Chapter Summary


  • A genome is all the genetic information that defines an organism.
  • Genomes of bacteria and archaea are made up of chromosomes and plasmids consisting of DNA.
  • Chromosomes of bacteria and archaea can be circular or linear, as can plasmids.
  • Functional units of DNA sequences include structural genes and regulatory sequences.


  • Noncoding DNA can constitute a large amount of a eukaryotic genome, while prokaryotes have very little noncoding DNA.
  • DNA is composed of two antiparallel chains of purine and pyrimidine nucleotides in which phosphate links the 5′ carbon of one nucleotide with the 3′ carbon of the next in the chain. The result is a double helix containing a deep major groove and a more shallow minor groove.
  • Hydrogen bonding and interactions between the stacked bases hold together complementary strands of DNA.
  • Supercoiling by topoisomerases compacts DNA into an organized nucleoid.
  • Bacteria, eukaryotes, and most archaea possess negatively supercoiled DNA. Archaea living in extreme environments have positively supercoiled genomes.
  • Type I topoisomerases cleave one strand of a DNA molecule and relieve supercoiling; type II enzymes cleave both strands of DNA and use ATP to introduce supercoils.


  • Replication is semiconservative, with newly synthesized strands lengthening in a 5′-to-3′ direction. It involves initiation, elongation, and termination.
  • Replication is initiated from a fixed DNA origin attached to the cell membrane. Initiation depends on the mass and size of the growing cell. It is controlled by the accumulation of initiator and repressor proteins and by methylation at the origin.
  • Elongation requires that primase (DnaG) lay down an RNA primer, that DNA polymerase III act as a dimer at each replication fork, and that a sliding clamp keep DNA Pol III attached to the template DNA molecule.
  • The 3-to-5proofreading activity of Pol III corrects accidental errors during polymerization.
  • DNA ligase joins Okazaki fragments.
  • Two replisomes, each containing a pair of DNA Pol III complexes, are fixed at the membrane, and DNA feeds through them.
  • Termination involves stopping replication forks halfway around the chromosome at ter sites that inhibit helicase (DnaB) activity.
  • Ringed catenanes formed at the completion of replication are separated by topoisomerase IV and the proteins XerC and XerD.


  • Plasmids are autonomously replicating circular or linear DNA molecules that are part of a cell’s genome and can be transferred to other cells.
  • Plasmids replicate by rolling-circle and/or bidirectional mechanisms.
  • Plasmids can be transferred between cells.


  • Eukaryotic chromosomes are always linear, doublestranded DNA molecules that replicate by mitosis.
  • A reverse transcriptase called telomerase is need ed to finish replicating the ends of a eukaryotic chromosome.
  • Histones (eukaryotic DNA-packing proteins) play a critical role in forming chromosomes.
  • Introns and pseudogenes are noncoding DNA sequences that make up a large portion of eukaryotic chromosomes.
  • Archaeal chromosomes resemble those of bacteria in size and shape, but archaeal DNA polymerases are more closely related to eukaryotic enzymes.


  • DNA restriction endonucleases used for DNA analysis cleave DNA at specific recognition sequences, which are usually 4–6 bp in length and produce either a blunt or a staggered cut.
  • Agarose electrophoresis will separate DNA molecules on the basis of their size.
  • Restriction endonuclease–digested DNA molecules were first cloned into plasmids in the early 1970s.
  • The polymerase chain reaction (PCR) will amplify one or two copies of a specific gene a millionfold.
  • The most commonly used DNA sequencing technique (Sanger technique) uses nucleotides that lack both the 2′ OH and 3′ OH groups to terminate chain elongation.
  • Entire genomes are sequenced by shotgun cloning of overlapping DNA fragments, each of which is sequenced. Overlapping regions are matched and joined by computer analysis until the entire genome is reconstructed.
  • Metagenomics uses rapid DNA sequencing and other genomic techniques to study consortia of microbes directly in their natural environment.