| Physiology•Biochemistry |
■Physiology ☉Poiseuille law: R=8ηL/πr4 ☉Chemoreceptor PaO2: peripheral: carotid body, aortic arch PaCO2: central: medulla pH: carotid body ☉Autoregulation: cerebral blood flow sensitive to PaCO2 coronary blood flow sensitive to PaO2 ☉O2 dissocation curve right shift: ↑↑CO2, 2-3-DPG, H+ ☉Apneustic center:長吸中樞（破壞後，呼吸變淺快） pH下降無法刺激呼吸中樞，因為H不過BBB ☉Respiratory quotient: CHO > Protein > Lipid ☉Pulmonary distribution PCO2: top< bottom PO2: top> bottom V/Q ratio: Top> bottom ☉Cell growth Angiogenesis: a/bFGF, VEGF TGFb: firogenesis, inhibitory to epithelial cells ☉Ccr > Cin = GFR (125 ml/min) > Curea Filtration fraction= GFR/RPF=1/4 CO只受efferent arteriole影響 Autoregulation則受afferent arteriole影響 ☉"U wave" not usually present; it could represent repolarization of the "Purkinje fibers" at the "far end" of the ventricular nerves. ☉Myoelectric Complex, Migrating Bursts of depolarization that move from the stomach to the ileocecal valve at regular frequency during the interdigestive period. The complex and its accompanying motor activity periodically cleanse the bowel of interdigestive secretion and debris in preparation for the next meal. ☉insulin-like growth factors (IGF's) polypeptides with high sequence similarity to insulin. They can trigger the same cellular responses as insulin, including mitogenesis in cell culture. IGF-II is thought to be a primary growth factor required for development while IGF-I expression is seen in later life.In addition to the insulin-like effects, IGF-I can also regulate cell growth and development, especially in nerve cells, as well as cellular DNA synthesis. ☉Hormones of the Digestive Tract 1. Gastrin Produced by pyloric mucosa Stimulated by Amino acids(tryptophane & phenylalanine) and peptides Stimulates parietal cells and Chief cells Maintains gastric mucosa Inhibited when pH falls below 2.5 2. Secretin Produced by upper small intestine mucosa Stimulates release of secretion #1 from pancreas (water & bicarbonate) 3. CCK (cholecystokinen) Produced by small intestine mucosa Stimulates contraction of gall bladder, Secretion #2 from pancreas (enzymes) ☉Colipase a small protein cofactor needed by pancreatic lipase for efficient dietary lipid hydrolyisis. Efficient absorption of dietary fats is dependent on the action of pancreatic triglyceride lipase. Colipase binds to the C-terminal, non-catalytic domain of lipase, thereby stabilising as active conformation and considerably increasing the overall hydrophobic binding site. Structural studies of the complex and of colipase alone have revealed the functionality of its architecture ☉Proximal Convoluted Tubule The Na-K-ATPase on the basolateral membrane of the PCT cells moves sodium out of the cells creating a lowered intracellular sodium concentration. This provides an impetus for the sodium in the PCT lumen to move into the cells via a sodium-proton antiporter. In exchange, protons are sent into the lumen where they combine with bicarbonate ions to form carbonic acid. （分泌最多氫離子） ☉DCT In the DCT, a luminal carbonic acid anhydrase converts the carbonic acid into H2O and CO2 which can enter DCT cells. Here they are back-converted by a second carbonic anhydrase. Protons are actively secreted in the DCT by a sodium-independent electrogenic ATPase, while the bicarbonate is recovered. The protons are buffered in the urine by "titratable" acids, primarily inorganic phosphate, with some contribution from others such as urate and creatinine. ☉CT The kidney can control pH to some extent by regulation of titratable acid. In states of acidosis, more phosphate is secreted to help buffer the load (leading to hypophosphatemia) while alkylosis promotes phosphate reabsorbtion. Ammonia production can augment proton excretion on an as-needed basis. Glutamine is converted in collecting tubute (CT) cells into ammonium and bicarbonate. The ammonium is exchanged with sodium in the lumen, and the ammonium remains charge-trapped in the lumen. The bicarbonate from the breakdown of glutamine is reabsorbed. Any ammonium that is not excreted is reabsorbed into circulation, and this is problematic because it is toxic. In the liver ammonium can be detoxified by conversion to urea, a process which consumes bicarbonate. Both hypercalcemia and hyperkalemia inhibit renal ammonium excretion. (Jack Welch, M.D., Ph.D.) ☉Nuclei of Hypothalamus Savage behavier: stimulation of Dorsomedial/destruction of ventromedial Polyphagia: lesion of ventromedial（ventral就是肚子） Oligophagia: lesion of lateral（流浪在社會邊緣） Circadian thythm: suprachiasmatic（在天空） Secretion: Oxytocin: PVN/ ADH: SON ☉Acidophic: Growth hormone(low in REM, hign when glucagon), Prolactin ☉神経繊維を伝わる信号の速度 分類 直径（マイクロメートル） 有髄 速度（ｍ/秒） 機能 Aα １２－２０ ＋ ７０－１２０ 運動神経 Aβ ５－１２ ＋ ３０－７０ 触覚、圧覚 Aγ ３－６ ＋ １５－３０ 筋紡錘に関する Aδ ２－５ ＋ １２－３０ 痛覚、触覚 B ＜３ ＋ ３－１５ 自律神経 C ０．４－１．２ - ０．５－２ 痛覚、反射、嗅覚 ■Biochemistry ☉Vmax/v=Km/S +1 v=1/2 Vmax時, S=Km Km越大，affinity越小 efficasy: Vmax/Kmax 1.competitive inhibition: Km↑, Vmax←→ 2.non-compatitive inhibition: Km←→, Vmax↓ 3.Un-compatitive inhibition: Km↓, Vmax↓ ☉Amino Acids 苯環：phenylalanine, triyptophan, tyrosine 酸：aspartic acid, glutamic acid 鹼：lysine, arginine, histidine Ketogenic: Leucine Keto-glutagenic: phenylalanine, tryptophan, tyrosine / lysine, Isoleucin ☉Alpha-helix 3.6 residues(1 helix)→→0.56 nm: 60 residues→→90 nm ☉Footprinting a method for determining the exact DNA sequence to which a particular DNA-binding protein binds. ☉Transamination: require Vit B6 (Pyridoxine) Alanine→Pyruvate Glutamate→α-ketoglutarate Aspartate→Oxaloacetate ☉Essential AA: Leu,Ile,Lys/ Met,Thr,Val/ Trp,Phe Essential FA: arachinoid acid(20:4), linoleic acid(18:2), lineoleic acid(18:3) ☉HDL: Apo A LDL: Apo B-100 VLDL: Apo CII Chylomicron: Apo B-48 ☉Purine: Glutamine + Aspartate + CO2 Thymidine: Glutamine + Aspartate + CO2 ☉Epinephrine→AC→cAMP↑→phosphorylase↑：分解 Insulin→→AC→cAMP↓→phosphotase活化glycose synthetase↑：合成 ☉Met, Val→→acetyl CoA→→TCA cycle→→12ATP→→共15ATP Glucose: 38 +2 ATP ☉Copper and the synthesis of elastin and collagen. Copper's role in connective tissue is linked to the enzyme lysyl oxidase. From a biochemical perspective, copper is a cofactor for the enzyme and a determinant of its activity in connective tissues. Lysyl oxidase catalyses a post-translational oxidation of certain lysine and hydroxylysine residues. ☉Overview of Prokaryotic Translation Initiation Steps in Formation of 70S initiation Complex (1) Dissociation of the 70S ribosome into the 30S and 50S subunits (IF-1); (2) Binding of IF-3 to 30S; (3) Binding of IF-1 and IF-2/GTP to 30S; (4) Joining of 30S/IF initiator tRNA and mRNA to form 30S initiation complex; (5) Binding of 50S to 30S complex, with loss of IF-1 and IF-3; (6) Dissociation of IF-2 with hydrolysis of GTP to GDP and Pi ☉Lesch-Nyhan syndrome →deficiency of the enzyme hypoxanthine-guanine phosphoribosyl transferase (HPRT), →overproduction of uric acid: HPRT normally plays a key role in the recycling of the purine bases, hypoxanthine and guanine, into the purine nucleotide pools. In the absence of HPRT, these purine bases cannot be salvaged, and instead are degraded and excreted ultimately as uric acid. ☉a-oxidation →3-methyl-branched fatty acids (such as phytanic acid) are taken up the diet. These compounds cannot be degraded by the normal peroxisomal b-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase (see the fourth step of b-oxidation). The solution for this dilemma is the alpha-oxidation pathway. →The first two steps are not in dispute: these two steps consist of the ligation of phytanate to phytanoyl-CoA, and the hydroxylation of phytanoyl-CoA. The long chain fatty acyl-CoA synthetase is capable of ligating CoA to phytanic acid. →Phytanoyl-CoA hydroxylase (PAHX) converts phytanoyl-CoA to a-hydroxylphytanoyl-CoA. Mutations in the gene encoding PAHX are responsible for ★Refsum's disease, a disorder resulting in neurological dysfunction and biochemically characterized by the accumulation of high levels of phytanic acid. ☉b-oxidation →The peroxisome handles the b-oxidation of many substrates. These include very long chain fatty acids (VLCFAs; both saturated and unsaturated), some long chain fatty acids, and long chain dicarboxylic acids (products of w-oxidation). Peroxisomes can also oxidize the side chains of eicosanoids, which are molecules important in short-range signaling and are derived from arachidonic acid. Peroxisomal b-oxidation also plays a role in bile acid synthesis. →Fatty acyl-CoA synthetase, Acyl-CoA oxidase, Catalase ☉Refsum disease →The three diagnostics are retinitis pigmentosa, peripheral polyneuropathy, and cerebellar ataxia. →associated with high levels of phytanic acid, caused by a deficiency in phytanoyl-CoA hydroxylase (a-oxidation pathway). Later studies identified the gene encoding for this activity (PAHX) ☉Glycogen Phosphorylase Glycogen phosphorylase catalyzes phosphorolysis of glycogen to glucose-1-phosphate.Two forms of the enzyme exist. The relatively "inactive" form 'b' has no phosphate, but can be converted to the more active form 'a' by action of the enzyme glycogen phosphorylase b kinase. ☉Methods of protein degradation 1.Lysosomal system - The primary lysosomes, budded from the Golgi complex, are bags of degradative enzymes. Over 50 different hydrolytic enzymes are contained in lysosomes, including proteases, nucleases, lipases, and carbohydrate-cleaving enzymes. 2. Cytosolic Degradation System - Because general proteases would hydrolyze virtually all cytoplasmic proteins, cells must have a way to distinguish proteins to be attacked from those to be left alone. →→Ubiquitin marking - The best-known cytoplasmic protein targeting system uses a protein called ubiquitin, a 76-residue polypeptide, found in virtually every eukaryotic cell. ☉Carbamyl phosphate synthetase (CPS) deficiency →a urea cycle defect that occurs when a deficient enzyme mediates the normal path for incorporation of ammonia. CPS deficiency is derived from catabolism of amino acids into a one-carbon compound, CPS (H2N-CO-PO32-). →Regulation of CPS I activity depends upon the levels of N-acetylglutamate (see N-Acetylglutamate Synthetase (NAGS) Deficiency). In cases of homozygous deficiency of CPS I, the ability to fix waste nitrogen is completely absent, which results in increasing levels of free ammonia with the attendant effects on the central nervous system. ☉Proteoglycans The majority of glycosaminoglycans(GAGs) in the body are linked to core proteins, forming proteoglycans (also called mucopolysaccharides). The specific GAGs of physiological significance are hyaluronic acid, dermatan sulfate, chondroitin sulfate, heparin, heparan sulfate, and keratan sulfate. Several genetically inherited diseases, for example the lysosomal storage diseases, result from defects in the lysosomal enzymes responsible for the metabolism of complex membrane-associated GAGs. These specific diseases, termed mucopolysaccharidoses (MPS) ☉deoxyspergualin (15-DSG) is an agent with immunosuppressive effects on both lymphocytes and monocytes ☉Iron ions undergo two important changes of oxidation state during digestion and absorption. 1.The first change occurs in the stomach. Here iron (III) is reduced to iron (II). This reduction is favored by the low pH. Reducing agents, such as ascorbic acid, assist this process. Reduction is important because iron (II) dissociates from ligands more easily than iron (III). 2.The second change occurs in the duodenum. The duodenum is bicarbonate-rich, and alkaline. In the alkaline environment ,heme is absorbed directly by the mucosal cells. Within the cells, the iron dissociates from it. free iron (II) ions are oxidized to iron (III), which is taken up by the mucosal cells in substantial amounts under all circumstances of nutritional iron status. ☉DNA Damage & Repair UV radiation - 260 nm is wavelength at which maximum absorption occurs for DNA Four ways to repair of T dimers in E. coli: A) Photoreactivation ★Light repair phr gene - codes for deoxyribodipyrimidine ★photolyase that, with cofactor folic acid, binds in dark to T dimer. When light shines on cell, folic acid absorbs the light and uses the energy to break bond of T dimer; photolyase then falls off DNA B) Excision Repair ★Dark repair Three types 1) UV Damage Repair (also called NER - nucleotide excision repair) ★Excinuclease (an endonuclease; also called correndonuclease [correction endo.]) that can detect T dimer, nicks DNA strand on 5' end of dimer (composed of subunits coded by uvrA, uvrB and uvrC genes). 2) AP Repair Repair of apurinic and apyrimidinic sites on DNA in which base has been removed. Base removed by radiation or DNA glycosylases which sense and remove damaged bases. ung gene codes for ★uracil-DNA glycosylase which recognizes and removes U in DNA by cleaving the sugar-nitrogen bond to remove the base. 3) Mismatch Repair Accounts for 99% of all repairs Follows behind replication fork. Two ways to correct mistakes made during replication: 1) 3'>5' exonuclease - proofreading 2) Mismatch repair C) Postreplicative (Recombinational) Repair If T dimer not repaired, ★DNA Pol III can't make complementary strand during replication. Postdimer initiation - skips over lesion and leaves large gap (800 bases). Gap may be repaired by enzymes in recombination system - lesion remains but get intact double helix. D) SOS Response ☉Functions of DNA Methylation 1. Protection from endonucleases designed to destroy foreign DNA (mainly bacterial DNA). ★Endonucleases are enzymes that cut DNA at specific points (i.e. a CG base pair). However, if the base pair is methylated then the very specific restriction enzyme will not recognize the DNA. Since human DNA and bacterial DNA are methylated differently, but each in an extremely specific manner, this defense mechanism allows for only foreign DNA to be destroyed by the endonucleases. 2. Regulation in gene expression. Experimental evidence has shown that in certain cells there are heavily methylated genes and these genes are not expressed. On the other hand cells that have non-methylated forms of these genes are expressed. An example of these is seen in★ housekeeping cells (cells that produce proteins used in "clean up" of cellular debris and dead organelles) in which cells with non-methylated genes for these cells continuously transcribe or produce the materials needed to make housekeeping cells. Also one of the★ X chromosomes in females is not expressed. A hypothesis for this phenomenon is linked to the ★heavy methylation of the inactive X chromosome. ☉The Edman reaction →involves a series of chemical reactions which, beginning at the amino terminus of a protein, remove one amino acid at a time, ultimately releasing a derivatized amino acid which can be chromatographically identified. Essentially, the Edman reaction consists of two chemical reactions which occur under different pH conditions. This allows release of amino acids from the N-terminus in a sequential manner. →The first reaction, the coupling step, occurs at a high pH. Phenylisothio-cyanate(PITC) in the presence of a base, reacts quantitatively with the free amino terminal amino group of a peptide to form a phenylthiocarbamyl-protein (PTC-protein). ☉CNBR (cyanogen bromide) When a protein is cleaved by the commonly used enzymes, the new C terminus gains a hydroxyl group, while the new N terminus gains a hydrogen. The activity of CNBR (cyanogen bromide) is unusual in that cleaves on the C-terminal side of methionine, converting it to a homoserine. ☉Michaelis-Menten Plot of the rate of an enzyme reaction or rate of transmembrane transport versus drug concentration. →"First Order" portion where velocity is directly proportional to the drug concentration and the"Zero Order" portion where the processes are saturated andfurther increases in drug concentration do not change the rate ofthe process. Note also that the Km is the drug concentration that produces 50% of the maximum velocity. →saturation(steady state): the enzyme is saturated by the substrate and becomes a bottleneck for the entire reaction. This is the essence of MM kinetics which is fundamentally different from a conventional chemical kinetics in which usually there are equal amount of reactants. ☉tight turns(4+2/3+3/2+4/1+5/6) Delta-turn - It is the smallest tight turn which involves only two amino acid residues and the intraturn hydrogen bond for a delta-turn is formed between the backbone NH(i) and the backbone CO(i+1). Gamma-turn - It involves three amino acid residues and the intraturn hydrogen bond for a gamma-turn is formed between the backbone CO(i) and the backbone NH(i+2). Beta-turn - A beta-turn involves four amino acid residues and may or may not be stabilized by the intraturn hydrogen bond between the backbone CO(i) and the backbone NH(i+3). Alpha-turn - An alpha-turn involves five amino acid residues where the distance between the Calpha(i) and the Calpha(i+4) is less than 7Å and the pentapeptide chain is not in a helical conformation. Pi-turn - It is the largest tight turn which involves six amino acid residues. |