Endosymbiotic Theory

Evidence for Theory of Endosymbiosis

• Mitochondria and chloroplasts share similarities with bacteria
• They are similar in size and shape to bacteria
• Both contain circular DNA, typical of prokaryotes
• They reproduce independently of the host cell
• Ribosomes resemble those of prokaryotes
• The mechanism of protein synthesis is more similar to those found in bacteria than eukaryotes
• Same antibiotics that inhibit protein synthesis on bacterial ribosomes also inhibit protein synthesis on mitochondrial and chloroplast ribosomes.

Prokaryotic Cells and Eukaryotic Organelles

• Similarities between prokaryotic cells and eukaryotic organelles provide striking evidence for a shared origins in endosymbiosis

Bacteria Nucleus

• Gemmata bacteria supports hypothesis that a plasma membrane may have surrounded the nuclear regions to form a nucleus
• Gemmata features a double membrane surrounding the nucleoid, akin to a eukaryotic nucleus

Eukaryotic evolution

• Eukaryotic host and the bacterial endosymbiont are a modern example of possible eukaryotic evolution A modern prokaryote can live inside a eukaryotic cell

Fossilized Prokaryotes

• Cyanobacteria-like fossils 3.0 to 3.5 billion years old, considered oldest known fossils

Classification of Eukaryotes

• Protista is catchall kingdom of mostly unicellular eukaryotes, grouped based on rRNA
• Fungi develop from spores or hyphal fragments, either unicellular or multicellular, cell walls of chitin
• Plantae are multicellular, have cellulose cell walls, and undergo photosynthesis
• Animalia are multicellular organisms without cell walls

Taxonomic Hierarchy

• Linnaeus developed series of subdivisions to plants and animals
• Eukaryotic species are closely related organisms that breed with each other

Classification of Prokaryotes

• Prokaryotic species is a population of cells sharing high genomic similarity
• Culture: bacteria grown in lab media, often from a clone
• Clone: population of cells the descend from a single parent cell
• Strain: genetically distinct cells within a clone

Classification of Viruses

• Viruses are not part of any domain, lack cells, and require a host
• Classification is vital, since a major worldwide cause of disease
• Viral species are viruses sharing similar characteristics, set apart from other species via various methods—morphology, genomes, enzymes, ecological niche, etc.
• Viruses are obligatory intracellular parasites

Viral Origins Theories

• Viruses arose from independently replicating nucleic acid strands
• Viruses came from degenerative cells dependent on association with another cell
• Viruses evolved with host cells

Microorganism Classification and Identification

• Classification: placing organisms in related species groups, according to known traits
• Identification: matching traits of an "unknown" organism against known organisms
• Clinical identification: using clinical labs for identification

Identifying Microorganisms in Clinical Microbiology

• Lab requisition forms specify specimen type and tests
• Transport media collects/transports pathogens, preservatives help viability
• Clinical Laboratory Scientists analyze biological specimens for testing and reporting

Conventional Microorganism Identification

• Morphology: cell shape and arrangement
• Differential staining: using Gram and acid-fast staining (limited use for cell wall-less bacteria or archaea)
• Biochemical tests: determining if bacterial enzymes are present

Biochemical Tests Details

• Uses enzymatic activities to differentiate bacteria
• Gives insight into species' ecological role
• Many tests are used to ID organisms
• Useful for treatment

Serology Based Identification

• The science is based on the examination of serum (part of the blood) and immune responses in serum, which will be discussed in depth chapter 18, for use in rapid, at-home COVID-19 tests

Whole Genome Sequencing Info

• DNA base composition gives clues for organism relatedness
• Done via guanine + cytosine percentage, where GC + AT = 100%
• Closely related organisms share similar quantities of various bases
• Online databases such as NCBI Genome Database archive hundreds of organism genomic sequences
• DNA sequencing is now used for both classification and identification

Nucleic Acid Amplification Tests

• Nucleic Acid Amplification Tests (NAAT's) amplify DNA of an unknown microorganism that cannot be cultured
• Reverse transcription PCR: used to find SARS-CoV-2, poliovirus, and MPOX viruses in sewage
• Produces enough microbial DNA for analysis

Question 1 Response

• A and B, the chloroplast and the mitochondria.

Question 2 Response

• Bacteria lacks a nucleus, has peptidoglycan and sensitive to antibiotics

Amino acids, Peptides, Glycans, Lipids

• Amino acids are building blocks for proteins
• Peptide: Amino acids (2 - 50) bond to make short amino acid chain
• Glycans: Term refers to carbohydrates, sugars, monosaccharides, oligosaccharides and polysaccharides.
• Saccharide: Sugar
• Monosaccharide: single sugar molecule
• Disaccharide: 2 monosaccharides bonded
• Oligosaccharide: few sugars, typically 3-15 bonded via glycosidic bonds
• Polysaccharide: many monosaccharides bonded via glycosidic bonds
• Lipid: Fatty acids and steroids
• Synthesize: to make

Binary Fission and Central Dogma

• Binary fission: Prokaryotic cell reproduction where cell divides into two daughter cells.
• Review central dogma at: https://www.pearson.com/channels/microbiology/learn/jason/ch-8-microbial-genetics/central-dogma-Bio-1

Prokaryotes and Eukaryotes

• All living cells fall into 2 categories, prokaryote or eukaryote
• Prokaryotes
  • Structurally smaller than eukaryotes
  • DNA: a single, circular chromosome, uncontained by a membrane
  • Prokayotes lack of organelles.
• Eukaryote DNA is packaged in multiple chromosomes inside a membrane-enclosed nucleus

Prokaryotic Cells Differentiated

• Thousands of bacteria species are differentiated by:
  • Morphology (shape)
  • Chemical composition
  • Nutritional needs
  • Biochemical activities
  • Energy sources

Bacterial Morphology / Shapes

• Average size: 0.2-2.0 μm diameter x 2-8 μm length
• Most bacteria are monomorphic (single shape)
• Some are pleomorphic (many shapes)
  • Coccus is spherical (plural: cocci, meaning berries)
  • Bacillus is rod-shaped (plural: bacilli, meaning little rods or walking sticks)
  • Spiral: comes in Vibrio, Spirillum, Spirochete shapes
  • Star-shaped: Staphyle (a bunch of grapes)
  • Rectangular: Streptos (a chain)

Cocci Bacteria

• Cocci are round, oval, elongated, or flattened

• Cocci may remain attached after division

  • Diplococci: occur in pairs
  • Streptococci: occur in chains
  • Tetrads: occur in groups of four
  • Sarcinae: remain attached in cubelike groups of eight
  • Staphylococci: grapelike clusters [Staphyle = grapes, Streptos = chain]

Bacilli Bacteria

• Bacilli (rod-shaped) divide along their short axis only
  • Single bacilli: form most bacilli as single rods
  • Diplobacilli: occur in pairs / Diplobacilli
  • Streptobacilli: occur in chains / Streptobacilli
  • Coccobacilli: look like cocci / Coccobacilli

Meanings of "Bacillus"

• “Bacillus” has two definitions in microbiology:
  1. Bacillus refers to a bacterial shape.
  2. Bacillus refers Bacillus anthracis.

Spiral Bacteria Traits

• All spiral bacteria have twists; they are never straight

  • Use flagella, propeller-like external appendages

• Bacteria with curved-rod shapes are called vibrios

• Spirilla: helical shape, similar to corkscrew, fairly rigid

• Spirochetes: helical, flexible; they use axial filaments

Shapes of Prokaryotes

• Stella = Star-shaped, varied environments
• Haloarcula = Rectangular & halophilic archaea

Cell Shape Differences

• Bacteria can show morphological plasticity

• Pleomorphic: cells that can take multiple forms

• Changes during growth: the cells get smaller with advancing age

• Nutrient limitations lead to increase of surface/volume ratio

  • Larger surface/volume is better because essential enzymes exist on the membrane.

• Response to environmental stresses: host immune responses, harsh conditions

Prokaryotic Cell Structure

• Characteristic structures in bacteria

• Prokaryotic cells lack membrane-enclosed organelles

• Every bacterium includes a cytoplasm, ribosomes, a plasma membrane, and a nucleoid

• Pretty much all bacteria include a cell wall

• Certain additional structures play vital, specific roles

  • Capsule (glycocalyx): used for bacterial virulence
  • Cell wall or flagella: help with bacterial identification
  • Cell wall: used as a target for antimicrobial agents

• Plasmids: carry data to resist antibiotics or production of toxins

Glycocalyx Composition

• Bacteria prefer attaching to surfaces instead of free-floating

• Glycocalyx

  • Many bacteria secrete Glycocalyx on the surface outside the cell wall
  • Made out of polysaccharide, polypeptide or both

• There are two types

  • Function: Glycocalyx defends cells and allows them to adhere to other cells:
  • Capsule: neatly organized, firmly adheres
  • Slime layer: unorganized, loose
  • Made of polysaccharide

Glycocalyx Functions:Virulence

• Can make a pathogen more virulent

  • Prevents phagocytosis: the ingestion/elimination of bacteria by host cells
  • Enables microbial attachment: helping microbes stick to body surfaces

• Helps in bacterial communities (ie. biofilms) like Streptococcus mutans attaching to teeth.

• Bacillus anthracis & Streptococcus pneumoniae are only virulent if they are encapsulated

• Protects against dehydration & can inhibit nutrient loss via viscosity

Flagella and Bacteria

• Flagella are filamentous cellular surface appendages to propel bacteria

• Flagella allows motile bacteria to move itself

• The three basic parts to the flagella are

  • Outermost flagellin region
  • Hook connects flagellum to the filament
  • Basal body grounds flagellum to the cell

• Bacteria is "atrichous" without flagella.

Flagella Rotation

• Bacterial flagella rotations are either clockwise or counterclockwise

• “Run” or “swim”: happens only when bacteria is moving in one direction for a certain amount of time [counterclockwise]

• “Tumble”: periodic, random, abrupt changes in direction [clockwise]

• Tumbling is from reversal rotation

• Runs are interrupted by tumbles

Flagella Arrangements

• Four Arrangements of the Flagella are:
  • Peritrichous: even dispersion
  • Monotrichous: single flagellum
  • Lophotrichous: 2+ flagella on cell end
  • Aphitrichous: flagella on each end

Advantage of Motility

• Is the movement of a bacterium toward or away from a particular stimulus
• Provides a bacterium a route to a good environment away from an adverse one.
  • Chemotaxis is the result of a chemical's presence
  • Phototaxis happens as a result of a light source
• Special stimulus receptors exist on motile bacteria
• Bacteria go toward the stimulus as a result of an attractant, which creates a positive chemotactic signal, bacteria runs
• Bacteria recoils from the stimulus as a result of a repellent, which creates a negative chemotactic signal, bacteria tumbles

Axial Filaments

• Found in spirochetes [Syphillis & Lyme Disease]
• Anchored at one end of a cell & filament
• Body rotates as move with outer sheath
  • Makes it so cell moves like a corkscrew

Differences Between Fimbriae and Pili

• Appendages made of protein pilin
• Made of Protein are shorter, thinner and straighter
• Two Types:

  • Fimbriae: Provide Attatchment, Contribute to Biofilm

    • Enable Certain Bacteria to adhere to surfaces
    • Can result in severe diarrhea as E. coli O157 attaches the intestine's lining
    • Colonization and disease may not occur because of an absence of fimbriae.

  • Pili: Motility and DNA Transfer between cells, contribute to antibiotic resistance

    • Gliding & twitching motility

Cell Walls of Bacteria

• The semirigid cell wall of the bacterial cell gives the cell its shape
• Nearly all prokaryotes are protected by a cell wall that surrounds the fragile cytoplasmic, or plasma membrane
• The environment outside poses threat if in contact
• Made of peptidoglycan [only in bacteria]
• Has pathogenicity = to cause disease
• Aids the action of a few particular antibiotics
• Can differentiate the species by chemical composition

Composition & Structure of Bacterial Cell Walls

• Peptidoglycan network called murein
• Composed of 2 repeating rows of disaccharide including:
  • N-acetylglucosamine (NAG)
  • N-acetylmuramic acid (NAM)
• Rows form glycans linked to polypeptides (proteins) structure
• This produces a protein lattice to shield from environment.

Bacterial Peptidoglycan

• Glycans are composed of NAM + NAG disaccharide
• Peptido are peptide links
• Tetrapeptide chains are made of 4 linked amino acids & attach to NAMs
• Bond between tetrapeptide to NAM links tetrapeptide to amino group on neighboring NAM

Peptidoglycan structure

• Repeating units: NAG
• Chains of N-acetylglucosamine (NAG) bound through a β-(1,4) glycosidic linkage
• 4 amino acids

Crosslinking Peptidoglycan

• There are 2 Bacteria Types where Crosslink Peptidoglycan:

   = Gram negative, Connected via direct cross [Thin]
  

  • Gram positives, connected through interbridge [Thick]

Penicillin and its Use

• Penicillin blocks the final linking of peptidoglycan rows by targeting peptide cross-bridges
  • Cell walls become weaker, and trigger cell lysis

Gram+ Cell Walls Components

• Gram+ walls have Thick peptidoglycan

• Teichoic acids span multi-layers of peptidoglycan to strengthen the cell wall.

• Peptidoglycan Layer: a cell wall link containing lipoteichoic acid

• Wall: contains teichoic acid that is linked from peptidoglycan layer Recognized by human immune +system [antigenic]

Peticoglycan and Gram+ Relations

• Periplasmic space is present between membrane and the cell wall

Gram- Cell Walls

• Has thin peptidoglycan, outer membrane

  • Peptidoglycan attaches lipoproteins in in periplasm & outer membrane

    -Protects periplasm located in membranes Inner side of the outer membrane

• Outer membrane made of lipopolysaccharide(lps), lipoproteins & phospholipids/barrier

  • Channel permeable of penicillin
  • Has nutrients to feed the cell from inner side - Gram (+) Do not contain teichoic acids

Lipopolysaccharide (LPS) Description

• Lps: Made of lipids & carbs & have a trio components:
  • Outer layer & its embed top with outer membrane
• Lipid - Die & Endotoxin are functions of Gram - during release
  • Responsible that caused fever, shock, Symptoms
• Core polysaccharide: attaches on Lipid - is role

Bacterial Peptidoglycan

• An o polysaccharide: Extends and is composed of sugar
• Recognized by human immune system [antigenic] as compared with Gram (+) calls that have teichoic

Atypical Atypical Cell Walls:

• Mycoplasmas: walls lack cells, need hosts to grow
• They slip thru bacterial filters because of there size and lack of walls.
• Unique since lack cell wall because of lipids made of sterols
• Most Human Pathogen [Mycoplasma Pmeumoniae and mild Preumoniae

ACID for Cell Walls:

• Fast Walls - Contain Peptidoglycan

  • Surface with Waxy Lipid (Myolic Acid) will stop dies. Polysaccharide is hold by Arabinogatan to the acud (P)Genera's such ad (Mycobacterim and Nocardia

Damage in relations to the cells Wall

Outer membrane is made to blocks access to penciling on cell membrane.

If the a' cell breaks down that peptidog'y cam with weakens gram positive

Question (3) Response

• C) Streptobacilli

Question (4) Response

• B) Pilí.

Question (5) Response

• B) The capsule allows escape from phagocytosis

Question (6) Response

• C) antibiotics are infective because no peptoglycan is there.