recept bind > enz chain > tf biochemistry signaling

Question 1

What are the main members of the Wnt signaling pathway?

Answer 1

The 3 main proteins of the Wnt pathway include Wnt, Frizzled (FRZ), and dishevelled (Dsh). Wnt proteins are ~400 amino acids, palmitoylated at ~24 conserved cysteine residues, and glycosylated.
The friizzled family receptor is ~700 aa, 7 transmembrane unconventional G protein coupled receptor that associates with the lipoprotein receptor (LPR5) to bind wnt.
Dishevelled (~700aa) is highly conserved and Wnt ligation causes monomers to polymerize at LPR5 and bind axin which releases b-catenin to perform transcription factor functions.
Downstream signaling related to Wnt binding: 6 proteins at binding site, 9 frizzled receptors, and 18 disheveled varieties. Variation by tissue type accounts for cellular specialization.
Dishevelled null mice are socially inept ?schizophrenia model.
axin-axix inhibitory protein, ~860aa,binding motifs
b-catenin ~780aa, multiple armadillo repeats, binding motifs, serine and threonine phosphorylation sites

Question 2

What phospholipid is bound by the Pleckstrin Homology (PH) domain?

Answer 2

Pleckstrin homology domain (PH domain) of a protein is 120 amino acids long which helps bind the protein to phosphatidylinositol lipids, and the beta-gamma subunit of heterotrimeric G protein

Question 3

What are c-Jun N-terminal kinases?

Answer 3

Stress stimuli (ultraviolet light or radiation, heat shock, and osmotic shock) activate various serine/threonine kinases that eventually phosphorylate cytosolic c-Jun N-terminal kinase (serine 63 and 73). c-JunP kinase moves to the nucleus, binds and phosphorylates transcription factor c-Jun (331 aa 35 kDa), on threonine and tyrosine. Also activates C-fos and other leucine transcription factor proteins responsive to cytokines, . There are 10 isoforms from three genes (JNK1-3). This pathway regulates growth, differentiation, survival, and apoptosis.

Question 4

What pathways contain proteins with the SH3 domain?

Answer 4

The SH3 domain (SRC homology 3 domain) contains ~60 amino acids that help form specific protein complexes. SH3 domains are found in protein families such as PI3 kinase, RasGTPase-activating protein, and C25. Signaling pathways affected relate to cytoskeleton, Ras kinase, and SRC kinase (small GTPases).

Question 5

What does MAP3 kinase do?

Answer 5

MAP3 kinase is a serine/threonine enzyme group protein kinase (~3k hits on OMIM) that activates this pathway. It has an ATP binding site, phosphorylates MAP2 kinase. 19 genes code for this enzyme which includes members of the oncogenic RAF family.
Important in embryogenesis, keratinocyte migration, T cell cytokine production, and B cell antibody production.

Question 6

How are the various forms of Phosphatidylinisitol (Ptdins) synthesized and what processes do they support?

Answer 6

Phosphoinisotol is attached to diacylglycerol at the 1 position. Phosphatidylinisitol 4 (Ptdins(4)) is phosphorylated at position 4 by PI4K. Phosphoinisitol 5 kinase phosphorylates position 5 creating Ptdins(4,5). Ptdins(4,5)P2 has 3 phosphate groups counting the 1 position. PI 3 kinase then phosphorylates position 3 creating Ptdins(3,4,5)P3, with 4 phosphate groups. Phospholipase C activated by GPCR then splits Ptdins(4,5)P2 into Ins(1,4,5) P3 and diacyl glycerol. Ins(1,4,5) then attaches to InsP3R which opens the calcium channel. The 4,5 positions are most important, other phosphorylated inositols are biologically active e.g. IP6, and Ptdins(4,5,)P2 to Ptdins(3,4,5) P3 which is involved with Rho GTPases.
Diacyl glycerol activates protein kinase C (serine/threonine kinase) by attaching protein kinase C to the cell membrane.
Ins(1,4,5)P3 (Inositol 1,4,5 triphosphate)
IP6 (phytic acid, inositol hexakisphosphate

Question 7

What is Janus kinase?

Answer 7

Janus kinase (JAK) is a family of intracellular cytokine receptor associated tyrosine kinases (120-140 kDa) with 7 janus homology domains (JH1-7) with JH1 being a tyrosine kinase acting on STAT transcription factors. JH 3-7 associate with proline rich domains of receptors and are activated by ligand binding. There are two active phosphate transferring sites one stimulatory, and another which negatively regulates it.

Question 8

What are AGC kinases?

Answer 8

AGC kinases contain protein kinase A (PKA, cAMP dependent protein kinase), cGMP-dependent protein kinase (PKG), and protein kinase C (PKC,serine/threonine kinase).
cAMP binds to regulatory unit of PKA freeing up kinase to use ATP to phosphorylate serine or threonine.
cGMP works similarly on other serine threonine substrates.
Protein kinase C responds to DAG or Ca to phosphorylate serine threonine usually to modify receptor sensitivity.

Question 9

what is HIF-1 -alpha ( hypoxia inducible factor)?

Answer 9

HIF-1-Alpha (HIF1A gene product) beta subunit forms a heterodimeric protein with the aryl hydrocarbon receptor nuclear translocator (Arnt). The N-terminus contains a DNA binding domain, and the C terminus recruits transcriptional co-regulatory proteins.The net result is formation of blood vessels in embryos and tumors, and migration of keratinocytes for epithelial healing.
A PAS domain HIF-1-alpha functions as a signal receptor combining to form transcription factors. First discovered on Period circadian protein, Aryl hydrocarbon receptor nuclear translocator protein, and Single-minded protein.
The HIF promoter binds NF-kB.

Question 10

What is fibroblast growth factor?

Answer 10

Fibroblast growth factors refer to over 100 family members of about 140 aa with 48 isoforms, heparin binding domain, nuclear localization signal, interacts with four different receptors that respond to over 100 different FGF ligands to activate receptor tyrosine kinase. This affects mesoderm induction, antero-posterior patterning, limb development, neural induction, neural development,[16] and in mature tissues/systems angiogenesis, keratinocyte organization, wound healing processes, and endocrine effects.
A point mutation in FGFR3 causes achrondoplasia.

Question 11

What does the RORγt (RAR-related orphan receptor gamma) gene do?

Answer 11

RAR-related orphan receptor gamma (RORγt) is a nuclear receptor transcription factor that binds to hormone response element genes (HRE) that are essential for lymphoid organogenesis lymph nodes and Peyer’s patches, especially important in generating Th17 cells and T regs.
Cholesterol and tretinoid (carboxylic acid of vit A) are ligands.

Question 12

What are Rab (RAS associated protein) proteins?

Answer 12

Rab proteins are small GTP ases (20–25 kDa) in all eukaryotes that hydrolyze GTP during signal transduction. 70 types.
Tyrosine kinase receptors cause Ras GDP to become Ras GTP (via RasGrf2 (guanine releasing factor,~1300aa) and Sos-son of seven less, Sos ~1300aa, a guanidine exchange factor, both GDP->GTP)
RasGTP then goes on to activate a serine/threonine kinase to phosphorylate raf-1 to MEK (mitogen activated protein kinase kinase) to MAPK, also MEKK (mitogen activated protein kinase kinase kinase) to SEK1 (MAP2K4 )to JNK’s.
Multiple proteins become phosphorylated and magnify the signal to detect (taste, smell, light), protein biosynthesis at the ribosome, control and differentiation during cell division, translocation of proteins through membranes, transport of vesicles within the cell. Rab proteins are active in tubulin and actin networks.

Question 13

How do CpG sequences in bacterial and viral DNA activate macrophages?

Answer 13

TLR9 ~1000 aa, Ig extracellular portion responds to unmethylated CpG sequences common in bacterial and viral DNA. Signaling begins with MyD88 binding via TIR (Toll/IL-1 Receptor) domains, which binds TRAF6 which induces Interferon regulatory factor five (IRF5) to go nuclear. Dimers form transcription factors that promote virus mediated activation of interferon, modulation of cell growth, differentiation, apoptosis, and immune system activity.
Snps associated with SLE and RA.

Question 14

What is the function of AMPK (adenosine monophosphate-activated protein kinase) ?

Answer 14

AMPK contains three proteins (alpha, beta, gamma). Increased concentration of AMP bind to the alpha and gamma units activating the kinase, (phosphorylation threonine 172) which phosphorylates-activates other kinases that affect Akt, P53, and P38 MAPK.
The net result is to inhibit anabolism and increase catabolism-autophagy.

Question 15

What receptor transmembrane protein uses Jak3 ( Janus kinase3) accessory protein?

Answer 15

Jak3 associates with the common gamma chain (CD132) participates in receptor complexes of at least six interleukins: IL-2, IL-4, IL7, IL9, IL 21. When partnered with other chains the receptor stimulates leukocyte formation and maturation: T cells, B cells, NK cells.

Question 16

How is release of IP3 from phosphatydlinisitol accomplished, and what is the fate of IP3?

Answer 16

Ligated G protein coupled receptors (5-HT2 serotonergic, alpha-1 adrenergic, calcitonin, H1 histamine, metabotropic glutamate, muscarinic, thyroid releasing hormone). activate phospholipase C which releases I3P from PtlI(3,4)P2. IP3 stimulates calcium channels on the ER. Such calcium release is important in muscle contraction.
Abnormal Huntingtin protein in Huntington’s Chorea and in Alzheimer’s disease may be especially sensitive due to the effect of mutated presenilin on IP3 sensitive calcium channels.
Protein kinase C is activated by binding to membrane bound diacyl glycerol.

Question 17

How is phosphatidylinositol generated ?

Answer 17

Class I PI3K’s produce phosphatydlinisitol phosphate (PtdI(3)P, PtdI(3,4)P2 and Ptins(3,4,5)P3. PI3K is activated by G protein-coupled receptors, and tyrosine kinase receptors.
Class I PI3K are heterodimeric with 8 genes and multiple splice variants
class II catalysts use PI and PI (3, 4)P2 and probably bind lipids in a calcium independent manner.
Class III produce PI(3)P from PI

Question 18

What are the differences between JAKS, JNKs and jun?

Answer 18

janus kinases (JAKS) are non receptor tyrosine kinases, that bind to cytokine receptors (growth hormone, prolactin, lectin, erythropoietin..) 1132 amino acids, 9 tryosines, SH2 domain, STAT proteins dock, get phosphorylated, go to nucleus, activate gene transcription.

c-Jun N terminal kinases JNKs (JNK1/2/3) 427 amino acid, threonine at position 183, 185, serine at 377. phosphorylates Jun transcription factor that regulates: histone deacetylase, apoptoses, determination of dorsal identity, programed necrotic cell death, TLR signaling, response to stress.

jun potent transcriptional activator, 272 amino acids, homolog of transforming gene noted in avian sarcoma virus. Necessary for synergistic transcriptional activity with Smad3. Pathways: Toll like receptor 2,4,9, and TGF-beta.

Question 19

How are mitogen activated protein kinases related?

Answer 19

Mitogen activated protein kinases (MAPKs) evolved from a common ancestor of cyclin dependent kinases into ERK, JNK, and four varieties of P38 kinases. MPK1 is 360 aa, has ATP binding and kinase motifs , cytoplasmic and nuclear signal proteins, SH3 domain. activated by threonine and tyrosine phosphorylation. They support transcription factors affecting cellular proliferation, gene expression, differentiation, mitosis, cell survival, and apoptoses.

Question 20

How does the Eph/ephrin signaling system work?

Answer 20

Eph receptors (16) are named after erythropoietin-producing hepatocellular carcinoma cell line on which the receptor was discovered. This orphan receptor was then recognized as part of the Eph/ephrin signaling combination where 2 cells stimulate each other. Ephrin-A (9 genes) ligands are glycosylphosphatidylinositol-linked and ephrin-B (5 genes) ligands are transmembrane proteins. Eph receptors have an intracellular tyrosine kinase domain which becomes active after ligation due to phosphorylation of tyrosine and serine residues in the juxtamembranous region of Eph.

Question 21

What are the main types of enzymatic catalytic cell membrane receptors?

Answer 21

The five major families of enzymatic catalytic receptors include

1) epidermal growth factor receptor (ERB1-4) tyrosine kinase
2) glial cell-derived neurotrophic factor (GRFa1-a4) tyrosine kinase
3) naturetic peptide receptor (NPR1-4) guanylyl cyclase
4) neurotrophin receptor (TrkA-p75) tyrosine kinase
5) toll-like receptor (TLR) receptors. tyrosine kinase

Question 22

What are some intercellular signaling proteins?

Answer 22

Intercellular signaling peptides and proteins include:
growth factors (endothelial growth factor, epidermal growth factor, fibroblast growth factor, nerve growth factor, platelet derived growth factor, TGF-beta)
ephrins-family of membrane-bound receptor protein-tyrosine kinases (EFNA1-B3), adipokine, agouti signaling protein,
connective tissue growth factor, cytokines ( interferons, interleukins, TNF), endothelin, hedgehog protein, parathyroid hormone related protein, somatomedin, metalloproteinase, Wnt Protein.

Question 23

What is the dual role of the lipoprotein receptor?

Answer 23

LRP5 (low density lipoprotein receptor-related protein 5) acts as a coreceptor with rfriizzled and Wnt to activate disheveled.
Loss of function patient results in osteoporosis-pseudoglioma syndrome. Gain of function mutations result in high bone mass.

Question 24

What are the mechanisms by which a signal from one cell can affect itself or another?

Answer 24

Signaling within, between, and among cells may be due to

1) intracrine signals produced by the target cell that stay within the target cell
2) autocrine signals produced by the target cell are secreted and affect the target cell itself
3) juxtacrine signals target adjacent-touching cells via protein or lipid, component, not of the cell membrane, including via gap junctions as in cardiac muscle nerve conduction.
4) paracrine signaling targets cells in the vicinity of the emitting cell-neurotransmitters
5) endocrine signals target distance selves while hormones.

Question 25

How does Notch signaling work?

Answer 25

Notch agcts as a receptor for ligands that are expressed on adjacent cells. The ligand may release part of the notch protein which then becomes a transcription factor for the receiving cell.

Question 26

What is a G protein coupled receptor?

Answer 26

G protein-coupled receptors have 7 transmembrane chains 35-55 kDa, ~290 aa linked to a heterotrimeric G protein . the transmembrane chains alter position with ligand binding and act like a guanine nucleotide exchange factor (NEF), replacing GDP to GTP.
G protein coupled receptors types (number) include:
A- (662), eicosanoid, neurotransmitter, purinergic, biogenic amine, olfactory
B- (15) secretin
C- (22) metabotrophic glutamine
D phernome receptor
E-cAMP receptor
F- fizzled/smoothened
D,E,F- (92)

Question 27

What is the difference between the P2X receptor and the P1 receptor.

Answer 27

The P2X receptor is made of multiple subunits consisting of two transmembranous portions, an external loop and intracellular and in C-terminals. The complex is activated by ATP and often serves as a calcium channel provoking smooth muscle contraction-bladder, vas deferens, heart muscle.
Adenosine receptors (P1) are G protein-coupled receptors with adenosine as the endogenous ligand. Signal transduction is affected through cAMP.

Question 28

What is vascular endothelial growth factor?

Answer 28

Vascular endothelial growth factor (121-206aa) ligates the VEGF Tyrosine kinase receptors (3 varieties) and are recognized in various combinations leading to multiple effects. Different combinations are responsible for embryonic growth of arteries, myocardial angiogenesis,lymphangiogenesis, and specialized lymphatics within bronchioles and about the placenta. Inhibitors are standard treatment for wet macular degeneration costing over 10 billion per year.
Vegf release stimulated by TNF in RA accounting for increased vascular permeability and angiogenesis.

Question 29

What does the Ras superfamily of proteins do?

Answer 29

The Ras superfamily is a group of small GTPases related to the Ras subfamily (RAt Sarcoma source). Ras contains a 6 stranded beta sheet and 5 alpha helices that binds GDP/GTP, and motifs for binding Mg, and guanine.
Ras controls cell proliferation,
Rho controls cytoskeletal dynamics/morphology,
Rab controls membrane trafficking,
Rap controls cellular adhesion,
Arf controls vesicular transport,
Ran controls nuclear transport,
Rheb activates mTORC1 pathway, and
Miro controls mitochondrial transport.
Receptor tyrosine kinases are a form of enzyme-linked receptors that activate Ras once phosphorylated by ligand binding.

Question 30

What factors bind to Ras and alter its GTPase activity?

Answer 30

The Ras GTPase is the Ga subunit of the heterotrimeric G protein large GTPase found in G protein receptors. GTPase activating proteins (GAPs) encourage GTP to GDP transition. Guanine nucleotide exchange factors (GEFs) release GDP which is then replaced by the abundant cytosolic GTP. Son of sevenless (Sos) and cdc25 have a RasGEF domain. Ras activity depends on GTP: GDP ratio as well as a factors like PI3K.

Question 31

How does the transcription factor Gata1 affect erythropoiesis and thrombopoiesis?

Answer 31

The GATA1 transcription factor is a member of the zinc finger transcription factor family. Near the N-terminal, a zinc finger binds strongly to FOG1 (friend of GATA) which accounts for its strong transcriptional activation. GATA1 is active in erythropoeisis and in thrombopoiesis. In strongly increases alpha spectrin production.

Question 32

What is the difference between phospholipase C and protein kinase C?

Answer 32

Phospholipase C releases IP3 from PIP2 which then stimulates IP3 sensitive calcium channels on the ER.
Protein kinase C is a serine threonine phosphatase that is activated by DAG and incased Ca++. It phosphorylates substrates near the cell surface and is important in signal transduction.

Question 33

What ligates the dectin 1 receptor?

Answer 33

Dectin 1 has a C-type lectin like domain with a Carbohydrate binding extracellular motif and recognizes fungi, mycobateria, and endogenous ligand on T cells. It is expressed on macrophages, neutrophils, eosinophils and dendritic cells. The cytoplasmic immunoreceptor tyrosine-based activation motif-ITAM, upon dimerization may stimulate tyrosine kinase which activate Syk kinases (spleen-tyrosine kinase) leading to respiratory burst, PGs, and release of many cytokines.
made from CLEC7A gene.

Question 34

What sort of protein is growth differentiation factor II?

Answer 34

Growth differentiation factor II (GDFII) a.k.a. bone morphogenetic protein (BMP-9) is a member of the transforming growth factor beta superfamily. It may be be the active factor causing rejuvenation when young blood is transfused into older subjects.

Question 35

What does the C2 domain of a cytosolic protein do?

Answer 35

A C2 domain of a protein targets it to the cell membrane by an 8 β strand structure coordinating 3 calcium ions. This serves to hold an enzyme to a cell membrane so that its target once transformed, remains in the membrane, thus improving the efficiency of signal transduction.
Used by PTEN, PI3-kinase.

Question 36

what are P2Y receptors ?

Answer 36

P2Y are 7 transmembrane G protein coupled receptors activated by ATP, ADP, UTP, UDP, and UDP-glucose. 12 human P2Y G protein-coupled receptors have been cloned, and are present on all human tissues. P2Y12 is a target for clopidogrel.
Mutations affect incidence of myocardial infarction, and cystic fibrosis.

Question 37

What are rhodopsin-like receptors?

Answer 37

Rhodopsin like G-protein-coupled receptors are a superfamily based on evolutionary relationships. There are 19 families including receptors for chemokines, opioids, somatostatin, neuropeptides, relaxin/insulin, complement, melatonin, and hormones.

Question 38

How does the glucocorticoid receptor work?

Answer 38

The glucocorticoid receptor is expressed by the gene NR3C1 (Nuclear Receptor Subfamily 3, Groups 1) which controls development, metabolism, and immune response. The GC receptor-GC complex is transported to the nucleus can act in the cytoplasm to repress proinflammatory proteins by preventing translocation of transcription factors.
Glucocorticoids regulate several thousand genes in a cell representing up to 20% of the express genome. Binding depends on the chromatin landscape which is tissue and cell type specific. There are at least 16 GR isoforms divided equally as GR alpha and GR beta. The awful form binds to cortisol but the beta form does not. The beta form can dimeze with the alpha form, decreasing its potency.

Question 39

Identify some processes the AP-1 transcription factor regulates.

Answer 39

AP-1 (activator protein 1) is a transcription factor belonging to c-Fos, c-Jun, ATF, and JDP families that regulate gene expression in response to cytokines, growth factors, stress, infections, differentiation, proliferation, apoptosis. Up regulates genes with thyroid hormone response element (TRE, a DNA sequence common to thyroid response elements) thus increasing response toTPA (phorbol acetate).

Question 40

How does cAMP coordinate gene regulation?

Answer 40

CREB (cAMP response element binding protein) a transcription factor binds binds DNA at CRE (cAMP response elements-a DNA sequence).