Session Start: Tue Sep 23 11:34:37 2008 Session Ident: #Chemistry [11:34] * Now talking in #Chemistry [11:34] * chemistry.gravitywaves.com sets mode: +nt [15:37] * che450 has joined #Chemistry [15:37] * che450 has quit IRC (Quit: Leaving) [15:55] * LA has joined #Chemistry [16:00] * DrSturm has joined #Chemistry [16:00] * pKa has joined #Chemistry [16:01] hi dr sturm, i had a question regarding the structure of TRNA, do we have to know the function of the TC and DHU arms? [16:01] * WAT has joined #Chemistry [16:01] No [16:02] can you explain the action of G-proteins [16:02] * pH has joined #Chemistry [16:02] * che450 has joined #Chemistry [16:02] You do not need to know anything about G-proteins [16:03] thanks [16:05] how about collagen maturation? [16:05] You need to understand collagen maturation [16:06] hi....Dr.Sturm....I have question for worksheet #5. Describe a common structural modification of circulating globular proteins and indicate which specific residues are midified? [16:06] my answer is are often modified to increase solubitlity [16:06] and [16:06] Glycosylation, attachment of a sugar to Ser, Thr, Tyr, Asn, Gln [16:06] enchance biological acitivity [16:06] is that coorect? [16:07] attachment of a sugar to a protein? [16:07] No, see answer above. [16:08] can you explain collagen maturation [16:08] please [16:09] * Phosphol has joined #Chemistry [16:09] on the effects of sat/unsat lipids, (WS#6: ) does the saturated lipid give the membrene less fluid? [16:09] * xxkdjks has joined #Chemistry [16:10] *membrane [16:10] Collagen's primary structure is unique w/ a Gly reisdue every third position, secondary structure tight alph-helices, tertiary structure triple helices and quaternary structure consists of fibrils [16:10] unstaurated fatty acids make a membrane less fluid, also cholesterol can make is less fluid [16:11] thanks [16:11] how do u define collagen? [16:11] * che450 has quit IRC (Quit: Leaving) [16:11] how does that happen? is it bec of the double bonds? [16:12] unique type of triple helix ,stabilized by crosslinked?is theis the definition of collagen? [16:13] Yes, the double bonds in unsaturated fatty acids [16:13] collagen is a structural (fibrous) protein [16:13] * che450 has joined #Chemistry [16:13] ok that makes sense, tnx [16:14] Yes, notice in the pictures the unsaturated fatty acids stick out at odd angles because of the double bonds which are rigid unlike single bonds [16:15] Can you please explain the Blood group antigens? [16:16] The bllod goups A, B, AB arise because of the different CHO structures found on the surface of a given individuals RBC's [16:17] which domain of a membrane protein is usually glycosylated? [16:17] Blood group antigens are another way that glycoproteins and glycolipids attached to the surface of membranes are important [16:17] The extracellular domain of a membrane is glycosylated [16:19] so then the glycoproteins contain vast amt of "bio info" due to glycosylation? [16:19] * xxkdjks has quit IRC (Quit: Leaving) [16:19] Yes, they allow cell-cell communication and recognition [16:19] * xxkdjks has joined #Chemistry [16:19] tnx [16:19] * hoffmann has joined #Chemistry [16:20] which domain of a protein is usually glycosylated? [16:20] The extracellular domain. [16:22] pumps and receptor are asymmetric because you can find them outside of the surface of the cell, as well with CHO's too, right? [16:23] * xxkdjks has quit IRC (Quit: Leaving) [16:24] Everything associated with a membrane is asymmetric. [16:24] * tRNA has joined #Chemistry [16:25] * Phosphol has quit IRC (Quit: Leaving) [16:26] * WAT has quit IRC (Quit: Leaving) [16:26] * Phospho has joined #Chemistry [16:27] * che450 has quit IRC (Quit: Leaving) [16:28] Can you describe the 4 subclasses of lipids and example of each [16:28] * kobe has joined #Chemistry [16:28] * che450 has joined #Chemistry [16:29] Fatty acids, triglycerides, phospholipids and sterols [16:30] Thank you [16:31] Can you describe a common structural modification of circulating globular proteins and indicate which specific residues are modified? Is it glycosilation and the residues are "o" linked to Ser and "N" linked to Asn [16:32] Yes, also Thr, Tyr and Gln [16:33] For the co-factor of Amino acids residues in collagen can we say "vitamin C" instead of ascorbic Acid [16:34] Do we need to know the sequence of DNA and transcribe it into mRNA? [16:34] where are Thr, Tyr and Gln linked? o or n? [16:34] which of the functional grps in the human body are capable of hydrogen bonding? [16:35] Vitamin C is fine [16:35] When it comes to tertuary and quaternary structures how does the hydrophobic effect is a major drving force in the conformation of protein in a aqueous enviroment [16:35] You do not need to transcribe DNA into mRNA but you should know how to transcribe codons into a protein [16:36] Thr, Tyr are "O" linked and Gln "N" [16:36] how do you define charged tRNA? [16:36] All of the "functional" groups are capable of H-bonding [16:37] tRNA carries the activated amino acid for incorporation into the growing protein [16:37] * cbone has joined #Chemistry [16:38] The types of RNA used in translations are they mRNA, tRNA, and rRNA? [16:39] * Don has joined #Chemistry [16:39] There are many types of RNA, we briefly discussed mRNA and tRNA [16:39] Do we need to know the steps for amino acis activation? [16:40] * pH has quit IRC (Quit: Leaving) [16:40] No. [16:40] what will be emphasized from the section on proteins? [16:41] Pretty much anything in the lecture notes and that we did in class is fair game [16:41] can you explain tertuary and quaternary structures how does the hydrophobic effect is a major drving force in the conformation of protein in a aqueous enviroment ? [16:42] Do we have to know the different antibiotics and Toxins [16:42] Do we need to know the detailes of integral membrane proteins? [16:43] Tertiary structure is the folding of the entire protein, quaternary is when two or more complete proteins come together to make one fully functioning protein [16:43] Yes, you need to know the antibiotics and toxins which inhibit transcription [16:44] Can you tell whch are the major components of ribosome in translation [16:45] Don't understand the question. [16:46] The function of the ribosomes is the site of the proten synthesis in translation? [16:46] do we need to know full detAIls of toxins ANd aNtibiotics related to trascription [16:46] * Don1 has joined #Chemistry [16:46] * Don1 has quit IRC (Quit: Leaving) [16:46] Yes and yes [16:46] Work sheet 4 question 4 says State the function of the ribosome in translation and list its major components [16:47] All you need to know is that the ribosomes are the sight for protein synthesis [16:47] *site [16:49] * Don has quit IRC (Ping timeout: 240 seconds) [16:49] can you please explain how do we compare water to a representative carboxylic acid? [16:50] A carboxylic acid is much more likely to ionize and hence is a stronger acid than water [16:51] do we need to know the shingosine of the sphingomyelin,or just know the different groups associated that make up the sphingolipid [16:51] For the collagen maturation are you going to ask the steps and what happen in each [16:52] Just that sphingolipids are an important part of membrane structure because of their amphiphilicity [16:52] You should know the steps in collagen maturation [16:53] Do we need to know the detailes of integral membrane proteins? [16:53] For collagen do we have to know the reaction the residues and the co-factor [16:54] You do not need to know the details of the two receptors: RTK's and G-proteins [16:54] Yes you should know the five specializations seen in collagen [16:55] Do we need to know the steps for amino acis activation? [16:55] * student has joined #Chemistry [16:55] No [16:55] will we have to diagram the action of g-proteins and Na/K ATPase? [16:56] No [16:56] what will we have to know about integral membrane proteins? [16:56] H0-Lysine---which make glycosilation it doesn't have a co-factor wright? [16:56] You do not need to know the details for the receptors everything else is fair game [16:56] ok [16:56] Which domain of a membrane protein is usually glycosylated and how do membrane glycoproteins may contain a vast amount of biological "information"? [16:57] Correct [16:57] extracellular dommain [16:57] * tRNA has quit IRC (Quit: Leaving) [16:57] The extracellular domain, the glycoproteins and glycolipids. [16:59] the sugar part of the glycoprotein contains the biological information correct? [16:59] The glyco-proteins and lipids allow cells to communicate and recognize eachother [16:59] * tRNA has joined #Chemistry [17:01] what is an important stabilizing modification of alpha-keratin? [17:02] disulfide bonds [17:02] * pKa has quit IRC (Quit: Leaving) [17:03] Do we need to know the 5 modifications of amino acid residues in collagen? [17:03] WS 6 says diagram (describe) the action of G-proteins, what is that you want [17:03] Don't need to worry about that for the exam [17:03] * testtaker has joined #Chemistry [17:04] * testtaker has quit IRC (Quit: Leaving) [17:04] WS#3,Question3, Can you please explain the Four features of sodiam bicarbonate that help effective buffer system? [17:04] * testtaker has joined #Chemistry [17:04] * testtaker has quit IRC (Quit: Leaving) [17:04] The bicarbonate equation is a great buffer because it can respond to changes in CO2, H+ and HCO3- [17:05] Tx [17:07] can you explain the hydrophobic effect? [17:07] * tRNA has quit IRC (Quit: Leaving) [17:08] "Like attracts like", hydrophobic residues tend to join together in the center (interior) of the protein while the hydrophilic residues remain on the outside exposed to water [17:08] * Phospho has quit IRC (Quit: Leaving) [17:09] I still don't understand the 4 features that make it an effective buffering system? can you number it off? [17:10] in elastin, what stands are connected to the desmosine [17:11] * Phospho has joined #Chemistry [17:11] * Phospho has quit IRC (Quit: Leaving) [17:11] Protein strands are connected together in a repeating uits called desmosine [17:11] what is the significance of the desmosine in elastin [17:12] It is the repeating structural unit that makes elstin tough [17:12] thaNks [17:12] Is this same as 4 way cross link of Lysine is desmosine? [17:13] The four protein strands connect together via Lys [17:13] do we need to know the heritable diseases related to collagen? [17:14] Yes, in as much detail as we went through on the board during class [17:16] can you describe a common structural modification of circulating globular protains, and indicate which specific residues are modified? is it Asn --> Ser? [17:17] Glycosylation, "O' link through Ser, Thr, Tyr, "N" link via Asn, Gln [17:17] * surrurr has joined #Chemistry [17:19] For worksheet 5, ques 6: Identify which domain of a membrane protein is usally gylcosylated? Is the answer "Receptors" [17:19] The extracellular domain [17:20] that is only for MEmbrane protein rytt [17:20] Yes, membrane proteins [17:21] do we need to know the diagram of the G-Proteins? or is it sufficient to know that G-proteins activate other membrane proteins which bind GTP? [17:22] Can you explain on how membrane gycoproteins may contain huge amount of biological information? [17:22] will we need ot know which subunits are affected by antibiotics and toxins? [17:23] The glyco-proteins and lipids allow cell-cell communication and recognition and also play a role in blood typing (htose associated w/ RBC's) [17:24] for case study 1, aspirin was the diagnosis and treatment was stomach pump,,how can I prepare for alternate diagnosis and their treatments [17:25] Can you go over delineate the steps in collagen maturation? [17:25] the rules for recognizing/diagnosing acidosis/alkalosis (the end of the "Acidosis/Alkalosis" lecture) [17:26] Basically the picture, followed by the legend in the lecture notes. [17:27] so basically takes place from nucleus to mitochondria to rough ER and then secretion [17:27] out of the cell [17:28] Yes, and specifically what happens in each compartment is in the legend below the diagram [17:30] what is 2ndary and tertiary structure of mature collagen and importance of glycin residues? [17:32] Gly cine every third residue ( primary structure) allows the tight collagen helix (secondary structure), then the triple helices (tertiary structure) then finally fibril formation (quaternary structure) [17:35] so gylcine residues basically helps the formation of primary, seconday, tertiary and quaternary stucture right? [17:35] Yes. [17:37] how a polypeptide can be hydrophobic, hydrophilic or amphilic based on its amino acid sequence (primary structure)? I think it depends on R group of amino acid is it right? [17:38] Yes, it depends on the chemistry of the "R" groups [17:40] what is the significance of enzyme glycosylation [17:40] If amino acid is basic or acidic will it be amphilic? [17:41] * PAINnthe has joined #Chemistry [17:41] Will what be amphiphilic? [17:42] Glycosylation provides high information content, allowing cell-cell communication and recognition [17:42] Can you clarify the 4 subclasses of lipids? [17:43] Fatty acids, triglycerides, phospholipids, sterols [17:43] If amino acid is basic or acidic will polypeptide be amphilic? [17:44] in future lectures, can you please slow down? it's hard for us to listen, write and attempt to process the information at the same time [17:44] All proteins are amphiphilic, they have both hydrophobic and hydrophilic residues, they can have "hydrophibic" patches [17:45] when choesterol impedes the motion of hydrocarbon tails providing less fluid, does that make membrane less stable [17:46] No, not really related to stability, really only makes a difference to animals whose body temperatures are low, i.e. hybernating bears [17:48] Membrane fluidty of saturated and unstatured lipids will be less membrane fluid on saturated compare to unstaurated and more membrane fluid on unstaturated compare to saturated and less membrane fluid on unsaturated compare to cholestorol? [17:48] Unsaturated fatty acids make the membrane less fluid [17:49] how about saturated fatty acids then? [17:49] is it vice versa [17:50] saturated fats pack more easily because they don't contain any double bonds (unsaturation), C-C single bonds can rotate freely [17:50] Is it okay to email you with questions for tomorrows test since I wasnt able to attend most of the chat room? [17:52] Yes, check the log for the chat room on the home page of the web site as many of your questions may have been answered. [17:54] Can you list four features which help sodium bicarbonate equilibrium equation an effective blood buffering system? [17:54] okay [17:55] * Phospho has joined #Chemistry [17:55] The ability of the equation (body) to respond to variations in concentration of CO2, H+ and HCO3- [17:55] Will we need to know the Henderson-Hasselbach equation? [17:56] No [17:57] O.K., any last minute questions? [17:57] Can you define wobble for me [17:57] Thank You [17:57] * PAINnthe has quit IRC (Quit: Leaving) [17:57] can you go over structural modification of circulating globular proteins and indicate which specific residues are modified? [17:58] Glycosylation, "O" linked Thr, Ser, Tyr, "N" linked Gln, Asn [17:58] does wobble that happen on first of last base of the codon [17:58] the third base [17:59] ok thaNks [17:59] how does non enzymatic glycosylation provide useful clinical information concerning diabetic patients? [18:00] Glycosylated Hb (AGE's) are a marker of long term blood glucose control [18:00] See you tomorrow. [18:00] thanks [18:00] * DrSturm has quit IRC [18:00] * Disconnected Session Close: Tue Sep 23 18:00:26 2008