Downloads and Links

DOWNLOADS

STUDENT INFORMATION SHEET (NRLR)

• Ch 151: student_profile_sheet_biochem.doc

• Ch 251: student_profile_sheet_gradstudent_word.doc

HANDOUTS

• Set 1: Review of Key Ideas from General and Organic Chemistry (PDF file): 2 slides per page- ch151-01-Review of Chemistry_2per (reloaded 2010.06.21, sorry for the missing link. Thanks for pointing it out.

EXERCISES

• elisa-virtual-lab worksheet    *  Link to HHMI Virtual Lab Page

LINKS

TEXTBOOK SITES

• BOYER TEXTBOOK SITE: http://bcs.wiley.com/he-bcs/Books?action=index&itemId=0471661791&bcsId=2779
  • animations, quizzes, cutting edge science topics, and more!
• MOLECULAR CELL BIOLOGY by Lodish, Berk, Zipursky, Matsudaira, Baltimore, Darnell site (many of the animations I use come from this textbook’s companion CD): http://www.whfreeman.com/lodish4e/index.htm
• Online version of Stryer’s Biochemistry (5th Ed.) from NCBI: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.TOC&depth=2
• Online version of Garrett and Grisham’s Biochemistry (2nd Ed.) at http://web.virginia.edu/Heidi/home.htm
• Books of the ASCB: http://www.ascb.org

ESSENTIAL BIOCHEMISTRY SITES

• A good review of cell biology: Inside the Cell by the US National Institute of General Medical Sciences <http://publications.nigms.nih.gov/insidethecell/index.html>. Onlie, PDF, and other materials.
• FoldIt! The Protein Folding Game (solve puzzles for science) by David Baker’s Lab and their friends. http://fold.it
• National Center for Biotechnology Information (NCBI) Main Site at http://www.ncbi.nlm.nih.gov/ or http://www.pubmed.org
• ExPASy Proteomics Server at the Swiss Institute of Bioinformatics, including UniProt and SwissProt databases for Proteins: http://www.expasy.ch/
  • guide to some ExPASy tools by Abi Go ’01at http://www.chem.admu.edu.ph/~nina/abi/index.html
• Protein [3-D Structure] Databank at http://www.pdb.org
• Protein structure viewing: Prof. Eric Martz’s site at http://www.molviz.org
• The world of proteins: Proteopedia with easy to use Java tools to look at the molecules in 3-D:  http://proteopedia.org/wiki/index.php/Main_Page
  • More structure-viewing sites are noted below under sites for self-study.

DATABASES GALORE

• The Human Protein Atlas: http://www.proteinatlas.org/
• MitoCarta: mitochondrial proteome: http://www.broadinstitute.org/pubs/MitoCarta/index.html
• Eukaryotic Pathogen Database: Malaria and more: http://eupathdb.org/eupathdb/
• Eucheuma denticulatum ESTs: http://www.inbiosis.ukm.my/eudbase/

PHILIPPINE-CENTRIC INFORMATION PORTALS

• Philippines: Health Research and Development Information Network (HERDIN) of the Philippine Council for Health Research and Development, DOST: http://www.herdin.ph/
• eHealth Philippines: http://www.ehealth.ph/
• Philippine Science Letters (an open access journal edited by Dr. Eduardo A. Padlan and Dr. Gisela P. Concepcion): http://www.philsciletters.org/
• Philippine Journals Online:  http://philjol.org/
  • Includes Philippine Agricultural Scientist, Philippine Scientist, Philippine Journal of Internal Medicine, Philippine Journal of Neurology, Philippine Journal of Otolaryngology Head and Neck Surgery, Philippine Journal of Psychology, Philippine Journal of Systematic Biology, Philippine Scientific Journal, and more.
• Philippine Journal of Science: http://philjournalsci.dost.gov.ph/ (full text for June 2010 issue out)
• Philippine eLib: http://www.elib.gov.ph/

GENERAL SITES FOR VIDEOS, LECTURES, and MORE

• Howard Hughes Medical Institute: http://www.hhmi.org/biointeractive/
  • must view for Pinoys: Our very own Toto Olivera and his cone snails! http://www.hhmi.org/biointeractive/biodiversity/lectures.html
  • See his Nemo-eating snails on his web site: http://www.biology.utah.edu/olivera/movies/
• BioVisions project at Harvard: http://multimedia.mcb.harvard.edu/
• iBioSeminars: http://www.ibioseminars.org and http://www.ibiomagazine.org
• Genetic Science Learning Center at the University of Utah: http://learn.genetics.utah.edu/
• Cold Spring Habor DNALearningCenter: http://www.dnalc.org/resources/animations/
• TED- technology, design, and generally cool ideas: http://www.ted.com
• NIH webcasts: http://videocast.nih.gov/
• MIT Open Courseware: http://ocw.mit.edu/OcwWeb/web/home/home/index.htm
• University of California Berkeley webcasts: http://webcast.berkeley.edu/
• University of California TV on demand: http://www.uctv.tv/ondemand/
• OpenMichigan: Resources from the University of Michigan: http://open.umich.edu
• Cell Biology animations: http://www.johnkyrk.com/
• Cell biology images and videos: http://cellimagelibrary.org
• Videos and more on molecular biology techniques: http://www.molecularstation.com/
• Amazing microscopy images at Florida State University’s Molecular Expressions site: http://micro.magnet.fsu.edu/primer/index.html
• Microscopy images fromthe Exploratorium: http://www.exploratorium.edu/imaging_station
• Life Sciences Education: http://www.lifescied.org; http://www.biosciednet.org/portal
• Inside the cell: http://publications.nigms.nih.gov/insidethecell/
• The Wellcome Trust- education resources
  • Genes, Genomes and Health issue of Big Picture, with links to activities like DNA origami:  http://www.wellcome.ac.uk/Education-resources/Teaching-and-education/Big-Picture/All-issues/Genes-Genomes-and-Health/index.htm

SITES FOR SELF-STUDY

Review of Chemistry: Hank Green’s Crash Course Chemistry channel: https://www.youtube.com/playlist?list=PL8dPuuaLjXtPHzzYuWy6fYEaX9mQQ8oGr

The European Bioinformatics Institute’s Train Online site <http://www.ebi.ac.uk/training/online/>

Online quizzing

• Biochemical compounds flash cards <http://quizlet.com/2448514/biochemical-compounds-flash-cards/>

Molecular viewing

• Viewing the basics about the biomolecules (requires Java): Version Biomodel-3v7a  – January 2007 by Angel Herráez, University of Alcalá de Henares, Spain
• Viewing nucleic acids: by Eric Martz, University of Massachusetts, USA
• Viewing DNA packaging: http://images.the-scientist.com/supplementary/video/dnapackaging/DNAi_packaging_vo2-sm.htm(
  Animation by Drew Berry. Used with permission from the Howard Hughes Medical Institute, © 2002. Read more: Navigating the Nucleosome – The Scientist – Magazine of the Life Sciences http://www.the-scientist.com/article/display/55229/#ixzz11TGWvToO)
• Viewing lipids and membranes: http://www2.uah.es/biomodel/en/model2/bilayer/ Eric Martz and Angel Herráez
• Viewing globular proteins: hemoglobin: Eric Martz, University of Massachusetts
• Viewing fibrous proteins: collagen: by Gretchen Heide Bisbort & Karl Oberholser, Messiah College, Pennsylvania, USA
• FoldIt! The Protein Folding Game (solve puzzles for science) by David Baker’s Lab and their friends. http://fold.it
• The Anatomy and Taxonomy of Proteins- http://kinemage.biochem.duke.edu/teaching/anatax/index.html- go through the links and check out the figures: great as a coloring book! Example: http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.3a3.77-1.html. [I’m so glad this is now online! And they’re by an academic grandmother, so I’m proud of it– besides, this is a protein classic!)

Gene expression and control

• Overview of gene expression: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=956592171
• Changes in gene expression, alleles, dominance: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=956612455
• Regulating genes from Nova: http://www.pbs.org/wgbh/nova/teachers/interactives/regulating-genes/index.html
• A video look at transcription from a single gene: http://www.the-scientist.com/blog/display/57561/
• Epigenetics
  • Ghost in Your Genes (companion site to the Nova TV special, with slides, animations, sample video, and more): http://www.pbs.org/wgbh/nova/genes/
  • Visualization prize winner for epigenetics from University of Utah: The Epigenetics of Identical Twins: http://learn.genetics.utah.edu/content/epigenetics/twins/
    • Other related material from the same site, e.g., the impact of pup-licking mothers: http://learn.genetics.utah.edu/content/epigenetics/
  • Science special issue video on epigenetics (2010 Oct 29): http://videolab.sciencemag.org/Featured/650920373001/1

DNA techniques

• Genome Editing
•  
  

  The short, layperson version: Jennifer Doudna on TED 2015 London: http://www.ted.com/talks/jennifer_doudna_we_can_now_edit_our_dna_but_let_s_do_it_wisely#

  •  

    The short, science version: Jennifer Doudna on iBioseminars, 2015: https://www.youtube.com/watch?v=SuAxDVBt7kQ

  •  

    The long version in the context of precision medicine: Jennifer Doudna at the Pacific Symposium on Biocomputing (PSB) 2016 in Hawaii (January 4-8, 2016): https://www.youtube.com/watch?v=3JhG5sVQlPY

  •  

    The other contenders from MIT from a neuroscience perspective: Feng Zhang at the Canada Gairdner Symposium: RNA and the New Genetics by the Gairdner Foundation, published on Nov 24, 2015: https://www.youtube.com/watch?v=yT5JeLVUgdo

  •  

    A panel discussion at the World Science Festival in New York, June 3, 2016: http://www.worldsciencefestival.com/2016/08/splicing-dicing-dna-genome-engineering-crispr-revolution/

  •  

    Biohacking clip: The $140 Mail-Order CRISPR Kit: Is Unregulated Biohacking the Future of Science? from Reason TV Published on Jun 20, 2016: https://www.youtube.com/watch?v=odE8dNcklks

• karyotyping of chromosomes: University of Utah (med students and biochem lab members, take note):
  • Introduction:  http://learn.genetics.utah.edu/content/begin/traits/scientists/
  • Activity: http://learn.genetics.utah.edu/content/begin/traits/karyotype/
  • Some materials on chromosmal aberrations that lead to genetic disorders: http://learn.genetics.utah.edu/content/begin/traits/predictdisorder/
• DNA electrophoresis self-study site at the University of Nebraska-Lincoln: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=1065724861
• Polymerase chain reaction self-study site at the University of Nebraska-Lincoln: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=968252315
• Real time or quantitative PCR (of emerging interest for diagnostics, such as for k-Ras testing in cancer, etc.), with review of PCR: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=1057077340
• Bacterial identification virtual laboratory at the Howard Hughes Medical Institute (absolute must-do): http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html
• Overview of genetic engineering at the University of Nebraska-Lincoln (absolute must-do; links below provide clarifications): http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957879329.
  • DNA extraction – DNA is extracted from an organism known to have the desired trait. http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957882007
  • Gene cloning – The gene of interest is located and copied. http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957884601
    • The mechanics of recombinant engineering (check this out to understand techniques): http://croptechnology.unl.edu/viewLesson.cgi?LessonID=959197140
    • Making and screening gene libraries: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=961796736
  • Gene modification – The gene is modified to express in a desired way by altering and replacing gene regions.
    • Gene design 1: Gene regions. http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957885210
    • Gene design 2: Gene constructs (important for understanding control of gene expression). http://croptechnology.unl.edu/viewLesson.cgi?LessonID=959031259
  • Transformation – The gene(s) are delivered into tissue culture cells, using one of several methods, where hopefully they will land in the nucleus and insert into a chromosome.
    • Plant tissue culture: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957885612
    • Transformation methods: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=958077244
    • Transformation events: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=958660409
  • Backcross breeding – Transgenic lines are crossed with elite lines to make highyielding transgenic lines.
    • Basic gene inheritance: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957885794
    • Backcross breeding: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=959009357
• Genetic engineering vs. breeding: http://croptechnology.unl.edu/viewLesson.cgi?LessonID=991751218
• Genome Consortium for Active Teaching: http://www.bio.davidson.edu/GCAT

Protein techniques lab

• Protein purification lab (thanks, Henson, for the link!) <http://home.btconnect.com/agbooth/archive/swingPP/ProtLab.html>
• ELISA vitual lab at HHMI: http://www.hhmi.org/biointeractive/vlabs/immunology/index.html
• description and photos from MIT
• Isolation of beta-galactosidase from E. coli
• Desalting and qualitative activity assay
• Running SDS-PAGE
• Bradford protein assay and staining the SDS-PAGE gel
• Western blot

Metabolism

• Glycolysis animation by IUBMB:  http://www.iubmb-nicholson.org/swf/glycolysis.swf
• A creative way to look at hexokinase: Glucose Wars by Mike Gibbs, uploaded by mikewoo, Sep 17, 2014:  https://www.youtube.com/watch?v=eRQQ5i0–l8

Introduction to the cell

• http://rosejames.weebly.com/cells.html (Rose James’s class site for cell biology has a umber of good links)
• A game to get to know the cell: http://cellcraftgame.com/

Cell Cycle

• Cell Cycle: <http://croptechnology.unl.edu/viewLesson.cgi?LessonID=979149292>
• Mitosis and the cell cycle from Harvard Outreach: <http://outreach.mcb.harvard.edu/animations/cellcycle.swf>
• Cell cycle checkpoints, especially spindle formation, in normal and cancer cells: <http://outreach.mcb.harvard.edu/animations/checkpoints.swf>
• Biochemical pathways of normal and cancer cells and apoptotic cells (mouse over the molecules to learn more): <http://outreach.mcb.harvard.edu/animations/biochem.swf>
• Introduction to the cell cycle game (about 10 minutes to play): <http://nobelprize.org/educational/medicine/2001/cellcycle.html>
• A cartoon version with some notes on techiques to visualize and synchronize the cell cycle: <http://www.cell-action.com/cell_cycle/cell_cycle.html>
• Cell biology and cancer for high school by the National Cancer Institute, NIH, USA) <http://science.education.nih.gov/supplements/nih1/cancer/default.htm>
• A cyclin is observed cycling: <http://www.the-scientist.com/blog/display/57561/>

Cell differentiation, development, and stem cells

• A Stem Cell Story by the European Stem Cell Consortium: http://www.eurostemcell.org/films
• A cartoon look at what is a stem cell from the Learn Genetics site of the University of Utah Genetic Science Leaning Center <http://learn.genetics.utah.edu/content/tech/stemcells/scintro/>
• Types of stem cells, from the same site: <http://learn.genetics.utah.edu/content/tech/stemcells/sctypes/>
• Embyogenesis and the origin of stem cells, from Harvard Outreach <http://outreach.mcb.harvard.edu/animations/embryo5.swf>
• A simplified visualization of gene expression on the chromosome during differentiation, also from Harvard Outreach <http://outreach.mcb.harvard.edu/animations/preloaderStemCells.swf>

Metabolism Game, with genetics too

• The Genomics Digital Lab: 7-day free trial available: http://www.genomicsdigitallab.com/gdl/default.cfm

Free games

• CellCraft: http://www.kongregate.com/games/CellCraft/cellcraft

OTHER TECHNIQUES PLACES

• Lab protocols: http://www.protocol-online.org
• Microscopy Resource Center by Olympus: http://www.olympusmicro.com/primer/java/index.html
• Flow cytometry instrument: Christopher Leukel, filmed by JD Holbrook, University of Utah, http://www.youtube.com/watch?v=nAfL4FXju1s&feature=related, December 16, 2008.
• ProfessorPamela Stanley’s lab at Albert Einstein Medical School/Yeshiva University in New York has a good compilation of tools. Dr. Jenny Aguilan, our Glycobiology (Ch 251.6) teacher is doing a postdoc there and shared with us the site: http://stanxterm.aecom.yu.edu/database.htm
• See also ch253.wordpress.com.

FUN STUFF

• Kevin Ahern’s Metabolic Melodies (Oregon State University) (http://www.davincipress.com/metabmelodies.html) and his Links to Biochem sites at http://www.davincipress.com/amazinglyfree.html. Songs are mainly Christmas carols, Beatles, showtunes, and more.
• The Biochemist’s Songbook: http://web.csulb.edu/~cohlberg/songbook.html
• Biochemical Songs from Musical Chemistry: http://musicalchemistry.jimdo.com/biochemical-songs/
• Jeff Cohlberg’s Biochemistry Songs: http://web.csulb.edu/~cohlberg/Cohlbergsongs.html
• PCR music video ad and links to PDF lyrics from Bio-Rad: http://bio-rad.cnpg.com/lsca/videos/ScientistsForBetterPCR/
• Some YouTube bits and pieces:
  • The Zheng Lab at Baylor College of Medicine’s Lady Gaga Bad Romance Parody “Bad Project” (http://www.youtube.com/watch?v=Fl4L4M8m4d0) is my current favorite. Check it out.
  • DNA Replication Rap to Backstreet Boys’ “I want it that way.” (Thanks, Kriska!): http://youtube.com/watch?v=dIZpb93NYlw (note that the H2 bonding they talk about is really just H-bonding…)
  • Protein synthesis: don’t let the formal opening narration by Paul Berg, 1980 Nobel prize for Chemistry fool you: the film soon leads to a classic 1970’s hippie version of protein synthesis directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University : http://youtube.com/watch?v=u9dhO0iCLww. Info and upload June 6, 2006 by “miraclemart.” I guess this is fun history of science as well– so that’s what our scientific forebears were up to back then. 😉

SOME FUN STUFF BY STUDENTS

• GLEE-pids by Genato, Gotico, Junio, Oracion, and Razonabe (1st sem 2010-2011): http://glee-pids.tumblr.com/
  • articles, videos, games, and some good good songs for reviewing lipids (for which we don’t have good songs from Professor Ahern’s collection)
• Biochemistry in Chemical Conditions by Alcantara, Daza, Dy, Madelar, Medina, and Yu (1st sem 2010-2011): http://biochemproj.blogspot.com/
  • includes articles  on osteoporosis drugs, dengue, antidepressants, dieting and weight loss, and a close-up look at a protein involved in cancer spread, and “The Biochem Song” to the tune of “September” of Earth, Wind, and Fire

• Food Demystified by the Food Mythbusters (Andalis, Calderon, Codia, Lim, and Roque, 1st sem 2010-2011) at http://fooddemystified.blogspot.com/
  • articles, puzzles, and links to TED.com videos on food.

ATENEO-RELATED

• Ateneo de Manila University
• Ateneo de Manila Rizal Library
• Ateneo de Manila Department of Chemistry

CHEMISTRY

• Periodic Table Site: Chemical Elements
• Periodic Table Site: Webelements
• Chemical Finder

MISCELLANEOUS

• Download Adobe Acrobat 8.0 , 20.8Mb (to read the PDF files in this site)
• Save paper: FinePrint can print on multiple pages, and has a free demo version for printing a few pages. www.fineprint.com