Viruses and Infections

Viruses & Infections

• Cell tropism: virus specificity for certain cell types, determined by virus surface proteins and host cell receptors.
• Virus must have compatible receptors for attachment and intracellular machinery for replication.
• HIV targets CD4+ T cells due to CD4 receptor presence.
• Direct effects of viral infections include cell lysis, cell fusion, and altered cell function.
• Indirect effects: immune response results in inflammation and tissue damage.
• Viruses can also cause cellular transformation, leading to cancer.
• The immune system resolves viral diseases.
• Innate immune system is the first line of defense; adaptive immune system uses T cells and antibodies.
• Cultivation of viruses requires inoculation of a living host because viruses need living cells to replicate.
• Enumeration methods: plaque assay (counting lysis zones), endpoint dilution assays, direct particle counting.
• Proper sterile techniques and controlled environments are needed to grow viruses accurately.
• Viroids consist of only RNA.
• Satellites consist of only nucleic acids.
• Viroids are small, circular RNA molecules infecting plants; they lack protein-coding genes and rely on host enzymes.
• Satellites are subviral agents needing a helper virus for replication and encode their own proteins.
• Prions are misfolded proteins causing neurodegenerative diseases by inducing normal proteins to misfold.
• Prions lack nucleic acids and spread via direct contact with infected tissue.
• Prions build up in the brain, causing nerve cell death and sponge-like holes, leading to memory loss, movement problems, death, Mad cow disease, and Creutzfeldt-Jakob Disease (CJD).

Microbial Growth

• Bacterial cell cycle entails binary fission: a single cell replicates its chromosome and divides into two identical daughter cells, involving growth, DNA replication, and cytokinesis.
• Eukaryotic cell cycle: cyclin includes interphase (G1, S, G2) and mitosis.
• FtsZ: protein forms a Z ring at the division site, guiding septum formation during cytokinesis, essential for division.
• Septation leads to formation of cross wall between 2 daughter cells
• Steps include: selecting a site for septum formation, Z ring assembly, cell wall synthesizing machinery assembly, constriction, and septum formation.
• ProteinFtsZ: tubulin homologous, is found in most bacteria and archaea.
• The MinCDE system in E. coli ensures Z-ring forms only in the middle
• MreB: an actin-like protein that helps maintain rod shape by directing cell wall synthesis and chromosome movement.
• ParA and ParB proteins involved in chromosome partitioning, segregate replicated chromosomes.
• ParA polymerizes to form filaments that pull DNA to a cell pole.
• ParB binds DNA at paS site near origin of replication, stabilizing the DNA.
• Penicillin-Binding Proteins (PBPs): enzymes that link peptidoglycan strands and help with cell wall remodeling.
• Autolysins: special PBPs that break down portions of the wall for new peptidoglycan insertion.
• Bactoprenol: lipid carrier transporting peptidoglycan precursors across the cytoplasmic membrane, delivering building blocks to growing wall and is essential for growth and maintaining cell shape.
• Cardinal conditions: minimum, optimum, and maximum physical conditions (temp, pH, osmolarity) for microbial growth
• Aerobes grow in the presence of atmospheric oxygen (O2), which is 20% O2, obligate aerobes require O2 to grow
• Anaerobes grow in the absence of O2, Facultative anaerobes grow with or without O2, but prefer O2
• Obligate anaerobes cannot grow in the presence of oxygen and aerobes grow without O2
• Microaerophiles require low oxygen levels (2-10% O2)
• Defined/synthetic media have ingredients defined with a chemical formula
• Complex media contains some ingredients of unknown chemical compositions (yeast)
• Selective media supports specific microbe growth by inhibiting others
• MacConkey agar selects for gram-negative bacteria
• Differential media distinguishes species by visible changes
• Blood agar distinguishes between hemolytic vs nonhemolytic bacteria
• MacConkey agar distinguishes between lactose fermenters vs nonfermenters
• Chemical composition can be defined (synthetic) complex, physical nature liquid, semisolid, solid, and supporting, enriched, selective, differential bacterial growth.
• Lag phase: cells adjust to environment, synthesizing new components, no division, and varies in length.
• Log (exponential) phase: rapid cell division and growth.
• Population is most uniform in chemical and physical properties
• Stationary phase: growth rate = death rate due to nutrient depletion.
• Reasons for stationary phase: nutrient limitation, limited oxygen, toxic waste accumulation, critical population density.
• Death phase: cells die as resources are exhausted, and viable cells decrease exponentially.
• Long term stationary phase: genetically adapted survivors persist, leading to natural selection and evolution.
• Oxygen reduced too reactive oxygen species (ROS): superoxide radical, hydrogen peroxide, hydroxyl radical.
• Aerobes produce protective enzymes: SOD, catalase, peroxidase.
• Superoxide dismutase (SOD): converts superoxide radicals to oxygen and hydroxide peroxide.
• Catalase: breaks hydrogen peroxide into water and oxygen.
• Peroxidase: converts hydrogen peroxide into water without releasing oxygen.
• Psychrophiles: thrive in cold (0-20°C) with unsaturated fatty acids in membranes for flexibility.
• Mesophiles: prefer moderate temp (20-45°C) including most human pathogens.
• Thermophiles: adapt to hot environments (45-85°C) using heat-stable proteins and saturated fatty acids.
• Hyperthermophiles: live in extreme heat (85-113°C) with specialized DNA protecting proteins and stable membranes.
• Halophiles: grow optimally in presence of salts.
• Biofilms are structured communities of bacteria embedded in a self-produced matrix (EPS – extracellular polymeric substance).
• Biofilms are ubiquitous in nature in water.
• Biofilms form through initial attachment to surface, maturation as cells produce EPS, and dispersion when some bacteria colonize new areas.
• Biofilms offer protection from antibiotics, environmental stress, and the immune system.
• Biofilms develop through attachment, growth, dispersal, and are common on medical devices and natural surfaces.
• Growth refers to population growth rather than individual cell growth
• pH: acidophiles, neutrophiles, and alkaliphiles.
  • Most bacteria & protist are neutrophiles
  • Most fungi are acidic and archaea are acidophiles
• Microbes cannot regulate internal temperature, optimum enzyme temperature, and high temperatures inhibit enzyme functioning and be lethal.
• Microbes on land and in water exist at 1 atm pressure, Barotolerant.
• The Barophilic require or grow more rapidly in high pressure and fatty acids change membrane to adapt high pressure.
• Radiation: mutations result in death, DNA damage repairable, mutations via cell mechanisms.
• Visible light: at high intensities, visible light generates singlet oxygen, a powerful oxidizing agent.

Control of Microbial Growth and Antimicrobial Chemotherapy

• Therapeutic dose: The minimum concentration of a drug needed to effectively treat an infection

• Balance between drug efficiency and safety (drug level requires for clinical treatment)

• Therapeutic index: toxic dose/therapeutic dose

• Toxic dose: drug level that becomes too toxic for the patient.

• The Kirby-Bauer test assesses bacteria sensitivity to antimicrobial agents.

• Antibiotic-impregnated paper disks are placed on agar plate with bacteria in question.

• As antibiotics diffuse through agar, they create a zone of inhibition where bacterial growth is prevented. Zone sizes determine susceptibility, intermediate resistance, or resistance to antibiotics.

• The Kirby-Bauer test measures bacterial susceptibility to antibiotics.

• Antibiotic impregnates discs being placed on the agar plate with bacteria.

• Clear zone size indicates drug effectiveness

• Standardized method for disk diffusion test; sensitivity/resistance is determined using tablets relating zone diameter with microbial resistance

• Table values are plotted to determine if an effective drug concentration in body can be reached.

• Intrinsic resistance: natural resistance due to structural features (e.g., gram-negative bacteria outer membrane).

• Mycoplasma resistance to B-lactam antibiotics and other cell wall inhibitors due to a lack of a cell wall

• Acquired resistance: resistance gained through mutations or horizontal gene transfer, changing a sensitive bacterium to a resistant one.

• Adaptive resistance: temporary resistance due to environmental stress that disappears when conditions change.

• Bacteria lack the mechanisms for antibiotic resistance and ignore the presence of antibiotics usually because they are embedded in biofilms that antibiotics cannot effectively penetrate or are growing too slowly to be inhibited.

• Drug-tolerant persistors lack antibiotic resistance and ignore antibiotic presence as they are in biofilms antibiotics can't penetrate or grow too slowly.

• Mechanisms of drug resistance: modify the target Abx, drug inactivation, minimize concentration of antibiotics cell, bypass reaction that is inhibited by agent,

• Overcome drug resistant: give drug concentration to destroy microbes or give 2 or more drugs concurrently and use drug only when it is necessary.

• Sterilant: kills all organisms including spores (autoclaving, ethylene oxide, hydrogen peroxide vapor)

• Disinfectants: kills most pathogens on inanimate surfaces. (bleach, phenol)

  • Phenolics: used in labs and hospitals, denature proteins, disrupt membranes
  • Alcohols: Inactivate some viruses, denature proteins, dissolve lipids
  • Halogens-lodine/chlorine act as disinfectant and sanitizer:
    • Iodine: skin antiseptic. Oxidizes cell constituents and iodinates proteins with endospores.
    • Chlorine: disinfectant, destroys vegetative bacteria and fungi, sporicidal

• Sanitizers reduce safe microbial levels in tissues such as alcohol.

• Antiseptics kill or inhibit microbes on living tissue (iodine)

• Bacteriostatic: inhibits bacterial growth without killing (tetracycline)

• Bactericidal: kills bacteria without lysing them (penicillin)

• Bacteriolytic: kills bacteria by lysing (bursting their cells lysozyme)

• Physical ways to control microorganisms: heat, radiation, filtration

• Mechanical: handwashing, air filters

• Biological: using bacteriophages to target Bacteria

• Antimicrobial drugs can be grouped based on their general targets such as cell wall synthesis inhibitors like penicillin that are 6-aminopenciillianic acid derivatives

  • B-lactam ring feature = essential Bioactivity
    • Penicillin inhibits enzymes for peptidoglycan crosslink blocking preventing cell wall synt. Only works on growing bacteria

• Naturally occurring penicillin's: penicillins V and G are narrow spectrum

• Semisynthetic penicillin's: broader spectrum with Bulkier side chains making them more difficult for B-lactamase enzymes to degrade

• Aminopenicillins broader coverage includes gram-neg bacteria : Cephalosporins are similar to penicillin and four categories depending on spectrum of activity are determined dependent on activity dependent on allergy

• Vancomycin inhibits cell wall synthesis and targets gram-+ bacteria.

• Protein synthesis inhibitors affect bacteria ribosomes that translate mRNA into proteins.

• Tetracyclines have a four ring structure which bind to ribosome structure and is static

• Macrolides contain erythromycin that attaches to ribosome subunit and inhibits protein elongation

• Lincosamines are produced by streptomyces and is used for anaerobic microbes.

• Chloramphenicol binds to 40S ribosomal subunit and inhibits transferase so its effevtive agains anaerobes and intracellular pathogens

• Oxazolidinones bind to 50S subunit targets rRNA and prevent formation of complex so its effective agains MRSA

• Nucleic acid synt inhibitor uses ciproflaxin that is usually toxic but targets polymearse that eukary doesnt have. Fluroquinolones synthethic target gyrase

• Metabolic inhibitors for sulfonamide is anabalog structural inhibit key enzymes for metabolism.

• Sulfa are related to inhibit acid syntehsis by inhibiting competetively a pathogen target that stops toxic sythsis

• Trimetoprim is a competitor that interferes for sythesis.

• Penicillin/cepahorin inhibits synthesis syntehsis

• Rifampin is a block in rna transcript

• Tertacycline is inhibits protein synths

• Sulfanimide blocks syntehis.

• What makes a drug toxic? -Lack of specificity, accuulation, allergy and cell disrution

• What is an action of tamiflu?

• inhibts infleunze enzyme and limited spread the virus

• Reverse for transcription intergration etc

• Acycolvir herpe virus

• zanamiaza block influnza enzyme

• Cidofovir- dna syntehse

• HAART drugs target reverse transcriptases, the protease, etc

• enaztativcally stop by modify

• altaraion sites to change antibacaterial sites

• metabolism law thermodyanmic energe from outside

• oragned enzyme pathway regualte catalyuzed

• 3 mechanisms impoatanct catabolize makes atpp.

• anabolize proteins dna

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coa auto hert autoto

• redox? gives of e to aceeptr.

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more negatrive greater more bette

• bonds chemjcal phosphate pep

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• conrast fermentr e acceptor r yield

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