February 6th Lecture Notes

Prokaryotic Diversity

Four postulates to prove a causal relationship between a microorganism and an individual:

1. The microorganism must be present in every case of the disease and absent from healthy individuals.

2. The putative causative agent must be isolated and grown in pure culture.

3. The same disease must result when the cultured microorganism is used to infect a healthy host.

4. The same microorganism must be isolated again from the diseased host.

Fall Into two domains: Bacteria and Archaea

Biofilms are highly resistant to anti-bacterial agents

Differences Between Prokaryotes and Eukaryotes

Unicellular
• Prokaryotes are single-celled
• Only eukaryotic cells can be multicellular
• Prokaryotes may stick together to form associations and biofilms
Cell size
• Size varies tremendously but is generally much smaller than eukaryotes
• Most prokaryotes are less than 1 mm in diameter
$Nucleoid <br>$• Prokaryotic chromosome is single, circular, double-stranded DNA
• Found in the nucleoid region of the cell
• Often have plasmids
Cell division and genetic recombination
• Most divide by binary fission, and don’t go through the mitosis process that
eukaryotes do
• Exchange genetic material extensively

February 8th Lecture Notes

Differences between Bacteria and Archaea

• Plasma membrane

  • The bonds are different

• Cell wall

  • Bacteria have peptidoglycan, archaea don’t.

• DNA Replication

• Gene Expression

Classification

Early Classification

1. Photosynthetic

2. Motile

3. Unicellular

4. Formation of spores

5. Is it a human pathogen?

Newer Classification

1. Amino acid sequences

2. Percent Guanine/Cytosine Content

Understand The Features of a Typical Prokaryotic Cell

Flagellum: a slender threadlike structure, especially a microscopic appendage that enables many microorganisms to swim.

Pilus: A pilus is a hair-like appendage found on the surface of many bacteria and archaea. The pilus of a bacteria cell helps the cell stick to surfaces.

Capsule: A capsule is a gelatinous outer layer secreted by a bacterial cell and that surrounds and adheres to the cell wall.

Cell wall: A structural layer surrounding some types of cells, just outside the cell membrane

Cell membrane: a biological membrane that separates and protects the interior of all cells from the outside environment

Chromosomal DNA: The primary genetical material, controlling the structure of proteins and hence influencing all enzyme-driven reactions

Shapes/ Arrangement of bacteria

• Cocci: Spherical

• Bacilli: Rod-shaped

• Sarilli: spiral

• Diplo-: Pair

• Strepto-: Chain

• Staphylo-: Cluster (like Grapes)

Major Groups of Prokaryotes

Proteobacteria: One of five bacteria phyla and is further divided into five classes Alpha - Epsilon

Gram-Positive / Negative Prokaryotes: Gram-positive will hold the stain (purple) as it has a thicker cell wall.

Prokaryotic Genetics

Conjugation: Pillus transfers genetic material from one cell to the next

Translation: DNA transfer via virus

Transformation: Naked uptake of DNA (could be from a dead cell or done artificially)

• Still subject to mutations!

Metabolism

Nutrients: Substances are needed for cells to build all of the molecules required to sustain life.

Macronutrients: Nutrincese that are required in a large amount

• Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, and Sulfur. CHONPS

Micronutrient: Nutrients required in a smaller amount

Acquisition of carbon:

Autotrophs: From inorganic CO2

• Photoautotrophs - energy from the sun

• Chemoautotrophs - energy from oxidizing inorganic substances

Heterotrophs: From organic molecules

• Photoheterotrophs – light as an energy source but obtain organic carbon made by other organisms

• Chemoheterotroph – both carbon atoms and energy from organic molecules

  • Humans are also an example.

Beneficial Prokaryotes

• Important for the carbon cycle.

• Medicine: Vaccines

• Important to the nitrogen cycle

• Many products are derived from prokaryotes: Wine, beer, cheese, etc.

• Genetic engineering: “Biofactories”

• Bioremediation: Able to remove pollutants from the atmosphere

February 13th Lecture Notes

Endosymbiosis

This is the idea that two organisms with a symbiotic relationship became one organism (mitochondria/chloroplast and cells)

The nuclear genome of a eukaryote is more closely related to archaea.

There are also more endosymbiosis events, other than the nucleus

Characteristics of a Eukaryotes

• Cells with nuclei surrounded by a nuclear envelope with nuclear pores

• Mitochondria

• Cytoskeleton of microtubules and microfilaments

• Flagella and cilia (if not currently, descended from an ancestor that did)

• Chromosomes organized by histones

• Mitosis

• Sexual reproduction by meiosis

• Cell walls (if not currently, descended from an ancestor that did)

Protists

Very diverse which makes classifying them very difficult.

• Can’t be classified as a plant: Gamites dry out

• Can’t be a fungus: They do not have chitin in their cell wall

• Can’t be classified as animals: they do not undergo embryonic stages.

Morphology

• Most are unicellular

• They vary in size from microscopic to hundreds of meters long.

• Some live in colonies/groups but others live like multicellular organisms

• Very high complexity and functionality

Metabolism

• Aerobic or anaerobic

• Photoautotrophs or heterotrophic

• Amoebas and some other heterotrophic protist species ingest particles by a process called phagocytosis

• Saprobes- heterotrophs that absorb nutrients from dead organisms or
  their organic wastes

• Mixotrophs- some protists can obtain nutrition by photoautotrophic or
  heterotrophic routes, depending on whether sunlight or organic nutrients
  are available.

Phagocytosis: (think of amoebas) Surrounding food and digesting and then releasing the food.

Transportation

Some have cilia that move them

Some use pseudopods

others use the flagella to swim

Life cycles

• Most are free living some are parasitic

• Asexual reproduction is common although sexual reproduction is possible and is associated with resistant cysts

  • Asexual reproductions result in offspring that are genetically identical to the parent

  • The downside to sexual reproduction is that only 50% of genetics get passed on. Another downside is finding a mate, no rizz :(. Less chance of less adaptive offspring.

  • How do you get genetic diversity?

    • Genetic mixing through crossing over during meiosis

  • Asexual reproduction is good in stable environments

  • Sexual reproduction is good in variable environments

February 17th Lecture Notes

Protists are very important to the environment as they produce oxygen.

• Many are symbionts: Think of coral

February 20th Lecture Notes

Most fungi are multicellular, and they all share their mode of nutrition: by eating dead organisms.

• most are saprobes, some are parasitic

The largest organism on earth is a fungus.

Animals and fungi are more related to one another than they are to plants.

Fungi do not photosynthesize and they do not have chloroplasts

Fungi

Thallus: The body of most fungi is multicellular mycelium

• consists of a vast network of threadlike hyphae

  • septate fungi have hyphae with cross walls

  • Nonseptate fungi are multicellular.

Cell walls have chitin and store glucose

Fungi can reproduce sexually and asexually.

February 22nd Lecture Notes

Symbiosis: Two organisms that live together (not mutualism)

Lichens

Symbiotic association between a fungus and a cyanobacterium or green algae

• Typically looks like fungus.

Fungi are important in nutrients cycling because they eat waste and dead things