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Friday, December 19, 2008

Web Source: Enzyme Assay Protocols

Alkaline Phosphatase


Ascorbate Oxidase


Acetyl CoA Synthase


Alanine Dehydrogenase


Alcohol Dehydrogenase


Aminolevulinate Synthase


Assay and Purification of Enzymes-Oxalate Decarboxylase; Chapter 5


Beta-galactosidase enzyme assay


Chymotrypsin


Chymotrypsinogen


Citrate Synthase


b-Galactosidase


Deoxyribonuclease


ELISA-Based Assay for Glycosyltransferases



Enzyme Assay (Presentation)


Enzyme Assay Protocol


Enzyme Assay Protocol (SudingLab)


Enzyme assay using ultra-low volume surface micromachined sensors


Gamma Glutamyl Transferase


Glucokinase



GDP-ase Assay



Glucose Oxidase


High Throughput Screening Using Enzyme Assay Microarrays


Hyaluronidase


Introduction to Enzyme Kinetics: Assay of beta-Galactosidase.


Invertase Assay


Isocitrate Lyase


Lactate Dehydrogenase


Malate Dehydrogenase


Malic Enzyme


NADH oxidase


KEX2 Assay


Kinase Enzyme Assay


Lipoxidase


Organelle Isolation and Marker Enzyme Assay (Multiple Protocols)


Peroxidase (Guaiacol Units)


Peroxidase (Purpurogallin Units)


PM ATPase Assay


Preparation of Cell Extract


PEP Carboxykinase


PEP Carboxylase


Pyruvate Carboxylase


Pyruvate Decarboxylase


Pyruvate Dehydrogenase


Pyruvate Kinase


Pyruvate Oxidase


Tyrosine Phenol Lyase


Xylitol Dehydrogenase


Xylose Reductase



Ribonuclease



SOLID-PHASE NON-SEPARATION ENZYME ASSAY



Trypsin



Trypsin Inhibitor



Trypsinogen



Wapedia - Wiki: Enzyme assay

Thursday, December 18, 2008

Web Source: Proteins and Structures

Circular dichroism
http://osu.orst.edu/dept/biochem/varselec.html


Evolution of chaperones
http://www.uni-erlangen.de/pharmakologie/arbeit/fitforli.htm


Green fluorescent protein Chime tutorial
http://www.biochem.mcw.edu/science_ed/Pages/gfp/exercise_1/chime/index.htm


Hyperactive molecules
http://www.ch.ic.ac.uk/chemical_mime.html


Hyperactive molecules: Part 2
http://www.ch.ic.ac.uk/hm_second.html


Introduction to Protein Structure

http://webhost.bridgew.edu/fgorga/proteins/default.htm


Large molecule problem set
http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/large_molecules_problems.html


Molecular origami
http://www.tc.cornell.edu/er/sci93/dis22origami/dis22origami.html


Protein Structure (Online Lecture)

http://lectures.molgen.mpg.de/ProteinStructure/index.html


Protein Structure (Video Resource)

http://video.google.com/videosearch?q=protein+structure&ie=utf-8&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&sa=X&oi=video_result_group&resnum=8&ct=title#


Protein and Peptide Structures (Tutorials)

http://www.bmb.uga.edu/wampler/tutorial/


Protein Data Bank (A Source of Studying)

http://www.rcsb.org/pdb/home/home.do


Principles of Protein Structure

http://www.cryst.bbk.ac.uk/PPS2/


Protein Structure (Animation)

http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html


Proteins

http://www.friedli.com/herbs/phytochem/proteins.html


Protein structure (from Wikipedia)

http://en.wikipedia.org/wiki/Protein_structure


Principles of protein structure
http://www.cryst.bbk.ac.uk/PPS2/course/index.html


Studying protein molecules with Chime
http://cti.itc.Virginia.EDU/~cmg/Demo/molecule.html


X-ray crystallography
http://www.imb-jena.de/www_sbx/manfred/teach/page1.html

Web Source: Amino Acids

Amino Acids Properties

http://prowl.rockefeller.edu/aainfo/contents.htm


Amino Acids (A Database)

http://www.bioscience.org/urllists/aminacid.htm


Amino acid-- Britannica Online Encyclopedia

http://www.britannica.com/EBchecked/topic/20691/amino-acid


Amino acid basics (Animations)

http://www.johnkyrk.com/aminoacid.html


Amino Acids

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AminoAcids.html


Amino Acids and Peptides

http://www.chem.qmul.ac.uk/iupac/AminoAcid/


Amino acids: Structures and properties
http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html


Amino Acids. Name Abbr. Linear structure formula

http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids_en.html


Amino acid (Wikipedia, the free encyclopedia)

http://en.wikipedia.org/wiki/Amino_acid


Amino Acids Section

http://www.nyu.edu/pages/mathmol/library/life/life1.html


A variety of properties of amino acids
http://prowl.rockefeller.edu/aainfo/contents.htm


Amino acids and peptide bonds
http://www.iacr.bbsrc.ac.uk/notebook/courses/guide/aa.htm


Amino acid frequencies in particular protein chains
http://asparagin.cenargen.embrapa.br/SCORPION/


Amino Acid Repository
http://www.imb-jena.de/IMAGE_AA.html


Chime structures of all the amino acids
http://www.clunet.edu/BioDev/omm/aa/aa.htm


Colorful photos of amino acids
http://micro.magnet.fsu.edu/micro/gallery/aminoacid/aminoacid.html


General Amino Acid Information
http://www.eng.uci.edu/~hslee/aminoacid.html

Images for amino acids

http://www.google.com/search?client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial&channel=s&hl=en&q=amino+acids&btnG=Google+Search


Introduction To Amino Acids

http://www.cryst.bbk.ac.uk/education/AminoAcid/overview.html


Online quizz on amino acids
http://info.bio.cmu.edu/Courses/BiochemMols/PQuiz/PQInst.html


Reference Guide for AMINO ACIDS

http://www.realtime.net/anr/aminoacd.html


The Amino Acids Collection

http://micro.magnet.fsu.edu/aminoacids/index.html


The Amino Acid Repository

http://www.imb-jena.de/IMAGE_AA.html


The Chemistry of Amino Acids

http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.html

Web Source: Nucleotide metabolism (Synthesis and Degradation of Nucleotides)

Nucleotide metabolism
http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html


Nucleotides and muscle metabolism
http://www.bmb.leeds.ac.uk/illingworth/muscle/#nucleotides


Nucleotide Metabolism

http://seqcore.brcf.med.umich.edu/mcb500/nucsyl/nucmetab.html


Nucleotide Metabolism

http://www.roberts-publishers.com/mcmurry/Chapter06.pdf


Purine and pyrimidine nucleotide metabolism in higher plants.

http://www.ncbi.nlm.nih.gov/pubmed/14658380


Purine and Pyrimidine Metabolism

http://library.med.utah.edu/NetBiochem/pupyr/pp.htm


Nucleotide metabolism (Homo sapiens)

http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=15869


Nucleotide Metabolism

http://www.bmb.leeds.ac.uk/illingworth/metabol/nucleo.htm


Nucleotide Metabolism (Q)

http://biochemistryquestions.wordpress.com/category/nucleotide-metabolism-q/


Nucleotide Metabolism

http://www.chemistry24.com/biochemistry/nucleotide-metabolism.html


Nucleotide Metabolism (Quiz Questions)

http://wps.prenhall.com/esm_horton_biochemistry_4/37/9595/2456409.cw/index.html


Nucleotide Metabolism. Nucleotide sources

http://www.rose-hulman.edu/~brandt/Chem330/Nucleotide_metabolism.pdf


AmiGO: nucleotide metabolic process Details

http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0009117&session_id=1623amigo1229589037

Web Source: Lipid Biosynthesis

Cholesterol metabolism
http://swnt240.swmed.edu/gradschool/webrib/goldstei.htm


Fatty Acid and Lipid Synthesis

http://dwb.unl.edu/teacher/nsf/c11/c11links/www.bact.wisc.edu/microtextbook/metabolism/lipidSyn.html


Lipid biosynthesis
http://www.ncbi.nlm.nih.gov/pubmed/7640528


Genomics Approaches to lipid biosynthesis
http://www.cropscience.org.au/icsc2004/symposia/3/5/156_ohlroggejb.htm


Lipid Biosynthesis and Its Coordination with Cell Cycle Progression

http://pcp.oxfordjournals.org/cgi/content/abstract/pci213v1


Lipid Biosynthesis

http://www.bmb.leeds.ac.uk/illingworth/metabol/lipids2.htm


Membrane dynamics related to lipid biosynthesis and apoptosis

http://www.bc.vet.uu.nl/BCHome/ProjCV/apoptosis.HTM


Mycobacterial lipids
http://bioscience.org/1997/v2/d/barrow/d387-400.htm


Evolution of Lipid Biosynthesis Enzymes and the Oxygen Cycle

http://www.eps.harvard.edu/people/faculty/pearsonlab/research/rs4/rs4.html


Lipid Biosynthetic Pathways

http://www.cem.msu.edu/~reusch/VirtualText/lipids.htm#synth

Wednesday, December 17, 2008

Biochemistry Graphics on the Web

Amino Acids & Proteins

Biochemistry Website at UCSB with Chime displays of amino acids and proteins.

Biological Sciences 102 Home Page at UC Davis.

Biomolecular Structures at Göteborg University (Sweden) shows molecules as Chime images with brief explanations.

Interactive Biochemistry at the University of Virginia. Some of the topics require Java to be enabled (Under Netscape's Options menu, choose Network Preferences..., then Languages.) The above link will open a new Netscape page (785 x 475). If you prefer, use a direct link to the same content.

Medical Biochemistry at Univ. Kansas Medical Center. Elegant Chime displays from a slow server.

Online Macrmolecular Museum at Kenyon College.

Structure and Packing of the Alpha Helix A detailed tutorial on the -helix and on the uses of the RasMol command line. From Duane Sears and coworkers at University California, Santa Barbara.

Structure and Packing of the Beta Pleated Sheet A detailed tutorial on the -sheet and on the uses of the RasMol command line. From Duane Sears and coworkers at University California, Santa Barbara.

The Biology Hypertextbook Home Page at MIT. Many topics are displayed as GIFs, with self-quizzes on each topic.

Web Biochemistry Amino acid and protein tutorials (with quizzes) at Curtin University in Perth, W. Australia.


Glycolysis

Design It Yourself Glycolysis Homepage. Stepwise quiz on the pathway.

Image map to KLOTHO files.

Metabolic Pathways of Biochemistry Major pathways are shown as 2-D (GIFs) or 3-D (Chime images) with each on a single page.

Select an EC number to obtain further information on enzyme and reaction catalyzed.

Step by Step Glycolysis. Fact Sheet; Reaction & Animation (Windows 3.1).

The Glycolysis Pathway View substrates, and products (GIFs); and enzyme structures (RasMol).


TCA Cycle

TCA Cycle Intermediates using Chime with capsule comments at Univ. Kansas Medical Center.

TCA Cycle Problem Solving (MS Windows Only).


General & Miscellaneous

Biochemistry: A Virtual Text, to accompany Biochemistry, 2nd edition by Mathews and van Holde. Mostly GIFs and JPEGs, but some structures can be viewed with RasMol or Chime.

Dictionary of Science and Technology, a cross-referenced source that explains all of the terms used here. Provides GIF graphics of some of the molecules.

O Dictionary Library for Hetero Compounds is a catalog of more than 1100 "hetero compounds" found in the Protein Data Bank. This comprehensive listing (150Kb) allows the user to view the molecules with the Chime plug-in. The same information in a linked seven page format (30K per page) is also available.

Periodic Tables of the Elements with clickable links to their chemical and physical properties, etc.

Principles of Protein Structure using the internet, the U.S. mirror site for the Birbeck College (U.K.) course. Detailed explanations and informative graphics on all aspects of the topic.

Swiss-Quiz Multiple choice questions on molecular biology, biochemistry, and genetics. (Perfect scores are rewarded with some Swiss chocolate!)

SourceDr. William McClure