CELL

<body topmargin=0 leftmargin=0 marginheight=0 marginwidth=0><script type="text/javascript"> ////// Compete ///////////////////// __compete_code = '667f89f26d96c30e99728fe6a608804d'; (function () { var s = document.createElement('script'), d = document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0], t = 'https:' == document.location.protocol ? 'https://c.compete.com/bootstrap/' : 'http://c.compete.com/bootstrap/'; s.src = t + __compete_code + '/bootstrap.js'; s.type = 'text/javascript'; s.async = 'async'; if (d) { d.appendChild(s); } })(); ////// Quantcast ///////////////////// function channValidator(chann) { return (typeof(chann) == 'string' && chann != ''); } function lycosQuantcast(){ var lb = ""; if(typeof(cm_host) !== 'undefined' && channValidator(cm_host)){ lb += cm_host.split('.')[0] + '.'; } if(typeof(cm_taxid) !== 'undefined' && channValidator(cm_taxid)){ lb += cm_taxid; lb = lb.replace('/',''); } else { lb = lb.replace('.',''); } return lb; } var _qevents = _qevents || []; (function() { var elem = document.createElement('script'); elem.src = (document.location.protocol == "https:" ? "https://secure" :"http://edge") + ".quantserve.com/quant.js"; elem.async = true; elem.type = "text/javascript"; var scpt = document.getElementsByTagName('script')[0]; scpt.parentNode.insertBefore(elem, scpt); })(); _qevents.push({ qacct:"p-6eQegedn62bSo", labels:lycosQuantcast() }); /////// Google Analytics var _gaq = _gaq || []; _gaq.push(['_setAccount', 'UA-21402695-21']); _gaq.push(['_setDomainName', 'angelfire.com']); _gaq.push(['_setCustomVar', 1, 'member_name', 'md/danil', 3]); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); ////// Lycos Initialization ///////////////////// var lycos_ad = Array(); var lycos_search_query = ""; var lycos_onload_timer; var cm_role = "live"; var cm_host = "angelfire.lycos.com"; var cm_taxid = "/memberembedded"; var angelfire_member_name = "md/danil"; var angelfire_member_page = "md/danil/celldeath/id26.htm"; var angelfire_ratings_hash = "1338606059:2f443503ba3f487c5a8eaf5c329bbab5"; var lycos_ad_category = {"dmoz":"kids_and_teens\/directories","ontarget":"&CAT=family%20and%20lifestyles&L2CAT=kids&CAT=family%20and%20lifestyles&L2CAT=teens","find_what":"paris"}; var lycos_ad_remote_addr = "38.107.179.221"; var lycos_ad_www_server = "www.angelfire.lycos.com"; var edit_site_url = "www.angelfire.lycos.com/landing/landing.tmpl?utm_source=house&utm_medium=landingpage&utm_campaign=toolbarlink"; </script> <script type="text/javascript" src="http://scripts.lycos.com/catman/init.js"></script> <script type="text/javascript"> (function(isV) { if (!isV) { return; } //this.lycos_search_query = lycos_get_search_referrer(); var adMgr = new AdManager(); var lycos_prod_set = adMgr.chooseProductSet(); var slots = ["leaderboard", "leaderboard2", "toolbar_image", "toolbar_text", "smallbox", "top_promo", "footer2"]; var adCat = this.lycos_ad_category; adMgr.setForcedParam('page', (adCat && adCat.dmoz) ? adCat.dmoz : 'member'); if (this.lycos_search_query) { adMgr.setForcedParam("keyword", this.lycos_search_query); } else if (adCat && adCat.find_what) { adMgr.setForcedParam('keyword', adCat.find_what); } for (var s in slots) { var slot = slots[s]; if (adMgr.isSlotAvailable(slot)) { this.lycos_ad[slot] = adMgr.getSlot(slot); } } adMgr.renderHeader(); adMgr.renderFooter(); }((function() { var w = 0, h = 0, minimumThreshold = 300; if (top == self) { return true; } if (typeof(window.innerWidth) == 'number' ) { w = window.innerWidth; h = window.innerHeight; } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) { w = document.documentElement.clientWidth; h = document.documentElement.clientHeight; } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) { w = document.body.clientWidth; h = document.body.clientHeight; } return ((w > minimumThreshold) && (h > minimumThreshold)); }()))); </script> <style> #body .adCenterClass{margin:0 auto} </style> <div style="background:#abe6f6; border-bottom:1px solid #507a87; position:relative; z-index:9999999"> <div class="adCenterClass" style="display:block!important; overflow:hidden; width:916px;"> <a href="http://www.angelfire.lycos.com/" title="Angelfire.com: build your free website today!" style="display:block; float:left; width:186px; border:0"> <img src="/adm/ad/angelfire-freeAd.jpg" alt="Site hosted by Angelfire.com: Build your free website today!" style="display:block; border:0" /> </a> <script type="text/javascript">document.write(lycos_ad['leaderboard']);</script> </div> </div> <div id="lycosFooterAd" style="background:#abe6f6; border-top:1px solid #507a87; clear:both; display:none; position:relative; z-index:9999999"> <div class="adCenterClass" style="display:block!important; overflow:hidden; width:916px;"> <div id="aflinksholder" style="float:left; width:186px;"> <a href="http://www.angelfire.lycos.com/" title="Angelfire.com: build your free website today!" style="display:block; border:0"> <img src="/adm/ad/angelfire-freeAd2.jpg" alt="Site hosted by Angelfire.com: Build your free website today!" style="display:block; border:0" /> </a> <div style="text-align:center"> <span style="color:#393939!important; font-size:12px!important; position:relative; top:-6px"> Sponsored by </span> <a href="http://www.listen.com/disty/index.jsp?from=lycos" target="_blank"> <img src="http://af.lygo.com/d/toolbar/sponsors/rhapsody_logo.jpg" alt="sponsor logo" title="Rhapsody"/> </a> </div> </div> <div style="float:left; width:728px; overflow:hidden"> <script type="text/javascript"> document.write(lycos_ad['leaderboard2']); </script> </div> </div> </div> <script type="text/javascript"> window.onload = function() { var f = document.getElementById("lycosFooterAd"); var b = document.getElementsByTagName("body")[0]; b.appendChild(f); f.style.display = "block"; } </script> <noscript> <img src="http://www.angelfire.com/doc/images/track/ot_noscript.gif?rand=971466" alt="" width="1" height="1" />  <iframe frameborder="0" marginwidth="0" marginheight="0" scrolling="no" width="728" height="90" src="http://ad.yieldmanager.com/st?ad_type=iframe&ad_size=728x90&section=280303"></iframe>  </noscript> <table cellpadding=0 cellspacing=0 border=0 height="100%"><tr> <td valign="top" width=168 BGCOLOR="#000000" TEXT="#F7F7FF" background="041a11c3.gif"> <div> <IMG SRC="2c6f2590.jpg" border=0 width="242" height="345" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><A HREF="id18.htm" TARGET="_top" TITLE="INTRODUCTION"><U>INTRODUCTION</U></A></div> <div> CELL</div> <div> <A HREF="id19.htm" TARGET="_top" TITLE="DEFINITION"><U>DEFINITION</U></A></div> <div> <A HREF="id20.htm" TARGET="_top" TITLE="CELL DEATH AND ADAPTATION"><U>CELL DEATH AND ADAPTATION</U></A></div> <div> <A HREF="id30.htm" TARGET="_top" TITLE="AMYLOIDS"><U>AMYLOIDS</U></A></div> <div> <A HREF="id28.htm" TARGET="_top" TITLE="APOPTOSIS"><U>APOPTOSIS</U></A></div> <div> <A HREF="id29.htm" TARGET="_top" TITLE="CRYSTALS"><U>CRYSTALS</U></A></div> <div> <A HREF="id27.htm" TARGET="_top" TITLE="CRITERIA"><U>CRITERIA</U></A></div> <div> <A HREF="id21.htm" TARGET="_top" TITLE="CAUSES"><U>CAUSES</U></A></div> <div> <A HREF="id22.htm" TARGET="_top" TITLE="NECROSIS"><U>NECROSIS</U></A></div> <div> <A HREF="id23.htm" TARGET="_top" TITLE="AGING"><U>AGING</U></A></div> <div> <A HREF="id24.htm" TARGET="_top" TITLE="FAVORITE LINKS"><U>FAVORITE LINKS</U></A></div> <div> <A HREF="id25.htm" TARGET="_top" TITLE="PICTURES"><U>PICTURES</U></A></div> <div> <A HREF="id32.htm" TARGET="_top" TITLE="My Photos"><U>My Photos</U></A></div> <div> <A HREF="id17.htm" TARGET="_top" TITLE="Contact Me"><U>Contact Me</U></A></div> </td> <td valign="top" BGCOLOR="#000000" TEXT="#F7F7FF"> <div> <FONT SIZE="5" COLOR="#99CC00" FACE="Arial" ><B>CELL AND DEATH    [CELL INJURY]</b></FONT>     <FONT SIZE="1" COLOR="#CCCC66" FACE="Arial" >|   <A HREF="index.htm" TARGET="_top" TITLE="CELL AND DEATH CELL INJURY"><U><B>home</b></U></A></FONT></div> <div> <A HREF="id18.htm" TARGET="_top" TITLE="INTRODUCTION"><U>INTRODUCTION</U></A>   |   <B>CELL</b>   |   <A HREF="id19.htm" TARGET="_top" TITLE="DEFINITION"><U>DEFINITION</U></A>   |   <A HREF="id20.htm" TARGET="_top" TITLE="CELL DEATH AND ADAPTATION"><U>CELL DEATH AND ADAPTATION</U></A>   |   <A HREF="id30.htm" TARGET="_top" TITLE="AMYLOIDS"><U>AMYLOIDS</U></A>   |   <A HREF="id28.htm" TARGET="_top" TITLE="APOPTOSIS"><U>APOPTOSIS</U></A>   |   <A HREF="id29.htm" TARGET="_top" TITLE="CRYSTALS"><U>CRYSTALS</U></A>   |   <A HREF="id27.htm" TARGET="_top" TITLE="CRITERIA"><U>CRITERIA</U></A>   |   <A HREF="id21.htm" TARGET="_top" TITLE="CAUSES"><U>CAUSES</U></A>   |   <A HREF="id22.htm" TARGET="_top" TITLE="NECROSIS"><U>NECROSIS</U></A>   |   <A HREF="id23.htm" TARGET="_top" TITLE="AGING"><U>AGING</U></A>   |   <A HREF="id24.htm" TARGET="_top" TITLE="FAVORITE LINKS"><U>FAVORITE LINKS</U></A>   |   <A HREF="id25.htm" TARGET="_top" TITLE="PICTURES"><U>PICTURES</U></A>   |   <A HREF="id32.htm" TARGET="_top" TITLE="My Photos"><U>My Photos</U></A>   |   <A HREF="id17.htm" TARGET="_top" TITLE="Contact Me"><U>Contact Me</U></A></div> <div> <IMG SRC="040f4010.gif" border=0 width="500" height="1" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> CELL</div> <div> <IMG SRC="0ac226b0.jpg" border=0 width="546" height="363" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> VULNEABLE ORGANELLES <FONT SIZE="2" COLOR="#0000FF" FACE="Arial" ><U><IMG SRC="0c995a40.jpg" border=0 width="405" height="420" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></U></FONT></div> <div> <IMG BORDER="0" SRC="Symb075c00b700c8ccffff00.gif" HEIGHT="13" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">membranes</div> <div> <IMG BORDER="0" SRC="Symb075c00b700c8ccffff00.gif" HEIGHT="13" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">mitochondria</div> <div> <IMG BORDER="0" SRC="Symb075c00b700c8ccffff00.gif" HEIGHT="13" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">cytoskeleton</div> <div> <IMG BORDER="0" SRC="Symb075c00b700c8ccffff00.gif" HEIGHT="13" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">DNA</div> <div> CELLULAR ORGANELLE CHANGES</div> <div> <B><IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">Cell Organelle Swelling</b></div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">cloudy swelling, hydropic degeneration, fatty change</div> <bR> <div> <B><IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">Metabolic Changes</b></div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">loss of ATP, enzymes activated by calcium</div> <bR> <div> <B><IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">Membrane Dissruptions</b></div> <bR> <div> <B><IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">Intracellular Accumulations</b> </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">lipid </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">protein </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">glycogen </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">pigments </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">breakdown products </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ccffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">lipofuschin</div> <div> If you're not familiar with the cell cycle, here's a very brief summary for you.</div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0"> Basically, the cell cycle is the "program" for cell growth and cell division (proliferation). </div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">There are 4 broad phases of the cell cycle: <I>G1</I><I> </I><I>(and</I><I> </I><I>G</I><FONT SIZE="1" COLOR="#FFFFFF" FACE="Arial" ><I>0</I></FONT><I>),</I><I> </I><I>S</I><I>,</I><I> </I><I>G2</I><I>, and </I><I>M</I>.</div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">The <I><U>G1 (Gap 1) phase</U></I><I> </I>is characterized by gene expression and protein synthesis. This is really the only part of the cell cycle regulated primarily by extracellular stimuli (like mitogens and adhesion). Anyway, this phase enables the cell to grow and to produce all the necessary proteins for DNA synthesis. Why is this important? Well, it primes the cell to enter the next phase: S (Synthesis) phase.</div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">During the <I><U>S phase</U></I>, the cell replicates its DNA...so it now has 2 complete sets of DNA. Why would the cell want 2 complete sets of DNA? This allows the cell to divide into two daughter cells, each with a complete copy of DNA. But, before the cell can do this, it needs to enter the third phase of the cell cycle: the G2 (Gap 2) phase.</div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">During the <I><U>G2 phase</U></I>, the cell again undergoes growth and protein sythesis (it needs enough proteins for 2 cells!)...priming it to be able to divide. Once this is complete (by the way, there are many <I>"checkpoints"</I> along the way!), the cell finally enters the fourth and final phase of the cell cycle: the M (Mitosis) phase.</div> <div> <IMG BORDER="0" SRC="Symb075c00b700f0ffffff00.gif" HEIGHT="16" WIDTH="24" ALIGN="bottom" HSPACE="0" VSPACE="0">During the <I><U>M phase</U></I>, the cell splits apart (called <I>cytokinesis</I>) into two daughter cells. Now, the cycle has been completed! What do the cells do know? Well, there are two choices...it can either start the cycle again by entering G1, or it can become quiescent by entering G<FONT SIZE="1" COLOR="#FFFFFF" FACE="Arial" >0</FONT> </div> <div> <IMG SRC="2e0a7370.gif" border=0 width="423" height="311" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><FONT SIZE="3" COLOR="#000080" FACE="Arial" >proteins involved in controlling the cell cycle. The main </FONT><B>families that I will discuss are the </b><B>cyclins</b><B> (especially cyclin D and cyclin E...and little about cyclin A), the</b><B> </b><B>cyclin-dependent kinases</b><B> (especially CDK4, CDK6, and CDK2), the </b><B>CDK inhibitors</b><B> </b><B>(especially p16, p21, and p27), and the </b><B>tumor supressor genes</b><B> </b><B>(especially Rb and p53). Because of the complexity of these pathways, I'll divide them into two separate pages: the </b><B>Rb pathway </b><B>and the </b><B>p53 pathway</b><B>.</b></div> <div> <B>Of course, one of the main clinical interests of cell cycle control is </b><B>cancer</b><B>. Cancer can be very briefly described as uncontrolled cell growth and proliferation (as well as </b><B>metastasis</b><B>, or the invasiveness of cancerous cells into other tissues). Therefore, research in understanding cell cycle control has many implications for cancer, especially for the development of therapeutics. Thus, throughout this page, as I describe each of the above proteins and their roles in controlling the cell cycle, I will also try to mention their abnormal role (either gain of function or loss of function) in cancer. </b></div> <div> Another critical protein in regulating the cell cycle is the tumor suppressor protein p53. In fact, p53 is the most frequently disrupted gene in cancer, illustrating its importance. What is p53 and why is it important? Well, p53 is a DNA-binding protein involved in regulating the expression of genes involved in cell cycle arrest (like p21WAF1/CIP1, check out my <U>Rb page</U> if you missed this!) and apoptosis (such as Bax check out my <U>Apoptosis page</U>!). Apoptosis is basically cellular suicide. So, as you can probably guess from its functions , p53 recognizes when something in the cell has gone wrong and either tells the cell to stop growing (so the cell can repair any damage that has been done) or if all else fails, tells the cell to kill itself (to prevent unregulated cellular growth...cancer) .</div> <div> Now, p53 protein levels are normally kept very low within the cell. However, once stimulated (see below), its protein levels are rapidly increased along with its half-life, while its mRNA levels remain relatively unchanged. What does this suggest? That the regulation of p53 at the protein level (not DNA or RNA level) is critical in its activation. An important negative regulator of p53 at the protein level is Mdm2, which is actually a p53-responsive gene. So, can you see the negative feedback loop here? P53 becomes activated (see below) and then increased Mdm2 levels. Mdm2 then inactivates p53, turning it off. As you can imagine, if you want to increase p53 protein levels within the cell, you are going to have to inhibit Mdm2.</div> <div> <FONT SIZE="3" COLOR="#66FFFF" FACE="Arial" ><B><IMG SRC="2e1b80e0.gif" border=0 width="440" height="270" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b></FONT>DNA damaging agents<FONT SIZE="4" COLOR="#008080" FACE="Arial" > (like radiation) induce </FONT>the activation of kinases (such as ATM and DNA-PK) that can phosphorylate a critical serine residue in the Mdm2-binding domain of p53. So, when p53 is phosphorylated here, it can no longer bind to Mdm2. Then, this is able to relieve Mdm2-mediated inhibition of p53, right? Why would DNA damaging agents activate p53? Well, if your DNA is damaged, you don't want to replicate it, right? If you did, you might produce cells with deleterious mutations, which might then lead to cancer. So, p53 recognizes when the cell has sustained DNA damage and halts the cell cycle so the cell can repair the damage, or in many cases, just tells the cell to kill itself (apoptosis).</div> <div> Another mechanism to inhibit Mdm2 is by oncogenes, constitutively active mutant proteins that continually tell the cell to grow (such as Ras). Why would oncogenes activate p53? Again, you don't want cells to grow uncontrollably, right? That's cancer! So, p53 recognizes when this happens and halts the cell cycle. However, oncogenes do not lead to the activation of ATM or DNA-PK, in fact, oncogenes don't even lead to the phosphorylation of p53 in the Mdm2-binding domain! So, how do oncogenes inhibit Mdm2? By inducing the expression of a tumor suppressor protein called p19ARF. Now, this is a really interesting protein (and relatively new!), so I'll spend a bit more time talking about it below.</div> <div> <I><B><IMG SRC="2e256b80.gif" border=0 width="342" height="440" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2e4b8200.gif" border=0 width="440" height="288" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b></I><I><B>p53 is the </b></I><I><B>MOST</b></I><I><B> </b></I><I><B>commonly disrupted gene in cancer. So, you know it has to be important. Now, is it necessary for normal cell cycle progression? p53 is a checkpoint. It recognizes when something has gone wrong (for example the DNA has been damaged or the cell is being stimulated by an oncogene) and immediately halts the cell cycle to prevent the cell from becoming cancerous. So, if you lose p53, your cell loses this important checkpoint and may go on to become a cancerous cell. Not only are p53 mutations found in cancer, but so are overexpression of</b></I><I><B> </b></I><I><B>Mdm2</b></I><I><B> </b></I><I><B>(which would act to inhibit p53) as well as the loss of </b></I><I><B>p19ARF</b></I><I><B>.</b></I><I><B>p16INK4a </b></I><I><B>is frequently disrupted in cancer? Well, remember, p19ARF is also at that same locus! And, since most of the disruptions that occur at this locus are </b></I><I><B>deletions</b></I><I><B>, it eliminates both p16INK4a and p19ARF! Now you can probably see why this is the second most disrupted locus in cancer. By eliminating these two tumor suppressor proteins, you lose the regulation (in part) of the Rb and the p53 pathway!</b></I></div> <bR> <DIV ALIGN="LEFT"></DIV> <div> <B><IMG SRC="2e5581b0.gif" border=0 width="600" height="539" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b></div> <div> Rittinger, K. <I>et al.</I> (1997). <I>Nature</I>, <B>388</b>: 693-697.</div> <div> This is the crystalized structure of Cdc42 bound to a non-hydrolyzable GTP analog (so it's stuck bound to GTP-like molecule) on the left interacting with it's GAP (see below). Pretty cool picture, eh? I think so!</div> <div> <FONT SIZE="3" COLOR="#00FFFF" FACE="Arial" ><B><IMG SRC="2e680b80.gif" border=0 width="384" height="440" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b></FONT><B>GDP-bound Cdc42 is bound to a GDI and is not tethered to </b><B>the membrane.</b><FONT SIZE="3" COLOR="#66FFFF" FACE="Arial" ><B> </b></FONT></div> <div> <B>The GDI is phosphorylated by other proteins (e.g. PKC) and releases Cdc42.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>The GDP-bound Cdc42 can then be tethered to the membrane via its geranylgeranyl group located at the C-terminus.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>Now associated with the membrane, a GEF can open Cdc42 so that the GDP is released.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>A GTP molecule can now bind to the vacant site in Cdc42, leading to its activation.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>The GTP-bound Cdc42 now can interact with its various downstream effectors leading to a variety of biological responses.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>The GTP is hydrolyzed by the intrinsic GTPase activity of Cdc42 as well as by GAPs, leaving GDP bound to Cdc42 and its subsequent inactivation.</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <div> <B>The GDP-bound Cdc42 can again be bound by GDIs, removed from the membrane, and returned to the cytoplasm…and the cycle is complete!</b><FONT SIZE="3" COLOR="#33FF66" FACE="Arial" ><B> </b></FONT></div> <bR> <div> <B><IMG SRC="2e7b85a0.gif" border=0 width="440" height="346" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b><B><IMG SRC="2e9df090.gif" border=0 width="479" height="265" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2ea1fb80.gif" border=0 width="287" height="440" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></b></div> <div> <FONT SIZE="2" COLOR="#FFFFCC" FACE="Arial" ><IMG SRC="2bdb55c0.jpg" border=0 width="437" height="604" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2bea19e0.jpg" border=0 width="417" height="414" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></FONT><B> <A NAME="heterochromatin"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A></b><B>Heterochromatin </b></div> <div> This is the condensed form of chromatin organization. It is seen as dense patches of chromatin. Sometimes it lines the nuclear membrane, however, it is broken by clear areas at the pores so that transport is allowed. Sometimes, the heterochromatin forms a "cartwheel" pattern. Abundant heterochromatin is seen in resting, or reserve cells such as small lymphocytes (memory cells) waiting for exposure to a foreign antigen. Heterochromatin is considered transcriptionally inactive</div> <div> <B> <A NAME="euchromatin"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A></b><B>Euchromatin </b></div> <div> Euchromatin is threadlike, delicate. It is most abundant in active, transcribing cells.<I> (See Alberts et al, Molecular Biology of the Cell, Garland Publishing, 1994, pp 351-352).</I> Thus, the presence of euchromatin is significant because the regions of DNA to be transcribed or duplicated must uncoil before the genetic code can be read</div> <div> <FONT SIZE="2" COLOR="#FFFFCC" FACE="Arial" ><IMG SRC="2bf1d190.jpg" border=0 width="285" height="281" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></FONT>Just before cell division (and after DNA synthesis), the chromatin condenses further into individual metaphase chromosomes. The dividing chromosomes appear as two chromatids. An electron microscopic view of a chromosome is shown in this photograph. The chromatids appear to be made of coiled loops of 20-30 nm <FONT SIZE="3" COLOR="#0000FF" FACE="Arial" ><U>nucleoprotein fibers</U></FONT>. <I>Modified from Bloom and Fawcett, A Textbook of Histology, Chapman and Hall, 12th edition, Figure 1-14 </I></div> <div> Can one define individual genes on chromosomes?</div> <div> In the section below, we will show the electron microscopic views that support the organization of DNA in chromosomes. First, we will look at how we can identify specific genes by cytochemistry. </div> <div> <FONT SIZE="3" COLOR="#FFFFCC" FACE="Arial" ><IMG SRC="2c04d7f0.jpg" border=0 width="333" height="383" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2c102050.jpg" border=0 width="258" height="261" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2c212e50.jpg" border=0 width="274" height="229" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></FONT> <A NAME="fish"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A>FISH</div> <bR> <div> A more precise way to identify genetic sequences and genes is via a technique called "Fluorescence In situ Hybridization" or FISH. This involves the use of DNA or oligonucleotides complementary to a nucleotide sequence on the chromosomes. These "cDNA probes" are conjugated to fluorescein, rhodamine, Texas red, or another fluorescent compound and then used to detect the sites of the gene on the individual chromosomes. This figure detects a sequence on chromosome 21 in a normal individual (white label). Note, there are two copies of this chromosome, each bearing the sequence. This probe is useful for the detection of Down syndrome which contains an extra chromosome 21. </div> <div> FISH has also been called "chromosome painting" and there are commercial kits available to detect multiple chromosomes in one section or metaphase spread. A recently developed kit is so colorful, it has been named "Joseph's coat". Each nucleotide probe is attached to a different fluorescent compound and they can be added together because they will attach to different chromosomes, or different regions of the nucleus or chromosomes. In this photograph, FISH was used to detect sequences in chromatin in interphase nuclei. A triple labeling protocol was applied to detect chromosome 2 (red; Texas red), 4 (blue, AMCA) and 8 (green, fluorescein).<I>Taken from Boehringer Mannheim Biochemicals "Non Radioactive In Situ Hybridization Application Manual</I></div> <div> <IMG SRC="2c385110.jpg" border=0 width="389" height="273" ALIGN="BOTTOM" HSPACE="0" VSPACE="0">To understand how the DNA and histones are organized in a chromosome, we must appreciate the fact that the nucleus is only 6 micrometers in diameter. The total length of DNA in the human genome is 1.8 meters. Thus, in order to pack the DNA into the nucleus as in the photograph of the metaphase chromosome , there must be several levels of coiling and supercoiling. There is nearly a 10,000-fold reduction in length in an interphase nucleus. Each chromosome contains 1 long molecule of DNA plus associated histones (basic proteins) which help in the condensation and regulation processes. In the following section, we will show an uncoiled chromosome and also visualize it with specific electron microscopic techniques. </div> <div> Visualize 10-30 nm fibers and  <A NAME="fibrils"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A>fibrils </div> <div> To look at chromatin, we can isolate nuclei and disrupt them. This will disperse the chromatin which can be spread on a water surface. This spread can be picked up on a plastic-coated grid and examined with the electron microscope</div> <div> <IMG SRC="2c41a760.jpg" border=0 width="538" height="374" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> The first level of organization you see is a tangle of 20-30 nm fibers. These are actually coils of the DNA and histones. The figure on the left shows the <FONT SIZE="3" COLOR="#0000FF" FACE="Arial" ><U>tangled chromatin fibers</U></FONT> in the left panel. Shearing forces can be used to further uncoil and stretch these fibers and the beaded filaments appear. The strands between the beads are segments of double stranded DNA. These are shown in the right panel</div> <div> <IMG SRC="2c57d1c0.jpg" border=0 width="381" height="540" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2c75e3c0.jpg" border=0 width="350" height="316" ALIGN="BOTTOM" HSPACE="0" VSPACE="0">Role of the Ribosome</div> <div> The route from the DNA code to the protein.</div> <div> <TABLE BORDER="0" CELLPADDING="1" CELLSPACING="1" WIDTH="451" BORDERCOLORLIGHT="#C0C0C0" BORDERCOLORDARK="#808080" FRAME="VOID" RULES="NONE" ALIGN="BOTTOM" HSPACE="0" VSPACE="0" > <tR> <tD VALIGN=CENTER HEIGHT= 229 WIDTH="447"><div> Before cell division, the DNA in our chromosomes replicates so each daughter cell has an identical set of chromosome. In addition, the DNA is responsible for coding for all proteins. Each amino acid is designated by one or more set of triplet nucleotides. The code is produced from one strand of the DNA by a process called "transcription". This produces mRNA which then is sent out of the nucleus where the message is translated into proteins. This can be done in the cytoplasm on clusters of ribosomes, called "polyribosomes". Or it can be done on the membranes of the rough endoplasmic reticulum. The cartoon to the left shows the basic sequence of transcription and translational events. </div> </tD> </tR> </TABLE></div> <div> <IMG SRC="2c819570.jpg" border=0 width="281" height="599" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><FONT SIZE="2" COLOR="#FFFFCC" FACE="Arial" >What happens at the site of the ribosome?</FONT></div> <div> <TABLE BORDER="0" CELLPADDING="1" CELLSPACING="1" WIDTH="445" BORDERCOLORLIGHT="#C0C0C0" BORDERCOLORDARK="#808080" FRAME="VOID" RULES="NONE" ALIGN="BOTTOM" HSPACE="0" VSPACE="0" > <tR> <tD VALIGN=CENTER HEIGHT= 401 WIDTH="441"><div> The code is actually translated on structures that are also made in the nucleus, called Ribosomes. These ribosomes provide the structural site where the mRNA sits. The amino acids for the proteins are carried to the site by "transfer RNAs,". In the cartoon to the left, these are shown as blue molecules. Each transfer RNA (tRNA) has a nucleotide triplet which binds to the complementary sequence on the mRNA (see the three letters at the bottom of each molecule). </div> <div> The tRNA carries the amino acid at its opposite end. One can trace and detect binding of a particular tRNA-amino acid complex to the mRNA by labeling that amino acid. It will bind to its tRNA. In the case to the left, Phenylalanine is bound to the tRNA which carries the complementary base code AAA (adenine-adenine-adenine). This triplet code would bind to the complementary sequence on mRNA UUU (uracil X3). The mRNA is shown as a green arrow. This cartoon shows the selective binding site on the mRNA which is attached in the ribosome. It also shows the tRNA carrying the Phenylalanine bound at the site In this particular assay which uses a polyuracil mRNA, only phenylalanine-bearing tRNA is bound and detected on the filter. </div> </tD> </tR> </TABLE></div> <bR> <div> <IMG SRC="2c990900.jpg" border=0 width="400" height="400" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> initiator tRNA is attracted to the region (carrying a methionine. It binds to the triplet code AUG.</div> <div> This then attracts the large ribosomal subunit which will bind to the small subunit. Note that it has an A site and a P site. These are different binding sites for the tRNAs. The cartoon below describes the next phase in the process. </div> <div> Elongation</div> <div> <IMG SRC="2cc74370.jpg" border=0 width="372" height="311" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2cdd52a0.jpg" border=0 width="469" height="298" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> <TABLE BORDER="0" CELLPADDING="1" CELLSPACING="1" WIDTH="445" BORDERCOLORLIGHT="#C0C0C0" BORDERCOLORDARK="#808080" FRAME="VOID" RULES="NONE" ALIGN="BOTTOM" HSPACE="0" VSPACE="0" > <tR> <tD VALIGN=CENTER HEIGHT= 454 WIDTH="441"><div>  <A NAME="polyribosomes"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A>Polyribosomes</div> <div> Clusters of ribosomes may sit on a mRNA and make proteins, each making a strand of polypeptides. These clusters are called polyribosomes. When they are free in the cytoplasm, they are called free polyribosomes (linked by the mRNA). Or, they may bind to rough endoplasmic reticulum.</div> <div> Ribosomes are visualized as small (20 X 30 nm) ribonucleoprotein particles. They are formed from two subunits. As you learned in the lecture on the <FONT SIZE="3" COLOR="#0000FF" FACE="Arial" ><U>nucleolus </U></FONT>, the subunits are produced in the nucleolus in organizing centers on certain chromosomes. The two ribosomal subunits leave the nucleus separately through the <FONT SIZE="3" COLOR="#0000FF" FACE="Arial" ><U>nuclear pores </U></FONT>. The pores are structured to allow transit of only the subunits. Whole ribosomes are formed outside in the cytoplasm. This prevents protein synthesis from occurring in the nucleus. Why might this be important? </div> <div> The above photograph shows a group of ribosomes in action. They are connected by a strand of messenger RNA which runs between the large and small subunits. They read the 3 nucleotide code for an amino acid and the appropriate transfer RNA brings the amino acid to the growing polypeptide chain. In this photograph, we see the growing peptide chain radiating at right angles to the mRNA. It extends from the base of the large ribosomal subunit.</div> <bR> </tD> </tR> </TABLE></div> <bR> <bR> <bR> <div> In this cartoon, note that the initiator tRNA complex has moved to the P site. This leaves the A site open for the next tRNA. In this case, we have Proline, which carries the complementary code GGC. Note that its binding site on the mRNA is CCG. After binding to the A site, the peptide bond between the methionine and proline forms. The empty tRNA carrying the MET leaves and the tRNA carrying the Proline moves to the P site. The ribosome moves to the next triplet code from 5' to the 3' direction (note arrow on mRNA). The tRNAs are moving from 3' to the 5' direction as the ribosome reads the code</div> <div> <IMG SRC="2cb413a0.jpg" border=0 width="321" height="314" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <bR> <div> The ribosome continues to read the code from the 5' to the 3' and amino acids are added to the growing peptide chain. This one shows the tRNA carrying the glycine amino acid coded by CCA. Its complementary bases are GGU.</div> <div> This continues until the stop codon is reached. This is highlighted in red in this figure and the next figure. </div> <div> The following cartoon shows what happens when the stop codon is reached.</div> <div> End of translation</div> <div> <FONT SIZE="3" COLOR="#FFFFCC" FACE="Arial" ><IMG SRC="2ca26510.jpg" border=0 width="550" height="337" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2ce17e40.jpg" border=0 width="535" height="228" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></FONT>Introduction to the  <A NAME="ribosome_endoplasmic_reticulum"><IMG BORDER="0" SRC="1x1.gif" HEIGHT="1" ALIGN="bottom" WIDTH="1" HSPACE="0" VSPACE="0" ></A>Ribosome-Endoplasmic Reticulum Unit </div> <div> <TABLE BORDER="0" CELLPADDING="1" CELLSPACING="1" WIDTH="439" BORDERCOLORLIGHT="#C0C0C0" BORDERCOLORDARK="#808080" FRAME="VOID" RULES="NONE" ALIGN="BOTTOM" HSPACE="0" VSPACE="0" > <tR> <tD VALIGN=CENTER HEIGHT= 169 WIDTH="435"><div> The left hand view of this cartoon shows the free polyribosomes connected by the mRNA. They are arranged in rosettes and these can be seen in the cytoplasm in conventional electron micrographs. The right hand view shows the arrangement of polyribosomes on the rough endoplasmic reticulum. Note that the growing polypeptide chain (which projects down from the large subunit) is inserted through the membrane and into the cisterna of the rough endoplasmic reticulum. </div> <bR> </tD> </tR> </TABLE></div> <div> <IMG SRC="2cfb21b0.jpg" border=0 width="434" height="283" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d0de000.jpg" border=0 width="478" height="256" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d126350.jpg" border=0 width="294" height="309" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <div> <IMG SRC="2d2abb80.gif" border=0 width="427" height="440" ALIGN="BOTTOM" HSPACE="0" VSPACE="0">golgi</div> <bR> <div> Tier I shows budding from ER that is arranged facing a central zone at one end of the Golgi complex. These buds become vesicles and are coated with COPII protein coats. </div> <div> Tier II The ER faces a central zone called a vesicular-tubular cluster (VTC). After they lose their COPII coat, they merge with the VTC's carrying the soluble and membrane proteins to the Golgi complex. </div> <div> Tier III illustrates the entire complex which is unique in the cytoplasm. It is termed the 'export complex' and contains unique proteins that suggest it is specialized for information flow to and from ER and the Golgi complex</div> <div> <IMG SRC="2d3256c0.jpg" border=0 width="549" height="364" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d44b8f0.jpg" border=0 width="587" height="399" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d5070b0.jpg" border=0 width="519" height="267" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d631af0.jpg" border=0 width="561" height="431" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d7a19f0.jpg" border=0 width="417" height="415" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d864f30.jpg" border=0 width="356" height="499" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2d9bebc0.jpg" border=0 width="702" height="188" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2da03650.jpg" border=0 width="515" height="357" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2db65af0.jpg" border=0 width="613" height="431" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2dc3f100.jpg" border=0 width="575" height="272" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2ddd5700.jpg" border=0 width="725" height="368" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2de1cc00.jpg" border=0 width="284" height="448" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"><IMG SRC="2dfcda40.jpg" border=0 width="461" height="420" ALIGN="BOTTOM" HSPACE="0" VSPACE="0"></div> <bR> </td> </tr></table></body>