AP Biology
Notes: Bacteria (structure)
Prokaryotes dominate the biosphere; they are the most numerous organisms and can be
 found in all habitats. Approximately 4000 species are currently recognizes, however, 
estimates of the actual diversity range from 400,000-4 million species. They are structurally 
and metabolically diverse.

Prokaryotes are smaller and lack membrane-bound organelles. Prokaryotes have cell 
walls but the composition and structure differ from those found in plants, fungi and protists. 
Prokaryotes also have simpler genomes. A small percentage can cause disease. Some are 
decomposers, key organisms in life-sustaining chemical cycles. Many form symbiotic 
relationships with other prokaryotes.

Bacteria and Archea

The traditional five-kingdom system recognizes one kingdom of prokaryotes (Monera) and
four kingdoms of eukaryotes (Protista, Plantae, Fungi, and Animalia). 

Archea: Believed to have evolved from the earliest cels. Inhabit extreme environments 
which may resemble the Earth's early habitats.

Bacteria: Considered the more "modern" prokaryotes, having evolved later in Earth's history. 
More numerous than Archaea. Differ from Archaea in structural, biochemical, and physiological
 characteristics.

A majority of prokaryotes are unicellular, although some aggregate into two-celled to
 several-celled groups. Others form true, permanent aggregates and some bacterial species
 have a simple multicellular form with a division of labor between specialized cells. Cells have 
a diversity of shapes, the most common being spheres (cocci), rods (bacilli), and helices
 (spirilla and spirochetes). One rod-shaped species measures 0.5 mm in length. Most have 
diameters of 1-5 microns.

A majority of prokaryotes have external cell walls that:
- maintain the cell shape
- protect the cell
- prevent the cell from bursting in a hypotonic environment
- differ in chemical composition and construction from the cell walls of protists, fungi, and plants

Peptidoglycan: modified sugar polymers cross-linked by short polypeptides. Exact
 composition varies among species. Some antibiotics work by preventing formation of the
 cross-links in peptidoglycan.

Gram-positive bacteria: have simple cell walls with large amounts of peptidoglycan, stain blue.

Gram-negative bacteria: have more complex cell walls with smaller amounts of peptidoglycan. 
Have an outer lipopolysaccharide-containing membrane that covers the cell wall. Stain pink.
 Are more often disease-causing (pathogenic) than gram-positive bacteria. Lipopolysaccharides 
are often toxic and the outer membrane helps protect these bacteria from host defense systems. 
They also impede entry of drugs into the cells, making gram-negative bacteria more resistant to
 antibiotics.

Many prokaryotes also secrete sticky, gelatinous substances that form a layer outside the cell 
wall called a capsule. Capsules also aid in adhesion to other cells (to form prokaryotic aggregates 
or facilitate attachment to host cells).

Motile bacteria use one of three mechanisms to move:

Flagella: Prokaryotic flagella differ from eukaryotic flagella in that they are:
- unique in structure and function; prokaryotic flagella lack the "9 + 2" microtubular 
   structure and rotate rather than whip back and forth like eukaryotic flagella
- not covered by an extension of the plasma membrane
- one-tenth the width of eukaryotic flagella

Filaments, composed of chains of the protein flagellin, are attached to another protein hook 
which is inserted into the basal apparatus. The basal apparatus consists of 35 different proteins.
 Their rotation is powered by the diffusion of protons into the cell. The proton gradient is maintained by an ATP-driven proton pump.

Prokaryotic movement is fairly random in homogenous environments but may become directional in a heterogenous environment. 

Taxis: Movement to or away from a stimulus. The stimulus can be light (phototaxis), a chemical
 (chemotaxis), or a magnetic field (magnetotaxis). Movement toward sa stimulus is a positive taxis
 while movement away from a stimulus is a negative taxis.

During taxis, bacteria moveby running and tumbling movements. It is caused by flagella moving
 coordinately about each other or in separate or randomized movements.

Prokaryotes lack the diverse internal membranes characteristic of eukaryotes. Some prokaryotes,
 however, do have specialized membranes, formed by invaginations of the plasma membranes. 
Infoldings of the plasma membrane function in the cellular respiration of aerobic bacteria. 
Cyanobacteria have thylakoid membranes that contain chlorophyll and function in photosynthesis.

Genophere: the bacterial chromosome, usually one double-stranded, circular DNA molecule. 
This DNA is concentrated in the nucleoid region, and is not surrounded by a membrane.
It also has very little protein associated with the DNA.

Plasmid: smaller rings of DNA having supplemental genes for functions such as antibiotic
 resistance or metabolism of unusual nutrients. Replicate independently of the genophore; 
can be transferred between partners during conjugation.

Reproduction
Asexual:
Neither mitosis nor meiosis occur in the prokaryotes. Reproduction is asexual by 
binary fission. DNA synthesis is almost continuous.

Sexual:
Transformation: The process by which external DNA is incorporated by bacterial cells.

Conjugation: The direct transfer of genes from one bacterium to another.

Transduction: The transfer of genes between bacteria by viruses.

Generation time is usually one to three hours, although it can be 20 minutes in optimal environments. Competition in natural environments is reduced by the release of antibiotic chemicals which
 inhibit the growth of other species. Optimal growth requirements vary depending upon the species.

Endospore: resistant cell formed by some bacteria. It contains one chromosome copy 
surrounded by a thick wall. When endospores form, the original cell replicates its chromosome 
and surrounds one copy with a durable wall. The original surrounding cell disintegrates, releasing 
the resistant endospore. Since some endospores can survive boiling water for a short time, 
home canners and food canning industry must take special precautions to kill endospores of dangerous bacteria. They may remain dormant for many years until proper environmental conditions return.