chapter 16

Bio1151 Chapter 16 9

The physical structure of nucleic acids such as _ANI_16,5 RNA or was discovered by Watson and Crick from photos of crystallography made by Rosalind Franklin.
- X-ray diffraction "photo 51" of DNA made by Rosalind Franklin provided clues for Watson and Crick (Nobel 1962) to discover the structure of DNA.
  Rosalind the "dark lady":
DNA is a double , with the sugar-phosphate backbones on the outside, and pairs of bases on the _act_16&C inside.
- DNA structure.
  Each nucleotide consists of a nitrogenous base (T, A, C, or G), the sugar deoxyribose, and a phosphate group.
  The 5' end of the polynucleotide is a phosphate, while the 3' end is a hydroxyl group of the sugar.
  The phosphate of one nucleotide forms a covalent bond with the sugar of the next, providing a "backbone" from which the bases project.
  Review:
- DNA double helix. Covalent bonds between nucleotides form two strands of sugar-phosphate backbones on the outside of the double helix. The complementary nitrogenous bases are paired in the inside, held together by hydrogen bonds. The 2 strands are antiparallel: they run in opposite 5' to 3' directions.
_act_16&B Weak bonds form between the complementary base pairs: (A) always pairs with (T), and (C) always pairs with (G).
- Base pairing in DNA.
  The pairs of nitrogenous bases in a DNA double helix are held together by hydrogen bonds.
  The geometry of the bases are the basis of base-pairing rules.
- Adenine (A) pairs with Thymine (T) by forming two bonds,
- Cytosine (C) pairs with Guanine (G) by forming three bonds.
  When DNA base-pairs with RNA, A pairs with U.
  Review:
- Nitrogenous bases. Adenine and guanine are purines, nitrogenous bases with two organic rings. Cytosine and thymine are pyrimidines, which have a single ring.
The base-pairing rules are used for DNA : each strand acts as a for building a strand.
- Semi-conservative replication of DNA. The parent molecule is a double helix (untwisted for simplification). The 2 strands are separated, breaking the hydrogen bonds between the bases. 2 "daughter" DNA molecules are produced, each consisting of one parental strand and one new strand.
The replication occurs in three phases: , , and .
- Initiation
  - Initiation.
    In eukaryotes, DNA replication begins at many origins of replication along each chromosome.
    The DNA unwinds at replication forks, forming multiple replication bubbles.
  - At the replication fork, helicase unwinds the double helix, as topoisomerase stabilizes the intact double helix. A short RNA primer is added by primase in the 5' to 3' direction, using the parental DNA as a template and following the base-pairing rules. Review:
  - In this micrograph, three replication bubbles are visible along the DNA of a cultured Chinese hamster cell.
- Elongation
  - Elongation. DNA polymerase III catalyzes the addition of a nucleotide to the 3' end of a growing new strand by the hydrolysis of a nucleoside triphosphate. This process is different along the leading and lagging new strands. Review:
  - DNA polymerase III elongates DNA strands only in the 5' to 3' direction.
    On the leading strand (where the 3' end of the new strand proceeds into the fork), DNA synthesis can proceed continuously.
  - On the lagging strand, synthesis must occur away from the replication fork, also in the 5' to 3' direction.
    DNA polymerase III elongates the lagging strand in short Okazaki fragments.
- Termination
- Termination.
  DNA polymerase I removes the RNA primer.
  DNA ligase joins the Okazaki fragments along the lagging strand.
  Review:
_act_16&D Summary: DNA replication
Base-pairing is about 99.999% accurate, an error occurs about 1 in base pairs. DNA can "proofread" during polymerization and replace most incorrect nucleotides.
- DNA proofreading.
  
  During DNA replication an incorrect base pair may be formed. The replication complex excises the incorrect base. DNA polymerase adds the correct base.
Uncorrected DNA can be repaired by nucleotide repair.
- Nucleotide excision repair.
  A thymine dimer, a type of damage often caused by excessive exposure to ultraviolet radiation.
  A nuclease enzyme cuts out (excises) the damaged nucleotides.
  DNA polymerase replaces it with a normal DNA segment.
  DNA ligase completes the process by closing the gap in the sugar-phosphate backbone.
The overall error rate is about 1 in 10 nucleotides, or 99.99999999% accurate.
The ends of linear eukaryotic chromosomes get with each round of replication.
- Shortening of linear DNA.
  DNA polymerase III cannot complete the 5' end on the new lagging strand.
  After removing the last RNA primer, each round of replication produces shorter DNA molecules.
- After the first round of replication, the new lagging strand is shorter than its template.
  After a second round, both the leading and lagging strands are shorter than the original parental DNA.
- Each chromosome terminates in a , that postpones the erosion of genes near the ends.
  - Eukaryotes have non-coding nucleotide sequences called telomeres at the ends of their linear DNA. The telomeres do not prevent DNA shortening, but postpone erosion of genes near the ends of chromosomes. Humans have a "Hayflick limit" of about 52 cell divisions before cellular death.
- Eukaryotic cells contain the enzyme to lengthen telomeres in gametes.
- An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells.
  This prevents shorter chromosomes being passed to future generations.
Eukaryotic DNA is packaged with proteins to form , which condense into visible chromosomes during mitosis.
- In eukaryotes, DNA is complexed with histone proteins forming "beads" called nucleosomes, which appear as 10-nm chromatin during interphase. A nucleosome has 8 histone molecules. A different proteins, H1, acts as a spacer between nucleosomes. continue Review:
- Chromosome structure.
  Interactions between nucleosomes cause the 10-nm fiber to coil into a 30-nm fiber.
  The 30-nm fiber forms looped domains that attach to a scaffold of non-histone proteins.
  The looped domains coil further during mitosis to form a 700-nm chromatid.
  Such tight packing makes the genes on the DNA inactive.

DNA proofreading.

During DNA replication an incorrect base pair may be formed.	The replication complex excises the incorrect base.	DNA polymerase adds the correct base.