Biochemistry SGD

• The roughly 3 × 10^9 base pairs of DNA that compose the haploid genome of humans are divided uniquely between 23 linear DNA units, the chromosomes. Humans, being diploid, have 23 pairs of these linear chromosomes: 22 autosomes and two sex chromosomes.

  
• Human genomic DNA, if extended end-to-end, would be meters in length, yet still fits within the nucleus of the cell, an organelle that is only microns (μ; 10^-6 meters) in diameter. Such condensation in DNA length, in part, is induced following its association with the highly positively charged histone proteins resulting in the formation of a unique DNA-histone complex termed the nucleosome.

  
• Nucleosomes


  • DNA wrapped around the surface of an octamer of histones

  
• Formation of chromatin


  1. Strings of nucleosomes form along the linear sequence of genomic DNA

  2. Chromatin can be more tightly packaged and condensed

  3. This ultimately leads to the formation of the chromosomes

  
• While the chromosomes are the macroscopic functional units for DNA transcription, replication, recombination, gene assortment, and cellular division, it is DNA function at the level of the individual nucleotides that composes regulatory sequences linked to specific genes that are essential for life.

  
• DNA replication, repair, and recombination


  Involves steps, phases of the cell cycle, and molecules responsible

  
• Errors in DNA replication, repair, and recombination can have negative effects on cellular and organismal integrity and health.
• Genetic information in DNA can be transmitted by exact replication or exchanged by processes like crossing over, recombination, transposition, and gene conversion. These provide adaptability and diversity but can also result in disease.

  
• Mutations are due to changes in the base sequence of DNA and may result from faulty replication, transposition, or repair. Abnormalities in gene products can be the result of mutations in transcribed protein coding, non-protein coding DNA, or non-transcribed regulatory-region DNA.
• Mutations in germ cells are transmitted to offspring (vertical transmission of hereditary disease). Mutations in somatic cells are passed on to successive generations of cells within an organism (horizontal transmission).
• Many diseases and most cancers are due to the combined effects of vertical transmission of mutations and horizontal transmission of induced mutations.
• Chromatin


  Chromosomal material in the nuclei of cells of eukaryotic organisms, consisting of DNA, histones, and non-histone proteins

  
• Chromatin


  • Contains very long double-stranded DNA molecules and a nearly equal mass of small basic proteins termed histones, as well as a smaller amount of non-histone proteins and RNA

  
• The double-stranded DNA helix in each chromosome has a length that is thousands of times the diameter of the cell nucleus.

  
• Histones


  Small family of closely related basic proteins that condense DNA and participate in gene regulation

  
• Core histones


  • H2A
  • H2B
  • H3
  • H4
• Histones


  • Carboxyl terminal two-thirds are hydrophobic, amino terminal thirds are rich in basic amino acids
  • Subject to at least six types of covalent modifications (acetylation, methylation, phosphorylation, ADP-ribosylation, monoubiquitylation, and sumoylation)
  • These modifications play important roles in chromatin structure and function
• Nucleosome


  Organizational unit of chromatin, composed of DNA wrapped around a histone octamer

  
• Nucleosomes are separated by ~30 bp of linker DNA, giving chromatin a "beads-on-a-string" appearance.

  
• Assembly of nucleosomes


  Mediated by chromatin assembly factors and histone chaperones

  
• Nucleosomes exhibit preference for certain DNA regions, likely related to DNA flexibility and presence of other DNA-bound factors.

  
• Higher-order chromatin structures


  • 10-nm fibril
  • 30-nm chromatin fiber
• Histone H1 appears to stabilize the 30-nm chromatin fiber.

  
• Interphase chromosomes have chromatin fibers organized into 30,000 to 100,000 bp loops or domains anchored in a nuclear matrix.

  
• Some genes or gene regions are mobile within the nucleus, moving to discrete loci upon activation.
• Active chromatin


  Transcriptionally or potentially transcriptionally active, with altered nucleosome structure, DNase I hypersensitive sites, and particular histone variants/modifications

  
• Inactive chromatin (heterochromatin)


  Densely packed, transcriptionally inactive
• Euchromatin (transcriptionally active chromatin) is replicated earlier than heterochromatin.
• Enhancer


  Interrupted nucleosomal structure caused by the binding of nonhistone regulatory transcription factor proteins

  
• Genes capable of being transcribed often have a DNase-hypersensitive site(s) in the chromatin immediately upstream

  
• Nonhistone regulatory proteins


  Involved in transcription control and maintaining access to the template strand

  
• Transcriptionally inactive chromatin


  Densely packed during interphase, referred to as heterochromatin
• Transcriptionally active chromatin


  Stains less densely, referred to as euchromatin

  
• Euchromatin is replicated earlier than heterochromatin in the mammalian cell cycle
• Constitutive heterochromatin


  Always condensed and thus essentially inactive, found in regions near the chromosomal centromere and at chromosomal ends (telomeres)

  
• Facultative heterochromatin


  At times condensed, but at other times actively transcribed and uncondensed, appearing as euchromatin

  
• One X chromosome in mammalian females is almost completely inactive transcriptionally and is heterochromatic, but decondenses during gametogenesis and becomes transcriptionally active during early embryogenesis

  
• Polytene chromosomes


  • Contain regions of condensed chromatin and lighter bands of more extended chromatin
  • Transcriptionally active regions are especially decondensed into "puffs" that contain the enzymes responsible for transcription and are the sites of RNA synthesis

  
• Fluorescence in situ hybridization (FISH)


  Technique that uses highly sensitive fluorescently labeled hybridization probes to map specific gene sequences within the nuclei of human cells, even without polytene chromosome formation

  
• Metaphase chromosomes


  • Possess a twofold symmetry, with the identical duplicated sister chromatids connected at a centromere
  • The centromere is an adenine-thymine (A-T)-rich region containing repeated DNA sequences that range in size from 102 (brewers' yeast) to 106 (mammals) base pairs
  • Metazoan centromeres are bound by nucleosomes containing the histone H3 variant protein CENP-A and other specific centromere-binding proteins, forming the kinetochore which provides the anchor for the mitotic spindle