Terms Medical Genomics
Little RNA processing; mRNA is already mature
Heavy RNA processing; mRNA is not mature, splicing needed
Monocistronic mRNA; contains only genetic information to translate only a single
protein chain (polypeptide) --> in Eukaryote
Polycistornic mRNA; mRNA carry several open reading frames each of which is
translated into a polypeptide --> in Prokaryote
Elongation; (E-P-A) amino acid added to growing polypeptide
Enzyme histone acetyltransferase (HATs) and Enzyme histone deacetylase (HDACs)
are for histone modification
Nuclear matrix; network of fibers found throughout the inside of a cell nucleus
(analogous to the cell cytoskeleton)
Insulator is a segment of DNA that function as a boundary between 2 genes. It
protects (insulates=isoleert) a gene from the regulatory effects neighboring genes.
Sequencing; determine nucleic acid sequence (order)
Cloning; technique to generate many copies
Polonies; combination colonies and polymerase (foundation next generation
sequencing)
Next generation sequencing/parallel sequencing; samples can be analyzed
simultaneously in a single reaction mixture
Blunt ends; equal ends
Ligation adapter; small double-stranded DNA with known sequence
Bridge amplification; principle the same as PCR but it happens on glass (flow cell),
new formed DNA stuck to the glass. Copy bend and interact with other primer.
Clone; collection of many identical items
Library; many different clones (entire information of vectors)
Shearing; breaking DNA into small pieces
Contigs; set of overlapping DNA, uninterrupted
Fingerprinting; bands on gel electrophorese that overlap are maintained rest is
digested.
Probes; stukje DNA dat bijv. met isotopen wordt gemerk en wordt gebruikt om een
bepaald DNA aan te tonen
,Chromosome walking; when probe is combinate with research for overlapping
restriction fragments
Identical; corresponding feature (kenmerk) shared between species
Similar; degree to which species share identicals
Homologous; similar due to common ancestry (voorouder)
• Orthologous; homologous characters with same function in species
• Paralogous; homologous characters with different function in species
Analogous; similar due to common evolution
Stringency; minimum number of matches that must be achieved to achieve a positive
score
Query; user provided sequence
BLASTP; protein query vs protein database
BLASTN; nucleotide query vs nucleotide database
BLASTX; translated DNA (nucleotide) query vs protein database
TBLASTN; protein query vs translated DNA (nucleotide database)
TBLASTX; translated DNA (nucleotide) query vs translated DNA (nucleotide)
database
E-value: probability that sequence with that score is found in database by
coincidence
Comparative genomics; genome sequence of different species are compared
Phylogeny; sequence of events involved in the evolutionary development of species
(phylogeny tree describes this)
Principle of parsimony; order of speciation with lowest number of evolutionary
changes is most likely to have occurred
Homology transfer; sequence similarity reflects functional (gene function) similarity
Synteny; conservation of blocks of order within 2 sets of chromosomes
Phylogenetic foot printing; compare phylogenetic distant (verre) species --> method
for identifying important non-coding DNA sequneces (mutations in this will lead to
disease)
Phylogenetic shadowing; compare phylogenetic close species --> method for food
printing closely related species
C-value paradox; genome size does not correlate with organism’s complexity
,Non-coding DNA;
• Isochores; spots where the base-pair composition may vary from the average
• Pseudogenes; duplication goes wrong
• Tandem (in the same direction) Repeats; copies of the same identical DNA
sequence behind each other
• Mobile elements (transposons and retroviruses); DNA can jump from spot to
spot
, Lecture 1 – Introduction
Wildtype allele; normal
Null allele; knock out
Mutant allele; knock in
Floxed allele; conditional knock out
1’ base 2’H 3’ OH 4’H 5’ phosphate group
RNA; 2’ OH instead of H, mostly single stranded
mRNA; encode proteins
rRNA; component of ribosome that from protein translation machinery
tRNA; couple amino acids to protein. Adapter molecule act between mRNA and
protein
• Has anti-codon that binds to mRNA
• Amino tRNA synthetase attach the correct amino acid to acceptor site
Promotor and transcription termination signal = transcription
Stop and start codon = translation
Prokaryotes; operons, little RNA processing, polycistronic mRNA, DNA in cytoplasm
Eukaryotes; introns and exons, heavy RNA processing, monocistromic mRNA, DNA
in nucleus
Poly-A-tail to 3’ end contributes to;
• Transcription termination
• Release of RNA polymerase from the template
RNA polymerase unwinds double helix:
• Antisense or template; RNA becomes complementary to this
• Sense or coding strand
Elongation; (E-P-A) amino acid added to growing polypeptide
Protease; cutting enzyme
C-terminus 3’
N-terminus 5’
Promotor; decrease gene expression
Little RNA processing; mRNA is already mature
Heavy RNA processing; mRNA is not mature, splicing needed
Monocistronic mRNA; contains only genetic information to translate only a single
protein chain (polypeptide) --> in Eukaryote
Polycistornic mRNA; mRNA carry several open reading frames each of which is
translated into a polypeptide --> in Prokaryote
Elongation; (E-P-A) amino acid added to growing polypeptide
Enzyme histone acetyltransferase (HATs) and Enzyme histone deacetylase (HDACs)
are for histone modification
Nuclear matrix; network of fibers found throughout the inside of a cell nucleus
(analogous to the cell cytoskeleton)
Insulator is a segment of DNA that function as a boundary between 2 genes. It
protects (insulates=isoleert) a gene from the regulatory effects neighboring genes.
Sequencing; determine nucleic acid sequence (order)
Cloning; technique to generate many copies
Polonies; combination colonies and polymerase (foundation next generation
sequencing)
Next generation sequencing/parallel sequencing; samples can be analyzed
simultaneously in a single reaction mixture
Blunt ends; equal ends
Ligation adapter; small double-stranded DNA with known sequence
Bridge amplification; principle the same as PCR but it happens on glass (flow cell),
new formed DNA stuck to the glass. Copy bend and interact with other primer.
Clone; collection of many identical items
Library; many different clones (entire information of vectors)
Shearing; breaking DNA into small pieces
Contigs; set of overlapping DNA, uninterrupted
Fingerprinting; bands on gel electrophorese that overlap are maintained rest is
digested.
Probes; stukje DNA dat bijv. met isotopen wordt gemerk en wordt gebruikt om een
bepaald DNA aan te tonen
,Chromosome walking; when probe is combinate with research for overlapping
restriction fragments
Identical; corresponding feature (kenmerk) shared between species
Similar; degree to which species share identicals
Homologous; similar due to common ancestry (voorouder)
• Orthologous; homologous characters with same function in species
• Paralogous; homologous characters with different function in species
Analogous; similar due to common evolution
Stringency; minimum number of matches that must be achieved to achieve a positive
score
Query; user provided sequence
BLASTP; protein query vs protein database
BLASTN; nucleotide query vs nucleotide database
BLASTX; translated DNA (nucleotide) query vs protein database
TBLASTN; protein query vs translated DNA (nucleotide database)
TBLASTX; translated DNA (nucleotide) query vs translated DNA (nucleotide)
database
E-value: probability that sequence with that score is found in database by
coincidence
Comparative genomics; genome sequence of different species are compared
Phylogeny; sequence of events involved in the evolutionary development of species
(phylogeny tree describes this)
Principle of parsimony; order of speciation with lowest number of evolutionary
changes is most likely to have occurred
Homology transfer; sequence similarity reflects functional (gene function) similarity
Synteny; conservation of blocks of order within 2 sets of chromosomes
Phylogenetic foot printing; compare phylogenetic distant (verre) species --> method
for identifying important non-coding DNA sequneces (mutations in this will lead to
disease)
Phylogenetic shadowing; compare phylogenetic close species --> method for food
printing closely related species
C-value paradox; genome size does not correlate with organism’s complexity
,Non-coding DNA;
• Isochores; spots where the base-pair composition may vary from the average
• Pseudogenes; duplication goes wrong
• Tandem (in the same direction) Repeats; copies of the same identical DNA
sequence behind each other
• Mobile elements (transposons and retroviruses); DNA can jump from spot to
spot
, Lecture 1 – Introduction
Wildtype allele; normal
Null allele; knock out
Mutant allele; knock in
Floxed allele; conditional knock out
1’ base 2’H 3’ OH 4’H 5’ phosphate group
RNA; 2’ OH instead of H, mostly single stranded
mRNA; encode proteins
rRNA; component of ribosome that from protein translation machinery
tRNA; couple amino acids to protein. Adapter molecule act between mRNA and
protein
• Has anti-codon that binds to mRNA
• Amino tRNA synthetase attach the correct amino acid to acceptor site
Promotor and transcription termination signal = transcription
Stop and start codon = translation
Prokaryotes; operons, little RNA processing, polycistronic mRNA, DNA in cytoplasm
Eukaryotes; introns and exons, heavy RNA processing, monocistromic mRNA, DNA
in nucleus
Poly-A-tail to 3’ end contributes to;
• Transcription termination
• Release of RNA polymerase from the template
RNA polymerase unwinds double helix:
• Antisense or template; RNA becomes complementary to this
• Sense or coding strand
Elongation; (E-P-A) amino acid added to growing polypeptide
Protease; cutting enzyme
C-terminus 3’
N-terminus 5’
Promotor; decrease gene expression
