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Chapter 4

Biology Chapter 4.docx

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McMaster University
Lovaye Kajiura

Biology Chapter 4: Nucleic Acids and the RNA World Bernard Ho September 16, 2010 Nucleic Acid − Polymers made up of nucleotides − Components of a nucleotide o Phosphate group bonded to o Sugar bonded to o Nitrogenous base − Mainly two types of nucleotides o Ribonucleotides  Ribose as sugar  -OH group bonded to second carbon in the ring o Deoxyribonucleotides  Deoxyribose is sugar  H group bonded to second carbon in the ring  Deoxy  lacking oxygen − − Nitrogenous base attached at C #1, phosphate group at C #5, C #3 OH is involved in bonding with next nucleotide − The different nucleotides − Nucleic acids form when nucleotides polymerize − Polymerization reaction involves the formation of a bond between the phosphate group of one nucleotide and the hydroxyl group of the sugar component of a nucleotide (phosphodiester bond) − Water is a bi-product − When nucleotides involve ribose, the polymer produced is ribonucleic acid (RNA) − When nucleotides involve deoxyribose, the polymer produced is deoxyribonucleic acid (DNA) − The sugar-phosphate spine of a nucleic acid is directional, as is the peptide-bonded spine of a polypeptide − In a strand of RNA or DNA, one end has an unlinked 5’ carbon, while the other end has an unlinked 3’ carbon (by convention, sequence of bases found in RNA or DNA strand is always written 5’  3’) o Bases are always added at the 3’ end of the growing molecule − Sequence of nitrogenous bases forms the primary structure of the molecule − Polymerization reactions are catalyzed by enzymes and is endergonic − The addition of one more phosphate groups raises the potential energy of the substrate molecules enough to make an endergonic reaction possible o Addition of a phosphate group  phosphorylation DNA Structure and Function − DNA and RNA have a sugar-phosphate backbone created by phosphodiester linkages and a sequence of four nitrogenous bases that extend from it − James Watson and Francis Crick determined the secondary structure of DNA past breakthroughs o They knew the molecule had a sugar-phosphate backbone o By analyzing nitrogenous bases in DNA samples from different organisms, Erwin Chargaff had established two rules  Total number of purines and pyrimidines in DNA is the same  Number of T’s and A’s in DNA and C’s and G’s in DNA are equal o By bombarding DNA with X-rays and analyzing how it scattered the radiation, Rosalind Franklin and Maurice Wilkins had calculated the distances between groups of atoms in the molecule  Length of one complete turn of helix = 3.4nm  Width of helix = 2.0 nm  Distance between bases = 0.34 nm o They arranged two strands of DNA side by side and running in opposite directions (5’  3’ vs. 3’  5’) (antiparallel) o Found that if the antiparallel strands were twisted together to form the double helix, the coiled sugar-phosphate backbones ended up on the outside of the spiral and the nitrogenous bases on the inside o For that to fit, the bases had to form purine-pyrimidine pairs o Adenine could form two hydrogen bonds with thymine and guanine could form three h
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