Molecular Flashcards
As well as the linear DNA chromosomes also contain proteins that..(5)
- Pack and Unfold the DNA within the nucleus e.g. histones
- Control DNA replication, repair and genetic recombination.
- Maintain chromosome integrity by protecting the end sequences e.g. telomerase
- Govern proper chromosome segregation during cell division
- Regulate gene expression e.g. RNA Primase, RNA polymerase
Placement of transcriptionally active genes vs inactive?
Activation of a gene is accompanied by migration from the periphery towards the centre of the nucleus
In nm the width fibre of chromatin vs when supercoiled?
10nm in interphase vs 30nm when supercoiled.- gets so much more densely packed.
DNA is wrapped around core.. made of … subunits, to make up a …stabilised by…
Histones
8 H subunits
Nucleosome
H1 linker proteins
Histone tail names?
H2A x2
H2B x2
H3 x2
H4 x2
The histone N- terminal tails are rich in ….
Significance?
lysines and arginines
Substrate for post-translational control
Significance of nucleosome free areas in the DNA?
Transcription factors can bind and RNA polymerase so can be translated.
What is the centromere? (brief function)
DNA sequence in which the kinetochore assembles and mediates chromosome segregation.
What is the kinetochore?
Protein complex found at the centromere that binds to the microtubules of mitotic spindle.
What is the telomere?
3 prime overhang repeat of TTAGGG, that maintains integrity and stops the shortening. It’s synthesised by the telomerase.
Why is telomere necessary?
Without there would be bases lost from the DNA during replication. DNA polymerase needs an RNA primer to elongate from, and at the 3prime end without when this is removed there would be a loss of bases.
Normally can use DNA polymerase to seal the gap, but there is no 5 prime for it to extend from, whereas with telomere another okazaki fragment can be added, and this gap sealed as normal by DNA ligase.
Why does the telomere not shorten over time?
It is maintained by telomerase. This is an enzyme which is a ribonucleoprotein. This acts as a template, with the sequence AAUCCCAAU, antisense to TTAGGGTTA. The first AAU binds to the 3prime strand, and using this as a DNA template strand adds GGGTTA. It then moves along with AAU binding so adding the next GGGTTA etc, adding 6 nucleotides at a time.
What is the centromere structure?
Repeated sequence making up alpha satellites, forming condensed transcriptionally inert heterochromatin.
Inner: connect so hold sister chromosomes together (cohesin to)- normal H3 histones, but DNA is demethylated at lysine 4.
Outer: connect to kinetochore- centromere specificH3 histones.
What are alpha satellites?
In the centromere these make up the DNA repeats that are docking sites for the kinetochore inner plate proteins, and outer plate to that, which the spindle Microtubules attach to.
How is the alpha satellite DNA structure different? Why?
The heterochromatin contains centromere specific H3 histones (Centromeric protein a variety specifically).
These help hold the sister chromatids together by adhesion molecules ensuring correct pairing.
Outer DNA is demethylated at lysine 4 but normal H3
What structure does the yeast kinetochore have?
It is basket in shape, which links one single nucleosome in the kinetochore to a microtubule..
Only …..% of eukaryotic genome codes for cellular proteins, and …% is just repeated sequence elements.
1.5%
50%
What are DNA transposons?
Mobile genetic elements that jump around the genome using the cut and paste method.
e.g. P-element in fly, Ac-Ds in Maize
How does the DNA transposons move in the genome?
Cut and paste method:
Transposase enzyme bind to cut the transposon out of the genome.
They are bundled into a mobile transposome.
This can be inserted into another location.
Problem with DNA Transposons?
They are powerful mutagens as they can change alleles (e.g. Ac-Ds colour change in the Maize when first discovered) or cause damaging mutations.
What are retroviral-like transposable elements? Insert into genome how?
E.g. HIV.
Viruses that use RNA transcriptase to convert their RNA into DNA which can be inserted into a genome.
How do retroviral-like transposable elements Insert into the genome?
E.g. HIV
Once the virus is in a host cell, it unenvelopes. The reverse transcriptase of the virus is used to conver the RNA into DNA (adds a DNA strand to the template RNA then this is uses as a template etc and Double stranded DNA is made)
This is then inserted into the host genome. This gene is then transcriped and translated into other viruses (RNA copies, envelope proteins, capsid proteins and reverse transcriptase) so the new virus can leave this host cell and invade another, inserting the DNA into other genome locations.
What are non-retroviral Poly-A retrotransposons?
The most abundant type, replicate via RNA intermediate using our own reverse transcriptase to replicate via copy and paste into the genome.
How to non-retroviral poly-A retrotransposons replicate?
The gene e.g. L1 element is transcribed into RNA. Our native endonuclease cleaves the new location DNA. Using the newly created 3prime as a primer and the RNA as a template, the top strand of nicked DNA is extended by our Reverse transcriptase. As this DNA strand is replicated normally, a new double strand with the retrotransposon is created. (page 291)
Summary of the difference between the three types of transposible elements?
- DNA Transposons- use cut and paste by transposase to move (in a mobile transposome) e.g. Ac-Ds
- Retroviral-like retrotransposons- e.g. HIV- code for all it needs e.g. reverse transcriptase, envelope and capsid and RNA
- Non-retroviral retrotransposons- e.g. L1 element, use our own enzymes, Nicks the DNA and uses its RNA as a template. Don;t need viral packing.
non-retroviral retrotransposons in disease?
Haemophilia
L1 or LINE-1, Long interspersed nuclear element
An insertion of this L1 element into the clotting protein Factor VIII can cause.
DNA topoisomersase function?
It prevents DNA Becoming tangled, reducing superhelical tension which is created due to unwinding during DNA replication.
How does DNA Topoisomerase work?
Type 1: Nicks and reseals only one strand by unwinding one around the other.
Type 2: Nicks and reseals both strands- more risky and ATP required.
DNA replication steps? (6)
- DNA helicase uses ATP to unwind the DNA and SSB proteins keep the strands apart.
- RNA primer is added by DNA primase.
- DNA polymerase adds the new bases from the primer in a 5’-3’ direction. This is continuous on the leading strand but for the lagging Okazaki fragments are added.
- Ribonuclease H removes the primer.
- DNA polymerase extends over the gap.
- DNA ligase seals the nick, using ATP.
What is the equation for DNA replication/ synthesis?
dNMPn + dNTP= dNMPn+1 + 2pi
dNMPn (Deoxyribonucleotide mono-phosphate Existing strand)
dNTP (Deo… triose phosphate- incoming nucleotide)
How is 2pi released from DNA replication/ synthesis?
The incoming nucleotide has three phosphates, so as it joins two are lost.
Initially this molecule is made of two Phosphates and 6 oxygen molecules and termed Pyrophosphate.
Pyrophosphatase then converts this (PPi) to 2 inorganic phosphates and ATP.
Where does the ATP needed for DNA ligase come from?
The breaking down of pyrophosphate to 2pi and ATP by pyrophosphatase.
Mutations in DNA helicase?
Werner Syndrome- premature aging
Bloom syndrome- short stature and predisposition to cancer
How does the processivity of DNA polymerase increase?
When it is associated with the sliding clamp, which is kept at the primer: template junction by a clamp loader.
ATP is bound to the DNA here also, and when DNA polymerase binds AMP+Pi is given off.
The association of the sliding clamp stops the polymerase falling off the DNA, but allows movement.
It is released at the 5’ of the proceeding Okazaki.
Use of the SSB proteins?
Single stranded binding proteins, keep the DNA open, and straighten out the chain without covering the bases, stopping hairpin helices forming.
How is a replication origin determined?
Destination determined in yeast by where there is an autonomously replicating sequence ARS element.
In humnas, near to certain genes e,g HBB or MYC, but no specific sequence just where there is a nucleosome free zone.
After determined where how does a replication origin open? (4 steps)
Formation of a Pre-replicative complex in the G1 phase:
- Origin recognition complex (ORC) binds to the replication sequence. This lays down the foundations for the Pre-replication complex.
- Helicase loading proteins bind to the ORC- cdc6 and CdE1.
- The helicase Mcm 2-7 binds to complete the formation of the Pre-RC.
- Origin activation- unwinding of DNA and recruitment of DNA polymerase in the S phase.
How is it decided whether the Pre-RC formation is activated etc? Why?
Cdk high: Current Pre-RC formation activated, but new Pre-RC formation is prevented
Cdk low: New Pre-RC formed, and any existing not activated.
This prevents more than one origin of replication opening at one time.
What is a hydrolysis reaction?
The separation of two molecules by using H2O
opposite of a hydrolysis reaction?
Condensation- two molecules join together and H20 is released.
What is an oxidation reaction?
Gain of oxygen (or loss of electrons)
The four bases can be mutated by which 4 reactions?
hydrolysis, condensation, methylation or oxidation
Deamination of which base causes what?
Cytosine is deaminated to uracil. NH3 and H20 are released.
Why is deamination of … base bad?
Deamination of cytosine causes it to become uracil, so when DNA replicates there will be an Adenosine inserted instead of a Guanine.
What is a UV pyrimidine Dimer?
Covalent linkage between two carbon atoms in adjacent pyramidines e.g. Thymine dimers or Tymine-cytosine etc,
Why is a UV pyramidine Dimer bad?
During DNA replication, there will be either a deletion, subsititution or arrest replication as DNA polymerase cant bind.
What is the impact of ultraviolet radiation on DNA?
Can cause Pyramidine dimers to form
What is depurination?
Removal of a purine, e.g. A or G, causing a base deletion.
What is ionizing radiation?
Double stranded DNA breaks, which are prone to degradation as they have to telemeres, then causing the loss of sequences.
What is a PH domain?
Involved in membrane binding and anchoring proteins to the membrane, proteins interract with the charged head of phospholipids
How do you experimentally get an epitope tagged protein?
Insert DNA of tag e.g. DYKDDDDK into the protein of interest DNA, introduce this into a cell and it will translate the protein with the tag, which can be purified.
Steps for an immunopull down to show interracting proteins?
- Tag the protein of interest with an epitope.
- Add other proteins to bind
- Use specific antibody to the epitope of the POI.
- Add protein A coated beads complimentary to the antibody (immunoprecipitation)
- centrifuge to recover the complex.
- identify the bound proteins by mass spectrometry or western immunoblotting.
What is an epitope tagged protein?
A protein tagged with a sequence known to us, so we can purify by using an antibody to the epitope.
What are these?
HA peptide YPYDVPDYA
Myc peptide EQKLISEEDL
Flag peptide DYKDDDDK
Common epitope tags for the POI for immunoprecipitation
What are these?
Glutathione-S-transferase (GST)
Hexa-histidine (6xHis)
Common protein tags for affinity chromotography.
GST affinity pull-down method?
Instead of an epitope being added in immunopull down, GST is added to the POI. The POI then binds to the Glutathione coated beads.
Other proteins are eluted, while the POI and bound proteins are later.
SDS PAGE or western blotting with antibodies are used to separate, or mass spectrometry to identify.
What is depurination?
Loss of a purine (A or G- Get pure drugs if u are A G)
Deletion.
Why is depurination bad?
When DNA replication happens a base will then be exised and lost.
What is deamination?
Deamination of a pyramidine, thus converting it to anotjer base, e.g. Cytosol deaminated to uracil.
NH3 and H20 given off.
What can ultra violet light cause to happen to bases in DNA?
UV pyramidine dimers.
Covalent linkage between 2 carbon atoms in adjacent pyramidines e.g. thymine dimers or tymine cytosol etc.
WHat is bad about UV pyramidine dimers?
Leads to either a base pair deletion, substitution or can arrest the DNA replication as DNA polymerase cant bind.
What can ionizing radiation do to DNA?
Cause double stranded breaks which then have exposed ends that are prone to degradation. They have to telemeres so can result in the loss of sequences before repaired.
Two methods for repairing ionizing radiation breaks in DNA?
Non-homologous end joining and Homologous recomibation.
WHat is the difference between the two methods of reparing ionizing radiation?
Non-homologous end joining is musch faster but less precise can result in loss of bases, whereas homologous recomination is the last line of defence and is more accurite.
How does non-homologous end joining work?
Quickly joins up the two broken ends of DNA, but this can cause loss of DNA due to degradation.
How does homologous recomination work after a DNA break? (short description)
Sister chromatids are recruited (often near just after replication anyway) and used to ensure there is no DNA loss. These are used as templates to repair any lost DNA bases.
How are sister chromatids used to repair DNA in homologous recomination?
- Exonuclease degrades the 5prime ends of the cut DNA back, to create resected sticky ends.
- DNA binding protein RecA promotes strand invasion (opening the sister chromatids strands so that he complimentary broken strand can bind)
- A heteroduplex is created (a DS molecule created by recomination from a different source- in this case two sister chromatids).
- A holiday junction is also created (crossing of the DNA)
- DNA polymerase synthesises new DNA using the sister chromatids as templates.
- The invading (damaged) strand is released nd the broken double helix of both reforms with DNA Helicase
- DNA synthesis continues using the repaired strand as a template.
- DNA ligase seals the nicks created.
What is base excision repair after?
After deamination of cytosol to uracil
Method of base excision repair?
After deamination c to U.
- The incorrect uracil base is recognised by DNA glycosylase and removed.
- AP endonuclease removes the sugar and Phosphodiesterase removes the phosphate so there is a gap in the DNA
- DNA polymerase adds the new nucleotide using the other strand as a template.
- DNA ligase seals the nick.
What is nucleotide Excision Repair used after?
Pyramidine dimer formation.
What is nucleotide excision repair method?
- Dimer recognised by Excision nuclease and the backbone of the DNA is cleaved a few bases either side of the dimer damage.
- DNA helicase removes the sliced single stranded fragment.
- DNA polymerase extends from the Primer:template junction using the other strand as a template.
- DNA ligase seals the nick.
What method is used to repair deamination of a DNA base?
Base Excision repair. (B and D both early in alphabet, whereas N and P later)
What method is used to repair a pyramidine dimer in DNA?
Nucleotide excsion repair. (B and D both early in alphabet, whereas N and P later)
Difference between endo and exonuclease?
Exonuclease removes nucleotides as the end of a DNA strand, whereas Endonuclease is in the middle.
What is a holliday junction?
A crossed structure created during recombination, where the DNA strands are separated so one can cross and bind to complimentary bases of another.
Enzyme that promotes strand invasion?
RecA
Method of homologous recomination? (non repairing)
- Spo11 Endonuclease makes the initial cleavage in the middle of the strands.
- Mre11 Exonuclease resects the 5 prime end degrading it to create a staggered double stranded break.
- Strand invasion catalysed by RecA.
- DNA synthesis catalysed by the DNA polymerase, and second strand captured by the strand invading, to make a double holliday junction.
- (look at picture) cuts and ligations of strands happens so recombination occurs.
What are the phases of the cell cycle?
Go- Gap phase where cell cycle is arrested
G1- Gap phase 1, checking environment is stable before going into the cell cycle.
S- Synthesis, interphase, all DNA is replicated.
G2- Gap phase two checking all of the DNA is replicated and envronemnt still favourable.
M- Mitosis, Segregation of the chromosomes into separate cells and cytokinesis.
Phases of Mitosis?
Interphase (DNA replication)
Prophase (Condensation of sister chromatids)
Prometaphase
Metaphase (mitotic spindle attatch to the kinetochore)
Anaphase (separation of chromatids)
Telephase (envelope reforms)
Two types of yeast replication?
Budding yeast: A bud forms off the yeast, and duplicate contents and this stretches into the bud which separates off into a new cell.
Fission yeast: Normal eukaryote way
Advantages of using yeast to study cell cycle?
- Rapid divisions once every hour
- Can be done haploid or diploid
- Cell cycle genes are highly conserved so good for studying our own mechanism
Why is an Xenopus a good biochemical model for cell cycle studying?
- easy to collect eggs
- Rapid division rate (every 30mins)
- Large size good for collecting purified proteins
- Can do RNA injection experiments on the oocyctes.
How would one experimentally do cell-free mitosis? Why?
Extract the cytoplasm of an egg cell, add the sperm to fertilise in a test tube.
Add ATP.
Can then add antibodies which can then target proteins in the solution and analyse the proteins present at each stage.
What are the three checkpoints in mitosis?
G1 to S- Is the environment favourable?
S to Prophase- Is all the DNA replicated? (negative signals)
Metaphase to Anaphase APC: Are all the chromosomes attatched to the spindle?
What varies to promote the cell cycle?
Cyclins. Cyclin levels vary and these bind to cdk’s (cyclin dependent kinases).
CDK’s then phosphorylate many proteins that are specific to certain stages of the cell cycle.
How are CDK’s regulated apart from Cyclins binding?
On phosphate activates, two inactivates.
Wee1 was phosphorylate in the inhibitory position to inactivate.
CDK 25 phosphatase can remove this nand activate it again.
p27 can also inactivate.
What is Anaphase promoting complex?
It is a ubiquitin ligase which ubiquitinises M and S cyclin, so promoting Anaphase.
The ubiquitination is then achieved by E1 and E2 enzymes under APC regulation.
Cdc20 activates APC.
APC also ubiquitinates ….. as well as the cyclins. why?
securin for destruction, enabling the eventual destruction of cohesin and thus sister chromatid separation
Difference between meisos and mitosis?
Homologue chromosomes, materal and paternal segregate, to give only half the total number= haploid 23 instead of 46.
How is gentic diversity increased further? (beyond just random assortment of chromosomes?)
Crossing over. Bivalents are formed which allow genetic recomination.
When in meiosis do the different chromatids separate?
Anaphase 1: The sister chromatids segregate.
Anaphase 2: Paternal and Maternal chromosomes segregate.
What facilitates the pairing of a bivalent?
Synaptonemal complex made of cohesin between the maternal and paternal chromosomes.
and base pairing of homologues.
Crossing over of chromosomes happens at a …..?
chiasma
Two reasons for homologous recombination?
- Align the chromosomes up ready for anaphase and facilitates the formation of the synaptonemal
- Allows for genetic recombination between paternal and maternal DNA on the same chromosome.
Word for abnormal number of chromosomes?
Aneuploid
…% of sperm are aneuploid and …% of eggs
4% sperm
20% egg
causes miscarriage/ downsyndrome (philadelphia chromosome)
Where would the kinetochore have to attatch to the spindle to secregate differently in meiosis?
In mitosis (and Meiosis 2) connected to each sister chromatid so the spindles pull them apart. In meiosis 1 they are attatched to the centre of two sister chromatids so they segregate together, and maternal and paternal segregate.
DNA dye that shows nuclei?
DAPI binds to A-T rich DNA causing it to fluoresce
How can T be seen in DNA replication?
BrDU is a thymidine analogue that subs for the base and can be detected by fluorescent antibodies.
Pulse treatment can be used to tell which cells are what?
In the S-phase of the cell cycle.
How do cyclins activate CDK?
Cause a conformational change
How are different proteins expressed when all cells have the same genome?
Transcriptional regulation, not all genes are transcribed, and therefore translated into proteins. Even after this the proteins may be modified etc to be different.
DNA binding proteins charge? Reach into the ….. of DNA
Positively charged Binding AA’s (DNA negatively charged due to the phosphate backbone e.g. gel electrophoresis
DNA major groove
DNA binding proteins will interract with the …… of the DNA in the major groove (4 details)
response element in the major groove- makesspecific interractions with the bases via hydrogen bonds and non-specific to the backbone due to the charge
On a molecular level how do DNA binding proteins e.g. transcription factors bind to the DNA response element?
Side chains of the bases are either hydrogen donors, acceptors, a hydrogen molecule or a methyl group, which can interract with amino acids of the transcriptionf actors
e.g. asparagine binding to adenine via two hydrogen bonds.
What are examples of DNA binding protein types?
Transcription factors, polymerases, nucleases,
e.g. via zinc fingers, leucine zippers, helix-loop- helix etc
Example of yeast transcription factor? Binds?
Rox1, known to bind to 8 sites in 3 yeast genes, which all have different affinity to the protein. (3 in HEM13, 4 in ANB1 and Rox1 tiself)
How can different affinities of response elepments to a transcription factor cause different levels of transcription?
E.g. ROX1 doesnt bind perfectly, so is on some of the time and off other times, and the amount of transcription is the ratio of time on vs time off, depending of its affinity to the response element.
What is a consensus sequence?
The average sequence that a DNA binding protein will bind to e.g. the most common bases at those positions
sequence logo uses this to create an image of the text with the more common bases appearing larger than less common ones.
What are permissive transcription factors also called?
General transcription factors
How do transcription factors regulate DNA transcription? (3)
- Interracting with the RNA polymerase complex to promote or repress
- Altering acetlyation of the DNA, to make it more or less accessible for transcription.
- Binding to other transcription factors
How does DNA looping occur?
Chromatin doesnt bend easily so for two proteins to interract and loop they have to be more than 500bp’s away.
How is the promiscuous nature of the enhancers modulated?
(that they can work at enhancing more than one gene) By insulator elements, these block this and prevent enhancers activating downstream genes.
Two types of insulator elements?
an enhancer-blocking function and a heterochromatin barrier function.
There may be many inputs of transcription regulation, how is this interpreted?
It is interpreted as a sum of all of the transcription activators and repressors, and whether these are strong or weak, to give the final level of transcription.
How does tryptophan regulate its own transcription?
If high the tryptophan repressor protein undergoes a conformational change so can bind to the DNA and represses proteins required for tryptophan synthesis, whereas if low tryptophan in the cytoplasm this protein is not bound to genes actve.
7 ways that transcription factors can be activated?
- Ligand binding
- Phosphorylation
- Release from the membran, separate from the TM part.
- unmasking, removal of an inhibting subunit
- Removal of a signal peptide so can go into the nucleus
- Addition of a second subunit
- Protein synthesis
Transcription factors can act …… to activate transcription the most by?
synergistically
Binding together helps prevent them falling off,
or the first may say unwind the DNA so the second can bind.