Biochemistry 6: DNA and Biotechnolog Nucleic Acid Structure Nucleic acids are polymers of nucleotides. Types include Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA). 1° Structure: Linear sequence of nucleotides. 2° Structure: Interactions between bases within the same molecule. In DNA, the bases are held together by hydrogen bonds. 2° structure is responsible for the shape of nucleic acid. RNA 2° structure has 4 basic elements: Loops, helices, bulges, and junctions. Loops include stem-loops (hairpin loops), tetraloops, and psuedoknots. 3° Structure: The location of the atoms in 3D space. 4° Structure: Interactions of nucleic acids with other molecules. Example: Chromatin interacting with histones. DNA Replication * See appendix for full diagram DNA Replication: The process of producing an identical replica of a DNA molecule. Occurs in the S (synthesis) phase of the cell cycle. DNA Repair Oncogenes: Develop from mutations of proto-oncogenes, and promote cell cycling. May lead to cancer. Oncogenes = stepping on gas pedal Tumor Suppressor Code for proteins that reduce cell cycling or promote Genes: DNA repair. Mutated Tumor Suppressor genes = cutting the brakes Proofreading: DNA Polymerase proofreads its work and excises incorrectly matched bases. The daughter strand is identified by its lack of methylation and corrected accordingly. Mismatch Occurs during G2 phase using the genes MSH2 and MLH1. Repair: Nucleotide Fixes helix-deforming lesions of DNA such as Thymine Excision Repair: dimers. A cut-and-patch process. Excision Endonuclease. Nucleic Acid Structure: Includes DNA structure and RNA structure. Base Excision Fixes nondeforming lesions of the DNA helix such as Repair: cytosine deamination by removing the base, leaving apurinic/apyrimidinic (AP) site. AP Endonuclease then removes the damaged sequence, which can be filled in with the correct bases. Eukaryotic Chromosome Organization 46 chromosomes in human cells. DNA is wound around histone proteins to form nucleosomes, which may be stabilized by another histone protein. As a whole, DNA and its associated histones make up chromatin in the nucleus. DNA Structure Chromatin: Heterochromatin: Dark, dense, and silent Euchromatin: Light, uncondensed, and expressed * See appendix for full diagram DNA: Deoxyribonucleic Acid. A macromolecule that stores genetic information in all living organisms. Nucleoside: 5-carbon sugar + nitrogenous base. NO PHOSPHATE groups Nucleotide: A nucleoside with 1 to 3 phosphate groups added. Nucleotides in DNA contain deoxyribose; in RNA they contain ribose. Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Uracil (U). In RNA, U replaces T, so A pairs wi U via 2 h-bonds. Watson-Crick Backbone of alternating sugar/phosphate groups. Always Model: read 5’ 3’. Two strands with antiparallel polarity wound into a double helix. Nitrogenous Purines: Adenine and Guanine. Made of two rings. Bases: Pyrimidines: Cytosine, Thymine, Uracil. Made of one ring. Chargaff’s Rules: # of Purines = # of Pyrimidines. A = T; C = G B-DNA vs Z-DNAMost DNA is B-DNA, forming a right-handed helix. Low concentrations of Z-DNA, with a zigzag shape, may be seen with high GC-content or high salt concentration. Denature / Denatured: Pulled apart Reannealed: Reannealed: Brought back together Telomeres: Ends of chromosomes. Contain high GC-content to prevent unraveling of the DNA. During replication, telomeres are shortened, but this can be partially reversed by telomerase. Centromeres: Located in the middle of chromosomes and hold sister chromatids together until they are separated during anaphase in mitosis. High GC-content to maintain a strong bond between chromatids. Acrocentric When the centromere is located near one end of the Chromosome: chromosome and not in the middle. Recombinant DNA and Biotechnology Recombinant DNA: DNA composed of nucleotides from 2 different sources Hybridization: The joining of complementary base pair sequences. Polymerase Chain See appendix for details Reaction (PCR): Electrophoresis: See appendix for details