RNA Structure

  1. function of mRNA
    conveys info from DNA to the translation machinery (ribosomes)
  2. function of tRNA
    works as an adaptor for amino acids in protein synthesis
  3. functions of some RNAs
    • Some RNA carry enzymatic activities.
    • Some RNAs have regulatory roles & control the level & translation of some mRNAs.
  4. how RNA differs from DNA
    • 1. Use of ribose instead of deoxyribose in the backbone (OH in the 2`position)
    • 2. Use of uracil instead of thymine. Lack of the methyl in 5' position
    • 3. RNA is single stranded but can fold on itself and make double strand structures within the molecule or it can make double strand structures with parts of other RNA molecules (important for many functions).
  5. Only some (not all) of RNA __ have double stranded RNA as their genetic material.
  6. RNA can fold back on itself & generate structures such as __
    • stem and loop (hairpin)
    • internal loops
    • bulges (unpaired bases within a double strand region)
    • junctions between a few double stranded regions
    • Image Upload 1
  7. Some base pairing are between distant bases & involves more than one structure which are named __
    • pseudoknots
    • Image Upload 2
  8. There are __ bonds between G & U
    • 2 hydrogen
    • Image Upload 3
  9. There are local regions of __ but not __ as seen in DNA
    • self base pairing;
    • long stretches of double helices
    • Image Upload 4
  10. Because of 2' OH, RNA double helices are closer to the structure of __
    • A-DNA (wide & shallow minor grooves & narrow deep major grooves)
    • This structure is not well suited for sequence specific recognition of RNA
    • Image Upload 5
  11. The sequence recognition of double helix RNA is achieved by relaying on the structure of __
    • hairpin loops, bulges, & distortions of non-canonical base pairs (e.g. tRNA)
    • Image Upload 6
  12. In the unpaired regions, the RNA backbone is __
    very flexible (high freedom in rotation of backbone)
  13. Making 3D foldings usually involve unusual base pairings such as __
    • base triple (U:A:U) & base-backbone interactions
    • Image Upload 7
  14. __ help the formation or stabilization of RNA 3D structures by __
    • Proteins;
    • shielding the negative charges of RNA backbone

    These 3D structures may have different conformations in equilibrium with each other.
  15. short sequences of RNA that change conformation upon binding with small molecules, such as metabolites (mostly in bacteria)
  16. Changes in the conformation of RNA causes __
    the termination of transcription
  17. In the presence of high levels of guanine, __
    • this base binds to the riboswitch & changes the conformation of the RNA. leads to termination of transcription & purines will not be made
    • Image Upload 8
  18. molecules that act as biological catalysts

    Similar to other enzymes, ribozymes have an active site, substrate interacting domains, and binding sites for co-factors

    • ex. RNaseP, cleaving 5' end of pre-RNA to generate mature tRNA
    • Image Upload 9
  19. __ is a nucleoprotein but the catalytic activity is carried out by the __
    RNase P; RNA part (The protein part only shields the negative charges of the 2 RNA molecules)
  20. an evolution based system to generate small RNA molecules that can bind to a particular molecule or protein: __. These generated RNAs (with binding ability) are known as __
    • SELEX; aptamers
    • Image Upload 10
  21. After several rounds of SELEX, the selected aptamers should have __
    • very high affinities for the ligand
    • Image Upload 11
  22. Upon interaction of an RNA with a metabolite, __
    → change in configuration of RNA → gaining the ability to bind a fluorophone → fluoresence

    • Only if both molecules are attached to the RNA, there will be fluorescence. This system can be used to monitor real time production of that metabolite within the cell
    • Image Upload 12
Card Set
RNA Structure
Week 1