

Back 72

Entrance into the cell with removal of envelope at the membrane.

Reverse transcription of one RNA genome begins in nucleocapsid.

Single DNA strand produced.

Reverse transcriptase uses this to make a complementary strand, forming dsDNA product.

Front 73

Retrovirus Replication (Part 2)

Back 73

dsDNA enters nuclease with integrase, which incorporates retroviral DNA into host genome to form provirus, which remains indefinitely.

Transcription of retroviral DNA.

Assembly and packaging of genomic RNA.

Budding of enveloped virions and release from cell.

Front 74

Retrovirus Life Cycle Visual

Back 74

Front 75

ICTV Criteria for Viral Classification -

5 Categories

Back 75

(1) Genome composition.

(2) Capsid Symmetry.

(3) Envelope.

(4) Size of the Virion.

(5) Host Range.

Front 76

David Baltimore

Back 76

Proposed the main distinctions among classes of viruses be:

The genome composition (RNA or

DNA).

The route used to express

messenger RNA (mRNA).

Front 77

7 groups of Baltimore Virus Classification

Back 77

Group I: Double-stranded DNA viruses.

Group II: Single-stranded DNA viruses.

Group III: Double-stranded RNA viruses.

Group IV: (+) single-stranded RNA viruses.

Group V: (–) single-stranded RNA viruses.

Group VI: RNA retroviruses.

Group VII: DNA para-retroviruses.

Front 78

Baltimore Virus Classification Visual

Back 78