Dynamic Cell- Caunt's

?
What are Kon and Koff?
Proportionality constants that describe the relationship between concentration and rate of association and dissociation (higher= higher propensity to associate/dissociate)
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What is the likelihood of interaction between to molecules determined by?
Concentration and affinity (affinity determined by complementarity in shape and chemistry- if high then bonds formed strong enough to withstand thermal jolting)
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What is the Kd?
The equilibrium constant. A measure of affinity (inversely proportional). It is the concentration of ligand required to occupy 50% of free ligand binding sites at equilbrium
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Why is the Kd of a hormone receptor so much lower (higher affinity) than a NT receptor?
HR: ligand secreted into blood, so conc v. low, hence must have high affinity. NT ligand secreted into synaptic cleft (low vol, hence high conc easier to achieve) so doesnt require such a high affinity (also requires high Koff to allow clearance)
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What are domains of a protein?
Polypeptides able to fold into a function unit independently of the rest of the protein
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What is the upper limit of the number of amino acids able to fold without error? so?
250- this is why multi domains evolved.
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What are the two types of protein domains?
Interaction and catalytic
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What are the most prelevant types of kinases in eukaryotes?
Ser/thr, tyr and lipid kinases (to form PIs)
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What kinases are relevant in bacteria?
His kinases (but mechanism of phosphorylation very different)
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How doe kinases ensure specificity to correct ser/thr/tyr?
Active site complementarity (signature target motifs around phospho-site) docking sites (allow binding of discrete regions of kinase away from active site) modular interaction domains (move kinase towards substrate) and scaffolds/adaptors (associate kina
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What is the benefit vs drawback of scaffolds?
They increase efficiency of signal transfer and deliver signals to specific substrates by binding two components together BUT they limit amplification as limits number of substrates
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What is glycosylation?
The addition of sugars
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What is ubiquitination?
The addition of proteins
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What is palmitoylation?
The addition of lipids
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What can a) phosphates b) acetyl groups c) methyl groups d) hydroxyl groups, be added to?
a) Thr/Ser/Tyr b) lys c)lys/arg/glu d)pro
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Give 3 subfamilies of G-protein Coupled receptors.
Yeast mating factors, rhodopsin receptors and olfactory receptors
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What %of drugs target GPCRs?
Over 45%
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What are GPCRs also known as?
serpentine/heptahelical receptors
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Which subunit in 'large' (trimeric) g-proteins are similar to 'small' g-proteins? What does this mean?
Alpha. They work in an analogous way (both GTPases)
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What does adenyl cyclase catalyse?
the formation of cAMP from ATP
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How many TM domains does adenyl cyclase have? How many catalytic domains?
12TM domains, and 2 intracellular catalytic domains (1 after every 6 TM domains)
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What are the properties of second messengers which make them good signalling molecules?
1) very small and highly diffusable 2) rapid change in concentration due to constantly being synthesised and degraded 3) can cause widespread/highly localised effects on target effectors.
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How many calcium binding sits and subunits does IP3 have?
4
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What experimental techniques can be used to study a) DAG b) IP3
a) Phenol esters e.g. TPA to imitate DAG action b) Ionophores e.g. ionomycin initiate IP3 gated channels
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what are the relative concentrations of calcium in a) cytosol b) ER c) extracellular
a) low b) high c) high
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Hence?
Energy is required to keep ca2+ out of cytosol
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Give three ways that [Ca2+] is conserved?
1) Na+/Ca2+ exchangers in the PM 2) Ca2+ ATPase pumps in the PM + ER 3)ca2+ binding proteins in the cytosol
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What 3 responses does the frequency of oscillations of ca2+ control?
1) oestrous cycle 2) smooth muscle contraction 3) gene transcription
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Describe CaM
A ca2+ binding protein, with no cayalytic activity of its own- but allosterically activates effectors
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Where is CaM found?
In all eukaryotic cells
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How many Ca2+ binding sites does it have?
4
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How many Ca2+'s must bind for full activity? Hence?
atleast two- hence sigmoidal response
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What does CaM-K stand for?
Ca2+/CaM dependent kinase
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For the NO signalling pathway to relax smooth muscles, name the a) writer b)eraser c) reader
a)NOS b) none-spontaneous oxidation of NO is very rapid c) GC
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Use the NO signalling pathway to explain (A) why CO is poisonous (B) why nitroglycin can be used as treatment for angina (pain cased by inadequate blood flow) and....
a) because it can act like NO b) because it can be transformed into NO (therefore relaxing smooth muscle and increasing blood flow)
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...(C) how viagra works
viagra targets cGMP phosphodiesterase in penis, so get a rapid accumulation of cGMP, hence relaxing blood vessels and increasing blood flow
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Name three members of of nuclear receptor family, and their derivatives
streoid hormones+vitamin D=cholesterol derivatives. thyroid hormose= tyr derivatives. reinoids =vitamina A derivatives
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Three examples of steroid hormones are a)cortisol b)testosterone c)oestrogen and progesterone. Name what these are each produced by and their effects
a) cortex of adrenal gland, metabolism b) leydig cells of testes, male secondary sexual characteristics promoted c) ovarian follicles, maturation of uterus
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What experiment can be used to demonstrate how nuclear receptors cause early and delayed waves of transcription?
Treatment of drosophila larvae with ecdysone
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What are polytene chromosomes?
Giant chromosomes composed of many parallel copies of genetic material
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What stage of replication can be visualised under the microscope?
interphase
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what does the addition of ecdysone cause?
puffs which appear and disappear, reflecting dynamic change in transcription
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Where does ecdysone receptor associate?
with first puffs
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What can the appearance of late puffs be blocked by?
protein synthesis inhbitors, e.g. cyclohexamide
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What does this show?
That there is a primary response (transcription factors, which turn off primary response genes and turn on secondary response genes) and secondary response to hormones
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What are immediate early genes?
Genes for which the transcription machinery is already there e.g. myc
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What does PTEN stand for?
Phosphatase and tensin homologue
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What experiments tell us about how receptors link to g-proteins?
Genetic experiments on the eye of drosophila
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How many structures is each eye made up of? What are these called?
800- ommatidia
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Each 800 structures comprises how many cells? And how many photoreceptor cells is the light focusing on?
22, 8
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Why is this such a good model?
It is not essential for life, and is easy to observe
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Which protein is the last to be recruited from epithelial sheet? What is it responsible for?
R7, UV detection
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What is the seventies mutant? What can it not do? hence what does it encode?
loss of R7. cannot UV taxis. encodes receptor.
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Card 2

Front

What is the likelihood of interaction between to molecules determined by?

Back

Concentration and affinity (affinity determined by complementarity in shape and chemistry- if high then bonds formed strong enough to withstand thermal jolting)

Card 3

Front

What is the Kd?

Back

Preview of the front of card 3

Card 4

Front

Why is the Kd of a hormone receptor so much lower (higher affinity) than a NT receptor?

Back

Preview of the front of card 4

Card 5

Front

What are domains of a protein?

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