CHAPTER 7

• Viral genomes


  • They contain nucleic acid as their genetic material, surrounded by a capsid of proteins
  • They are not cellular organisms, since they rely on host cells for replication
  • Most viruses have a limited host range, or spectrum of cell types, that it will infect

  
• Viral genome


  The sum of the genetic material in the virus
• Characteristics of selected viral genomes

  • Parvovirus (ssDNA, 5.0 Kb, 5 genes)
  • Fd (ssDNA, 6.4 Kb, 10 genes)
  • Lambda (dsDNA, 48.5 Kb, 71 genes)
  • T4 (dsDNA, 169.0 Kb, 288 genes)
  • TMV (ssRNA, 6.4 Kb, 6 genes)
  • Influenza virus (ssRNA, 13.5 Kb, 11 genes)
  • HIV (ssRNA, 9.7 Kb, 9 genes)

  
• Viral genome assembly


  Packaging into the capsid

  
• Bacterial chromosomes


  • They are circular, a few million nucleotides in length, and possess a few thousand different genes
  • Structural gene sequences account for the majority of the DNA
  • The nontranscribed regions between genes are called intergenic regions
  • They have a single origin of replication

  
• Bacterial chromosomes have 1-4 copies per cell

  
• Repetitive sequences dispersed throughout the bacterial genome may play a role in gene expression, DNA folding, DNA replication, and genetic recombination

  
• Compacting the bacterial chromosome

  1. Formation of loop domains

  2. DNA supercoiling

  
• DNA supercoiling


  Twisting forces that further compact the DNA
• Negative supercoiling in living bacteria

  Creates tension of the DNA that can be released by DNA strand separation, enhancing genetic activities such as replication and transcription
• DNA gyrase


  Enzyme that introduces negative supercoils
• Topoisomerase I


  Enzyme that relaxes negative supercoils
• Drugs that block bacterial gyrase function are an alternative to cure bacterial infection
• Eukaryotic chromosomes


  • They are located within the nucleus of the cell
  • Chromatin is the DNA-protein complex that is found within eukaryotic chromosomes
  • The size of an organism's genome is not necessarily an indication of the number of genes, as the additional DNA is due to the accumulation of repetitive sequences

  
• Salamanders: Plethodon richmondi vs. Plethodon larselli

  • The genome of P. larselli is over twice the size of P. richmondi, but the two species have very similar traits. The additional DNA in P. larselli is due to the accumulation of short repetitive DNA sequences that do not code for genes and present in many copies.

  
• Functionally important sequences in eukaryotic chromosomes

  • Origins of replication (necessary for DNA replication, spaced about every 100,000 base pairs)
  • Centromeres (DNA sequences necessary for proper chromosome segregation during mitosis and meiosis, with two types: point centromeres and regional centromeres)
  • Telomeres (at the end of the chromosome, prevent translocations and chromosome shortening, and protect against exonuclease enzymes)

  
• Eukaryotic chromosomes may contain from a few hundred to a few thousand genes
• Eukaryotic chromosomes


  • They are usually linear
  • A typical chromosome is tens of millions to hundreds of millions of base pairs in length
  • Eukaryotic chromosomes occur in sets, with many species being diploid (2 sets of chromosomes)
  • Genes are interspersed throughout the chromosome
  • Each chromosome contains many origins of replication spaced about every 100,000 base pairs
  • Each chromosome contains a centromere that forms a recognition site for the kinetochore proteins
  • Telomeres contain specialized sequences located at both ends of the linear chromosome
  • Repetitive sequences are commonly found near centromeric and telomeric regions, but they may also be interspersed throughout the chromosome

  
• Sequence complexity


  The number of times a particular base sequence appears throughout the genome
• Types of sequences based on sequence complexity

  • Nonrepetitive sequences (found once or a few times, includes structural genes)
  • Moderately repetitive sequences (found from a few hundred to a few thousand times)

  
• Telomeres


  • Prevent chromosome translocations and shortening
  • Required for proper segregation during mitosis and meiosis

  
• Centromeric and telomeric regions

  • Repetitive sequences are commonly found

  
• Eukaryotic chromosomes


  • Contain many origins of replication approximately 100,000 bp apart
  • Kinetochore proteins link the centromere to the spindle apparatus

  
• Sequence complexity in eukaryotic genomes

  • Nonrepetitive sequences (found once or a few times)
  • Moderately repetitive sequences (found from a few hundred to few thousand times)
  • Highly repetitive sequences (found tens of thousands or millions of times)

  
• Highly repetitive sequences


  • Alu sequence in humans (a retroelement)
• Compacting eukaryotic chromatin


  • Interaction with special proteins
  • Allows for the dynamic structure of DNA
  • Differences in compaction level between interphase and M phase
  • Chromatin remodeling influences gene expression through transcription

  
• Nucleosome


  • Repeating structure unit in a eukaryotic chromosome
  • Double-stranded DNA wrapped around an octomer of histone proteins
  • DNA makes 1.65 negative superhelical turns around the octomer
  • Involves 146 base-pairs
  • Nucleosomes connected by linker regions of 20 - 100 bp

  
• Histone proteins


  • Basic proteins containing a large number of lysine and arginine amino acids
  • Allow binding to DNA backbone via electrostatic and hydrogen bonding

  
• Histone octomer


  • Consists of two each of H2A, H2B, H3, and H4 histone proteins
  • Histone protein H1 is a linker

  
• Nucleosome structure revealed experiment

  1. Digest DNA with DNase I

  2. Measure molecular mass of resulting DNA fragments using gel electrophoresis

  3. Linker DNA more accessible to DNase I than DNA bound to core histones

  4. DNase I cuts in linker DNA, producing DNA pieces around 200 bp long

  
• The beads-on-a-string model of chromatin structure is correct
• 30 nm fiber


  • Nucleosomes associate with each other to form a 30 nm diameter structure
  • Histone H1 involved in this level of compaction
  • 30 nm fiber shortens total DNA length seven-fold
  • Originally proposed to be in a solenoid formation, now believed to be in a three-dimensional zig-zag

  
• Radial loop domains


  • Chromatin organized into loops of 25,000 to 200,000 base pairs
  • Interaction between 30 nm fiber and nuclear matrix via matrix-attachment sites (MARs) or scaffold-attachment sites (SARs)
  • Important for gene regulation and chromosome organization in the nucleus

  
• Heterochromatin


  • Highly compacted regions of DNA
  • Constitutive heterochromatin always exists as heterochromatin
  • Facultative heterochromatin may convert between euchromatin and heterochromatin
• Euchromatin refers to less condensed regions of chromatin
• The steps in eukaryotic chromosomal compaction lead to the metaphase chromosome