Session Start: Tue Oct 21 11:49:36 2008 Session Ident: #Chemistry [11:49] * Now talking in #Chemistry [11:49] * chemistry.gravitywaves.com sets mode: +nt [15:58] * dyco has joined #Chemistry [15:59] * roar has joined #Chemistry [16:01] * sn2 has joined #Chemistry [16:02] * sn2 has quit IRC (Quit: Leaving) [16:03] * pm has joined #Chemistry [16:04] * DrSturm has joined #Chemistry [16:04] Hi dr. Strum, how is ethanol used as fuel in the body? [16:04] * guest has joined #Chemistry [16:05] * guest has quit IRC (Quit: Leaving) [16:05] * BPG has joined #Chemistry [16:05] Ethanol furnishes 7 Kcal/g, over 90% of ingested ethanol is metabolized in the liver through oxidation. [16:05] Hi! do we need to memorize the coorperativity? [16:05] * carino has joined #Chemistry [16:06] Can we provide the abbreviated names for the vitamins instead of the entire name, i.e. B2 for riboflavin [16:07] Don't understand "memorize the cooperativity" [16:07] * folate has joined #Chemistry [16:07] Abbreviations are fine as long as they are correct [16:07] * elrey has joined #Chemistry [16:07] coorperativity for oxygen? [16:07] Dr. strum What are the harmful action of AO species in cells [16:08] React with amino acids in proteins, lipids in membranes, bases in DNA and damage them [16:08] what exactly do we have to know about NAD+ and NADP+? [16:08] Do we need to know the structure of AMP ADP ATP [16:08] You have to understand the concept of cooperativity [16:09] thanks [16:09] see you tomorrow in class [16:09] You have to know the electron carrying parts of NADH and FADH2 and the five bases (A, T, C, G, U) [16:09] * BPG has quit IRC (Quit: Leaving) [16:09] What are the 2 reaction that nucleotides can undergo and biochemical importance [16:10] Ribonucleotides are the Monomeric Units of Nucleic Acids [16:10] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [16:10] Nucleotide Derivatives: [16:10] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [16:10] dr.strum what do u mean by caroteniods being quenchers of singlet oxyegen=acting as cellular antioxidants [16:10] * Hb has joined #Chemistry [16:10] Ribonucleotides are the Monomeric Units of Nucleic Acids [16:10] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [16:10] Nucleotide Derivatives: [16:10] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [16:10] As far as the lecture on Enzymes: Catalysis and Kinetics...do we need to know the TYPES OF ENZYMES REACTIONS? MICHAELIS-MENTEN EQUATION, LINEWEAVER-BURKE PLOT, and the Competitive and Non-competitive inhibiton graphs? [16:10] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [16:11] Do we need to know diagrame of a triacylglycerol [16:11] You need to know the types of enzyme reactions and understand all of the graphs [16:12] You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [16:12] How absorbed and transported [16:12] Sorry [16:12] in the energy diagrams, what happens at the transition state? [16:13] How folate is absorbed and transported [16:13] Absorption and Transport: a model for all water soluble vitamins [16:13] >Conversion to a more readily absorbed form. [16:13] >Links with a binding protein. [16:13] >Conversion to a transport form to cross membrane into plasma. [16:13] >Transported from plasma to target tissues. [16:13] The transition state is the half way point between the substrate and products [16:14] Dr.Sturm, do we need to know the infant respiratory distress syndrome? [16:14] Yes. [16:14] How the vitamin c, e and the carotenoids act cellular antioxaants. [16:14] * surrurr has joined #Chemistry [16:15] They scavenge (quench) the AO species [16:15] Why is Alkaline Phophatase an Isoenzyme? [16:15] * Hb has quit IRC (Quit: Leaving) [16:16] It has two distinct forms one comes from bone cells and one from liver cells [16:16] Protein quality? [16:16] was the significance of low ethanol intake [16:17] Ethanol intake results in excess calories and an increase in adipose tissue (fat) [16:18] Essential amino acids, easily digested [16:18] el rey is that you gerardo? [16:21] ALT and Glutamyl Transpeptidase correlation? [16:22] * kobby has joined #Chemistry [16:22] how can creatine phosphokinase and lactate dehydrogenase be used to diagnose myocardial infarction [16:22] Glutamyl transpeptidase is general for liver disorder while ALT is specific for hepatitis [16:22] do we need to memorize the complete name of the AOs or can we just write LOO* for Lipid peroxyl ? [16:22] Can you describe the relationship of Bohrr effect to O2 binding by Hb and explain the physiological significancee of this effect? [16:22] Following a heart attack the cardiac cells lyse spilling their contents into the blood. [16:22] Creatine Phosphokinase (CPK)- MB isozyme appears first w/in 24 hrs., normal w/in 48 hrs. [16:22] Lactate Dehydrogenase (LDH)- H4 isozyme may persist for two weeks [16:23] You can use AO structures as long as they are correct [16:23] ok. tnx [16:23] Bohr (Proton) Effect: [16:23] O2 binding to Hb is sensitive to physiological pH changes. [16:23] i.e. Contracting Muscle- lactic acid is produced, hence the H+ concentration increases, pH decreases -------->promotes O2 dissociation (fulfills greater requirement for O2). [16:23] H+ antagonizes the binding of O2 to Hb. [16:23] In lungs, higher pH increases affinity of Hb for O2 (reverse of what is happening in muscle). [16:25] What isapparent Km? [16:25] The Km for an enzyme with an inhibitor present [16:26] Can you define transition state? [16:26] The mid point between the substrate and product [16:26] what us energy of activation? [16:26] is* [16:27] do we need to know all serum enzymes of just the 3 major ones talked about [16:27] The energy barrier between the substrate and products that must be over-come for the reaction to proceed [16:27] For this test, we need to only had to know the 5 bases and the NADH and FADH2 reactions, right? [16:27] Do we have to memorize Structures: AMP, ADP, ATP, B2, Pyridoxal Phosphate? [16:27] All serum enzymes [16:27] what is free of energry? [16:27] Do we have to memorize Reactions: Vitamin A & E, Folic Acid, Functions of Pyridoxal Phosphate, Mechanism of Chymotrypsin Action? [16:28] You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [16:28] what's the difference between ribonucleoside and ribonucleotide? [16:28] Doc, does Hb alternate between T and R states as you go from tissue to lungs, when talking about e.g the Bohr effect? [16:28] "side" is the base + ribose, "tide" is the base + ribose + phosphate [16:29] Don't know what you mean by "alternate" [16:29] can you define free of energy? [16:29] how do we compare the relative reactivities of AO species ? [16:29] The difference in energy between substrate and product [16:29] it's in T state in the tissues, but nothing's mentioned when we talk about the lungs [16:30] Least reactive to most reactive or most to least [16:30] can you define rate limiting step and reaction specificity? [16:30] In lungs, higher pH increases affinity of Hb for O2 (reverse of what is happening in muscle). [16:31] The rate limiting step controls the rate for a pathway, an enzyme is specific for a certain reaction [16:31] my question then is, is Hb in the R state at this point? [16:31] least to most reactive ? [16:32] In tissues it goes from R to T, opposite in lungs Tense to Relaxed [16:32] ah, thanks [16:32] AO species list them least to most reactive or most to least reactive [16:32] Tx [16:33] can you define catalysis and prosthetic group [16:34] A catalyst lowers the Ea in a reaction, a prosthetic group is an organic co-factor that is covalently bound to a protein [16:35] are the Fatty acids, Phospholipids- cell mambrane, and Sterol three classes of lipids ? Then what are the specific function for cholesterol, and fatty acids ? [16:36] Yes, cholesterol is the precursor to all steroid hormones, fatty acids provide energy [16:37] is cpk=creatine+atp [16:37] what is the importance of non functional plasma enzymes as a diagnostic tool? [16:37] are cholesterol and phospholipids classified as non essenstial Fatty acids? and Omega3 essential? [16:38] CPK is the enzyme that catalyzes the phosphorylation of creatine [16:38] Do we need to know the structures of choline, ethanolamine, serine etc? [16:38] The appearance of such enzymes in the plasma reflects destruction of cells from which these enzymes originate. [16:39] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [16:39] the definition of heavy chain [16:40] A protein that is part of an Ab [16:40] are chol and phospolipids considered non essential fatty acids? [16:41] while Omega 3 an essential FA? [16:41] * MB has joined #Chemistry [16:41] The three essential fatty acids are linolenic, linoleic and arachidonic [16:41] Do we need to be able to draw the Lineweaver-Burke plot? [16:42] You need to understand the graphs [16:42] Do we need to know the table on the first page of the Nucleotide/Lipid handout , or just know that Ribonucleoside = base + ribose, and Ribonucleotide = base + ribose + phosphate group? [16:43] do we need to know the diagram for triglycerol [16:43] Just the deifinitions for ribonucleoside and -tide [16:43] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [16:44] can you define allostery? [16:44] Do we need to know the different variations of phospholipids? [16:45] what happens in hydroxylation of lys and pro under post-translational modication [16:45] Work sheet 7 Q3 discuss the binding of Co to the iron-heme comlex ? [16:45] The attachment of a molecule at an allosteric site that affects the protein in a stimulatory or inhibitory way [16:45] Pro and Lys are hydroxylated [16:46] Heme actually has a greater affinity for CO than O2 [16:46] can you explain how folate is absorbed and transported? [16:46] when an inhibitor binds to the allosteric site, is it guaranteed to change the shape of the active site? [16:46] Absorption and Transport: a model for all water soluble vitamins [16:46] >Conversion to a more readily absorbed form. [16:46] >Links with a binding protein. [16:46] >Conversion to a transport form to cross membrane into plasma. [16:46] >Transported from plasma to target tissues. [16:47] how vitamin C E and Cartotenoids act as antiodants? [16:48] No, not necessarily [16:48] do we need to know the post translational modifications (PTM) that regulate enzymes...or just to know that PTM regulate enzymes? [16:48] They scavenge (quench) AO species [16:48] Don't need to know the specific modifications [16:50] Do we need to know the function, source, deficiencies of Folic acid and cobalamin? [16:50] Yes [16:51] Do we need to know the different variations of phospholipids? [16:51] No. [16:52] what about the functions, and RDAs of all 9 water soluble vitamins? [16:52] you need to know the table but not the RDA's [16:52] was difference between protease and proenzyme [16:53] Can you dicuss phospholipids, including sphingomyelin, and their importance as lung surfactants. [16:53] * biochem has joined #Chemistry [16:54] -In utero, the developing fetus exists in a fluid environment, the lungs are collapsed (oxygenation occurs across the placenta). [16:54] -At birth the newborn is suddenly exposed to air, the lungs must expand and fill w/ air. [16:54] -Because of the high surface tension, caused by H-bonding of water molecules, this requires a significant amount of energy. [16:54] -The energy barrier is decreased with Lung Surfactant: phospholipids, primarily DPPC (Lecithin) and proteins. These amphiphilic compounds form "sheets" in an aqueous environment reducing the surface tension between water molecules and decreasing the energy barrier. [16:54] -This surfactant prevents lung collapse in newborns as well as adults. [16:54] would you classify serine proteases as exoprotease's [16:54] Endoproteases [16:54] * carino has quit IRC (Quit: Leaving) [16:55] what's the definition for protein quality? [16:56] Describe two reactions nucleotides can undergo and discuss their biochemical importance. [16:56] Contains the essential amino acids and is easily digested [16:56] Ribonucleotides are the Monomeric Units of Nucleic Acids [16:56] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [16:56] Nucleotide Derivatives: [16:56] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [16:57] is it simple ester formation and triacylglycerol formation? [16:57] Triglycerides are formed via esterification of fatty acids to the glycerol backbone [16:58] so then what's the other reaction nucleotides udergo? [16:58] how do NAD+ and NADPH+ function in energy producing pathways? [16:58] That is two [16:58] Ribonucleotides are the Monomeric Units of Nucleic Acids [16:58] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [16:58] Nucleotide Derivatives: [16:58] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [16:58] do we need to know which amino acids play role in trypsin and elastase mechanisms [16:59] Yes, the same catalytic triad, His, Ser, Asp as for chymotrypsin [17:01] worksheet 13, #3 - in addition to oxidative cellular damage, what other harmful actions can be listed? [17:01] how is NAD+ oxidized? [17:01] That's it. [17:02] can you explain how folate is absorbed and transported [17:02] When NADH reduces a substrate it is oxidized and when it oxidizes a substrate it is reduced [17:02] do we need to know specifics of how antioxidants quench AO [17:02] Absorption and Transport: a model for all water soluble vitamins [17:02] >Conversion to a more readily absorbed form. [17:02] >Links with a binding protein. [17:02] >Conversion to a transport form to cross membrane into plasma. [17:02] >Transported from plasma to target tissues. [17:03] thanks [17:03] Just that the antioxidants scavenge (quench) the AO species [17:03] so, NAD+ is oxidized and NADP+ is reduced... will this be enough , or would need us to explain "HOW" the redox happens? [17:04] You need to know the electron carrying parts of NADH, FADH2, that means draw them [17:04] ok.tnx [17:04] NAD+ and NADP+ are basically the same except that NAD+ does not have a phosphate group on it [17:06] how would we explain NAD+ and NADP+ containing enzymes function in energy producing pathways? ...is it electron transfer carriers in cells involved in oxidation reduction rxns? [17:06] Yes. [17:07] same goes for FAD correct? [17:07] Yes. [17:08] * biochemM has joined #Chemistry [17:08] what is apparent Km? vs just plain Km [17:09] do we need to know process ethanol takes to form acetyl CoA [17:09] Apparent Km is the Km for an enzyme with an inhibitor present [17:09] No. [17:10] what about the triacylglycerol formation? [17:10] I don't know if you answered this one already ( if you did let me know) what effects does bpf have on hemoglobin affinity for o2 and how it facilitates oxygen release to tissues? [17:10] do we have to know what the FAB and Fc definitions? [17:11] BPG is produced in the RBC from the metabolism of glucose [17:11] BPG lowers the affinity of Hb for O2 [17:11] Accumulation of BPG is a characteristic of active metabolism and increased O2 requirements by the tissue. [17:11] In lungs, when O2 is bound, the cavity where BPG binds becomes to small, thus the increased affinity for O2 in the lungs. [17:11] how can we define a hapten? [17:12] A hapten is a small molecule which can elicit an immune response only when attached to a large carrier such as a protein; the carrier may be one which also does not elicit an immune response by itself. [17:13] * fatmanin has joined #Chemistry [17:13] Is it good that if just say that hapten is the small set of features on Ag surface? [17:13] Yes [17:15] why is a combined analysis of plama glutyl transpeptidasee and alanine aminotransferase is desirable for diagnosis hepatitis in patient? [17:15] * carino has joined #Chemistry [17:16] Two reactions that nucleotides undergo and bio. importance? [17:16] Glutamyl transpeptidase is general for liver disease and ALT is specific for hepatitis [17:16] Ribonucleotides are the Monomeric Units of Nucleic Acids [17:16] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [17:16] Nucleotide Derivatives: [17:16] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [17:17] do we have to know the classes of lipids or just the essential lipids? [17:18] Both [17:18] * roar has quit IRC (Quit: Leaving) [17:19] * OHic has joined #Chemistry [17:20] Do we have to know the 9 water soluble vitamins along with the major functions and RDA? [17:20] * mm has joined #Chemistry [17:20] * elrey has quit IRC (Quit: Leaving) [17:20] * elrey has joined #Chemistry [17:20] Yes, but not the RDA's [17:21] triacylglycerol formation, equation(s) or structures? [17:21] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [17:22] How about the struture of the Myoglobin? [17:22] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [17:23] do you only need to know myoglobin is a dimer [17:24] so beside the strutures of NADH, FADH2, and five bases( A, T, C, G, U) do we need to memorize other strutures? [17:24] Mb is not a dimer, it is a single protein with a heme prosthetic group [17:24] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [17:24] how can I explain how NAD+ and NADP+ containing enzymes function in energy producing pathways. [17:25] They function as electron carriers in oxidation/reduction reactions [17:26] how about on the antibody, do we need to know the Vaccines? [17:26] What about the key metabolic pathways in which NAD+, NADP+ and FAD participate? [17:26] NADH: Key Metabolic Pathways: glycolysis, citric acid cycle, respiratory chain, amino acid metabolism [17:27] FADH2: Key Metabolic Pathways: amino acid deamination, purine degradation, citric acid cycle, fatty acid oxidation [17:27] how does the antibody bind to its antigen? [17:27] Through ionic interactions [17:27] the hypervairable are involved right? [17:28] Also the Vaccinces? [17:28] Can you compare and contrast ribonucleoside and ribonucleotide. [17:28] The hypervariable regions are at the tips of the Ab and that is where antigen binding occurs [17:28] * Vitamins has joined #Chemistry [17:28] THE CDRS are the hypervariable regions? [17:28] "side" base + ribose; "tide" base + ribose + phosphate [17:28] Yes. [17:29] so we still need to know the Vaccines? [17:29] yes. [17:29] Dr. sturm can you tell me effect of CO2 on hemoglobin affinity for oxygen and the physiological relevance of this effect? [17:30] CO2 is a byproduct of metabolism. [17:30] Accumulation of CO2 is a characteristic of active metabolism and increased O2 requirements by the tissue. [17:30] CO2 lowers the affinity of Hb for O2 so that in the tissues O2 is released. [17:30] In lungs CO2 is kept lower by expiration increasing the affinity of Hb for O2 (reverse of what is happening in tissues). [17:31] Do we need to know all 10 of the principal serum enzyme and their uses in clinical diagnostic? [17:31] Yes [17:31] Where it says describe the following terms associated with enzymes what do we have to say for coenzyme and prosthethic group.? [17:33] A co-enzyme is an orgain co-factor that is easily removed (not covalently bound) to the enzyme; a prosthetic group is an organic co-factor which is covalently attached to a protein [17:34] Dr. Sturm, could you tell me if I need to know the struture of AMP, ADP, and ATP? [17:35] You said that we don't have to know the RDA for the soluble vitamisns [17:35] No, You need to know the electron carrying parts of NADH, FADH2 and the five bases (A, T, C, G, U) [17:35] No RDA's [17:36] does a non competitive inhibitor cause Vmax and Km to decrease? [17:36] yes [17:36] thank you [17:37] Can you explain how NAD+ and NaDP+ containing enzymes function in energy producing pathways? [17:37] They carry electrons in oxidation/reduction reactions [17:37] I thought non-competitive inhibitor only cause Vmax to decrease and Km increase [17:39] 1 over Km increases which translates to a decrease in the enzymes affinity for its substrate (Km) [17:39] * elrey has quit IRC (Quit: Leaving) [17:41] is it the same thing for flavin (FAD) containing enzymes function in energy producing pathways? [17:41] Yes. [17:41] Is Base+Ribose+phosphate group a sufficient definition for ribonucleotide? [17:42] Yes. [17:43] What are interactions with control proteins and zygomens? [17:43] Do we need to know that CPK, LDH and Amylase are dimer, tetramer, and monomer, respectively? [17:43] or how long they persist in the blood after a heart attack? [17:44] Zymogen (Proenzymes): Inactive large precursors of the active form of a protein. The enzymes are activated by removal of a portion of the peptide chain (proteolysis). [17:44] Yes on CPK, LDH and Amylase [17:44] For this question: Define isozyme and nonfunctional plasma enzyme and discuss the importance of nonfunctional plama enzymes as diagnostic tool? [17:44] Can you describe the two reaction nucleotides can undergo and discuss their biochemical importance? [17:45] Control proteins have two parts a regulatory and catalytic subunit that associate/dissociate making the enzyme inactive/active [17:45] Ribonucleotides are the Monomeric Units of Nucleic Acids [17:45] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [17:45] Nucleotide Derivatives: [17:45] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [17:46] Doc, the 3 classes, functions, and e.g of lipids [17:46] Fatty acids, triglycerols, sterols [17:47] Are we going to have to demostrate/draw/point out on a lineweaver-burke plot the vmax, km, competitive inhibition and non competitive inhibition for the exam? [17:47] * MB has quit IRC (Ping timeout: 240 seconds) [17:48] Perhaps. [17:49] Do we need to know the 6 types of enzymes reactions: tranferase, hydrolase, oxidoreductase, lygase, and isomerase [17:49] Yes. [17:50] What is there to say about a heavy chain? light chain? [17:50] * biochemM has quit IRC (Quit: Leaving) [17:50] They are proteins that make up an Ab [17:52] Dr, Sturm, what is the compare and contrast Ribonucleoside and Ribo nucleotide [17:52] * MB has joined #Chemistry [17:52] "side" is Base + Ribose; "tide" base + Ribose + Phosphate [17:52] Doc, I'm coming up short on the functions of the 3 lipid class [17:53] and describe two reactions nucleotides can undergo and discuss their biochemical importance [17:53] for interaction with a control protein, the attachment of an inhibitory subunit is the cAMP right? [17:53] * beerlover has joined #Chemistry [17:54] Fatty acids produce energy, triglycerides store fatty acids, cholesterol is the precursor for all steroid hormones [17:54] Ribonucleotides are the Monomeric Units of Nucleic Acids [17:54] Nucleotides (ribonucleotides) can be linked sequentially to form nucleic acids (store and transmit genetic information). [17:54] Nucleotide Derivatives: [17:54] Many biosynthetic reactions in carbohydrate metabolism require nucleotide derivatives. [17:54] Dr, Sturm. what is the describe two reactions nucleotides can undergo and discuss their biochemical importance [17:55] O.K., we have time for one or two more questions. [17:55] O.K. we have time for one or two more questions [17:55] Do we need to know the types of enzyme RXNs? [17:56] Dr, Sturm. what is the describe two reactions nucleotides can undergo and discuss their biochemical importance [17:56] the inhibitory subunit in the Inhibition of enzyme activity with control group is cAMP right? [17:56] We have time for one or two more questions [17:56] o we need to know the types of enzyme RXNs? [17:56] We have time for one or two more questions [17:56] Dr, Sturm. what is the describe two reactions nucleotides can undergo and discuss their biochemical importance [17:56] could you tell me please [17:56] do we need to know the types of enzyme RXNs? [17:56] what is it [17:56] Yes, you need to know the types of enzyme reactions [17:57] so we pretty much have to know everything [17:57] Thanks for your help DR. S [17:57] what antioxident is effective against a hydroxyl radical [17:57] The reactions of nucleotides has been answered several times check the log [17:57] Thats a good [17:57] ? by kobby [17:57] Vitamin C [17:58] Good luck everyone!!!!! [17:58] * DrSturm has quit IRC [17:58] do we have to know the 6 ways proteins can undergo post-translational modications [17:58] * beerlover has quit IRC (Quit: Leaving) [17:58] * Disconnected Session Close: Tue Oct 21 17:58:33 2008