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95 Cards in this Set
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- Back
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methylmalonic aciduria
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deficiency in methylmalonic coA mutase which results in excess methylmalonic acid, autosomal recessive, coA is derived from vitamin B.
methylmalonyl coA normally gets converted into succinate |
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efficient enzymes for all biochemical reactions
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most go on the order of 10^11 to 10^18
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exopeptidases
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cleave terminal amino acid residues
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enzymes
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contain an active site, active site contains residues that have specific interactions,
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serine proteases
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enzymes that include proteolytic enzymes, blood coagulation, immune response cell differentiation
have a catalytic triad: serine, histidine, and aspartate, this allows serine to become an alkoxide at neutral pH binding is specific, has specificity pockets |
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mechanism of serine protease
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1. Substrate bound in correct orientation
2. Attack by alkoxide of serine 3. Transition state stabilization by hydrogen bonds 4. Acyl enzyme intermediate formed and C-terminal peptide formed 5. Attack by a water 6. Transition state stablization 7. Other half of peptide (N-terminal peptide) NOTE: enzyme is regenerated at the end NOTE: they are endopeptidases |
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chymotrypsin
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serine protease that best exemplifies lock and key model
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lysozyme
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induced fit model, cleaves polysaccharide backbone, acid hydrolysis
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enzyme velocity
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change in product over change in time
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michaelis menten kinetics application
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V=Vmax[S]/ (Km+[S])
not esential for the enzyme to be pure equation allows for calculation for proper substrate range Km is characteristic fo rthe enzyme |
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kcat
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can be measured when the enzyme is saturated with substrate, requires normally a purified enzyme or a known amount of enzyme present
vmax=kcat[Et] |
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Enzymes in blood plasma
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presence of elevated enzyme activity in blood plasma may indicate tissue damage
Enzymes are compartamentalized EX: creatine kinase (CK2) post myocardial infarction alkaline phosphatase in blood (should be in bone) |
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An enzyme can have...
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more than one substrate
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two defects in methylmalonic aciduria
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deficient enzyme or not enough B12
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example of control of enzyme activity
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ethylene glycol poisoning, ethylene glycol gets utilized by alcohol dehydrogenase which results in glycoaldehyde and a lot of metabolic nasties, can inhibit enzyme using intoxicating amounts of ethanol
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enzymes are regulated by
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1. changes in protein concentration
2. changes in intrinsic activity of enzymes (phosphorylation, zymogen granules) 3. changes in substrate concentration, sometimes the product, or the inhibitor |
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pH and temperature
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can really inhibit enzyme activity at extreme pH and temperature
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Zymogens
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active site residues are out of sync until a proteolysis results in proper arrangement of a.a.'s
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blood clotting cascade
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inactive forms of prothrombin and thrombin, cascade, prothrombin is cleaved to make thrombin, thrombin makes fibrinogen to fibrin, which aids in clotting by forming cross linking
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prothrombin
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has two domains, left domain has no activity, right one has activity! two clips make thrombin!
Has y carboxylation that allows for Ca2+ ions to bind so that it can bind to the membrane, vitamin K works with gamma carboxylase |
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thrombin
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is an active serine protease, need to have ile16 in the right position, it is made on a membrane surface
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warfarin
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is a vitamin K analagoue that inhibits gamma carboxylase thus acting as an anti-clotting drug
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example of irreversible inhibitors
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antithrombin, trypsin inhibitor
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inhibition of elastase in lung tissue
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alpha 1 antitrypsin does this, deficiency in alpha 1 antitrypsin can result in lung damage because lack of inhibition of elastase from neutrophils
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smoking
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smoking can cause oxidation of alpha anti-1 tryspin, leading to emphysema!
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which residues are frequently phosphorylated
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serine, threonine, tyrosine, can affect enzyme activity if these residues are near to an active site!
Phosphorylation in activation loops can drastically change activity |
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protein phosphatase
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removes phosphates
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protein kinase
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adds phosphate groups
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inhibitors of enzyme activity
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competitive inhibitors
non-competitive inhibitors irreversible inhibitors |
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DIFP
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irreversible inhibitor that covalently binds and doesn't allow serine protease to work
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competitive inhibitors
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resemble the substrate and then don't allow substrate to bind to the active site, they increase the Km without affecting the Vmax
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non-competitive inhibitors
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bind to something elsewhere on the active site (can be reversible or irreversible)
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antithrombin
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another example of an irreversible inhibitor
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uncompetitive inhibition
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lowers Km and Vmax
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mixed inhibition
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lowers Vmax and increases Km
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allosteric enzymes
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contain multiple subunits
don't follow michaelis menten kinetics, have binding sites for affector molecules, generally more regulatory |
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ATCase
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classic example of an allosteric enzyme, CTP acts as a negative allosteric effector whereas ATP acts as a positive allosteric effector
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bioenergetics
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process of making and breaking chemical bonds in a molecule
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catabolism
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involves breakdown to make ATP
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anabolism
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use ATP to make for biosynthetic work, mechanical work etc
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free energy
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arbitrary term to help define energy changes, DG=DH-TDS, delta S is related to changes in concentration
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delta g is sensitve
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to changes in products and reactants
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equation
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delta G=G+RTlnQ
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reactions are reversible
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they result in a change in the sign of the reaction
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activation barrier
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all reactions have a reaction barrier, stabilization by a catalyst lowers the energy transition state, catalyst, does not alter equilibrium
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enzyme is optimized
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for also binding to the transition state, not only the substrate!
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reactions in the body
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not at equilibrium (except for death)
reaction can be driven by removing product concentration |
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E2F
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Needed for transcription of RNA for proteins required for synthesis and cell growth, normally sequestered by pRB protein
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pRB
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when not phosphorylated, sequesters E2F so that it can't allow transcription to occur, however when it is phosphorylated by cyclin/cdk complex (D or E cyclin) it allows cell cycle to occur because pRB protein dissociates from E2F
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pRB mutant
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regulation of E2F is lost and cell replication and growth is unregulated
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role of p53 in halting DNA damage and apoptosis
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DNA damage results in p53 (which can lead to apoptosis), p21, and then inhibition of Cyclin/Cdk complex
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p53 phosphorylation
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p53 is a substrate for phosphorylation of many events, this allows it to stabilize!
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genes regulated by p53 have...
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response elements that act on them
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p21
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binds to cyclin/Cdk complex and also to PCNA to inhibit growth
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p53 absence
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doesn't allow for p21 induction, resulting in lack of inhibition,
also results in a lack of apoptosis |
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tumor supressors and actions
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RB: retinoblastoma
p53: sarcomas, carcinomas, NF-1: neuroblastoma APC: colon and stomach |
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proto-oncogenes
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genes that if mutated, can have implications for cancer, proto-oncogenes code for proteins involved in cell signaling or in cell growth checkpoints
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tumor signaling
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many tumors just keep on generating their own signals, allowing for continuous growth
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signal transduction
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certain receptors penetrate the plasma membrane and have receptor activity, phosphorylation of tyr residues allow other molecules to be active
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alterations in signal transduction linked to cancers
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excess growth factor
defective growth factor receptors defective signaling molecules altered regulation of transcription factors |
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Ras
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responsible in part of signal transduction pathway, ras gets activated by GTP, if it can't go back to GDP it becomes constantly active, problem!!!
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NF-1 and neurofibromin
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NF-1 encodes neurofibromin, NFbmin contains a GAP domain, associated with a defective ras protein
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overexpression of c-fos and c-jun
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c-myc and c-jun (AP-1) overexpression leads to cancer
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myc gene
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encodes a transcription factor that affects 15% of all genes
it binds to enhancer sequences and recruits histone acetyltransferases |
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burkitt's lymphoma
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chromosome 8 and c-myc can lead to constitutive expression of c-myc
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cyclin deregulation
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can lead to malignancies
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viruses causing cancer
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SV-40 can sequester RB and p53, resulting in cell transcription factor still working
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HPV
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has multiple domains that affect multiple sites for cancer
E6: proteolysis of p53, E7: protein product capable of binding RB! |
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FAP
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loss of APC gene and loss of other genes and mutations results in a dangerous cancer
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how do we control glucose after meal?
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B islet cells release insulin which stimulates glucose uptake
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insulin travels through bloodstream
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binds to receptors on muscle and blood cells and involves a bunch of intermediates that result in receptor translocation
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general overview of signal transduction
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primary stimuli (growth factors)
receptors second messengers cascade enzymes and adaptors outputs |
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signaling pathways
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intracrine: within the cell
paracrine: nearby cell autocrine: secreted by cell and acting on the same cell it secreted endocrine: chemicals that travel through bloodstream to affect other cells neuroendocrine: secreted by neuronal cells through blood |
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catecholamines
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time course: seconds
time course: one second receptors: plasma membrane change in membrane potential or second messenger |
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peptides/proteins
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time: minutes/hours
receptors on plasma membrane trigger 2nd messengers or kinases |
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steroids
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time: hours or days
receptors: cytoplasm or nucleus regulate RNA transcription or stability |
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adenylate cyclase cascade
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receptor-G-protein, adenylate cyclase, cAMP, protein kinase A, phosphorylation of enzymes.
G alpha with GTP gets dissociated from beta and gamma subunit and get associated with adenylate cyclase |
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adenylate cyclase
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ATP changes to AMP
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phosphodiesterase
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degrades cAMP
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cAMP activates
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protein Kinase A
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protein kinase A
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regulates both glycogen breakdown and synthesis, phosphorylation of glycogen phosphorylase by PKA modulates its activity
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cAMP different effects in different cells
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glycogenolysis in liver cells
relaxation in muscle cells, different cells have different substrates for PKA! |
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cholera
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toxin binds to alpha subunit, making it continuously active (ADP ribosylation), causes block in Na+ transport resulting in continuous Cl- and water transport into lumen
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Gq signaling pathway
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agonist binds, alpha binds to GTP, alpha GTP binds to Phospholipase C which cleaves PIP2 to IP3 and DAG
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IP3
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causes calcium release and NOS or protein kinases are activated,
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calcium release
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calcium functions through calmodulin, which is a protein modulator, can affect Cam dependent Kinase or NOS proteins
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neural signals and vasodilation
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acetylcholine causes release of Ca2+ which binds to calmodulin in endothelial cells affects NO synthase resulting in NO release, causing vasodilation by action on guanylate cyclase, which produces cGMP, viagra works through this way
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tyrosine kinase receptors
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extracellular hormone binding leads to activation of intracellular protein kinase, phosphorylates targets on tyrosine, receptors themselves are kinases,
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mechanism of tyrosine kinase function
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ligand receptor dimerization
cross phosphorylation major substrate is receptor itself |
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receptor phosphorylation results in recruitment of proteins
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SH2 domains of proteins bind to phosphorylated proteins (C-terminal to pTYR),
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ras pathway
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insulin binds to tyrosine receptor, it dimerizes, cross phosphorylation, IRS particle comes in and gets phosphorylated and then binds to GRB2
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GRB2
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has SH2 (IRS-1) and SH3 domains (SOS)
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SOS
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guanine nucleotide exchange factor converts Ras GDP to Ras GTP
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phosphoinositide 3 pathway
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insulin binds to receptor, receptor dimerizes, receptor gets phosphorylated activates p85 and p110 and then it creates PIP3 which activates Pdk, Rac, and AKT which allows for transcription factors
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steroid hormone receptors
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hormone binds to a specific receptor in cytoplasm-conformational change and moves to the nucleus to affect targeted genes
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