Microbiology

Fungi

  • General characteristics
    • Made of hyphae filaments.
    • Parasitic hyphae = haustoria
    • A mass of hyphae is called mycelium.
    • Have cell wall made of chitin.
    • All fungi are heterotrophs - they are either parasites or saprobes.
    • Lichens = fungi + algae. Algae provides food, fungi provides water and protection.
    • Mycorrhizae = fungi + plant roots. Plant provides food, fungi provides more absorption surface area.
    • Yeast, molds, mushrooms are all fungi.
  • General aspects of life cycle
    • Can be sexual or asexual.
    • Reproduces via spores or mycelial fragmentation.
    • Most fungi have both a haploid and a diploid stage of life cycle.

Virus structure

  • General structural characteristics (nucleic acid and protein, enveloped and nonenveloped)
    • Nucleic acid can be DNA or RNA, single stranded or double stranded.
    • Protein coat covers the nucleic acid.
    • Some viruses have an envelope derived from the host's cell membrane, while others lack it (nonenveloped).
      • Enveloped viruses bud off the host's membrane.
      • Nonenveloped viruses cause the host to burst to release viral particles.
    • Smaller than bacteria.
  • Lack organelles, nucleus: Viruses don't have any organelles or a nucleus. The genetic material is simply packed inside a protein coat.
  • Structural aspects of typical bacteriophage
    • bacteriophage
    • Head stores genetic material.
    • Sheath provides a passage way for genetic material to be injected into the host bacteria.
    • Tail fibers attach to the host bacteria.
  • Genomic content RNA or DNA: Viruses can contain either RNA or DNA as their genomic content. Out of the RNA viruses, those that convert their genome into DNA inside their host are called retroviruses.
  • Size relative to bacteria and eukaryotic cells: Viruses are roughly 100 times smaller than bacteria, and 1000 times smaller than eukaryotic cells.

Viral life cycle

  • Self-replicating biological units that must reproduce within specific host cell: Viruses can not replicate by themselves. They depend on the host's replication organelles to replicate. The host's ribosomes will make the necessary protein coats and polymerases that replicate the viral genetic material. Retroviruses contain their own reverse polymerase to convert RNA to DNA before the host's polymerases take over.
  • Generalized phage and animal virus life cycles:
    • attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic material
    • use of host synthetic mechanism to replicate viral components: Host's ribosomes synthesize the necessary enzymes. Host's ATP provides necessary energy. The host also provides the raw materials such as nucleotides and amino acids.
    • self-assembly and release of new viral particles: The coat proteins and viral genetic material will assemble into viral particles all by themselves.
  • Retrovirus life cycle: integration into host DNA
    • First, retrovirus enters the host.
    • The viral reverse transcriptase then converts the viral RNA genome into double-stranded DNA.
    • A virally encoded enzyme called integrase adds in the viral DNA into the host's genome at a random place.
    • When the host replicates, the viral DNA gets replicated also.
  • Transduction: transfer of genetic material by viruses
    1. Virus infects cell: host DNA degraded into fragments, viral DNA takes over control.
    2. Host DNA fragment gets packed into virus progeny by accident.
    3. Virus progeny infects another cell, injects previous host's DNA fragment.
    4. Fragment enters cell, find its homologous counterpart, and crossover.

Prokaryotic cell: structure, bacteria

  • Lack of nuclear membrane, mitotic apparatus: Bacteria do not have a membrane-enclosed nucleus. Their genetic material is located in an irregular region called the nucleoid. Bacteria do not have spindles and asters that make up the eukaryotic mitotic apparatus. Instead, the prokaryotic cytoskeleton helps pull the replicated DNA apart.
  • Lack of typical eukaryotic organelles: Bacteria don't have Golgi, ER, mitochondria, chloroplasts.
  • Major classifications of bacteria by shape: bacilli (rod-shaped); spirilli (spiral shaped); cocci (spherical); eubacteria; archaea
    • Eubacteria are the bacteria we encounter every day, while Archaea are the prokaryotes that inhabit extreme environments (high salt, temperature, or chemicals).
  • Presence of cell wall in bacteria: bacterial cell wall is made of peptidoglycan, a polysaccharide-protein molecule. In contrast, plant cell wall is made of cellulose and fungi cell wall is made of chitin.
  • Flagellar propulsion, mechanism
    • Bacterial flagella is made of flagellin. In contrast, eukaryotic flagella is made of microtubules.
    • The mechanism of the bacterial flagella is rotation. A rotor at the base of the flagella drives the rotation, powered by a proton or sodium gradient. (Compare this to eukaryotic flagella, which is powered directly by ATP)

Prokaryotic cell: growth and physiology

  • Reproduction by fission
    • DNA replicates
    • Replicated DNAs separate by attaching to the cell membrane as the cell elongates (in contrast to mitosis, no spindle fibers needed).
    • Cytokinesis divides the parent cell into two daughter cells.
  • High degree of genetic adaptability, acquisition of antibiotic resistance
    • Mutation
    • Transformation: bacteria take in plasmids and DNA fragments and integrates them into the genome.
    • Transduction: bacteriophages undergoing lysogenic life cycle incorporate the viral DNA into the bacterial genome.
    • Conjugation: Bacteria transfer DNA between one another through the sex pilus.
  • Exponential growth: Bacterial growth starts off being exponential because of the nature of binary fission. Later, when food becomes short, and it gets crowded, growth slows and eventually plateaus.
  • Existence of anaerobic and aerobic variants
    • Obligate aerobe = must have oxygen for growth.
    • Obligate anaerobe = dies when oxygen is present.
    • Facultative anaerobe = doesn't need oxygen for growth, but grows better with oxygen.
  • Symbiotic relationships
    • Parasitic = bacteria benefits at the expense of the host. Disease causing bacteria are examples of parasitic relationships.
    • Mutualistic = both bacteria and host benefits. For example, the E. Coli in your gut; the natural flora on your skin.
    • Commensalistic = one benefits while the other has no effect.

Prokaryotic cell: genetics

  • Existence of plasmids, extragenomic DNA, transfer by conjugation
    • Plasmids are double stranded DNA.
    • A plasmid can exist and replicate independently of the genomic DNA, or be integrated into it.
    • Plasmids are inherited.
    • Plasmids are not essential for growth and reproduction in the wild.
    • Conjugation transfers genetic material between bacteria via a pillus.
      • A bacteria able to make the pillus (F+) has a plasmid that contains the pillus genes.
      • F+ bacteria can transfer the plasmid to an F- bacteria.
      • Conjugation can also transfer some genomic DNA (because F+ plasmid can integrate into the chromosome).
  • Transformation: incorporation into bacterial genome of DNA fragments from external medium
    • When a bacteria dies, it lyses and spills many DNA fragments into the environment.
    • Another bacteria encounters these DNA fragments, takes them in, and integrates them into its own genome.
    • If the DNA fragments contained an antibiotic resistant gene, then the transformation just made the bacteria antibiotic resistant.
  • Regulation of gene expression, coupling of transcription and translation
    • Regulation at the transcription level: some genes are actively transcribed, while others are not. Activaters and inhibitors modulate the transcription of a gene.
    • Regulation at the translation level: Some mRNA gets translated more. In prokaryotes, mRNAs with better Shine-Dalgarno sequence are translated more. In eukaryotes, translation regulation can involve adding more polyAs to mRNA (longer mRNA life time), modulating the translation machinery (phosphorylation of initiation factors), or storing mRNAs to be translated at a later time (mRNA masking).
    • Prokaryotes regulate gene expression predominantly at the transcription level (eg. Operons, in which inducers increase transcription, and inhibitors decrease transcription). Eukaryotes have more regulation at other levels, and can also undergo RNA splicing, which can splice RNA in different ways to make different mRNAs.
    • For more eukaryotic gene regulation, click here
    • Transcription-translation coupling: in prokaryotes, translation occurs as the mRNA is being transcribed (no RNA processing in prokaryotes).
    • In a coupled transcription-translation system, regulation by attenuation can occur for the Trp gene:
      • When cell is full of Trp, translation occurs fast because of abundant Trp amino acid. This fast ribosome movement across the transcribing mRNA causes the Trp mRNA transcription to terminate. Because Trp is not needed.
      • When cell is starved of Trp, translation occurs slower because Trp amino acid is lacking. This slower ribosome movement across the transcribing mRNA causes the Trp mRNA to be made to its completion.