User:Cody Couperus/Sandbox 3: Difference between revisions

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-==Cathepsin D==
+==RNA==
 ==Introduction==
-Cathepsin D (CD) is an apartic acid protease generally found in the lysosome of cells, but is also found intracellularly, extracellularly, and in endosomes. Its pH optimum is at an acidic pH (4-6).
+-single stranded polynucleic acid
-CD important for protein degradation, but many physiologically relavent functions have been idenfified.
+-Transcribed from DNA by family of RNA polymerases
-It is a heterodimer, with a 14 kD light chain and 34 kD heavy chain, activated from Procathepsin D autocatalytically and with assistance from cysteine proteases. Between the two lobes is an extended active site that accomidates 8 residues. CD specificity is gained by active site preference for hydrophobic residues. At the base of the active site are the two aspartate residues involved in catalysis of peptide bonds.
+-Functional roles include functional transfer for protein synthesis, catalysis, cellular regulation
-==Activation==
+-Degraded by....
-==Catalytic Mechanism==
+==Products of Transcription==
+Names/functional roles
+==Post/Co-transcriptional modifications==
+==Degradation pathways==
+==Structure General==
+Summary of - how to build a 3D structure from a linear medium. Practical considerations. How to think about
+folded polymers.
+Backbone
+Ribose
+Bases + base pairing
+Forces: stacking (VDW), hydrogen bond, hydrophobic effect, electrostatic
+==Primary Structure==
+Sequence
+Maybe some statistics?
+==Structure (building blocks)==
+Stem loop
+Coaxial helices
+Kink-turn
+Hook-turn
+Ribose zipper
+Kissing loops
+Hairpin loops
+Pseudoknots
+A-minor interactions
+A-major interactions
+Tetraloop-receptor motifs
+T-loop motif
+Triple stranded RNA
+RNA quadruplex structuers
+Metal chelation