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Both chapters provide a deep dive into the other organisms that aren't…

- - - - An infectious particle consisting of genes packaged in a protein coat
      - Types
        
        Capsid Shapes
        
        Helical Viruses
        
        These have rod-shaped capsids
        
        Icosahedral Viruses
        
        These have polyhedral capsids with 20 triangular facets
        
        Complex Viruses
        
        Bacteriophages
        
        These have complex structures with an icosahedral head and a tail apparatus
        
        Enveloped Viruses
        
        A membranous envelope derived from the host cell, containing viral glycoproteins
    - - Viral Genomes
        
        May consist of:
        
        Double-stranded DNA
        
        Single-stranded RNA
        
        Double-stranded RNA
        
        Single-stranded DNA
        
        Viruses are classified as DNA viruses or RNA viruses
        
        Retrovirus
        
        A unique class of RNA animal viruses known for their complex replication cycles
        
        They possess an enzyme called reverse transcriptase, which allows them to transcribe their RNA into DNA
        
        Viruses can have both linear and/or circular DNA
      - Capsids and Envelopes
        
        Capsid
        
        The protein shell that encloses a viral genome
        
        May be rod-shaped, polyhedral, or more complex in shape
        
        Built from protein subunits called capsomeres
        
        Viral Envelopes
        
        A membrane, derived from membranes of the host cell, that cloaks the capsid, which in turn encloses a viral genome
        
        Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell
        
        Bacteriophages (Phages)
        
        Viruses that infect bacteria
  - - - A type of phage replicative cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage
        
        It is replicated along with the chromosome and does not kill the host
      - Steps
        
        Integration
        
        After a phage injects its DNA into a bacterial cell, the DNA circularizes and integrates into the bacterial chromosome
        
        Replication
        
        The prophage is replicated along with the host's DNA during cell division
        
        This causes for the passing of the viral DNA to daughter cells
        
        Dormancy
        
        The prophage remains dormant
        
        It will remain dormant until an environmental trigger induces it to exit the chromosome
        
        Switch to Lytic Cycle
        
        Once induced, the prophage can initiate the Lytic Cycle
        
        This leads to the production of new phages and eventual lysis of the host cell
    - - A type of phage replicative cycle resulting in the release of new phages by lysis (and death) of the host cell
        
        Ultimately results in the destruction of the host cell
      - Virulent Phage
        
        A phage that replicates only by a lytic cycle
        
        Ex: T4 Bacteriophage (infects E. coli bacteria)
      - Steps
        
        Attachment
        
        The phage attaches to the surface of a bacterial cell
        
        Using its tail fibers to bind to specific receptors
        
        Entry and Degradation
        
        The phage injects its DNA into the host cell
        
        This leads to the degradation of the host's DNA
        
        Synthesis
        
        The phage DNA takes over the host's cellular machinery to produce phage proteins and replicate its genome
        
        Self-Assembly
        
        New phage particles are assembled from the synthesized components
        
        Release
        
        The host cell bursts (lyses), releasing 100 to 200 new phage particles
        
        They can then infect other cells
    - - Temperate Phages
        
        A phage that is capable of replicating by either a Lytic or Lysogenic Cycle
        
        Ex: Lambda Phage
        
        Lytic Cycle
        
        The phage injects its DNA into the host, leading to the production of new phages and eventual lysis (destruction) of the host cell to release the progeny
        
        Lysogenic Cycle
        
        The phage DNA integrates into the bacterial chromosome, becoming a prophage
        
        This allows the phage DNA to be replicated along with the host's DNA without killing the host cell
        
        The prophage can later exit the host genome and enter the lytic cycle under certain conditions
      - Prophage
        
        A phage genome that has been inserted into a specific site on a bacterial chromosome
  - - - Bacteria
        
        Restriction Enzymes
        
        Specialized proteins found in bacteria that serve as a defense mechanism against foreign DNA
        
        CRISPR-Cas System
        
        A sophisticated defense mechanism found in bacteria and archaea, acting like an immune system to protect against viral infections, particularly from bacteriophages
        
        CRISPR System
        
        DNA sequences in the bacterial genome that contain short, repetitive palindromic sequences interspersed with "spacer" DNA
        
        The spacer DNA corresponds to fragments of DNA from past viral infections
        
        Cas Proteins
        
        These are CRISPR-associated proteins that work with the CRISPR sequences
        
        When a bacterium is infected by a phage, the CRISPR region is transcribed into RNA, which is then processed into short RNA strands
        
        The short RNA strands bind to Cas proteins, forming a complex; this complex uses the RNA as a guide to identify and cut the DNA of the invading phage
      - Vaccines
        
        A harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
        
        Epidemic
        
        A widespread outbreak in a certain region or country
        
        Pandemic
        
        A global outbreak
    - - An infectious agent that is a misfolded version of a normal cellular protein
      - Can be transmitted in food, act slowly, and are virtually indestructible
      - Ex: Mad Cows Disease
    - - Horizontal Transmission
        
        Enter through damaged cell walls
      - Vertical Transmission
        
        Inherited the virus from a parent
- - - - Coccus
        
        A spherical-shaped bacterium
      - Bacillus
        
        A genus of rod-shaped, gram-positive bacteria
      - Spirillum
        
        A bacteria characterized by its spiral shape
      - Terminology
        
        Staph
        
        Cluster of groups
        
        Strept
        
        Chains
    - - Cell Wall
        
        Maintains the shape, protects the cell, and prevents bursting in a hypotonic environment
        
        Peptidoglycan
        
        A type of polymer in bacterial cell walls consisting of modified sugars cross-linked by short polypeptides
        
        The bacterial cell wall contains peptidoglycan
        
        Gram Stain
        
        A staining method that distinguishes between two different kinds of bacterial cell walls
        
        Gram-Positive
        
        Stains purple
        
        Has more peptidoglycan
        
        Can have a capsule
        
        Gram-Negative
        
        Stains Pink
        
        Has less peptidoglycan
        
        Has an outer membrane
        
        Impedes the use of antibodies
        
        Can have a capsule
        
        Archaeal walls contain a variety of polysaccharides and proteins, but lack peptidoglycan
      - Capsule
        
        A dense and well-defined layer of polysaccharide or protein that surrounds the cell wall and is sticky
        
        Slime Layer
        
        A not well organized capsule
        
        Protects against dehydration, and some capsules shield pathogenic prokaryotes from attacks by their host’s immune system
      - Endospores
        
        A thick-coated, resistant cell produced by some bacterial cells when they are exposed to harsh conditions
        
        Some bacteria from metabolically inactive endospores when water or nutrients are lacking
    - - Pili
        
        Also called a sex pilus or conjugation pilus
        
        In bacteria, a structure that links one cell to another at the start of conjugation
      - Fimbriae
        
        A short, hairlike appendage of a prokaryotic cell that helps it adhere to the substrate or to other cells
      - Flagella are the most common structures used by prokaryotes for movements
        
        Flagella
        
        Long, whip-like appendages that enable cellular movement
        
        Can have more than one
      - About half of all prokaryotes exhibit taxis
        
        Taxis
        
        The ability to move toward or away from a stimulus
    - - Membrane folding in bacteria is to compact space and to increase surface area
      - Bacteria has circular chromosomes, plasmids, and nucleoid region
  - - - Prokaryotes reproduce quickly by binary fission and can divide every 1-3 hours under optimal conditions
        
        Binary Fission
        
        A method of asexual reproduction
        
        The cell grows to roughly double its size; the DNA of the bacterial chromosome, which is circular, begins to replicate at a specific site called the origin of replication
        
        As replication proceeds, the origins move to opposite ends of the cell; the cell elongates, and once replication is complete, proteins cause the plasma membrane to pinch inward, dividing the cell into two daughter cells, each with a complete genome
      - Key Features of Prokaryotes
        
        They're small
        
        They reproduce by binary fission
        
        They have short generation times
      - F Factor
        
        Plasmid
        
        Cells containing the F Plasmid (F+ Cells) function as DNA Donors
        
        F Plasmid
        
        A form of the F factor, a piece of DNA that enables bacteria to form pili and transfer DNA during conjugation
        
        An F+ Cell can convert an F- Cell to an F+ Cell if it transfers an entire F Plasmid to the F- Cell
        
        If only part of the F Plasmid's DNA is transferred, the recipient cell will be recombinant
        
        Cells lacking the F Factor (F- Cells) are recipients
        
        Chromosome
        
        Hfr cells, named for high frequency of recombination
      - R Plasmids
        
        Antibodies kill most bacteria, but not those with R Plasmids, plasmids that carry resistance genes
        
        R Plasmids
        
        A type of bacterial plasmid that carry genes conferring resistance to antibiotics, such as tetracycline or ampicillin
    - - Role of Oxygen
        
        Obligate Aerobes
        
        Requires O2 for cellular respiration
        
        Obligate Anaerobes
        
        Poisoned by O2 and live by fermentation or use substances other than O2 for anaerobic respiration
        
        Facultative Anaerobes
        
        Use O2 if it is present or carry out fermentation or anaerobic respiration it not
      - Nitrogen
        
        Some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3) in a process called nitrogen fixation
        
        Nitrogen Fixation
        
        A biological process where atmospheric nitrogen (N₂) is converted into ammonia (NH₃), making nitrogen accessible to plants
      - Cooperation
        
        Prokaryotes may cooperate to use resources unavailable to individual cells
        
        Nitrogen-fixation is isolated in cells called heterocysts that prevent oxygen penetration
        
        Heterocysts
        
        Specialized cells found in some filamentous cyanobacteria
        
        These cells are crucial for nitrogen fixation, a process that converts atmospheric nitrogen into a form usable by plants and other organisms
        
        Photosynthetic cells exchange carbohydrates for the fixed nitrogen produced by the heterocysts