1.2 - ACELLULAR MICROBES: VIRUSES, SATELLITES, VIROIDS, PRIONS

what are most viruses

bacteriophages

what are acellular entities

• viruses

• satellites

• viroids

• prions

What are acellular entities?

Infectious agents are not made of cells that lack metabolism and require a host to replicate.

What are viruses made of?

Nucleic acid (DNA or RNA) surrounded by a protein coat

Why can’t viruses reproduce independently?

They lack metabolic and replication machinery

What are satellites made of

nucleoc acids and proteins coat sometimes

what are satellites

Require a helper virus to infect and replicate ususally in plants

what are viroids made of

Circular single-stranded RNA which lack proteins

what are viroids

interfere with host gene expression

what are prions made of

made of only proteins

why are prions infectious

because they cause normal proteins to misfold

what can prions lead to

spongiform encephalopathies ( brain disease)

examples of Prions

BSE ( mad cow disease)

Scrapie (Sheeo)

CJD (humans)

Why are viruses considered emerging and evolving threats?

Viruses mutate rapidly, allowing them to evolve, adapt to new hosts, and emerge as new pathogens

How can viruses be useful in therapy?

Viruses can be used in gene therapy, vaccine development, and phage therapy to treat bacterial infections.

What role do viruses play in aquatic ecosystems?

influencing population control and nutrient cycling.

How do viruses affect organic matter in ecosystems

Viral infection causes cell lysis, converting particulate organic matter into dissolved organic matter.

How do viruses contribute to global nutrient cycles?

Viruses play a role in the global carbon and nitrogen cycles by releasing nutrients back into the environment

How do viruses influence evolution?

transfer genes between bacteria via horizontal gene transfer (transduction).

Why are viruses important in molecular biology research?

Viruses serve as model systems and are sources of key enzymes, such as reverse transcriptase (RT).

what does it mean if viruses are obligate intracellular pathogens

they are incapable of replication outisde host cells

Why can’t viruses replicate outside host cells?

They lack the metabolism and cellular machinery needed for replication.

How do viruses replicate differently from cells?

Viruses are assembled from separate components rather than growing and dividing.

What are the main parts assembled during viral replication?

Nucleic acid and protein subunits are synthesised separately and then assembled into virions.

Why do viruses depend on host ribosomes?

Viruses lack the genetic information needed for protein synthesis.

What host processes do viruses hijack?

Protein synthesis, energy production, and replication machinery

What is a virion?

A virion is the complete, infectious form of a virus outside a host cell.

What is the typical size of a virion?

Virions are approximately 10–400 nm in diameter.

Why can virions only be seen using electron microscopy?

They are too small to be resolved by light microscopy.

What structure is found in all virions?

A nucleocapsid.

What is a nucleocapsid?

It consists of viral nucleic acid (DNA or RNA) surrounded by a protein capsid - forms the essential structural core

What is the function of the capsid?

It protects the viral genome and helps transfer it into the host cell - functions as the protein coat of the virus

what are capsids made up of

protein subunits called protomers.

what are the names of the 3 capsid structures

1. hellical

2. Icosahedral

3. Complx

describe the strcutre of a hellical capsid

• hollow tubes with protein walls, with its size determined by the nucleic acid length

  • A piece of coiled RNA surrounded by repeated of a protein sub unit called a protomer. 

describe to structure of a iscosahedral capsid

An icosahedral capsid is a viral protein shell shaped like a regular polyhedron with 20 identical triangular faces and 12 corners (vertices

Why do viruses use an icosahedral shape?

: The icosahedral shape is strong, stable, and efficient, allowing the virus to enclose its genome using the fewest protein subunits.

what is a capsomer

ring or knob-shaped protein units, made of either 5 or 6 protomers. 

Capsomer, made up of 5 subunits is called a

Pentamers

Capsomer made up of 6 subunits is called a

Haxamer

describe a complex caspisd

• head resembles a icoshedral and a tail is helical. 

• they have tail fibers

binal symmetry is

• when the head resembles a icoshedral and a tail is helical. 

Do all virions have envelopes?

No. Only some viruses are enveloped.

what is the envolpe

• outer, flexible, lipid membranous layer which surrounds the nuclear capsid

where do viral envelopes come from

the host celll plasma membrane when undergoing replication

some viruses have enzymes packaged inside them what do these do ?

• They subvert the immune system to trick the host immune system so that it doesn’t work properly.

What is the role of spike proteins?

Spike proteins bind to host cell receptors, enabling viral entry

What is the main function of viral DNA or RNA?

Viral nucleic acid functions as hereditary material, not as an enzyme.

Can viral genomes encode proteins?

Ye, but these proteins are made by host ribosomes.

What else do viral genomes contain besides genes?

They contain regulatory elements that conswhen and how viral genes are expressed in the host

What structural forms can viral genomes take?

Viral genomes can be single- or double-stranded, linear or circular, and segmented or non-segmented

how can we classify viruses

disease, host, morphology, serology and sequence

what is the most important and widely used system to classify viruses based on

• the type of genome and how the virus replicates.

what does the Baltimore Classification System (BCS) groups viruses according to:

• Whether the genome is DNA or RNA

• Whether it is single- or double-stranded

• How the virus produces mRNA

how many classes of vruses are there according to the BCS

7

BCS - class 1

dsDNA viruses

• Genome: Double-stranded DNA

• Replication similar to host DNA

• mRNA made using host or viral RNA polymerase

• DNA → mRNA

BCS - class 2

ssDNA viruses

• Genome: Single-stranded DNA

• First converted into double-stranded DNA

• Then transcribed into mRNA

ssDNA → dsDNA → mRNA

BCS - group 3

dsRNA viruses

• Genome: Double-stranded RNA

• Host cannot read dsRNA

• Virus carries RNA-dependent RNA polymerase

• Enzyme makes mRNA from dsRNA

dsRNA → mRNA (using viral enzyme)

BCS - group 4

Positive-sense ssRNA viruses

• Genome: RNA (+)

• Genome itself acts as mRNA

• Can be translated immediately

RNA (+) = mRNA

BCS - group 5

Negative-sense ssRNA viruses

• Genome: RNA (−)

• Cannot be translated directly

• Must be copied into RNA (+) first

• Virus carries RNA-dependent RNA polymerase

RNA (−) → RNA (+) → mRNA

BCS - group 6

RNA reverse-transcribing viruses

• Genome: RNA (+)

• Uses reverse transcriptase

• RNA → DNA → integrated into host genome

• Host then produces mRNA

RNA → DNA → mRNA

BCS - group 7

DNA reverse-transcribing viruses

• Genome: dsDNA

• DNA is transcribed into RNA

• RNA is reverse-transcribed back into DNA

• mRNA produced during this cycle

DNA → RNA → DNA → mRNA

what are the 6 stages in the viral replication cycle

1. attachment

2. penetration/uncoating

3. transcription and translation

4. replication

5. Assembly

6. Release

stage 1 of the viral replication cycle

• Attachment via specific host receptor binding

• Trigger the ability to enter the cell 

Stage 2 of the viral replication cycle

• Penetration/uncoating of the nucleocapsid.

• Exposing their nucleic acid in the cytoplasm of the host 

Stage 3 of the viral replication cycle

• Transcription and translation of viral proteins.

Stage 4 of the viral replication cycle

• Replication of the viral genome. so the cell makes lots of copy of the viral genome and proteins 

Stage 5 of the viral replication cycle

• Assembly of viral progeny(Little baby virueses)

Stage 6 of the viral replication cycle

• Release from the host cell.

• Must avoid overcoming the host immune response.

what human receptor does SARS-CoV-2 spike protein attaches to

• ACE2.

How do animal viruses enter host cells?

Animal viruses enter host cells by attaching to specific receptors and entering either by membrane fusion or receptor-mediated endocytosis.

What determines how a virus enters a host cell?

Whether the virus is enveloped or non-enveloped determines its entry mechanism.

How do enveloped viruses enter cells via membrane fusion

Viral fusion proteins cause the viral envelope to fuse directly with the host cell membrane, allowing the nucleocapsid to enter the cytoplasm.

What is receptor-mediated endocytosis in enveloped viruses?

The virus binds to a host receptor, triggering the host to engulf it into an endosome.

What happens to enveloped viruses inside the endosome?

Fusion proteins cause the viral envelope to fuse with the endosomal membrane, releasing the viral genome into the cytoplasm

How do non-enveloped viruses enter host cells?

They usually enter by receptor-mediated endocytosis or by direct injection of their nucleic acid.

What happens after endocytosis of non-enveloped viruses?

The virus undergoes uncoating, where the capsid breaks down and releases the viral genome.

Why don’t non-enveloped viruses use membrane fusion?

They lack a lipid envelope, so they cannot fuse with host membranes.

Why is receptor-mediated endocytosis important for viruses?

It allows viruses to exploit a normal host cell process to gain entry into the cell.

What do 5′ and 3′ mean in DNA and RNA strands?

They describe the direction of the nucleotide backbone, based on the carbon numbering in the sugar molecule.

How are the two strands of DNA oriented?

One strand runs 5′ → 3′, and the other runs 3′ → 5′ in opposite directions

Which DNA strand resembles mRNA?

The 5′ → 3′ strand, because it has the same orientation and coding information as mRNA (except T instead of U).

What is meant by “positive-sense” RNA?

Positive-sense RNA has the same sequence and orientation as mRNA, so it can be directly translated by ribosomes.

Why can’t negative-sense RNA be translated by ribosomes?

Ribosomes can only read positive-sense (mRNA-like) sequences, not complementary RNA.

How do negative-sense RNA viruses make proteins?

They must first convert their genome into positive-sense RNA using RNA-dependent RNA polymerase.

What is a viral replication factory?

A specialised membrane-bound area inside a host cell where viruses replicate and assemble

Which host organelle is commonly used to form viral replication factories?

The endoplasmic reticulum (ER).

How do viruses form replication factories?

They induce expansion and rearrangement of host cell membranes to create protected compartments.

Why do viruses use membrane-bound replication complexes?

To protect viral components from host immune detection

How do replication factories improve viral replication?

They concentrate viral genomes, proteins, and enzymes in one location.

How do replication factories help viruses evade the immune response?

Membranes shield viral nucleic acids from immune sensors inside the cell

What processes occur inside viral replication factories?

• Genome replication

• protein synthesis coordination

• virus assembly.

Who makes viral proteins inside an infected cell?

Host ribosomes translate viral mRNA to produce viral proteins.

Where does bacteriophage assembly occur?

In the cytoplasm of the bacterial cell

Why does bacteriophage assembly occur in the cytoplasm?

Bacteria do not have a nucleus

hat is the first major structure assembled in a bacteriophage?

The prohead (empty capsid precursor).

What happens after the prohead is formed?

The viral DNA is packaged into the prohead.

What structure is added after DNA packaging in a bacteriophage?

The base plate.

Which components form the bacteriophage tail?

Base plate proteins, the tube, and the sheath.

What is the final component added to the bacteriophage?

Tail fibres, which help the phage attach to bacterial cells.