Microbiology basics

• Microbiology Lecture 1 Notes cover the classification of protists and microorganisms, cellular structures and differences, bacterial morphology and taxonomy, and the characteristics of bacteria, viruses, and other microorganisms.

Classification of Protista

• Higher protists (eukaryotic) include algae (except blue-green algae), protozoa, and fungi.
• Lower protists (prokaryotic) include bacteria and blue-green algae.

Units of Measurement

• 1 cm = 10 mm
• 1 mm = 1000 micro.m = 1 million nano m

Classification of Microorganisms

• Major groups include algae, protozoa, fungi, bacteria, and viruses.
• Some organisms (rickettsiae and chlamydiae) are intermediate between bacteria and viruses.
• Bacteria, fungi, and protozoa belong to the kingdom of protists and are differentiated from animals and plants by being unicellular or relatively simple multicellular organisms leading a parasitic existence.
• Viruses are unique, acellular, metabolically inert organisms that can replicate only within living cells, making them obligate intracellular parasites.

Differences Between Viruses and Cellular Organisms

Structure

• Cells have a nucleus or nucleoid (in bacteria) with DNA, surrounded by cytoplasm for energy generation and protein synthesis.
• Viruses have an inner core of DNA or RNA but no cytoplasm, depending on the host for energy and proteins (metabolically inert).

Reproduction

• Bacteria reproduce by binary fission, where a parent cell divides into two similar cells.
• Viruses disassemble, produce nucleic acid and protein copies, and then reassemble within a host cell to replicate.
• Bacteria can replicate extracellularly, except for rickettsiae and chlamydiae, which require living cells for growth, similar to viruses.

Viral Replication Process

• Attachment to host cell.
• Entry into the cell.
• Uncoating to release genetic material.
• Transcription/mRNA production.
• Synthesis of virus components.
• Virion assembly and release.

Prokaryotes vs. Eukaryotes

• Prokaryotes are organisms without a true nucleus.
• Eukaryotes (fungi, protozoa, and humans) have cells with a nucleus.
• Prokaryotes have a single, circular DNA molecule without a nuclear membrane. Plasmids may be also present.
• Eukaryotes have a true nucleus with multiple chromosomes surrounded by a nuclear membrane.

Genetic and Cellular Organization

• Prokaryotes have DNA in the cytoplasm without a nuclear membrane versus eukaryotes with DNA in a membrane-bound nucleus.
• Prokaryotes possess a single, haploid chromosome, while eukaryotes have multiple, diploid chromosomes.
• Prokaryotic DNA is associated with histone-like proteins, whereas eukaryotic DNA is complexed with histone proteins.
• Prokaryotes divide via binary fission, but eukaryotes divide via mitosis and exchange genetic information during sexual reproduction.

Cellular Organization

• Prokaryotes have cytoplasmic membranes containing hopanoids, while eukaryotes contain sterols.
• Energy metabolism is associated with the cytoplasmic membrane in prokaryotes versus mitochondria in eukaryotes.
• Photosynthesis in prokaryotes is associated with membrane systems, while eukaryotes have chloroplasts in algal and plant cells.
• Flagella consist of one protein (flagellin) in prokaryotes but have a complex microtubular structure in eukaryotes.
• Ribosomes are 70S in prokaryotes and 80S in eukaryotes.
• Eubacteria have peptidoglycan cell walls, but eukaryotes have polysaccharide cell walls (cellulose or chitin).

Svedberg Unit

• Theodor Svedberg won the 1926 Nobel Prize for chemistry for his work in colloid chemistry.
• The "Svedberg unit" measures the velocity of sedimentation and the molecular weight of proteins.

Eubacteria vs. Archaebacteria

• Prokaryotes are divided into eubacteria and archaebacteria.
• Eubacteria include common bacteria and human pathogens.
• Archaebacteria rarely cause human disease and live in extreme environments.
• Recent studies found archaebacteria in the oral cavity, but their role in oral health is undetermined.

Bacterial Morphology

Shape

• Determined by the rigid cell wall.
• Bacteria classified into cocci (spherical), bacilli (rod-shaped), and spirochaetes (helical).
• Pleomorphic bacteria have variable shapes.

Size

• Ranges from 0.2 to 5 μm. Smallest ones are about the size of poxviruses. Longest bacilli can be the same length as yeasts and human RBCs(7 μm).

Common Bacterial Forms

• Coccus
• Capsulated diplococci
• Cocci in chains (e.g., streptococcus) and clusters (e.g., staphylococcus)
• Bacillus
• Capsulated and flagellated bacillus (e.g., Escherichia coli)
• Curved bacilli (e.g., Vibrio spp.)
• Spore-bearing bacilli (e.g., Clostridium tetani)
• Spirochaete

Bacterial Arrangement

• Bacteria arrange themselves according to the plane of cell division as pairs (diplococci), chains (streptococci), clusters (staphylococci), or palisades (corynebacteria).

Gram-Staining Characteristics

• Bacteria can be classified into Gram-positive (purple) and Gram-negative (pink) based on cell wall staining characteristics.
• Gram-staining is useful for identification and therapy, as Gram-positive bacteria are more susceptible to penicillins.

Bacterial Cell Structure

Protoplast

• Includes the cytoplasmic membrane, cytoplasm, nucleus, and cell organelles.

Cell Wall

• Bacteria have a rigid cell wall that protects a fluid protoplast.

External Structures

• Flagella: whip-like filaments for motility.
• Fimbriae and pili: structures for surface adhesion.
• Glycocalyx (slime layer): polysaccharide coating for adherence.
• Capsule: a gelatinous layer composed of polysaccharide and protein.

Flagella

• Whip-like filaments that act as propellers for movement. Composed by flagellin.
• Arrangements:
  • monotrichous (single polar flagellum)
  • amphitrichous (single flagellum at each end)
  • lophotrichous (tufts of flagella at one or both ends)
  • peritrichous (flagella all over the surface)
• Most bacilli (rods) possess flagella, but most cocci do not and are therefore non-motile.
• Spirochaetes move by using flagellum-like structure called the axial filament, which wraps around the cell producing undulating motion.

Fimbriae and Pili

• Fine, hair-like filaments shorter than flagella that extend from the cell surface.
• Pili composed of protein subunits (pilin), mediate bacteria's adhesion.
• Sex Pili forms attachment between bacteria during conjuagation.

Glycocalyx (Slime Layer)

• Is polysaccharide coating that covers outer surfaces of many bacteria and allows bacteria to adhere.

Capsule

• Amorphous, gelatinous layer surrounds bacterium composed mostly of polysaccharide. It can be composed of protein in some spores (e.g. Bacillus anthracis)
• Important because it mediates the adhesion, inhibits phagocytosis, and used as antigens in certain vaccines
• Diagnosed using Quellung reaction

Cell Wall

• Provide rigidity.
• Multilayered outside the cytoplasmic membrane and is porous and permeable
• Made of peptidoglycan (protein + sugar). Some are covered by an outer membrane.
• The peptidoglycan varies in thickness and chemical composition
• Peptidoglycan (murein and mucopeptide) derived from peptide and sugars (glycan)

Gram-Positive and Gram-Negative Bacteria

• Gram-positive and Gram-negative bacteria have differing cell wall structures and components.
• The Gram-positive cell contains a thick peptidoglycan layer and teichoic acids. No outer membrane involved.
• The Gram-negative cell wall complex outer membrane composed of LPS, lipoprotein, and phospholipid.
• Porins in gram cells allow transport molecules across the outer membrane.
• The 0 antigen of LPS and lipid A are embedded in the membrane.
• Antibiotics have difficulty penetrating the outer membrane. Because their cell wall is thinner they are susceptible to penicillins.

LPS (Lipopolysaccharide)

• Is highly toxic is known as an Endotoxin.
• Cannot be produced by Gram-positive because they do not have LPS in their cell walls.
• Responsible for disease symptoms such as fever and shock
• Mycobacterium tuberculosis's cell wall contains mycolic acids making gram staining impossible so use acid-fast

Bacteria with Defective Walls

• Some can survive with defective cell walls. myoplasmas and L-forms, (spheroplasts and protoplasts)
• Mycoplasmas: do not possess a cell wall and do not need hypertonic media for their survival.
• L-forms: lack cell walls and unstable/osmotically fragile. Only can survive with hypertonic conditions.

Cytoplasmic Membrane

• Lies just inside the peptidoglycan layer of the cell wall. It is composed of a phospholipid bilayer

Cytoplasmic Membrane Functions

• Active transport and selective diffusion of molecules and solutes.
• Electron transport and oxidative phosphorylation in aerobic species.
• Synthesis of cell wall precursors.
• Secretion of enzymes and toxins

Mesosome

• Convoluted invagination of the cytoplasmic membrane that function as origin of the transverse septum (splits the cell in half) and the DNA binding site.

Cytoplasm

• Comprises inner nucleoid regiuon and the amorphous matrix (contains ribosomes, nutrient granules, metabolites and ions).

Genetic Material (Nucleoid)

• Comprises a single, supercoiled, circular chromosome that contains about 2000 genes, approximately 1 mm.
• Division undergoes semiconservative replication bi-directionally from a fixed point.

Ribosomes

• Ribosomes are the sites of protein synthesis. Bacterial ribosomes differ from those of eukaryotic cells in both size and chemical composition.
• Prokaryotes: 70s
• Eukaryotes: 80s

Bacterial Spores

• Spores are formed because of adverse conditions and nutrients sources, carbon, and nutrients are scarce.
• Spores are formed by Bacillus (anthrax agent) and Clostridium (tetanus and botulism).
• The spore develops the vegetative cell containing bacterial DNA, small amount of cytoplasm, cell membrane, peptidoglycan, very little water and a keratin-like coat.
• A spore forming bacteria grown vegetative then divides via binary fission if there are available nutrients or conditions.

Spore Formation

• DNA condenses self in the center of the cell.
• DNA dives into two complete copies and the cell membrane invaginates to form.
• Next peptidoglycan between the two membranes forms the spore cortex
• Next dipicolinic is formed inside the spore. Calcium enters and water removed outside.
• A protein coat forms outside. The spore becomes mature. Sometimes it forms exosporium.
• The spores are resistant to environment conditions. Enzyemes destro the mother cell and released the mature spore. This coat conatins calcium dipicolinate.

Spores

• Are metabolically inert, resistant to heat, dehydration, radiation, and chemicals and can remain dormant for many years.
• Once they degrade through enzyemes it reforms bacteria again.

Endospores Clinical Relevance

• Extraordinary resistant towards heat and chemicals cannot be easily achieved by boiling or autoclaving. Used to evaluate sterilization efficiacy of autoclaves (Bacillus stearothermophilus)

Taxonomy

• The classification and categorization of organisms, using diagnostic microbiology. Bacteria and fungi are protists.

Bacterial Classification

• Is somewhat phenotypical (artificial traits) opposed to genotypically.
• Includes morphology. staining properties (grams), cultural requirments, bio chemical reactions and antigenic structure.

Genotypic Traits

• Is useful and import and exploits gentle characteristics to see DNA patterns through bacterial DNA.

Recent Researchs

• Bacterial habitats in humans have a flora that cannot be cultured using routine test for unculturable,

How Organisms Get Their Names

• Beginning taxonomic kingdom, division, subdivision, order, family, genus and species

Naming Scientific

• Scientific name or organism is a binomial combination of generic + species.
• Is written in italics (genus abbreviated, and species not capital)
• When used adjective do not italicize

Questions about microbiology, with a focus on bacteria, viruses and cell features. Covers characteristics, classification, and reproductive processes. Tests knowledge of nanometers, cell walls, and bacterial capsules.