BCH 304: Determination of Nucleic Acids and The Protein Data Bank

Flashcards about Nucleic Acids Determination and The Protein Data Bank

What detergent is used in the isolation of plant DNA to complex with carbohydrates?

Cetyltrimethylammonium bromide (CTAB)

What is the purpose of washing the DNA pellet with 70% ethanol during plant DNA isolation?

To remove traces of CTAB and chloroform

What is the ideal A260/A280 ratio for pure DNA?

1.8-2.0

What does a low A260/A280 ratio indicate?

Presence of contaminants such as proteins

What are three classes of total RNA?

Ribosomal, messenger, and transfer RNA

Which method is commonly used to recover total RNA intact from plant materials?

The phenol-chloroform method

What treatment inactivates contaminating RNases in solutions used for RNA isolation?

Rinsing glassware with 1% diethyl pyrocarbonate solution

What type of data do protein data provide?

Crystallographic or 3-dimensional structural data about proteins and nucleic acids

What structural determination methods are used to obtain data for the Protein Data Bank (PDB)?

X-ray crystallography, NMR spectroscopy, and Cryoelectron microscopy

What is the purpose of the Protein Data Bank (PDB)?

A repository or database where biologists and biochemists make available or publish macromolecular structure information

List three websites to search for the Protein Data Bank (PDB).

www.wwpdb.org, www.pdbe.org, www.rcsb.org/pdb

What is the PDB accession code?

A unique alphanumeric identifier for each PDB structure in the database

Name a program that can be used to visualize 3-D structures of PDB files.

Pymol, VMD, Rasmol, MDL Chime, UCSF Chimera, Swiss-PDB Viewer, StarBiochem, Sirius, Vis Prot3DS, Discovery Studio etc