ThoughtQuestionsforBIOC212.pdf

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Department
Anatomy & Cell Biology
Course
ANAT 212
Professor
Jason Young
Semester
Fall

Description
ANSWERS TO THOUGHT QUESTIONS FOR BIOC 212 If you disagree with an answer provided, please do so with a comment (Ctrl+Alt+M) instead of deleting it, so we can discuss it. Feel free to add as much as you like/see relevant or change wording into something more coherent. WE CAN DO THIS! :D Lecture 01 ­ Folding 1 Which amino acid side chains can form these interactions? Hydrophobic interactions A,C,E,Q,F,G,H,I,K,L,M,N,P,R,T,V,W,Y Hydrogen bonds C,D,E,R,K,H,N,Q,S,T,Y Van de Waals interactions all ionic bonds D,E,R,K,H disulfide bonds C Lecture 02 ­ Folding 2 HSP70 Cycle Hsp­70­ATP Hsp70­ADP Substrate is Bound: No Yes Hsp70 DNAJ Yes No (transfered to Hsp70) Co­chaperone DNAJ NEF interaction with Hsp70 Lecture 03 ­ Folding 3 Compare and Contrast Substrate ATP ADP no nucleotide how does it bind Bound: to substrate Hsp70 No Yes No single site in cleft Chaperonin Yes No No multiple sites (top ring) around ring Hsp90 Yes No No ??? ● GR v. HSF1 ○ Glucocorticoid Receptor ■ Is bound by a chaperone to keep it’s conformation stable until a steroid allows it to enter into its native state. ○ HSF1 ■ The monomer is bound by Hsp90, until heat shock causes proteins to unfold, and it binds those proteins en lieu of the HSF1. The HSF1 is then free to bind with two other monomers to form the active trimer which upregulates Hsp production Lecture 04 ­ Folding 4 ● What  could be the effects of phosphorylation, acetylation and methylation on side chains on: ○ Recognition of N­end rule degrons ■ N­end rule detects: basic, large hydrophobic ■ Both phosphorylation and acetylation add acidic groups. This can possibly: ● Save small basic residues by neutralizing them ● Save some (not huge) hydrophobic residues by making them polar ■ Methylation adds a hydrophobic residue. This can possibly: ● Promote degradation of medium hydrophobic residues, which can be pushed to cross the threshold of hydrophobicity ● Promote degradation of acidic residues with medium/long hydrophobic sequences that would otherwise not be degraded ○ Recognition by chaperones ■ Chaperones recognize exposed hydrophobic sequences. ● Acetylation and phosphorylation of these sequences can cause them not to be detected (although I doubt this happens, because this would promote unfolded proteins to go undetected). ● Much more probable is the methylation of proteins causing them to be recognized and bound by chaperones, by creating exposed hydrophobic sequences ○ Attachment of ubiquitin ■ If K­48 (where Ub binds to signal degradation)  is bound to an acetyl, phosphatidyl or methyl group, it’ll be inaccessible to Ub, and therefore avoid degradation ■ If K­63 (where Ub binds to signal different mechanisms) is bound to an actyl, phosphatidyl or methyl group, it’ll be inaccessible to Ub and therefore not send out those signals... Lecture 05 ­ Membranes 1 Compare and Contrast Size Polarity (head hydrophobicity groups) Phospholipids > amino acid Very Polar, various Very non­polar  amino acid Free Fatty Acids
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