cell biology final exam

Voltage-gated potassium channels

(Kv) channels play an important role in propagating action potential in neurons during the repolarizing phase.Kvs consist of 4 identical subunits, each with 6 helices. The selectivity filter lined by 20 oxygen atoms, arranged in 4 potential K+-binding sites. The size is for K+- (1.33 A) while too loose for Na+ (0.95 A).Ions passing through the pore are dehydrated.

what do Receptor Tyrosine Kinases (RTKs) bind, and what does it affect?

(RTKs) bind polypeptide ligands that regulate cell proliferation, growth, differentiation or migration.

Wiskott-Aldrich Syndrome proteins

(WASp proteins) are key regulators of actin cytoskeleton. N-WASP is auto-inhibited. Relief of auto-inhibition requires the cooperative binding of two proteins: GTP-bound Cdc42 (a small G protein) to the G protein binding domain (GBD) and PIP2 to the basic domain (B). Since both inputs are required for strong activation, the 2 inputs have an AND relationship. SH3 domains from proteins such as Nck can substitute for Cdc42 by binding to proline-rich regions of N-WASP. (Cdc42 OR Nck) AND PIP2 →activation od N-WASP

Gated Ion Channels (what kinds of things do they do, properties)

- Show ion selectivity. - Not constantly open and fluctuate between an open and a close state. - Sustained activation usually results in desensitization of these channels. - Very important in human physiology. Local anesthetics such as novocaine block voltage gated Na channels. Calcium channel blockers are used to treat high blood pressure. Neurotransmission relies of ligand-gated channels AMPA and NMDA (ketamine, pcp, nitrous oxide). Ligand-gated ion channels (LGICs) mediate intercellular communication by converting the appearance of a signal into an flux of specific ions in the membrane. They are integral membrane proteins with an ion channel that spans the membrane. Under resting conditions, the channel is closed, and signal triggers a conformational change that opens the gate.Note that while in most cases the signal is a chemical (neurotransmitters etc), in some cases, voltage or mechanical force opens the channel.

Optimized spatial organization in retina (how it makes it fast)

- Signaling proteins are very densely packed on the surface of rod disc membrane →activated proteins along the cascade immediately encounter the next protein. - Two-dimensional diffusion on the membrane increase the likelihood of productive interactions compared to three-dimensional diffusion in solution. - PDE6 is almost a "perfect enzyme": one activated it works at almost the diffusion-limited rate. - Signaling depend on small molecules: cations and cGMP which diffuse very fast.

How are signaling proteins are built to function as switches?

1- Many signaling molecules act as a simple allosteric switch, whereby the active conformation of the protein is stabilized in the presence of a stimulatory covalent modification (ie phosphorylation etc) or ligand binding. Activation of a kinase upon phosphorylation of the activation loop.

Patched:

12 transmem helices. binds extracellular domain. Not a gpcr

Signaling by TLRs

13 members of the TLR family in humans, each bind a distinct pathogen-specific structural motif such as dsRNA, ssRNA, flagellin, lipopolysaccharides... activation of an important transcription factor: NF-κB. Activation of TLRs activates NF-κB through phosphorylation, polyubiquitylation and degradation of the inhibitory subunits (IκBs). The common regulatory step in this cascade is the activation of an IκB kinase (IKK) complex.

How are signaling molecules built to function as input/output devices? (3 ways, one example for each)

2- Some proteins achieve input/output control by acting as modular allosteric switches. In these types of proteins, regulatory domains can provide switching function. For example, in protein tyrosine phosphatase Shp2 the catalytic domain is constitutively active. However, in the basal state, two SH2 domains autoinhibit the phosphatase activity. 3- Multiple polypeptides can interact non-covalently to form a protein-complex allosteric switch. Protein kinase A (PKA) has a catalytic kinase domain and a regulatory domain. Binding of cAMP to the regulatory subunit causes the release of the regulatory subunit and activation of the kinase catalytic domain. 4- In addition to changes in conformation or interactions, another simple and common way to change protein activity in response to inputs is to change its subcellular localization. The transcription factor Pho4 is normally localized in the cytoplasm. Proper signals can result in its translocation to the nucleolus and transcription of the downstream genes.

what sort of Feedback can cause output levels to oscillate

3-component negative feedback loop, or a 2-component negative feedback loop with intrinsic delay can yield oscillations. But they are damped oscillations with inconsistent amplitude.

coherent feed-forward

A coherent feed-forward loop is composed of three components: Two transcription factors X and Y, where the former regulates the latter, and a target gene Z, where X and Y both bind the regulatory region of Z and jointly modulate the transcription rate

A network that only responds to sustained inputs (what must be true of its "architecture"? three requirements

A detector for a sustained input can be built from a -coherent feed-forward architecture. -The speed at which the signal travels down the 2 divergent branches must differ -and the downstream node must act be an AND gate.

Properties of a hysteretic system

A hysteretic system could display memory by locking into a high-output state upon a transient increase in input. An extreme form of hysteresis is an irreversible system, in which no decrease in the input is sufficient to restore the system to low-input system.

state machines

A synchronous sequential circuit, consisting of a sequential logic section and a combinational logic section, whose outputs and internal flip-flops progress through a predictable sequence of states in responds to a clock and other input signals. A generic state machine switches between two different states (0 and 1) when provided with specific inputs. An automatic door will open when it detects motion.The door has 2 states: closed or open.Sensor: motion detector. A cell can be viewed as a device that can exist in many distinct states such as: dividing, quiescent, apoptotic. With specific signals providing instructions to switch from one state to another. Individual proteins and pathways within a cell also can be considered as a state machine.

Example of how a feedback loop can cause output oscillation (cytokines)

After stimulation with cytokines the inhibitors IκB are degraded. Then NF-κB translocates into the nucleus, where it activates the expression of feedbacks that modulate the nuclear localization. The nuclear localization of NF-κB can be oscillatory upon TNF-α. Expressing knocked-in GFP fused to NF-κB upon TNF-α. Each line in the plot represents a different cell in the same population under the same treatment.

Gated channels share a similar overall structure in what ways

All gated channels share similarities in overall topology. All composed of multiple similar or identical subunits arranged in a ring structure in the plane of the membrane. With 2 to 5 subunits in the ring. In few cases, the channel is a monomer (possibly made from fusion of monomers through evolution). Each subunit consists of 2 to 6 hydrophobic α-helices that span the membrane and connected by loops of varying length. The specific physical properties of the pore (size of the pore, electrostatic properties, side chain of the amnoacids facing the pore...) determine which molecules can go through.

Switchlike Response

An enzyme can show switchlike response if it is activated in a cooperative manner. Signaling systems can respond to signal amplitude in a graded or a digital manner Response to hormone or stress. Developmental fate decision.

Positive feedback loops in the T cell activation network amplify a small input

As few as 10 antigenic peptide-MHC complexes presented by an antigen-presenting cell can lead to robust activation of a cognate T cell. Positive feedback loops in the T-cell activation pathway play an important role in amplifying the small stimulus. 1- Formation of the immune synapse leads to receptor and signaling-protein clustering →enhancement and amplification of signaling proteins. 2- The immunological synapse only contain a few non-self peptide complexes (agonist) within a sea of self peptides (non-agonist). However agonist-receptor complexes can interact with non-agonist-receptor complexes: activated Lck can recruit nearby receptor→signal amplification. 3- T cells once activated secrete cytokine IL-2. IL-2 is a mitogen and stimulates the same cell (autocrine loop) as well as nearby cells (paracrine loop). This leads to expansion of a single cognate T cell into a clonal army of activated T cells. 4- Production of DAG →activation of RasGRP (GEF) →Ras activation (Ras-GTP).Ras-GTP stimulates Sos which is a GEF and further activates Ras.

Fan-in and Fan-out network architecture

Aside from forming cascades (nodes linked in series), nodes can be linked in fan-in (one node is controlled by multiple upstream inputs) or fan-out (one node controls multiple downstream nodes) fashion.

Signaling network architectures

At the simplest level, nodes in a signaling network represent individual signaling components (proteins etc) while links are regulatory relationships between nodes.Positive link = activation. Negative link = repression. double negative (two inhibits in a row = positive for the last node in sequence.)

AND GATE) ex (cdk)

Binding of cyclin AND phosphorylation of the activation loop are both required for the full CDK activity

"or" gate

But one of those inputs has an "or" branch Bc its an or gate, if one goes away the other is still sufficient.

PDZ domains recognize...

C-terminal peptide motifs PDZ domains are one of the most common modular protein-interaction domains that play a central role in organizing diverse cell signaling assemblies. These domains specifically recognize short C-terminal ∼5-residue motifs. Structure of the PDZ domain and mechanism of peptide recognition. PSD-95 PDZ domain (shown in red) with a bound peptide (N-KQTSV-C, shown in blue). Affinity in the low micromolar range (1-10 μM).

simplified t cell cascade in order

CD45 activates Lck->Lck phosphorylates immunoreceptor tyrosine-based activation motifs (ITAMs) -> CD3 and ζ-chains serve as binding sites for Zap-70. -> Once bound, Zap70 gets activated by Lck.-> Zap-70 phosphorylates LAT and SLP-76(scaffold for..):-> recruitment of GADS (adaptor), Sos (GEF), PLCγ and downstream proteins such as Nck and VAV ->triggers cytoskeletal rearrangement PLCγ+PIP2 →IP3 and DAG →Ca2+ →activation of calcineurin (a phosphatase)→NFAT goes to nucleus.DAG →activation of MAP kinase pathway →AP-1 activation.pAP-1 AND NFAT →IL-2 gene expression.

CAP in bacteria

Catabolite activator protein (CAP) acts as a glucose sensor. It activates transcription of the operon, but only when glucose levels are low. CAP senses glucose indirectly, through the "hunger signal" molecule cAMP.

Adaptation of Photoreceptors

Changes in visual sensitivity with sustained change in light level , allows for the visual system to respond to a broad range of light intensities. Sunlight has about 10^22 per meter squared per second, and there exists 100,000,000 perceived changes in light level Activated rhodopsin binds and activate a GPCR kinase (GRK) which phosphorylates rhodopsin →recruitment of arresting to rhodopsin →blocks G protein binding and promotes rhodopsin internalization. Activated PDE6 has GAP activity which promotes inactivation of transducing. Closing of the cation channels leads to decrease in the Ca2+ concentration →increase the activity of guanylyl cyclase →increase the levels of cGMP.

Two general strategies for information transfer across the membrane:

Concerted conformational changes for receptors with multiple membrane spanning segments. Dimerization or oligomerization of receptors that span the membrane only once (single-pass receptors). (can bring two kinases into contact w eachother) Sometimes there can be some rotation for the kinases to face eachother. (Concerted conformational changes cannot be transmitted across the membrane by single-pass receptors.)

Engagement of T cell and antigen-presenting cell

Dendritic cells and T cells directly contact and scan each other for proper interaction partners. Multiple other cell-cell interactions are required for activation of T cell. These interactions are mostly adhesion, co-receptor or co-stimulatory in nature.The T cell acts like an AND gate that requires multiple inputs for its activation.

Diabetes

Diabetes, is a disease caused by a broken feedback loop involving the hormone insulin. The broken feedback loop makes it difficult or impossible for the body to bring high blood sugar down to a healthy level.Insulin decreases the concentration of glucose in the blood. Glucagon does the opposite: it increases the concentration of glucose in the blood.Diabetes happens when a person's pancreas can't make enough insulin, or when cells in the body stop responding to insulin

bad effects of modular domain rearrangement?

Domain rearrangement is a powerful mechanism for generating new functions, but it can also lead to novel disease.In some human leukemias, a chromosomal translocation leads to the fusion of self-organizing SAM domain from the gene TEL to the tyrosine kinase Abl. The resulting chimeric protein is constitutively clustered →transphosphorylation and stabilization of the active conformation of the catalytic kinase domain →oncogenic transformation The Philadelphia chromosome is generated by the translocation of the tip of chromosome 9 (encoding Abl) to chromosome 22 (encoding BCR). This generates a hybrid protein containing a coiled-coiled domain of BCR at the N-terminus fused to Abl→dimerization of Abl →cancer. The drug imatinib inhibits the Abl kinase is a successful example of kinase inhibitor for cancer therapy.Imatinib binds to the active site and decrease the activity of the kinase. Leukemia: chromosomal translocation, results in fusion of cell organizing sam domain onto a kinase. The extra piece is a polymerizatuon protein, kinases stick together. Every kinase needs another to be active, so theres a cluster of active kinases that keep signaling Dimerized kinase from philadelphia chromosome too: inhibitor imatenib binds where atp supposed to bind, inhibits atp binding.

Wnt signaling (species its present in, what its important for)

Drosophila segment polarity gene wingless The Wnts are secreted lipid-modified glycoproteins and comprise a large family of nineteen proteins in humans. The most fundamental form of the pathway consists of a Wnt ligand from a secreting cell, its cognate receptors on the surface of a receiving cell, and signal transducers within the receiving cell. Wnt signaling is involved in virtually every aspect of embryonic development and also controls homeostatic self-renewal in a number of adult tissues. Germline mutations in the Wnt pathway cause several hereditary diseases, and somatic mutations are associated with cancer of the intestine and a variety of other tissues. Homolog is integrated or "int" in humans.

What is the role of the Sex Hormone Binding Globulin (SHBG)?

During pregnancy, SHBG production is activated and the levels of SHBG increase by five-fold to ten-fold. The high SHBG levels during pregnancy may serve to protect the mother from exposure to fetal androgens that escape metabolism by the placenta. it binds hormones very tightly

NOR GATE ex

Either of the negative phosphorylation input by Wee1 kinase and inhibitory ligands (p27) is sufficient to inhibit activation of CDK

Interaction domains that recognize phospholipids

FYVE domains, found in endocytic proteins, typically bind to PI(3)P. This interaction is weak. To increase the affinity for membranes, they insert hydrophobic sidechains into the membrane. Moreover, they form dimers and oligomers.

Feedback loops

Feedback architecture is responsible for many of the complex biological behaviors we see in signaling.Feedback is observed when the output from a given node follows a path of links that return to regulate the node of origin.

what is one core requirement for oscillations (you missed: the caveat)

Feedback can cause output levels to oscillate Negative feedback is a core requirement for oscillations. But a simple negative feedback loop without proper delays or steps cannot achieve oscillation and mostly function as an output limiter.

general retina and photosensing info

First cell type in retina to receive light is photoreceptor. Rod and cone. Rod shape cells are for low light. Then other cell types integrate signal to send to brain Photoreceptor detects w specialized surface filled w receptors, gpcrs (rodopsin), g protein, phosphodiesterase, ion channel. Rodopsin senses light, so you have a lot of it. In dark cell is depolarized (when there are no photons). Thers a constitutively activated g cyclase, gmp produces active ion channel. When receptor (g protein) is activated and light is sensed, a phosphosdiesterase is activated to break down cgmp. Closes ion channel. Conformational change between cys and trans to activate protein. Level of cgmp controls polarization Low level light can be detected thru big amplification Each g protein activates an enzyme, enzyme breaks down a lot of cgmps, closes many ion channels. "Clusters" packed disks of proteins, all proteins in pathway right next to eachother. Balanced ration, receptor has most surface area. Immediate activation.

gates interacting?

Gates can stack on top of eachother. Where actin branches grow: this protein is autoinhibited (a piece that inhibits itself). Has two domains that interact with the output domain and inhibit. Two inputs: pip 2 lipid, and cdc42 gp protein. Both inputs required; "and". But one of those inputs has an "or" branch Bc its an or gate, if one goes away the other is still sufficient.

Membrane Guanylyl Cyclase Receptors (mGCs)

General function: regulation of fluid volume and movement (eg in kidney, smooth muscle). In the basal level the kinase homology domain (KHD) is phosphorylated and the guanylyl cyclase (GC) domain is inactive. The KHDs possess some of the residues that are present in active protein kinases, but residues that are required for mediating the phosphotransfer reaction are either missing or mutated. Ligand binding (atrial natriuretic peptide (ANP)) →ATP binding to the KHD domain →activation of the GC domain. Dephosphorylation of the KHD →release of ATP →Inactivation of GC domain. Membrane guanylyl cyclase receptors. mGCs: important in kidney to control secretion of fluid from body. Receptors have enzymatic domain, kinase homology. Looks like kinase but missing pieces for phosphorylation. Kinase homol domain binds atp, then enzymatic domain becomes active (the gianylyl cyclase part).

IPTG

Gratuitous inducer of lac operon: inactivates repressor but is not broken down by β-galactosidase

Signaling network in the photoreceptor cells. How does the rod cell maintain its depolarized state?

Guanylyl cyclase is constitutively active:GTP→cGMP.cGMP opens a special kind of ligand-gated cation channel →net flow of Na+and K+ into the cell. Positive ions coming into the cell keep the cells depolarized.Light activate rhodopsin (a GPCR) →activated Gα (transducin) activates phosphodiesterase 6 (PDE6) →hydrolyze cGMP to GMP →cation channel closes.

the real answer to that cholera question

Gα has GTPase activity, meaning it hydrolyzes GTP to make GDP.If it cannot hydrolyze GTP, it stays bound with GTP. Which means it stays active. the cholera inhibits g alpha GTPase activity

which hormones can pass through plasma membrane

Hydrophobic hormones such as steroid hormones (estrogen, testosterone, hydrocortisone, progestrone), vitamins A and D, thyroid hormones can pass through the plasma membrane and act through nuclear receptor (NR) superfamily of transcription factors.Nuclear receptors bind to the target DNA via an N-terminal DNA binding domain and activate gene expression programs.Testosterone (and similar hormones) have 3 forms. 1%-2% floats around on its own in the blood, called "free" testosterone. About half of the remaining hormone is loosely attached to albumin. 40% to 70% of total testosterone travels around with a protein called sex hormone binding globulin (SHBG).

talked (tick marks):

I

digital vs analog

In biology its a little more subtle. Signals: digital vs analog. Digital: 0 or 1, there or not there. But analog has a range, half, 0.2, 0.6. Less than two volts=0, five or more =1 but we "digitize" signals to simplify

β-catenin in presence and absence of wnt

In the absence of Wnt, β-catenin is degraded by acytosolic destruction complex. In the presence of Wnt, a complex of Frizzled (a GPCR) and LRP forms.Tail of LRP becomes phosphorylated and accessible and Frizzled complex recruits Disheveled (DVL) →recruitment of axin →disruption of destruction complex. β-catenin goes into nucleus and initiate transcription of certain genes. Beta-catenin kept in cytoplasm Once you have signal, receptor (frizzled) which is a gpcr and single trans memb receptor "lrp" destroys complex by recruiting part of it to the membrane, so that trans factor can go into nucleus. Key protein in recruitment is "disheveled"

Sonic Hedgehog signaling in primary cilium:

In the absence of the ligand sonic hedgehog (Shh), the target receptor Patched (Ptc) is localized to the cilium and inhibits the activity of Smoothened (Smo). In this case transcription factor Gli get phosphorylated and partially degraded. The truncated Gli acts as a transcription repressor.In the presence of Shh, Smoothened gets phosphorylated, binds to arrestin and gets translocated to the cilium by motor proteins. Gli is also not phosphorylated and act as transcription activator. smoothened protein, a gpcr. The key is that in intercellular interface of receptor there is a lock in off that breaks in on. Cholesterol important for activation

Molecular memory

In the simplest form, changes in the output are transient, persisting only as long as the input is maintained (similar to a door buzzer).Some signaling systems response require permanent changes in output to persist beyond the duration of a transient input →Molecular memory

NF-κB, active and inactive states

In unstimulated cells, the NF-κB proteins are predominantly localized in the cytoplasm and are associated with a family of inhibitory proteins known as IκBs. NF-κB -IκB interaction blocks the ability of NF-kB to bind to DNA and results in the NF-kB complex being primarily in the cytoplasm due to a strong nuclear export signal in IkBa. Activation of TLRs activates NF-κB through phosphorylation, polyubiquitylation and degradation of the inhibitory subunits (IκBs). The common regulatory step in this cascade is the activation of an IκB kinase (IKK) complex.

incoherent feed-forward

Incoherent feed-forward loops in biology and engineering. a In biology, a Type 1 incoherent feedforward loop (I1-FFL) is characterized as an input, X, which activates both an intermediate (Y) and the ultimate output (Z), while Y represses or inhibits Z.

Transcriptional promoters can integrate input from multiple signaling pathwaysExample:

It is important T-cell become activated when there is a strong stimuli present. When T-cell is activated one of the important outputs is the activation of interleukin-2 (IL-2) promoter and production and secretion of cytokines.The ERK MAPK pathway leads to phosphorylation and activation of AP-1.However, transcription from IL-2 promoter requires NFAT. dephosphorylation and activation of NFAT is through Ca2+/calcinuerin (a phosphatase) pathway.Synergic interaction of AP-1 and NFAT results in the expression of IL-2 promoter.This guarantees that only robust and sustained T-cell activation will result in gene expression (AND gate).

one example of Synthetic toggle switches with memory

Lac repressor (lacl) inhibits expression of GFP.TetR inhibits expression of lacl.Therefore, TetR expression promotes expression of GFP.

T cell receptor (TCR) signaling network

Lck is a Src family tyrosine kinase that is associated with a co-receptor (CD4). CD45 activates Lck by dephosphorylating a tyrosine in its inhibitory C-terminal tail. The inhibitory kinase Csk opposes CD45 and phosphorylates the C-terminal tail of Lck to stabilize the closed autoinhibited conformation.Loss of CD45 causes hyperphosphorylation of the Lck C-terminal tail and markedly reduces the amount of active Lck. Because active Lck amounts are reduced, T cell development is impaired when TCR signaling is required. T cell receptor (TCR) signaling network CD45 is a receptor-type protein tyrosine phosphatase Once MHC-TCR complex formed, Lck phosphorylates immunoreceptor tyrosine-based activation motifs (ITAMs) within the TCR-associated CD3 and ζ-chains (denoted as the TCR complex) which then serve as binding sites for Zap-70. Once bound, Zap70 gets activated by Lck. Zap-70 phosphorylates LAT and SLP-76.These two proteins act as scaffolds for recruitment of GADS (adaptor), Sos (GEF), PLCγ and downstream proteins such as Nckand VAV as part of machinery that triggers cytoskeletal rearrangement.PLCγ+PIP2 →IP3 and DAG →Ca2+ →activation of calcineurin (a phosphatase)→NFAT goes to nucleus.DAG →activation of MAP kinase pathway →AP-1 activation.pAP-1 AND NFAT →IL-2 gene expression.

Proteolysis in notch signaling

Ligand is Delta, presented by a different cell.TACE: a metalloprotease -> first cut and allow the second cleavage.Pulling force on the ligand is necessary to expose the cleavage site. This is one of the few cases that signaling by a single TM receptor does not require dimerization or clustering.

Three major cell-surface receptor families enable cells to respond to signals from their environment

Ligand-gated ion channels (LGICs), the G-protein-coupled receptors (GPCRs), and the receptor tyrosine kinases (RTKs). These receptors are intrinsically allosteric: signal transduction involves "communication over a distance" between spatially distinct yet conformationally linked binding sites.

what Light causes in photoreceptor cells

Light causes hyperpolarization of photoreceptor cells, inhibiting glutamate release.

c elegans retreat mechanism (you forgot: names.)

Like the single-celled organisms the worm retreats from noxious chemicals, but its decision is more finely judged. A single sensor, the neuron labeled ASH in the brain's wiring diagram, controls this behavior by driving a "retreat" command interneuron, AVA, which shuts down the "forward" motor neurons and activates the "backward" motor neurons.The worm uses more than 1,700 different types of receptor molecule for chemoreception. the sensor ASH collects signals from various types of receptor for noxious stimuli that require an aversive response; ASH couples its output to a single neuron that executes a command: Scram! Neurons in worm: bends muscles on one side. 2 neurons, one for each side. Receptors for good things, and receptors for bad things. All good receptors in "move forward" neuron, all bad-thing receptors in "bend/change direction" neuron.

Tyrosine phosphatase receptors

Many protein tyrosine phosphatases have a TM and extracellular domain and thought to act as receptors too. In many cases the ligand is not known. It is thought, in the unliganded receptor, the phosphatase domain is active. Ligand binding and clustering results in inactivation of the phosphatase domain. The net result of ligand binding to RTKs and RTPs is the same: Net increase in tyrosine phosphorylation in the vicinity of the receptor.

Recombining interaction domains and catalytic domains to build...?

Many signaling enzymes are regulated by modular interaction domains. nSuch an architecture can create an allosteric switch.

Mechanism of gating of the voltage-gated channels

Many voltage-gated channels have a similar design principle. Several positively charged residues (usually Arg) in a "voltage sensor" domain (helices 3 and 4) are translocated through the membrane in response to voltage change. The resulting conformational change opens the channel. This functionality is modular. Changing the sequence and number of positive residues can affect the sensitivity of the channel. Some channels require multiple inputs to open

What do we mean by "modular" and why is it useful?

Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. (the watchmaker metaphor)

what do Toll-like receptors (TLRs) activate (ie the end goal of that pathway)?

NF-κB

How is NF-κB signaling terminated?

Negative feedback loop: IκBα is one of the earliest induced NF-kB targets; it is fully re-synthesized within less than one hour after stimulation and subsequently enters the nucleus and removes NF-κB from its cognate DNA.

Negative feedback loops helps t cells how?

Negative feedback loops prevent and limit T cell misactivation Activation of T cell requires detection of MHC-peptide by TCR as well as co-stimulatory signal (such as CD28 binding to B7).Competing binding of inhibitory motifs (ITIMs) with B7 has inhibitory effect on the activation. Phosphorylation of an activated TCR can lead to recruitment of SH2 containing ubiquitin ligases of the Cbl family which can result in the degradation and downregulation of the TCR complex.

Membrane permeable signaling: NO

Nitric oxide (NO) is an important signaling molecule that modulates flow of blood through vasculature. NO binding increases the activity of the enzyme soluble guanylyl cyclase (sGC). Because half-life of free NO is few seconds, it can transmit signal between adjacent cells. NO activates sGC by directly binding to the ferrous core which results in conformational changes leading to the activation of the catalytic domain. By this mechanism, the sGC activity can be stimulated by about 5000-fold.

what two things can "threshold" be?

Note: "threshold" can be concentration, or can be amount of time that needs to pass after introduction of signal.

Signaling by Nuclear Receptors

Nuclear receptors ligand-regulated transcription factors that are activated by steroid hormones, such as estrogen and progesterone, and various other lipid-soluble signals, including retinoic acid, oxysterols, and thyroid hormone. Unlike most intercellular messengers, the ligands can cross the plasma membrane and directly interact with nuclear receptors inside the cell, rather than having to act via cell surface receptors. Once activated, nuclear receptors directly regulate transcription of genes that control a wide variety of biological processes, including cell proliferation, development, metabolism, and reproduction In the absence of signal, the NRs often reside in the cytosol in complex with hsp90 and other proteins. Ligand binding usually results in a conformational change, dimerization and transfer of the NR to the nucleus. In some cases, NRs are bound to the target DNA but by association with transcriptional co-repressors, and are inactive. Ligand binding induces a conformational change that causes the release of the repressor complex.

Bacterial chemotaxis (what is it an example of?)

One of the best studied examples of adaptation in cell signaling is found in bacterial chemotaxis. Bacteria can sense a gradient of chemorepellent and swim away from the source. They do so by performing a biased random walk which they achieve through alternating tumble and swim phases. Chemotaxis: reduction in tumbling frequency to drive swimming toward attractant. A stepwise increase in chemorepellentresult in a transient increase in the probability of tumbling, followed by a return to a steady-state basal probability.

How do biological systems integrate multiple inputs?

One simple but effective way for signaling proteins to integrate multiple inputs is to have multiple post-translational modifications within the same peptide. The functional output of having a single modification versus two modifications could be very different.Lys9 at the N-terminal tail of histone H3 methylated →recruit HP1 →gene silencing.Phosphorylation of Ser10 by Aurora-B kinase block HP1 binding. AND NOT gate

How can the photoresponse be so rapid

Optimized spatial organization: the organization of signaling proteins and their properties lead to efficient and rapid communication.

How might the T cell discriminate between antigenic and non-antigenic interactions?

Over a million non-antigenic peptide complexes are unable to activate the T cell, while as few as 10 antigenic peptide complexes are sufficient to fully activate the T cell. Non-self peptide binds with lifetime at least 10 fold longer than self-peptide. Thus TCR may use the lifetime of receptor engagement to discriminate between self and non-self signals.

Overlaying a positive feedback on oscillatory circuits can...

Overlaying a positive feedback on oscillatory circuits can result in robust oscillators with consistent amplitudes.

PDZ domains recognize what?

PDZ domains are one of the most common modular protein-interaction domains that play a central role in organizing diverse cell signaling assemblies. These domains specifically recognize short C-terminal ∼5-residue motifs. Structure of the PDZ domain and mechanism of peptide recognition. PSD-95 PDZ domain (shown in red) with a bound peptide (N-KQTSV-C, shown in blue). Affinity in the low micromolar range (1-10 μM). Pdz domains: protein traction domain, important for assembling protein synapse in brain. Recognizing c tail of protein. Always a valine at the end. Found in many scaffold proteins, transmem, ion channels Pdz organizes proteins in synapse. Scaffold, anchor channels and receptors.

Example of building complexity of function by combining interaction domains

PLC-δ has a PH domain that selectively binds PI(4,5)P2 which is also a substrate for its catalytic domain. The interaction thus concentrate the enzyme at regions of the membrane that are enriched for its substrate.

paramecium size, and response to encounters immovable obstacles

Paramecium, a single-celled protozoan, measures up to 350 μm × 50 μm, 300,000-fold larger than E. coli. It can swim 50 fold faster than E. coli. In E. Coli. Chemotaxis relies on diffusion of intracellular messenger molecules. For a Paramecium that is 100-fold longer than E. coli , diffusion from " head " to " tail " would be 10,000-fold slower, about 40 s. At the first bump it throws its cilia into reverse and backs off by a few millimeters. Then it does a quick twiddle, switches to forward, and sets off in a new direction. This avoidance response is fast (completed within a fraction of a second) and it has to be. Futile activity wastes time and energy; moreover, the immovable object might be a predator! Electrical signals spread much faster: a change in membrane voltage initiated at the head reaches the tail in milliseconds.Electrical signaling for the avoidance response requires several new components: First, a mechanoreceptor is needed to detect initial bump. This involves a specialized cation channel inserted into the cell membrane. Stretch on the membrane deforms the channel, opening it to Na+ ions that rapidly depolarize the membrane (<100 μs). Second, depolarization opens voltage-sensitive calcium channels that admit a rush of calcium ions further depolarizing the membrane, opening still more calcium channels, and so on. This positive feedback produces a robust response that recruits calcium channels across the entire membrane. They open briefly, then close and inactivate. The two components (stretch-gated sodium channel plus voltage-gated calcium channel) cooperate to deliver a synchronous pulse of calcium over the cell's entire surface.

when does receptor dimerization occur, and what does it do?

Problem with having only one transmembrane domain? Harder to change shape. Single pass receptor strategy: when ligand comes, it can dimerize them! Receptors with a single TM segment form higher order assemblies upon ligand binding Ligand simultaneously bind two different receptors through extracellular interactions and result in dimerization. Dimerization makes it much more likely that the receptors will phosphorylate each other and keep each other phosphorylated due to their proximity Also provide docking site for downstream binding partners. Ligand binding →control the proximity/orientation of intracellular signaling/enzymatic domains.

Modifying the strength or duration of output

Responses in the cells can be transient→lasting only as long as the stimulus or even less.Other signaling responses can last for very long periods, even after the input stimulus is gone →cellular memory.Input signal might only be detected by a small number of receptor molecules. This requires amplification. One fundamental mechanism for signaling systems to amplify output is through the use of enzymes - one activated enzyme can act on many substrate molecules.A higher levels of signal amplification will occur if multiple amplifying enzymes are linked into a cascade.The degree of amplification can be limited by the number and localization of downstream signals.

how Combination of interaction domains can be used as a scaffold for assembly of signaling complexes?

Scaffold proteins is one of the major classes of multidomain signaling proteins. Scaffold: proteins that form complexes by bringing multiple proteins tg. Can also control output of signal. Protein grb2: has an sh2 domain, can bind phos tyr, can then initiate ras or another pathway w substrates. Depending on where localized, can produce unique output In some cases, scaffolds or adaptor proteins decide the fate of the signal: example is Grb2 couples an activated RTK (such as PDGFR) to downstream effectors. Grb2 contain 1 SH2 domain and 2 SH3 domains. The SH2 domain binds to the phosphorylated receptor. The SH3 domains can bind to Sos (a GEF for Ras) or Cbl(a ubiquitin E3 ligase). Grb2 takes a phosphotyrosine-based input and converts it into a specific output.

how Ligand gated ion channels play a central role in neurotransmission?

Signal transmission at the synapse involves release of neurotransmitters (acetylcholine, dopamine, serotonin, Noradrenaline, glutamate, GABA...) at the presynaptic site and binding to a ligand-gated ion channel at the postsynaptic side.The opening of these channels can initiate or inhibit an action potential. -Arrival of an action potential at the axon terminal open voltage-gated calcium channels. -Influx of Ca2+ triggers the exocytosis of some of the vesicles containing neurotransmitter. - The released neurotransmitter molecules bind to receptors on the postsynaptic membrane. These receptors are ligand-gated ion channels (fast: millisecond) or GPCRs (often slow: 10s of milliseconds). -Reuptake: The neurotransmitter is taken back into the presynaptic neuron by active transport. All the neurotransmitters except acetylcholine use this method. Acetylcholine is removed from the synapse by enzymatic breakdown into inactive fragments. The enzyme used is acetylcholinesterase.

Problem: It would be uneconomical to maintain high levels of all possible proteins and processing enzymes when only a subset is needed at a given moment. what is the bacterias solution?

Solution: the bacteria refrains from synthesizing proteins for uptake and digestion until a taste receptor binds the target molecule. A receptor's binding affinity determines the concentration at which protein synthesis becomes economical.

different responses/different "thresholds"

Some signaling systems show response that are proportional to the input level, whereas others only becomes activated above a given threshold. Some signaling respond immediately upon stimulation, whereas others require sustained input before switching on.

T cell signaling: controlling the launch of an adaptive immune response

Specialized antigen-representing cells such as dendritic cells take-up pathogen derived material to break down into small peptide fragments. Fragments bind to the Major Histocompatibility Complex (MHC) and displayed on the outside the cell while the cells migrating to the lymph nodes. At lymph nodes they interact with T lymphocytes (T cells) through MHC-non-self peptide-TCR complex, which activates the T cell.Once activated, T cell will clonally proliferate and differentiate into killer and helper T cells.This results in launching of a complex response, including killing of the infected cells, stimulation of B cells to produce antibodies.

nonreceptor tyrosine kinases (examples, what they do)

T cell receptor, cytokine receptor, a third one I missed. they must recruit a kinase. dont have their own enzyme Many cell-surface receptors do not have intrinsic catalytic domains, instead their intracellular portions interact noncovalently with proteins with catalytic activity (like kinases, proteases). this is one such receptor.

how Fast negative feedback loop can block activation by short stimulation time inputs

The Lck tyrosine kinase generates the first positive signal of TCR activation.However, it also generate a negative signal: phosphorylation of Shp1 which then binds to LCK and dephosphorylate downstream targets of Lck. If the activating signals received by the T cell are sustained enough, then this leads to gradual accumulation of activated MAPK ERK. ERK phosphorylate Lck at Ser59 which disrupts interaction of Lck with Shp1.ERK provides a slow, delayed positive feedback loop that overrides the fast Shp1 negative feedback.

Some examples of ligand-gated ion channels that play a central role in neurotransmission

The acetylcholine receptors at the neuromuscular junction are excitatory neurotransmitter-gated cation channels. These channels are non-selective and can pass Na, K and Ca. Activation of the channel cause muscle to contract. Ionotropic glutamate receptors (iGluRs) are tetrameric glutamate-gated ion channels.The composition and amount of these channels change during development.

Some properties of domains

The globular proteins generally have a hydrophobic core surrounded by a hydrophilic outer layer. These interactions are important to stabilize the global structure and help create channels and binding sites for enzymes. While most signaling domains fold as a single unit, there are a few classes of domains that composed of several repeats of a smaller conserved unit: WD40. Interaction domain can act as readers of the post-translational modification. The interaction domain can function to form larger complexes (If they are in separate proteins). Domains can also be for other interactions - protein lipid interactions. Require zinc ions.

key regulatory node in photoreceptor signaling.

The levels of the second messenger cGMP is a key regulatory node in photoreceptor signaling.Note: the cells is constantly paying energy for this highly responsive signaling system, in the form of constant resynthesis of GTP.

How photoreceptor cells sense and amplify light inputs?

The molecular signaling machinery in the photoreceptor cells of the eye function to detect light and convert it to the signal that can be efficiently transmitted to the optic nerve. Light input detected by the retina leads to an action potential in ganglion cells that transmits the information to the brain Light causes hyperpolarization of photoreceptor cells, inhibiting glutamate release. ~100 million rhodopsin molecules per photoreceptor cell.

After one light exposure how does photoreceptor reset to enable detection of further changes in light

The photoreceptor cell signaling network contains several negative feedback loops that mediate adaptation: Even in constant light the activation of the photoreceptor cell is transient.Because of this adaptation photoreceptor cells have a wide dynamic range.

feed-forward activation

The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway

Synthetic toggle switches with memory (IPTG)

The system initiated with IPTG for 6 hours to express fluorescence (write), and then grown 5 hours without IPTG. Afterwards, the cells were treated with aTc for 7 hours to turn off GFP expression (Erase) then removed. Cells remained in low fluorescent.

building complexity of function by combining interaction domains

Throughout evolution distinct domains can recombine and become linked with other domains. Complexity can increase without increase in gene numbers.proteins encoded by the human genome have a richer assembly of domains than do their counterparts in invertebrates or yeast.

Hedgehog signaling

Transcription factor Gli: Zinc Finger domains of Gli1/2/3 bind the consensus sequence GACCACCCA. Can be activator or repressor of transcription depending on proteolytic processing. Trans factor: gli. Zinc finger containing proteins binds dna. Sequence consensus: they find this sequence in genome and bind it. Can be an activator or repressor of transcription, depending on where its cleaved. If cleaved in middle it is activator. Smoothened (SMO): is a GPCR. cholesterol is necessary for SMO activationPatched (ptc): was cloned as a segment-patterning gene in Drosophila. Contains 12 transmembrane helices. Sonic Hedgehog (SHH): The ligand for the Patched receptor. It is a protein, and the functional form is ~ 20 kDa Gli gets phosphorylated, partuially degraded, acts as transcription repressor Specific recognition between Ptch1 and Shh.T he ShhN-Ptch1 interface is primarily mediated by polar and charged residues. ECD1 and ECD2 each contribute multiple acidic residues for interaction with the Lys/Arg patch that lines the pseudo-active site groove of ShhN. The reported resolution for the interface is approximately 3.8 Å.

how ptms affect eachother

Two aas next to eachother; one can acquire phos, the other can be methylated. These two ptms affect eachother. If methylation, chromatin silencing. But if phosphorylation, phosphate inhibits binding of silencing factor, so there is gene expression. Silencing only happens w methylation and no phosphorylation.

Membrane permeable signaling: Oxygen

Under normal oxygen levels, proline hydroxylase (PHD) is activated →Transcription factor HIF-1a (hypoxia inducible factor) is hydroxylated and recognized by VHL ub-ligase →degradation of HIF-1a.Translocation of HIF to the nucleolus results in upregulation of certain genes, specifically ones associated with reprogramming cells from oxidative to glycolytic metabolism. Overall design is like many other pathways.Transcription factors chose between 2 different genetic programs.A sensor detects the level of a molecule (oxygen) and through a series of changes (PTM, p-p interaction, localization) it controls the output (transcription of certain genes).

Wd40 can bind

Wd40 can bind dna, phosphorylated peptides

structure and specificity of SH2 domains, plus example

When we talk domain, they are not 100% the same in terms of amino acid sequence. SH2 domains are ~ 100 amino acids on length with a central β sheet that separates the domain into two binding pockets: the pTyr pocket and the specificity pocket. An arginine (+) deep in the pocket interacts with the phosphate (-) pTyr. The SH2 domain of the Src kinase binds to pYEEI because the isoleucine fits into a hydrophobic pocket in the specificity pocket of this SH2. The SH2 domain in Grb2 specifically chooses a peptide with asparagine in +2 due to favorable hydrogen bonding and the β-turn conformation favored by asparagine.

Structure and specificity of SH2 domains

When we talk domain, they are not 100% the same. SH2 domains are ~ 100 amino acids on length with a central β sheet that separates the domain into two binding pockets: the pTyr pocket and the specificity pocket. Example of cooperativity between domains:Tandem SH2 modules from Zap-70.Their distance from each other allow recognition of a specific target position at a specific orientation on the TCR tail (called ITAM).ITAMs=immune receptor activation motifs. Generally sh2 domain has 2 binding pocket: phosphotyrosine pocket (arginine in pocket to make hydrogen bonds w tyrosine) Other pocket: specificity pocket: allow sh2 domain to bind a specific peptide. It recognizes the context of the peptide, surrounding aas.

what controls kinase activation

Whether activation loop is phosphorylated

what is different (with regards to modularity) about WD40?

While most signaling domains fold as a single unit, there are a few classes of domains that composed of several repeats of a smaller conserved unit: WD40. WD40 repeat domains is an example of a case that knowing only the identification of the domain cannot always explain their function because they have a wide range of binding properties. Shown interacting with DNA or a peptide.There are examples of domains with very different amino acid sequence and biochemical activities that fold onto a similar 3D structure.Domains with the same overall structures (indicated by very similar arrangement of α helices and β sheets) can recognize different ligands.

why do t cells need an and gate?

You want system not to respond to every tiny input, otherwise you would have too much noise and overactive immune system. So only respond if theres a serious issue. T activation requires from 2 diff pathways. One is to mapk pathway to phosphorylate ap1, which binds dna This alone isnt enough to promote IL3 genes. Robustness means you need a second and component: Ca dependent pathway to activate diff trans factor.

Noncovalent coupling of receptors to kinases

a common signaling strategy Many cell-surface receptors do not have intrinsic catalytic domains, instead their intracellular portions interact noncovalently with proteins with catalytic activity (like kinases, proteases). Example: nonreceptor tyrosine kinases.

Insulin receptor

a constitutively dimer (monomers are linked by disulfide bonds). Insulin binding change the conformation of an existing receptor dimer to bring the intracellular kinase domain closer to each other. Insulin receptor: already a dimer, but kinases are held apart and binding brings them together.

double negative feedback loop

a feedback loop in which the inhibitor of the signal is inhibited, ultimately leading to a positive feedback loop

Bacterial chemotaxis is controlled by

a negative feedback adaptation system Chemorepellent activates the chemotaxis receptor →activates the CheA protein (kinase). CheA phosphorylates CheY →binds to the flagellar motor to induce tumbling. Regulatory node:Receptor activity requires its methylation on key aspartate residues through activity of the methylase CheR which is constant. The activity of the demthylase CheB is controlled by CheA. CheA phosphorylates CheB →activation of CheB →demethylation of the receptor→downregulation.

Combination of interaction domains can be used as

a scaffold for assembly of signaling complexes Scaffolds have binding sites for multiple partners and function to nucleate assembly of large multiprotein complexes.External input signals is required to promote binding.

the three special networks:

adaptation, oscillation, bistable switch and hysteresis.

Phosphodiesterase is special, why?

almost a perfect enzyme -- limited only by diffusion and concentration

How is the photoreceptor cell able to detect low light, even a single photon?

amplification. The tapetum lucidum is a layer of tissue in the eye of some animals. Lying immediately behind the retina, it is a retroreflector reflects visible light back through the retina, increasing the light available to the photoreceptors. The tapetum lucidum contributes to the superior night vision of some animals.

what positive feedback does

amplify

Circadian rhythm is..

an example of oscillatory system. PER protein was found to be a nuclear protein and to shuttle between the cell nucleus and the cytoplasm in a temporally regulated manner, suggesting PER is a transcription regulator. timeless, an additional gene influencing the circadian clock showed that the levels of timeless mRNA also cycled with a 24h period, and that TIM could bind directly to PER, affecting its nuclear localization and abundance by blocking PER degradation.

The primary cilium:

another key in hedgehog signaling. The primary cilium is a long, thin organelle protruding from the apical surface of almost all cell types, most commonly from epithelial cells. Primary cilia are particularly important during development, with a suite of inherited developmental disorders known as the "ciliopathies" resulting from mutations in genes encoding cilia proteins. every cell has primary scillia, like a little hair. Inside, microtubule. Hub of signalling. Scillia pathway diseases associated w malfunction. Antennae.

how is Tyrosine phosphatase shp2 regulated

autoinhibits

Signaling by TGFβ receptor

begins with the binding of a ligand to a TGFβ type II receptor. Ligand binding induces formation of complexes containing 2 copies of RI and RII. The RII is a serine/threonine receptor kinase which catalyzes the phosphorylation of RI. pRI binds R-SMAD and phosphorylates it. pR-SMAD dissociates from the receptor and bind to co-SMAD (eg SMAD4) through an amino acid stretch that became available upon phosphorylation. The phosphorylated RSMAD/coSMAD complex enters the nucleus where it binds transcription promoters/cofactors and causes the transcription of DNA.

Adaptation allows

cells to control output duration

Phosphodiesterase (PDE)

cytosolic enzyme that deactivates and degrades cAMP

Proteolysis

decomposition of proteins. irreversible: most likely to be used for systems that must respond decisively and strongly to a signal without ability to control the signal once initiated.

Wide dynamic range lets us see...

detail, shades of light. This adaptation allows large dynamic changre. 3 neg feedback loops 1 receptor itsef. Very quickly deactivated aftr activating. Internal part gets phos, special family called gpcr kinases. Then binds "arrestin" blocks binding g protein, gets rid of receptor Say you have a receptor. If didnt have this process, one photon gives signal, eye cant process a second photon. But w this process, one receptor goes in, fresh receptor comes out. Recycling resets system for new activation.

BAR domains

dimeric, banana shaped structures that bind preferentially to and stabilize curved regions of the plasma membrane domains consisting of coiled coils that form long, thin, curved dimers with a positively charged concave surface. BAR domain proteins assemble into crescent-shaped scaffolds and favor membrane curvature. proteins with BAR domains can polymerize into a superstructure that favors and maintains the curvature BAR domains form coiled-coil sequences that adopt a banana-shaped structure. The concave surface of this dimer is typically positively charged and thus has affinity for biological membrane (tend to have a net negative charge). The curved shape means they bind with the highest affinity to membranes with a specific degree of curvature that matches the curvature of BAR domain: formation of endocytic vesicles.

toggle switches

double negative feedback loop with two triggers

Proteins with multiple pTyr motifs function as

dynamically regulated scaffolds

arrestin

enzyme that participates in desensitization of GPCRs by phosphorylating them after they have been activated by ligand binding

EGF

epidermal growth factor change the conformation of the receptor to increase the affinity of the receptors for each other. receptor has one binding site and its binding reveals a receptor dimerization motif. each single signal molecule binds a site on one of the receptors, causing them to have higher affinity for eachother (they must both be bound, 2 signaling molecules required)

Negative feedback allows (give an example with ca)

fine-tuning of output Negative feedback loops provide a way to make the output of a signaling system more precise, instead of maximize the output level. External stimuli can open Ca2+ channels resulting in increased concentration of cytoplasmic Ca2+. However, [Ca2+] > 0.6 μM induces uptake of Ca2+ by mitochondria →limiting the [Ca2+] in the cytoplasm.

speed of Signaling through GPCRs

generally slow (100-500 ms). One exception is in the eye.

operon

genes that work together

PDZ domains are often found...

in scaffold proteins as multiple tandem arrays and/or linked to other kinds of modular protein-interaction domain. Many transmembrane receptors, ion channels, adhesion proteins have PDZ binding motif. PDZ-containing proteins are major organizers of the postsynaptic density. PDZ domain-containing scaffolds organize cell-cell signaling junctions.

Negative feedback loop can be used to

increase the output precision. Using just one inducible promoter, cell to cell variability of expression is large. A negative feedback loop through a repressor provides a self-correcting mechanism that proportionally represses transcription.

Logic gates process...

information from multiple inputs Example of the AND gate was in the CAR-T paper. It is important to remember that biological logic gates are not truly digital (0 or 1). The physiological inputs (concentration of protein, lipids, ligands) usually vary continuously over a range of values, as opposed too being either present or absent. Therefore, the output usually has a range and is not all or nothing.

Cyclin-dependent kinase (CDK) acts to... (concise and vague)

integrate a wide variety of both activating and repressing inputs.

There are four major classes of membrane receptors

ion channel receptors, 7 helix transmembrane receptor, receptor w intrinsic enzymatic activity, enzyme associated receptor (recruiter receptor)

Cytokine receptor: what type of receptor is it? (just the name)

is a Jak: Janus Kinase.Janus was a Roman god with 2 faces

Hysteresis

is an irreversible, switch-like behavior that can occur between two steady-states in a system. The state in which a system resides depends not only on the current conditions, but also on the history of the system. In these system the input stimulus required to keep the system in the active state is lower than the input required for triggering the initial transition from basal to active state.

When photon hits retinol

it switches between cis and trans conformation. It is unique among gpcrs- bc is has to be very very fast.

what negative feedback does

limit the output

Certain plant protein kinases are regulated by...

modular light-gated domains Light interacts with Flavin mononuclease of the Light-oxygen-voltage-sensing domain (LOV domain). This triggers a conformational change that leads to the dissociation and activation of the kinase domain and phosphorylation of the substrate. Another domain: lov domain. In plants. Triggers conf change when it sees light. Is a kinase. If it receives light, a piece goes from alpha helix to unstructured. Unstructure opens it up. Researchers use for synthetic switch. light-> protein exported out of the cell

Bistable switch

molecular mechanism which has two stable steady states that can be interconverted by some external signal type of positive feedback

Fibroblast growth factor (FGF)

needs 2 different ligands to bring two monomers together. Stable dimers only form when two heparin sulphate oligosaccharides combine with receptor ligand complexes.

Histidine binds what metal?

nickel

Proteins domains are...

not modular There are examples of domains with very different amino acid sequence and biochemical activities that fold onto a similar 3D structure. Domains with the same overall structures (indicated by very similar arrangement of α helices and β sheets) can recognize different ligands.

PDGF

platelet derived growth factor forms a ligand dimer, each one engages one receptor. (so both the signal, and the receptor, are dimers)

Serine/threonine receptor kinases, tgf beta receptor

similar idea, forming dimer. Tgf beta: a little asymmetry, one subunit binds ligand, recruits second subunit and phosphorylates it. Second unit performs signaling.

The effector for canonical Wnt signaling?

the β-catenin transcription factor.

Immune checkpoint inhibitors

these drugs basically take the "brakes" off the immune system, which helps it recognize and attack cancer cells Immune checkpoints are a normal part of the immune system. Their role is to prevent an immune response from being so strong that it destroys healthy cells in the body. The checkpoint and partner proteins can bind together and send an "off" signal to the T cells. This can prevent the immune system from destroying the cancer.Immunotherapy drugs called immune checkpoint inhibitors work by blocking checkpoint proteins from binding with their partner proteins. This prevents the "off" signal from being sent, allowing the T cells to kill cancer cells.

Protein domains

they are modular A domain represents a polypeptide sequence that can fold independently into functional unit, and is typically between 35 and 250 amino acids. 1) To mediate interaction with other proteins →interaction domains.SH2, SH3, C1, C2, PH ... 2) To catalyze enzymatic reactions →catalytic domains.kinase, phosphatase, GEF, GAP ...

Phosphorylated stat goes

to nucleus.

interaction domains

to what extent does development in one area depend on or influence development in another area Interaction domain can act as readers of the post-translational modification.The interaction domain can function to form complexes (If they are in separate proteins).Or the interaction domain could induce a conformational change that alters the activity of other domains.

Signaling systems can distinguish between _____ types of inputs?

transient and sustained input In some cases, signaling systems in cells need to measure the duration of an input.In designing sliding automatic doors, in winter or summer for example, it is not desirable for the door to open in response to brief motions (noise for example people just walking by the door and not wanting to enter).Also, The door has to stay open until a sustained period has passed during which no motion is detected, to avoid accidentally closing the door on a person.

Jaks

type of kinase. The FERM and SH2 domains together are responsible for binding to the receptor. This provides the specificity required to target a particular JAK to a particular receptor chain. The pseudokinase domain, adopts a typical kinase fold it is catalytically defective. It modulates (turns down) the activity of the C‐terminal tyrosine kinase domain. All JAKs are tyrosine kinases. Binding of the ligand to cytokine receptor reorients the receptor/JAK dimers, which activates JAKs. Activated JAKs in turn, phosphorylate the residues on the cytoplasmic tail of the cytokine receptor to create "docking sites" for recruitment of downstream STAT proteins with SH2 domains. Upon binding, STAT gets phosphorylated, dimerizes and translocate to the nucleus as we saw previously.

adaptation

type of negative feedback Adaptation is the ability of a system to respond and then reset itself even in the continuing presence of a stimulus. Adaptation allow shutting off output when it is harmful or toxic in excess, or costly for the organism.Adaptive system couples response to relative changes in the input, not its absolute level, thus allowing system to respond to much wider range of inputs levels.

oscillation

type of negative feedback Biological oscillations are found in all living creatures, from simple cells to complex multicellular organisms. Examples of biological oscillations are circadian rhythm, hibernation cycles, cell division cycle, menstrual cycle, pulsatile release of hormones, heart beats and respiration. ex: Estrogen concentration in a woman's life from puberty to menopause. body temp over the day.

Bistable response

underlies more permanent outputs Positive feedback loops are usually associated with amplifier response. A positive feedback loop with proper regulatory step can trigger a bistable switch. The bistable switch is one of the important regulatory motifs in cell signaling. = When the input crosses a threshold, the output increases to a high, active state. Bistable systems make use of hysteresis to remain in the active state.

bacteria lac operon

when glucose is off the menu, it can use lactose. This requires lactose detectors to call for 2 proteins: a membrane transporter to admit lactose and an enzyme, galactosidase, to digest it. The genes coding these proteins are adjacent in E. coli 's DNA, comprising an operon (genes that work together). Their expression is blocked by a repressor. The repressor is the lactosedetector which, upon binding allolactose (an isomer that always accompanieslactose) changes shape and releases from the DNA. This allows RNA polymerase to move off and transcribe the operon. The system can do calculations: IF lactose present ANDNO glucose, then GO. By encoding the transporter (lacY encodes Beta-galactoside permease) and the digestive enzyme (lacZ encodes β-galactosidase) together, one sensory signal can evoke all necessary components in the correct ratios.The system can do calculations: IF lactose ANDNO glucose, then GO.The bacteria has a memory of about 1 second. The microbe easily lives like a Zen master: in the moment. Feed the cell, and in an hour, it is gone, divided among its progeny. Once lactose is sensed, it can make expression of genes to digest it. Normally genes are repressed, lactose binds lactic repressor (lactose seeps into bacteria) and repressor is released. But you want to do this only when theres no glucose - so you need 2 sensors, one to sense glucose, one for lactose. Glucose sensor required for activation of genes. Senses glucose thru hunger signal, cAMP. Camp goes up when hungry, binds cap, activates cap. Then repressor must be released from dna: only when lactose present.

For proteins that traverse the lipid bilayer, the transmembrane portion almost always consists of (number, and property)

α-helical segment comprised of 20-25 amino acids. Part inside lipid is hydrophobic, use hydrophobic aa. You need 20-25 aas to go thru membrane. The hydrophobic side chains of amino acids in the transmembrane segment interact with hydrophobic fatty acid chains in the membrane.