Biofilms
Define biofilm. Where are they typically found?
Biofilm: A community of bacteria attached to a surface and each other surrounded by an extracellular matrix made of biological polymers.
Found anywhere wet (drain pipes, faucets, rocks in bodies of water, teeth, showerheads, toothbrush)
What structures are found in all viruses?
- Genome
- Capsid
What three ways can newly synthesized virions be released from a cell?
1) Budding (enveloped cells only)
2) Lysis
3) Exocytosis in vesicles
What is an obligate intracellular parasite?
An organism or infectious agent that relies solely on its host cell for energy, metabolic intermediates, and protein synthesis. Essentially, it requires a host to survive and reproduce. A virus is an obligate intracellular parasite.
What is a prion? What is a virioid?
Prion: acellular infectious agent made of protein. Mainly infects the central nervous system
Viroid: acellular infectious agent made of a single-stranded RNA. Does not contain any protein. Mainly infects plants
List and describe the four stages of biofilm formation.
Attachment:
- Planktonic cells attach to a surface via random collisions with the surface. This can be assisted by their pili/fimbriae
- Production of a sticky matrix
- Bacteria are induced to express biofilm-specific genes. These genes recruit other bacteria and aid in forming the sticky layer around them.
Colonization:
- Intracellular communication (quorum sensing)
-Growth
- Polysaccharide formation
- Loss of flagella (removes motility)
Development:
- Further growth and polysaccharide formation
Dispersal:
- Breaking off of a part of the biofilm to begin a new one somewhere else. Can be an entire section or a planktonic shower.
- Triggered by environmental factors like nutrient availability
How is the viral genome different than the genome of a host cell?
- Can be made of DNA or RNA (instead of just DNA)
- Can be single-stranded or double-stranded (not just double)
- Can be circular or linear
- Much smaller
- MUST carry or encode RNA-dependent RNA-polymerase if it is an RNA virus
Which step in the replication cycle of a virus determines the host or tissue specificity of the virus?
Attachment: There MUST be a receptor on the host cell in order for protein attachment to occur (very precise and specific process)
Several stages in viral multiplication involve specific host machinery. Why is it less likely that successful chemotherapeutic agents could be found that would affect these stages?
By targeting the host cell’s machinery to shut down the production of viruses, you would also shut down the host cell’s metabolic functions, effectively inactivating and killing the host. When a host cell dies, it releases the viral particles anyways, so this does not solve the problem.
Where do enveloped viruses normally acquire their envelope from?
From membranous internal organelles in the host cell. This could be the nuclear membrane, the ER, or the cellular membrane.
What are four different advantages to biofilm living?
1) Trap and concentrate nutrients
2) Prevent detachment from a surface and one another
3) Increased communication (quorum sensing) and swapping of genes (chance for increased immunity)
4) Self-defense. A much higher concentration of antibiotics must be used to kill a biofilm than individual bacteria
What is a positive strand? What is a negative strand?
Positive strand: in an RNA virus, this strand contains the exact same base sequence as the viral mRNA. Can be used as the mRNA strand directly to begin synthesizing proteins
Negative strand: this strand has a base sequence that is complementary to viral mRNA. It therefore must be transcribed into the positive strand before it can be used to make protein
How is the lysogenic cycle different than the lytic cycle?
The lysogenic cycle does not kill the cell while the lytic cycle will lyse the cell which subsequently kills the cell.
Lysogeny allows the viral genome to incorporate itself into the host genome. This is called a prophage. The prophage is then replicated with the host cell's genome as the cell divides. It can lie dormant for a long time. When stress occurs, the viral genome is excised from the host cell's genome and it enters the lytic cycle.
What kind of damage can viral infection impose on a host cell?
1) Death via lysis
2) Altering a host cell's genetic material
3) Transforming the host cell into a cancerous cell (ANIMAL VIRUSES ONLY)
What is latency? How is it different than lysogeny?
Latency only occurs in animal viruses. The animal virus may or may not incorporate into the host cell's DNA and will lie dormant until stress occurs. The main difference is that if incorporation does occur, the viral genetic material will PERMANENTLY remain embedded in the host's DNA. When stress occurs, the virus will shed viruses, but the original viral DNA will remain in the host.
Examples: shingles, herpes
What is the significance of Pseudomonas aeruginosa biofilms?
These specific biofilms produce polysaccharides that prevent antibiotic penetration. Therefore, they are very difficult to treat.
As opportunistic pathogens, they infect the lungs, blood, urinary tract, skin, ears, etc. They are very dangerous to human health.
What is reverse transcriptase? Which types of viruses must carry it?
It is an enzyme that converts an RNA genome into DNA. This goes against the central dogma of genetics. Retroviruses must have it. These are classes VI and VII of virus on the chart.
What are three ways that a virus can enter a host cell?
2) Membrane fusion: envelope and membrane fuse together and the nucleocapsid is taken into the cell. The capsid gets degraded by the host cell enzymes
3) Phagocytosis: the virus pushes through the cytoplasmic membrane and takes some of the membrane with it. The cell will close up after the virus enters. The membrane around the virus is then degraded once it fully enters.
What are the four possible outcomes of an animal virus once it infects a host cell?
1) Virulent (lytic) infection: results in the lysis of the host cell and the release of the virus. This is the MOST COMMON outcome
2) Latent infection: viral DNA exists in the host's genome and the virions are not produced. It leaves the host cell unharmed unless lysis is triggered under stress. The virus is present in the host cell, but it is NOT replicating
3) Persistent infection: the release of virions is slow and the host is not lysed. The host cell continues to grow and the virus makes more virions
4) Transformation: a virus converts the host cell into a tumor cell
What is an autoinducer and what does it do?
It is a specific signaling molecule that is used in quorum sensing. In this process, the autoinducer is used to sense the cell density of the bacteria in the surrounding area. This molecule diffuses freely across the cell membrane in either direction. When there is a high concentration of bacteria in the area, they are also sending out these signal molecules. This would force the autoinducers back into the bacterial cells and notify them that there is a high cell density of other bacteria in the area.
The autoinducer then binds to transcriptional activator proteins to trigger the transcription of the specific genes needed.
What is the role of biofilms in dental caries?
Acidic glycoproteins in saliva form a thin, organic layer that bacteria (mainly Streptococcus) attach to. When sugar is introduced to the mouth, the bacteria are fed and they undergo lactic acid fermentation. The corrosive lactic acid produced breaks down the tooth's enamel and produces dental caries.
Genome: ssRNA + virus. 30 kb
Capsid: vital for binding, contains nucleocapsid N
Envelope: contains envelope protein E (a small, integral membrane protein. This protein is involved in many aspects of the viral life cycle (assembly, budding, envelope formation, and pathogenesis). Also contains spike protein (S). There are 12 spike proteins
Describe the Sars-CoV2 replication cycle
Attachment: "S" spike protein on virus attaches to ACE2 receptors
Entry: Endocytosis occurs via phagocytosis followed by the fusion of the envelope with the endocytic membrane. The nucleocapsid is uncoated in the cytoplasm
Synthesis: ssRNA + acts as mRNA. The negative strand is synthesized as a template. This occurs in the cytoplasm
Assembly: Occurs in cytoplasm. Acquires envelope from the golgi
Release: Budding
What is the difference between antigenic drift and shift? Be detailed!
Antigenic drift: small, gradual changes in the viral antigens over time due to mutation.
Antigenic shift: major, immediate changes in the viral antigens due to gene reassortment. It only occurs in the influenza virus. It leads to the immediate change of one or both of the major NA or HA viral glycoproteins (spike proteins). Occurs when two different influenza viruses infect the same cell and their antigens get "mixed-and-matched". This creates a new, hybrid version of the flu for which humans do not have antigens. It leads to much more serious outbreaks of the flu.
How are both bacterial viruses and animal viruses grown in a lab?
Bacterial: A pure culture of bacterial hosts is inoculated in a liquid medium or spread as “lawns” on the surface of an agar plate and then inoculated with a virus suspension. Requires a cell culture.
Animal: They are cultivated in tissue cultures which are cells obtained from an animal organ and grown in sterile glass or plastic vessels containing an appropriate culture medium. The tissue culture media are often complex, containing a wide assortment of nutrients including blood serum and other highly nutritious substances to feed the animal cells and antimicrobial agents (which are present to prevent bacterial growth)