Please only use for repetition. If you want to use the questions on your smartphone here is a file always having
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.
->Anymemo
->in tab format (should work with iPhone apps)
I have tested neither
Using the questions you should be able to revise MOST of the knowledge covered in the Usadel part. The part of Prof Frentzen is NOT covered here.
Usually the answers are a bit on the short side and would NOT be sufficient if they came in the exam.
Der Quizz beinhaltet den allergrößten Teil des geprüften Sachwissens . Seien Sie aber auch auf Techniken und machen Sie sich Gedanken zu dem Zusammenhang. Die Antworten sollen Ihnen meist nur einen Denkanstoss geben und sind i.A. zu kurz für die Beantwortung einer Klausurfrage.
RNA can act as an enzyme and can serve as a store of genetic information.
DNA as a molecule is very long. It needs to fit into a cell or into the nucleus
No but they have similarly positively charged proteins, like IHF (Integration host factor)
H2a, H2b, H3, H4
As an outer particle, additional packing
~146b
micrococal DNAase digestion, the nucleosme protects the DNA, then run the fragments on a gel
incomplete digestion
–Acetylation (Ac)
–Ubiquitination (Ub)
–Methylation (Me)
–Phosphorylation (P)
–Sumoylation (Su)
Histone acetylase
PRC2 (polycomb repressive complex) silences genes via histone modification, PRC1 maintains this silencing state
A plant PRC1 like protein
Histone 3 Lysine 27 triple methylated
It is associated with genes.
Metyhlation of Cytosines
By nucleosome remodelling factors. These can change the localization of the nucloesomes with respect to the DNA
-Bromodomain (binds acetylated lysines)
-Chromodomain (binds methylated lysines)
Methylated cytosines are less chemically stable, so more likely to undergo deamination, which changes the base to thymine (also a valid base)
It distinguishes new from "old" DNA (new DNA is hemimethylated) also it distinguishes foreign from own DNA
Enzymes recognizing specific sites in the DNA and cutting the DNA
No animals use mostly CG sites, Plants CG, CHG, CHH
These are symmetric, so maintaince methylation is easy
Through silencing
See the Drosophila example
Through silencing
Transposons get reactivated, and subsequently the plants get less and less fit
See the maize B-I example
Basically this defines the centromer sites, point centromers are very small, regoin centromers hundreds of kilobases, in holocentric centromers there is no defined region (whole chromosome)
it solved the "end" problem by prolonging special structures "telomeres" at chromosome ends.
Purin versus Purin exchange
Purin versus Pyrimidin exchange, or vice versa
tuatomeric structures of DNA bases
cell internal metabolies, e.g. reactive oxygen species
external chemicals e.g. alkylation agents
radiation e.g. UV or X-ray
deamination
Direct reversal of the damage by photolyases
The protein transfers the alkyl group onto itself, as this is irreversible the protein is no enzymes and is thus "used up" . But it can still act as a regulator (see there)
Its role is in mismatch repair MutS recognizes a mismatch, MutH a hemimethylated strand and nicks the strand; be prepared to explain the mechanism
damaged bases are removed by glycosylase (there are many different ones) AP site is recognized by an endonuclease, it cleaves the backbone and the hole is filled 3/17
For bulky lesions
Translesion polymerases, they are able to polymerize in a non-templated fashion when damage has occurred
The TLs polymerase are error prone and just ensure that DNa can be replicated, this often leads to mutations. It can safeguard replication though ´
Normally LexA is blocking the syntehsis of SOS genes by binding to a DNA operator. If RecA bind ssDNA it is activated and cleaves LexA. Cleaved LexA can't bind to the operator anymore, SOS genes are read. =>2/27,28
They play a role in the eukaryotic damage reponse e.g. to double strand breaks.
Cell cylce control, replication fork stabilization, replication origin control
See slide
Non homologous end joining, joining DNA ends, it is predominant in non dividing cells. (G1 phase)
A double stranded break is repaired by simply joining the ends potentially after trimming a few bases by a nuclease.
DNA ends are resected, regions of microhomology are found, DNA pairs, gaps are filled and overhangs trimmed
Resection occurs to generate 3' overhangs, one of the 3' overhangs invades an intact duplex, generating a heteroduplex and a displacement loop,
new DNA is synthesized, until this can pair with the other 3' overhang. Then repair replication and synthesis (Probably helpful if you could draw a diagram here)
It plays a role in homology directed repair, where it has nuclease and helicase activity and in the end generates 3' tails after encountering Chi sites.
Special DNA sequences recognized by the recBCD complex.
Werner Syndrome
Bloom Syndrome
Rothmund Thomson Syndrome
It loads onto the single stranded DNA and helps in strand exchange it also plays a role in homologous recombination
DNA is changed and is afterwards a copy of the homologous chromosome. This can lead to a loss of heterozygosity
The switching uses homology directed repair. There are three loci the active MAT locus and two silent loci one carrying alpha and one a information.
The endonuclease HO cuts in the MAT locus and either the information of alpha or a is copied there potentially changing the mating type.
No this depends on how the junction is cleaved
Movement of the holiday junctions
After a double strand break, DNA is resected and bound by proteins which help in inavding the other duplex. DNA
is synthesized from the invading strand. The displaced strand of the D-loop is captured by the remaining 3' end.
DNA synthesis occurs and holiday junctions form 3/41
They are similar and the initial processes are almost the same
single strand nick leads to a ds break after strand separation. One strand of the "broken off" end invades the
"whole" part a D-loop structure is formed, DNA synthesis occurs, the displaces strand is captured by the lagging strand
lagging strand synthesis is restarted and after clevaged the fork is restored see
Resection occurs to generate 3' overhangs, one of the 3' overhangs invades an intact duplex, generating a heteroduplex and a displacement loop,
new DNA is synthesized. The displaced strand from the D-loop is not captured. Here lagging strand synthesis starts occuring => 3/50
Potentially loss of heterozygousity
Potentially this Replication is not as precise as normal replication 4/58f
Recombination on the same chromosome
Unequal crossover between chromatids or between homologs can lead to deletions and duplications
Crossing over between different chromosomes can lead to DNA translocation
See graph there
transposition / transposable elements
Autonomous elements encode the enzymes needed to move. Non-autonomous elements lack these and rely on enzymes of Autonomous elements
High
They are inactive e.g. due to mutation (also see first lecture)
The gene function or regulation can be affected potentially resulting in disease
No in general not, but be aware of the special cases
Class I elements are retrotransposons that move via an RNA intermediate, Class II elements are DNA only transposons 5a/11
It has terminal inverted repeats and a transposase gene.
LTR and non LTR
Class II elements can likely cross the species barrier
Cut and Paste
Nick and Paste
E.g. pathogenicity factors and antibiotica resistance
A bacterial cut and paste DNA element only encoding its own transposase
Two simple transpons (IS elements) flanking (another) gene(s)
Two
The transposase cuts in trans, i.e. they cut the other end that they don't bind
GCATxxxxTransposonxxxxGCAT
Upon insertion a piece of DNA is duplicated, when the transposon leaves, this duplicated DNA can remain -> a footprint
When the transposon leaves and the resulting gap can be repaired by homology directed repair from a transposon free site, the original state can be restored and no footprint remains
Antibodies joining of different pieces, more possible antibodies, several possible fragments for each V D J pieces
They could be related as there are certain similarites both in the enzymes as well as in the signal DNA sequences
A DNA mobile element. It was only recently introduced into Drosophila by crossing the species barrier.
Using microinjection this is a way to make transgenic flies.
This is a fish transpon which was no longer active. Using the consensus sequence the ancestral working state could be restored
This is a fish transpon which was no longer active. Due to mutations the inserted transposons became "dormant"
LTR and non-LTR elements
long terminal repeat
>LTR=== GAG, PR, IN, RT-RH ===LTR>
INtegrase, GAG, PRotease, RT-RnaseH reverse transcriptase+ RNAse activity
ENV for extracellular stage
It can get lost due to homologous recombination between the elements
Explain the additional elements retroviruses have
very high
Reverse Transcription is error prone. reverse transcription is part of the life cycle.
ORF1/ORF2 and polyA
a stretch of Ts that pair with the polyA tail
DNA methylation both prevents transposase expression and transposon end activity
It is active in germ line but not somatic cells.
They block transcription of certain transposons.
It preferably inserts into heterochromatin
If transposons preferably insert in a location close to the donor site.
Conservative site-specific recombination
They are topoisomerases
Serine and Tyrosine type
Tyrosine recombinases break DNA and form DNA-3P-tyrosine linkage, Serine recombinases break DNA and form a DNA 5P-serine linkage
See the sequence in the lecture
See the sequence in the lecture
a (tyrosine) recombinase that recognizes lox sites.
To delete DNA between two lox sites, this is often used as a tool where Cre is expressed under a specfic promoter. After Cre expression, a piece of DNA is removed and for example a tissue specific knockout is made.
attP, attB -> attL, attR
phage lambda recombination
RNA has U instead of T and ribose instead of deoxyribose.
Initiation, Elongation, Termination
RNA polymerase I (large ribosomal RNA), II (mRNA), III (tRNA and 5S rRNA)
They have an additional polymerases (apart form I, II , III) to transcribe regulatory RNAs
3/4 <x< 4/4 or the main load
It can become phosphorylated
It contacts the promoter
-35 and -10 element
very active
TATAAT
Proteins binding to sigma factors and inhibiting their function
It is exported through the incomplete flagellum apparatus
TATA box
TATA binding protein TBP
RNA polymerase is in position and the DNA is not yet opened, then the complex of polymerase and promoter is called closed complex
RNA polymerase has opened up the transcription bubble
RNA polymerase is not immediately working fully instead it enters cycles of abortive initiation resulting in short pieces of RNA being released. This is likely due to a loop of eukaryotic TFIIB and bacterial sigma factors extending into the polymerase
When the loop of TFIIB/sigma inserted into the RNA polymerase is displaced and the polymerase breaks away from the promoter
It becomes phosphorylated
Incubate RNA polymerase holoenzyme with radioactive nucleotides. Run products on gel and visualize with Xray film
locked nucleic acids (these are locked in a conformation more favourable for hybridization)
10< x <100 (20-50 nt/s)
When there is some pausing after only 35-50 bp have been synthesized by RNA polymerase
Short complementary regions in the nascent transcript forming hairpins or weak DNA-RNA hybrids
Elongation factors
RNA polymerases reverses direction, most recently made RNA separates off from DNA, this protruding end can be chopped off
This is often capping, happening while RNA is still being made
It is phosphorylated at additional serines
It helps in nuclease degradation, elongation termination of transcript, mRNA processing, export from the nucleus and directing translation
7-methylguanine is lined via a 5'-5' triphosphate to the 5' end of the RNA. (In more complex eurkaryotes 2' O of ribose in the second and third base gt methylated) 6a/37
removal of 5' phosphate (PPP-RNA -> PP-RNA), addition of GMP (GPPP-RNA), methlyation of guaanine m7GPPP-RNA)6a/38
histone chaperons
Changes in supercoiling
A site where bacterial RNA polymerase terminates transcription without any additional factors
An inverted repeat that forms a stem loop in the RNA, and a polyA (DNA) region, that leads to less stable AU base pairs
An enzymatic terminator
The former make a hairpin and have a poly A region the latter (Rgho) don't
RNA Polymerase III
eu. RNA Pol III doesn't need the RNA hairpin 6a/46
It is coupled to 3' end processing
They get polyadenylated
No, the nascent transcript is cleaved first and then the polyA tail is added.
torpedo and allosteric model
It must specifically recognize its right regulatory sequence e.g. through a protein domain
In the major grove all bases can potentially be distinguished this is not necessarily the case for the minor grove
positively charged amino acids, as the DNA is negatively charged
helix-turn-helix, homeodomain, zinc finger....
See the slides
low glucose, lactose available -> strongly on
low glucose, lactose not available -> off
high glucose, lactose available -> weakly on
high glucose, lactose not available -> off
The two component signal transduction pathway features a histidine kinase.
No it can also occur during elongation and termination
When transcription termination is actively prevented
HIV
Riboswitches are RNA regions that can directly bind a small molecule that controls the RNA secondary structure, regulating transcription or translation
see 103 (you would need to explain that there are 4 blocks, where 3+4 form a terminator but there is a small ORF with lots of Trp causing eventual staalling making 2 pair with 3) ...
It cleaves it into short pieces
siRNA -> silencing (Give some details about AGO, Dicer etc)
They can spread between cells.
When a construct is brought into a genome in normal sense orientation and both the introduced gene and the endogenous gene are silenced 7/29
double stranded
Yes siRNAs for example can target regions for Cytosine methylation or histone modifications
five
Production of siRNA
See slide: RNA Pol makes pri-mRNA which is cleaved into pre-miRNA (Drosha), exported from the nucleus (Exportin), there pre-miRNA is cleaved by Dicer and finally RISC complex is formed (what is not shown there is strand selection... just fro your info)
The strand of a miRNA that is usually (or probably better: more often) degraded
Transcription factors
Cleaving, splicing, polyAdenylation, Capping, Editing
no
5' and 3' structures (e.g. cap) hairpins, splicing
See slides
GTP
They can mimic tRNAs
The Shine Dalgarno sequence (be prepared to explain how it works as well)
The Sequence A/GXXAUGG which is helping in recognizing the "right" AUG in eukaryotes
See corresponding slide
No it ids highly accurate
bacterial quality control, in bacteria, see slide
Selenocytstein, see slide
yes
(p)ppGpp which is synthesised through RelA
ferritin : be prepared to explain the mechanism
ferritin : be prepared to explain the mechanism
Explain the mechanism in general!
Explain the EJC and where you would normally encounter splice sites and how this can be used to find premature stop codons
These prevent hydrophobic patches to aggregate
GroEL binds, later GroES a switch occurs exposing different hydrophilic/hydrophobic regions, protein gets refolded
Potein disulfide oixidase, it both oxidises and swaps disulfide bonds
BSE, Scrapie, nvCJD, GSS ....
No yeast also has prions
Certain yeast prions can be cured by chaperons
Protein regions which autocatalytically "splice" themselves out of the protein. They can be used in chemical semi-synthesis
Acylation, Prenylation, GPI anchors
It is related to inteins and it is modified with cholesterol
They can become more soluble and spacious
modified AA, give at least on example each
see slide you must include E1, E2, E3
Often one E1, several E2 and very many E3
degradation in the proteasome
degrade (certain!) ubq marked proteins
see slide
see slide
see slide: recognition of sequence/ribosome stops/SRP-ribo gets recognized by SRP-receptor/peptide chain moved to translocator
protein SU as well as 7S RNA
importins/exportins
via GTP /see slides for the cylces
Multiple compartments that need to be targeted : thus TIM/TOM TIC/TOC
Multiple compartments that need to be targeted : thus TIM/TOM TIC/TOC