Biology and Chemistry Workshop

Biology and Chemistry Workshop Sat 16 Oct 2010 14:00 till Sat 16 Oct 2010 19:00 What: Biology and Chemistry Workshop Tagline: Yet another Hsb Meetup! Where: HSB Brussels,Belgium Cost: 0 Who: U_go URL:

 Date changed to Saturday 16 of october

What

This will be a beginners workshop, things I (U_go) want to cover :

• Biology for beginners
  • focus on genetics
  • theory on how to make GMOs
  • also have fun with microscopes
• Chemistry for fun
  • biology requires special stuff but we can have fun with some chemistry
  • See Chemistry_experiments_1o1

Biology

• Introduction on cells
• Genetics, DNA and how it works
• Where to find DNA sequences
• How to program bacteria
• BioBricks
• Introduction on what to do next (get DNA, insert it in bacteria)

Who

• U_go

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notes

___ Chemistry 1o1 ___

mendeliev's table of elements: http://www.ptable.com/?lang=us

neutrons change the weight, not the behavior

      1         : nr of electrons in diff layers

1  : nr of protons H hydrogen  : name 1.00794  : average mass

                 (as there is a some deuterium en tritium it is not equal to 1)

adding neutrons doesn't change behavior of atoms

       2 : 2 electrons on first layer
       1 : 1 electron on second layer

3 Li

what keeps an atom together? Strong nuclear force http://en.wikipedia.org/wiki/Strong_interaction

last column: noble gasses; inert left: akalines : release OH right:acids : release hydrogen

solvent : brownian motion : particles moving because of temperature

C-N-O and H are basics for organic chemistry Fe : used for instance in hemoglobine Mg : eg in clorophyl

fun videos each element comes with a very entertaining video that explains the properties of the element.

http://www.periodicvideos.com/

___ Biology ___

dna is one molecule (in fact 2 molecules, each strand of the helix is one molecule) dna is an acid and reacts well with base

4 bases {A,T,C,G}
A-T
C-G

sugars: cycle(s) with one oxygen and 4or5 carbon atoms etc saccharose

___ Genomes ___

3 main groups of organisms

- bacteria: difficult to see with microscope (eg diameter of red blood cell 7 micron, diameter of bacteria - 1 micron) - archaea (looks like bacteria, but with very different dna, living in very exotic environments - eg vulcanic lakes, ice etc) - eukaryota (complex cells, groups) plants, fungi, animals

bacteria - escherichia coli duplicates every 20min cells in human body duplicate every 24h (eg skincells,..)

fly -- drosophila melanogaster -- small genome

yeast 13 Mbp (mega-base-pairs) 16 chromosomes 25% common genome with man

human 3Gbp

uniprot.org mrgene.com

biobricks.org promoter-rbs-gene-stop

partsregistry.org

protein viz pymol/rasmol

find proteins: www.pdb.org

http://fold.it/portal

Download complete genomes :

=> Main repository ftp://ftp.ensemblgenomes.org/pub/

=> Bacteria E. coli ftp://ftp.ensemblgenomes.org/pub/bacteria/release-5/fasta/e_coli_k12/dna/E_coli_K12.EB1.dna.chromosome.Chromosome.fa.gz

=> Fly D. melanogaster ftp://ftp.ensemblgenomes.org/pub/metazoa/release-6/fasta/drosophila_melanogaster/dna/ (5 chromosomes : X, Y, 2, 3, 4)

___ Genomics ___

=> Green Fluorescent Protein http://www.uniprot.org/uniprot/P42212

=> PyMOL ! Might need to register http://www.pymol.org/ http://packages.ubuntu.com/lucid/pymol (Lucid) http://sourceforge.net/projects/pymol/develop (SVN) => Alternative : RasMol http://en.wikipedia.org/wiki/RasMol

=> Green Fluorescent Protein (GFP) on Protein Database (PDB) http://www.pdb.org/pdb/explore/explore.do?pdbId=1B9C

___ Hands on ___

>Mysterious sequence ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTGGTCCCAGTTCTTGTTGAATTAGAT GGCGATGTTAATGGGCAAAAATTCTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACA TACGGAAAACTTACCCTTAATTTTATTTGCACTACTGGGAAGCTACCTGTTCCATGG CCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTCTCAAGATACCCAGAT CATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAA AGAACTATATTTTACAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTT GAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGAT GGAAACATTCTTGGACACAAAATGGAATACAACTATAACTCACATAATGTATACATC ATGGGAGACAAACCAAAGAATGGCATCAAAGTTAACTTCAAAATTAGACACAACATT AAAGATGGAAGCGTTCAATTAGCAGACCATTATCAACAAAATACTCCAATTGGCGAT GGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCCAAA GATCCCAACGAAAAGAGAGATCACATGATCCTTCTTGAGTTTGTAACAGCTGCTAGG ATTACACATGGCATGGATGAACTATACAAA