Microorganism Classification and Replication

• Microorganisms are classified by their structure, chemical composition, biosynthetic pathways, and genetic makeup.
• There are five major groups of microorganisms that can cause infections in humans including bacteria, protozoa, fungi, helminths, and viruses.

Important Features

• Cells have a nucleus or nucleoid containing DNA surrounded by cytoplasm.
• Viruses lack cytoplasm and contain either RNA or DNA as their genetic material.
• Viruses rely on the host cell's machinery for protein synthesis and energy generation and can't produce their own proteins.
• Cells replicate either by binary fission (prokaryotic cells) or mitosis (eukaryotic cells).
• Viruses replicate by producing multiple copies of their nucleic acid and protein, then reassembling into multiple progeny viruses.
• Binary fission is the division of one parent cell resulting in two identical daughter cells.
• Cells contain both RNA and DNA, whereas viruses only contain either RNA or DNA.

Types of Cells

Non-Cellular Organisms

• Viruses contain either RNA or DNA as their genetic material, but do not have organelles or biosynthetic machinery.
• Bacteriophages are viruses that infect bacteria.
• Viroids are single-stranded, covalently closed, circular RNA molecules that exist as base-paired, rod-like structures.
  • They have not been proven to cause disease in humans.
• Prions are altered conformations of normal cellular proteins that can autocatalytically form more copies of themselves.
  • Prions are infectious particles associated with subacute progressive, degenerative diseases of the central nervous system.
  • An example of prion diseases is Creutzfeldt-Jakob disease
  • Misfolded proteins can induce misfolding in normal variants of the same protein (leads to cellular death)
• Prions cause transmissible spongiform encephalopathies
• Prions are extremely resistant to chemicals, heat, and radiation.
• Incineration is the most effective method of disposal for prion-contaminated materials.
• Creutzfeldt-Jakob disease aka Subacute spongiform encephalopathy.
• fatal neurodegenerative disease acquired by consuming prion infected brain or nervous tissue.
• neurodegenerative dx acquired via injection.

Bacterial Taxonomy

• Bacterial taxonomy is the area of biological science that encompasses classification, nomenclature, and identification of organisms.
• It establishes and maintains records of key characteristics of clinically relevant microorganisms.
• It facilitates communication by assigning universal names to clinically relevant microorganisms.
• An organism's name consists of two parts: the genus and the species.
• Bacteria: Escherichia coli
• Domain: Bacteria
• Phylum: Proteobacteria
• Class: Gammaproteobacteria
• Order: Enterobacterales
• Family: Enterobacteriaceae
• Genus: Escherichia
• Species: Coli
• Subspecies: Escherichia coli O157:H7
• Subspecies are a group within a species that are physically and genetically different from the rest of the group.
• Biotype: same species with the same genetic makeup but displays differential physiologic

Bacterial Genetics

• Genome is the genetic information in a cell (chromosome and plasmids)
• Chromosomes are structures containing DNA that physically carry hereditary information withing genes.
• Bacteria contain a single, unpaired (haploid) chromosome.
• Genes are segments of DNA that code for functional units.
• DNA is a macromolecule of repeating nucleotides.
• Nucleotides contain a nitrogenous base (adenine, thymine, cytosine, or guanine), deoxyribose, and a phosphate group.
• Base pairs always occur in a specific way: Adenine - thymine and Cytosine - guanine
• Genotype is the genetic makeup of an organism.
• Phenotype refers to the expressed properties of an organism.
• Gene expression is affected by transcription and translation.
• Transcription is the transfer of DNA-bound protein synthesis instruction to mRNA.
• Translation occurs at the ribosomes and is mediated by mRNA-linked amino acids.

• Genetic exchange and diversity is important for the organism to survive and evolve
• Mutations include induced or spontaneous heritable alterations of DNA sequences.
• Causes of mutations include chemicals, radiation, and viruses
• Base substitution: one base is insterted in place of another. (a.) DNA polymerase makes an error (b.) A mutagen alters the hydrogen bonding
• Frameshift mutation: insertion or deletion of one or two base pairs, disrupting the reading frame.
• Deletion: large excisions of DNA
• Insertions: change genes change genes and integration of new DNA
• Results of mutations:
  • Missense mutation: a codon causes a different amino acid to be inserted.
  • Nonsense mutation: a codon causes a termination that stops protein synthesis prematurely.
  • Silent mutation- mutation has no effect on protein's structure or function
• Function lost to mutation may be reversed:
  • Genotypic reversion (true) - restoration at the site of DNA alteration
  • Phenotypic reversion (suppression) restoration of an activity lost to mutation
  • DNA transferred from donor to recipient can integrate to the host cell chromosome.
• Homologous recombination involves DNA with pairing to exchange.
• Nonhomologous recombination is the addition of new genetic material to the chromosomes.
• Conjugation is bacterial cell transfer or genetic material.
• Transduction is phage-mediated transfer of host DNA sequences (Generalized and Specialized).
• Transformation is the direct uptake through cell wall by competent bacteria

Pathogenesis

• Virulence is a quantitative measure of pathogenicity and is measured by the number of organisms needed to cause disease.
• LD50 is the lethal dose to kill half the hosts and ID50 (50% infectious dose) is the number of organisms needed to cause infection in half the host.
• Virulence factors are Flagella, Pili, Capsule, Endospores, Toxins.

Bacterial Cell Structures

• The cell envelope is composed of macromolecular layers that surround the bacterium.
• The cell wall (murein layer or peptidoglycan layer) is the outermost component, and provides osmotic pressure and gram stain properties.
• It made primarily of peptidoglycan.
• Not found in mycoplasma
• Lipoprotein cross-links the peptidoglycan and outer membrane in gram-negative bacteria.
• The outer membrane provides a barrier to the cell.
• Can also serve as primary permeability barriers to hydrophilic and hydrophobic compounds.

The Components in Gram-Positive and Gram-Negative Cell Walls

• Periplasmic space is located between the cell membrane and outer membrane in Gram -.
• Periplasmic space contains hydrated peptidoglycan, penicillin-binding proteins, hydrolytic enzymes, and oligosaccharides
• Located in gram - cells
• Bayer's junction is the region where is inner leaflet in the gram - outer membrane.
• External layer: capsule
• Capsule is a well-defined outer structure.
• B. anthracis exception: polypeptide capsule
• P. multocida: hyaluronic acid capsule
• The capsule protects the bacteria from phagocytosis and is demonstratedin media containing Milk or Serum.
• Glycocalyx is polysaccharide fibrils that surround bacterial wall.
• Sometimes is called slime layer
• Associated with adhesive properties
• Has a granular appearance due to polyribosomes and inclusions
• Contains prominent antigenic sites

Bacterial Nucleus

• The bacterial nucleus is generally called the nucleoid or nuclear body.
• Not surrounded by a nuclear membrane
• Consists of polyamine and magnesium ions bound to negatively charged, circular, supercoiled, double-stranded DNA, small amounts of RNA, RNA polymerase, etc.

Bacterial Cytoplasm

• Contains ribosomes and various types of nutritional storage.
• Does not contain organelles.
• The cell membrane contains various functions.
• Has a sedimentation coefficient of 70S composed of 30S and 50S subunits
• Are the sites of action of many antibiotics that inhibit protein biosynthesis
• Are small, circular, extrachromosomal, double-stranded DNA molecules
• Metachromatic granules serve as energy source; food reserves.
• Appendages include flagella and Pili.
• Flagella contains protein appendages of the cell and motility.
• Peritrichous: flagella all around

Types of Flagella

• Atrichous: no flagella
• Monotrichous: flagella located at one pole
• Lophotrichous: tuft of flagella at one or both poles
• Amphitrichous: single flagella at each pole

The Ways to Demonstrate Motility

• Hanging drop.
• Flagellar stains.
• Semi-solid medium
• Pili (fimbriae) are short protein subunits mostly gram - bacteria.
• Endospores are a survival response to adverse environments and have multi-layered coating.

Types of Toxins

• Exotoxins: secreted proteins by gram +/- bacteria.
• Cytotoxins: kills host cells.
• Neurotoxins: act on nerve cells.
• Enterotoxins: act on gastrointestinal tract, causes GI and diarrhea.
• Pyrogenic Exotoxins: releases cytokines.
• Tissue Invasive Exotoxins: allow bacteria to destroy and tunnel through tissue.
• Endotoxins are structural components in gram- bacteria only.
• Bacterial Growth includes increase in cell numbers resulted in the biomass of the bacteria.

Phases

• Lag phases: cells increase w/vigorous activity.
• Exponential Growth: cells divide rapidly.
• Stationery Phase: due to depletion of nutrient production is slowing.