MIC102 MT1

UC Davis Sam Munoz Diaz Spring 2025

What is a microbe?

“free living organisms so small that are only visible under the microscope”

What are some exceptions to microbes?

• Visible to the naked eye

  • Ex. Epulopiscium fishelsoni

• Can only live within cells (no free living; intracellular parasite)

  • Ex. Mycobacterium leprae

  • Ex. Viruses

How are bacteria, fungi, archaea, protists, viruses, prions classified? (Cellular/Acellular)

Cellular: fungi, protists, bacteria (prokaryotes), archaea (prokaryotes)

Acellular: Viruses, prions

How are microbes classified?

phylogenetically

What do we want in a gene to be good for phylogenetics?

• selectively neutral

• conserved regions (for PCR primers)

• Shared across all organisms to be analyzed (16s rRNA- “universal” gene)

What are the three domains of life?

Archaea, Eukaryotes, Bacteria and relatives

Why are microbes important? Global reason

• photosynthestic bacteria (cyanobacteria) oxygenated the planet (cooling the planet)

• Microbes are involved in global biogeochemical cycles (carbon, nitrogen)

Why are microbes important (within your body)

• Roughly 9/10 of the cells in your body are microbes

• 10k different species make up human microbiome

• Gut bacteria helps make vitamin B and K

What kind of diseases do microbes cause?

• Bacterial

  • Food poisoning (E. coli/ Salmonella), STIs (gonorrhea), TB

• Viral

  • Food poisoning (Norovirus), STIs (HPV/HIV/Herpes), Influenza, Ebola

• Fungal

  • Ringworm

• “Protist” (microbial eukaryote)

  • Giardia

Resolution needs to be ___ than what were trying to see (bacteria are ~1µm)

smaller

What kind of staining would kill the cells

Safranin and Crystal Violet in the Gram stain

Phase Contrast

Increase the contrast by changing the quality of light, can see movement

Fluorescence

• Fluorochromes that emit light of specific wavelengths when excited by light of a different wavelength

• Can be an external dye, attached to a molecule such as an antibody or DNA probe

• Can be engineered into genes and viewed in living cells

Electron Microscopy

• Magnifies up to ~500,000x

• n=0.005nm; d=~0.2nm

• Scanning EM: to view exterior (surfaces, “outside”)

• Transmission EM: to view internal structures, smallest specimens

Where does life come from? The Endosymbiotic Theory

1. Infoldings in the plasma membrane gave rise to end-membrane components, including a nucleus and endoplasmic reticulum

2. In a first endosymbiotic event, the ancestral eukaryote consumed aerobic bacteria that evolved into mitochondria

3. In a second endosymbiotic event, the early eukaryote consumed photosynthetic bacteria that evolved into chloroplasts

What are the three domains of life?

Bacteria, archaea, eukarya

Plasma membrane

Selectively permeable barrier, mechanical boundary of a cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis), detection of environmental cues for chemotaxis

Gas vacuole

An inclusion that provides buoyancy for floating in aquatic environments

Ribosomes

protein synthesis

Inclusions

storage of carbon, phosphate, and other substances; site of chemical reactions (microcompartments); movement

Nucleoid

Localization of genetic material (DNA)

Periplasmic space in gram negative and gram positive bacteria

Gram-negative bacteria: contains hydrolytic enzymes and binding proteins for nutrient processing and uptake

Gram-positive bacteria: may be smaller or absent

Cell wall

protection from osmotic stress, helps maintain cell shape

Capsules and slime layers

Resistance to phagocytosis, adherence to surfaces

Fimbriae and pili function

Attachment to surfaces, bacterial conjugation and transformation, twitching

Flagella

Swimming and swarming motility

Endospore

Survival under harsh environmental conditions

External Structures in a Prokaryotic cell (3)

• Appendages: Flagella, pili/fimbriae

• Glycocalyx: capsule, slime layer

• S-layer

Envelope structures in prokaryotic cell (4)

• Outer membrane with LPS

• Lipoprotein

• cell wall

• cell membrane

Internal structures in prokaryotic cell (6)

• cytoplasm

• cytoskeleton

• nucleoid/chromosome

• ribosomes

• inclusions

• endospore

What kind of linkages do Eukaryotes and Archaea use?

• Eukaryotes: Ester linkage

• Archaea: Ether linkage

Which traits do solutes need to be able cross across a phospholipid bilayer?

• Small, uncharged, polar molecules

  • water, urea, glycerol, ethanol

• hydrophobic molecules

  • steroids, O2, CO2, N2

What types of solutes cannot cross a phospholipid bilayer?

• large, uncharged polar molecules and ions

  • H+, monosaccharides

Isotonic Solution Effect

No net movement of water particles, Cell membrane is attached to cell wall

Hypertonic Solution Effect

Water particles move out of the cell. Cell membrane shrinks and detaches from cell wall (plasmolysis)

Hypotonic Solution Effect

Water particles move into the cell. Cell wall counteracts osmotic pressure to prevent swelling and lysis

Isotonic Solution Meaning

A solution that has the same solute concentration as another solution. There is no net movement of water particles, and the overall concentration on both sides of the cell membrane remains constant

Hypertonic Solution Meaning

A solution that has a higher solute concentration than another solution. Water particles will move out of the cell, causing crenation

Hypotonic solution meaning

A solution that has a lower solute concentration than another solution. Water particles will move into the cell, causing the cell to expand and eventually lyse

Cell walls protect against what kind of stress?

osmotic

Penicillin inhibits what?

cell wall synthesis

How does penicillin inhibit cell wall synthesis?

• Incubation in isotonic medium

• Protoplast transfers to hypotonic medium

• Swelling due to sudden H2O influx

• Lysis (bursts)

Some differences in gram-positive and gram-negative peptidoglycan (murein)

Gram positive: Pentapeptide, tetrapeptide (Gly5, L-Lys)

Gram-negative: direct link, DAP (diaminopimelic acid)

Similarities: NAG (N-acetylglucosamine), NAM (N-acetylmuramic acid)

Bacteria Gram-Positive Stains

Has enough membrane to stain with crystal violet stain

Gram Negative Stain

Does not have enough membrane to stain (plasma membrane, peptidoglycan, outer-membrane)

Which envelope is more complex, gram-negative or gram-positive?

Gram-negative

Lipopolysaccharide (LPS) O-antigen/O-polysaccharides traits

• vary between species

• recognized by immune system

• can be used to ID by “O-antigen” type

What is LPS also known as?

“Endotoxin” released when cell dies

Which is most directly responsible for septic shock events?

Lipid A

Porins

Channel/gate that allows for selective permeability in the outer-membrane

Increases permeability of outer membrane to small and hydrophilic molecules

Acid-Fast Bacteria

Waxy layer that makes cells resistant to acids, and soaps

Does slow nutrient uptake and growth

Hard to get rid of and is programmed to hunt for phage against Mycobacterium (HHMI SEA PHAGES)

Mycoplasmas

• lack cell wall completely (many antibiotics target cell-wall synthesis

• Use sterols extensively in their membranes

• Live on or inside host cells

What can be found outside of the cell wall?

• Glycocalyces

  • capsule

  • slime layer

• S-layers

What do flagella consist of?

• filament

• hook

• basal body

Bacterial pilus made and function

assembled from pilin monomer into a helix; can be rapidly assembled and disassembled to a change length. Can be attachment point for viruses

Function: Conjugation, attachment (“fimbra”) with adhesions at tip, twitching motility

Nucleoid (Cell Interior)

DNA is not strictly separated from rest of cell

Transcription and translation occur together

Organizes DNA

Genome size

~Potentially 10MB or more

Genome size corresponds to complexity

What type of chromosome do bacteria typically have?

A singular circular chromosome

What helps bacterial DNA form supercoiled loops

DNA-binding proteins

How are repulsive charge effects of DNA neutralized in bacteria?

By cations binding to the DNA

What enzymes control supercoiling in bacterial DNA?

DNA gyrase and Topoisomerase I

Role of DNA gyrase in bacterial supercoiling

Utilizing ATP to actively wind DNA into negative supercoils

What does “Reverse Gyrase” do?

Actively winds DNA into a positive supercoil

How does Topoisomerase I function in bacteria?

Does not use ATP and allows DNA to relax towards a less supercoiled state

Difference between positive and negative supercoiling

Positive supercoiling occurs with left-handed twists, while negative supercoiling occurs with right-handed twists

What does the interior of the nucleoid exclude?

ribosomes

What happens when genes are transcribed?

They are unspooled and made available to RNA polymerase along the surface of the nucleoid

How quickly do ribosomes have access to new mRNA transcripts?

almost immediately

Cytoplasm density

very dense to keep local concentration high

Cytoplasm crowding

aids protein folding and other chemical reactions

Specialized Structures- Gas Vesicles: Function

Can tune buoyancy for optimum light gathering

Specialized Structures- Gas Vesicles: Common in?

Aquatic photosynthetic microbes like Cyanobacteria

Specialized Structures- Gas Vesicles: Protein shell permeability

Protein shell permeable to gas but impermeable to water

Note: Gas diffuses to reach equilibrium and is not pumped in or stored in higher concentrations

Specialized Structures- Thylakoids: Function Thylakoids: Function

Enhance light-gathering abilities of photosynthetic bacteria by greatly increasing the membrane surface area

Specialized Structures: Thylakoids: Made up of

Stacks of membrane sac with shared lumen

Specialized structures- Thylakoids: Similar structures

Similar structures made by chemolithotrophs

Specialized functions- Carboxysomes: function

Used in bacteria that fix CO2

Enhance the function of RubisCo

Specialized structures- Carboxysomes: Made of

protein shells

Specialized structures- Carboxysomes: Similar structures

Heterotrophic bacteria sometimes have similar structures

Enterosomes: no RuBisCo but allow to metabolize other compounds with harmful intermediates

Specialized Structures- Storage granules: Also known as?

Refractile inclusion bodies

Specialized Structures- Storage Granules: function

Store useful materials when in abundance for later use when materials are lacking

Specialized structures- Storage granules: Inorganic materials commonly stored

Sulfur, calcium, phosphate

Specialized structures- Storage granules: Types of organic polymers stored

Polyhydroxyalkanoates (PHA)

Specialized structures- Magnetosomes: What are they

Membrane-bound, iron-containing structures in certain bacteria

Specialized structures- Magnetosomes: Function

Several crystals are chained together to act as compass needle

Specialized structures- Magnetosomes: Location in cell

Attached to cell membrane

Specialized Structures- Magnetosomes: Primary compounds found in it

Fe₃O₄ (Magnetite) or Fe₃S₄ (greigite)

What are 5 specialized functions of bacteria?

• Magnetosomes

• storage granules

• Carboxysomes

• Thylakoids

• Gas Vesicles

Bacteria vs Archaea: Plasma membrane lipids

Bacteria: Ester-linked phospholipids form a lipid bilayer

Archaea: Glycerol dieters form lipid bilayers; glycerol tetraethers form lipid monolayers

Bacteria vs Archaea: Cell wall constituents

Bacteria: Peptidoglycan is present in nearly all; some lack cell walls

Archaea: very diverse but peptidoglycan is always absent: some consist of S-layer only, others combine S-layer w/polysaccharides or proteins or both; some lack cell walls

Bacteria vs Archaea: Inclusions present?

Yes to both, including gas vacuoles

Bacteria vs Archaea: Ribosome size

70S for both

Bacteria vs Archaea: Chromosome structure

Bacteria: most are circular. double stranded (ds) DNA

Archaea: All known are circular, dsDNA

Bacteria vs Archaea: Plasmids present

Bacteria: yes, circular and linear dsDNA

Archaea: yes, circular, dsDNA

Bacteria vs Archaea: External structures

Bacteria: Flagella, fimbriae (pili) common

Archaea: Archaella, pili common

Bacteria vs Archaea: Capsules or slime layers

Bacteria: Common

Archaea: Rare

Archaeal envelopes membranes

Can provide more rigidity and structure than bacterial membranes

What is a different linkage and acid that bacteria and archaea have?

Linkage in Archaea: Lysozyme-insensitive

Acid in Archaea: N-Acetyltalosaminuronic acid

Acid in Bacteria: N-Acetylmuramic acid

Bacteria vs Archaea: Archaeal Ribosomes

Somewhat “intermediate” between bacteria and Eukaryotes

Bacteria vs Archaea: Proteins

Archaea can use histone-like proteins in chromosome management; other nucleoid-associated proteins are similar in use to Bacteria but differ in structure