Chemistry 332 - Spring 1996
Elements of Organic Chemistry II

Professor Carl C. Wamser

Chapter 16 - Lipids and Nucleic Acids

• general term for biomolecules that are water-insoluble but soluble in organic media
  (in biological systems this usually means membrane-bound)
  
  
• categories of lipids:
  • fatty acids - long chain carboxylic acids (C₁₂ - C₂₀)
    
    
  • fats and oils - triesters of fatty acids and glycerol (triglycerides)
    (monoglycerides are monoesters, diglyecrides are diesters)
    (function as energy storage materials)

• phosphatides - phosphate esters of glycerol (+ fatty acids)
  (membrane constituents)

• steroids - polycyclic structure with specific substituents
  (hormones, special functions)

• prostaglandins - cyclic structure with long chains
  (hormones, special functions)

• fats are solids, oils are liquids (same basic triglyceride structure)
• serve as insoluble deposits that can be retrieved for energy

• all natural fatty acids have an even number of carbon atoms, since they are synthesized from acetate (C₂) subunits
• natural unsaturated fatty acids have cis double bonds
  cis-double bonds lead to a lower melting point
  unsaturated and polyunsaturated fats are also more easily digestible

• basic hydrolysis of fats (saponification) generates soaps
  (the sodium salts of fatty acids)

• the ionic head group is water-soluble, the nonpolar tail insoluble
• soaps tend to aggregate in micelles, where nonpolar dirt dissolves

• the natural analog of the soap structure:
  a polar phosphate head group
  two nonpolar tails

• phospholipids with two tails tend to make planar bilayer aggregates

• other lipids are found in the nonpolar environment of membranes
• proteins often have a nonpolar and polar part, and are membrane-bound

• cholesterol is the precursor to most other steroids: vitamin D, bile salts, hormones

• the sex hormones and birth control pills are steroids

• 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

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

• 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

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

• nitrogen base + sugar + phosphate(s) = nucleotide
• ATP = adenosine triphosphate is used as an energy storage molecule
  hydrolysis to ADP releases 8 kcal/mole
  coupling of ATP hydrolysis helps to drive reactions that would ordinarily be unfavorable

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

• 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

• 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)

• 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)

• 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

• 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
  (Table 16.3 will be provided for quizzes and exams)
• 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)

• 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

• sizes of DNA molecules measured in kilobases (1000s 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

• draw structures for representative examples of fats, fatty acids, unsaturated fats, soaps, phospholipids, steroids, nucleosides, nucleotides
• recognize how the structures are appropriate for their particular biological functions
• identify the complementary base pairs in DNA and RNA
• identify the codons for amino acids and their sequence in DNA, m-RNA, and t-RNA
• describe the processes of DNA replication, transcription, and translation