Hoofdstuk 1: moleculaire opfrisser
➢ What is ‘modern’ biotechnology?
♥ In vitro propagation, cell & tissue culture
♪ disease-free, clean, well-defined material
♥ Molecular markers
♪ improved selection; diagnostics
♥ Genetic engineering
♪ recombinant DNA, transgenics; diagnostics
♥ Omics technologies
♪ High throughput data collection; technologies
♪ DNA, RNA, protein, metabolites
♪ Bioinformatics, computational biology
➢ Hierarchy of biological organization
♥
➢ Prokaryotes <-> Eukaryotes
♥ (almost) all organisms contain DNA, RNA and protein
♥ different ways of storing DNA
♪ Nucleus in eukaryotes
♥ complexity versus efficiency ?
♪ prokaryotes (Escherichia coli):
❖ small, unicellular, efficient
♪ eukaryotes (plant, human):
❖ large, multicellular, subcellular, complex
♥ Genes of eukaryotes are split
♪ DNA not co-linear with mature RNA, but longer
❖ primary transcript is ~ as long as the DNA
♪ RNA undergoes further modification
❖ in which parts of the RNA are removed
❖ modification is called: splicing
• the removed parts are called ‘introns’ or ‘intervening sequences’
• introns may have a function
• intron splice sites are conserved
• various mechanisms exist for splicing
➢ Differentiation: a conceptual issue
♥ all cells of an organism contain the same DNA, (yet, not all that DNA is identical),
yet, not all cells use the same DNA, therefore, not all cells look the same.
♪ differential use of the same genetic information gives different results
♪ how is the differential usage organized?
♥ disease is often caused by errors in or misuse of the genetic material
➢ Biological information transfer (central dogma)
, ♥
♥ Much more complex!
♪
♥ DNA (makes DNA) makes RNA makes protein (makes metabolites makes action makes phenotype)
♪ DNA makes DNA: replication
❖ by DNA polymerase
❖ in 5’ -> 3’ direction only
❖ in nucleus
❖ requires beginning (= primer)
❖ involves numerous other factors and proteins
• e.g. DNA ligase
❖ Applications:
• PCR
exponential amplification of DNA
uses DNA polymerase and two opposing primers
rounds of DNA denaturation and DNA synthesis
○ smart tric: DNA polymerase from thermophilic organism (e.g. Thermus aquaticus -> Taq polymerase)
many, many applications
○ detection; mapping; mutagenesis; gene isolation; sequencing; cloning
Read length and pairing
○ Short reads are problematic, because short sequences do not map uniquely to the genome.
○ Solution #1: Get longer reads.
○ Solution #2: Get paired reads.
• DNA sequencing
➢ What is ‘modern’ biotechnology?
♥ In vitro propagation, cell & tissue culture
♪ disease-free, clean, well-defined material
♥ Molecular markers
♪ improved selection; diagnostics
♥ Genetic engineering
♪ recombinant DNA, transgenics; diagnostics
♥ Omics technologies
♪ High throughput data collection; technologies
♪ DNA, RNA, protein, metabolites
♪ Bioinformatics, computational biology
➢ Hierarchy of biological organization
♥
➢ Prokaryotes <-> Eukaryotes
♥ (almost) all organisms contain DNA, RNA and protein
♥ different ways of storing DNA
♪ Nucleus in eukaryotes
♥ complexity versus efficiency ?
♪ prokaryotes (Escherichia coli):
❖ small, unicellular, efficient
♪ eukaryotes (plant, human):
❖ large, multicellular, subcellular, complex
♥ Genes of eukaryotes are split
♪ DNA not co-linear with mature RNA, but longer
❖ primary transcript is ~ as long as the DNA
♪ RNA undergoes further modification
❖ in which parts of the RNA are removed
❖ modification is called: splicing
• the removed parts are called ‘introns’ or ‘intervening sequences’
• introns may have a function
• intron splice sites are conserved
• various mechanisms exist for splicing
➢ Differentiation: a conceptual issue
♥ all cells of an organism contain the same DNA, (yet, not all that DNA is identical),
yet, not all cells use the same DNA, therefore, not all cells look the same.
♪ differential use of the same genetic information gives different results
♪ how is the differential usage organized?
♥ disease is often caused by errors in or misuse of the genetic material
➢ Biological information transfer (central dogma)
, ♥
♥ Much more complex!
♪
♥ DNA (makes DNA) makes RNA makes protein (makes metabolites makes action makes phenotype)
♪ DNA makes DNA: replication
❖ by DNA polymerase
❖ in 5’ -> 3’ direction only
❖ in nucleus
❖ requires beginning (= primer)
❖ involves numerous other factors and proteins
• e.g. DNA ligase
❖ Applications:
• PCR
exponential amplification of DNA
uses DNA polymerase and two opposing primers
rounds of DNA denaturation and DNA synthesis
○ smart tric: DNA polymerase from thermophilic organism (e.g. Thermus aquaticus -> Taq polymerase)
many, many applications
○ detection; mapping; mutagenesis; gene isolation; sequencing; cloning
Read length and pairing
○ Short reads are problematic, because short sequences do not map uniquely to the genome.
○ Solution #1: Get longer reads.
○ Solution #2: Get paired reads.
• DNA sequencing
