User:Cody Couperus/Sandbox 3 - Revision history

Cody Couperus at 18:50, 16 February 2016

Cody Couperus — Tue, 16 Feb 2016 18:50:07 GMT

←Older revision		Revision as of 18:50, 16 February 2016
Line 2:		Line 2:

	==Introduction==		==Introduction==
		+
	-single stranded polynucleic acid		-single stranded polynucleic acid
		+
	-Transcribed from DNA by family of RNA polymerases		-Transcribed from DNA by family of RNA polymerases
		+
	-Functional roles include functional transfer for protein synthesis, catalysis, cellular regulation		-Functional roles include functional transfer for protein synthesis, catalysis, cellular regulation
		+
	-Degraded by....		-Degraded by....

Line 14:		Line 18:
	==Degradation pathways==		==Degradation pathways==
	==Structure General==		==Structure General==
-	Summary of - how to build a 3D structure from a linear medium. Practical considerations. How to think about folded polymers.	+	Summary of - how to build a 3D structure from a linear medium. Practical considerations. How to think about
		+	folded polymers.
		+
	Backbone		Backbone
		+
	Ribose		Ribose
		+
	Bases + base pairing		Bases + base pairing
		+
	Forces: stacking (VDW), hydrogen bond, hydrophobic effect, electrostatic		Forces: stacking (VDW), hydrogen bond, hydrophobic effect, electrostatic

	==Primary Structure==		==Primary Structure==
	Sequence		Sequence
		+
	Maybe some statistics?		Maybe some statistics?

Cody Couperus at 18:49, 16 February 2016

Cody Couperus — Tue, 16 Feb 2016 18:49:23 GMT

←Older revision		Revision as of 18:49, 16 February 2016
Line 26:		Line 26:
	==Structure (building blocks)==		==Structure (building blocks)==
	Stem loop		Stem loop
		+
	Coaxial helices		Coaxial helices
		+
	Kink-turn		Kink-turn
		+
	Hook-turn		Hook-turn
		+
	Ribose zipper		Ribose zipper
		+
	Kissing loops		Kissing loops
		+
	Hairpin loops		Hairpin loops
		+
	Pseudoknots		Pseudoknots
		+
	A-minor interactions		A-minor interactions
		+
	A-major interactions		A-major interactions
		+
	Tetraloop-receptor motifs		Tetraloop-receptor motifs
		+
	T-loop motif		T-loop motif
		+
	Triple stranded RNA		Triple stranded RNA
		+
	RNA quadruplex structuers		RNA quadruplex structuers
		+
	Metal chelation		Metal chelation

Cody Couperus at 18:48, 16 February 2016

Cody Couperus — Tue, 16 Feb 2016 18:48:54 GMT

←Older revision		Revision as of 18:48, 16 February 2016
Line 25:		Line 25:

	==Structure (building blocks)==		==Structure (building blocks)==
		+	Stem loop
	Coaxial helices		Coaxial helices
	Kink-turn		Kink-turn

Cody Couperus at 18:46, 16 February 2016

Cody Couperus — Tue, 16 Feb 2016 18:46:32 GMT

←Older revision		Revision as of 18:46, 16 February 2016
Line 1:		Line 1:
-	==~~Cathepsin D~~==	+	==RNA==

	==Introduction==		==Introduction==
		+	-single stranded polynucleic acid
		+	-Transcribed from DNA by family of RNA polymerases
		+	-Functional roles include functional transfer for protein synthesis, catalysis, cellular regulation
		+	-Degraded by....

-	~~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).~~	+	==Products of Transcription==

-	~~CD important for protein degradation, but many physiologically relavent functions have been idenfified.~~	+	Names/functional roles

-	~~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.~~	+	==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

-	==~~Activation~~==	+	==Primary Structure==
		+	Sequence
		+	Maybe some statistics?

-	==~~Catalytic Mechanism~~==	+	==Structure (building blocks)==
		+	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

Cody Couperus at 06:15, 18 May 2014

Cody Couperus — Sun, 18 May 2014 06:15:04 GMT

←Older revision		Revision as of 06:15, 18 May 2014
Line 8:		Line 8:

	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.		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.
		+
		+	==Activation==
		+
		+	==Catalytic Mechanism==

Cody Couperus: New page: ==Cathepsin D== ==Introduction== Cathepsin D (CD) is an apartic acid protease generally found in the lysosome of cells, but is also found intracellularly, extracellularly, and in endosom...

Cody Couperus — Sun, 18 May 2014 05:25:41 GMT

New page: ==Cathepsin D== ==Introduction== Cathepsin D (CD) is an apartic acid protease generally found in the lysosome of cells, but is also found intracellularly, extracellularly, and in endosom...

New page

==Cathepsin D==

==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).

CD important for protein degradation, but many physiologically relavent functions have been idenfified.

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.