Microbiology Ch. 13

2013 Report of ICVT

- 6,000 viruses belong to 2,828 species, 455 genera, 103 families, and 7 orders.

Largest size of virus

- 800 nm

T4 Phage (dsDNA)

- A double-stranded DNA phage. - Phage takes over a bacterial cell, directing that cell to synthesize new phage particles. - Viewed as a 5-step process (attachment, genome entry, synthesis of phage proteins and genome, assembly, and release).

Phage Induction

- Lets the phage escape from the damaged host. - Induced into people. - People have HIV or an illness. - Goes from lytic stage to lysogenic.

Synthesis

- Third stage. - Cell begins to synthesize after T4 DNA is injected into a host cell and some genes of that DNA are being transcribed. - Not all phage-encoded proteins are synthesized. - Made in a sequential manner during course of infection. - Holds early and late proteins.

A single nucleic acid, either DNA or RNA, never both. Provides a useful method to classify the viruses.

A virus contains what kind of nucleic acid, what is it? What type of method does it provide?

ssRNA

Viroids characteristically are composed of:

The nucleic acid

Which part of the attached bacteriophage enters through the host cell wall?

dsRNA, (+)

_____ viruses carry replicase to synthesize (__) strand.

Provirusues

- Part of latent infections. - A silent viral genome. - Cannot be eliminated from the body. - Can recur.

Use RNA as a template to make DNA.

Retroviruses are unique in that they:

FALSE

T or F Bacterial cells are harder to grow than animal cells.

TRUE

T or F Viruses require a live organisms as a host to grow.

The International Committee on Viral Taxonomy (ICVT)

- Keeps an online database and publishes a report describing key features, classification, and nomenclature of recognized viruses.

Antigenic Drift

- Mutations lead to antigenic variation and allow some RNA viruses to adapt to selective pressures. - Occurs as mutations accumulate in gene encoding key viral proteins. EX: influenza viruses.

Superinfection

- Once you get infected, you cannot get infected a second time. - Depends on the lysogen. - CANNOT GET INFECTED ONCE YOU CAUGHT THE BUG!!

Replicative Form (RF)

- A double-stranded DNA. - One strand of RF is used as a template to make mRNA as well as multiple copies of the phage's single-stranded genome. - ONCE IT IS REPLICATED, YOU CAN COPY IT.

M13

- A filamentous phage that initiates infection by attaching to a protein on the F pilus of E.coli. - Produces single-stranded and double-stranded DNA. - Its single-stranded DNA genome enters the cytoplasm of the bacterial cell when the host cell DNA polymerase synthesizes the complementary strand. - Has to transcribe into mRNA to make proteins (NEEDS DNA POLYMERASE TO DO THIS!!!) - The double-stranded DNA is referred to as a replicative form (RF). - The phage coat proteins molecules are inserted into the host cell's cytoplasm to obtain the membrane. - At the same time, the phage-encoded proteins form pores that span the cytoplasmic and outer membrane to form a gas so they can leave.

Tropism

- A specific tendency for the virus to attach to the receptor. EX: dogs do not contract measles from humans.

Replicase

- A virally encoded RNA polymerase. - RNA- dependent RNA polymerase. - Able to synthesize a strand of RNA from an RNA template. - Lacks proofreading and allows antigenic drift.

SOS repair

- Activates a protease that destroys the repressor protein that is responsible for maintaining the intergration of the prophage. - Triggers from outside the DNA that can turn on the lytic cycle. - Uses phage induction and lysogenic conversion.

Alternating Receptor Sites

- Alter or cover specific receptors on cell surfaces which prevents the phage from attaching. - Requires an attachment. - May have other benefits to bacteria that can produce toxins, capsules, slime layer (biofilms), or mask receptors.

Reverse transcriptase

- An RNA-dependent DNA polymerase which synthesizes DNA from an RNA template. - Runs counter to the central dogma of molecular biology in that an RNA molecule that is used as a template to make DNA. - Synthesizes a DNA strand. - Uses RNA genome as a template to make one strand of DNA. - Complementary strand is synthesized to make a double-stranded DNA. - Once the DNA is copied, it cannot be eliminated from the cell.

CRISPR System

- Bacterial cells that survive some phage infections retain small segments of phage DNA, incorporating them into bacterial genome. - Includes a spacer. - Includes the spacer sequences, its transcribed and then cut into small RNA called crRNAs.

Persistent Infections

- Can continue with or without symptoms for years, or even the life of the host. - Contains Chronic and latent infections.

Lysogenic Conversion

- Certain properties where cells adapt to. - Immune system does not recognize lysogenic conversion.

Lysogeninc Conversion

- Changes in the phenotype of a lysogen as a consequence of the specific prophage it carries.

Acute Infections

- Characterized by a sudden onset of symptoms of a relatively short duration. - Result in a burst of virions being released from infected host cells. - Virus-infected cells often die, the host may survive. - The immune system of the animal host may eliminate the virus over a period of days to months. EX: influenza, mumps, and poliomyeltis.

Capsomeres

- Composed of identical subunits - Arranged in a precise manner to form the capsid.

Prions

- Composed solely of proteins. - Violates the central dogma of replication that requires nucleic acid to act as a template for replication of macromolecules. - NOT MADE UP OF NUCLEIC ACIDS!!! - Linked to slow, always fatal to humans, and to animal diseases. - Transmissible only within species. - Proteins accumulate in neural tissues.

Viroids

- Consistently solely of small single-stranded RNA molecules that form a closed ring used for hydrogen bonding. - One-tenth of the size of the smallest infectious viral RNA genome known. - ONLY INFECTS PLANTS--> where it causes serious diseases.

Lambda Phage

- DNA excised from chromosomes only about once per 10,000 divisions of lysogen. - Will go to the lytic route to infect something else.

Filamentous Phages

- DOES NOT DESTROY THE HOST CELL. - Single-stranded DNA that looks like long fibers. - Causes productive infections (process does not kill the host cell). - Uses M13 phage as a model.

(+) and (-) strands

- Designation that indicated which strand is used as the template for RNA synthesis. - These strands genomes can be transcribed to produce mRNA. - mRNA is a (+) strand. - mRNA is translated to make proteins.

Restriction-Modification System

- Enables bacterial cells to target something viral. - Protects bacteria from phage infection by quickly degrading incoming foreign DNA. - Goes through restriction and modification enzymes.

Penetration and Uncoating

- Enveloped viruses enter the host cell by one or two mechanisms: FUSION W/ HOST MEMBRANE or ENDOCYTOSIS.

Lytic (virulent) Phase

- Exits the host at the end of the infection cycle by lysing the cell. - Destroys the host cell in the process.

Attachment

- First stage. - Particles collide with their host cells by chance. - A phage attaches by means of a protein on its tail to a receptor on the host cell surface or appendage such a pilus. - Receptors used by phages perform functions for the cells.

Lambda Phage as Model

- Has linear chromosomes and 2 ends that are complementary single-stranded that overhangs that joins together inside of the host cell to form a circular molecule of DNA. - Either direct lytic infection or intergrate into the E.coli chromosomes. - ALWAYS TARGETS THE CELL.

Temperate Phages

- Have an option of either lytic infection (productive infection) or incorporating their DNA into the host cell genome.

Uncoating

- IN VIRUSES, nucleic acid separates from its protein coat before the start of replication. - May occur with entry of the virion into the cell, or after the final intracellular destination for viral replication that has been reached.

Key Characteristics of ICVT

- Include the GENOME STRUCTURE (type of nucleic acid and strandedness) and HOST INFECTED (plants, archaea, animals, and bacteria).

Retroviruses

- Include the human immunodeficieny virus (HIV. - Has a (+) strand RNA genome. - Carries reverse transcriptase within the virion.

Prophage

- Intergrated phage DNA. - Replicated along with the host cell chromosome. - When the cell divides, the prophage is passed onto the cell's progency. - Later, the prophage can begin the process that leads to a productive infection.

Fecal-oral Route

- Known as enteric viruses. - Enteric means relating to the intestines.

Release

- Lysozyme is produced late into infection. - Enzymes digest the host cell wall from within, causing the cell to lyse, which releases the phage. - Contains a burst size.

Replication of RNA Viruses

- Majority of RNA viruses are single-stranded. - Replicate in the cytoplasm. - Replication requires encoded RNA polymerase (replicase).

Spikes

- Many animal viruses have this protein structure. - Sticks out from either the lipid bilayer of enveloped viruses OR the capsid of non-enveloped viruses. - Goes into the EUKARYOTIC cells. - Out-punching that has the ability to attach the cells.

Genome

- May be linear or circular. - May be double-stranded or single-stranded. - In viruses, it can have a single-stranded DNA or double-stranded DNA.

Replication of DNA Viruses

- Most DNA viruses replicate in the nucleus of the host cell. - Uses host cell machinery for DNA synthesis as well as gene expression. - Often code for DNA polymerase. - Allows replication even if the host cell is not actively replicating its own chromosome.

Release

- Most enveloped viruses are released by budding. - Viral protein spikes insert into host cell membrane. - Making proteins accumulate; then nucleocapsids are extruded. - Covered with matrix protein and lipid envelope. - Non-enveloped viruses released when host cells die, by apoptosis initiated by virus or host.

Productive Infections

- Part of Lytic Phase. - Viral infections result in the formation of new viral particles. - They go to the cell, it gets released into a surrounded area to lyse the other cells, then goes around to kill/infect cells.

Expression of viral genes

- Part of Synthesis of viral proteins. - Capsid proteins and any enzymes required for replication.

Generalized Transduction

- Results from a packaging error during phage assembly. - ALWAYS LYTIC!!! - Some phages degrade the bacterial chromosome into fragments during lytic infection. (infection of the cell) - ABILITY TO ALLOW DNA OR RNA TO ENTER THE HOST CELL. - Uses generalized transducing particles.

Specialized Trandsuction

- Results from an excision mistake made by a temperate phage during its transition from a lysogenic to a lytic cycle. - ALWAYS LYSOGENIC!!! - Short piece of flanking bacterial DNA is removed; a piece of phage DNA remains. - The excised DNA contains BACTERIAL and PHAGE GENES. - It is replicated then becomes incorporated into phage heads.

Plaque Assays

- Routinely used to quantitate phage particles in samples such as sewage, seawater, and soil. - Double layer of agar is used; top layer (soft agar) --> inoculated with a bacterial host and phage containing specimen. - The bacteria present in the soft agar multiplies rapidly, producing a turbid layer of dense lawn of bacterial growth. - Done by using different dilutions of phase suspension.

Matrix Protein

- Sandwiched between the nucleocapsid and the envelope. - Unique to the enveloped viruses. - Something that only non-enveloped viruses will have.

Genome Entry

- Second stage. - Bacteriophage injects its genome into the cell. - T4 degrades a small portion of the cell wall, using an enzyme located in the tip of its tail. - Enzyme is known as T4 lysozyme (functions similar to the lysozyme found in tears and eggs)

Spacer

- Segments of phage DNA. - Inserted into a chromosomal region called CRISPR. - Provides a historical record of past phage infections. - Allows bacterial cells as well as its progeny to recognize. - Blocks subsequent infections by same types of phages.

Single-Stranded DNA (ssDNA)

- Similar to ssDNA viruses. - Except the compliments are to a single-stranded DNA molecule. - Must be synthesized to generate a double-stranded (+/-) molecule) - Genes can be expressed to produce the encoded proteins.

Single-Stranded RNA

- Single-stranded (+) RNA is used as mRNA. - + RNA = mRNA. - Neede to make protein. - + is always need for protein.

Virus 2 categories

- Some infect prokaryotic cells, other infect eukaryotic cells. - Both groups are viruses, but the ones that infect bacteria are known as bacteriophages, or phages.

Enveloped Viruses

- Some viruses have an envelope --> a lipid bilayer outside the capsid. - Have a lipid bilayer envelope from the host cell . - Not all membranes will do this. - More susceptible to disinfectants b/c the chemicals damage the envelope, making the viruses non-infectants.

Arboviruses (arthropod borne)

- Spread by arthropods often can infect widely different species. - Usually biological vectors. - When an infected arthropod takes a blood mean from the animal, it transmits the virus. - Comes from mosquitoes and ticks that can transfer things.

Titer

- The concentration of infectious phage particles in the original phage suspension.

Lysogen

- The infected cell. - The cell is infected by a virus that takes the lysogenic route.

Lysogenic Infection

- The latter situation. - When a virus takes its own DNA and incorporates it into the host cell. - The intergrated phase DNA, called prophase, is replicated along with the host cell chromosome.

Phages

- Have tail fibers, that attach to the host cells. - Contains proteins on the end. - Made to adhere to the surface of the cells. - Needs to do this to get to nucleic acid.

Zoonotic viruses

- Causes zoonoses. - Goes from animal to human. - EX: herpes.

Mad Cow Disease

-Killed more than 170 people in England.

Synthesis of multiple copies of the viral genome

-Part of synthesis of viral proteins. - The viral protein that is made are sometimes synthesized as polyprotein that is cleaved by viral proteases into individual proteins. - Most DNA viruses multiply in the nucleus.

Complete, extracellular virus particle

A virion is a (an):

2 categories of cells they can infect.

How many groups can viruses be broken down to and to do what?

SOS repair will fix it.

If DNA gets damaged by UV light exposure, what will repair it?

Only produced during reactivation.

In latent infections, the virions are:

Matrix protein

In the region of budding, the inside of the plasma membrane becomes coated with:

Metabolically inert

Outside of living cells, viruses are:

Lysogenic phages

Phages that can either replicate & cause cell lysis or integrate their DNA into host DNA are:

Plaques

- Circular zones of clearing, form in the lawn due to cell lysis caused by the phage. - Each plaque represents a plaque-forming unit (PFU) initiated by a single phase particle infecting a cell.

Smallest size of virus

- 10 nm - 10 genes

Only infect E. coli that have pili

Filamentous phages...

TM or EM microscope

Viruses are too small to see with a light microscope, what kind is recommended to use?

Inside living, activating, metabolizing cells

Viruses can only multiply in what conditions?

DNA Viruses RNA Viruses Reverse transcribing viruses

What are some replication strategies of viruses that can be divided into 3 categories?

Alternating Receptor Sites Restriction-Modification System CRISPR System

What are the 3 mechanisms that confer bacterial resistance to phage infection?

Attachment Penetrating and Uncoating Synthesis Assembly Release

What are the steps of generalized infection cycle of animal viruses?

Nucleocapsid

- The capsid together with the nucleic acid it encloses.

Attachment Genome Entry Synthesis Assembly Release

What are the steps of the T4 model?

Icosahedral (spherical) Helical (cylindrical) Complex ("catch off category")

What are the three different shapes of viruses?

Lytic Temperate Filamentous

What are the three general types of phage infections of bacteriophages?

Lysogenic Conversion Superinfection

What are two different consequences of lysogency?

Microbes not organisms

What are viruses, and what are they not?

The host cell has to make more copies of itself.

What does a virus need to do to obtain certain components?

No ribosomes No ability to make energy/ATP No origin of replication

What is something that viruses do not have?

Viruses Virion Receptor Host cell

_______ have protein components that allow the ______ to attach (absorb) to specific ________ sites on ____ ____. MUST ATTACH TO THE HOST CELL.

Fusion

- Part of penetration and uncoating. - The lipid envelope of the virion fuses with the cytoplasmic membrane of the host cell. - Non-enveloped viruses have no lipid envelope, cannot fuse to host membrane to enter cells. - The virions can only enter via endocytosis. - Once in the endosome, the nucleocapsid is released in the cytoplasm. RESULT = the nucleocapsid is released directly into the cytoplasm.

Endocytosis

- Part of penetration and uncoating. - Virions that enter endocytosis take advantage of the receptor-mediated endocytosis. - A normal mechanism by which cells bring is a certain extracellular material into the host. - The viral particles bind to the receptors than normal trigger and facilitate the process.

Chronic Infections

- Part of persistent infections. - Continous production of low levels of virus particles. - In some cases: the infected cell services and slowly releases viral particles. - In other cases: the infect cell lyses, but only a small proportion of cells is infected at any given time.

Burst Size

- Part of release. - Number of phage particles is released per one phase. - 200 are released from one process of the cycle, in a 30 minute process. - These phage particles them infect any susceptible cells in the environment.

Defective Particles

- Part of specialized transduction. - The phage particles do not carry the entire set of phage genes --> leads them to be defective. - DEFECTIVE PARTICLES ARE RELEASED AS THE HOST CELL LYSES. - When a defective phage injects its DNA into another bacterial cell, both PHAGE and BACTERIAL DNA enter.

Late proteins

- Part of synthesis. - Structural proteins (capsid, tail); produced toward end of the cycle. - Produces everything later into the phase. - Puts the protein capsid to the tail which makes the virus.

Early proteins

- Part of synthesis. - Translated within minutes. - A nucleus that degrades the host cell's DNA. - Then proteins that modify a subunit of the host cell's RNA polymerase so it no longer recognizes bacterial promoters. - Shuts everything down. - Produced by nuclease by the ribosomes in the host cells. - Breaks down the DNA host cells into small fragments. DESTROYS EVERYTHING.

Intergration Process

- Part of the lambda phage. - Uses phage-encoded enzymes (intergrase). - Inserts the phage DNA into the host cell chromosome into a specific site. - Replicated with the host chromosome prior to division. - Can be excised from the host chromosome by a phage-encoded enzyme. ( THIS IS THE START OF THE LYTIC INFECTION) - Uses a repressor to prevent phage-encoded enzymes.

Generalized Transducing Particles

- Phage heads that contain only bacterial genes in place of phage genes CANNOT direct a phage replication cycle. - The particle can bind to another bacterial cell (new host) and injects its DNA. - The bacterial DNA can intergrate into the recipient cell can be transferred.

Repressor

- Prevents expression of the gene required for excision. - Essential for maintaining the lysogenic state. - Prevents phage-encoded enzymes.

Attachment/absorbtion

- Process of attachment is same in all virus-cell infections. - Animal viruses have attachment proteins or spikes on their surfaces. - Viruses will bond to the receptors. - Need multiple receptors so it can attach and recognize. - The host cell in us is different in animal viruses. (they will have different reactions to infections of bacterias). - Usually glycoproteins are on the cytoplasmic membranes (recognized by the animal viruses). - Often more than one is required (EX: HIV binds to 2). - Specific receptors (tropism) is required, limited range of viruses. - Can only infect a single species.

Assembly

- Produces new phage particles when multiple copies of the phage genome and the structural components are produced. - Complex, multistep process. - Once phage head is formed, DNA is packed into it. - The tail is attached then followed by the tail spikes. - Some self-assemble. - The protein joins together spontaneously to form a specific structure.

Synthesis of Viral Proteins

- Production of viral particles in an infected cell require 2 distinct but interrelated events: 1) expression of viral genes to produce STRUCTURAL and CATALYTIC PROTEINS. 2) synthesis of multiple copies of the viral genome.

Apoptosis

- Programmed cell death. - Prior to release of the viral particles. - The immune response of an animal: directed toward eliminating the virus that can lead to the same process. - Virions are release from the dead cells that may invade any healthy sells in the area.

Modification Enzyme

- Protects the host cell's own DNA from the action of the restriction enzyme. - Does this by adding methyl groups to the nucleobases recognized by the restriction enzymes. - Will methylate the incoming phage DNA before the restriction enzyme has acted. - The phage DNA will not be degraded allowing it to replicate and lyse the host cell. - The DNA of the phage progeny could be defrauded by different restriction-modification system.

Assembly and Maturation

- Protein capsids form. - Brings together genomes and enzymes that are packaged to form a nucleocapsid. - Viruses are structurally diverse. - Non-enveloped viruses mature fully and take place in nucleus or in organelles of cytoplasm. - Viruses will deposit protein into the host cytoplasmic membrane. - Then, the nucleocapsid binds to these regions of the membrane before exiting the host cell. - Some DNA assembles their nucleocapsids in the nucleus of the host cell.

Capsid

- Protein coat. - Protects the nucleic acids from enzymes and toxic chemicals in the environment. - It is complete. - Holds extracellular virus particles. - Carries any enzymes required by the virus for infection of host cells.

Restriction Enzymes

- Recognizes specific short nucleotide sequences in foreign DNA or RNA (such as a phage DNA, then will cut the sequence). - Destroys things inside the bacterial that are foreign. - Cannot degrade methylated DNA. - Will degrade incoming phage DNA, but not the host DNA. - Played important role in biotechnology revolution. - Gives scientists, a tool to remove genes from one DNA molecule, so they can be joined together.

Double-Stranded DNA (dsDNA)

- Replication is simple. - Follows central dogma of molecular biology. - Has two complementary strands: (+) and (-) strands. - Serves as a template for DNA replication.

Prions accumulating tissues

- The neurons die. - Tissues develop holes. - Brain function deteriorates. - Sponge-like appearances of the brain tissues(transmissible spongiform encephalopathies --> refers to all prion diseases). - PRIONS LACK A NUCLEIC ACID!!!! - Uninfected animals synthesize a normal neuronal protein that is identical in amino acid sequence to a prion protein.

Classification of Viruses

- The species name is the name of the disease the virus causes. - EX: polioviruses causes poliomyeltis - Virus end is used for the genus name. - Viruses commonly referred to only by the species name.

Bacteriophage

- The virus that infects that bacterial cell.

F Pilus

- Used for conjugation when one cell is passed from one another passing through DNA bacterial cells.

Features of a Virus

- Viewed as genetic information: DNA or RNA contained within a protective coat. - INERT PARTICLES, incapable of particles, incapable of metabolism, replication, or motility. - No ability to replicate or survive outside the cell. - They are INERT when outside the cell. - When inside the cell, they have direct activities that have profound effects on the cell.

Latent Infections

- Viral genome (provirus) remains silent in the host cell; it can reactivate. - Some viruses do not intergrate into the host cell chromosomes. - Replicated independently into host genome, like a plasmid. - Uses proviruses. - Can later be reactivated. - Some viruses exhibit both.

Virion

- Viral particles that consist of nucleic acid surrounded by a protein coat.

Non-enveloped (naked) viruses

- Viruses lack an envelope. -More resistant to disinfectants. - All phages are non-enveloped viruses. - Most disinfectants will destroy the envelope of the cell wall.

Respiratory Route

- Viruses transmitted through the respiratory route. - EX: the flu

Antigenic Shift

- When a new subtype of a virus is formed by reassortment between different strains of a virus or even between different viruses