Organic Chemistry III
	Professor Carl C. Wamser
Chem 336 - Spring 2009	Chapter 28 Notes

Nucleic Acids

Nucleic Acids

• huge molecules that carry the genetic information for an organism
• a polymer composed of phosphate esters linking sugars, with specific nitrogen bases attached to each sugar unit

Deoxyribose

• in RNA, ribose is the sugar, specifically beta-D-ribofuranose
• in DNA, 2-deoxyribose is the sugar, also with the beta furanose structure

The Nitrogen Bases

• pyrimidine bases have a 6-membered ring with two nitrogens
  cytosine, uracil (found in RNA), and thymine (found in DNA)

• purine bases have two rings with four nitrogen atoms
  adenine and guanine

Nucleosides

• nitrogen base + sugar = nucleoside
• one-letter codes imply the nucleoside (add "d" for deoxy)
  
  C = cytosine
  U = uridine
  T = thymidine
  A = adenosine
  G = guanosine

Nucleotides

• nitrogen base + sugar + phosphate(s) = nucleotide
• ATP = adenosine triphosphate is used as an energy storage molecule

Polynucleotides - DNA and RNA

• polymers of DNA or RNA are named from 5' end to 3' end

Base Pairing

• specific H-bonding can take place between bases on adjacent strands
  in DNA: A & T base pair, G & C base pair
  in RNA: A & U base pair, G & C base pair
• the base pairing requires antiparallel directions of the two strands
  the optimum structure for base pairing is a double helix

Replication of DNA

• note that each strand of DNA contains enough information to duplicate its partner
• DNA is replicated by uncoiling and creating new partners for each strand
• replication is done by an enzyme, DNA polymerase, using nucleotide triphosphates (like ATP)

Transcription of Genetic Information from DNA to RNA

• information from DNA is transcribed by copying onto messenger RNA (m-RNA)
• the m-RNA message matches the original DNA (complementary to the DNA being copied)

Translation of the Genetic Information into Protein Biosynthesis

• m-RNA brings the genetic information to ribosomes, where protein biosynthesis takes place
• m-RNA message is read sequentially by its 3-letter codons
• as needed, individual amino acids are brought to the ribosomes by transfer RNA (t-RNA)
• t-RNA specifically recognizes both the code for an amino acid and its particular amino acid

The Genetic Code

• each amino acid is represented by a three-letter code
  the code is expressed as it appears on the m-RNA, from 5' to 3' direction
• special features of the genetic code (like a language)
  • no punctuation - exact starting spot is crucial, must always move by 3 units
  • there is a "stop" code
  • duplicate codes - most amino acids have multiple codes
  • single-letter changes (especially in the last spot) usually don't cause a serious misreading of the code
    (however, sickle-cell anemia is caused by a single error in the structure of hemoglobin, in which 6-Glu is erroneously replaced by 6-Val)

Why is the OH Missing in DNA?

• RNA (both m-RNA and t-RNA) is meant to recycle readily to read and write messages
• DNA is meant to remain stable
• hydrolysis of the phosphate esters of nucleic acids is enhanced by the 2'-OH group
  in the absence of the 2'-OH group, the phosphate esters are very stable to hydrolysis

DNA Sequencing

• sizes of DNA molecules measured in kilobases (thousands of base pairs)
• specific cleavages of DNA can occur with restriction enzymes
• smaller fragments are more easily identified and reassembled into the original
• the Human Genome Project is an attempt to map the entire human genetic information in DNA