The joys of last-minute cramming

[tarigwaemir]

Lowell House, on the Feast of St. Gerald

I give up. There are about two weeks of practice problems that I haven't really looked at, but I don't care anymore. Am going to get up early tomorrow, shower, and read through key experiments before chemistry. I skimmed the textbook and took the practice exams cold (got the equivalent of one entire problem wrong on each, which means I am screwed), so I know most of the material but not the details.

Some notes on things I must memorize (and hopefully have memorized), so feel free to ignore.

Lariat formation: 2' OH of branch point A in the middle of the intron attacks phosphate of the guanine nucleotide at the 5' splice site in a transesterification reaction that kicks out the 5' exon as the leaving group (in other words, a phosphodiester linkage between phosphate and 3' OH of the adjacent upstream nucleotide is broken) and the lariat structure itself can be visualized as the branch point A with both 2' and 3' phosphodiester linkages

Aminoacylation: deprotonate the carboxy group on the amino acid and have nucleophilic oxygen attack ATP, releasing pyrophosphate and resulting in aminoacyl-AMP complex, which in turn is attacked at the ester carbon by the 3' OH of the tRNA

Peptide bond formation: the amino group on the incoming amino acid attacks the ester carbon in a transesterification reaction that kicks out the tRNA as leaving group and transfers the peptide chain to the incoming tRNA

(Amazing what patterns you find, just by writing things out. All of the above reactions are basically the same. Nucleic acids aren't very creative, apparently.)

Recombination:

• RecBCD - helicase and endonuclease; cuts both 5' and 3' end until chi site, after which it cuts only 5' end
  
• RecA - mediates strand invasion, searches for homologous sequences and forms duplexes; binds to the 3' single-stranded overhang in long extended helix
  
• RuvA and Ruv B - mediate branch migration; binds at Holliday junction (the pretty symmetrical structure)
  
• RuvC - resolves Holliday junction; recognizes RuvA and RuvB complex

Transcription:

• -35 and -10 promoter elements - bound by σ factor
  
• UP element - bound by C-terminal domain of α subunit
  
• TBP - binds to TATA box; binds at minor groove and causes kink in DNA
  
• TFIID - binds to TATA box
  
• TFIIA and TFIIB - bind to promoter region; recruited by TBP-TFIID-promoter complex
  
• TFIIH - contains kinase domain that phosphorylates serine and threonine residues in CTD-domain of RNA polymersase III and releases it from transcription initiation complex

Splicing:

• U1 snRNP - contains RNA complementary to 5' splice site
  
• U2 snRNP - contains RNA complementary to branch point; binds so that branch point A is exposed in a bulge
  
• U4, U5 and U6 snRNP - recruited by U1-U2-pre-mRNA complex, releases U1 snRNP
  
• U4 and U6 snRNP - contain complementary snRNA, result in release of U4 and creation of catalytic center for splicing

Translation:

• IF3 - dissociates large subunit from small subunit, recruits IF1 and IF2
  
• IF1 and IF2 - assemble initiation complex of small subunit, mRNA and initiator tRNA; requires 1 GTP
  
• Ef-Tu - delivers charged tRNA to A site; requires 1 GTP
  
• Ef-Ts - regenerates Ef-Tu-GTP from Ef-Tu-GDP
  
• Ef-G - translocation of incoming tRNA from A to P and exiting tRNA from P to E; requires 1 GTP
  
• RF1 or RF2 - recognizes stop codon and recruits RF3
  
• RF3 - catalyzes hydrolysis of peptidyl-tRNA linkage; requires 1 GTP
  
• RRF - releases tRNA from ribosome; analog of tRNA that binds in A site, requires 1 GTP

I think I remember most of that, although I need to review initiation pathways for transcription and translation. Should do that tomorrow morning as well. Hopefully I'll get up early--if I'm stressed enough, that is.

Yours &c.