Bacteriophage Biology Quiz

Bacterial Definitions

• Bacteriostatic agent: Stops the multiplication of bacteria. Multiplication resumes after removing the agent.
• Bactericidal agent: Kills the bacterial cell. The process is irreversible; bacterial multiplication won't occur even after removing the agent.

Actions and Definitions

• Sterilization: The process of eliminating all microbial flora.
• Disinfectant: A substance used to inactivate microorganisms in specific areas (e.g., tables, floors), but is too toxic for use on human tissue.
• Disinfection: The inactivation of microorganisms from surfaces (inanimate objects).
• Antisepsis: Applying bactericidal or bacteriostatic substances to kill or inhibit the growth of pathogenic flora in wounds.
• Asepsis: All measures that prevent contamination from infectious agents.
• Conservation: Preventing spoilage of degradable products (e.g., food, drugs) by microbial agents.

Physical Agents

• Heat:
  • Dry heat sterilization: flaming, dry heat oven.
  • Moist heat sterilization: boiling, pasteurization, tyndallisation, autoclaving.
  • Dryness (desiccation)
  • Lyophilisation: gradual drying in vacuum at low temperatures (-40°C to 70°C).
• Mechanical pressure
• Osmotic pressure
• Radiations
• Ultrasounds
• Electricity
• Filtering: Passing thermo-sensitive fluids through sterilizing filters to capture microorganisms.

Chemical Agents

• Phenol and derivatives: Bactericidal action by lysing bacterial cells.
• Alcohols: Weaker than phenol; act bactericidally only on vegetative forms.
• Halogens and halogenated compounds: Often used as antiseptics and disinfectants (e.g., chlorine, iodine); have powerful bactericidal and sporicidal action.
• Acids and bases: Bactericidal action by distorting bacterial proteins.
• Salts: Heavy metals have the strongest bactericidal effect.
• Formaldehyde and Glutaraldehyde
• Gaseous disinfectants: Ethylene oxide is the best for dry surfaces.
• Soaps and detergents (surfactants)
• Metabolic antagonists
• Dyes
• Others: Hydrogen peroxide, potassium permanganate.

Biological Agents: Bacteriophages

• Bacteriophages: Viruses that can lyse bacterial cells (lytic bacteriophages) or not (symbiotic bacteriophages).
• Morphology and chemical composition:

  • DNA phages

  • RNA phages

  • The head contains nucleic acid core and a protein shell (capsid). The nucleic acid core is mainly DNA and makes up about 50% of the dry weight. The protein shell gives the head a polygonal shape with identical protein subunits forming a hexagonal prism.

  • The tail is used for attachment to the bacterial cell surface. It has three sections: lacunar middle, contractile sheath and basal terminal plate. The plate has attached tail fibers.

• The tail can exist in two functional phases: relaxed and contracted stages.
• In addition to the normal form, there may be bacteriophages without tails and also filamentous bacteriophages.
• RNA phages have a specific morphology with a molecular weight of 4x10^6 Daltons, self-complementary complex tertiary structure and capsids composed of 180 subunits (capsomeres). They are involved in chromosome conjugation and lysogenization of intestinal bacteria.

Types of Interrelations Between Bacteriophages and Bacteria

• The bacteriophage is a bacterial virus, with bacteria as its host.

• Attachment to the bacterial surface occurs through receptors.

• Lyso-sensitive bacteria allow the attachment and entry of bacteriophages.

• Lyso-resistant bacteria do not allow this attachment and entry.

• Lytic relation: Phages penetrate the cell, causing cell death and releasing new bacteriophage particles.

• Steps of the lytic cycle:

  • Adsorption
  • Penetration
  • Intracellular replication (DNA phage replication, then RNA phage replication)
  • Maturation of phage particles
  • Release of phage particles

• Adsorption: The attachment of the phage to receptors on the surface of a lyso-sensitive bacterial cell.

• Penetration: The phage injecting its nucleic acid into the bacterium.

• Intracellular replication: Viral DNA replicates, using host cell machinery, and new phage components are synthesized.

• Maturation: Assembled phage particles and components are produced.

• Release: Newly formed phages are released, usually by cell lysis.

• Symbiotic relation: Entry of the bacteriophage into the bacterial cell without causing lysis, with genetic material integration into the bacterial chromosome (called lysogeny). -Prophages: bacteriophages able to establish a symbiotic relationship with specific host bacteria. The stages of the symbiotic phage infection are adsorption, penetration of phage nucleic acid, circularization of DNA phage and coupling circular DNA phage with bacterial DNA. -Lysogenic bacteria are resistant ('immune') to infection by the same bacteriophage due to the release of a 'repressor' substance inhibiting the multiplication of the lytic phage inside the cell. -Inducing agents lead to the inactivation of the repressor, therefore, causing a change of certain cell properties (called 'conversion').

Bacterial Genetics

• Bacterial genetics: Studies heredity and variability in bacteria.
• Heredity: The property of living organisms to pass on specific characteristics to their offspring.
• Variability: Hereditary changes in bacteria.
• Genetic material organization in bacteria: The bacterial genome consists of replicons, which are functional genetic units that can replicate independently. This includes the bacterial chromosome and extrachromosomal genetic elements (such as plasmids and transposable elements).

Bacterial Heredity

• Bacterial characteristics are genetically determined; their expression is reflected in the phenotype.
• The bacterial genome consists of replicons (genetic configurations that replicate independently).
  • Bacterial chromosome
  • Extrachromosomal genetic elements
  • Genetic transposable elements

Bacterial Nuclear Area

• The bacterial nuclear area (nucleoid) is the irregularly shaped region that contains the genetic material (DNA) within the cytoplasm.

DNA Structure

• DNA is composed of two complementary strands with reverse polarity, following the Watson and Crick model.
• These strands are formed by nucleotides composed of: deoxyribose, phosphoric acid, and nitrogenous bases (adenine, guanine, cytosine, thymine).

DNA Replication

• The double helix structure of DNA in bacteria allows for semi-conservative replication at specific sites.
• The DNA opens up like a zipper using DNA gyrase.
• Each existing strand acts as a template for the synthesis of a complementary strand by DNA polymerase.

Extrachromosomal Elements

• Plasmids: Extra-chromosomal genetic formations (circular DNA molecules) that can replicate independently of the bacterial chromosome. Plasmids can be conjugative, meaning they can transfer independently to other bacterial cells; or non-conjugative (they need the help of another conjugative plasmid or bacteriophage). Episomes are a type of extrachromosomal element that can either replicate autonomously or integrate into the chromosome.

  • Genetic determinants: Essential genes for replication, but also accessory genes for bacterial survival or virulence factors (e.g., antibiotic resistance, toxins). Some plasmids have no observable effect (cryptic plasmids).
  • Resistance plasmids: Circular DNA molecules with genes that confer resistance to one or more types of antibiotics.
  • Virulence plasmids: Carry genetic determinants enabling bacteria to produce virulence factors (e.g., toxins, colonization factors).
  • F plasmid (plasmid for sex): Carries genes for DNA transfer during bacterial conjugation and it can integrate into the bacterial chromosome mediate chromosomal gene transfer.
  • Col Plasmids: Contains genes for antibacterial polypeptides (bacteriocins) which can kill other bacterial strains.

• Genetic Transposable Elements: (IS - Insertion sequences; Tn - Transposons.) Fragments of genetic material that can move from one location to another within the genome.

• This movement can alter bacterial genes and characteristics, potentially contributing to bacterial variability.

Bacterial Variability

• Phenotype variation: Changing bacterial properties by adapting to environmental conditions without altering the genome.
• Genotype variation: Changes resulting from genome modifications (mutations, genetic material transfer).
• Variation in bacteria is attained through:
  • Mutations (spontaneous/induced)
  • Transfer of genetic material (transformation, transduction, conjugation, transposition)

Bacterial Mutations

• Mutations: Spontaneous or induced changes in the bacterial genome, altering the nucleotide sequence of a gene. - Point mutations: affect one nucleoid, potentially reversible. - Extended mutations: affect multiple genes

• Causes of mutations:

  • Copying mistakes during self-replication due to speed
  • Exposure to mutagens (e.g., X-rays, UV radiation, biological agents) which modify the base sequences.

• Consequence of mutations: Individuals with new characteristic traits, such as antibiotic resistance, or pathogenicity.

Transfer of Genetic Material

• Transformation: Transfer of pure DNA from a donor to a recipient cell.
• Competence: The state where the recipient bacterium allows foreign DNA incorporation.
• Competence-positive cells display specific surface antigens ('power factor') to facilitate and allow a more porous and electropositive cell wall. The cell's ability to take up foreign DNA.
• Transduction: Transfer of genetic material by bacteriophages. This can either be generalized transduction (any gene can be transferred) or specialized transduction (only certain genes are transferred).
• Conjugation: Transfer of genetic material through cell-to-cell contact.
• Transposition: Integration of a transposable genetic element into a different place in the genome. Transposable elements, based on their structure and mechanism of translocation, fall into three classes: I, II, and III.

Antibacterial Chemotherapy

• Definition: Chemotherapeutics are any substance that inhibits (or kills) microorganisms (bacteria) in small doses. (Can be lethal - bactericidal, or prevent multiplication – bacteriostatic).
• Mechanisms of action:
  • Metabolic competitive antagonism
  • Inhibition of bacterial cell wall synthesis
  • Alteration of cytoplasmic membrane function
  • Inhibition of bacterial protein synthesis
  • Inhibition of bacterial nucleic acid synthesis

Cell Wall Synthesis Inhibitors

• Betalactams (penicillins and cephalosporins): Inhibit cell wall synthesis by binding to enzymes involved in the final stage of cross-linking of peptidoglycan chains (PBPs). This leads to secondary accumulation of murein subunits, thus activating the autolytic enzyme system. Resulting in bacterial cell lysis.
• Glycopeptides (vancomycin, teicoplanin): Interfere with peptidoglycan elongation.
• Bacitracin: Used locally for skin infections; high toxicity.
• Isoniazid, cycloserine, ethionamide: Used in treatment of tuberculosis.

Surface and Cytoplasmic Membrane Inhibitors

• Surfactants (polymyxins): Destruct bacterial cytoplasmic membrane phospholipid structures.
• Amphotericin B, Colistin, Imidazole, Gramicidin Also destruct bacterial membrane by a similar mechanism.

Protein Synthesis Inhibitors

• Aminoglycosides: Block formyl-methionyl-t-RNA binding to ribosomes (preventing polypeptide chain initiation) and affect the decoding information on m-RNA.
• Tetracyclines (tetracycline, doxycycline): Block aminoacyl-t-RNA attachment to ribosomes, thus inhibiting protein synthesis.
• Chloramphenicol: Inhibit peptide bond formation between amino acids.
• Macrolides (clarithromycin, azithromycin): Inhibit ribosome translocation of peptide chains.
• Lincosamides (clindamycin): Bind to ribosomes, preventing peptide bond formation.
• Fusidic acid: Blocks protein synthesis by binding elongation factor to the polypeptide chain on the ribosome.

Nucleic Acid Inhibitors

• Rifampicins: Bind to DNA-dependent RNA polymerase, blocking RNA synthesis.
• Quinolones (nalidixic acid, ciprofloxacin, norfloxacin, ofloxacin etc): Block DNA gyrase, responsible for DNA supercoiling.
• Sulphonamides: Inhibit folic acid synthesis, which is important for DNA and RNA synthesis. Co-trimoxazole is an example.
• Sulfones (e.g., dapsone): Are related to sulphonamides and used to treat certain bacterial infections (e.g. leprosy).

Resistance Mechanisms and Types

• Natural resistance: Inherent characteristic of certain bacterial species.
• Acquired resistance: Resistance developing in susceptible species. This is influenced by different mechanisms such as:
  • Production of enzymes that inactivate the antibiotic (e.g., penicillinase).
  • Decreased permeability of the bacterial cell wall or cytoplasmic membrane to the antibiotic.
  • Development of excess complementary enzymes.
  • Alteration of intracellular target (e.g., modification of ribosomal protein).
  • Increase in synthesis of substances which interfere with the antibiotic action (e.g., para-amino benzoic acid synthesis in the case of sulfonamides).
• Resistance types:
  • Monovalent: Resistance to one antibiotic.
  • Multivalent: Resistance to multiple antibiotics.
• Rhythm of resistance appearance (determined by antibiotic): The rate of resistance development for different classes of antibiotics can differ in terms of swiftness (fast - streptomycin type; intermediate - erythromycin type; slow - penicillin type).

Bacterial Taxonomy and Morphology

• Bacterial taxonomy: The science of classifying and naming bacteria.
• Bacterial cell structure: Characteristics, shape and dimensions, structural components of the cell wall and the spore form.
  • Classification of cocci (spherical, oval, etc).
  • Different settlement patterns of cocci.
  • Bacteria classification in based on bacilli forms.
    • Different settlement patterns of bacilli.
      • Isolated
      • In chains
      • In palisades. .
    • Bacterial morphological forms: coccobacillus, vibrios, spiral bacteria (e.g. spiral, spirochetes, spirochaetes)
• Bacterial cell division: The reproduction process of bacteria involving septation and separation and division of nuclear material.

Microorganism Basic Classification

• Basic classification between prokaryotes and eukaryotes: Differences in cell structure, presence of organelles (such as mitochondria), cell size, nucleus.
• Prokaryotes are smaller than eukaryotes and don't have organelles or a nucleus.

Bacterial Cell Structure

• General characteristics of prokaryotic cells:
• Dimensions, generally small (1-10 μm).
• Organization is typically unicellular, forming populations.
• Major component
  • Nucleoid/Nucleus: Region containing the genetic material (DNA), no nucleus or nucleolus.
  • Cytoplasmic membrane: A thin elastic membrane that regulates passage of substances between the cell and its environment.
  • Cell wall: Provides shape, structural support and protection, and is the target of some antibiotics
  • Cytoplasm: Unpartitioned region containing enzymes, ribosomes, and various inclusions.
• Additional peripheral elements:
  • Annex Elements: Cilia, fimbriae, capsules.
  • Spores: Dormant resistant stage of some bacteria.