Universal Features

Central Dogma of Life Excluding retroviruses

DNA -> RNA -> Proteins

Universal Structure and Processes

Cell Membranes

DNA structure and replication

RNA Synthesis (A,C,G,U)

RNA Polymerase

Ribosomes for translation

Metabolic pathways

Universal genetic code (codons/amino acids)

Prokaryotes

Heterotrophs

Gets nutrients elsewhere.

Doesn't make food themselves.

Prokaryotes Bacteria and Archaea

Have a single circular double stranded DNA.

Replicate by binary fission, not mitosis.

They move around by spinning a flagella like a propeller.

• Flagella are made from flagellin proteins

• The flagellin proteins are outside the cell membrane.

No organelles.

Carry plasmids

Extra little pieces of DNA.

Independent tiny circles of DNA.

Can carry antibiotic resistance genes.

Horizontal Gene Transfer Lateral Gene Transfer

Can occur in more complex organisms such as aphids absorbing bits of fungi.

Conjugation

"Bacterial Sex" via plasmids.

Transformation

Uptakes/absorbs environmental/external DNA bits.

Transduction

Phage virus-mediated transfer of genomic bits.

Endosymbiotic Theory

Chloroplasts in plants came from engulfing cyanobacteria and not killing it.

Mitochondria came from engulfing proteobacteria and not killing it.

Bacteria

Gram Stains

Bacteria have peptidoglycan, eukaryotes don't.

Detects the presence of an outer layer of peptidoglycan.

Gram Positive

One cell wall with large peptidoglycan layer outside.

Gram Negative

Two cell walls with small peptidoglycan layer in-between.

Antibiotics

Inhibit the ribosomes in bacterial cells.

These selectively target bacteria and don't kill archaea or eukaryotes.

Common Phyla

Actinobacteria

Antibiotics were first discovered as natural weapons in actinobacteria against other bacterias.

Cyanobacteria

First cells to photosynthesis sunlight -> O2.

Bacterial Shapes

Bacteria Shapes

Rod-shaped

Spherical

Spiral

Locations

• Different bacteria grow in different environments.
• Such as oxygen environments (aerobic/anerobic).

Bacteria can communicate via pheromones. Can trigger bioluminescence among colonies.

Bacterial Colonies

Archaea

Archaea

Have no peptidoglycan.

Extremophiles

Hyperthermophiles

Hadobacteria

Thermophiles

Cell Specialization

Fixation

Taking inorganic compounds and combining it with molecules into organic compounds.

Metagenomics

We sample DNA from the environment and identify organisms by DNA sequencing.

Cell Types

Spores

Hearty cells survive harsh conditions, can reactivate later to reproduce.

Heterocysts

For nitrogen fixation.

Vegetative Cells

For carbon fixation, photosynthesis.

Pathogens

Pathogens

Can outcompete and outgrow, causing illness.

Common Pathogens

• Chlamydias
• Spirochetes
• Proteobacteria

How to Identity a Pathogen

_Koch's Postulates

• Is present in every case of the disease.
• Organism must be cultured from the sick patient.
• Bacteria must be able to induce the disease.
• Bacteria must be recoverable from newly infected individuals.

Study Guide

• What are some common, universal, conserved processes and/or structures in ALL cellular life?
  • DNA -> RNA -> Protein synthesis. DNA is universal in call life.
• What are the three big domains of life?
  • Archaea, prokaryotes, and eukaryotes.
• Which domain is more closely related to us? Which is/are prokaryotic; which is/are eukaryotic?
  • Archaea are most closely related to us. Archaea and prokaryotes are prokaryotic.
• What are the kingdoms of life? Which kingdom is most closely related to us?
  • Animals, plants, fungi, protozoa, bacteria, archaea. Fungi is most closely related to us.
• Name characteristics of prokaryotes that makes them different from our cells (eukaryote cells).
  • They have circular DNA and their flagella, if they have one, is located outside the cell membrane.
• What are plasmids? Why are they important?
  • Tiny circles of DNA that are easily transferrable among prokaryotes.
• Name at least two reasons why bacterial cells seem less closely related to eukaryotic cells (our cells) than archaeal cells.
  • They have peptidoglycan and they are susceptible to antibiotics.
• What is the basis for classifying bacteria into Gram +/- strains?
  • If peptidoglycan exists outside the cell wall, then it's gram+.
  • If peptidoglycan is sandwiched between two cell walls, and can't be stained, then it's gram-.
• What is a common cellular target for many common antibiotics/medicines for infections?
  • Ribosomal production in prokaryotes.
• Why are there horizontal lines crisscrossing the phylogenetic tree, between the three domains of life? What two processes does that depict/show? What data supports this?
  • That's the endosymbiotic theory, horizontal gene transfer, how we acquired mitochondria and chloroplasts.
• Describe 3 ways genes commonly shared, or new genes acquired, in prokaryotes.
  • Bacterial sex, phage-virus mediated, picking them up from their environment.
• How do horizontal gene transfers (HGT) complicate phylogeny? How do we overcome that to study microbial species relationships and understand cellular evolution?
  • It makes it so there's not a linear relationship back to a shared root. We look at multiple genes.
• Describe the HGT phenomenon in aphids.
  • Aphids picked up carotenoid production from fungi of the plants they feast on.
• What steps would be required for Archaea cells to give rise to Eukaryotes?
  • They would have to become multicellular.
• Why are archaeal microbes cells less understood than bacterial microbes? How can we study more Archaea species?
  • They live in extreme environments. By accurately reproducing their environment and food sources.
• What is a "mixed microbial community" and name an example in:
  • A diverse collection of microbes living in a shared space.
  • aquatic environments
    • Tide pools
  • terrestrial environments
    • Hot springs
  • a healthy human
    • The gut lining.
  • an unhealthy human
    • An open wound.
  • plants
    • On their leafs/flowers
  • animals
    • Their anus
• What conditions are different between the skin and intestine/gut habitats in humans? Does that affect whether bacteria or archaea live there? Does it affect the species present?
  • The gut has little to no oxygen, so only certain types of bacteria can live there. The skin is oxygen-rich and has a different variety of species present. Archaea prefer to live in extreme environments, maybe your low pH stomach.
• How is human (or other animals, or plants) colonization with prokaryotes advantageous?
  • They help aid in digestion and metabolize nutrients in the gut. Takes some the burden off our own bodies.
• How do Prokaryotes move? What type of motion do they undergo? What are prokaryotic flagella structurally made of?
  • They use move their flagella in circular, propeller, motions to move.
  • The flagella is made from flagellin protein and is outside the cell membrane.
• Why do we say that Hadobacteria and Hyperthermophilic bacteria are similar, and likely closely related to the first ancient cells on Earth? What was ancient Earth's environment like?
• Why are Actinobacteria interesting? What do they produce? What can they cause?
  • They naturally produce antibiotic compounds that we have replicated and now use as our antibiotic medicine.
• Staphylococcus epidermidis is a common skin bacterium that lives with us. A related bacterium, Staphylococcus aureus (textbook Fig. 18.6), is usually harmless but can become an opportunistic pathogen and can be resistant to antibiotics. MRSA is a pathogenic S. aureus variant, sometimes called “flesh-eating bacteria.”
  • What does MRSA stand for?
    • Methicillin resistant Staphylococcus aureus
  • What is methicillin?
    • An antibiotic
• Why are Cyanobacteria significant regarding photosynthesis?
  • They were first to perform photosynthesis and eukaryotic cells absorbed (horizontal gene transfer; endosymbiotic theory) them to gain photosynthetic abilities.
• In filamentous colonial-type Cyanobacteria:
  • In what different forms do they exist?
    • Rods, spheres, and spirals? Or colonies
  • What three types of cells exist, and what is the function of each?
    • Vegetative: carbon fixation
    • Spores: survive harsh conditions.
    • Heterocysts: nitrogen fixation
• What does "fixation" mean, as in Carbon or Nitrogen fixation?
  • Taking molecules from the environment, such as nitrogen or carbon, and turning those into organic compounds.
• Why are proteobacteria important evolutionarily?
  • They are great and producing energy and eukaryotic cells absorbed (horizontal gene transfer; endosymbiotic theory) them to gain ATP production.
• Why do we call archaea “extremophiles”?
  • They evolved to live in very harsh conditions such as in hot springs.
• What are some common pathogenic bacteria?
  • Proteobacteria,
• What pathogen is related to Vibrio fischeri? Why is V. fischeri interesting to study as a model organism?
• Which Archaea phylum is thought to be most closely related to Eukaryotes? What is the sister phylum for Eukarya in the phylogenetic tree?
• Name some famous places with Archaea extremophiles.
  • Old faithful, great salt lake.
• Based on oxygen need/usage, how does that impact our human relationship with prokaryotes? Which are non-pathogenic?
• Are most bacteria pathogens? How do we define pathogens?
  • No, we just study mostly pathogens. Pathogens are microbes that cause us illness, using Koch's Postulates.