Virus/Bacteria

Why are viruses not a true cell?

• they are obligate intracellular parasites that need to be inside of a host cell to express genes and reproduce

  • uses host cell machinery (enzymes, cell energy, cell structures like ribosomes, etc.)

What components do ALL viruses have?

• nucleic acid core

  • DNA or RNA

  • single or double stranded

• capsid

  • protein coat of the virus

  • 2 different capsid shapes

    • icosahedral - 20 sided w/ nucleic acid in center

    • helical - rod-shaped (capsomeres wind about nucleic acid)

What is a capsid?

protein coat of the virus

Describe the two types of capsids

icosahedral - 20-sided (nucleic acid in center)

helical - rod-shaped (capsomeres wind about nucleic acid)

What are components that only SOME viruses have?

• envelope (aka membrane)

  • surrounds capsid

  • produced from host cell membrane; also contains viral proteins

  • may have spike-like projections (glycoproteins)

• enzymes

  • usually needed for viral replication or transcription of genes (i.e. RT)

What is the definition of a viral infection?

The nucleic acid of the virus enters the host cell

Name the four types of viruses based on capsid shape and envelope and describe them

Enveloped polyhedron

• ex. HIV/Flu

Naked polyhedron

• ex. Adenovirus, cold virus

Enveloped spiral

• TMV, helical capsid

Naked spiral

• ORF virus (scabs from sheep)

How do plant viruses enter the plant cell?

Via an insect vector that pierces thick cell wall and injects the virus

What are the steps of viral infection?

1. Adsorption

2. penetration

3. uncoating

4. synthesis

5. assembly

6. release

ACRONYM TO REMEMBER: APUSAR

Describe the adsorption stage of viral infection/reproduction

• binding to host cell, viral protein—cell receptor interaction

• host cell specific - each type of virus can only infect a limited number of host cells

Describe the penetration stage of viral infection/reproduction

• entry into cell

  • non-enveloped viruses use receptor mediated endocytosis

  • enveloped viruses’ viral envelope fuses with the plasma membrane of the host cell → capsid enters host cells

Describe the uncoating stage of viral infection/reproduction

• disassembly of infecting virus (removal of outer structures to expose nucleic acid

Describe the synthesis stage of viral infection/reproduction

• synthesis of viral components such as capsid proteins, viral enzymes, envelope proteins, nucleic acid

  • remember that viral genome often contains a gene that produces an enzyme that degrades host cell DNA/alter host cell RNA poly → host cell can’t transcribe/translate its own genes → virus can hijack cell’s energy to manufacture its own proteins and genome

Describe the assembly stage of viral infection/reproduction

• assembly of different virus components to product intact virus that can infect another host cell

• capsid surrounds genome + enzymes that need to be encapsulated in the intact virus

Describe the release stage of viral infection/reproduction

• enveloped virus

  • viral proteins are inserted into host cell membrane

  • nucleocapsids accumulate at sites where proteins are inserted

  • virus buds out of cell - modified host cell membrane becomes viral envelope

• non-enveloped

  • lysis occurs (host cell death)

Describe the structure and form of entry for bacteriophages

• structure: includes icosahedral head + tail

• special form of entry

  • viral tail fiber proteins bind host cell receptors

  • nucleic acid is injected into host cell as tail contracts; all viral structures including capsid are left outside of cell

What are the two alternative forms of infection?

Lytic and lysogenic

Describe the lytic cycle

• complete viral life cycle that ends in lysis of host cell (host cell death)

• virus directs the production of lysozyme that breaks open host cell to release viruses

• viruses that kill host cells in this way → lytic viruses + virulent

NOTE: not all bacteria are killed once infected by a lytic virus, some bacteria have protective restriction enzymes that recognize and chop up foreign DNA

Describe the lysogenic cycle

• host cell is NOT killed

• phage DNA enters cells → integrates into bacterial chromosome → phage genome now called prophage

• prophage expresses gene for repressor protein that shuts off activity of other viral genes → VIRUS ENTERS A LATENT STAGE

• when bacterial cell reproduces, it replicates prophage genome with its own → each new bacterial cell contains viral genome

• stimulants such as chemicals/radiation can induce prophage to be excised from bacterial genome → virus undergoes lytic cycle

What are temperate phages?

virus that can undergo a lytic or lysogenic cycle

What is transduction with respect to the lysogenic cycle?

• method that increases variation in bacterial genome

• during assembly some of the host DNA will become encapsulated in a capsid.

• phage may go on to “infect” another bacterium with HOST DNA

What are the three major types of viruses based on type of genetic material/method of replication?

1. DNA

2. RNA

3. retroviruses

Describe the life cycle of a DNA virus

reference this diagram and remember APUSAR

Describe the life cycle of an RNA virus

• similar to DNA viruses, the virus enters the cell and the genome is uncoated

• assembly and release are similar to DNA viruses

• DIFFERENCE:

  • RNA acts as an mRNA for immediate translation and as a template to produce more RNA genome

  • some of the genes need to be translated first before replication b/c virus needs to produce enzyme that uses RNA as template in order to produce more of the RNA genome.

    • host-cell doesn’t contain an RNA dependent RNA poly)

Provide examples of DNA viruses

herpes, Hepatitis B, smallpox, papilloma

Provide some examples of RNA based viruses

polio

rabies

influenza

rhinovirus

Describe the life cycle of a retrovirus

• retroviruses contain RNA genomes that are changed into DNA genomes → then integrated into host cell DNA

  • integration into host cell DNA allows the host machinery to transcribe viral Genes → viral replication

• carry reverse transcriptase (RT)

  • transcribes RNA into DNA (this enzymes lowkey makes a lot of mistakes → why HIV mutates so fast)

NOTE: HIV has two identical strands of RNA inside the capsid (idk why, gotta ask)

Describe the function of integrase in retroviruses

• enzyme that enables the virus to insert its reverse-transcribed genetic material into the DNA of a host cell

Describe the function of protease in retroviruses

brought in with virus during infection cleaves polyprotein into separate function proteins (remember that viruses don’t have introns)

Describe the types of antibiotics that are used to treat HIV

• AZT - nucleotide base analog inserted into the DNA as reverse transcription takes place

  • RT will sometimes add AZT in chain instead of nucleotide → b/c AZT is a chain terminator → incomplete genome → viral life cycle stops

• Protease inhibitors - binds to and inhibits protease enzyme from cleaving polyprotein into functional proteins by competitively binding to protease active site

• (integrase inhibitors do the same thing but with integrase)

Describe what vaccines and are and what they consist of

• consists of an altered (attenuated) virus that’s been inactivated by removal of certain genes/proteins that make it unable to cause disease

• vaccine is recognized as a foreign substance → initiates immune response → production of antibodies + WBCs that target for antigens of the virus

  • some vaccines just consist of the antigens rather than a whole virus

Describe Interferons

• chemical naturally produced by viral-infected cells that’s secreted into the surrounding environment and helps prevent infection of nearby cells

What are the examples we have to know about DNA viruses that cause cancer

Hep B → can cause liver cancer after a prolonged infection of ~20 years

HPV → can cause cervical cancer

Describe the hypothesis for the origin of viruses

• evolved as fragments from cellular genomes that acquired specialized packaging

• may have evolved from plasmids or transposons

• evidence - many viral genes are very similar to hots cellular genes and in fact are more similar to host genes than to genes found in other types of viruses.

What are prions?

• infectious agent that contains no nucleic acid

• abnormally folded proteins that interacted with normal cellular proteins in the brain and change them into abnormal proteins

  • accumulation of the abnormally folded proteins causes disease

What are viroids?

• naked pieces of RNA, very short, 200-400 bases, circular (shorter than a typical virus which is ~ 2000 nucleotides)

• cause disease mainly in plants but there are no protein codes in the RNA

• circular RNA may be broken down by dicers into siRNA → silence mRNA in plant cell → reduction in yield

Describe the two domains that prokaryotes are divided into

Bacteria

• includes most prokaryotes

Archaea

• more primitive prokaryotes

• live in extremely challenging habitats

  • methanogens - produce methane by reducing CO₂ with H₂ (strictly anaerobic)

  • halophiles - require high salt concentration to live

  • thermophiles - live in extremely hot environments

Are eukaryotes more closely related to Archaea or Bacteria domain?

Archaea (more recent last common ancestor)

Fill in this chart comparing the three domains of life

What are the three main cell shapes for bacteria?

bacilli - rod-shaped

cocci - spherical

spirilli (spirochetes) - helical/spiral

Describe the components of bacterial cell structure

All have:

• cell wall

• plasma membrane

• cytosol

• ribosomes

• DNA

  • circular chromosome (no histones, basically no other protein)

  • plasmids

    • the small circular sections of DNA

    • replicate independent of main chromosome

    • often contain genes for antibiotic resistance

Some have:

• flagella

  • for motility

  • anchored to cell wall + plasma membrane

  • bacteria can have 0, 1, or more flagellum

• pili

  • extensions from cell that aid in attachment from host

  • some pili are important in exchange of genetic material (conjugation)

• capsule

  • polysaccharide, slimy film outside cell wall

  • can make bacteria more pathogenic - evade phagocytosis by white blood cells

  • also can aid attachment to host

What are episomes

plasmids that can integrate into the main chromosome

Conjugation

• transfer of DNA by cell-to-cell contact (plasmid/part of chromosome is transferred)

  • occurs across sex pilus coded for by genes on plasmid called F (fertility) factor

    • only F⁺ or Hfr cells have this plasmid

• F⁺ or Hfr donor "cell transfers DNA to an F^- recipient cell

  • btwn F⁺ and F^-

    • F⁺ cell’s pili attach to F^- cells → F factor transferred

    • F^- cells become F⁺ cells

• Hfr and F^-

  • Hfr cell is an F⁺ cell where the plasmid is integrated within the chromosome

  • F factor DNA has a break

  • part of the F factor AND the attached chromosome move through the conjugation pilus into F^- cell

  • pilus breaks down before last part of F-factor is transferred → F^- cell REMAINS F^-

  • parts of Hfr chromosome transferred into F^- cell can recombine with F^- chromosome

  • extra DNA ending up outside the chromosome during the recombination process are degraded by enzymes

Transformation

DNA is taken up PASSIVELY from surroundings (think Griffith experiment)

Transduction

• pieces of DNA are transferred from one bacterium to another by a viral vector

• General Transduction

  • lytic cycle →host DNA is fragmented → random pieces are packaged in the viral capsid during viral replication

  • virus infects another cell → carries pieces of DNA from the last host

  • first host cell DNA can integrate itself into second host cell DNA

Gram Positive vs Gram Negative Bacteria

• gram positive

  • less pathogenic

  • thick, peptidoglycan layer and RETAINS stain → appear purple

• gram negative

  • more pathogenic

  • thinner peptidoglycan layer → doesn’t retain stain → appears pink

  • has outer membrane made of lipopolysaccharides (LPS/endotoxin) → causes disease