T6 Flashcards
How does passing on of information differ between genetic and epigenetic inheritance?
Genetic inheritance passes on exact copies of the original code sequence, whereas epigenetic inheritance usually very limited and may not pass on at all.
Describe position effect variegation.
A breakage event in chromatin leading to previous euchromatin areas (transcribing genes) being incorporated into heterochromatin and vice versa.
What is the position effect in regards to genes.
Position of genes, in euchromatin or heterochromatin, determines whether the gene is expressed or not.
What nucleosomal histone-modifications can be found on lysine and serine?
Lysine: acetylation, monomethylstion-trimethylation
Serine: phosphorylation
Where does most histone modification take place?
On the “relatively unstructured N-terminal “histone tails”.
What enzymes are responsible for histone modification?
HATs (histone acetyl transferases) and HDACs (histone deacetylase complexes). Histone methyl transferase and histone demethylases.
How are the histone modification enzymes recruited?
Rough action of gene regulatory proteins.
What’s the effect of acetylation of lysine on the histone N-terminal tail?
Loosening of chromatin structure through loss of charge.
What is the main purpose of histone modification?
Attraction of proteins that stretch chromatin appropriately.
What are the functions of histone variants and when are they transcribed?
They mediate added function of the histone such astrascriptional activation, centromere function and kinetochore assembly, FNA repair and rcombination, gene expression and chromosome segregation, transcriptional repression ans X-chromosome activation. They’re transcribed throughout the interphase, vs. most histones in S phase.
What is the histone code hypothesis?
The hypothesis of histone covalent modification (extending, mosified histone tails) and variation being a code, read by code-reader complexes that modify bucleosome function (transcription, chromatin form etc.).
How are specific chromatin modifications spread for long distances along a chromosome?
With the aid of a reader-writer complex. A gene regulatory protein binds to free DNA, attaches a histone modifying enzyme (writer). A code-reader protein then reads the modification, a new writer enzyme attaches and so on, creating reader-writer complexes.
How is chromatin remodeling limited?
Through barrier sequences in DNA, ex. HS4. A barrier sequence contains for example a cluster of binding sites for histone acetylase enzymes (acetylases and deacetylases), which moderates the possibility of methylation of lysine.
Explain how histone reader-writer complexes can cause chromatin condensation.
ATP-dependent chromatin remodeling complexes attach to the junction of the reader-writer complex formed as reading enzymes replace writing enzymes. The modification thus spreads along the chromatin.
How are histones involved in centromere formation?
The kinetochore-attaching histone is modified in H3. Other histones around are densely packed.
What defines the centromere?
Repeats of A-T-rich alpha satellite DNA. However, this sequence can be missing and rather it is the protein complex associated with the centromere that seems most essential.
What is the role of the initial seeding event in centromere formation?
It is required for de noco centromere formation. It involves histone with the CENP-A variant of histone H3 and happens in humans readily on the A-T-rich repeating satellite DNA-sequences.
Describe the formation of the centromere.
- Centric heterochromatin displays banding of CENP-A H3 histone areas with corresponding CENP-A negative areas, dimethylated at lysine 4.
- Centric chromatin coils form so that CENP-A histone H3 areas contact the inner kinetochore plate.
- Pericentric heterochromatin starts at either end of centric heterochromatin.
How are the centromeric structures of chromatin inherited in replication?
Modified histone components remain bound to replicated DNA and the bind their appropriate components (CENPA-A H3 remains with the DNA).
How are hetero-eu-patterns transferred to replicated DNA.
Histone modification is activated in replicated DNA by specific regulator sequences and modifying proteins, securing passing on of original structure.
What’s an alternative to chromatin-associated protein for epigenetic inheritance?
Networks of signaling molecules that control gene expression.
What is a lampbrush chromosome?
The theorized structure of all eucarytotic chromosomes in interphase. Paired sister chromosomes intertwine. Each chromosome has a structure where bigger loops alternate with shorter, more condensed (wavy chromomeres) areas of chromatin. There are 4 copies of each loop in every diploid cell. Most of the DNA is contained outside of the loops. Proteins forms scaffolding for the chromatin to rest on.
What are polytene chromosomes and what are they useful for in DNA research.
Multiple copies of the same chromosome lined laterally and joined to a large unit. Antibody staining allows for investigating of chromayin associated regulatory proteins.
What is a chromosome puff in relation to polytene chromosomes?
A stretch of uncondensed polytene chromosome, visible through microscopy.
What can be said about homologuous chromosome position in the nucleus in general and during very active transcription.
The position of the two homologuous chromosomes don’t necessarily coincide but during active transcription they diffuse to nuclear neighbourhoods for gene expression.
How is the eu-heterochromatin barrier enforced?
By barrier proteins:
- Tethering to nuclear pore complex
- Binding to nucleosomes
- Recruitment of histone-modifying enzymes hinders heterochromatin zone from spreading
How are reactions in the nucleus effectivated?
Through macromolecular forming of distinct biochemical environments (proteins polymerize with attached components).
Name two purposes for the highly condensed form of DNA in chromosomes.
- Easy separation of sister chromatids (they’re disentangled)
- Keeps fragile DNA from breaking during sister chromatid separation
What is the role of condensins?
The condensin proteins aid in compactin of DNA into chromosomes.
What are the different levels of DNA packing in chromosomes?
- DNA double helix
- Bead-on-a-string chromatin
- 30 nm chromatin fibre
- chromatin fiber waves 300 nm
- condensation of waving
What is the SMC protein dimer?
Part of condensin complex that fastens chromatin loops together in a key ring kind of fasion.
Where is condensin found on a condensed chromosome?
Along the medial part, along with ex. telomerase II.
What gives rise to genetic variation and subsequently new species?
Errors in the DNA regulatory mechanisms, transposons.
Define purifying selection.
“selection that eliminates individuals carrying mutations that interfere with important genetic functions”
How can different species be genetically linked to a common ancestor?
Almost perfect conservation of basic RNA and DNA utilization genes (mRNA machinary etc.).
What is a phylogenetic tree?
A tree of descendance, relating species to each other and to common ancestors.
What does comparison of human and mice genome tell us?
Coding sequences are generally more similar, substitutions are more common than addition/deletions and gene order in a chromosome is the same.
Explain the difference in the size of vertebrate and Fugu (pufferfish) genome.
Slowing down of DNA addition, coupled with ‘cleansing’ of the genome of non-critical information.
Multispecies sequence comparison - what’s it useful for?
Identifying common important DNA sequences of unknown function.
What are human accelerated regions?
Regions of DNA in where rapid mutation has taken placr, leading to human species divergence.
What are possible fates of duplicated genes?
Silencing, removal or divergence. (tetramer Hb vs. primordial monomer Hb)
Give an example of a result of duplication and divergence seen in mammals today.
Separate forms of β-chain of Hb, adult and foetal.
How does recombination of exons lead to encoding of new proteins?
Through intron expansion (duplication of sequences on either sides of exon).
What are SNPs (single-nucleotide polymorphisms?
Points in genome sequence where one big part of the population has one nucleotide, whilst another part has another.
How is the studying of polymorphism clinically relevant?
Future drug therapies will take into account individual genetic traits, including polymorphic ones, when deciding on dosage, duration etc.
Does one type of signal activate only one type of GPCR?
No. Ex. adrenaline can activate nine different GPCRs.
Outline the G proteins trimeric structure.
α, β and γ (gamma) subunits, Alpha and gamma are covalebtly attached to membrane lipids. Alpha binds GDP/GTP.
What are the steps of GPCR activation?
- GTP binds to alpha subunit.
- Target protein or RGS (regulator of G protein signaling) is bound which has GAP activity (alpha-subunit-specific GTPase-actuvating protein).
- Activation of G protein continues as long as ligand is bound to receptor.
name the cAMP synthesis/breakdown regulators.
Synthesized by adenylyl cyclase. Degraded by cAMP phosphodiesterase.
What’s the difference between Gs and Gi?
Gs (stimulatory G protein) activates membrane bound adenylyl cyclase, whilst Gi (inhibitory G protein) inhibits it. Tjeir different types of G proteins that can be coupled to receptors.
What two toxins are widely used in G protein targeted experiments?
Cholera toxin (chronic activation of GPCR) and Pertussis toxin (chronic inactivation of GPCR).
Outline the intracellular GPCR signal transduction.
- Adenylyl cyclase is activated by Gi GPCR
- Inactive PKA, connected to AKAPs (A kinase anchoring proteins), are phosphorylated to yield two active PKA monomers
- Monomers enter the nucleus
- PKA phosphorylates/activates CREB (cyclic AMP response element binding protein)
- CREB recruits CBP (CREB binding protein)
- Gene transcription is activated
What alternatives are there to PKA mediation of cAMP in cells?
Ion-channels in olfactory sensing. GEF that activates Rap1 monomeric GTPase.
Outline PIP hydrolysis.
- Phospholipase C-β hydrolyses PIP2 (phosphatidylinositol derivative attached to cell membrane) into diacylglycerol (remains attached) and IP3 (cytosol)
- Diacylglycerol activates protein kinase C
- IP3 releases Ca^2+ from the ER
Outline the reaction path of GPCRs with PIP2s.
- GPCR is activated
- It activates phospholipase C-β
- PIP2 is hydrolyzed
- Diacylglycerol attaches to inactive protein kinase C
- IP3 releases Ca^2+ from ER
- Ca ions activate protrin kinase C
How are calcium depleted ERs refilled?
Store-operated Ca^2+ channels in plasma membrane are activated, Ca^2+ sensor proteins in ER mediate intake.
Distinguish between conventional and atypical PKCs.
Only conventional PKCs are activated eith the diacylglycerol + Ca^2+ mechanism.
How is ER-contained calcium-release controlled?
- Through IP3-receptors (require IP3 and are inactivated by high amounts of calcium ions)
- Through ryanodine receptors (receptors activated by Ca ion binding, positive feedback)
How do Ca^2+-flux heavy cells (neuro/musculo) differ from other cells in calcium transport?
In addition to ER calcium pump, Ca-binding protein, ATPase Ca-pump and mitochobdrial Ca-intake nerves and muscles couple Ca-efflux to Na^+ influx
What kind of calcium influx phenomenons can be seen in cells?
Spikes and oscillations.
What is the role of the allosterically, stepwise activated calmodulin protein?
Regulation of enzymes and membrane transport proteins (ATP dependent Ca transporter).
What is a CaM-kinase?
Ca^2+/calmodulin-dependent kinases phosphorylate gene regulatory proteins such as CREB and thus regulate transcription.
Outline the functions of CaM-kinase II.
Maintains activeness after the activating Ca^2+/calmodulin signal has died out, thanks to autophosphorylation (molecular memory).
How do GPCRs regulate ion channels?
Directly: alpha subunit inhibits adenylyl cyclase, beta subunit binds to K-ion channels and open them.
Indirectly: stimulating channel phosphorylation: PKA, PKC, CaM-kinase, or through causing of destruction of nucleotides controlling ion channels.
How do GPCRs control olfactory/visual sensing?
Through control of cNUCLEOTIDE (cAMP etc.) gated ion channels.
Explain the signaling method of sense receptors.
Hyperpolarization that follows increase in cNUCLEOTIDE effectively turns off receptor cell inhibition. cGMP phosphodiesterase subsequently lowers the cGMP levels when stimulation (light) stops.
What enzymes aid in control of visual sensing?
Rhodopsin kinase, arrestin and cGMPphosphodiesterase.
How is a sensory stimuli relayed so that it causes neural voltage response?
Through cascade amplification.
What are the three modes of desensitization for GPCRs?
- receptor inactivation
- receptor sequestration
- receptor down regulation
What’s the mechanism behind GPCR desensitization?
It is dependent on the phosphorylation by PKA, PKC or GRKs. Only activated GPCRs can activate GTKs to polyphosphorylate/deactivate them.
What is the arrestin mode of action mechanism?
Prevention of interaction between receptor and G protein AND adaptor between receptor and clathrin-dependent endocytosis machinery for receptor mediated endocytosis.
