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Academia Ghetto Thread

Started by Mesozoic Mister Nigel, September 05, 2014, 05:51:06 PM

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LMNO

Thanks! I'll do some reading!

Mesozoic Mister Nigel

You're welcome! Glad to be able to turn you on to something new.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Mesozoic Mister Nigel

These are a fraction my notes from mol bio. They aren't worth reading, I'm just posting them because I'm losing my fucking mind after transcribing them. There are 72 pages (12 point single-spaced) of this shit.

BI 334
11/20/2014
Class notes

   The Tryptophan operon
o   operator is a regulatory sequence within operon
   Operator (& all regulatory sequences) are DNA
   Trp repressor requires tryptophan to bind trp operator
o   Tryptophan binds repressor, which binds operator
o   Trp repressor changes shape when bound to tryptophan
   Attentuation – in e. coli only – A unique regulatory process that involves regulation of transcriptional termination by translation
o   Trp leader mRNA has two trp codons
o   Trp leader region can form alternative secondary structures
o   One of these structures is a termination factor
   High levels of trp cause formation of termination factor & thereby attenuation of transcription
   Negative regulation – bound repressor protein prevents transcription: addition of ligand removes protein (can also work in opposite direction)
   Positive regulation: binding of protein promotes transcription by increasing binding of transcription factors
   Lambda bacteriophage lifecycle
o   Lambda regulatory region (att) can act as activator or repressor depending on where it binds to the DNA
o   Binding is moved by a single base pair to determine whether it is operator or repressor
   Lambda repressor is a dual role operon
   Lac operon encodes genes that allow cells to encode lactose
o   Lac operon responds to presence of lactose very quickly
o   Lac repressor binds to inverted repeats to prevent transcription
o   Lac operon allows transcription in presence of lactose when glucose is absent
   CAP works in combination with lac
o   CAP is sensitive to glucose levels and binds to operator in absence of glucose
   Inducer (in the case of lac, lactose) changes conformation of the repressor (in this case, lac) so that it doesn't fit into the major groove and cannot bind.
   CAP: Catabolite gene Activator Protein
o   Positively regulated by glucose
   Gal operon – allows galactose metabolism
   HU works with Gal & causes looping & repression of Gal operon
   AraBAD promoter region – arabinose
   Lac repressor binds several sites at once that are far apart, causing looping
o   Increases effective concentration of protein
o   DNA cannot make a 90 degree bend more than every 200 base pairs
o   Activation at a distance – RNA looping
   Rrn operons contain rRNA & tRNA genes
   UP element increases transcription of rrn operons
o   rRNA 7 tRNA more abundant in faster growing e coli cells
o   There are 7 operons in e coli
   rRNA operons are subject to feedback regulation
   Regulators are dimerized for precision
   Repressors bind as tetramers to allow looping
Eukaryotic transcription regulation
   General transcription factors
   There are several thousand gene regulatory proteins (8% of gene)
o   Dozens of signals effect gene
   Eukaryotes don't have operons
o   Genes in a pathway require coordinated regulation
   Mediator complex required for activated transcription
   Regulatory proteins @ 5-10% of gene
   Sequences that bind regulatory proteins are enhancers
   Enhancers:
o   Can act at a distance
o   Can be up or downstream of initiation site
o   Orientation-independent
o   Yeast equivalent is UAS, an upstream factor
   Activation domain activates polymerase when close to it
   Activators are modular – can be moved to other DNA sequences
   Activators have two functional domains that are independent of each other and can be separated; the activating domain (ACT) and the DNA-binding domain (DBD)
   Zinc fingers
   2-hybrid screen
   HATs – histone acetyltransferases (acetylation)
   HDACs – Histone deacetylases (deacetylation)
o   Activated DNA is more open, less compact
   Gene activation is synergistic
   The activation process in eukaryotes has many steps and the order of the steps is gene-specific
   Eukaryotic repressors can be direct:
o   Competitive DNA binding
o   Masking the activation surface
o   Direct interaction with general transcription factors
   Eukaryotic repressors can be indirect
o   Recruitment of chromatin remodeling factors
o   Recruitment of histone deacetylases
o   Recruitment of histone methyl tranferase
   Co-activators/co-repressors
   Enhanceosome
o   DNA-bending protein
   Spatial transcriptional regulation
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


S

... making diagrams showing the interlinked pathways worked better for me than listing the steps, in Biochem and Molecular Cell Biology. Form IS function, at that level, and drawing an arrow was easier to remember than the full text of pages of notes. First thing I did on every exam was flip to a blank back page and draw out all the diagrams I had made myself.

... it's such a miserable rush.

Mesozoic Mister Nigel

#289
Quote from: S the Mad on December 08, 2014, 05:08:23 AM
... making diagrams showing the interlinked pathways worked better for me than listing the steps, in Biochem and Molecular Cell Biology. Form IS function, at that level, and drawing an arrow was easier to remember than the full text of pages of notes. First thing I did on every exam was flip to a blank back page and draw out all the diagrams I had made myself.

... it's such a miserable rush.

Sounds like you didn't have a shitty instructor, and merely understanding mechanisms was adequate for you to pass the exams.

But of course, obviously typing up my notes from class makes it clear that I'm not studying in any other way.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Cain

Zinc fingers suck.  I don't want fizzy fingertips  :sad:

Mesozoic Mister Nigel

Quote from: Cain on December 08, 2014, 08:16:14 AM
Zinc fingers suck.  I don't want fizzy fingertips  :sad:

They're the WORST.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Mesozoic Mister Nigel



The fact that I only need 75% on the Ochem final tomorrow to keep my A is REALLY not helping motivate me to study, here.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Mesozoic Mister Nigel

I submitted my piece of the Powerpoint and a 4-page paper to my Systems Science group project folder yesterday. We were all supposed to have pieces in by last night so we could compile and edit today.

Amount of submissions from teammates: 0.

I hate team projects.

Theoretically I should warm up my studio so I can finish my meta-representation, which I decided would be cool to do in glass, LOL. It's 40 degrees down there. This is something I should have thought of in advance, what with it being December.

Bitterness and Finals overcome me. No amount of caffeine can sweeten my attitude.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Mesozoic Mister Nigel

My neurophysiology book sits here, mocking.

It's my favorite class this term, but I'm fucking over it.

"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Doktor Howl

Quote from: Mesozoic Mister Nigel on December 08, 2014, 11:53:52 PM
My neurophysiology book sits here, mocking.

It's my favorite class this term, but I'm fucking over it.




No loafing.

Do not question the system.
Molon Lube

Mesozoic Mister Nigel

I also realized far too late that we won't be getting our projects back, and the meta-representation I proposed is worth about $175.

Fuck.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Mesozoic Mister Nigel

Quote from: Doktor Howl on December 08, 2014, 11:54:26 PM
Quote from: Mesozoic Mister Nigel on December 08, 2014, 11:53:52 PM
My neurophysiology book sits here, mocking.

It's my favorite class this term, but I'm fucking over it.




No loafing.

Do not question the system.

I'm probably going to end up with a B in Mol Bio and you know what? I DON'T EVEN CARE ANYMORE.
"I'm guessing it was January 2007, a meeting in Bethesda, we got a bag of bees and just started smashing them on the desk," Charles Wick said. "It was very complicated."


Doktor Howl

Quote from: Mesozoic Mister Nigel on December 08, 2014, 11:58:09 PM
I also realized far too late that we won't be getting our projects back,.

What?
Molon Lube

Doktor Howl

Quote from: Mesozoic Mister Nigel on December 08, 2014, 11:58:50 PM
Quote from: Doktor Howl on December 08, 2014, 11:54:26 PM
Quote from: Mesozoic Mister Nigel on December 08, 2014, 11:53:52 PM
My neurophysiology book sits here, mocking.

It's my favorite class this term, but I'm fucking over it.




No loafing.

Do not question the system.

I'm probably going to end up with a B in Mol Bio and you know what? I DON'T EVEN CARE ANYMORE.

You sound as if you might be questioning The System.
Molon Lube