Exam 1: Ch 3 Protein Purification and Analysis Flashcards Preview

Cellular and Molecular Biology > Exam 1: Ch 3 Protein Purification and Analysis > Flashcards

Flashcards in Exam 1: Ch 3 Protein Purification and Analysis Deck (34):

overall task

to separate (resolve) a protein from others based on physical or chemical differences


3 most widely used characteristics for separating proteins

size (length or mass)

net electrical charge

binding affinity for specific ligands



weight of a sample (in daltons or AMU) where density is the ratio of its mass to volume (g/L)


proteins vary greatly in ____ but not ____

mass, density



two particles in suspension with different masses or densities settle to the bottom of a tube at different rates

heavier or more dense molecules settle (sediment) faster than lighter or less dense molecules


2 purposes centrifugation is used for

preparative technique to separate one type of material from another

analytical technique to measure physical properties of macromolecules


differential centrifugation

separation of water-soluble proteins from insoluble cellular material

cell organelles and fragments form a pellet at the bottom of the tube, and proteins are in the supernatent


rate-zonal centrifugation

separation of water-soluble proteins through a solution of increasing density called a density gradient (often sucrose)

proteins separate into bands/disks based on their mass



technique for separating molecules under an applied electric field

dissolved molecules move through an electric field at a speed determined by their charge to mass ratio



SDS ionic detergent denatures multimeric proteins

electrophoresis in polyacrylamide gel separates by size b/c of sieving action (small moves faster)

SDS binds proteins proportional to length of pp chain


2D gel electrophoresis

combines SDS-PAGE with a pH gradient

1st separates proteins by charge then by mass

negative charge migrates toward anode, positive toward cathode until reach isoelectric point (pH when net charge of protein is 0)


liquid chromatography

sample placed on a packed column of spherical beads in a cylinder and flows down via gravity or a pump

nature of the beads separate by mass, charge, or binding affinity


gel filtration chromatography

separates proteins by mass

beads in columns have tunnels

small proteins get trapped in tunnels and move slowly, big proteins filter right through (more quickly)


ion-exchange chromatography

separates proteins by charge

beads have carboxyl groups ( - ) or amino groups ( + )

negatively charged proteins get stuck to amino beads, and positive charged proteins get stuck to carboxyl beads

elute with high [ ] of salt solution


affinity chromatography

ligands or mother molecules that bind to the protein are covalently attached to beads

antibody affinity, immunoaffinity are commonly used



detects presence of a molecule of interest as it is separated from other molecules

uses a distinctive characteristic of the protein like binding a specific ligand, catalyzing a specific rxn, or being recognized by a specific antibody


chromogenic and light-emitting enzyme rxns

enzyme assays detect loss of substrate or formation of product

chromogenic substrates change color during the rxn


antibody assays

antibodies specifically recognize the epitope of an antigen

presence of the epitope visualized by labeling antibody with an enzyme that is fluorescent or radioactive

green fluorescent protein found in jellyfish is used


detecting proteins in gels

proteins embedded in 1 or 2D gels not usually visible

must label or stain proteins while they're in the gel or electrophoretically transfer the proteins to a membrane of nitrocellulose and then detect them

proteins dyed with organic dye or silver based stain


immunoblotting (Western blotting)

separate proteins and then identify a specific protein of interest by using 2 diff antibodies

1st antibody binds to epitope on target protein

2nd antibody binds to 1st antibody and has an enzyme or other molecule attached that generates color or light (chemiluminescence)


epitope tagging

biosynthetically or chemically attaching epitope to an unrelated protein

antibodies generated by injecting intact protein or a fragment of the protein into a rabbit to induce antibody formation


specific activity

amount of radioactivity per unit of material

measured in disintegrations per minute (dpm) per millimole



time required for half the atoms to undergo radioactive decay

shorter half-life equals higher specific activity



one atom in a radiolabeled molecule that is in a radioactive form


common radioisotopes used





how is radioactivity detected

geiger counter: handheld

scintillation counter: mix with liquid containing fluorescent compound that emits a flash of light when it absorbs radiowaves


pulse-chase experiment

trace changes in intracellular location of proteins over time

radiolabeled compound attached to cellular molecule of interest "pulse"

"chase" is incubation period when samples are taken to determine location of the pulse


mass spectrometry

determine mass of a protein or fragments

ratio of mass of a charged molecule to its charge



4 key features of a MS

ion source that transfers protons to the protein

mass analyzer in a vacuum separates ions of basis of different m/z

detector measures relative abundance of each ion in the sample

computer data system calibrates instrument


tandem MS/MS

ions break protein into short peptides (less than 25 aa) at the peptide bonds

can determine aa sequence via deduction


determine primary structure with gene sequences

MS performed to find mass fingerprint (list of MW of peptides from the protein)

MWs used to search a genome database to ID the sequences


x-ray crystallography

beams of x-rays passed through a protein crystal to determine 3D structure

creates an electron density map that is analyzed and fit to a molecular model


cryoelectron microscopy

protein sample frozen in liquid helium to preserve structure

then examined in frozen state by a cryoelectron microscope


NMR spectroscopy

3D structure of proteins less than 200 aa studied this way

concentrated protein solution placed in magnetic field and effects of radio frequences on nuclear spin states of different atoms studied

determines distances between atoms