MOLECULAR BIOLOGY 

 


 LINKS         note:  some chime programs run only on netscape

Plug-Ins.  Some links below require plug-ins (software for special effects, like motion or audio).  Usually the application will link to another site for down-loading the plug-in. 
atoms and chemical bonds [Freeman  Chapter 2a ]
back to top
water and pH [Freeman Chapter 2b]

 
macromolecules [Freeman  Chapter 3 Bio103]      textbook figures
Protein Motors [Freeman  Chapter 5  Bio103 cells]
Protein Channels, receptors, and transporters [Freeman  Chapter 5b Bio103 membrane]
DNA  (Freeman  Chapters 11-17)
   
CODONS: Genetic Code Table adapted from  http://molbio.info.nih.gov/molbio/gcode.html :
 
    T    C      A      G
T TTT Phe (F)
TTC "
TTA Leu (L)
TTG " 		TCT Ser (S)
TCC "
TCA "
TCG " 		TAT Tyr (Y)
TAC
TAA Ter
TAG Ter 		TGT Cys (C)
TGC
TGA Ter
TGG Trp (W)
C CTT Leu (L)
CTC "
CTA "
CTG " 		CCT Pro (P)
CCC "
CCA "
CCG " 		CAT His (H)
CAC "
CAA Gln (Q)
CAG " 		CGT Arg (R)
CGC "
CGA "
CGG "
A ATT Ile (I)
ATC "
ATA "
ATG Met (M)		 ACT Thr (T)
ACC "
ACA "
ACG " 		AAT Asn (N)
AAC "
AAA Lys (K)
AAG " 		AGT Ser (S)
AGC "
AGA Arg (R)
AGG "
G GTT Val (V)
GTC "
GTA "
GTG " 		GCT Ala (A)
GCC "
GCA "
GCG " 		GAT Asp (D)
GAC "
GAA Glu (E)
GAG " 		GGT Gly (G)
GGC "
GGA "
GGG "
back to top
BIOTECH TOOLS  (Freeman  Chapter 12 and Chapter16-17 )    
  1. Restriction  enzymes  are nucleases; they cut DNA or RNA into fragments ( Box  15.1, p.302).  (In bacterial cells, the natural function of restriction enzymes is to destroy the nucleic acids of enemies.)  Also see picture from last year's textbook.  Eco-ri is the most famous restriction enzyme, but there are at least a hundred different restriction enzymes, each of which attacks a different palandromic sequence.  Restriction enzymes are used to create cuts and fragments for DNA analysis and also for genetic engineering.
  2. Fragments produced by restriction enzymes have different lengths.  Fragments are sometimes called RFLPs (pronounced "riff-lips"), especially when the different lengths reflect differing alleles or at least individual differences. 
  3. Electrophoresis separates and sorts fragments according to their lengths, box 15.2, p. 308.   Electrophoresis and autoradiography (Fig.12.12c) are explained in more detail on p. 50 (Box 3.2). Want to see RFLPs eletrophoresed?  
  4. Probes are oligonucleotides, short pieces of RNA or single-stranded DNA.  Probes work by hybridizing with single strands of DNA or RNA; it's called hybrid (new meaning) because the probe and its target are from different critters.  The probe and its target have complementary base sequences; so they stick together by hydrogen bonds between the complementary pairs, just like a primer will stick to DNA in replication or transcription.  Radioactive or fluorescent probes are especially useful in research.  Can you figure out why?  
    • A probe can ID specific base sequences on the electrophoresis gel or on blots (box 15.2, p. 309) which absorb the fragments from the gel. 
    • A probe can also pinpoint the location of a gene on a chromosome (as seen in Freeman CD activity 16.1) or to find which colonies of genetically engineered bacteria have the right DNA sequence (as seen in Freeman CD activity 17.1).
    • Probes can also be used in vivo; one example is in situ hybridization which is used to tell which genes are active in specific tissues.  The mRNAs which have been transcribed can be detected with radioactive or fluorescent DNA probes (Box 19.1). 
    • probes have many other uses 
  5. PCR, fig. 12.11, uses primers and polymerase and temperature cycles to replicate DNA in huge quantities.  
  6. How can we sequence a gene?  =What is the base sequence of this DNA? (fig. 12.12)   DNA base sequence determination:  The Sanger (dideoxy) procedure is still used in some professional laboratories today, even though there are machines which determine the base sequence faster.  The newer procedures are based on the same principles as dideoxy sequencing described on p. 242.    Study fig 12.12.
  7. Ligase enzyme can make recombinant DNA  for genetic engineering or GM (genetic modification).  Ligase "glues"  fragments together, usually into circles of DNA, called plasmids (which are natural) or BACs (bacterial artificial chromosomes).   (Recombinant DNA is not expressed (cannot work) unless it is adjacent to promoter DNA segments, fig. 13.5, 13.6.) (In live normal cells, the natural function of ligase is to combine the Okazaki fragments of the lagging strand in DNA replication, fig. 12.9 #7)
  8. DNA can be synthesized in the lab, but synthetic DNA is used mostly as probes or sometimes as deliberate mutations, tiny inserts into recombinant DNA.   (DNA used for genetic engineering is always recombinant DNA, involving genes from natural sources, partly because real genes are too long to be synthesized practically and partly because the proteins which would be translated do not fold into functional and predictable tertiary shapes. Scientists don't know enough about proteins yet.)  You don't have to know how they synthesize DNA.   You can buy synthetic DNA at www.operon.com, among other places.
  9. How can we make recombinant DNA?  see tool #7 above
  10. If we don't want to use PCR to get extra DNA, are there natural methods to clone genes? note:  this is a different use of the term "clone."   It's not enough to have different meanings for "hybrid"--  we have to make things confusing to keep muggles from using genetic engineering.
  11. What if we just needed to "enslave" some bacteria or yeasts so that they would make a human protein we needed, like insulin or growth hormone or a clotting factor for hemophiliacs?  Answer:  We could just put the genes into some cells, feed the new transgenic cells and let them replicate until we have vats them transcribing the genes and then translating them into the proteins we need.  Then we "sacrifice" them and extract the proteins we need.  
  12. How can we do put new genes into people or crops or a transgenic host? Answer:  Recombinant DNA can be incorporated into cells by vectors (viruses, plasmids, artificial chromosomes).   Viruses usually are able to find their way into host cells without much help, but other vectors have to be injected with liposomes or "gene guns" or pulses of electric current  which penetrate the host cell membranes.  If you're HIV-positive, you're transgenic.   Interested in the AIDS Gateway site?
  13. How do you know if your vector worked?  Answer:  Reporter genes are "markers" of success. They often produce some fluorescent signal or some other observable trait which gives the scientist hope that the other recombinant DNA in the vector has been incorporated and will be expressed.  That's the real reason for "glow in the dark" tobacco or tomatoes, etc.  
  14. Another way to test for the presence of transgenic genes or to screen for particular alleles  :  measure its expression with probes for its mRNA on microarrays, sometimes called gene chips.   Learn the details at http://vector.cshl.org/dnaftb/36/concept/index.html.    buy one  or go to www.microarrays.com or http://www.genemachines.com/products.html     Learn More at http://bioinformatics.phrma.org/microarrays.html 
    excellent student paper on gene chips.  
    Latest details on microarray modifications, especially for in situ hybridization http://www.the-scientist.com/yr2002/oct/lcprofile1_021028.html 
    The BioChipNet database:  http://www.biochipnet.de/
  15. In situ hybridization is yet another way to tell which genes are working.  The mRNAs which have been transcribed can be detected with radioactive or fluorescent DNA probes (Box 19.1)
  16. Where can you get reporter genes or other genes to play transgenic games with? Answer:   Recombinant genes and cDNA genes (complementary to mRNA, without introns,) are stored in plasmids in gene libraries.  The raw materials (natural genes) are also stored in seed banks, and sperm banks and other tissue vaults, usually within vials submerged in liquid nitrogen (very very cold).  Other useful natural genes are often found in bacteria and fungi which have evolved adaptations for particular environmental problems and opportunities (for example, the bacteria which destroys "roundup" herbicide).    want to buy some cDNA? 
  17. Should you look through an entire genome or could you just search the haplotypes?  A haplotype is the collection of all the key genetic changes present in an individual,  but a "genome" is the entire set of the DNA from all 23 pairs of chromosomes and the mitochondria too (sometimes) and a "genotype" is an individual's status at a single location in the DNA (sometimes IDed  with SNPs).  See example at http://www.sciencemag.org/cgi/content/full/294/5547/1719/F2 
    hapmap http://www.washingtonpost.com/wp-dyn/articles/A37999-2002Oct29.html
  18. PIP (percentage identity plot) "compares two or more genomic sequences of a megabase or less in
    length, and returns information about the resulting alignments in a
    variety of formats, ranging from graphical summaries of the matching
    regions to nucleotide-level details." "A pip has a panel of dots that marks the degree of identity, usually
    between 50% and 100%, along a DNA sequence between two
    species. "  http://www.the-scientist.com/yr2002/dec/research3_021209.html 
Enzymes  [Freeman  Chapter 3c ]
back to top
Cellular Respiration  [Freeman  Chapter 6; ]
How to use clickable charts:
  • overview (KEGG, Kyoto U.) charts:
    • reactant or product (named near the O, with reaction arrows pointing to/from it):  click on the O of a reactant or product, and it gives you another page with 2-D structures and other information about the molecule.
    • enzyme: click on an enzyme's number in a blue box  within the reaction arrow, and it gives you another page of details on that enzyme, including diseases.  Then you can copy the name of the enzyme, and go to
      • Molecules-R-US, and enter the name in the search box to find choices for a chime-type rotating 3-D picture
      • or enter the name at Protein Data Bank Search-Lite and click choices for the enzyme versions and then click your choice for viewing methods (one of the chimes works best on our lab computers)
    • further detail:  click on rounded boxes, and it takes you to another chart or a diagram showing more detail
  • WALL CHART VERSION:  ExPASy  (Expert Protein Analysis System) Detailed Charts are electronic versions of the huge metabolic charts many biologists and biochemists use.  (Dr. Jann's is inside her office door; there's a prize there for the first person to find it.)
    • each reactant or product is named within a non-clickable box, often with its structure shown nearby.  But you may be able to link to other pictures of its structure from its enzyme page (next).
    • enzyme:  click on the blue name of an enzyme, and it gives you another page with more detail and more links.  For most enzymes, I think the easiest way to get a 3-D chime structure is to paste the enzyme name at Molecules-R-US or Protein Data Bank Search-Lite.
    • MORE detail is simply the loading of adjacent charts.
      back to top
Photosynthesis     Botany (Phytochemistry unit)