Additional study material
to accompany
Analytical Biochemistry Fall 2004
Updated
December 2, 2004
INDEX:
UV-visible spectroscopy
Cell
disruption and protein purification
Antibodies
Electrophoresis
Protein mass spectrometry
DNA
Cloning
strategies examples from the literature
Polymerase chain reaction
Fluorescence spectroscopy
Radioactivity methods
Centrifugation
UV-visible spectroscopy:
[UV-Visible
absorption spectroscopy, a tutorial from Sheffield-Hallam
University, Sheffield, UK]
[The
electromagnetic spectrum]
[Why is
the sky blue? Rayleigh scattering!]
[The
Beer-Lambert Law]
[Deuterium Lamp]
[Diffraction
Grating]
[Light
detectors: Photomultipliers and photodidodes]
[Choosing
the Detector for your Unique Light Sensing Application]: a
comparison paper from Perkin-Elmer Corp.
[Diode-array
spectrophotometer]
[An
example of the application of optical difference spectroscopy to the
study of enzymes]
Cell
disruption and Protein purification:
[Breaking
Up Isn't Hard To Do: A cacophony of sonicators, cell bombs, and grinders],
from The Scientist
[Ultrasonic homogenizers]
and [Mechanical
tissue grinders]
The [Protein Purification Handbook] (large
.pdf file) from [Amersham
Biosciences]
[HiLoad gel filtration columns from Pharmacia]
[Sephadex G25 for desalting and gel-filtration]
[Calibrating
a gel filtration column]
[Packing spheres:
Kepler's conjecture]
[Ion exchange chromatography on Sephadex]
Antibodies:
Rockland
Immunochemicals for Research
[Mike's
Immunoglobulin Structure/Function External Links Page]
[The home page
for the textbook Immunology, by J. Kuby]
[Formation
of precipitin complexes]
Electrophoresis:
Arne Tiselius,
father of electrophoresis; Nobel Prize in Chemistry, 1948.
[Introduction
to Electrophoresis]: from the Cell Biology Laboratory Manual
Gustavus Adolphus College, St. Peter, MN, USA.
[Detailed instruction manual for 2-D Gels from
Amersham-Pharmacia]
[Take
a look at a 2-D protein gel] from the [Swiss-Prot 2D-PAGE database]
[The Electrophoresis Society]:
an international organization founded to improve and promote technologies necessary
for biomolecular separation and detection.
Protein Mass spectrometry:
[Nobel Prize
in Chemistry - for their development of soft desorption ionisation methods for
mass spectrometric analyses of biological macromolecules]
[Mass
Spectrometry Links and Resources]
[A
review article on MALDI MS of proteins]
A good introduction to [MALDI-TOF
MS]
and a [review
on electrospray MS of proteins]
Electrospray
: Principles and Practice (review article from J. Mass Spectr.)
[Protein
sequencing by mass spectrometry]
[DNA
sequencing by mass spectrometry]
[Guelph
gets its own MALDI-TOF MS instrument]
DNA:
[Restriction enzyme
database]
[T4
Polynucleotide Kinase]
[Southern
blotting] A schematic diagram (used in the lecture)
[Southern
blotting] A detailed lab. protocol; Department of Human and
Clinical Genetics, Leiden University Medical Center, Netherlands
[Northern
blotting] A detailed lab. protocol; Univ.
Gesamthochschule Kassel, Germany
[Example
of a Southern blot]
[Example
of a Northern blot]
[Using
an RFLP to trace the sickle-cell gene in a pedigree]
[DNA
fingerprinting with RFLPs]
[cDNA
synthesis methods] A page from the University of Durham, U.K.
[Exons and introns: split genes: The Nobel Prize in
Physiology or Medicine, 1993]
[Cloning vector database]
[LacZ
-Complementation and E. coli cloning systems] A page from
the Department of Biology at U.C. Santa Cruz
[Plasmid
and phage vectors - introduction] A page from Oklahoma State
University
[Prokaryotic
Expression Vectors] A page from the Institute of Molecular
Biophysics, Florida State University
[Plasmid vectors]
(Stratagene Corp.)
[Cloning
vectors] A page from the University of Mississippi
[Slide
show on cloning methods] A page from McGill University
[RT-PCR]
an animation
Cloning
strategies: examples from the literature
Screening
by hybridization to a probe designed on the basis of a peptide sequence
Screening
an expression library with an antibody
Selection
of clones by complementation of biological function
Positional
cloning
Cloning
by identification of sequences in GenBank database
[Dideoxy
DNA Sequencing]
[DNA
sequencing with dye primers or "dye-deoxy" terminators]
[Mapping
and Sequencing the Human Genome] a WWW page at the Human Genome
Project
[Paul Berg,
Walter Gilbert, and Frederick Sanger, The Nobel Prize in Chemistry 1980]
Polymerase Chain Reaction:
[The polymerase
chain reaction]
[A
nice animated cartoon of the PCR process]
[The Polymerase Chain
Reaction (PCR) Jump Station: The ultimate Web page
for information
and links on all aspects of PCR]
[Kary
B. Mullis and Michael Smith, The Nobel Prize in Chemistry 1993]
Fluorescence spectroscopy:
[An
interactive Jablonski diagram]
[Quantitative
fluorometry]
[Fluorescence
spectroscopy of biosystems]
[Stopped-flow
apparatus]
[Fluorescence
resonance energy transfer]
Radioactivity methods:
[Liquid
scintillation counting] - a comprehensive and informative set of
pages about LSC, prepared for a course at UCLA - highly recommended.
[Radioisotopes]:
a comprehensive intro. from Texas A&M University; decay modes and
kinetics, scintillation counting, etc.
[Nuclear
chemistry] (from the "Virtual University North")
Isotopes: [The
band of stability]
[Neutrino Physics]
(from Duke Univ.)
[Radiation
Units]: Curie, Roentgen, Rad, Rem, Becquerel, Gray, and Sievert;
(from the Oak Ridges Associated Universities.)
[ICN Radiochemicals]:
a commercial supplier of radiolabelled compounds.
[Liquid
scintillation counting] - another nice introduction, from Dept. of
Chemistry and Physics at The Nottingham Trent University, U.K.;
this covers everything we will discuss in class, and more.
Centrifugation:
[Centrifugation]
- a detailed Web page from Texas A&M: OK for an introduction ...
[Archimedes'
Principle] (in case you have forgotten it!) and the wonderful (if apocryphal)
story
of its [discovery].
Theodor Svedberg,
the inventor of the ultracentrifuge; Nobel Prize in Chemistry, 1926.
[Sorvall
Centrifuges]
[National Analytical Ultracentrifugation
Facility at the University of Connecticut]
["Centrifuge
Improvements Put New Spin On A Laboratory Workhorse" (from: The
Scientist 9[5]:18, Mar. 06, 1995)]
[Spinning
with Dave: David Yphantis's contributions to ultracentrifugation, Correia
et al., Biophys
Chem. 108: 23-42, 2004]
[The
CENTRIFUGE HELPER page calculates relative centrifugal force]
[Density
Gradient Centrifugation]
[Density
gradient media] (Amersham)
[Density
gradient centrifugation] (Axis-Shield; click on "Techniques" to see many
specific density-gradient applications)
[Meselson-Stahl
experiment (Semiconservative replication of DNA)]
["Biotech
And Drug Industry Interest Fueling The Centrifuge Revolution"];
article from "The Scientist", 1996
[Stokes'
Law] Univ. of Virginia
[Sucrose
density gradient: Example:
application to study protein oligomerization]
[The
Determination of Molecular Weights by Sedimentation Equilibrium]
(Beckman)
[Sedimentation
equilibrium: Example: application to determination of protein MW]