Biology and Chemistry Workshop
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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
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
