I am just a newbie undergrad (graduating next quarter ) lab rat. I've done a lot of PCRs, minipreps, transformation. Basically the standard stuff. All of them involve solutions like Tris, NaOH, EDTA, acetic acid, SDS. I kind of know what all these solutions do on their own, but not within the context of these different protocols. I just want a clarification on what all these solutions do exactly:

Miniprep
-3 solutions are generally used: 1) glucose, tris, EDTA. 2)NaOH, SDS. 3)Acetate, Glacial acetic acid

PCR
-MgCl, Thermophilic buffer, DMSO (sometimes), Glycerol (sometimes)

Electrophoresis
-TAE, EtBr

Gel extraction. We use the Qiagen kit for gel extraction.
-Why add the ethanol after we dissolve the agarose.
-I see buffer TE or EB a lot in storing DNA/Cell. What exactly are these buffers.

Every lab probably do stuff a bit differently. If I am missing something, please enlighten me.

1) glucose, tris, EDTA.
in order to resuspend cells without osmotic breakage : tris EDTA : pH stability, glucose : getting appropriate osmolarity to avoid water transfert from the bacterias.
2)NaOH, SDS.
Lysis of cells (SDS is deteegent, alomst same as in toothpaste
3)Acetate, Glacial acetic acid
acidification of pH of solution that drives precipitation of genomic DNA and all debris

Mg++: helps transferts of phosphate that is necessary for elongation,
Thermophilic buffer : look in the datasheet of the enzyme,
DMSO (sometimes) : by increasing stringency, helps reduncing the non specificity of annealing process, Glycerol (sometimes) : i don't know

Electrophoresis
-TAE tris acetate EDTA : tris if for buffering ans acetate is for adjusting pH to the required value.
EtBr : by it's particular structure, it can intercalate DNA and RNA (a currently open topic deals with intercalation of RNA by EtBr)


Gel extraction. We use the Qiagen kit for gel extraction.
-Why add the ethanol after we dissolve the agarose : dissolution of agarose release the DNA from agarose and ethanol addition (but i think it's probably isopropanol) drive a general hydrophobication of the solution and helps bounding to the column of the DNA
-I see buffer TE or EB a lot in storing DNA/Cell. What exactly are these buffers. TE : 10mM tris EDTA pH8, EB is 10mM tris pH 8


you know what : google helps too.