LESSON 8: Molecular Structure of DNA and RNA

• 4 Criteria in Identifying DNA as the Genetic Material

  1. Information
  2. Transmission
  3. Replication
  4. Variation
• August Weismann and Carl Nageli (1880) - championed the idea that a chemical substance within living cells is responsible for the transmission of traits

  • Chromosome Theory of Inheritance - chromosomes are carriers of genetic material
• Frederick Griffith (1928) - studied a type of bacterium known then as pneumococci and now classified as streptococcus pneumoniae
• 2 Forms of S.pneumoniae

  1. smooth strains - capsule allows the bacteria to escape attack by mouse's immune system; kill the mouse
  2. rough strains - destroyed by the animal's immune system
• transforming principle - unidentified substance causing transformation
• transformation - change in cell function by transfer of an unknown substance

  • current definition: change in genotype and phenotype due to assimilation of external DNA by the cell
• MH Dawson and JL Alloway (1930) - in vitro transformation experiment
• Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) - used established biochemical purification procedures and prepared bacterial extracts from type S strains containing each type of these molecules

  • isolation of transforming substance
• Avery et al. Experiment

  • if no DNA extract was added, no type S bacterial colonies were seen on petri plates
• Alfred Hershey and Martha Chase (1952) - centered their research on the study of a virus known as T2

  • this virus infects Escherichia coli bacterial cells and is therefore known as bacteriophage
• capsid or phage coat - external structure of the T2 phage

  • composed entirely of protein with several different peptides
  • DNA is found inside the head of the T2 capsid
• Hershey-Chase (Blender Experiment)

  They used radioisotopes to distinguish proteins from DNA

  • sulfur atoms (³⁵S) - found in proteins but not in DNA
  • phosphorus atoms (³²P) - found in DNA but not in proteins
• Hershey-Chase (Blender Experiment)

  gieger counter - used to measure radioactivity

  • heavy bacterial cells sediment to the pellet, while lighter phages remain in the supernatant
• Hershey-Chase (Blender Experiment) Results

  • ³⁵S Experiment - 80% of the ³⁵S was labeled in the supernatant and the remaining 20% was in the pellet
  • ³²P Experiment - 70% of the ³²P label was in the pellet while the remaining 30% was in the supernatant
• DNA and RNA are known as nucleic acids, derived from the discovery of DNA by Friedrich Meischer in 1869
• nuclein - novel phosphorus-containing substance from the nuclei of WBCs found in waste surgical badges

  • was determined that they are acidic molecules, meaning they release [H+] and have negative charge at neutral pH
• 4 Levels of Complexity

  1. Nucleotides form the repeating structural units of nucleic acids
  2. Nucleotides are linked together in a linear manner to form a strand of DNA or RNA
  3. Two strands of DNA, and sometimes RNA, interact with each other to form a double helix
  4. The 3-D structure of DNA results from the folding and bending of the double helix
• nucleotide - repeating structural unit of both DNA and RNA
• 3 Components of a Nucleotide

  1. phosphate group
  2. pentose sugar
  3. nitrogenous base
• 2 Types of Sugars

  1. deoxyribose
  2. ribose
• 2 Categories of Bases

  1. Purine: adenine (A) and guanine (G), containing a double-ring structure
  2. Pyrimidine: thymine (T), cytosine (C), and uracil (U), containing single-ring structure
• 2 Types of Nucleotides

  1. deoxyribonucleotide
  2. ribonucleotide
• nucleoside - no phosphate group attached
• Deoxyribonucleic Acid - sugar is always deoxyribose; bases are adenine, thymine, guanine, and cytosine
• Ribonucleic Acid - sugar is always ribose; bases are adenine, uracil, guanine, and cytosine
• Nucleotide Structure

  Carbon residues in the pentose are numbered 1' through 5' (the prime) distinguishes these residues from those in the base, which are numbered without using a prime notion)
• Nucleotide Structure

  The base is attached to the 1' position of the ribose, and the phosphate is attached to the 5' position
• Pentose in Nucleotides

  The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose
• Pentose in Nucleotides

  The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, which forms a 5'-3' phosphodiester linkage
• Linkages in a Nucleotide

  The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring
• base + sugar = nucleoside
• base + sugar _ phosphate(s) = nucleotide
• ribose + adenine = adenosine

  ribose + guanine = guanosine

  ribose + cytosine = cytidine

  ribose + uracil = uridine
• phosphodiester linkage - the linkage in DNA or RNA strands

  • the backbone is negatively charged due to a negative charge on each phosphate
• In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar

  • This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5''-end and 3'-end
• Phoebus Levene (1909) - determined correctly that:

  • DNA is made up of chains of nucleotides
  • a nucleotide is a phosphate linked to a sugar linked to one of four nitrogenous bases
  • nucleotides link in series phosphate to sugar
• Phoebus Levene (1909) - incorrectly came up with the Tetranucleotide hypothesis

  • repeating tetramer: orders of bases exist in a fixed repetitive sequence, thus all bases appear in equal ratio
• model building - one method that proved important in the discovery of the structure of the DNA double helix
• Linus Pauling (1950s) - proposed that regions of proteins can fold into a secondary structure known as a helix

  • built large models by linking together simple ball-and-stick units
  • proposed the alpha helix secondary structure in proteins
  • incorrect with the Triple helix DNA model
• Errors with the Triple Helix DNA Model

  1. phosphates groups were shown as neutral molecules (must be negative)
  2. phosphates organized in the core for the helix: negative charges on oxygen would repel
  3. bases facing outwards