• These are commensal or mutualistic segments of DNA found in bacteria that float separately from the chromosome and are not needed for basic maintenance of the bacterial cell.
• Plasmids cannot survive or replicate without their bacterial host.
• Plasmids may not be essential to host survival, but they can confer some real advantages, such as resistance to antibiotics, promoting bacterial genetic transfer, the ability to manufacture toxins
  • exotoxins - secreted into the medium
  • endotoxins - bound to the plasma membrane of the bacterium
  ...etc.
• Plasmids may also sometimes be found in eukaryotic cells--usually plants and fungi.
• The fact that they are usually found in mitochondria and chloroplasts harkens back to the Endosymbiont Model of Eukaryote Evolution!
• No eukaryotic plasmids are known to benefit the host cell, and some are pathogenic.
• Plasmid DNA is generally small, ranging from less than 10 kb to slightly more than 100.

• This is found in mitochondria (mtDNA) and chloroplasts (cpDNA).
• In any given cell, these organelles are usually (though not always) genetically identical.
• Organelle DNA is primarily there to govern the function of the organelles themselves.
• The organelle genome usually encodes the enzymes necessary for the energy transducing reactions (cellular respiration or photosynthesis) taking place in the organelle.
• Because they are intimately involved in energy transduction, mtDNA and cpDNA can have profound effects if they mutate. Errors in mtDNA, for example, can result in mitochondrial myopathies which cause profound muscle weakness and other problems.
• These are almost always maternally inherited. ("Eve's DNA")
• Nuclear DNA also participates in manufacturing enzymes for organelle function; the organelles cannot function without nuclear DNA.
• However, the genes in the nucleus and the genes in the organelles are different from one another. There is NO OVERLAP and NO DUPLICATION.

• Viruses are non-living particles consisting of DNA or RNA in a sometimes-ornate protein capsule.
• They cannot replicate without commandeering the cellular machinery of a live host cell.
  (Viruses that infect bacteria to do this are called bacteriophages.)
• Viral genomes may be double stranded DNA, single stranded DNA or RNA (retroviruses). (Living cells always have double-stranded DNA.)
• When infective, the viral genome may either be incorporated into a host's chromosome or it may form a bit of DNA separate from the host's chromosome.
• Before it can be replicated or used to make viral proteins, the viral DNA is converted to double-stranded DNA like that of the host.

• These are the genomes of the true bacteria, and usually (not always) they are present as a single, circular chromosome.
• The single chromosome is located in a large central area called the nucleoid (or nucleoid region). This is held together in a live bacterium, but falls apart when the bacterium is lysed (to yield a great, big string of DNA). (See the dramatic figure in your text)
• Introns and exons exist in prokaryotes, but are very rare.
• Some bacterial genes code for proteins that are all used in the same function or process. Such genes are often located adjacent to each other on the chromosome, and are always transcribed together as a single mRNA that can be used for translation of all the proteins needed for that function or process.. The entire functional group of genes is called an OPERON.
• Operons are uncommon in eukaryotes (at least as far as we know).
• The bacterial chromosome has a few associated proteins, but their function has not been completely elucidated. (They might be involved in formation of the nucleoid).

• These are the chromosomes enclosed in the eukaryotic nucleus.
• Diploid (2n) cells contain two copies of the genome. Haploid (n) cells contain only one copy.
• n = the number of chromosomes in one complete copy of the genome.
• HOMOLOGOUS PAIRS of chromosomes are those which carry matching portions of the genome. Think of them as "mated pairs." They contain the same gene loci, though they may have different alleles of the genes at those loci.
• The exceptions are the heteromorphic SEX CHROMOSOME, which have have non-homologous loci, and undergo minimal crossing over.
• A chromosome that is not a sex chromosome is called an AUTOSOME
• A cell can be stopped in mid-mitosis, its metaphase chromosomes extracted and lined up in homologous pairs and photographed. Such a depiction of the chromosome complement is known as a KARYOTYPE. The karyotype yields important information, from chromosome number to physical markers on the chromosomes.

For Pondering

The study of interspecific genomic differences and their consequences is known as COMPARATIVE GENOMICS, and holds great promise for the future discovery of the causes (and potential treatments) of many heritable diseases that are found in diverse species.

CYTOGENETICS

CYTOGENETICS is the study of the physical properties and genetic nature of the chromosomes.

The c'somes are usually studied while in condensed form, during mitosis. But the landmarks seen in condensed c'somes are assumed to be the same as when the chromosomes exist as diffuse, uncondensed CHROMATIN. (During the part of the cell cycle when the cell is not actively dividing.)

Useful physical properties of chromosomes include:

• size (relative to the others in the genome)
• position of centromere (location of the kinetochore, which is the proteinaceous structure to which sister chromatids attach during mitosis)
  • telocentric (centromere at the end)
  • acrocentric (centromere very close to the end)
  • metacentric (centromere in the center)
  • submetacentric - almost in the center
• nucleolar organizer number and position(s).
  (nucleolus: visible region in nucleus where portions of the ribosomes (rRNA) are being assembled. This happens at a specific location (or locations) on the DNA known as the nuclear organizer.
• chromomere patterns - function unknown. These are little thickenings along the chromosome, easily viewed during prophase of mitosis or meiosis. Especially large chromomeres are called "knobs."
• Heterochromatin patterns. Portions of the chromosome are generally present as either tightly coiled heterochromatin (not actively transcribed) and euchromatin (able to be transcribed). Certain stains can be used to show these regions, which have characteristic patterns.
• Banding patterns: (transverse bands along the length of the chromosomes)
  • G bands (made visible with Giemsa stain) - rich in A-T bonds
  • R bands (made visible with reversed Giemsa stain) - rich in G-C bonds
  • Q bands (made visible with qunacrine hydrochloride)
  • Polytene bands - found only in certain cells which have a highly secretory function (e.g. dipteran salivary glands; Malpighian tubules (excretory), gut lining, footpad (flies smell with their feet!), mammalian liver cells.

  Polytene ("many stranded" (tene is Latin for "thread") chromosomes result from endomitosis: repeated chromosome duplication without separation. Multiple copies of the chromosomes lie together in a big bundle, and don't separate.

  Polytene chromosomes have been useful in allowing the physical study of things like deletion mutations, because they are so easily visible.

  In Drosophila cells, there are 8 chromosomes. But in cells containing polytene chromosomes only FOUR chromosomes are visible during mitosis, because the homologs appear to "fuse" during this process. At some point, the four fused homologs also fuse together at the chromocenter, a knot of fused heterochromatin (very tightly coiled chromatin) on either side of the centromeres of all four participating homologous pairs.

  Function? Unknown. It's all very strange and mysterious.

Structure of the Eukaryotic Chromosome

DNA strand is wound on little lumps of DNA/histone called NUCLEOSOMES. These histones are octamers (composed of 8 subunit proteins, two of each of four types of histones).