Bio Exam 2 Review PDF

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Exam 2 Review...

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Bio Exam 2 Review Kd: high = low affinity, vice versa 

Pull down assay, see what sticks - NOT a good experiment for this

Enzyme Activity: 3 way can alter protein activity 

Encourage precise molecule orientation for rxn. to happen

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Rearrange electrons in substrate, crating partial charges that favor reaction

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Strain molecule to force it towards transition state

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Enzyme concentration constant unless stated otherwise

Allosteric Regulation: regulates portion of proteins that’s not active site, can still change conformational state of active site, positive or negative regulation

Post Translational Modification: 

Ubiquitin mediated proteolysis, phosphorylation, covalent modification,

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Cleaving of signal sequence, etc. NOT alternative splicing

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Ex. p53: upregulates CDK inhibitors which completes translation but stops this and cell cycle - different forms of modification decides what p53 helps out with

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Study more examples like Ras and motor proteins (help microtubule and spindle formation, need to “walk”)

Protein Trafficking: 

Made in cytosol, needs signal sequence

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Ones that function in cytosol don’t have signal sequence

ER: 

entry signal, N-terminus, hydrophobic chains and a few charges aa’s, signal cleaved upon entry

Retention in ER lumen: 

entry signal AND retention signal, N-terminus (entry) and C-terminus (retention), charges aa’s, entry sequence is cleaved - retention signal is not

Mitochondria: 

Entry signal, N-terminus, interspersed + charged aa’s, cleaved upon entry

Nucleus: 

Import (NLS) and/or export (NES), within ass sequence, not on a terminus, lots of positive aa’s in a row, no protein enters folded and signal is not cleaved

Peroxisome: 

Within aa sequence, + charged aa’s, signal is not cleaved

(more in-depth info about this on slides)

GAP and GEF: 

GEF: nucleus, remove GDP from binding pocket of RAN allowing GTP to diffuse in

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GAP: cytoplasm, hydrolysis of GTP -> GDP

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Import: importin binds to cargo w/NLS, goes into nucleus, GEF makes Ran-GDP -> Ran-GTP, goes out of nucleus, which binds to importin to let go of cargo, GAP makes Ran-GTP -> Ran-GTP, importin unbinds and can rebind to cargo

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Export: eportin bound to cargo, GEF makes Ran GTP -> GDP, goes out of nucleus, GAP makes Ran-GDP -> GTP, lets go of cargo

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Practice Q: What would be the consequences of the following mutations on nuclear export? o

NEED to identify: location, function, mechanism, result

o

A non-functional Ran-GAP? 

In cytoplasm, function is hydrolysis of GTP -> GDP, if it’s bound to GTP it cannot let go of exportin or cargo protein, results in accumulation of exportin bound in cytoplasm

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A non-functional Ran-GEF?

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In nucleus, function is GDP removing from binding pocket -> GTP diffusing in, needs to ind to exportin, protein will not get into nucleus

Coding: 

Promoter: controls how much mRNA is transcribed an where it begins, noncoding region

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Start codon: transcription begins

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Stop codon: transcription ends, 3 different codes

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Coding region always on internal segment, the Cap 5’ UTR, 3’ UTR and poly-A tail serve other functions (ex. protection)

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***

RNA types: 

mRNA: “coding” carries nucleotide sequence from DNS to then be translated

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tRNA: “transfer” link between mRNA and amino acids, transfers them to ribosomes

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rRNA: “ribosomal”, non-coding intertwines ***

Central Dogma: DNA -> RNA -> Protein TF’s: 

General: required at every promoter, help polymerase attach

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Regulatory: promoter specific o

Negative regulation: prevents transcription of particular genes

o

Positive: activator, increases transcription

Operons: 

Series of genes transcribed at same time in multi-gene mRNA, mainly in prokaryotes but can exist in eukaryotes

RNA Polymerase: synthesis of RNA from existing DNA, not sequence specific, needs help to bind to DNA 

Prokaryotes: sigma factors

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Eukaryotes: Basal transcription factors

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Transcription initiated: RNA polymerase not sequence specific...