Unit 3 MIC102

WQ2025 Sam Diaz Munoz

What does a virus consist of?

• membrane

• nucleic acid

• protein shell

• Spike protein

Can viruses infect every type of cell? (bacteria/eukaryotes)

Yes, although viruses have some specificity, they can still infect different organisms or cells

Are there more viruses than hosts?

Yes, 10³¹ total viruses and are the largest reservoir for genetic diversity on earth (more viruses than stars)

What is a virus and what do they lack (2)?

Obligate intracellular parasites that don’t encode all necessary components for their reproduction (must replicate genome in cell of host organism)

• Lack complete translation machinery

• Lack complete energy generation machinery

Not all viruses cause disease and can be beneficial to the host. Name 5 examples and how they’re beneficial.

• Vibrio cholera: requires infection by bacteriophage, which carry toxins for gut invasion

• Mouse herpes virus infection: can protect against bubonic plaque

• Cucumber Mosaic Virus (CMV): improves drought tolerance in plants

• White clover mosaic virus: repels fungus gnats

• Protists: serve as a source of nutrition

Healthy adults have more than __ types of virus infecting

5

What are the viral origins of how you were born?

• Placentation arose from horizontal gene transfer from retroviruses

• Syncytiotrophoblasts involved in placental formation use a viral protein syncytin

  • (note: syncytiotrophoblasts are proteins from viral organs that promotes cells to get together and get multinucleated cells that helps in forming placenta)

What are the 5 main steps to the viral life cycle?

1. translation and replication

2. packaging and assembly

3. exit

4. free virus

5. attachment

What are the two primary activities viruses need to accomplish within the cell?

Transcription of their viral proteins, and replication of their viral genome

• These activities are completed with a mix of viral and host proteins and enzymes

  • Sometimes viruses encode their own enzymes and could in theory use the host’s

Why is it difficult to classify viruses based on genes?

There is no universal gene shared among viruses such as ribosomal RNA

Why is hard to find conserved regions in viral genomes?

Viral genomes evolve rapidly, making it difficult to find conserved regions and nucleotide not under selection

How are most viruses classified?

Most virologists classify viruses according to their nucleic acids using the Baltimore Classification

T4 phage

Tip proteins degrade peptidoglycan and allow ejection of DNA into host

dsDNA virus replication

• Circularizes inside the cell

• Rolling-circle replication style is possible/likely

• genome copies packed into capsid

ssDNA (+) virus replication

• (+) ssDNA acts as template to make (-) strand

• dsDNA molecule available for transcription

• dsDNA (-) strand available to synthesize more (+) strand for genome

ssRNA (+) replication

• Sense strand ready for translation

• Viral RNA encodes and RNA replicase (creates (-) template then use that to replicate (+) strand)

ssRNA (-) virus replication

• Contains a prepackaged RNA replicase; (-) RNA not immediately useable for translation

• RNA molecule is often attached to the capsid to keep it accessible to the replicase

dsRNA replication

• viral replicase is included in virion

• generates (+) strand RNA for translation

• Replicates both strands for genome replication

Retrovirus replication

• (+) ssRNA

• Prepackaged viral reverse transcriptase generates a (-) ssDNA

• (-) ssDNA is template for (+) strand DNA

• dsDNA is integrates into host genome using an integrate encoded by virus

• Host RNA polymerase transcribes new viral genomes off this integrates dsDNA

What is the eclipse period in viral protein synthesis?

The period after genome insertion and before vision completion when no viral particles are detectable

What must happen if a virus in not (+) RNA?

mRNA must be transcribed

What is the role of early proteins in adenovirus replication?

Early proteins direct the cell to replicate viral DNA and make later proteins

When are completed intracellular virus particles formed in adenovirus?

When DNA and late proteins are assembled

Packaging and Exit from the Cell Process

• capsids are formed through capsomer self-assembly

• nucleic acids packaged into completed capsids

• capsids complete, non-enveloped virus ready for exit

• Enveloped circuses bud off from host cell

Why are viral processes good targets for antiviral drugs?

Many viral processes are unique to viruses, making them effective targets for drugs

What is the best practice to avoid antiviral drug resistance?

Use multiple different types of drugs when possible

What. is viral latency?

A state where the virus is inside the host cell but does not proliferate or damage the cell

What are the two main ways viruses can maintain latency?

• Episome: Viral DNA maintained as an extrachromosomal element (varicella zoster)

• Prophage/Provirus: viral genome integrated into the host chromosome

What must viruses do to maintain latency?

• Avoid host cell destruction

• Avoid activating viral replication

What can cause a virus to reactivate from latency?

Stress, immunological suppression, or physiological changes in the host

What can latency do to the host?

• Protection from other infections

• Chronic diseases

• Cancer (cell transformation, regulatory sequences)

• Endogenous retrovirus

What type of genome does λ phage have ?

double-stranded DNA (dsDNA)

How does λ phage DNA circularize upon entry into the host cell?

Using sticky ends, DNA ligase joins them

• Circularization protects viral DNA from host exonuclease

Where does λ phage integrate into the host chromosome?

at the attB site

Selective Toxicity

Antibiotics are primarily toxic to bacteria but not eukaryotes

Spectrum of Activity

How many types of bacteria an antibiotic is effective on

Bacteriostatic

inhibit

bacteriocidal

kill

How do we measure susceptibility?

• Through minimal inhibitory concentration: the lowest concentration of a drug that will prevent the growth of an organism

• Kirby Bauer Assay makes testing many antibiotics at once easy

How does bacteria develop resistance in penicillin?

Through beta lactamase enzymes

How do antibiotics work?

Attack bacterial target necessary for cell function

• cell wall

• cell membrane

• DNA synthesis

• RNA synthesis

• Protein Synthesis

• Metabolism

What are the 4 main categories of antibiotic resistance mechanisms?

• Alter target (ex. mutations in PBPs stop methicillin from binding)

• Degrade antibiotic (ex. beta-lactamase cuts open penicillins)

• Modify Antibiotic (ex. adding methyl, acetylene, hydroxyl groups to kanamycin)

• Remove antibiotic from cell (ex. multi drug transport NorA in S. aureus)

Why are multidrug exporters a growing problem?

One multi drug resistance (MDR) efflux pump can provide resistance to many different types of antibiotics

How are multi drug exporters similar to ABC transporters?

They function similarly but are usually powered by the proton motive force (PMF) instead of ATP

Why can bacteria develop drug resistance quickly?

Bacteria are efficient at evolving new functions and can transfer resistance genes between cells

What is the typical rate of spontaneous resistance to a given antibiotic?

Approx 1 cell in 10⁷

What mechanisms allow bacteria to transfer resistance genes?

• Conjugation

• Insertion elements

• Transduction

How can using multiply-linked antibiotics help delay resistance?

Developing resistance to two drugs at once is much harder than to one, though still possible with MDRs

Airborne (bacterial diseases: modes of transmission)

inhalation of infectious particles leading to infection of respiratory tract

Diphtheria and it’s symptoms (airborne)

• Diphtheria toxin is absorbed by circulatory system and inhibits protein synthesis in cardiac, kidney, and nervous tissues

  • Symptoms include nasal discharge, pseudomembrane forms, fever, cough, paralysis

• Vaccines consist of inactivated toxin and is effective

What are some examples of mycobacterium (airborne)

• Bacteria with use mycotic acids in cell walls: acid-fast

• M. avian complex (most common pathogen group in U.S.)

• M. tuberculosis (M.bovis and M. africanum) causes tuberculosis

  • Infects macrophages

What are some treatments of tuberculosis?

• combination of antibiotic therapy

• Multidrug resistant Mtb have been found

• Skin tests for reaction from sensitized T cells by injecting a purified protein derivative

Arthropod-borne (bacterial diseases: modes of transmission)

Insects are common vectors; not common for bacteria as viruses and protists

What is Lyme disease? (arthropod-borne)

• tick-borne transmission of spirochete Borrelia

• Rodents and other wild animals natural hosts

• Initial symptom of target -shaped skin lesion and flu-like symptoms with second stage including neurological effects, heart inflammation, arthritis

Plague (arthropod-borne)

• caused by Yersinia pestis that spreads by fleas from animal to animal, direct contact, and airborne person to person

• Multiplies in vlood and lymph rapidly once in body

• Symptoms include hemorrhage, fever, headache, exhaustion, extreme lymph node swelling

Direct Contact (Bacterial diseases: modes of transmission)

transfer of bacteria to/from skin, underlying tissue, mucous membranes

• STIs are common forms of disease spread

Chlamydia (direct contact)

• Asymptomatic carriers

  • Symptoms include burning feeling, discharge and can spread and create pelvic inflammatory disease

Gonorrhea (direct contact)

• Infects mucous membranes of genitourinary tract, eye, etc

• Use pili and surface protein to adhere to microvilli of mucosal cells

  • Symptoms include painful urination, yellow pus, frequent urination

Staphlyoccus infections (direct contact)

• normal inhabitants of skin, upper respiratory tract, intestine; pus-forming (pyogenic)

• Staph tends to cause disease due to its rapid growth and toxin production

Food/water contamination (bacterial disease: modes of transmission)

• commonly cause E. coli gastroenteritis

  • Symptoms include: diarrhea, inflammation (gastroenteritis), fever

• E. coli is common and most strains are harmless/commensal

Opportunistic infection

• microbes can come from our microbiome or from environment

• Typically only cause disease in immune-compromised hosts

Antibiotic-associated colitis (opportunistic infections)

Clostridium difficile: normal gut microbe

• antibiotic treatment can upset gut microbiome balance, allowing C. dif to flourish, leading to diarrhea, colitis, due to constant inflammation and cell death

Influenza Virus

• Multiple (-) RNA strands

• Enveloped

• Relatively sensitive to heat, drying, acid

What are the two important envelope proteins in influenza virus?

• Hemagglutinin (H): causes RBCs to stick together, used to bind target cells

• Neuraminidase (N): cleaves sugars that bind viral particles, in order to facilate exit

Antigenic Drift (viral evolution)

• minor changes in H and N proteins

• Tend to cause minor epidemics every 2 years

• mutations in H and N make flu virus slightly harder

Antigenic Shift (viral evolution)

• Major changes to H and N proteins

• Tend to cause pandemics every decade

• Caused by reassortment of H and N proteins

HIV/AIDS: how does it spread

• Human Immunodeficiency Virus (+RNA retrovirus)

• Spread through direct contact with blood, breastmilk, or sexual fluids

• Untreated HIV leads to Acquired Immunodeficiency Syndrome (AIDS)

What does HIV consist of?

• Enveloped virus

• 2 copies of RNA genome

• Viral spike proteins help attach to susceptible host T-helper cells

• gp120 protein allow binding to CD4 receptor

How does HIV enter and work inside the body?

• HIV enters through endocytosis

• Uncoating and reverse transcription of genome into DNA

• Integrase inserts genome into host chromosome

• Integrated virus can replicate slowly over time