cell biology 7 Flashcards

1
Q

G protein–coupled receptors (GPCRs)

A

a large protein family of receptors that sense molecules outside the cell and activate inside signal transduction pathways and, ultimately, cellular responses. They are called seven-transmembrane receptors because they pass through the cell membrane seven times. The ligands that bind and activate these receptors include light-sensitive compounds, odors, pheromones, hormones, and neurotransmitters, and vary in size from small molecules to peptides to large proteins. G protein–coupled receptors are involved in many diseases, and are also the target of approximately 40% of all modern medicinal drugs. There are two principal signal transduction pathways involving the G protein–coupled receptors: the cAMP signal pathway and the phosphatidylinositol signal pathway. When a ligand binds to the GPCR it causes a conformational change in the GPCR, which allows it to act as a guanine nucleotide exchange factor (GEF). The GPCR can then activate an associated G protein by exchanging its bound GDP for a GTP. The G protein’s α subunit, together with the bound GTP, can then dissociate from the β and γ subunits to further affect intracellular signaling proteins or target functional proteins directly depending on the α subunit type. GPCR tend to dimerize but it is not clear if this is necessary to function.

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2
Q

GPCRs structure

A

GPCRs are integral membrane proteins that possess seven membrane-spanning domains or transmembrane helices. The extracellular parts of the receptor can be glycosylated. These extracellular loops also contain two highly conserved cysteine residues that form disulfide bonds to stabilize the receptor structure. Some seven-transmembrane helix proteins (channelrhodopsin) that resemble GPCRs may contain ion channels, within their protein.

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3
Q

GPCRs structure-function relationship

A

In terms of structure, GPCRs are characterized by an extracellular N-terminus, followed by seven transmembrane (7-TM) α-helices (TM-1 to TM-7) connected by three intracellular (IL-1 to IL-3) and three extracellular loops (EL-1 to EL-3), and finally an intracellular C-terminus. The GPCR arranges itself into a tertiary structure resembling a barrel, with the seven transmembrane helices forming a cavity within the plasma membrane that serves a ligand-binding domain that is often covered by EL-2. Ligands may also bind elsewhere, however, as is the case for bulkier ligands (e.g., proteins or large peptides), which instead interact with the extracellular loops, or, as illustrated by the class C metabotropic glutamate receptors (mGluRs), the N-terminal tail. The class C GPCRs are distinguished by their large N-terminal tail, which also contains a ligand-binding domain. Upon glutamate-binding to an mGluR, the N-terminal tail undergoes a conformational change that leads to its interaction with the residues of the extracellular loops and TM domains. The eventual effect of all three types of agonist-induced activation is a change in the relative orientations of the TM helices (likened to a twisting motion) leading to a wider intracellular surface and “revelation” of residues of the intracellular helices and TM domains crucial to signal transduction function (i.e., G-protein coupling). Inverse agonists and antagonists may also bind to a number of different sites, but the eventual effect must be prevention of this TM helix reorientation. The structure of the N- and C-terminal tails of GPCRs may also serve important functions beyond ligand-binding. For example, The C-terminus of M3 muscarinic receptors is sufficient, and the six-amino-acid polybasic (KKKRRK) domain in the C-terminus is necessary for its preassembly with Gq proteins.[35] In particular, the C-terminus often contains serine (Ser) or threonine (Thr) residues that, when phosphorylated, increase the affinity of the intracellular surface for the binding of scaffolding proteins called β-arrestins (β-arr).[36] Once bound, β-arrestins both sterically prevent G-protein coupling and may recruit other proteins, leading to the creation of signaling complexes involved in extracellular-signal regulated kinase (ERK) pathway activation or receptor endocytosis (internalization). As the phosphorylation of these Ser and Thr residues often occurs as a result of GPCR activation, the β-arr-mediated G-protein-decoupling and internalization of GPCRs are important mechanisms of desensitization.

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4
Q

GPCRs ligand binding

A

the ligands of GPCRs typically bind within the transmembrane domain. However, protease-activated receptors are activated by cleavage of part of their extracellular domain.

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5
Q

GPCRs conformation change

A

It is known that in the inactive state, the GPCR is bound to a heterotrimeric G protein complex. Binding of an agonist to the GPCR results in a conformation change in the receptor that is transmitted to the bound Gα subunit of the heterotrimeric G protein. The activated Gα subunit exchanges GTP in place of GDP which in turn triggers the dissociation of Gα subunit from the Gβγ dimer and from the receptor. The dissociated Gα and Gβγ subunits interact with other intracellular proteins to continue the signal transduction cascade while the freed GPCR is able to rebind to another heterotrimeric G protein to form a new complex that is ready to initiate another round of signal transduction.

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6
Q

hetertimeric G protein

A

These proteins are activated by G protein-coupled receptors and are made up of alpha (α), beta (β) and gamma (γ) subunits, the latter two referred to as the beta-gamma complex. Gα subunits consist of two domains, the GTPase domain (the deactivating part), and the alpha-helical domain. The β and γ subunits are closely bound to one another and are referred to as the beta-gamma complex. Upon activation of the GPCR, the Gβγ complex is released from the Gα subunit after its GDP-GTP exchange. The free Gβγ? complex can act as a signaling molecule itself, by activating other second messengers or by gating ion channels directly. The GDP dissociation is the rate limiting step and the conformation change in GPCR enzymaticaly favors this dissociation. The high concentration of GTP in the cytoplasm ensures that GTP will replace GDP.

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7
Q

G-protein activation/deactivation cycle

A

When the receptor is inactive, the GEF domain may be bound to an also inactive α-subunit of a heterotrimeric G-protein. These “G-proteins” are a trimer of α, β, and γ subunits (known as Gα, Gβ, and Gγ, respectively) that is rendered inactive when reversibly bound to Guanosine diphosphate (GDP) (or, alternatively, no guanine nucleotide) but active when bound to Guanosine triphosphate (GTP). Upon receptor activation, the GEF domain, in turn, allosterically activates the G-protein by facilitating the exchange of a molecule of GDP for GTP at the G-protein’s α-subunit. The cell maintains a 10:1 ratio of cytosolic GTP:GDP so exchange for GTP is ensured. At this point, the subunits of the G-protein dissociate from the receptor, as well as each other, to yield a Gα-GTP monomer and a tightly interacting Gβγ dimer, which are now free to modulate the activity of other intracellular proteins. The extent to which they may diffuse, however, is limited due to the palmitoylation of Gα and the presence of an isoprenoid moiety that has been covalently added to the C-termini of Gγ. Because Gα also has slow GTP→GDP hydrolysis capability, the inactive form of the α-subunit (Gα-GDP) is eventually regenerated, thus allowing reassociation with a Gβγ dimer to form the “resting” G-protein, which can again bind to a GPCR and await activation. The rate of GTP hydrolysis is often accelerated due to the actions of another family of allosteric modulating proteins called Regulators of G-protein Signaling, or RGS proteins, which are a type of GTPase-Activating Protein, or GAP. In fact, many of the primary effector proteins (e.g., adenylate cyclases) that become activated/inactivated upon interaction with Gα-GTP also have GAP activity. Thus, even at this early stage in the process, GPCR-initiated signaling has the capacity for self-termination.

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8
Q

Guanine nucleotide exchange factors (GEFs)

A

activate monomeric GTPases by stimulating the release of guanosine diphosphate (GDP) to allow binding of guanosine triphosphate (GTP).

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9
Q

Kinase

A

What they really do is adding phosphate groups (bulky, negatively charged) to proteins, which in turn can regulate their activity. The action of kinases (phosphorylation) is opposed by the action of phosphatases (dephosphorylation). Kinases can be classified based on the amino acid residue they phosphorylate (Ser and Thr; or Tyr), their substrate, their activation, or their phylogenetic relationship. There are much more kinases (388 S/T; 518 overall) than phosphatases (38 S/T; ~130 overall), meaning that a single phosphatase has to oppose the action of many kinases. This has lead to the traditional view that phosphatases are less specific and less regulated; this may be true in comparison to many kinases, but there is both substrate selectivity and regulation of activity among phosphatases. Ser/Thr and Tyr have phosphorylatable hydroxyl (-OH) groups, and chemically, a phosphorylation reaction catalyzed by a kinase is a nucleophilic attack of such hydroxyl group onto the γ-phosphate of an ATP molecule. A kinase catalyzes this by promoting an ideal positioning of the reaction partners.

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10
Q

Structure and Regulation of Protein Kinases

A

A kinase domain consists of a small and large. ATP binds in the cleft between the lobes; interaction of the substrate is usually mostly with the large lobe. A “closed conformation” of the glycine rich loop in the small lobe forces the γ-Phosphate of the ATP into the right position for phosphorylation (a fast reaction). An “open conformation” of the glycine rich loop then allow exchange of the generated ADP for a new ATP (a slow reaction). Thus, kinase activity is thought to require alternating open and closed conformations. The active conformation of all kinases is highly conserved. This presents a problem for making specific inhibitors for individual kinases. However, the inactive conformations are not, since there are many ways to distort conformation to prevent activity (an opportunity for specific inhibitors, now also realized by the pharmaceutical industry). Generally, the ATP binding pocket is somehow distorted in inactive conformations (glycine rich loop; C-helix; activation loop). In many but not all kinases, the activation loop has to be phosphorylated for full activity. Another common regulatory theme is block of the active site by an inhibitory “pseudo-substrate” sequence.

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11
Q

MAP kinase cascades

A

are examples how kinases are activated by other “upstream” kinases. MAP kinase stands for “mitogen activated protein kinase”, but the activating “mitogen” (something that induces cell division) is far upstream in the activation… and this upstream signal does not even have to be a mitogen.

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12
Q

Calcineurin

A

a protein phosphatase also known as protein phosphatase 3, and calcium-dependent serine-threonine phosphatase. also called Protein Phosphatase 2B. When an antigen-presenting cell interacts with a T cell receptor on T cells, there is an increase in the cytoplasmic level of calcium, which activates calcineurin, by binding a regulatory subunit and activating calmodulin binding. Calcineurin induces different transcription factors (NFATs) that are important in the transcription of IL-2 genes. IL-2 activates T-helper lymphocytes and induces the production of other cytokines. In this way, it governs the action of cytotoxic lymphocytes. The amount of IL-2 being produced by the T-helper cells is believed to influence the extent of the immune response significantly. Its activity is inhibited by both cyclosporin and tacrolimus. Both bind to an “immunophilin” (cyclophilin for cylcosporin; FKBP-12 = FK506 binding protein for tacrolimus) which then inhibits phosphatase activity of Calcineurin.

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13
Q

mTOR

A

Sirolimus = rapamycin = rapamune: immunosuppressant; can be used in combination with additional drugs in case of high risk for calcineurin inhibitor associated nephrotoxicity. Binds to FKBP-12 which then inhibits kinase activity of mTOR (not phosphatase activity of calcineurin)

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14
Q

cyclosporin

A

immunosuppressant indicated against graft rejection after transplantation. Ciclosporin binds to the cytosolic protein cyclophilin (immunophilin) of lymphocytes, especially T cells. This complex of ciclosporin and cyclophilin inhibits calcineurin, which, under normal circumstances, is responsible for activating the transcription of interleukin 2.

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15
Q

rapamycin

A

Unlike the similarly named tacrolimus, sirolimus is not a calcineurin inhibitor, but it has a similar suppressive effect on the immune system. Sirolimus inhibits the the production of interleukin-2 (IL-2) via action on mTOR, and thereby blocks activation of T and B cells. Binds to FKBP-12 which then inhibits kinase activity of mTOR (not phosphatase activity of calcineurin)

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16
Q

Kinases as pharmacology targets

A

Calcineurin (=Protein Phosphatase 2B) and mTOR (a Ser/Thr kinase) inhibitors (cyclosporin and rapamycin) are important immuno-suppressants. A Tyr kinase is the target of Gleevac, a highly successful drug in therapy of chronic myeloid leukemia.

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17
Q

CaMKII

A

a serine/threonine-specific protein kinase that is regulated by the Ca2+/calmodulin complex. The sensitivity of the CaMKII enzyme to calcium and calmodulin is governed by the variable and self-associative domains. This sensitivity level of CaMKII will also modulate the different states of activation for the enzyme. Initially, the enzyme is activated; however, autophosphorylation does not occur because there is not enough Calcium or calmodulin present to bind to neighboring subunits. As greater amounts of calcium and calmodulin accumulate, autophosphorylation occurs leading to persistent activation of the CaMKII enzyme for a short period of time. Low frequency stimulation (low Ca) calcineurin wins, it is more sensitive, leading to long term depression. High frequency stimulation -> high Ca2+ -> CaMKII wins (gets more sensitive in the process).

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18
Q

regulators of synaptic strength

A

CaMKII and Calcineurin (a Ca2+ regulated kinase and phosphate, respectively) are important mediators of long term potentiation and long term depression (LTP and LTD) of synaptic strength, respectively. (These forms of changes in the strength of connection between neurons are thought to underlie higher brain functions, especially learning and memory). (Slides 17+18). This is another example of Ca2+ as a node in signal transduction; depending on the pathway it activates, it can have opposite cellular effects.

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19
Q

Calcium signaling

A

Calcium can act in signal transduction resulting from activation of ion channels or as a second messenger caused by indirect signal transduction pathways such as G protein-coupled receptors.

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20
Q

Calcium signaling through ion channels

A

Movement of calcium ions from the extracellular compartment to the intracellular compartment alters membrane potential. This is seen in the heart, during the plateau phase of ventricular contraction. In this example, calcium acts to maintain depolarization of the heart. Calcium signaling through ion channels is also important in neuronal synaptic transmission.

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21
Q

Calcium as a secondary messenger

A

These include muscle contraction, neuronal transmission as in an excitatory synapse, cellular motility (including the movement of flagella and cilia), fertilisation, cell growth or proliferation, learning and memory as with synaptic plasticity, and secretion of saliva. Other biochemical roles of calcium include regulating enzyme activity, permeability of ion channels, activity of ion pumps, and components of the cytoskeleton. Specific signals can trigger a sudden increase in the cytoplasmic Ca2+ level up to 500–1,000 nM by opening channels in the endoplasmic reticulum or the plasma membrane. The most common signaling pathway that increases cytoplasmic calcium concentration is the phospholipase C pathway. Many cell surface receptors, including G protein-coupled receptors and receptor tyrosine kinases activate the phospholipase C (PLC) enzyme. PLC hydrolyses the membrane phospholipid PIP2 to form IP3 and diacylglycerol (DAG), two classical second messengers. DAG activates the protein kinase C enzyme, while IP3 diffuses to the endoplasmic reticulum, binds to its receptor (IP3 receptor), which is a Ca2+ channel, and thus releases Ca2+ from the endoplasmic reticulum. Depletion of calcium from the endoplasmic reticulum will lead to Ca2+ entry from outside the cell by activation of “Store-Operated Channels” (SOCs). This inflowing calcium current that results after stored calcium reserves have been released is referred to as Ca2+-release-activated Ca2+ current (ICRAC). Many of Ca2+-mediated events occur when the released Ca2+ binds to and activates the regulatory protein calmodulin. Calmodulin may activate calcium-calmodulin-dependent protein kinases, or may act directly on other effector proteins. Besides calmodulin, there are many other Ca2+-binding proteins that mediate the biological effects of Ca2+.

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22
Q

resting concentration of Ca2+

A

The resting concentration of Ca2+ in the cytoplasm is normally maintained in the range of 10–100 nM. To maintain this low concentration, Ca2+ is actively pumped from the cytosol to the extracellular space and into the endoplasmic reticulum (ER), and sometimes in the mitochondria. Certain proteins of the cytoplasm and organelles act as buffers by binding Ca2+. Signaling occurs when the cell is stimulated to release calcium ions (Ca2+) from intracellular stores, and/or when calcium enters the cell through plasma membrane ion channels.

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23
Q

EF hand

A

a helix-loop-helix structural domain or motif found in a large family of calcium-binding proteins. The EF-hand motif contains a helix-loop-helix topology, much like the spread thumb and forefinger of the human hand, in which the Ca2+ ions are coordinated by ligands within the loop. The EF-hand consists of two alpha helices linked by a short loop region (usually about 12 amino acids) that usually binds calcium ions. EF-hands also appear in each structural domain of the signaling protein calmodulin and in the muscle protein troponin-C. Upon binding to Ca2+, this motif may undergo conformational changes that enable Ca2+-regulated functions as seen in Ca2+ effectors such as calmodulin (CaM) and troponin C (TnC)

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24
Q

Calmodulin (CaM)

A

a calcium-binding messenger protein expressed in all eukaryotic cells. CaM is a multifunctional intermediate messenger protein that transduces calcium signals by binding calcium ions and then modifying its interactions with various target proteins. CaM mediates many crucial processes such as inflammation, metabolism, apoptosis, smooth muscle contraction, intracellular movement, short-term and long-term memory, and the immune response. CaM is expressed in many cell types and can have different subcellular locations, including the cytoplasm, within organelles, or associated with the plasma or organelle membranes. Many of the proteins that CaM binds are unable to bind calcium themselves, and use CaM as a calcium sensor and signal transducer. CaM can also make use of the calcium stores in the endoplasmic reticulum, and the sarcoplasmic reticulum. CaM can undergo post-translational modifications, such as phosphorylation, acetylation, methylation and proteolytic cleavage, each of which has potential to modulate its actions. It contains four EF-hand motifs, each of which binds a Ca2+ ion. Each Ca2+ coordinated with 5 oxygens (1 backbone, 3 aspartates, 1 glutamate.

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25
Q

Roles of calmodulin

A

Calmodulin binds to and confers Ca2+ regulation to a large number of other proteins, including ion channels, protein kinases and phosphatases, and cyclic nucleotide phosphodiesterases. The EF-hand motif of calmodulin is found in many other Ca2+ effectors, including parvalbumin (a cellular Ca2+ buffer), calpain (a Ca2+-activated protease) and troponin. There are also many Ca2+-binding motifs that do not resemble C2 domains or EF hands.

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26
Q

C2 domain

A

a protein structural domain involved in targeting proteins to cell membranes. The typical version (PKC-C2) has a beta-sandwich composed of 8 β-strands that co-ordinates two or three calcium ions, which bind in a cavity formed by the first and final loops of the domain, on the membrane binding face. Many other C2 domain families don’t have calcium binding activity. C2 domains are frequently found coupled to enzymatic domains; for example, the C2 domain in PTEN, brings the phosphatase domain into contact with the membrane where it can dephosphorylate its substrate, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), without removing it from the membrane

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27
Q

stem-cell niche

A

Stem-cell populations are established in ‘niches’ — specific anatomic locations that regulate how they participate in tissue generation, maintenance and repair. The niche saves stem cells from depletion, while protecting the host from over-exuberant stem-cell proliferation. It constitutes a basic unit of tissue physiology, integrating signals that mediate the balanced response of stem cells to the needs of organisms. Yet the niche may also induce pathologies by imposing aberrant function on stem cells or other targets. The interplay between stem cells and their niche creates the dynamic system necessary for sustaining tissues, and for the ultimate design of stem-cell therapeutics. Cells, matrix glycoproteins and the three-dimensional spaces they form provide ultrastructure for a stem-cell niche. The contact between these elements allows molecular interactions that are critical for regu- lating stem-cell function. Secreted proteins offer a paracrine measure of control, but non-protein components of the local microenviron- ment also affect stem-cell function.

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28
Q

The niche as a target in cancer therapy

A

If can- cer is organized in a manner similar to normal tissue, with a minor subpopulation of stem cells, an attendant blood supply and a unique microenvironment, there might be a similar dependence of the stem cells on a cancer niche. If the components of this niche could be demonstrated and targeted, it would be of considerable interest to modify the relative support of the stem-like cells of cancer. The idea that the niche might be a druggable target would be extremely appealing as an adjunctive and entirely independent means of targeting malignant cells.

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29
Q

Adult tissue stem cells

A

First, a population of tissue stem cells should be maintained over long periods of time, often the entire lifetime of the organism (“longevity”). And second, these long-lived stem cell populations should be able to gen- erate the differentiated cell types of the tissue. Most adult stem cells can generate multiple cell types (“multipotency”), yet examples also exist in which they only generate offspring of a single lineage. Stem cells are commonly believed to di- vide very infrequently (“quiescence”), and when this occurs, to generate one rapidly cycling daughter cell, while the other daughter replaces the parent stem cell (“asymmetric cell division”). Most adult stem cells are lineage-restricted (multipotent) and are generally referred to by their tissue origin (mesenchymal stem cell, adipose-derived stem cell, endothelial stem cell, dental pulp stem cell, etc.).

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30
Q

transit-amplifying (TA) cells

A

The rapidly cycling daughter cells, also called transit-amplifying (TA) cells, are responsible for building tissue mass. TA cells typically undergo a limited number of cell divisions, after which they termi- nally differentiate.

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31
Q

Induced pluripotent stem cells

A

a type of pluripotent stem cell that can be generated directly from adult cells. Since iPSCs can be derived directly from adult tissues, they not only bypass the need for embryos, but can be made in a patient-matched manner, which means that each individual could have their own pluripotent stem cell line. iPSCs are typically derived by introducing a specific set of pluripotency-associated genes, or “reprogramming factors”, into a given cell type. The original set of reprogramming factors (also dubbed Yamanaka factors) are the genes Oct4 (Pou5f1), Sox2, cMyc, and Klf4. While this combination is most conventional in producing iPSCs, each of the factors can be functionally replaced by related transcription factors, miRNAs, small molecules, or even non-related genes such as lineage specifiers.

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32
Q

Limitations of the transcription factor approach for IPSC

A

Throughput: the throughput of successfully reprogrammed cells has been incredibly low. Genomic Insertion: genomic integration of the transcription factors limits the utility of the transcription factor approach because of the risk of mutations being inserted into the target cell’s genome. Tumors: another main challenge was mentioned above – some of the reprogramming factors are oncogenes that bring on a potential tumor risk. Inactivation or deletion of the tumor suppressor p53, which is the master regulator of cancer, significantly increases reprogramming efficiency. Incomplete reprogramming: reprogramming also faces the challenge of completeness. This is particularly challenging because the genome-wide epigenetic code must be reformatted to that of the target cell type in order to fully reprogram a cell.

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33
Q

cancer stem cells (CSCs)

A

are cancer cells (found within tumors or hematological cancers) that possess characteristics associated with normal stem cells, specifically the ability to give rise to all cell types found in a particular cancer sample. CSCs are therefore tumorigenic (tumor-forming), perhaps in contrast to other non-tumorigenic cancer cells. CSCs may generate tumors through the stem cell processes of self-renewal and differentiation into multiple cell types. Such cells are proposed to persist in tumors as a distinct population and cause relapse and metastasis by giving rise to new tumors. Cancer stem cells are also capable of resurrection after morphological and biochemical apoptosis by evoking blebbishield emergency program.[1] Therefore, development of specific therapies targeted at CSCs holds hope for improvement of survival and quality of life of cancer patients, especially for patients with metastatic disease.In brief, CSC can be generated as: mutants in developing stem or progenitor cells, mutants in adult stem cells or adult progenitor cells, or mutant differentiated cells that acquire stem like attributes. Some researchers favor the theory that the cancer stem cell is generated by a mutation in stem cell niche populations during development.

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34
Q

Stem cell niche

A

refers to a microenvironment where stem cells are found, which interacts with stem cells to regulate cell fate. The word ‘niche’ can be in reference to the in vivo or in vitro stem cell microenvironment. During embryonic development, various niche factors act on embryonic stem cells to alter gene expression, and induce their proliferation or differentiation for the development of the fetus. Within the human body, stem cell niches maintain adult stem cells in a quiescent state, but after tissue injury, the surrounding micro-environment actively signals to stem cells to promote either self-renewal or differentiation to form new tissues. Several factors are important to regulate stem cell characteristics within the niche: cell-cell interactions between stem cells, as well as interactions between stem cells and neighbouring differentiated cells, interactions between stem cells and adhesion molecules, extracellular matrix components, the oxygen tension, growth factors, cytokines, and the physicochemical nature of the environment including the pH, ionic strength (e.g. Ca2+ concentration) and metabolites, like ATP, are also important. The stem cells and niche may induce each other during development and reciprocally signal to maintain each other during adulthood.

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35
Q

Cellular Signal Transduction

A

Extracellular Signal = Ligand -> Transmembrane Receptors -> Activation of intracellular Signal Transducers -> Modulation of Channels and Enzyme Effectors -> Production of Diffusible Second Messengers -> Regulation of Target Protein Phosphorylation by Kinases and Phosphatses -> specific cellular responsees

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36
Q

agonist

A

favors the conformation change in the receptor and triggers activation

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37
Q

antagonist

A

binding blocks receptor activation, usually through competive binding. 50% of all non anti-biotic prescription drugs act through these receptors.

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38
Q

Bordella Pertussis (whooping cough)

A

PTX: Pertussis Toxin-ADP ribosylates Gαi/o family near the C-terminus of α subunit to lock the G protein heterotrimer in the inactive state by preventing receptor coupling. No activation.

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39
Q

Vibrio cholera (Cholera)

A

CTX: Cholora Toxin-ADP ribosylates Gαs near the GTP binding site of the α subunit to inhibit GTPase activity thus converting the G protein to the active state even without receptor activation. No deactivation.

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40
Q

Diversity in Signaling through G protein-coupled Receptors

A

Ligands- different neurotransmitters, hormones and peptides -> GPCRs- bind to different receptor classes & subtypes -> Receptors couple to different G protein transducers -> G proteins regulate different Effector enzymes and channels -> Resulting in production of different Second Messengers -> Protein Phosphorylation- control of different kinases and phosphatases acting on different target substrates -> specific cellular responses

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41
Q

Postganglionic Efferents

A

Includes those released by Sympathetic Branch- adrenergic transmission at target organs- norepinephrine (NE) released at synapses and epinephrine (adrenaline) released into blood by the adrenal glands and the Parasympathetic branch- muscarinic cholinergic transmission at target organs- acetylcholine (Ach) released at synapses. In general sympathetic and parasympathetic oppose each other in regulating target organ functions/ Sympathetic fight or flight response. Examples in cardiovascular and pulmonary system

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42
Q

Adrenergic Receptors

A

Include beta1AR and alpha1AR

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43
Q

Muscarinic receptors

A

includes m2 AchR and m3 AchR

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44
Q

β1ΑΡ

A

a beta-adrenergic receptor, and also denotes the human gene encoding it. It is a G-protein coupled receptor associated with the Gs heterotrimeric G-protein and is expressed predominantly in cardiac tissue. Gs renders adenylate cyclase activated, resulting in increase of cAMP. cyclic AMP works by activating protein kinase A (PKA, or cAMP-dependent protein kinase). PKA phosphorylates L-type Ca2+ Channels, Ryanodine Receptors (RyR) in SR (Ca2+ release channels) and contractile proteins. Ca2+ influx increases, increased heart rate and contraction. Agonists- Norepinephrine, Epinephrine or Isoproterenol. (antagonists- propanolol or metoprolol)

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45
Q

α1ΑΡ

A

a G protein-coupled receptor (GPCR) associated with the Gq heterotrimeric G-protein. It consists of three highly homologous subtypes, including α1A-, α1B-, and α1D-adrenergic. Catecholamines like norepinephrine (noradrenaline) and epinephrine (adrenaline) signal through the α1-adrenergic receptor in the central and peripheral nervous systems. α1-Adrenergic receptors are members of the G protein-coupled receptor superfamily. Upon activation, a heterotrimeric G protein, Gq, activates phospholipase C (PLC), which causes an increase in IP3 (by cleaving PIP3) and calcium. This triggers further effects, primarily through the activation of an enzyme Protein Kinase C. This enzyme, as a kinase, functions by phosphorylation of other enzymes causing their activation, or by phosphorylation of certain channels leading to the increase or decrease of electrolyte transfer in or out of the cell. IP3 and DAG second messenger levels increase. IP3 binds to IP3-Receptor in ER and releases Ca2+ DAG-PKC stimulates Ca2+ influx (L-type Channel). Ca2+ stimulates smooth muscle contraction. Peripheral vasconstriction decreases blood flow to skin increasing blood pressure (and also helps shift blood flow to heart, lungs, and skeletal muscle).
Agonists- Norepinephrine, Epinephrine or Phenylephrine

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46
Q

m2-muscarinic cholinergic receptor (m2 AchR)

A

M2 muscarinic receptors act via a Gi type receptor, which causes a decrease in cAMP in the cell, generally leading to inhibitory-type effects. They appear to serve as autoreceptors. In addition, they modulate muscarinic potassium channels. In the heart, this contributes to a decreased heart rate. They do so by the G bèta gamma subunit of the G protein coupled to M2. This part of the G protein can open K+ channels in the parasympathetic notches in the heart, which causes an outward current of potassium, which slows down the heart rate. The agonist is acetylcholine. parasympathetic > sympathetic
input. cAMP second messenger levels decrease. Protein Kinase A (PKA) activity decreases. L-type and RyR Ca2+ Channels phosphorylation decreases (phosphatases). Ca2+ influx decreases leading to decreased heart contraction . Opening K+ channels leads to Membrane hyperpolarization and decreased excitability. Decreased Ca2+ influx through L-type Ca2+ channels. Decreased heart rate and contraction.

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47
Q

m3 AchR

A

is coupled to Gq and Stimulates phospholipase C (PLC) Ca2+ and lipid signals. Like the M1 muscarinic receptor, M3 receptors are coupled to G proteins of class Gq, which upregulate phospholipase C and, therefore, inositol trisphosphate and intracellular calcium as a signalling pathway. The calcium function in vertebrates also involves activation of protein kinase C and its effects. Because the M3 receptor is Gq-coupled and mediates an increase in intracellular calcium, it typically causes constriction of smooth muscle, such as that observed during bronchoconstriction. However, with respect to vasculature, activation of M3 on vascular endothelial cells causes increased synthesis of nitric oxide, which diffuses to adjacent vascular smooth muscle cells and causes their relaxation and vasodilation, thereby explaining the paradoxical effect of parasympathomimetics on vascular tone and bronchiolar tone. Indeed, direct stimulation of vascular smooth muscle M3 mediates vasoconstriction in pathologies wherein the vascular endothelium is disrupted. IP3 and DAG second messenger levels increase. IP3 binds to IP3-Receptor in ER and releases Ca2+. DAG-PKC stimulates Ca2+ influx (L-type channel). Ca2+ stimulates smooth muscle contraction, which leads to Bronchoconstriction

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48
Q

phosphodiesterase (PDE)

A

any enzyme that breaks a phosphodiester bond. The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate the localization, duration, and amplitude of cyclic nucleotide signaling within subcellular domains. PDEs are therefore important regulators of signal transduction mediated by these second messenger molecules. Inhibitors of PDE can prolong or enhance the effects of physiological processes mediated by cAMP or cGMP by inhibition of their degradation by PDE. Sildenafil (Viagra) is an inhibitor of cGMP-specific phosphodiesterase type 5, which enhances the vasodilatory effects of cGMP in the corpus cavernosum and is used to treat erectile dysfunction.

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49
Q

beta-2 adrenergic receptor

A

a beta-adrenergic receptor within a cell membrane which reacts with adrenaline (epinephrine) as a hormone or neurotransmitter affecting muscles or organs. his receptor-channel complex is coupled to the Gs G protein, which activates adenylyl cyclase, catalysing the formation of cyclic adenosine monophosphate (cAMP) which then activates protein kinase A, and the counterbalancing phosphatase PP2A. The assembly of the signaling complex provides a mechanism that ensures specific and rapid signaling. A two-state biophysical and molecular model has been proposed to account for the pH and REDOX sensitivity of this and other GPCRs.

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50
Q

GPCR desensitization

A

GPCRs can be desensitized following activation by agonists by becoming phosphorylated by members of the family of G protein-coupled receptor kinases (GRKs). Phosphorylated receptors are then bound by arrestins, which prevent further stimulation of G proteins and downstream signaling pathways.

51
Q

G protein-coupled receptor kinases (GRKs)

A

are protein kinases that phosphorylate only active GPCRs. G-protein-coupled receptor kinases (GRKs) are key modulators of G-protein-coupled receptor (GPCR) signaling. Phosphorylation of the receptor can have two consequences: Translocation: The receptor is, along with the part of the membrane it is embedded in, brought to the inside of the cell, where it is dephosphorylated within the acidic vesicular environment and then brought back. This mechanism is used to regulate long-term exposure, for example, to a hormone, by allowing resensitisation to follow desensitisation. Alternatively, the receptor may undergo lysozomal degradation, or remain internalised, where it is thought to participate in the initiation of signalling events, the nature of which depending on the internalised vesicle’s subcellular localisation. Arrestin linking: The phosphorylated receptor can be linked to arrestin molecules that prevent it from binding (and activating) G proteins, in effect switching it off for a short period of time. This mechanism is used, for example, with rhodopsin in retina cells to compensate for exposure to bright light. In many cases, arrestin’s binding to the receptor is a prerequisite for translocation. For example, beta-arrestin bound to β2-adrenoreceptors acts as an adaptor for binding with clathrin, and with the beta-subunit of AP2 (clathrin adaptor molecules); thus, the arrestin here acts as a scaffold assembling the components needed for clathrin-mediated endocytosis of β2-adrenoreceptors.

52
Q

β-arrestin

A

In response to a stimulus, GPCRs activate heterotrimeric G proteins. In order to turn off this response, or adapt to a persistent stimulus, active receptors need to be desensitized. The first step is phosphorylation by a class of serine/threonine kinases called G protein coupled receptor kinases (GRKs). GRK phosphorylation specifically prepares the activated receptor for arrestin binding. Arrestin binding to the receptor blocks further G protein-mediated signaling and targets receptors for internalization, and redirects signaling to alternative G protein-independent pathways, such as β-arrestin signaling. In addition to GPCRs, arrestins bind to other classes of cell surface receptors and a variety of other signaling proteins. b-arrestin also couples GPCRs to activation of additional downstream signaling pathways such as the JNK and ERK (shown to the right) MAP kinase pathways. There are even biased agonists/antagonists that can preferentially activate b-arrestin signaling over G-protein signaling. Example: The b-blocker carvidilol antagonizes G-protein signaling but activates b-arrestin signaling to ERK.

53
Q

β−αδρενεργιχ ρεχεπτορ σιγναλινγ τηρουγη Γσ ανδ χΑΜΠ προδυχτιον ιν τηε λυνγ

A

cAMP second messenger levels increase. Protein Kinase A (PKA) is activated by cAMP. PKA phosphorylation inhibits smooth muscle contraction. Smooth muscle relaxation leading to bronchodilation (and dilation of vasculature supplying blood to lungs,heart and muscle)

54
Q

How can we classify protein kinases?

A

1) Phosphorylated residue: Ser/Thr (S/T) or Tyr (Y) (Tyr kinases: src, fyn)
2) Substrate protein: Myosin light chain kinase (MLCK), Phosphorylase kinase, EF2 kinase, etc. but several kinases have many substrates (PKA, PKC, CaMKII). 3) Activating stimulus: (Mitogen activated protein kinase (MAPK)) Receptor linked: EGF receptor; Insulin receptor. Second messenger: PKA (cyclic AMP) PKC (Ca2+; diacyl-glycerol) CaMKII (Ca2+/CaM). cyclins: CDK2. 4) Phylogenic relationsship: how they are related to each other evolutionary. AGC: PKA, PKG and PKC containing

55
Q

Structure of ATP

A

The structure of this molecule consists of a purine base (adenine) attached to the 1’ carbon atom of a pentose sugar (ribose). Three phosphate groups are attached at the 5’ carbon atom of the pentose sugar. It is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the ribose sugar is first converted to deoxyribose by ribonucleotide reductase.

56
Q

Ser/Thr and Tyr structure

A

contain hroxyl groups which can be phosphorylated. Tyr is much more bulky therefore majority of kinases cannot p both ser/thr and tyr

57
Q

Phosphorylation

A

Phosphorylation is a nucleophilic attack of the hydroxyl group (of an S/T) to the γ-P of ATP

58
Q

Structure of PKA

A

There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine amino acid, which has been shown to be involved in ATP binding. In the central part of the catalytic domain, there is a conserved aspartic acid, which is important for the catalytic activity of the enzyme. close conformation: Glycine loop positions γ-P for phosphorylation reaction. open conformation: Glycine loop allows exchange of ADP with ATP. open/ closed conformation does not equal active/ inactive. While PKA has served as a structural model for the protein kinase superfamily, all previous structures of the catalytic subunit contain a phosphorylated activation loop.

59
Q

regulation of protein kinases

A

Because protein kinases have profound effects on a cell, their activity is highly regulated. Kinases are turned on or off by phosphorylation (sometimes by the kinase itself - cis-phosphorylation/autophosphorylation), by binding of activator proteins or inhibitor proteins, or small molecules, or by controlling their location in the cell relative to their substrates. Active conformations highly conserved among kinases;
Problem for drug development, BUT: Inactive conformations not to same extent. Usually at least 2 of the 4 distorted in inactive state: Activation loop, C helix, Glycine rich loop (incl. stable open or close conformation), “ATP binding pocket”. Additionally: Block by pseudo-substrate peptide (of regulatory region or subunit). Regulation can also occur by Inhibitory protein interaction and Activating protein interaction: CDK2

60
Q

c-Raf1

A

The c-Raf protein is part of the ERK1/2 pathway as a MAP kinase kinase kinase (MAP3K) that functions downstream of the Ras subfamily of membrane associated GTPases.

61
Q

MKK1

A

The protein encoded by this gene is a member of the dual-specificity protein kinase family that acts as a mitogen-activated protein (MAP) kinase kinase. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act as an integration point for multiple biochemical signals. This protein kinase lies upstream of MAP kinases and stimulates the enzymatic activity of MAP kinases upon activation by a wide variety of extra- and intracellular signals. As an essential component of the MAP kinase signal transduction pathway, this kinase is involved in many cellular processes such as proliferation, differentiation, transcription regulation and development.

62
Q

ERK1

A

The protein encoded by this gene is a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act in a signaling cascade that regulates various cellular processes such as proliferation, differentiation, and cell cycle progression in response to a variety of extracellular signals. This kinase is activated by upstream kinases, resulting in its translocation to the nucleus where it phosphorylates nuclear targets.

63
Q

MAPK/ERK pathway

A

Overall, the extracellular mitogen binds to the membrane receptor. This allows Ras (a GTPase) to swap its GDP for a GTP. It can now activate MAP3K (e.g., Raf), which activates MAP2K, which activates MAPK. MAPK can now activate a transcription factor, such as myc. Receptor-linked tyrosine kinases such as the epidermal growth factor receptor (EGFR) are activated by extracellular ligands. Binding of epidermal growth factor (EGF) to the EGFR activates the tyrosine kinase activity of the cytoplasmic domain of the receptor. The EGFR becomes phosphorylated on tyrosine residues. Docking proteins such as GRB2 contain an SH2 domain that binds to the phosphotyrosine residues of the activated receptor. GRB2 binds to the guanine nucleotide exchange factor SOS by way of the two SH3 domains of GRB2. When the GRB2-SOS complex docks to phosphorylated EGFR, SOS becomes activated. Activated SOS then promotes the removal of GDP from a member of the Ras subfamily (most notably H-Ras or K-Ras). Ras can then bind GTP and become active.

64
Q

Tacrolimus

A

an immunosuppressive drug that is used mainly after allogeneic organ transplant to reduce the activity of the patient’s immune system and so lower the risk of organ rejection. Tacrolimus is a macrolide calcineurin inhibitor. In T-cells, activation of the T-cell receptor normally increases intracellular calcium, which acts via calmodulin to activate calcineurin. Calcineurin then dephosphorylates the transcription factor NF-AT (nuclear factor of activated T-cells), which moves to the nucleus of the T-cell and increases the activity of genes coding for IL-2 and related cytokines. Tacrolimus prevents the dephosphorylation of NF-AT.

65
Q

Fasudil

A

a potent Rho-kinase inhibitor and vasodilator.

66
Q

NMDA-R

A

a glutamate receptor, is the predominant molecular device for controlling synaptic plasticity and memory function. Activation of NMDA receptors results in the opening of an ion channel that is nonselective to cations with a reversal potential near 0 mV. Calcium flux through NMDARs is thought to be critical in synaptic plasticity, a cellular mechanism for learning and memory.

67
Q

long-term potentiation

A

Glutamate binds to postsynaptic AMPARs and another glutamate receptor, the NMDA receptor (NMDAR). Ligand binding causes the AMPARs to open, and Na+ flows into the postsynaptic cell, resulting in a depolarization. NMDARs, on the other hand, do not open directly because their pores are occluded at resting membrane potential by Mg2+ ions. NMDARs can open only when a depolarization from the AMPAR activation leads to repulsion of the Mg2+ cation out into the extracellular space, allowing the pore to pass current. Unlike AMPARs, however, NMDARs are permeable to both Na+ and Ca2+. The Ca2+ that enters the cell triggers the upregulation of AMPARs to the membrane, which results in a long-lasting increase in EPSP size underlying LTP. The calcium entry also phosphorylates CaMKII, which phosphorylates AMPARs, increasing their single-channel conductance.

68
Q

AMPA-R

A

a non-NMDA-type ionotropic transmembrane receptor for glutamate that mediates fast synaptic transmission in the central nervous system (CNS). AMPA receptors (AMPAR) are both glutamate receptors and cation channels that are integral to plasticity and synaptic transmission at many postsynaptic membranes. One of the most widely and thoroughly investigated forms of plasticity in the nervous system is known as long-term potentiation, or LTP.

69
Q

Sources and sinks of Ca

A

Unlike other signals which are generated by catalytic enzymes, Ca2+ enters the cytoplasm (resting ca 50-100 nM) from “sources” where it can be ~2 mM. Thus, onset of Ca2+ signals is far more rapid than that of other signals. Ca2+ is moved out of the cytoplasm into “sinks.” At one time or another, identical structures serve as sources or sinks. Sources/sinks of calcium include ER/SR, extracellular space, mitochondra, and nuclear envelope.

70
Q

Movement from sources into cytoplasm

A

Ion Channels (passive, electrochemically downhill). Plasma membrane: Voltage- and ligand-gated Ca2+ channels (eg nACh and glutamate), store-operated Ca2+ channels (Orai1). Ca2+ moves from outside cell into cytoplasm. ER/SR, (nuclear envelope): IP3 receptors, ryanodine receptors. Ca2+ moves from lumen of ER/SR to cytoplasm. Mitochondria Mitochondrial uniporter, permeability transition pore (MPTP). Direction depends on Ca2+ gradient. MPTP contributes to cell death during stroke and myocardial infarction.

71
Q

Orai 1

A

a calcium selective ion channel. Orai channels play an important role in the activation of T-lymphocytes. Orai channels are activated upon the depletion of internal calcium stores, which is called the “store-operated” or the “capacitative” mechanism. Upon activation of phospholipase C by various cell surface receptors, inositol trisphosphate is formed that releases calcium from the endoplasmic reticulum.

72
Q

PIP2

A

Functions as an intermediate in the IP3/DAG pathway, which is initiated by ligands binding to G protein-coupled receptors activating the Gq alpha subunit. PtdIns(4,5)P2 is a substrate for hydrolysis by phospholipase C (PLC), a membrane-bound enzyme activated through protein receptors such as α1 adrenergic receptors. The products of the PLC catalyzation of PIP2 are inositol 1,4,5-trisphosphate (InsP3; IP3) and diacylglycerol (DAG), both of which function as second messengers. In this cascade, DAG remains on the cell membrane and activates the signal cascade by activating protein kinase C (PKC). PKC in turn activates other cytosolic proteins by phosphorylating them. The effect of PKC could be reversed by phosphatases. IP3 enters the cytoplasm and activates IP3 receptors on the smooth endoplasmic reticulum (ER), which opens calcium channels on the smooth ER, allowing mobilization of calcium ions through specific Ca2+ channels into the cytosol. Calcium participates in the cascade by activating other proteins.

73
Q

•Movement from cytoplasm into sinks

A

Transporters are much slower than ion channels because they are working against the electrochemical gradient (active, against electrochemical gradient). Ca2+ pumps use ATP to move Ca2+ out of cytoplasm into extracellular space (PMCA pumps) or into lumen of ER/SR (SERCA pumps). Na+/Ca2+ exchangers (NCX, RetX) extrude Ca2+ out across plasma membrane or from mitochondria into cytoplasm. NCX exchanges {3 Na+}:{1 Ca2+}, deriving energy from Na+ gradient.

74
Q

plasma membrane Ca2+ ATPase (PMCA)

A

a transport protein in the plasma membrane of cells and functions to remove calcium (Ca2+) from the cell. Since it transports Ca2+ into the extracellular space, the PMCA is also an important regulator of the calcium concentration in the extracellular space.

75
Q

SERCA pumps

A

SERCA resides in the sarcoplasmic reticulum (SR) within muscle cells. It is a Ca2+ ATPase that transfers Ca2+ from the cytosol of the cell to the lumen of the SR at the expense of ATP hydrolysis during muscle relaxation.

76
Q

sodium-calcium exchanger

A

an antiporter membrane protein that removes calcium from cells. It uses the energy that is stored in the electrochemical gradient of sodium (Na+) by allowing Na+ to flow down its gradient across the plasma membrane in exchange for the countertransport of calcium ions (Ca2+).

77
Q

•Cellular Ca2+Buffers

A

Cytoplasmic buffers restrict the spatial spread of Ca and create distinct signaling domains (eg plasma membrane vs. ER/SR) Proteins that bind calcium play a crucial role in Ca2+ signaling. The cytoplasmic buffers (e.g., parvalbumin) tend to restrict the spatial and temporal spread of Ca2+. The buffers also serve as a temporary storage site for Ca2+ while the relatively slow transport processes are operating. In the ER/SR lumen, high-capacity low affinity buffers (e.g., calsequestrin) allow large quantities of Ca2+ to be stored without the generation of a large gradient in the concentration of free Ca2+.

78
Q

Calsequestrin

A

a calcium-binding protein of the sarcoplasmic reticulum. The protein helps hold calcium in the cisterna of the sarcoplasmic reticulum after a muscle contraction, even though the concentration of calcium in the sarcoplasmic reticulum is much higher than in the cytosol. It also helps the sarcoplasmic reticulum store an extraordinarily high amount of calcium ions.

79
Q

Ca effectors

A

Surface Membrane Potential: Ca2+ channels, Ca2+-activated channels (Neuronal bursting, cardiac pacemaking). Protein Kinase C (Translocation to the membrane). Synaptotagmin (Ca2+-dependent fusion of synaptic vesicles). Calmodulin (multiple downstream targets)

80
Q

Synaptotagmin

A

a Ca2+ sensor in the membrane of the pre-synaptic axon terminal

81
Q

Protein kinase C (PKC)

A

a family of protein kinase enzymes that are involved in controlling the function of other proteins through the phosphorylation of hydroxyl groups of serine and threonine amino acid residues on these proteins. PKC enzymes in turn are activated by signals such as increases in the concentration of diacylglycerol (DAG) or calcium ions (Ca2+). Hence PKC enzymes play important roles in several signal transduction cascades. The C2 domain acts as a Ca2+ sensor and is present in both conventional and novel isoforms, but functional as a Ca2+ sensor only in the conventional.

82
Q

troponin

A

is integral to muscle contraction in skeletal muscle and cardiac muscle, but not smooth muscle. When the muscle cell is stimulated to contract by an action potential, calcium channels open in the sarcoplasmic membrane and release calcium into the sarcoplasm. Some of this calcium attaches to troponin, which causes it to change shape, exposing binding sites for myosin (active sites) on the actin filaments. Myosin’s binding to actin causes crossbridge formation, and contraction of the muscle begins.

83
Q

How can Ca be both a trigger for contraction and relaxation?

A

Maintained depolarization activates voltage-gated Ca2+ channels, which trigger Ca2+ release from nearby RyRs, a global Ca2+ increase, and vascular smooth muscle contraction. RyR causes large, localized Ca2+ increase, hyperpolarization via activation of nearby Ca2+-activated K+ channel, closing of voltage-gated Ca2+ channels, and vascular smooth muscle relaxation

84
Q

How Ca pathway activates helper T-lymphocytes

A

1)Peptide/MHC complex binds to plasma membrane T-cell receptors (TCR’s). 2) TCR’s aggregate, trigger activation of associated tyrosine kinase. 3) Activation of phospholipase C, generation DAG and IP3. 4) Activation of IP3R’s in ER and depletion of ER Ca2+ store. 5) Activation of a Ca2+ channel (Orai1) in plasma membrane. 6) Ca2+-calmodulin binds to calcineurin (a phosphatase). 7) Dephosphorylation of NFAT (nuclear factor of activated T cells). 8) NFAT translocates to nucleus & acts as a promoter for IL-2 gene. R91W mutation in Orai1 causes severe immuno-deficiency

85
Q

Mutations in RyR2 (the cardiac RyR)

A

cause familial polymorphic ventricular tachycardia. Ordinarily, Ca2+ release via RyR2 is synchronized with Ca2+ entering during the cardiac action potential. Mutations can result in a component of delayed release, triggering a delayed depolarization via the Na:Ca exchanger and thus trigger an arrhythmia.

86
Q

Obstacles to Using iPS Cells for Clinical Applications

A
  1. The development of alternative strategies for reprogramming adult skin cells into iPS cells without the use of viral vectors. 2. The development of efficient, safe methods for homologous recombination. Genome editing technologies such as CRSPR are useful. 3. The development of efficient methods for differentiating genetically corrected iPS cells into tissue specific lineages.
87
Q

Remaining obstacles for using iPS cells for clinical applications

A
  1. Demonstrating that iPSC-derived adult stem cell lineages are genetically stable 2. Demonstrating that iPSC-derived adult stem cell lineages will not be rejected by the patient’s immune system
88
Q

androgen receptor (AR)

A

a type of nuclear receptor that is activated by binding of either of the androgenic hormones testosterone or dihydrotestosterone in the cytoplasm and then translocating into the nucleus. The AR is a ligand- dependent transcription factor that controls the expression of specific genes. The binding of the AR to its native ligands 5α-dihydrotestosterone (DHT) and testosterone initiates male sexual development and differentiation.

89
Q

prostate cancer

A

In prostate cancer, the cells of these prostate glands mutate into cancer cells. The prostate glands require male hormones, known as androgens, to work properly. Androgens include testosterone, which is made in the testes; dehydroepiandrosterone, made in the adrenal glands; and dihydrotestosterone, which is converted from testosterone within the prostate itself. Androgens are also responsible for secondary sex characteristics such as facial hair and increased muscle mass. The androgen receptor helps prostate cancer cells to survive and is a target for many anti cancer research studies. As such, prostate cancer is treated by depriving tumors of androgens such as DHT and testoster- one or blocking their actions. However, the effect of this type of treatment is transient, as patients relapse after developing a castration-resistant form of the disease that is usually due to increased levels of AR expression or mutations that cause the AR to be resistant to antiandrogens. Prostate cancer is the most common cancer in men. Approximately 30,000 US men die from PCA. Mainstay of management for advanced disease is hormonal therapy, targeting the androgen receptor (AR). The most important recent developments in the medical treatment of prostate cancer have been focused AR

90
Q

AR structure

A

Like other members of the nuclear receptor family, the AR consists of three major functional domains: (i) the N-terminal domain (NTD), followed by (ii) the DNA binding domain (DBD), and (iii) the C-terminal ligand binding domain (LBD), which is connected to the DBD by a flexible hinge region

91
Q

How the androgen receptor functions

A

The AR resides in the cytoplasm when not associated with an androgen. Testosterone is the most common androgen. Upon ligand binding inhibitory chaperones are dissociated and AR moves to the nucleus. AR undergoes homo-dimerization and binds to the androgen-responsive elements of the DNA. After binding, AR recruits co-activators and gene expression occurs. In its normal state it is in the cytoplasm and associates with heat shock protein. Once binds with testerone it moves to nucleuse forms a dimer then a co-acteivator binds to dimer and this complex binds to DNA to promote transcription.

92
Q

Hormonal therapy in PCA

A

Reduce testosterone: Surgical orchiectomy or medical castration (e.g. leuprolide). Gonadotropin releasing hormone (GNRH) agonist (and now antagonists) (overloads system shutting down testosterone production). Anti-androgen (generally regarded as inferior to above) or Block receptor activity with an anti-androgen (e.g. bicalutamide). Three main sources of androgen in PCA: Testis – 90-95% of systemic testosterone, Adrenal glands 5-10% of systemic testosterone, and Intracrine androgen production in the prostate cancer cells themselves (will not be detected systemicaly because it is produced in the cells itself).

93
Q

AR antagonist

A

First generation = flutamide and bicalutamide. Action likely via association of these antiandrogens with the AR’s ligand binding domain. Competes with agonists to block androgen binding to the AR’s ligand binding domain. Interferes with co-activator binding

94
Q

Mechanisms of resistance to hormone therapy in PCA

A

1) AR activation via non-gonadal testosterone. 2) Overexpression of AR. 3) AR mutation leading to promiscuous AR activation. 4) Truncated form of AR, with constitutive activation of the ligand binding domain

95
Q

cytochrome P (CYP) 17

A

The microsomal enzyme cytochrome P (CYP) 17 plays a key role in androgen production. Abiraterone is a specific and potent inhibitor of CYP 17. Blocks testosterone production from all 3 sources. acts upon pregnenolone and progesterone to add a hydroxyl (-OH) group at carbon 17 of the steroid D ring (the hydroxylase activity), or acts upon 17-hydroxyprogesterone and 17-hydroxypregnenolone to split the side-chain off the steroid nucleus (the lyase activity)

96
Q

abiraterone

A

a drug used in combination with prednisone in metastatic castration-resistant prostate cancer (formerly hormone-resistant or hormone-refractory prostate cancer) – i.e., prostate cancer not responding to androgen deprivation or treatment with antiandrogens. side effects include hypokalemia, edema, and hypertension. Mineralcortacoid excess (high corticosterone and low aldosterone) leads to main side effects of abiraterone. Is a type of chemical castration. Abiraterone inhibits 17 α-hydroxylase/C17,20 lyase (CYP17A1), an enzyme which is expressed in testicular, adrenal, and prostatic tumor tissues.

97
Q

Targeting AR directly

A

Large drug screens were performed based on function and the structure of the ligand binding domain of the AR. Activity of first generation antiandrogens was questioned due to modest AR binding affinity. MDV3100 (enzalutamide) was identified. Has 5-8 fold great affinity than bicalutamide for AR binding.

98
Q

Enzalutamide

A

an androgen receptor antagonist drug. Mechanism of action: Inhibits nuclear translocation, Inhibits Co-activator recruitment, Inhibits DNA binding of AR. No known partial agonist properties, which can be seen with first generation antiandrogens such as bicalutamide. Prevents the nuclear translocation of AR and AR binding to DNA.

99
Q

cell adhesion

A

For most mammalian cell types, adhesion to other cells or the extracellular matrix (ECM) is critical for cell survival (together with the presence of growth factors). Most of these cells undergo apoptosis when kept in suspension or grown in agar (an inert gel), even in the presence of nutrients and growth factors. However, as cancer cells become increasingly malignant they can survive in suspension, i.e., they become anchorage-independent. Cell adhesion occurs whenever cells touch appropriate substrata. These may be appropriate other cells or the ECM. In a number of tissues cells are relatively sparse and held in place by an ECM scaffold. Cell adhesion is quite selective. For example, some cells adhere to and grow on fibronectin (e.g., fibroblasts) while others (e.g., most neurons) die on fibronectin but prosper on laminin. Similarly, a specific cell type “A” may adhere to and grow in conjunction with cell type “B” but not cell type “C”. This selectivity depends on the presence or absence of appropriate adhesion molecules and their ligands.

100
Q

intercellular junctions.

A

Most of the adhesions just discussed are not morphologically identifiable. However, in certain tissues, especially epithelia, cells form specialized, morphologically distinct devices called intercellular junctions. a type of structure that exists within the tissue of some multicellular organisms, such as animals. Cell junctions consist of multiprotein complexes that provide contact between neighbouring cells or between a cell and the extracellular matrix.

101
Q

extracellular matrix (ECM)

A

A significant fraction of tissue and organ volume is extracellular space filled by an intricate network of macromolecules, the extracellular matrix (ECM). The ECM consists of a variety of proteins and polysaccharides that are secreted and assembled in close association with the cells that synthesized them. The relative amount of ECM in different tissues varies greatly, from connective tissues, where the ECM may occupy the bulk of the volume, to brain, where it is a very minor component only. The ECM serves not only as a scaffold for cells but also participates in regulating various cell functions (survival, differentiation, migration, proliferation, and shape). In connective tissues, the ECM macromolecules are synthesized and secreted primarily by fibroblasts or specialized members of the fibroblast family, such as chondroblasts (in cartilage) or osteoblasts (in bone).

102
Q

ECM Components

A

The ECM consists of four major classes of molecules: glycosaminoglycans (GAGs), usually linked covalently to proteins to form proteoglycans; fibrous proteins, such as collagen and elastin; multidomain adapter proteins, such as fibronectin and laminin; water and many solutes. The proteoglycan molecules from a highly hydrated gel in which the fibrous and multidomain proteins are embedded. Nutrients, metabolites, hormones, etc. readily can diffuse through the ECM. The fibrous proteins give it its mechanical properties. The ECM typically is amorphous, but it may form a distinct structure, the basal lamina. Two of the basal lamina’s characteristic components are collagen IV and laminin

103
Q

glycosaminoglycans (GAGs)

A

GAGs consist of unbranched polysaccharide chains composed of disaccharide repeats. One of the sugars is always an amino sugar (such as N-acetyl-glucosamine), usually sulfated. The second sugar typically is uronic acid (e.g., glucuronic acid). Sulfation and carboxyl groups convey to the GAGs a high negative charge and, thus, the capacity to become highly hydrated. GAGs typically exhibit an extended conformation, fill very large volumes relative to their mass, and readily form gels. Some common GAGs are: hyaluronan, chondroitin sulfate, dermatan sulfate, heparan sulfate and keratan sulfate. They differ in disaccharide composition, sugar linkage, and location of sulfate groups. Example: hyaluronan (or hyaluronic acid) is composed of glucuronic-acid–N-acetyl-glucosamine disaccharides. Single chains may contain up to 25,000 disaccharide units. Hyaluronan is atypical, however, in that it is generally not linked to protein. They are attached to protein typically to a serine with a tetrasaccharide linker. They can differ greatly in size. depending on where the sulfation is changes the type of GAGs (eg heperin). They can also have different mixtures of dysaccharide repeats. One of the biggest role is to create a morphogen gradient across the cell surface. This keeps signaling molecules in place and helps maintains gradients in signaling molecules. Sometimes these signaling molecules will bind to GAGs and signle or sometimes they will bind and become inactive and therefore they must be cleaved before they can become active. Endothelial cells’ plamsa membrane is rich in GAGs. Leukocytes will use GAGs to slow down with selectins which recognize specific GAGs. Selectins will bind to GAGs due to high association constant (Ka), selectins are unique because they also have a reallly high dissociations constant (Kd). Therefore they attach and let go really quickly. This rolling is key for the leukocyte to move around safetly. Triple negative breast cancer cells go to bone first because of the GAGs that they bind to.

104
Q

Proteoglycans (PGs)

A

PGs are covalently linked complexes of GAGs and protein, typically of very high molecular weight. The “core protein” has attached to serines special link tetrasaccharides, and these serve as the primers for polysaccharide assembly. These post-translational modifications take place chiefly in the Golgi complex. The polymerized sugars maybe modified further (e.g., sulfation). PGs contain at least one GAG chain but may carry many, and the GAG chains can be very long, typically about 80 monosaccharides. The PG aggrecan, for example, contains over 100 GAG chains. As a result, the total mass of an aggrecan molecule is about 3x106 daltons. PGs are likely to play an important role, e.g., in the filtering function of the kidney glomerulus and as “reservoirs” of growth factors and proteases, which they may bind, and whose activity they may modify. Thus, they are not simply space-filling, inert components of the ECM. Some PGs are membrane-bound molecules, anchored via a transmembrane core protein tail or linked via a GPI anchor. PGs and GAGs may assemble to form higher-order aggregates. Aggrecan is an example: About 100 aggrecan monomers (each ~3x106 MW) may be bound non-covalently to a hyaluronan chain via pairs of link proteins. Such complexes may exceed MW 108.

105
Q

Collagens

A

Collagens are fibrous proteins and the most abundant proteins in mammals (about 25% of protein mass). About 25 distinct collagen subunits have been identified. They are known to assemble into about 20 different collagens. Collagen I is the most common form, abundant in connective tissues (see Connective Tissue). Collagen IV is characteristic of the basal lamina. Collagen I mutations are relatively frequent. They interfere with osteogenesis and cause skeletal dysplasias. Procollagen are secreted but do not fit in normal vesicle. There is special packaging with very long vesicle for transportation. Tropocollagen are covalently linked with each other to form long collagen fibers. Multiple different types and will either form rope like structure or sheet like structure. One of the most common component of any ECM.

106
Q

Elastin

A

Elasticity, an important property of many tissues (skin, lungs, blood vessels, etc.), is provided by a network of elastic fibers in the ECM. Elastin is a fibrous protein of distinct chemistry and function.

107
Q

Multidomain adapter proteins

A

The ECM contains several proteins with multiple domains that act as binding sites for other matrix macromolecules and for adhesion molecules on the surfaces of cells. These proteins include, e.g., fibronectin, laminin and tenascin. Thus, such proteins help to organize the matrix and to attach cells to it.

108
Q

Fibronectin

A

A signaling molecule, a large, dimeric glycoprotein whose two large subunits are linked together by disulfide bonds. Each subunit is folded into a series of functionally distinct binding domains. Serially repeated, smaller modules make up each of these domains. The main module is the “type III fibronectin repeat”, which binds to integrins. This repeat contains the characteristic Arg-Gly-Asp (RGD) binding sequence. Other domains bind to collagen, heparin or serve self-association. Thus, secreted fibronectin assembles in the ECM into highly insoluble fibronectin fibrils. Fibronectin null mutant mice are early embryonic lethal. It is a heterotrimer with base and two arms, Coiled coil alpha helical domain and globular domains with multiple different binding domains (self association binding to eachother, collagen binding, cell binding-> bind to intigrins, and heparin binding). Some cells will only bind to fibronectin and some will only bind to laminin, this allows cells to move in a specific manner. this is important in development and in an adult with immune system. They can also initiate signaling cascade.

109
Q

Laminin

A

another very large protein, composed of three subunits (α,β,γ) that form an asymmetric, disulfide-linked cross with the longer arm formed by a helical structure containing long stretches of all three subunits. Laminin is found in the basal lamina only (hence its name). Several isoforms of the laminin subunits assemble in different combinations to form a large protein family. Many laminins can self-assemble into a network via interactions between ends of their arms. Laminins, like fibronectins, have numerous binding sites for cells (integrins; see below) and other ECM proteins that link them to collagen (type IV). Some laminin mutations have been linked to nephrotic syndrome (glomerular filtration defect) and to neuromuscular junction/muscle innervation problems in children.

110
Q

Regulation of the ECM

A

Like any other structure in the body, the ECM must be turned over in an ordered manner. This is achieved by the secretion of extracellular proteases. Typically these proteases are either “matrix metalloproteases” (MMP). These may be substrate-selective (such as collagenases) or quite promiscuous. Extracellular protease activity is particularly important in tissue remodeling during development and in cell invasion of tissues (leukocytes reaching an inflammation site; cell migration in development; neurite outgrowth; cancer cell metastasis). Advancing cells are known to secrete proteases to clear the migration path. However, functions are more complex. Protease activity may unmask cryptic cell binding sites to promote cell binding or migration, may promote cell detachment, may activate (proteolytically) growth factors, or may release ECM- bound extracellular signals. Extracellular protease activity thus must be highly regulated. Loss-of-function mutations of matrix metalloproteases (MMP) 2 or 13 cause inherited osteolysis/arthritis syndromes and bone dysplasias. Overexpression of some MMPs, specifically MMP2, MMP9 and MMP14, correlates with high invasiveness and poor prognosis in many cancers. Cleaving ECM releases signaling molecules that could either provide further positive or negative feedback to the mobile cell. This is another way to guide cells. Some can cleavage cell to cell adhesion. Many different kinds for specificity.

111
Q

Cell Adhesion Molecules

A

As stated before, cell adhesion molecules are not simply adhesive devices: For adhesion and force generation against the ECM or other cells, they form a trans-membrane link with the cytoskeleton. When bound to a ligand, CAMs signal their engagement via conformational change to the cell interior, thus affecting cell function. There are many different known CAMs. The majority of these are sizable transmembrane glycoproteins (MW ~ 100-150 kDa). Because of the severe consequences (developmental and other) loss-of-function of a CAM may result in embryonic lethality. Two types of leukocyte adhesion deficiencies have been identified: Type I, affecting a particular integrin. Type II, affecting a selectin, a CAM involved in leukocyte rolling (the initial contact with vascular endothelial cells, prior to adhesion and extravasation).

112
Q

Cadherins

A

These are single-pass transmembrane glycoproteins that operate as homodimers. The extracellular domains contain 5 repeats that are stabilized by Ca2+ to form a rod-like structure. This means, cadherin binding is Ca2+-dependent. Cadherins bind to other cells via cadherins on the juxtaposed cell surface (homophilic binding) in a zipper-like fashion. They are very common in intercellular junctional complexes. Cadherins form complex when they touch eachother which attracts actin to create stability. Extracellular component will dimerize in a Ca dependent manner. then dimer can hook up with opposing dimer molecule. The intra cellular domain does not bind directly to actin filaments or MTs. beta and alpha catenin is an intermediary. This is why beta catenin is mutated in cancer (allows cell to loose cell-cell adhesion). beta catinin is also TF in Wnt pathway. when beta catenin is P by APC and is degraded. When APC is not active beta catenin goes to nucleus for transcription

113
Q

Ig Superfamily (IgSF) CAMs

A

IgSF CAMs also are single-pass transmembrane glycoproteins engaged in a usually homophilic binding mechanism (there are important exceptions). However, IgSF members do not form dimers, and binding does not require Ca2+. Binding is mediated by multiple Ig domains. Closer to the membrane, IgSF CAMs usually contain a couple of fibronectin type III domains.

114
Q

Integrins

A

These are the “classic” adhesion molecules interacting with the ECM. Thus, their binding is heterophilic. Integrins are composed of α/β heterodimers. Many different α and β sub- units exist (both are transmembrane glycoproteins). They are mixed and matched to some degree. Since both subunits participate in ligand binding, this results in a large variety of integrins with distinct binding selectivities. Typical ligands are the ECM proteins laminin, fibronectin, collagen, etc. (many involving the RGD sequence). Alpha gets clipped that remains attached with sulfate bond. Actin cytoskelton attaches to intracellular domain to provide support. Are not just attachment molecules, also have signaling capacity. Cells move by disengaging back end adhesion. Integrins are then internalized and moved to front where new adhesions are formed. Forms focal adehsion complex for signaling many together forms focal adhesions sites, which attract many other molecules (kinases, src). There are many different alpha and beta subunits allowing specificity in bind (eg laminin only or only fibronenctin), guiding movement. Signaling usually send survival pathway when they are ligated to something. If not ligated cell will die. This is why cells cant live in suspension (exception is cancer). Classic way to bypass this is Src pathway. Src is activated and cell doesnt care if it is attached.

115
Q

CAM-Associated Cytoplasmic Proteins

A

Because of the relative structural weakness of membranes, CAMs must be linked to the cytoskeleton. This is achieved by a variety of proteins associated with the cytoplasmic tails of CAMs. Such proteins include, in all cases, actin-binding proteins (vinculin, talin, α-actinin, etc.). Cadherins have very specific additional associated proteins, the catenins. In addition to providing the cytoskeletal link, CAM-associated proteins also are involved in the regulation of adhesion, in the control of actin polymerization, and in cell signaling mediated by CAMs. For example, assembly of adhesion sites requires the action of protein tyrosine kinases, whereas disassembly and detachment appears to require protein kinase C activity. Members of the Rho family of small GTPases involved in the regulation of F-actin polymerization also are associated with certain CAMs. It follows that CAMs are paired on the cytoplasmic face of the membrane with complex protein assemblies that serve mechanical, controlling, and signaling functions. It is not surprising, therefore, that these adhesion sites play major roles in cell differentiation/development and cancer. In development, CAMs change as cells differentiate. Cams are requered for synaptic junction. They are indeptendent of Ca. There are different classes which lead to different signaling cascades.

116
Q

Cams role with cancer

A

One of the early signs of carcinogenesis is a change in CAM(s). This is accompanied by (and may be the reason for) perturbed cell polarity and cytoarchitecture. Cadherin down-regulation appears to be a prerequisite for the dispersal of epithelium- derived cancer cells. Anchorage independence of cancer cells results from mutations in proteins of the signaling apparatus associated with cell adhesions. Certain catenins are known to be tumor suppressors. This means that loss of catenin function promotes carcinogenesis.

117
Q

docetaxel

A

microtubule based targeted chemotherapy.

118
Q

Prostate-specific antigen (PSA)

A

PSA is present in small quantities in the serum of men with healthy prostates, but is often elevated in the presence of prostate cancer or other prostate disorders. The United States Preventive Services Task Force (USPSTF, 2012) does not recommend PSA screening, noting that the test may result in “overdiagnosis” and “overtreatment” because “most prostate cancer is asymptomatic for life,” and treatments involve risks of complications including impotence (erectile dysfunction) and incontinence. It is not specific to prostate cancer but is specific to prostate tissue so is useful if prostate is removed.

119
Q

Ketoconazole

A

anti fungel, side efffect is adrenal supression. Effects cyp 17

120
Q

Types of cell movement

A

invasice proogression of primary tumor, 2d cell migration, elongated motaility in 3d, round shape motility in 3d

121
Q

3d cell motility

A

will make temporary pseudopods (by depolarizing actin filaments releasing tension allowing expansion in that direction) and then move based on these attachments. You don’t have a permenent leading edge. In dense ECM you don’t have space to make pseudopods. Instead they have to make space with the use of podosome (same thing as invadasom which is used in cancer).

122
Q

podosome

A

are cylindrical, actin-rich structures found on the outer surface of the plasma membrane. It is activated by Src signaling. Needs to make hole is ECM with MMP.

123
Q

MMP2, 9, and 14

A

These MMP can digest collagen 4 which makes up the basement membrane. This is used for cancer to be able to become metastic. There are drugs that target these proteins but there were major side effects.

124
Q

src

A

a non-receptor protein tyrosine kinase protein that in humans is encoded by the SRC gene. This protein phosphorylates specific tyrosine residues in other proteins. An elevated level of activity of c-Src tyrosine kinase is suggested to be linked to cancer progression by promoting other signals. c-Src can be activated by many transmembrane proteins that include: adhesion receptors, receptor tyrosine kinases, G-protein coupled receptors and cytokine receptors.