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Chapter 4

Textbook and Class Notes Collaborated - Week 1 - Unit 1 - Chapter 4 - BIO 1A03

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McMaster University
Margaret Fahnestock

Bio 1A03 Unit One: The Molecules of Life Chapter 4: Nucleic Acids and The RNA World  Two attributes to distinguish life from non-life o Reproduction – the ability of something to make a copy of itself o Metabolism – the ability to acquire particular molecules and use them in controlled chemical reactions that maintain conditions suitable for life and that contribute to growth o To many biologists, the presence of a plasma membrane is also required for life, because enzymes and reactants are contained inside a cell by a plasma membrane 4.1 What Is a Nucleic Acid?  Nucleic Acids: Polymers made up of monomers called nucleotides  3 components of a nucleotide: o Phosphate Group o Sugar  Organic compound with a carbonyl group and several hydroxyl groups  C#3 OH is involved in bonding with the next nucleotide  C#1 is attached to the nitrogenous base  C#5 is attached to the phosphate group o Nitrogenous Base  Ribonucleotides - Sugar is ribose; has an –OH group bonded to C#2 in the ring o Purines: Adenine (A) and Guanine (G) o Pyrimidines: Cytosine (C) and Uracil (U)  Deoxyribonucleotides - Sugar is deoxyribose; has an –H bonded to the C#2 in the ring o Purines: Adenine (A) and Guanine (G) o Pyrimidines: Cytosine (C) and Thymine (T)  DNA and RNA are Polynucleotides  The ribose problem o When formaldehyde molecules are heated in solution, they react with one another to form almost all of the sugars that have five or six carbons o The ease of forming these sugars creates a problem – in modern experiments, the various pentose’s and hexoses are produced in approximately equal amounts, but it seems logical to predict that ribose would have had to be particularly abundant for RNA or DNA to form in the prebiotic soup  The origin of pyrimidine o Origin-of-life researchers have yet to discover a plausible mechanism for the synthesis of cytosine, uracil and thymine molecules prior to the origin of life o Purines are readily synthesized by reactions among hydrogen cyanide (HCN) molecules How Do Nucleotides Polymerize to Form Nucleic Acids?  Nucleic acids form when nucleotides polymerize  Phosphodiester linkage/bond: Condensation reaction between the phosphate group of one nucleotide and the hydroxyl group of the sugar component of another nucleotide o -C-O-P-O-C o A phosphodiester linkage joins the C#5 on the ribose of one nucleotide to the C#3 carbon on the ribose of the other o Figure 4.2, page 73  Chain of phosphodiester linkages in a nucleic acid acts as a backbone and is directional o One end has an unlinked 5’ carbon, which the other end has an unlinked 3’ carbon o The sequence of bases found in RNA or DNA is always written in a 5’  3’ direction  When RNA or DNA is synthesized, bases are added at the 3’ end of the growing molecule o Figure 4.3, page 74  The sequence of nitrogenous bases forms the primary structure of the molecule  Polymerization reactions that form nucleotides are catalyzed by enzymes –polymerization reactions are endergonic Bio 1A03  Polymerization reactions can take place in cells because the free energy of the nucleotide monomers is first raised by reactions that add two phosphate groups to the ribonucleotides and deoxyribonucleotides – creating nucleotide triphosphates o Molecules that have phosphate groups attached in this way are said to be phosphorylated  The addition of one or more phosphate groups raises the potential energy of the substrate molecules enough to make an endergonic reaction possible o Figure 4.4, page 74; Nucleotide Triphosphate 4.2 DNA Structure and Function What is the Nature of DNA’s Secondary Structure?  James Watson and Francis Crick, 1953 in the journal Nature presented a model for the secondary structure of DNA  What Watson and Crick were working with: o Chemists had worked out the structure of nucleotides and knew that DNA polymerized through the formation of phosphodiester linkages – they knew that the molecule had a sugar-phosphate background o By analyzing nitrogenous bases in DNA samples from different organisms, Erwin Chargaff had esta
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