1. Things to read[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]

1.1. DNA

Additional Evidence That DNA Is the Genetic Material

• It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group
• In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next
• This evidence of diversity made DNA a more credible candidate for the genetic material

• Two findings became known as Chargaff’s rules(The base composition of DNA varies between species, In any species the number of A and T bases are equal and the number of G and C bases are equal)
• The basis for these rules was not understood until the discovery of the double helix

 

Building a Structural Model of DNA: Scientific Inquiry

• After DNA was accepted as the genetic material, the challenge was to determine how its structure accounts for its role in heredity
• Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure
• Franklin produced a picture of the DNA molecule using this technique
• Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical
• The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases
• The pattern in the photo suggested that the DNA molecule was made up of two strands, forming a double helix

• Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA
• Franklin had concluded that there were two outer sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior
• Watson built a model in which the backbones were antiparallel (their subunits run in opposite directions)
• At first, Watson and Crick thought the bases paired like with like (A with A, and so on), but such pairings did not result in a uniform width
• Instead, pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray data
• Watson and Crick reasoned that the pairing was more specific, dictated by the base structures
• They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C)
• The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C

Many proteins work together in DNA replication and repair

• The relationship between structure and function is manifest in the double helix
• Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material

The Basic Principle: Base Pairing to a Template Strand

• Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication
• In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules
• Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand
• Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new)

A chromosome consists of a DNA molecule packed together with proteins

• The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein
• Eukaryotic chromosomes have linear DNA molecules associated with a large amount
  of protein
• In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid
• In the eukaryotic cell, DNA is precisely combined with proteins in a complex called chromatin
• Chromosomes fit into the nucleus through an elaborate, multilevel system of packing
• Chromatin undergoes changes in packing during the cell cycle
• At interphase, some chromatin is organized into a 10-nm fiber, but much is compacted into a 30-nm fiber, through folding and looping
• Interphase chromosomes occupy specific restricted regions in the nucleus and the fibers of different chromosomes do not become entangled
• Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis
• Loosely packed chromatin is called euchromatin
• During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin
• Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions
• Histones can undergo chemical modifications that result in changes in chromatin organization

 

1.2. TATA Box

RNA Polymerase Binding and Initiation of Transcription

• Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point
• Transcription factors mediate the binding of RNA polymerase and the initiation of transcription
• The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes