BIOL 200

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BIOL 200
2012-09-22 17:27:50

third lecture
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  1. Backbone is comprised of?
    • repeating phosphate pentose units. 
    • Sugar phosphate backbone
    • Oriented to the outside of the double helix 
    • Doesnt contain information 
  2. 5' end 
    free phosphate group on the 5' carbon of the terminal sugar
  3. 3' end
    free hydroxyl on the 3' carbon of the terminal sugar
  4. ____________keeps neucleiotides bonded covalently 
    Phosphodiester bond
  5. In what direction does the DNA and RNA synthesis proceed in 
    5' to 3' direction
  6. Where is information found in DNA 
    • Base pairs
    • Stacked on top of one another forming parallel planes
  7. What is the orientation of the polynucleotide strands in the double helix?
  8. Adenine bonds with 
    • Thymine 
    • 2 hydrogen bonds
  9. Cytosine bonds with 
    • Guanine 
    • 3hydrogen bonds 
  10. Bases are stabilized with?
    Primarily with Hydrogen bonds
  11. Most DNA in cells is right or left handed helix?
    Right handed helix
  12. B form of DNA
    • -In B form the majority of time 
    • -2 helical grooves (Major and minor grooves)
    • -This is important  because it is where protein interacts with the nucleic acid. Basically protein acess to basse pairs

  13. A DNA
    • In very low humidity (and dehydrated samples), the B form of DNA changes to the A form. Also RNA-DNA and RNA-RNA helices exist in the A form.
    • Found in in vitro 
  14. Z DNA
    • Short DNA molecules of alternating purine and pyrimidine nucleotides
    • Adopt a left-handed helix conformation known as the Z form
    • Z DNA is also transiently formed shortly after transcription and, as such, is a tag for actively transcribed genes.
  15. B DNA can_____ about it's long axis. Which is important why?
    • It can bend along its long axis
    • It is important in DNA- protein interactions and in the folding of DNA into compact condensed structures 
  16. DNA denaturation andrenaturation is important when?
    During DNA replication and intranscription. It is also exploited in many techniquesin molecular biology and genomics.
  17. Tm ??
    • It is a function of GC conent because it takes more energy because of the 3hydrogen bonds 
    • As we increase the percentage of CG bonds the higher the Tm temperature. 
  18. Can RNA fold
    • Yes, it has many secondary structures 
    • hairpin
    • stem-loop 
    • psedoknot
  19. Proteins?
    Function is derived from the 3 dimentional structure, and the 3 dimentional structure is specified by the amino acid sequence.

    Three dimentional structure= conformation 
  20. Primary structure?
    • They have a bias
    • What binds amino acids together is the peptide bond

    • Linear arrangement
    • Also use the term residue=amino acid within the peptide/polypeptide
  21. Secondary Structure 
    • Refers to interactions at a local level 
    • Folding of localized regions of a polypeptide chain 
    • Stabilizing non-covalent interactions, forming as example:
    • Alpha helices
    • Beta sheets
    • Beta turns

    Non covalent interactions=random coil 
  22. Alpha helix
    • H bonds (stabilizes)
    • R- group point outwards
  23. Beta sheets
    • Laterally packed strands 
    • H-bonding between backbone of the beta strands 
    • not very long
    • parallel or antiparallel
    • pleated 
    • R groups points outwards
  24. Beta Turns
    stabolilized by H bonds
  25. Why is Proline compact?
    Because ring structures forces a natural bend. In other words the bends are rich in glycine and proline 
  26. Tertiary structures
    • Long range of folding with a polypeptide chain 
    • Stabilized by:
    • hydrophobic interactions between non polar side chains
    • hydrogen bonds between polar side chains 
    • disulfide bond between cysterine residues
    • Provides a compact structure of alpha helices, beta sheets and turns
  27. Quaternary structure
    • Some protein need association with other polypeptides
    • Example:
    • Potassium Ion Channel; nearly identical polypeptides that create the channel. It takes 4!
  28. Supramolecular Structure
    • Macromolecular assemblies
    • Usually>1 megadaltons in size 10's to 100's of polypeptides chains(as well as other macromolecules)
  29. Motif and Domain 
    • 3 different motifs
    • a) coiled- hydrophobic residue 
    •              - found in very fibrous proteins 
    • b) Ef Hand/ helix loop-helix motif
    •               - ionic bonds involving a Ca2+ 
    •              -Ca2+ binding protein 
    • c) Zinc finger motif
    •              -allows polypeptides to interact with DNA          and RNA 
    •              - RNA and DNA binding proteins

    • Many polypeptides are composites of different combinations of motif/ domains
    • * concerve domain,interchange of domain....which create new protein