Sunday, June 17, 2012

Biological Sciences 4 (Microbiology: Fungi, Virus, Bacteria))


Day 7: 

Fungi, virus, archea and bacteria.

A. Fungi
Fungi have cell walls like plants, but have multiple nuclei. 

Made of hyphae filaments (a mass of these is called mycelium).
Lichens = fungi + algae (algae provide food, fungi provide water and protection).
Mycorrhizae = fungi + plant roots. Fungi add more surface area for absorption.

1. General Characteristics
Cell wall made of chitin. Use glucose for energy, heterotrophic (parasites or saprosites). Convert sugar into alcohol and release CO2. Yeast, molds, mushrooms.

2. General Aspects of Life Cycle
Sexual or asexual. Reproduced with spores or mycelial fragmentation. Most fungi have both haploid and diploid stage.

B. Virus Structure
May have spikes, has a protein coat, nucleic acid on the inside.

1. General Structural Characteristics (Nucleic Acid and Protein, Enveloped and Nonenveloped)
Viruses have nucleic acid (DNA or RNA) inside a protein coat. Nucleic acid can be single or double stranded. A virus may have a host's cell membrane providing an envelope (lysogenic cycle). A virus without an envelope cause the host cell to burst and release viral particles like a spider egg sac hatching (lytic cycle).

2. Lack of Organelles and Nucleus
Viruses are much too small to contain organelles and nuclei.

3. Structural Aspects of Typical Bacteriophage
Bacteriophages posses a horn (labeled as tube in the above picture) they use to spear bacterial cells. They posses a head encasing nucleotides, a tail end (to attach to bacteria) and a sheath (where the horn/tube is stored).

4. Genomic Content (RNA or DNA)
Virus may have RNA or DNA. Either nucleotide sequence may be double or single. Viruses come in vanilla, chocolate, or double scoop of vanilla, or double scoop of chocolate. 

If the virus changes from RNA to DNA in the host, it is a retrovirus.

5. Size Relative to Bacteria and Eukaryotic Cells
Viruses are much smaller then bacteria and eukaryotic cells. 

Viruses are 100 times smaller then bacteria and 1000 times smaller then eukaryotic cells.

C. Viral Life Cycle
Virus can not reproduce without a host cell. The host cell copies the genetic information of the virus. 

1. Self-Replicating Biological Units that Must Reproduce within Specific Host Cell
The host cell's ribosomes make the protein coat and polymerases that replicate the viral genetic material. 

Retroviruses have reverse polymerase to convert RNA to DNA, within the cell.

2. Generalized Phage and Animal Virus Life Cycles
Finds a host, attaches to the host using tail or spikes, inserts genetic material, replicates inside the host.

A. Attachment to Host Cell, Penetration of Cell Membrane or Cell Wall, Entry of Viral Material
Virus use spikes, sticky protrusions or tails to attach to a host cell. Penetration of the cell membrane is facilitated by enzymes. Entry of viral material is facilitated by a tube.

B. Use of Host Synthetic Mechanisms to Replicate Viral Components
Ribosomes of the host cell synthesize enzymes. The host's ATP is used for energy. The nucleotides and amnio acids come from the host as well. Virus says "I ate the rest of your amino acids and nucleotides, thanks for letting me use your ribosomes. By the way you are out of ATP in the guest bathroom."

C. Self-Assembly and Release of New Viral Particles
The coat proteins and viral genetic material assembles itself prior to lysis.

3. Retrovirus Life Cycle, Integration into Host DNA, Reverse Transcriptase
Similar to other viruses, retroviruses enter a host, then however, the retrovirus converts its RNA into double-stranded DNA, then integrase adds the viral DNA into the host genome randomly, as the host replicates the viral DNA does also.

4. Transduction, Transfer of Genetic Material by Viruses
Virus sometimes move DNA by accident, small fragments get packed into virus progeny by accident and it travels to new host cells with the virus, where the DNA may find its homologous counterpart and crossover.

D. Prokaryotic Cell: Bacteria Structure
Prokaryots are mostly bacteria, which contain DNA within cell walls, but lack membrane bound organelle.

1. Lack of Nuclear Membrane and Mitotic Apparatus
The nucleus is not bound by a membrane, it is lumped together in the nucleoid region. The bacterial cytoskeleton pulls the DNA apart, so there are no mitotic apparatuses. 

2. Lack of Typical Eukaryotic Organelles
Processes take place in the cell cytoplasm, as membrane bound organelles are absent.

3. Major Classifications: Bacilli (Rod-Shaped), Spirilli (Spiral-Shaped), Cocci (Spherical); Eubacteria, Archaebacteria
Bacilli include Bacillus anthracis and E. coli, spirili include Borrelia burgdorferi (Lyme disease), Cocci include Streptococcus pharyngitis (strep throat), Eubacteria includes Chlamydia trachomatis (the most popular STD in America), Archaebacteria can be square shaped such as Haloquadratum walsbyi.

4. Presence of Cell Wall
Mycoplasm do not have cell walls. All other bacteria have cell walls made of peptidoglycan, a polysaccharide-protein molecule.

5. Flagellar Propulsion
Bacteria flagellas are made of flagellin (not microtubules). Rotation occurs at the base of the flagella powered by a proton or sodium gradient (not ATP).

E. Prokaryotic Cell: Growth and Physiology
Bacteria grow on every surface and in every climate on Earth. High genetic variance allows bacteria to survive and adapt. Bacteria is only limited by competition of other bacteria for food and space.

1. Reproduction by Fission
Bacteria duplicate themselves. DNA is copied and attaches to the cell membrane, as the cell membrane expands the DNA is separated, cytokinesis occurs dividing the daughter cells.

2. High Degree of Genetic Adaptability, Acquisition of Antibiotic Resistance
Natural mutation occurs (sometimes resulting in antibiotic resistance), transformation due to adding plasmids into the genome occurs, transduction due to bacteriophages adding viral DNA into the genome occurs, and conjugation between bacteria occurs (often causing antibiotic resistance).

3. Exponential Growth
When no crowding, waste or lack of food is involved bacterial growth is exponential, because of the binary fission process.

4. Existence of Anaerobic and Aerobic Variants
To occupy each available niche, some bacteria grow in low oxygen (obligate anaerobe), high oxygen (obligate aerobe) or either condition (facultative anaerobe).

F. Prokaryotic Cell: Genetics
Bacteria can pick up DNA from the environment.

1. Existence of Plasmids, Extragenomic DNA, Transfer by Conjugation
Plasmids are inherited double stranded DNA, a plasmid can exist and replicate independently of the main genome or as a part of it. Plasmids are extra, not essential. Conjugation is transfer of genetic material through a sex pillus. Genetic material may include geonome DNA.

2. Transformation (Incorporation into Bacterial Genome of DNA Fragments from External Medium)
Bacteria can pick up new DNA, when they die they leave the DNA around, other bacteria can uptake the DNA and use it, this gives resistant bacteria the ability to make non-resistant bacteria resistant. MRSA, VRE ext.

3. Regulation of Gene Expression, Coupling of Transcription and Translation

  • Gene expression is regulated predominately at transcription: Operons (activator and inhibitors) modulate which genes are actively transcribed.
  • Gene expression is regulated at translation: some mRNA gets translated more (due to better Shine-Dalgarno sequences).
  • Transcription-translation coupling: translation occurs at the same time as the mRNA is being transcribed. Regulation by attenuation can occur for the Trp gene (when cell is full of Trp, translation occurs quickly and more Trp is not transcribed), which affects ribosome speed.

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