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Flashcards in BIOCHEM gen Deck (75):
1

How is protein kinase B activated by mTOR?

Protein kinase B (PKB, Akt-V-AKT murine thymoma viral oncogene homolog 3) is a serine/threonine-specific protein kinase, is phosphorylated at threonine 308 by PIP3 and phosphoinositide dependent kinase one (PDK1). MTORC2 then phosphorylates Akt1 at serine 473 producing activated Akt1 which then activates or deactivates multiple substrates.
Other pathways also activate Akt1 including non-receptor tyrosine kinase and cAMP via protein kinase A (PKA, cAMP dependent protein kinase) in the presence of insulin.

2

What is the difference between cytochrome C oxidase-complex 4, cytochrome b-C1, and cytochrome c?

Cyotchrome C oxidase is complex IV, a large integral mitochondrial membrane complex composed of 28 cytochrome subunits (COX-1 through 8) containing two hemes (cytochrome a and a3) and two copper centers using 14 assembly subunits.
Cytochrome b-C1 is Complex 3 and contains 11 subunits, 3 respiratory subunits, 2 core proteins, and 6 low molecular weight proteins. Reduced ubiquinol donates electrons to ferricytochrome c and ferrocytochrome c then passes them to complex 4.
Cytochrome c is a small protein, 100 aa, 17k daltons, with 1 heme unit that uses its Fe to shuttles electrons from Complex 3 to Complex 4.
COX can mean cytochrome oxidase or cyclo-ooxygenase, renamed PTGS (ProsTaGlandin Synthase).

3

What proteins are reduced by thioredoxin?

Thioredoxin is a 12-kD antioxidant protein with a C-X-XC motif, that reduces other proteins via cysteine thiol-disulfide exchange. Substrates include ribonuclease, choriogonadotropins, coagulation factors, glucocorticoid receptor, and insulin.

3

What is PTEN (phosphatase and tensin homologue)?

PTEN dephosphorylates phosphorylated tyrosine based signaling molecules which decreases rapid cellular division. It preferentially dephosphorylates phosphatidylinositol-3,4,5-triphosphate to PI(4,5) which prevents Akt phosphorylation. The C2 domain binds to phospholipid membranes thus bringing the active site close to membrane-bound PIP3.
PTEN acts as a tumor suppressor gene.
Mutations result in multiple harmartomas.

5

How does NADPH-oxidase (cytochrome b(-245)) work?

In the resting cell, NADPH oxidase is an enzyme complex on the cell membrane or phagosome containing Cytochrome b(-245), a heterodimer of p91-phox beta (phox for phagocyte oxidase) CYBB, and p22-phox alpha (CYBA) polypeptides. The 2 heme groups and FAD along with other essential cytosolic proteins p47-phox, p67-phox, p40-phox, a Rho GTPase-binding protein forms the oxidase complex which attracts NADPH (absorption band at 558 aka cytochrome b(558)).
NADPH transfers 2 electrons across membrane to 02 creating 2 H2O2 and 2 H+ into cytosol where it is transferred across membrane via proton channel to balance lost electron.
cytochrome c reductase is complex 3 and cytochrome c oxidase is complex 4.

6

What are oncogenes?

Oncogenes are homologs of normal cellular genes in which a mutational change results in constitutive activation and gain of function.

6

What type of channel binds Hepcidin?

Hepcidin is a 25 amino acid hormone derived from an 84 amino acid pro hormone by a pro hormone convertase (turin). It inhibits iron transport out of cells by binding to the iron exporter channel (ferroportin) of enterocytes and macrophages.
Increase causes anemia, mutations result in juvenile hemachromatosis.
Hemopexin with apolipoprotein E binds the lipoprotein receptor for F3 internalization.

8

how does NF-Kb work?

NF-Kb generates p50-relA dimer (after ikBa is phosphorylated and released that bind response elements where additional factors mediate inflammation.
NFkB activates transcription of exogenous retroviruses.

9

What is the peroxisome?

Peroxisomes are single membrane organelles drived from the endoplasmic reticulum that replicate by fission. Peroxisomal target signal at the C-terminus (PTS1) or N-terminus of a protein target it for peroxisome assembly. Peroxisomes are involved in long chain fatty acids catabolism, biosynthesis of plasmalogens (ether phospholipids), and 10% of pentose phosphate shunt enzyme activity.
Peroxisome contain oxidative enzymes-catalase, D amino acid oxidase, uric acid oxidase producing H2O2 (absent human). Peroxisomes oxidize about 25% of ingested ethanol.

10

What is the structural role muramyl dipeptide?

Muramyl dipeptide C19H32N4011 is a peptidoglycan constituent of both gram-positive and gram-negative bacteria.

10

What different types of blotting procedures are used to identify cellular molecules?

Southern blot uses known DNA and probes with DNA samples. Procedure named after Edwin Southern. A northern blot uses electrophoresis to separate cellular RNA, blots it onto nylon membrane, uses labeled RNA or DNA or oligonucleotide probes with at least 25 complementary bases to identify type of cellular RNA. A reverse northern plot uses isolated known DNA fragments on a membrane and probes with cellular RNA to develop an expression profile for that tissue.
A Western blot separates unknown protein by electrophoresis on nitrocellulose and probes with a known antibody. Far-Western blotting probes a Western blot w post translational modification with a non-antibody binding protein to detect protein-protein interaction. An Eastern blot probes proteins separated by electrophoresis (SDS-PAGE gel) for post-translational modification to detect lipids, carbohydrates, or phosphorylation. A Far-Eastern blotting (developed in Japan) uses (high-performance thin layer chromatography (HPTLC) to separate phospholipids which are then transferred to a membrane and probed by ligand binding or mass spectroscopy.

12

What are the 3 fiber types formed by actin?

Human actin contains more than 30 isoforms composing three different types of fibers. α-actin appears in contractile structures, β-actin at the expanding edge of cells, and γ-actin found in stress fibers. ACTA1 codes for the α-isoform, predominant in skeletal muscle. The monomeric form is called G-actin (Globular), and F-actin (filamentous) when polymeric. Actin fibers develop from double helix formation in the cytoskeleton due to ADP ATP binding. The most common forms are ATP-G-actin, and ADP-F-actin.

13

What is an ABC transporter?

ABC transporters are a transmembrane large protein (some >2100 aa) family (5 types, multiple members) that use their cytoplasmic ATP-binding cassette (ABC) domain, to transport ( metabolic products, lipids, steroids and drugs) or regulate (if loose transmembrane domain). Mutants act in mendelian or polygenetic manner as in cystic fibrosis, macular degeneration.

13

What enzyme does metformin activate to inhibit mTOR?

Metformin inhibits mTOR by activating AMPK (adenosine monophosphate-activated protein kinase). Activated AMP kinase inhibits fatty acid and protein synthesis, mitochondrial respiration, up regulates glycolysis, and autophagy.

14

What is an HCN channel (c=cyclic)?

Hyperpolarization-activated cyclic nucleotide-gated channel (pacemaker channel) is composed of multiple units of 6 membrane-spanning domains which includes a voltage sensing domain, a cation permeable channel and a cyclic nucleotide-binding domain (cAMP). 4 genes code for the subunit HCN1 through HCN4(variable sensitivity to cAMP) which are expressed primarily in the heart and central nervous system-pacemaker cells.

15

How does smooth muscle contract?

Contraction is initiated by a calcium-regulated phosphorylation of myosin, rather than a calcium-activated troponin system. Myosin-actin filaments are attached to dense bodies anchored to intermediate filaments producing linear contracting series.
Smooth muscle contraction starts with calcium entry via ligand gated and voltage-gated slow calcium channels. Calcium pumps, sodium/calcium exchangers, and sodium potassium exchangers are active.

16

What is special about pannexin transmembrane channels?

Pannexin is the transmembrane 426 aa protein responsible for gap junctions and hemi channels between intracellular and extracellular space allowing passage of ca ions and small molecules such as ATP. ATP then ligates the P2X7 purinergic receptor (ligand gated ion channel, 595 aa) leading to the release of IL-1 beta, IL-6, and TNFalpha.

17

What is the function of caveolae in smooth muscle?

Caveolae are microdomains of lipid rafts on cell membranes specialized for cell signaling events and ion channels. Receptors include prostacyclin, endothelin, serotonin, muscarinic receptors, adrenergic receptors, second messenger generators (adenylate cyclase, phospholipase C), G proteins, kinases (protein kinase C, protein kinase a) and ion channels (L-type calcium channels, ATP sensitive potassium channels, calcium sensitive potassium channels).

18

What are Cadherins?

Cadherins are cell membrane 720 aa proteins (>100 types) with large N-terminal extra cytoplasmic domains which are important in cell adhesion. Adhesion is calcium dependent with a small intracellular C-terminal. Cadherin 11 is increased in the skin in scleroderma.

19

What do P2Y. purinergic G protein-coupled, ( x-ligand gated) receptors do?

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.

20

What are Cadherins?

Cadherins are cell membrane 720 aa proteins (>100 types) with large N-terminal extra cytoplasmic domains which are important in cell adhesion. Adhesion is calcium dependent with a small intracellular C-terminal.
Cadherins cross link cell membranes at adherins junctions. Viculins and catenins hold actin filaments to the intracellular portions of the cadherins.
Cadherin 11 is increased in the skin in scleroderma.

21

What is the structure of the T tubule link to the sarcoplasmic reticulum?

The sarcolemma T Tubule contains the calcium channel dihydro-pyridine receptor (Cav1.1, Calcium channel, voltage-dependent, L type, alpha 1S subunit, CACNA1S) with a calcium channel alpha-delta subunit. This attaches to the ryanodyne receptor (Ry 1) on the sarcoplasmic reticulum. Calsequestrin and triadin associate with the rynodyne receptor holds 80 Ca++/mol. MTOR(FK506, FKBP12) and calmodulin associate with the myoplasmic portion of the ryanodine receptor.

22

How does elevated calcium levels in the sarcoplasm result in muscle contraction?

High levels of calcium within the sarcoplasm cause troponin C to unblock myosin binding to actin filament. This results in ADP and inorganic phosphate in the myosin head to leave the myosin head which binds and flexes moving up the axin filament. ATP binds, myosin head releases, myosin hydrolyses the ATP, the head moves up again as long as calcium is there.

23

What is the result of ROS generation by NADPH Oxidase?

ROS kills bacteria and fungi by inactivating critical metabolic enzymes, initiating lipid peroxidation, or liberating redox-reactive iron which then produces indiscriminate oxidants. SOD (Superoxide dismutase) destroys ROS and inhibiting SOD increases ROS effectiveness.

24

What does the C2 domain of a cytosolic protein do?

A C2 domain of a protein targets it to the cell membrane by an 8 β strand structure. 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.

25

What is tensin?

Tensin is a 220 kda multi-domain protein that links integrin heterodimers to the plasma membrane, binds to actin filaments, and contains a phosphoserine binding domain. It is an important component linking the extracellular membrane, actin cytoskeleton, and signal transduction.

26

What does the term PHOX mean when associated with a protein?

Phosphinooxazolines (PHOX) are a class of reactive chiral ligands and are components of NADPH oxidase. The composition of the enzyme varies with phagocytic cells (GP 91 PHOX), and non-phagocytic cells (Nox family). In both cases reactive oxygen species are formed and NADPH becomes NADP+.

27

What is the difference between alpha one micro globulin and beta-2 microglobulin?

Alpha one microglobulin (A1M) is a 183 amino acid protein shaped as a basket that binds and the degrades heme, an oxidizing agent and free radical generator. Beta-2 microglobulin (B2M) is a 99 amino acid protein associated with HLA class I.

27

What is transglutaminase?

Transglutaminase has an SH bond that reacts with free amine groups (protein or peptide bound lysine) which releases NH3, and forms an protein-C=0(acyl)-S-enzyme bond. Then another free amide group replaces the S-enz bond, thereby connecting two large proteins and releasing the enzyme. P1-C=0 -N-P2 This reaction characterizes factor 13 stabilization of fibrin clots, and plays a role in skin and gut permeability.Nine human genes code for various transglutaminases.

27

What does the mevalonic pathway do?

The mevalonic pathway is important in the production of dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP) which are important in terpanoid synthesis, protein prenylation, cell membrane maintenance, hormones, routine anchoring, and N-glycosylation.

29

What metabolic defect in substrate utilization can affect the electron transport chain to increase reactive oxygen species production?

Any defect that decreases the concentration of mitochondrial matrix NADPH will result in excess of direct oxidation at complex 1, and 3 with increased production of reactive oxygen species.

31

What is Hemopexin?

Hemopexin is a beta-1B-glycoprotein that that binds heme, preventing ROS formation.
The low-density lipoprotein receptor-related protein 1 (LRP1, CD 91) is a receptor for apolipoprotein E and hemopexin resulting in receptor mediated endocytosis and iron transport.
Dysfunction results in Alzheimer' s disease, and atherosclerosis via the macrophage receptor.
Haptoglobin also binds heme and both are decreased (consumed during intravascular hemolysis).

32

define oxidation.

The substances that to be oxidized if it loses electrons and increases its oxidative state. An oxidizing agent easily removes electrons from other atoms thus increasing their oxidative state. Oxygen is an oxidizing agent because it is easily reduced by gaining electrons and becoming water.
Leo the lion goes ger. Leo=loss of electrons means oxidation, ger=gain of electrons means reduction.

33

What sort of protein is growth differentiation factor II?

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

34

How is tryptophan (C11H12N2O2) related to NAD?

Tryptophan is metabolized to kynurenine (C10H12N2O3) by tryptophan dioxygenase, an important step on the way to the synthesis of NAD (nicotinamide adenine dinucleotide).

34

What is the role of kynurenine in the immune response?

Kynurenine (C10H12N203) is produced by indoleamine 2,3-dioxygenase from tryptophan. Dependent biological functions include dilating blood vessels during inflammation, and regulating the immune response.
Synthetic L-Kyn in coculture of bone marrow-derived dendritic cells skews the differentiation of T cells to Treg cells rather than Th17 cells. Formation depletes tryptophan stores which depress growth of T cells and bacteria.

35

What is Klotho?

Klotho is a glucouronidase that modifies the FGF23 receptor (FGFR1(IIIc)), so that FGF23 signaling can affect Na+,K+ ATPase, restore parathyroid sensitivity and affect calcium metabolism. Klotho can be released from the plasma membrane by ADAM10 and ADAM17.
Klotho is related to longevity possibly by decreasing vitamin D levels by affecting the function of the TRPV5 calcium channel. Overexpression of klotho is associated with longevity (mice 25% increase) and is associated with increased cognition in human populations. Klotho-deficient mice show increased production of vitamin D and premature aging which is reversed by vitamin D deficiency.

36

What is the role of FGF23 in kidney function?

Fibroblast growth factor-23 (FGF-23) is released by bone in response to calcitriol and binds to FGF23R bound to klotho. It decreases the expression of a sodium-phosphate cotransporter thus decreasing phosphate reabsorption by the kidneys. It also causes decreased calcitriol synthesis. Gain of function mutation in FGF 23 (resists proteolytic cleavage) results in autosomal dominant hypophosphatemic rickets, loss of function leads to familial tumor calcinosis.

37

What ligates the dectin 1 receptor?

Dectin 1 is a C-type lectin with a carbohydrate binding extracellular motif and a cytoplasmic tyrosine-based activation motif. It recognizes fungi and is expressed on macrophages, neutrophils and dendritic cells. It is a costimulatory molecule for CD4 and CD8 T cells.
made from CLEC7A gene (C type LECtin).

38

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

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.

39

How does the transcription factor Gata1 affect erythropoiesis and thrombopoiesis?

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.

40

What factors bind to Ras and alter its GTPase activity?

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.

41

What sort of calcium channel is TRPV5?

TRPV5 is the transient receptor potential cation channel subfamily V expressed mainly on kidney epithelial cells for calcium reabsorption. It has six transmembrane-spanning domains with multiple phosphorylation and glycosylation sites. Activity is increased by klotho. TRPC6 (transient receptor potential cation channel, subfamily C, member 6) is activated by St. John's wort and decreased by klotho.

42

What is vascular endothelial growth factor?

Vascular endothelial growth factor gene has 8 exons and produces multiple factors of varying amino acid length - 121 to 206. VEGF Tyrosine kinase receptors come in three 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.

44

How big are microfilaments?

Microfilaments (actin) are 7 nm wide. intermediate filaments (proteins with alpha-helical rod domain) are 10 nanometers.
Myosin filaments are several hundred molecules thick, about 15 nm in diameter.
Microtubules are 25 nm wide.

45

What are some members of the Ras superfamily of proteins, and what do they do?

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.
Receptor tyrosine kinases are a form of enzyme-linked receptors that activate Ras once phosphorylated by ligand binding.
Members include:
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,
Rag RRAGA gene,Adenosine diphosphate ribosylation factor-1 GTPase ( member of the Arf small GTPase binding proteins of the Ras superfamily) is required for mTOR activation and lysosome localization by glutamine.
Rheb activates mTORC1 kinase, and displays guanine nucleotide exchange activity.
Miro controls mitochondrial transport.

46

How does mTORC1 increase production of reactive oxygen species?

mTORC1 increases cytosolic glycolysis and decreases oxidative phosphorylation thus lowering O2 demand and allowing excess O2 to form reactive oxygen species.

47

What are some of the structural components of smooth muscle cells?

Dense bodies in smooth muscle are composed of alpha-actinin attached to actin filaments along with vimentin and desmin.
Multiple integrens in the cell membrane (attached to extracellular molecules) are attached to Talin which support multiple vinculin attachments which when activated binds F actin.
Actinin is a micro filament protein dimer necessary for the attachment of actin filaments to Z line.
Contractile actin is attached to adherens junctions along with vinculin and cytoskeletal actin.
Vimentin, a 455 aa helical protein monomer forms a coiled coil dimer to produce intermediate filaments particularly in mesenchymal cells. Used to anchor organelles within the cytosol
desmin is a 52 kDa protein expressed only in vertebrates to form intermediate type III filaments near the Z line in sarcomeres.
vinculin is a 117 kDa protein with 1066 amino acids that binds to talin and alpha actinin to form cell-cell and cell-matrix junctions. It also has binding sites for F-actin, paxillin, and lipids.
Smooth muscle myosin fiber consists of two myosin chains (MYH11 gene).

48

How are purinoceptors originally P1 and P2 currently defined?

P1 receptors are G protein-coupled adenosine receptors, and P2 are divided into P2X and P2Y. P2Y receptors are also G protein coupled and respond to other nucleotides including ATP, ADP, UTP, UDP, and UDP-glucose. P2X receptors are ligand-gated ion channels respond to ATP.
The P2X receptor is made of multiple subunits consisting of two transmembranous portions, an external loop and intracellular C terminus. The complex is activated by ATP and often serves as a calcium channel provoking smooth muscle contraction-bladder, vas deferens, heart muscle.
The P1 adenosine receptors are divided into A1 (ADORA1 gene) is inhibitory decreasing heart rate. The A2A adenosine receptor (ADORA2A) is stimulatory increasing cAMP, coronary dilatation. The A2B receptor (ADORA2B) is stimulatory resulting in bronchospasm and the A3 receptor (ADORA3) is inhibitory causing cardiac muscle relaxation and inhibition of neutrophil degranulation.

49

What are some of the structural components of smooth muscle cells?

Dense bodies in smooth muscle are composed of alpha-actinin attached to actin filaments along with vimentin and desmin.
Multiple integrens in the cell membrane (attached to extracellular molecules) are attached to Talin which support multiple vinculin attachments which when activated binds F actin.
Actinin is a micro filament protein necessary for the attachment of actin filaments
Contractile actin is attached to adherens junctions along with vinculin and cytoskeletal actin.
Vimentin, a 455 aa helical protein monomer forms a coiled coil dimer to produce intermediate filaments particularly in mesenchymal cells.
Desmin (52 kDa) is used to anchor organelles within the cytosol and forms intermediate type III filaments near the Z line in the sarcomeres of vertebrates.
vinculin is a 117 kDa protein with 1066 amino acids that binds to talin and alpha actinin to form cell-cell and cell-matrix junctions. It also has binding sites for F-actin, paxillin, and lipids.
Paxcillin is a 76 kD protein with multiple binding sites especially the cytoplasmic tail of beta integrin, tyrosine kinases, including focal adhesion kinase (F AK).

51

How do tuberous sclerosis proteins affect mTOR?

TSC2 (tuberin, tuberous sclerosis 2) is a peripheral membrane protein that combines with TSC1 (hamartin, peripheral membrane protein) in cells to become a cytosolic dimer, a GTPase activating protein (GAP) that inhibits rheb (RAS homolog enriched in brain) GTPase by dephosphorylatiion. Otherwise Rag C/D binds GTP ->Rag A/B, attracts mTOR->mTORC1.
The TSC1/TSC2 heterodimer is a sensitive to upstream signals (Akt) that result in increased or decreased mTOR activation and can function as a tumor suppression gene when dimerized.

52

What subunits comprise the heterotrimeric G protein of the G protein coupled receptor?

The heterotrimeric G protein has an alpha subunit ~354 aa which in the resting state binds GDP and beta-gamma complex. There are 4 families of G alpha subunits based on sequence homology. Gi family inhibit adenylate cyclase or activate phosphodiesterase. Gs family activate adenylate cyclase, Gq family activate phospholipase C, and the G12/13 family activate the Rho family of GTPases. The G beta gamma complex can attach to ligand gated ion channels (G protein-coupled inward rectifying potassium channels) or L-type calcium channels, or bind to histamine receptors and activate phospholipase A2

53

How are G protein coupled receptors turned off?

Homologous desensitization of activated GPCR refers to down regulation by the receptor, and heterologous desensitization refers to down regulation by a different receptor via phosphorylation of the intracellular receptor domain. In the case of adenylate cyclase, the activated protein kinase A phosphorylates the adenylate cyclase which then stops working.
G protein-coupled receptor kinases (GRKs) phosphorylate active GPCRs (PKA, PKC) according to receptor domains, G protein subunits, lipids, anchoring proteins, and calcium sensitive proteins. This may result in endocytosis with recycling or destruction of the receptor, or arrestin binding and ciathrin-mediated endocytosis.

54

What subunits comprise the heterotrimeric G protein of the G protein coupled receptor?

Heterotrimeric G protein receptors have an alpha subunit ~354 aa which in the resting state binds GDP and beta-gamma complex. There are 4 families of G alpha subunits based on sequence homology. Gi family inhibit adenylate cyclase or activate phosphodiesterase. Gs family activate adenylate cyclase, Gq family activate phospholipase C, and the G12/13 family activate the Rho family of GTPases. The G beta gamma complex can attach to ligand gated ion channels (G protein-coupled inward rectifying potassium channels) or L-type calcium channels, or bind to histamine receptors and activate phospholipase A2

54

How are G protein coupled receptors turned off?

Homologous desensitization of activated GPCR refers to down regulation by the receptor, and heterologous desensitization refers to down regulation by a different receptor via phosphorylation of the intracellular receptor domain. In the case of adenylate cyclase, the activated protein kinase A phosphorylates the adenylate cyclase which then stops working.
G protein-coupled receptor kinases (GRKs) phosphorylate active GPCRs according to receptor domains, G protein subunits, lipids, anchoring proteins, and calcium sensitive proteins. This may result in endocytosis with recycling or destruction of the receptor, or arrestin binding and ciathrin-mediated endocytosis.

55

What are small GTPases?

Small GTPases are G proteins found in the cytosol that are homologous to the alpha subunit of heterotrimeric G-proteins, ~700 aa, that function independently to hydrolyze GTP to GDP. Guanosine nucleotide dissociation inhibitors (GDI) maintain small GTPases in the inactive state.

57

How are small GTPases turned off?

Guanine nucleotide exchange factors (GEF) activate GTPase by exchanging GDP for GTP. GTPase activating proteins (GAPs) increase the intrinsic rate of GTP hydrolysis, releasing phosphate group not phosphorylising. The GDP is then released slowly unless exchanged by a GEF.

58

What is the ligand that opens the P2X cation permeable ion channel.

P2X cell membrane receptors ( x-ligand gated, y-g protein coupled) are cation-permeable ion channels (trimers of 2 transmembrane subunits with intracytoplasmic n and c terminals) that open in response to ATP.They are important in cardiac rhythm and contractility, vascular tone, nociception and chronic pain, contraction of urinary bladder, platelet aggregation, macrophage activation, apoptosis, and neuronal-glial integration.
Pannexin is a much larger channel that permits ATP transmembrane transport.

59

How many functional types of cell membrane surface proteins are there?

Membrane proteins may function as:
1) membrane receptors- ion channel-linked receptors, enzyme linked receptors, G protein coupled receptors
2) transport proteins channel/pores, electrochemical potential driven transporters, primary active transporters, group transporters, transport electron carriers
3)membrane enzymes-oxido/reductase, transferase, hydrolase
4) cell adhesion molecules.

60

How many types of enzyme linked receptors are there?

Enzyme-linked receptors include the enzymes:
tyrosine kinase, tyrosine kinase associated receptors, receptor like tyrosine phosphatase, receptors serine/threonine kinases, type 1 guanylyl cyclases (type 2 are soluble) and histidine kinase associated receptors (uses ATP to phosphorlylate aspartate residues).
Tyrosine kinase receptors are the largest group responding to growth factors. Most of these receptors dimerize with their ligands in order to activate further signal transduction.

61

What are the phospholipase is A-C in the fossil kinases A-C?

Phospholipase A1 catalyzes the cleavage of the sn-1 position of phospholipids, forming a fatty acid and a lysphospholipid. Phospholipase A2 cleaves the SN-2 position. Phospholipase B can cleave both the SN-1 and SN-2 positions.Phospholipase C catalyzes the cleavage of I3P.
Phosphokinase A does not exist, phosphokinase be is a KT and phosphokinase C is a serine/threonine kinase activated by binding to diacylglycerol.

62

What is the role of FGF23 in kidney function?

Fibroblast growth factor-23 (FGF-23) is released by bone in response to calcitriol and acts to decrease the expression of a sodium-phosphate cotransporter thus decreasing phosphate reabsorption by the kidneys. It also causes decreased calcitriol synthesis. Loss of function mutation in FGF 23 results in autosomal dominant hypophosphatemic ricketts

63

What genes control mitochondrial replication?

Replication of mitochondrial DNA is controlled by nuclear respiratory factor (NRF)-1/NRF-2 and mitochondrial transcription factor A (Tfam).

64

What is the difference between mTORC1 and mTORC2?

mTORC1 is the nutrient/energy/redox sensor which is stimulated by insulin, growth factors, serum, amino acids, and oxidative stress.
mTORC2 is an important regulator of cytoskeleton, F-actin stress fibers, protein kinase C and Akt phosphorylation. Additional phosphorylation of Akt by PDK-1 (phosphoinositide-dependent kinase one).

65

How does mTORC1 inhibit autophagy?

Activated mTORC1 phosphorylates Atg 13 (autophagy related protein 13) which prevents autophagosome construction at the plasma membrane.

66

What is a tetratricopeptide repeat (TPR) ?

the tetratricopeptide repeat is a structural motive of 34 amino acids forming scaffolds to mediate protein protein interactions. They form 3-16 motifs that fold together and in a linear solenoid domain called TPR domain.

67

How many types of phosphoinosotide-3-kinase are there?

The phosphoinositide-3-kinase family consists of four classes:
class I responsible for PI(3)P , (PI (3, 4,) P 2), and (PI (3, 4, 5,) P3), which are activated by G protein-coupled receptors and tyrosine kinase receptors.
Class 2 probably binds calcium in a non-aspartate residue
class III or similar to class I and structure but have two units one catalytic and one regulatory
class IV are more distantly related closer to ataxia telangiectasia mutated and are protein serine/threonine kinases.

68

What 3 proteins make up the cytoplasmic NFkB complex?

Cytoplasmic NFkB consists of a heterodimer p50 and Rel held together by IkB

69

What is the function of the following motifs-RGS, DEP, PDZ, PTB, RBD, PX, pH, PX, CGL?

RGS domain promotes GTP hydrolysis by the elf a subunit of hetrotrimeric G proteins thereby inactivating and switching off G protein-coupled receptor signaling.
DEP domain targets membranes.
PDZ domains bind GPCRs (G protein coupled receptors).
PTB domains bind phospho tyrosine.
RBD domains bind Ras.
PX for phosphoinositides-binding.
PH for phosphatydlinisitol binding.
PXA associated with PX.
CGL (G protein gamma subunit-like) or binding G protein beta subunits.

70

How do G protein coupled receptors work? I

G protein coupled receptors act as G protein activating factors (GAP) where in guanine nucleotide-binding proteins change from GDP to GTP permitting them to participate in signaling. They spontaneously hydrolyze to GDP. The binding of G protein to their G protein coupled receptor can be modified by phosphorylation of serine/threonine sites near the carboxy terminal intracellular domain. PKC and PKA may participate.
There are hetrotrimeric G proteins (large, alpha, beta, gamma subunits) and small G proteins (small GTPases).

71

What is the function of CBS domains in AMPK (5' AMP-activated protein kinase)?

5' AMP-activated protein kinase (AMPK) is a heterotrimeric protein with alpha beta and gamma subunits coded by seven genes. The gamma subunit contains 4 CBS domains (cystathionine beta synthase) forming to Bateman domains that bind AMP. This enzyme regulates intracellular systems-glucose uptake, Beta-oxidation of fatty acids, GLUT4 synthesis, and mitochondria synthesis by sensing AMP: ATP ratio. Inhibition of energy consuming pathways also occurs-fatty acid synthesis, protein synthesis.

72

How does AMPK affect cholesterol synthesis?

AMPK is a cofactor in the synthesis of cholesterol and fatty acids. Fatty acid synthesis requires cAMP-dependent protein kinase as well, in order for acetyl CoA carboxylase to be inactivated by phosphorylation, and inhibit acetyl CoA->malonyl CoA. AMPK is a cofactor in the reversible phosphorylation of HMG CoA (3-hydroxy-3-methylglutaryl-CoA) reductase which makes it inactive. HMG CoA combines 2x 5C mevalonic acid to make the 10C Geranyl, 15 C farnesyl, 30C squalene and eventually the 27C cholesterol.

73

What is the role of IQGAP1 in cytoskeletal structure?

IQGAP1 (ras GTPase-activating-like protein) is a scaffold protein which organizes the actin cytoskeleton, transcription, and cellular adhesion during the cell cycle. It is found in the nucleus, plasma membrane, and cytoplasm in all tissue types.
E-cadherin is a transmembrane protein that binds to beta catenin in the cytosol, then beta binds to alpha catenin and the whole complex thereafter to actin. When E-cadheriin binds to adjacent cell E-cadherin , beta-catenin associates with IQGAP1. Strong adhesion develops when Actin associates with Rac/Ccd42, GDP, and Rho GDI

74

What is vitamin C and how does it work?

Vitamin C is ascorbic acid, a reducing agent that protects cells from ROS. It is a cofactor and procollagen maturation performing hydroxylation which permits triple helix formation.
Peptidases are than necessary to make the procollagen into mature fibrils, When absent results in Earlos Danlos syndrome.

75

Name the short chain dicarboxylic acids.

Pyruvic acid is 2-oxoprapanoic acid
oxalic acid is ethanedioic acid C 2
malonic acid is propanedioic acid C 3
Succinic Acid Is butanedioic acid C 4