Session Start: Tue Nov 11 13:09:10 2008 Session Ident: #Chemistry [13:09] * Now talking in #Chemistry [13:09] * chemistry.gravitywaves.com sets mode: +nt [15:29] * klassyx has joined #Chemistry [15:30] hi all [15:45] * BeatlesR has joined #Chemistry [15:57] * BeatlesR has quit IRC (Read error: Connection reset by peer) [15:58] * pollo has joined #Chemistry [16:00] * DrSturm has joined #Chemistry [16:00] * kobby has joined #Chemistry [16:00] hello professor [16:01] * Nerdboy has joined #Chemistry [16:02] dr sturm do you want us to know the 5 steps for the lagging strand [16:02] hi professor what is a replisome [16:03] * ProfSturm has joined #Chemistry [16:06] * DrSturm has quit IRC (Ping timeout: 240 seconds) [16:06] You need to know the five steps for lagging strand synthesis [16:07] * ProfSturm has quit IRC [16:07] * DrSturm has joined #Chemistry [16:07] hi, my question is, in the RNA synthesis and processing section, how do you define: initiation, elongation, and termination? [16:07] can you tell me what a replisome is [16:08] If you e-mail me your definitions I will let you know if they are correct. [16:08] okay thanks [16:09] To actually initiate and sustain DNA replication requires many other proteins and enzymes which assemble into a large complex called a replisome. It is thought that the DNA is spooled through the replisome and replicated as it passes through. So the place where DNA synthesis occurs. [16:10] im still confused about the lagging and leading strand. is the lagging strand 3' to 5' and vice versa for leading? [16:10] Hi Dr, in drawing the G-C, A-T base pairs, is there a specific way you'll want to see the H-bonding? [16:11] No as long as you have the correct H-bonding with eachother, i.e. like the picture in the lecture notes [16:11] ok, thanks [16:13] * delpee has joined #Chemistry [16:13] Both leading and lagging strands go 5' to 3' becuase that is the only way the DNA Polymerase works [16:13] * delpee1 has joined #Chemistry [16:13] So the lagging strand is synthesized in short segments [16:14] so would that mean the lagging strand works backwards then? [16:14] Yes that is one way to look at it [16:14] ah i see thank you [16:16] professor, back to my question about some definitions, so transcription initiation is the completed assembly of transcription factors and RNA polymerase bind to the promoter [16:17] * Gene has joined #Chemistry [16:17] * delpee has quit IRC (Ping timeout: 240 seconds) [16:17] Initiation: The initiation of transcription is directed by DNA sequences called promoters which tell the RNA polymerase where to begin transcription. The subunits that enable RNA polymerases to recognize and bind promoters are called initiation factors. The initiating nucleotide can be either a purine or pyrimidine. [16:18] ok, i see [16:19] for the DNA mutations, do we need to know the diseases for DNA defects? [16:19] No. [16:20] Do we need to know the detailed functions of RNA promoters I,II,III [16:20] No [16:21] what are the names of the set proteins that hold down leading and lagging strands [16:21] Don't understand the question [16:21] Can you please explaine NER ? [16:22] A 29 nucleotide segment of damaged DNA is then unwound, the gap is filled (DNA polymerase) and the nick sealed (ligase). [16:23] for topoisomerase do we only need to know that it removes positive supercoils or do we need to know the extra details like the types of antibiotics, etc. [16:23] * robo has joined #Chemistry [16:24] What is mis match repair? [16:24] Topoisomerase is an enzyme that removes the positive supercoils that form as the fork is unwound by the helicase. [16:24] You need to use complete sentences or I might not understand what you are saying [16:24] * pollo has quit IRC (Quit: Leaving) [16:25] ah i see, sorry [16:25] * biochem has joined #Chemistry [16:25] * rambo has joined #Chemistry [16:26] Sometimes DNA polymerase incorporates an incorrect nucleotide during strand synthesis and the 3' to 5' editing system, exonuclease, fails to correct it. These mismatches as well as single base insertions and deletions are repaired by the mismatch repair mechanism. Mismatch repair relies on a secondary signal within the DNA to distinguish between the parental strand and daughter strand, which contains the replication error. Because DNA repl [16:26] * pie has joined #Chemistry [16:27] Do we need to know the regulation of damage control ? means gene p53, p21 gaad45 [16:27] No. [16:27] do we need to know the drug names associated with inhibitors of dna replication [16:28] I left right after the quiz on thursday. Is the exam still covering the RNA synthesis and processing? [16:28] Just be able to list them, i.e. substrate analog, intercalating agents etc. [16:29] Everything since Exam 2. We covered both "DNA Mutation and Repair" and "RNA Synthesis and Processing" last Wednesday [16:30] * pie has quit IRC (Quit: Leaving) [16:30] can you explain "initiation"? what part of this process do we have to know? [16:30] Do we need to follow the pink work sheet or the lecture material for the purine and pyrimidine metabolism ? I mean it is very easy to remember from pink sheet. [16:31] * happybun has joined #Chemistry [16:31] Initiation: The initiation of transcription is directed by DNA sequences called promoters which tell the RNA polymerase where to begin transcription. The subunits that enable RNA polymerases to recognize and bind promoters are called initiation factors. The initiating nucleotide can be either a purine or pyrimidine. [16:31] * happybun has quit IRC (Quit: Leaving) [16:31] The pathways as drawn on the hand-outs along with the additional information presented on the board in class. [16:32] i have one more question, for the exam do you want us to know how to translate DNA into structures (i.e. we had a question like that on the first exam where we had to translate DNA from 3 letters) [16:33] No. [16:33] okay thank you [16:33] * Nerdboy has quit IRC (Quit: Leaving) [16:34] for the structures, we have to know how to connect base pairs, right? [16:34] What is elongation - Elongation is RNa polymerase links riboneucleotides together in 5' to 3 direction ? Is that right? [16:34] Yes, show the H-bonding between the bases [16:34] Yes, that is correct. [16:36] professor, during promoter clearance process, the RNA polymerase removes the promoter, what is the purpose of this? [16:37] RnaseH removes promoter sequences [16:38] Does anyone have a strategy for memorizing the pathways? I'm having a hard time. [16:38] what is the role of protein MutS in mismatch repair system [16:38] Focus on the reactions that have enzymes involved in them [16:39] * TREETOP has joined #Chemistry [16:39] i had to write them each segment over and over till i got them right [16:40] MutS basically anchors the mismatched sequence so it can be repaired [16:41] May you please explian mismatch repair? [16:41] Sometimes DNA polymerase incorporates an incorrect nucleotide during strand synthesis and the 3' to 5' editing system, exonuclease, fails to correct it. These mismatches as well as single base insertions and deletions are repaired by the mismatch repair mechanism. Mismatch repair relies on a secondary signal within the DNA to distinguish between the parental strand and daughter strand, which contains the replication error. Because DNA repl [16:42] Do we need to know the function of mut S, H and L [16:42] No [16:42] * rambo has quit IRC (Quit: Leaving) [16:42] thanks [16:43] * bunny has joined #Chemistry [16:44] * TREETOP has quit IRC (Quit: Leaving) [16:45] professor, so elongation is: the RNA polymerase traverses the template strand and produce the exact copy of the coding strand from 5'-> 3' with the exception that T is replaced by U, is that a complete definition yet? [16:46] do we need specifics on diseases from defects in dna repair mechanisms,,,such as xeroderma pigmentsum [16:46] Plus: RNA polymerase links ribonucleotides together in a 5' to 3' direction. The polymerase induces the 3' hydroxyl group of the nucleotide at the 3' end of the growing RNA chain which attacks (nucleophilic)the a phosphorous of the incoming ribonucleotide [16:46] No diseases [16:47] are there specific structures showing the H-bonding of the pyrimidine and purines or we need to draw the indivdual structures and their H bonding? [16:48] i see, thank you [16:48] You need to draw C H-bonding with G, A H-bonding with T or U [16:50] If Origin is the site for DNA synthesis on chromosome , and then what is origins? [16:51] so that means individual structures and then connecting them with the hydrogen bonds? [16:52] Origin: DNA synthesis starts at a specific place on a chromosome called an origin.?? [16:52] Yes individual structures just like in the lecture notes for "Nucleotides: Composition and Structure" [16:52] can you explain rho-dependent termination process? [16:53] * biochem has quit IRC (Quit: Leaving) [16:53] Don't need to know the rho dependent process. [16:53] * Nikki has joined #Chemistry [16:53] can someone help me with my homework? [16:54] This chat room is for college level biochemistry questions. [16:55] so in the termination process, you only need us to know the rho-independent process [16:55] Termination: Certain DNA sequences function as signals that tell the RNA polymerase to terminate transcription. The DNA of a terminator sequence encoded an inverted repeat and an adjacent stretch of uracils. [16:56] i see, thank you professor [16:57] * Nikki has quit IRC (Quit: Leaving) [17:00] * bunny has quit IRC (Ping timeout: 240 seconds) [17:03] * Jay has joined #Chemistry [17:04] Dr, ws #14 - qu.6 - definition of groove [17:04] * hhhh has joined #Chemistry [17:05] * bunny has joined #Chemistry [17:06] do we need to know rna polymerase promoters [17:06] Dr. Sturm, is the picture under the Secondary Structure of Nucleic Acid (the structures of T-A and C-G) of the first handout correct? [17:06] Do you want us to draw the back bone part too or just write "sugar"? [17:07] A groove is the gap fomed as the DNA forms a double helix [17:08] Promoters: The initiation of transcription is directed by DNA sequences called promoters which tell the RNA polymerase where to begin transcription. The subunits that enable RNA polymerases to recognize and bind promoters are called initiation factors. The initiating nucleotide can be either a purine or pyrimidine. [17:08] No the lecture notes for "Nucleotides: Composition and Structure" under Secondary Structure of Nucleic Acids [17:09] Just write sugar [17:10] so that picture is wrong? where can I see the correct drawing? [17:11] Is the defination of template - Existing strand of DNA ? [17:12] No that pictures is correct [17:13] Template: Nucleotide incorporation is determined by base pairing with the template strand of the DNA. The template is the DNA strand, also called the sense strand, that is copied by the RNA polymerase into a complementary strand of RNA called the transcript. The DNA strand that is not copied is know as the antisense strand. [17:13] You need to use complete sentences. [17:14] The picture of the C-G and A-T base pairs with H-bonding in the notes, "Nucleotides: Composition and Structure", is correct [17:15] What is primer? [17:15] do we need to know details of inhibitors of dna replication or just list them [17:15] * bunny has quit IRC (Ping timeout: 240 seconds) [17:15] Just list the inhibitors [17:16] Primer: DNA synthesis requires a primer usually made of RNA. A primase synthesizes the ribonucleotide primer ranging from 4 to 12 nucleotides in length. DNA polymerase then incorporates a dNMP onto the 3' end of the primer initiating leading strand synthesis. [17:16] do we need to know details of DNA repair mechanisms like MutS MutL etc [17:17] Not MutS, MutL [17:19] should we know TFIIH [17:19] No. [17:19] * jun has joined #Chemistry [17:20] how does recombination repair work? [17:20] or should i just not bother knowing? [17:21] So the template is copied into a complementary strand of DNA for DNA synthesis ? [17:21] The cell replicates past the damage and comes back later to fix it. [17:21] why is renaturing important for replication and transcription [17:23] For DNA synthesis the DNA is denatured, parent and daughter, then one strand from each is replicated. [17:23] * guest has joined #Chemistry [17:23] * Gene has quit IRC (Quit: Leaving) [17:23] DNA that has not "renatured" formed a double helix would not be functional [17:24] * Gene has joined #Chemistry [17:25] if we check the lecture material for DNA synthesis, the template is DNA strand copied in to complementary strand of DNA. [17:26] Can we just use that defination for template? [17:26] So a strand from the parent and one from the daughter is denatured then serves as a template for replication [17:26] we dont need to draw atp correct? [17:26] Do not need to draw ATP [17:26] Are we required to know the 3 possible mechanisms for semiconservative DNA replication? [17:27] No [17:27] Just this one: two replication forks are initiated at the origin and as synthesis proceeds the two forks migrate away from one another. This type of replication is called bi-directional. Most organisms, including mammals, use bi-directional replication. [17:27] what is the secondary structure of RNA [17:28] The secondary structure of RNA consists of a single polynucleotide. RNA can fold so that base pairing occurs between complementary regions. RNA molecules often contain both single- and double-stranded regions. The strands are antiparallel and assume a helical shape. [17:29] Are we required to know specific names of inhibitors of DNA replication or just the 4 types? [17:29] how many questions are there for the test [17:30] 34 [17:31] is the whole handout about pyrimidine metabolism about the synthesis? or is the second part degredation and third salvage? [17:31] what is Telomerase? [17:32] Purines is synthesis, degradtion, slavage and regulation, Pyrimidines mainly synthesis and regulation [17:33] Do we need to know the diagram on the first page of the Nucleotides: Composition and Structure handout? [17:33] and we must know all the steps correct? [17:33] * jun has quit IRC (Ping timeout: 240 seconds) [17:33] Telomerase is an enzyme that extends the 3' ends of a chromosome by adding numerous repeats of a six base pair sequence until the 3' end of the lagging strand is long enough to be primed and extended by DNA polymerase. [17:34] What is primer? [17:34] Just the over-view: DNA ---> RNA ---> Protein [17:34] * DNA has joined #Chemistry [17:34] Primer: DNA synthesis requires a primer usually made of RNA. A primase synthesizes the ribonucleotide primer ranging from 4 to 12 nucleotides in length. DNA polymerase then incorporates a dNMP onto the 3' end of the primer initiating leading strand synthesis. [17:35] * bunny has joined #Chemistry [17:35] Thanks [17:35] What do we have to know about the regulation of PRPP amidotransferase? [17:36] Hi! Is RNaseH the same as DNA pol I? [17:37] should we know about alpha-amanitin? [17:37] PRPP Amidotransferase is activated by PRPP and inhibited by IMP, GMP and AMP [17:37] Is RnaseH defination is an enzymes removes the Rna from OKAZAKI fragment? [17:38] Yes for Rnase definition and no it is not the same as DNA Polymerase I [17:38] Don't need to know alph-amanitin [17:38] DNA polymerase digests the RNA primers and replaces them with DNA in the 5' to 3' direction correct? [17:39] No [17:39] It uses the RNA primers as a starting point for synthesis [17:40] Should we know specific details about the 3 modifications from hnRNA to mRNA? [17:40] Just be able to list them. [17:40] Do we need to know the detailed process of DNA replication? [17:41] whats the purpose of HGRPT in salvage cycle of purines [17:41] Don't understand the question, you need to be able to define the terms on the vocabularly list handed out in class [17:41] do we need to know all the drugs names? [17:42] No drug names [17:42] How much detail should we know about the 3 RNA pol promoters? [17:42] Just be able to define Promoter [17:44] what do we need to know about CPS II and it's regulation? [17:45] Carbamoyl Phosphate Synthetase II (CPS-II) differs in several ways from its isoform (CPS-I), the enzyme which provides carbamoyl phosphate for the Urea cycle (see "Protein Turnover / Ammonia Metabolism"). [17:45] 1. CPS-II is located in the cytoplasm, CPS-I mitochondria [17:45] 2. Glutamine not Ammonia is the Nitrogen source [17:45] 3. CPS-II does not require N-acetylglutamate as an allosteric activator [17:45] 4. CPS-I is found only in Liver and Kidney, CPS-II in most tissues [17:45] Regulation: it is activated by PRPP [17:47] * DNA has quit IRC (Quit: Leaving) [17:47] Dr, does UTP play a role in CPS-II regulation? [17:48] Are we required to know all the enzymes that deal with purine and pyrimidine metabolism? [17:48] how does ASP function in pyrimidine synthesis [17:49] * eeeeeeks has joined #Chemistry [17:49] what do we need to know about the regulation of damage control of dna mutation and repair? and types of diseases? [17:50] Yes CPS-II is inhibited by UTP [17:50] ok [17:50] Only the ones on the lilac hand-out [17:50] can we appreviate methotrexate with MTX [17:51] It is used to synthesize carbamoyl aspartate [17:51] Yes, abbreviations are always fine as long as they are correct.............. [17:52] Dr, would it be ok to draw the flow charts on the test paper when we start ? [17:53] i.e the purines/pyrimidines [17:53] You can use the back of the test for drawings [17:54] ok [17:54] Do we need to know all the RNA polymerases? [17:54] Just a definition for RNA Polymerase [17:54] would you suggest to focus more on purine metabolism or pyrimidine metabolism [17:55] * confused has joined #Chemistry [17:55] * confused has quit IRC (Quit: Leaving) [17:55] Wouldn't choose one over the other but I would focus on reactions with enzymes associted with them [17:56] ok thank you [17:56] Rna polymerase [17:56] * confused has joined #Chemistry [17:56] hi professor, do we need to know the medication names? and their functions? [17:57] Sorry I mean What is the defenation for RNA polymerase [17:57] Should we know all the causes of DNA mutation in detail? [17:57] RNA polymerase links ribonucleotides together in a 5' to 3' direction. The polymerase induces the 3' hydroxyl group of the nucleotide at the 3' end of the growing RNA chain which attacks (nucleophilic)the a phosphorous of the incoming ribonucleotide. [17:57] * klassyx has quit IRC (Ping timeout: 240 seconds) [17:57] Thanks [17:58] Causes of DNA mutation are not on the list [17:58] do we need to know treatment for gout/ [17:58] Any last questions? [17:58] how many question on exam [17:58] 34 [17:58] Yes you need to know about allopurinol [17:58] do we need to know the medication, drug names? [17:59] thanks, Dr [17:59] No drug names other than allopurinol [17:59] You are welcome. [17:59] thanks [17:59] O.K., E-mail if you have more questions tonight. [17:59] * guest has quit IRC (Quit: Leaving) [17:59] * DrSturm has quit IRC [17:59] have a good one, see u tomorrow [18:00] i am still confused [18:00] * Disconnected Session Close: Tue Nov 11 18:00:16 2008