Please only use for repetition. If you want to use the questions on your smartphone a file having will be upoloaded
And here a pre-formatted file for AnyMemo for Android. The latter program is GPLed so it should always be free for you and you can check the source code. Please note that I didn't check it much apart from - the file loads the first few answers seem to be ok.
NEW File in tab format
Using the questions you should be able to revise MOST of the knowledge.
(Der Quizz beinhaltet den allergrößten Teil des geprüften Sachwissens . Seien Sie aber auch auf Techniken und machen Sie sich Gedanken zu dem Zusammenhang.
This can be achieved via the c-Value 1/47
There are many, even in relatively "simple" organisms 1/53
Sequencing will become (is) cheaper than storage so computer science has to be pushed and find new solutions. (Often a suggestion is throw the data away but the cost for the experiment is not taken into account)e.g. 1/24
mRNA, rRNA, tRNA, snRNA, miRNA, ... 2/4
this depends on the promoter (more detailed answer needed!) 2/9
-35 and -10 element 35 and 10 bases upstream of promoter. TTGACA TATAAT Some might have an additional UP element 2/10
See picture, you would rather see a figure and would have to explain it 2/15
See picture, you would rather see a figure and get an idea on how to interpret it. It is enough to have a rough idea about pseudocounts 2/15
only about a third, but almost all might have a TATA or TATA like box 2/21
see figure 2/24
TATA binding protein 2/25
see 2/28ff
in the major grove
Fragments are incubated with and without nuclear proteins that might bind. In the fraction with potential binding protein a band is “retarded” moved to apparently higher size 2/39
DNA fragments are treated with and without DNA binding proteins; afterwards the fragments are digested with DNAse, binding proteins protect : a footprint is visible on the gel 2/40
Explain either 2/47 affinity purification, 2/47 clone based and/or 2/48 Y1H
Explain either SELEX 2/41 and/or PBM 2/42
ESTs can be mapped onto the genome and splice sites be found 2/58f
See figure 2/59 for an overview
Figure at the end of the lecture: Cis Elements, core cis Elements, Introns, alternative Exons, Exons, splice modifiers e.g. ISE
The RNA needs to be reverse transcribed into cDNA first, e.g. using an oligo dT primer 3A/2-3
For each sample a “constitutive” product is monitored as well. The PCR reaction is Stopped after various cycle numbers (or just at one cycle number) or competitive PCR see question 3A/6
The reference gene is used to standardize the amount of RNA, this would assume that the expression of the reference gene is constant under the assayed conditions, which might not always be the case 3A/6-7
A standard which is very similar to the target (e.g. some different length but using the same primers!) is added in known amounts to the reaction mixture, where band intensities are equal one can determine the amount 3A/8
Sybergreen (like Etidiumbromide) intercalates in double stranded DNA, which is produced by PCR, the more dsDNA is made, the higher the absorbance. The reaction mix is almost like normal PCR+ Sybergreen 3A/10
Probes which hybridize to ssDNA are added to the PCR mix, these have two dyes, one absorber and a quencher, which quenches the signal by resonance transfer if both probes are close. Once polymerase comes by the probe is depolymerized thus the probes are far from each other => signal increases 3A/9-10
The number of cycles that have been run when a a certain Fluorescence threshold has been reached 3A/9
The Ct values of gene of interest and a "standard" are simple subtracted 3A/13
At least three BIOLOGICAL reps, High quality RNA, Digest RNA with DNAse I to remove genomic DNA, Use a good reverse transcriptase with no RNase H activity, Test cDNA, Design good primers, Standardize and use a master mix, Test at least 4 potential reference genes, Perform real time PCR on test and reference genes at the same time (and use melting curves), One should determine the best reference genes, Calculate transcript abundance using efficiency 3A/18
See figure 3A/26
wafer is silanated-> start,Linker is added, UV light deprotects linker but not where a mask is shielding UV light, nucleotide with protection is added, UV light with shielding and repeat, finally capping reagent is added 3A/30-33
perfect match and mismatch probes, the PM are complementary the MM have a mismatch in the 13th of 25 nucleotides 3A/35,36
This is necessary in order to compare arrays and thus samples, as one might have different amount of RNA extracted, a different laser intensity, different washing conditions etc.
One big assumption is that not too many genes are changing, or in other words most genes stay more or less the same 3A/44
One knows where the probes are on a gene and can order them 5' to 3' Synthesis often starts from the 3' poly A tail so one can see how the signal changes from 3' to 5' 3A/56
dideoxyy method, uses ddNTPs flourescently labelled, extension stops, mix is run on gel in CE for a proper answer see 3B/8-15
The intensities for the different dyes (translates to TCGA) at each position, from the peaks the sequence can be read 3B/15
A base quality score, no it is not linear, 10 units decrease the error rate by 10fold 3B/15
Nucleotides are flowed in one after the other, upon incorporation PPi is released which is converted by Sulfurylase to ATP which is used by luciferase to produce light. Apyrase uses up unused nucleotides for a proper answer see 3B/17-25
Homopolymers of the same Base, while the produced light gets more intense with more PPi released, it is difficult to distinguish longer stretches 3B/16-27
dGTP, dTDP, dCTP, dATP-alpha S. The latter is used as it is not recognized by luciferase instead of ATP but can be used by the polymerase 3B/27
Nucleotides are flowed in in a sequence, as they become incorporated H+ is released this is detected by sensors 3B/36
Homopolymers of the same base, while the produced H+ gets more intense with more bases incorporated in each cycle, it is difficult to distinguish longer stretches for a proper answer see 3B/35
Nucleotides are blocked and fluorescently labeled, all are flowed in at the same time, the cell is imaged, the block and label removed and a next cycle commences 3B/42
Overlay/Layout/Consensus 3B/49ff and kmer/de Bruijn based graph 3B/55ff
only 4 shown, as this is easy to display ATCG=>TCGA=>CGAG TATA=>ATAA =>TAAT GAGT=>AGTA=>GTAT, three generates one component in the graph only
Bringing contigs together, i.e. joining these by e.g. pieces of reads originating from two sides of a stretch of DNA where the middle is unknown, the unknown part is padded with Ns, this is done to get fewer and large pieces 3b/58ff
This is the Gene ontology, an ontology to classify genes. One can use it to look for groups of genes which are commonly up or down regulated 3C
A controlled vocabulary is giving only a certain set of "controlled" words that should be used to describe something. As these are controlled there is no ambiguitiy and we know what we speak of. 3C
basically as summary of lecture 3C
be mindful about the topology 3C/18
Be careful 3C doesn't bring in a lot of things but can be used to make sense of data.
If genes are correlated across a large number of arrays, the MIGHT have a similar function 3C/25
Be prepared to interpret Figure 4/2 showing a C0T graph?
E.g. Transposable elements (transposons) are fragments of DNA that can move around in the genome and insert at target sites 4/3
No 4/3
Yes indeed 4/3
Elements that replicate via DNA (II DNA transposons) or RNA (I, or Retrotransposons) intermediates. 4/4
Mutator, Merlin, PiggyBac, P, Transib, PIF-Harbinger, hAT, TC1-Mariner, ... 4/9
See 4/12ff
After insertion of a DNA transposon the target site is duplicated, after excision this duplication remains 4/14
After insertion of a DNA transposon the target site is duplicated, after excision this duplication remains 4/15
After excision of a transposon, homology directed repair of a transposon free site, restores the state before the transposon inserted, i.e no footprint 4/14
Helitrons are Class II transpons, that seem to replicate via a rolling circle mechanism. In any case they are characterized by the RepHel protein 4/23ff
An odd transposon potentially related to DNA viruses 4/30
No some transposons have been domesticated, where the DNA binding domain is often reused (also they might contribute to plasticity of the genome) 4/33ff
The DNA binding function 4/33ff
Class I: Copia, Gypsy, Bel-Pao, Retrovirus, ERV 4/43
See 4/49
Riboswitches, protein binding sRNAs,base-pairing sRNAs (cis-, trans-encoded); CRISPR RNAs
cis-encoded: located on the antisense strand of the target RNA, perfect complementarity to target mRNA, act negatively (mRNA degradation, Transcription termination)
See 5/9 , important features: DNA repeats, Unique spacers, CAS genes
During phage infection, new spacers corresponding to sequences of this phage are integrated into existing CSIPR arrays.
miRNAs: encoded in the genome by specific MIR genes; regulate developmental and physiological events; two Cleavage processes (Drosha, Dicer)
See 5/20
Drosha (cleaves pri(mary)-miRNA to pre-miRNA), Dicer (cleaves pre-miRNA to miRNA duplex), RISC complex (removal of one strand of miRNA, binding of complementary target mRNA, degradation of target mRNA)
Structure: PAZ domain for recognition of 3‘ end of miRNA; RNAse domain for cleavage of target RNA
See 5/29
See 5/36
RNA-Polymerase IV (production of siRNA) and RNA-Polymerase V (Recruitment of ARGONAUTE to DNA)
PIWI-interacting RNAs; Transposon control in germ cells and stem cells in animals
See 5/53-55
posttranscriptional regulation, posttranslational modification, different splicing and polyA isoforms 6/3
Usually these do not complete coincide (but it is not always as bad as in 6/4)
Differential gel electrophoresis, it is used to compare protein amounts. Proteins are labelled by a fluorescent label and run on a 2D Gel 6/7
No, the mixture would be too complex there would be overlapping Signals Due to Multiple Charged States & overlapping Signals Due to Natural Isotope Abundance 6/9
Matrix assisted Laser Desorption ionization. Analyte embedded in matrix a laser pulse (right wavelength) is given which ionizes matrix+analytes 6/14
The ions originating from the matrix 6/14
Electrospray Ionization details from 6/15 needed a drawing will help
Just some principle needed, e.g. quadropole has four rods, and selects based on m/z ratio ....
Quad 1 can be used to select an ion, Quad 2 is used as a collision cell, in quad 3 resulting fragment ions are scanned for 6/23
An ion trap based instrument useful in elucidating structure especially if MS/MS is not too meaningful 6/27
Several algorithms don't sequence peptides based on the ion, but compare spectrum obtained to simulated spectra 6/31ff
see 6/41 ff
SILAC, iTRAQ, ICAT or digestion with H2 18O
For a protein a heavy,stable ion labelled peptide is ordered and this is used to tune the instrument, afterwards the peptide of interest is injected with the synthetic one and quantified 6/56
genetic markers are testes for linkage, linkage can be expressed in cM to relate markers to each other. More detail from 7/7ff needs to be given
Restriction Fragment length Polymorphism, a SNP causes the creation or deletion of a restriction site in the DNA. DNA can be cut with the restriction enzyme run on a gel, blotted and interrogated with a (radioactive) probe hybridizing to that stretch of DNA 7/23
Single nucleotide polymorphism. E.g. using Illumina Golden gate (explain the assay!) 7/28ff
Where markers are assigned to physical location on the chromosome 7/31
Cut with different restriction enzymes either alone or in combination, determine the “restriction map” by combinatoric analysis 7/33
pulsed field gel electrophoresis 7/37
DNA is stained and immobilized (kind of stretched) restriction enzymes added, the DNA shrinks a bit, gaps become visible these are visualized 7/41
See 7/47
Genome wide association mapping. In a population phenotypes are correlated to markers.... 7
Usually relatively common allels with low penetrance/effect size 7/63
LD is the “nonrandom association of alleles at different loci.” 7/67
Population structure 7/72ff
That the structure shown reflects the geographic location somewhat (TRICKY BONUS: Explain why this might be the case) 7/75
Based on the number of publications, it probably is 7/53
one gets an information about the cellular components, potentially their physiological state etc
GC-MS uses "hard" ionization LC-MS a soft one, the latter tries to keep the molecule intact.
Electron impact, the molecule is bombarded with an electron and often "falls apart". In a GC-MS system one often finds EI 9/5
Electron impact, the molecule is bombarded with an electron and often "falls apart". In a GC-MS system one often finds EI 9/5
How do you explain a quantitative trait by simple Mendelian gentics?
Multiple loci involved
What is Heritability genetically
proportion of total variance within a population attributable to genetic factors