viruses and bacteriophages

what is a virus ?

genetic element that cannot replicate independently

obligate intracellular parasites

viral replication requires…

a host

viruses are incapable of

conserving energy

metabolism/synthesis of organic molecules

virion

extracellular form of virus that facilitates transmission from one host cell to another

what organisms can viruses infect ?

prokaryotes, eukaryotes, and other viruses

capsid

protein shell that surrounds viral genome

nucleocapsid

viral genome + capsid

naked virus

virus without outer envelope

enveloped virus

has outer layer with lipoprotein mem

what are capsomeres ?

individual protein molecules arranged in repeating pattern to form capsid

how are nucleocapsid assembled

by spontaneous self-assembly or host folding assistance

most viruses that affect eukaryotic cells are…

enveloped

what kind of symmetry do rod-shaped viruses have ?

helical eg. TMV

what determines the length and width of a helical virus ?

length - nucleic acids

width - size and arrangement of capsomeres

what kind of symmetry do spherical viruses have ?

icosahedral eg. HPV

what is the most efficient capsid arrangement and why ?

icosahedral - required fewest capsomeres

what symmetry types are seen in bacteriophages like T4 ?

icosahedral head and helical tail

joined by a collar

what is the source of lipids in the viral envelope ?

host cytoplasmic membrane

what do envelope proteins do ?

mediate host cell attachment and specificity

why are few plant / bacterial viruses enveloped ?

presence of rigid cell walls

why are enveloped viruses more easily destroyed ?

enveloped disrupted by handwashing and sanitisers

neuraminidase

enzyme inside some virions

degrades glycan structure on glycoproteins and lipids

allows liberation of viruses from cell

what is the smallest known viral genome ?

1.75 kb ssDNA single strand Circovirus

what is the largest known viral genome ?

2.5 Mb dsDNA Pandoravirus

which viral genomes are typically smaller RNA or DNA ?

RNA genomes

viroid

naked infectious RNA - no capsid

what forms can viral genomes take ?

DNA or RNA

single or double stranded

linear or circular

what is the difference between +sense and -sense RNA?

+sense is like mRNA

-sense is complementary and must be transcribed

what does the Baltimore classification scheme categorise ?

viruses based on genome type and replication strategy

how do viruses enter prokaryotic vs eukaryotic cells ?

prokaryotes - nucleic acid entry

eukaryotes - whole virion

what are the 5 phases of viral replication ?

attachment, penetration, synthesis, assembly, release

class VI (retroviruses) only infect…

animals

what is a lytic infection ?

virus replicates and lyses host cell

what characterises a one step viral growth curve ?

sudden increase in virus particles after host cell lysis

what is a temperate virus

virus that can enter either lytic or lysogenic pathway

what is a prophage

dormant phage genome integrated into host genome

what does the cl (lambda repressor) protein do ?

promotes lysogeny by repressing lytic genes

what does the Cro protein do ?

promotes lytic cycle by repressing cl expression

what are possible outcomes of animal virus infection ?

lytic infection, persistent infection, latent infection or transformation (cancer)

where does replication usually occur in animal viruses ?

host nucleus

what type of viruses are easiest to grow in the lab ?

bacteriophages

lytic vs lysogenic

lytic - virus immediately replicates, destroys host cell

lysogenic - virus integrates genetic material into hosts genome and lies dormant as prophage, doesnt kill host

what is a plaque assay ?

method to quantify infectious viruses by counting plaques on a bacterial lawn

direct counting of virion particles is done using…

electron microscope

what is a plaque ?

clear zone where viruses have lysed host cells

what does PFU stand for ?

plaque forming units

measure of infectious virus particles

why is PFU usually lower than direct electron microscopy counts ?

not all virions are infectious

conditions may not support infection

what are subviral agents

infectious entities that resemble viruses but are not

titer calculation

titer (PFU/mL) = number of plaques / DF x vol. plated (mL)

titer

conc. of infectious virus particles in original sample

can non-pathogenic prions exist ?

yes - some may play adaptive roles eg. MAVS

prion

infectious particles that lack nucleic acids

do prokaryotes have immune cells ?

no - they use molecular defence mechanisms instead

what are 3 defence mechanisms used by prokaryotes ?

restriction modification (RM) system

receptor modification

toxin-antitoxin systems

what is CRISPR ?

Clustered Regularly Interspaced Short Palindromic Repeats

prokaryotic adaptive immune system that provides heritable protection

how do RM systems work ?

bacteria produce restriction enzymes that cut foreign DNA at specific sequences

methylate own DNA at same sites to prevent self attack

what are spacer sequences in CRISPR ?

segments of past viral DNA used as “memory” to recognise future infections

what do Cas proteins do ?

nucleases that cut viral DNA during reinfection