BIOCHEM gen Flashcards
emphasis on reactions supporting immune activity
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.
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).
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.
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.
PTEN is ubinquinated by WWP1 (WW containing E3 ubiquitin -protein ligase1). WWP1 can be inhibited by indole 3-carbinol an extract of broccoli, which then preserves PTEN thus improving tumor suppression.
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.
What are oncogenes?
Oncogenes are homologs of normal cellular genes in which a mutational change results in constitutive activation and gain of function.
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.
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.
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.
What is the structural role muramyl dipeptide?
Muramyl dipeptide C19H32N4011 is a peptidoglycan constituent of both gram-positive and gram-negative bacteria.
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.
A far-Western blot 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 blot (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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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+.
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.
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.
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.
