[SCM] massXpert mass spectrometry suite: debian packaging branch, upstream, updated. 41a70205093791df401b34b6867e830c5a46d1f9
Filippo Rusconi
rusconi at mnhn.fr
Wed Apr 15 15:42:52 UTC 2009
The following commit has been merged in the upstream branch:
commit 4c119488c89aaadfe01dd71839a81caf429a0880
Author: Filippo Rusconi <rusconi at mnhn.fr>
Date: Sun Apr 5 20:44:46 2009 +0200
Removed files not related to the source tree. Added files related to MSWindows.
diff --git a/windows-installer/massxpert.iss b/massxpert.iss
similarity index 76%
rename from windows-installer/massxpert.iss
rename to massxpert.iss
index a88bcee..82b7729 100755
--- a/windows-installer/massxpert.iss
+++ b/massxpert.iss
@@ -5,9 +5,12 @@
[Setup]
AppName=massXpert
-;;;;;;;;; BEWARE THE VERSION
-AppVersion=1.6.9
-AppVerName=massXpert, version 1.6.9
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; BEWARE THE VERSION
+AppVersion=2.0.0
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; BEWARE THE VERSION
+AppVerName=massXpert, version 2.0.0
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; BEWARE THE VERSION
+
AppPublisher=Filippo Rusconi
AppPublisherURL=http://www.massxpert.org/
AppSupportURL=http://www.massxpert.org/
@@ -21,8 +24,10 @@ DisableProgramGroupPage=yes
LicenseFile=C:\Program Files\massxpert\doc\COPYING
OutputDir=C:\devel\massxpert\windows-installer
-;;;;;;;;; BEWARE THE VERSION
-OutputBaseFilename=massxpert-1.6.9-setup
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; BEWARE THE VERSION
+OutputBaseFilename=massxpert-2.0.0-setup
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; BEWARE THE VERSION
+
Compression=lzma
SolidCompression=yes
Uninstallable=yes
@@ -41,9 +46,6 @@ Name: "{pf}\massxpert\locales"
Name: "{pf}\massxpert\data"
Name: "{pf}\massxpert\doc"
Name: "{pf}\massxpert\doc\usermanual"
-Name: "{pf}\massxpert\doc\usermanual\pdf"
-Name: "{pf}\massxpert\doc\usermanual\html"
-Name: "{pf}\massxpert\doc\usermanual\figures"
Name: "C:\Documents and Settings\{username}\.massxpert"
[Files]
@@ -54,9 +56,7 @@ Source: "C:\Program Files\massxpert\plugins\*.dll"; DestDir: "{pf}\massxpert\plu
Source: "C:\Program Files\massxpert\locales\*.qm"; DestDir: "{pf}\massxpert\locales"; Flags: recursesubdirs createallsubdirs
Source: "C:\Program Files\massxpert\data\*"; DestDir: "{pf}\massxpert\data"; Flags: ignoreversion recursesubdirs createallsubdirs
Source: "C:\Program Files\massxpert\doc\COPYING"; DestDir: "{pf}\massxpert\doc\";
-Source: "C:\Program Files\massxpert\doc\usermanual\figures\*"; DestDir: "{pf}\massxpert\doc\usermanual\figures"; Flags: ignoreversion recursesubdirs createallsubdirs
-Source: "C:\Program Files\massxpert\doc\usermanual\html\*"; DestDir: "{pf}\massxpert\doc\usermanual\html"; Flags: ignoreversion recursesubdirs createallsubdirs
-Source: "C:\Program Files\massxpert\doc\usermanual\pdf\*"; DestDir: "{pf}\massxpert\doc\usermanual\pdf"; Flags: ignoreversion recursesubdirs createallsubdirs
+Source: "C:\Program Files\massxpert\doc\usermanual\*"; DestDir: "{pf}\massxpert\doc\usermanual\"; Flags: ignoreversion recursesubdirs createallsubdirs
Source: "C:\devel\massxpert\windows-installer\readme.txt"; DestDir: "{pf}\massxpert"; Flags: isreadme
; NOTE: Don't use "Flags: ignoreversion" on any shared system files
diff --git a/windows-installer/readme.txt b/readme-windows.txt
old mode 100755
new mode 100644
similarity index 90%
rename from windows-installer/readme.txt
rename to readme-windows.txt
index 3184b18..d77fd6b
--- a/windows-installer/readme.txt
+++ b/readme-windows.txt
@@ -4,10 +4,10 @@ Wellcome to the massXpert program readme.txt file
The Program and the Data were installed in C:\Program Files\massxpert.
-DOCUMENTATON
-++++++++++++
+DOCUMENTATION
++++++++++++++
-Documentation (in HTML and PDF formats) is available in C:\Program Files\massxpert\doc\userman.
+Documentation in PDF format is available in C:\Program Files\massxpert\usermanual.
USER FILES
@@ -54,4 +54,4 @@ Happy massXpert'ing !
And do not forget to report bugs !
Filippo Rusconi,
-Author developer of massXpert
\ No newline at end of file
+Author developer of massXpert
diff --git a/usermanual/doc-stuff/glossary.html b/usermanual/doc-stuff/glossary.html
deleted file mode 100644
index ce8928d..0000000
--- a/usermanual/doc-stuff/glossary.html
+++ /dev/null
@@ -1,1777 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
-<head>
-<style type="text/css"> .abbreviation {background: #fbb} .acronym {background: #fbf} .admin {background: #ff7} .definition {background: #fbb} .example {background: #aff;} .entryID {font-style: italic} .note {background: #ffa;} .see {background: #ccc} .seeAlso {background: #fdb} .synonym {background: #ffb} .term { font-size: large; font-weight: bold; } .termEntry { padding: 1px 1px 1px 1px; margin: 1px 1px 1px 1px; border: thin solid blue; } .title {font-size:20; font-weight: bold;} </style>
-</head>
-<body>
-<ul>
-<li>
-<a name="three-10helix" id="three-10helix"></a><em>three-10helix</em>:
- <div class="term">3-10 helix</div>
-<div class="synonym">
-<em><strong>synonym:</strong></em>3(10) helix</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Infrequently used motif of secondary structure, occurs most often as a single
-turn transition. Similar to , but more tightly coiled than alpha helix, with 3
-residues per helical turn, and 10 atoms in the ring closed by the
-hydrogen bond.
- </p>
- </div>
-</li>
-<li>
-<a name="alphaHelix" id="alphaHelix"></a><em>alphaHelix</em>:
- <div class="term">alpha helix</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Common motif of secondary structure. Polypeptide chain formining a helical
-arrangement in which one full turn contains 3.6 residues and 13 atoms, and
-can therefore also be refered to as 3.6 13 helix.
-Usually right handed but occasionally also left-handed.
- </p>
- </div>
-</li>
-<li>
-<a name="aminoAcid" id="aminoAcid"></a><em>aminoAcid</em>:
- <div class="term">amino acid</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A compound containing both an acidic and amino group. There are twenty naturally
-occuring amino acids from which proteins are built.
- </p>
- </div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>aa</div>
-<ul>
-<li>
-<a name="alanine" id="alanine"></a><em>alanine</em>:
- <div class="term">alanine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>ala</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>A</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-One of the most commonly found amino acids, with a methyl group as a side chain.
-A non-essential amino acid, it is biosynthesized directly from pyruvate.
- </p>
- </div>
-</li>
-<li>
-<a name="arginine" id="arginine"></a><em>arginine</em>:
- <div class="term">arginine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>arg</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>R</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Basic amino acid. Arginine can be made from ornithine by mammals in the
-Krebs-Henseleit urea cycle but arginine rapidly breaks down to
-urea.
- </p>
- </div>
-</li>
-<li>
-<a name="asparagine" id="asparagine"></a><em>asparagine</em>:
- <div class="term">asparagine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>asn</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>N</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with uncharged polar side chain.
- </p>
- </div>
-</li>
-<li>
-<a name="asparticAcid" id="asparticAcid"></a><em>asparticAcid</em>:
- <div class="term">aspartic acid</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>asp</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>D</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with acidic side chain. The ionised form is known as aspartate.
- </p>
- </div>
-</li>
-<li>
-<a name="cysteine" id="cysteine"></a><em>cysteine</em>:
- <div class="term">cysteine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Cys</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>C</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-An amino acid with a thiol side chain. Cysteine is neutral, polar and found on
-the surface of proteins. Cysteine plays a special role in protein structure due
-to covalent disulphide links.
- </p>
- </div>
-</li>
-<li>
-<a name="cystine" id="cystine"></a><em>cystine</em>:
- <div class="term">cystine</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A term found in older literature referring to two disulphide linked cysteine
-residues.
- </p>
- </div>
-</li>
-<li>
-<a name="glutamicAcid" id="glutamicAcid"></a><em>glutamicAcid</em>:
- <div class="term">glutamic acid</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Glu</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>E</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with acidic side chain. The ionised form is known as glutamate.
- </p>
- </div>
-</li>
-<li>
-<a name="glutamine" id="glutamine"></a><em>glutamine</em>:
- <div class="term">glutamine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Gln</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Q</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with amide side chain, uncharged and polar.
- </p>
- </div>
-</li>
-<li>
-<a name="glycine" id="glycine"></a><em>glycine</em>:
- <div class="term">glycine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Gly</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>G</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Simplest of the naturally occuring amino acids, with no side chain.
-Glycine is often located at bends or folds in proteins.
- </p>
- </div>
-</li>
-<li>
-<a name="histidine" id="histidine"></a><em>histidine</em>:
- <div class="term">histidine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>His</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>H</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with imidizole side chain. It's charged state ina protein is
-very dependent on its local environment.
- </p>
- </div>
-</li>
-<li>
-<a name="isoleucine" id="isoleucine"></a><em>isoleucine</em>:
- <div class="term">isoleucine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Ile</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>I</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with a hydrophobic aliphatic side chain. Isomer of leucine.
- </p>
- </div>
-</li>
-<li>
-<a name="leucine" id="leucine"></a><em>leucine</em>:
- <div class="term">leucine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Leu</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>L</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with a hydrophobic aliphatic side chain. Isomer of isoleucine.
- </p>
- </div>
-</li>
-<li>
-<a name="lysine" id="lysine"></a><em>lysine</em>:
- <div class="term">lysine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Lys</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>K</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with primary amine side chain. Positively charged under physiological
-conditions.
- </p>
- </div>
-</li>
-<li>
-<a name="methionine" id="methionine"></a><em>methionine</em>:
- <div class="term">methionine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Met</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>M</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with sulphur-containing hydrophobic side chain.
- </p>
- </div>
-</li>
-<li>
-<a name="phenylalanine" id="phenylalanine"></a><em>phenylalanine</em>:
- <div class="term">phenylalanine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>phe</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>F</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Phenylalanine is a naturally occurring aminoacid (L-isomer). The <i>D-isomer</i>
-can be found in some bacterial metabolites. It is one of the essential amino
-acids, and is aromatic, hydrophobic, and neutral thus it is found buried in
-protein structures.
- </p>
- </div>
-</li>
-<li>
-<a name="proline" id="proline"></a><em>proline</em>:
- <div class="term">proline</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Pro</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>P</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Cyclic amino acid
- </p>
- </div>
-</li>
-<li>
-<a name="serine" id="serine"></a><em>serine</em>:
- <div class="term">serine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Ser</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>S</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with neutral polar side chain.
- </p>
- </div>
-</li>
-<li>
-<a name="threonine" id="threonine"></a><em>threonine</em>:
- <div class="term">threonine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Thr</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>T</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with neutral polar side chain
- </p>
- </div>
-</li>
-<li>
-<a name="tryptophan" id="tryptophan"></a><em>tryptophan</em>:
- <div class="term">tryptophan</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Trp</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>W</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with aromatic side chain
- </p>
- </div>
-</li>
-<li>
-<a name="tyrosine" id="tyrosine"></a><em>tyrosine</em>:
- <div class="term">tyrosine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Tyr</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Y</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with aromatic side chain
- </p>
- </div>
-</li>
-<li>
-<a name="valine" id="valine"></a><em>valine</em>:
- <div class="term">valine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>Val</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>V</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Amino acid with aliphatic side chain
- </p>
- </div>
-</li>
-</ul>
-</li>
-<li>
-<a name="amphipathic" id="amphipathic"></a><em>amphipathic</em>:
- <div class="term">amphipathic</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A compound containing both hydrophobic and hydrophilic groups. Many
-cell components are amphipathic and tend to form structures in which the
-nonpolar, hydrophobic parts are hidden from water, whereas polar, hydrophilic
-parts are exposed to water.
- </p>
- </div>
-</li>
-<li>
-<a name="barrel" id="barrel"></a><em>barrel</em>:
- <div class="term">barrel</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-All-beta class of protein folds include sandwich and barrel topology. Barrel
-folds are made of single beta-sheets that twist and coils upon itself, mostly
-the first strand of the beta-sheet hydrogen bond to the last strand. The strand
-directions of the two opposite sides of the barrel fold are roughly orthogonal.
-Most barrel folds are closed. Barrels are defined by the number of beta-sheets
-(n) and staggering or shear of the sheets (S).
- </p>
- </div>
-</li>
-<li>
-<a name="base" id="base"></a><em>base</em>:
- <div class="term">base</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A heterocyclic component of nucleic acids
- </p>
- </div>
-<ul>
-<li>
-<a name="purine" id="purine"></a><em>purine</em>:
- <div class="term">purine</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, bicyclic, basic compound that occurs in nucleotides of
-DNA and RNA. The purines in DNA and RNA are adenine and guanine.
- </p>
- </div>
-<ul>
-<li>
-<a name="adenine" id="adenine"></a><em>adenine</em>:
- <div class="term">adenine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>A</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, bicyclic, basic purine that occurs in nucleotides of
-DNA and RNA. It is one member of the base pair A-T
-(adenine-thymine).
- </p>
- </div>
-<div class="seeAlso">
-<em><strong>see also:</strong></em>purine</div>
-<div class="seeAlso">
-<em><strong>see also:</strong></em>thymine</div>
-</li>
-<li>
-<a name="guanine" id="guanine"></a><em>guanine</em>:
- <div class="term">guanine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>G</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, bicyclic, basic purine that occurs in nucleotides of DNA
-and RNA. It is one member of the base pair G-C (guanine-cytosine).
- </p>
- </div>
-</li>
-</ul>
-</li>
-<li>
-<a name="pyrimidine" id="pyrimidine"></a><em>pyrimidine</em>:
- <div class="term">pyrimidine</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, cyclic, basic compound that occurs in nucleotides of DNA
-and RNA. The pyrimidines in DNA are cytosine and thymine. Those in RNA, are
-cytosine and uracil.
- </p>
- </div>
-<ul>
-<li>
-<a name="cytosine" id="cytosine"></a><em>cytosine</em>:
- <div class="term">cytosine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>C</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of
-DNA and RNA. It is one member of the base pair G-C (guanine-cytosine).
- </p>
- </div>
-</li>
-<li>
-<a name="uracil" id="uracil"></a><em>uracil</em>:
- <div class="term">uracil</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>U</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of
-RNA. It is able to form a base pair A-U (adenine-uracil).
- </p>
- </div>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-<li>
-<a name="betaSandwich" id="betaSandwich"></a><em>betaSandwich</em>:
- <div class="term">beta sandwich</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-All-beta class of protein folds include sandwich and barrel topology. Two
-beta-sheets are usually twisted and packed so their strands are aligned in
-sandwich folds. There are a few special cases of orthogonal sandwich
-folds.
- </p>
- </div>
-</li>
-<li>
-<a name="betaSheet" id="betaSheet"></a><em>betaSheet</em>:
- <div class="term">beta sheet</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Common secondary structure motif in proteins. Polypeptide chain in extended
-conformation, sheet formed of strands lying either parallel, antiparallel,
-or both. Beta sheets can be planar,twisted or form barrels.
- </p>
- </div>
-</li>
-<li>
-<a name="carbohydrate" id="carbohydrate"></a><em>carbohydrate</em>:
- <div class="term">carbohydrate</div>
-<div class="synonym">
-<em><strong>synonym:</strong></em>saccharide</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Carbohydrates are polyhydroxy-carbonyl compounds which generally have the sum
-formula (CH2O)n. An essential component of living organisms, they are used as
-storage compounds, energy metabolism intermediates, structural building blocks,
-and for the modification of proteins.
- </p>
- </div>
-</li>
-<li>
-<a name="catalysis" id="catalysis"></a><em>catalysis</em>:
- <div class="term">catalysis</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Catalysts accelerate chemical reactions by lowering the free energy of
-activation. They combine with the reactants, giving a transition state with less
-free energy than the uncatalyzed reaction. Formation of the reactant products
-regenerates the free catalyst. Enzymic catalysis is the same except for a
-measurable saturation effect (Michaelis Menten).
- </p>
- </div>
-</li>
-<li>
-<a name="catalyticTriad" id="catalyticTriad"></a><em>catalyticTriad</em>:
- <div class="term">catalytic triad</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Arrangement of three amino acids Ser-His-Asp(or Glu) which greatly increses the
-nucleophilic character of the serine.
- </p>
- </div>
-</li>
-<li>
-<a name="CATH" id="CATH"></a><em>CATH</em>:
- <div class="term">CATH</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A hierarchical classification of protein structural relationships
- </p>
- </div>
-</li>
-<li>
-<a name="chaperone" id="chaperone"></a><em>chaperone</em>:
- <div class="term">chaperone</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Chaperones are a set of proteins required for formation of proper tertiary
-structure, acting as catalysts by increasing the rate of the folding processes.
-Examples include protein disulphide isomerase and BiP.
- </p>
- </div>
-</li>
-<li>
-<a name="chiral" id="chiral"></a><em>chiral</em>:
- <div class="term">chiral</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Chirality means 'handedness' of molecules. Chirality is the description and
-classification of the optical and geometrical properties of molecular centres,
-axises or planes. Thus, chirality gives rise to different types of isomers.
-Chiral molecules do not coincide with their mirror image.
- </p>
- </div>
-</li>
-<li>
-<a name="circularDichroism" id="circularDichroism"></a><em>circularDichroism</em>:
- <div class="term">circular dichroism</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Substances that are optically active rotate the plane of linearly polarised
-light. Optical rotation of proteins is used to determine alpha helix coiling,
-and factors influencing the transition between alpha helix and random
-coil.
- </p>
- </div>
-</li>
-<li>
-<a name="codon" id="codon"></a><em>codon</em>:
- <div class="term">codon</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Specific triplets of mononucleotides in the DNA chain, called codons, correspond
-to specific amino acids or to start and stop of translation by the ribosome.
-The 64 possible triplets of bases in a codon code for 22 amino acids and stop
-codons. The start codon encodes for methionine.
- </p>
- </div>
-</li>
-<li>
-<a name="collagen" id="collagen"></a><em>collagen</em>:
- <div class="term">collagen</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Fibrous protein rich in glycine and proline that forms distinct triple-stranded
-helices. Major compound of the extracellular matrix and connective tissues.
- </p>
- </div>
-</li>
-<li>
-<a name="configuration" id="configuration"></a><em>configuration</em>:
- <div class="term">configuration</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The covalent linkages that make up a molecule. To change the configuration of a
-molecule one has to break and make new bonds.
- </p>
- </div>
-</li>
-<li>
-<a name="conformer" id="conformer"></a><em>conformer</em>:
- <div class="term">conformer</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Various nonsuperimposible three-dimensional arrangements of atoms that are
-interconvertible without breaking covalent bonds are called conformations. Atom
-naming conventions describe different conformations. Ramachandran used computer
-models of small polypeptides to find stable conformations.
- </p>
- </div>
-</li>
-<li>
-<a name="covalentBond" id="covalentBond"></a><em>covalentBond</em>:
- <div class="term">covalent bond</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A covalent bond exists between two atoms if they share electrons between them.
-One pair of electrons forms a single bond, and two pairs form a double bond.
-However, in quantum chemical terms an increase in electron density between the
-atoms also spreads over the rest of the molecule, particularly with delocalised
-bonding.
- </p>
- </div>
-</li>
-<li>
-<a name="crystallography" id="crystallography"></a><em>crystallography</em>:
- <div class="term">crystallography</div>
-<div class="synonym">
-<em><strong>synonym:</strong></em>x-ray crystallography</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-By using X-ray diffraction methods, crystals may be identified, their structure
-determined, and sizes measured. Crystallography can also be applied to powdered
-substances that are not crystalline but displaying some regularity of
-molecular structure. Crystallographic models show covalent skeletons, bond
-angles and lengths but not the actual space occupied by the molecule.
- </p>
- </div>
-</li>
-<li>
-<a name="cytoskeleton" id="cytoskeleton"></a><em>cytoskeleton</em>:
- <div class="term">cytoskeleton</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Fibrous network in the cytoplasm of an eukaryotic cell that shapes the cell and
-gives it the ability to move. Cytoskeleton consists mainly of microtubuli,
-actin and intermediate filaments.
- </p>
- </div>
-</li>
-<li>
-<a name="deltaHelix" id="deltaHelix"></a><em>deltaHelix</em>:
- <div class="term">delta helix</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Delta helices are left handed helices recently found in an NMR study of LAC
-repressor head piece.
- </p>
- </div>
-</li>
-<li>
-<a name="disulphideBond" id="disulphideBond"></a><em>disulphideBond</em>:
- <div class="term">disulphide bond</div>
-<div class="synonym">
-<em><strong>synonym:</strong></em>disulfide bond</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The bond formed by oxidation of the thiol groups of two cysteine residues.Often
-a stabilizing force in protein structure. Found mainly in secretory and
-membrane bound proteins.
- </p>
- </div>
-</li>
-<li>
-<a name="domain" id="domain"></a><em>domain</em>:
- <div class="term">domain</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Protein domains are areas of specific tertiary structure. These discrete
-portions of a protein have their own function. This discrete portions of a
-protein have their own function or stable folding structure.
- </p>
- </div>
-</li>
-<li>
-<a name="electrostatic" id="electrostatic"></a><em>electrostatic</em>:
- <div class="term">electrostatic</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Electrostatic attraction between ions of opposite charge holds the ions firmly
-in place and close together. Electrostatic interactions are one of the
-non-bonded interactions between protein molecules.
- </p>
- </div>
-</li>
-<li>
-<a name="enantiomer" id="enantiomer"></a><em>enantiomer</em>:
- <div class="term">enantiomer</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Enantiomers are two mirror images of a chiral molecule. They cannot be
-structurally superimposed. Each enantiomer rotates plane polarised light in a
-different direction (either D for clockwise or L for anti-clockwise).
- </p>
- </div>
-</li>
-<li>
-<a name="endoplasmicReticulum" id="endoplasmicReticulum"></a><em>endoplasmicReticulum</em>:
- <div class="term">endoplasmic reticulum</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>ER</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Cellular organelle in which synthesis of secreted proteins occurs.
- </p>
- </div>
-</li>
-<li>
-<a name="enzyme" id="enzyme"></a><em>enzyme</em>:
- <div class="term">enzyme</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Macromolecular substance able to catalyze a specific chemical reaction.
-Originally restricted to proteins, there have been discoveries of RNAs
-functioning as enzymes (designated ribozymes).
- </p>
- </div>
-</li>
-<li>
-<a name="enzymeClassification" id="enzymeClassification"></a><em>enzymeClassification</em>:
- <div class="term">enzyme classification</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>EC</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-System in which enzymes can be classified in hierachical groups according to
-function.
- </p>
- </div>
-<div class="seeAlso">
-<em><strong>see also:</strong></em>enzyme</div>
-</li>
-<li>
-<a name="exocytosis" id="exocytosis"></a><em>exocytosis</em>:
- <div class="term">exocytosis</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The directed transport of macromolecules from the cell by a vesicle mediated
-process.
- </p>
- </div>
-</li>
-<li>
-<a name="fold" id="fold"></a><em>fold</em>:
- <div class="term">fold</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The secondary structural units of helices and sheets form the basis of a
-classification for families of proteins. Each different topology is considered
-as a fold.
- </p>
- </div>
-</li>
-<li>
-<a name="foldase" id="foldase"></a><em>foldase</em>:
- <div class="term">foldase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Foldases assist in the correct folding of polypeptides.
- </p>
- </div>
-</li>
-<li>
-<a name="geneticCode" id="geneticCode"></a><em>geneticCode</em>:
- <div class="term">genetic code</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Genetic code is the sequence of codons along the DNA, that can be translated
-into an amino acid sequence. The DNA sequence of a gene can be used to predict
-the mRNA sequence, and the genetic code can in turn be used to predict the amino
-acid sequence.
- </p>
- </div>
-</li>
-<li>
-<a name="glycosidicBond" id="glycosidicBond"></a><em>glycosidicBond</em>:
- <div class="term">glycosidic bond</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A special kind of acetal bond linking sugars in polysaccharides together.
- </p>
- </div>
-</li>
-<li>
-<a name="glycosylation" id="glycosylation"></a><em>glycosylation</em>:
- <div class="term">glycosylation</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The addition of oligosaccharides to particular residues
-on a protein. This modification can be both co-translational and
-post-translational, occuring in the endoplasmatic reticulum and golgi.
-Three different forms of glycosylation can be distinguished: N-linked
-oligosaccharides, O-linked oligosaccharides and glycosyl-phosphatidylinositol
-(GPI-) anchors.
- </p>
- </div>
-</li>
-<li>
-<a name="Golgi" id="Golgi"></a><em>Golgi</em>:
- <div class="term">Golgi</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Membrane-bounded organelle in eukaryotic cells which is mainly involved in
-protein sorting and secretion. Many post-translational modifications occur in
-the golgi (among others the late stages of glycoslylation).
- </p>
- </div>
-</li>
-<li>
-<a name="greekKey" id="greekKey"></a><em>greekKey</em>:
- <div class="term">greek key</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Topology for a small number of beta sheet strands in which some interstrand
-connections go across the end of barrel or, in a sandwich fold, between beta
-sheets. Named after geometric motif on greek pottery.
- </p>
- </div>
-</li>
-<li>
-<a name="hairpinTurn" id="hairpinTurn"></a><em>hairpinTurn</em>:
- <div class="term">hairpin turn</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Beta hairpin turns or bends occur between two antiparallel beta-sheets, usually
-containing proline residues. There are also helix hairpin turns.
- </p>
- </div>
-</li>
-<li>
-<a name="helix" id="helix"></a><em>helix</em>:
- <div class="term">helix</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A helical arrangement of a protein chain forming a major part of secondary
-structure. Can be described by the N m notation where 'N' is number of residues
-per helical turn and 'm' is number of atoms including hydrogens in the ring
-closed by the hydrogen bond.
- </p>
- </div>
-</li>
-<li>
-<a name="homology" id="homology"></a><em>homology</em>:
- <div class="term">homology</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Evolutionary relationship stemming from a common ancestor that is inferred from
-a sequence comparison between two or more structures.
- </p>
- </div>
-</li>
-<li>
-<a name="hydrogenBond" id="hydrogenBond"></a><em>hydrogenBond</em>:
- <div class="term">hydrogen bond</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Electrostatic interaction between an hydrogen atom and an electronegative atom,
-such as oxygen, nitrogen or fluoride. Its strength is 5kJ/mol, and it is enough
-to fold a polyaminoacid in its characteristic structure. An hydrogen bond is
-key to the interaction between biological molecules.
- </p>
- </div>
-</li>
-<li>
-<a name="isoelectricPoint" id="isoelectricPoint"></a><em>isoelectricPoint</em>:
- <div class="term">isoelectric point</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The pH at which a protein carries no net elecric charge.
- </p>
- </div>
-</li>
-<li>
-<a name="isomer" id="isomer"></a><em>isomer</em>:
- <div class="term">isomer</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Isomer is one of two or more molecules with identical chemical compositions, but
-differing arrangements of atoms. Two isomers may differ in their physical,
-chemical, and biological properties.
- </p>
- </div>
-</li>
-<li>
-<a name="jellyroll" id="jellyroll"></a><em>jellyroll</em>:
- <div class="term">jellyroll</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Jellyroll is a variant of the greek key topology. A small number of beta-sheet
-strands have interstrand connections. Both ends of a sandwich or a barrel fold
-are crossed by two interstrand connections.
- </p>
- </div>
-<div class="seeAlso">
-<em><strong>see also:</strong></em>greek key</div>
-</li>
-<li>
-<a name="kinase" id="kinase"></a><em>kinase</em>:
- <div class="term">kinase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Kinase is a generic name for enzymes that attach a phosphate to a protein,
-opposite in action to phosphatases. These enzymes are important metabolic
-regulators.
- </p>
- </div>
-</li>
-<li>
-<a name="Klotho" id="Klotho"></a><em>Klotho</em>:
- <div class="term">Klotho</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Database of biochemical compounds
- </p>
- </div>
-</li>
-<li>
-<a name="ligase" id="ligase"></a><em>ligase</em>:
- <div class="term">ligase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that joins substituents together covalently, with ATP cleavage.
-Ligases form the 6th class of enzymes in the International Classification
-(EC.6).
- </p>
- </div>
-</li>
-<li>
-<a name="lipase" id="lipase"></a><em>lipase</em>:
- <div class="term">lipase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that catalyzes a process involving the cleavage of lipid. There are a
-range of such enzymes (EC.3.1)
- </p>
- </div>
-</li>
-<li>
-<a name="lysosome" id="lysosome"></a><em>lysosome</em>:
- <div class="term">lysosome</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Membrane-bounded organelle found in eukaryotes, involved in protein degradation.
-The lumen of lysosomes has an acidic pH.
- </p>
- </div>
-</li>
-<li>
-<a name="mannose" id="mannose"></a><em>mannose</em>:
- <div class="term">mannose</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Mannose is a monosaccharide. It is an aldohexose, 2 epimeric to glucose.
-D-Mannose is part of the core of N-linked oligosaccharides. In high mannose or
-in hybrid N-linked structures, mannose is found in the outer branches.
- </p>
- </div>
-</li>
-<li>
-<a name="MEDLINE" id="MEDLINE"></a><em>MEDLINE</em>:
- <div class="term">MEDLINE</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Database of scientific bibliography. References can be searched by different
-fields like: title, author, journal,substance, etc. MEDLINE is not a public
-database. However, it is possible to access a subset in molecular genetics at
-the NCBI.Medline is supported by MESH headings, of which ENTREZ is a subset.
- </p>
- </div>
-</li>
-<li>
-<a name="conformation" id="conformation"></a><em>conformation</em>:
- <div class="term">native conformation</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Physiologically folded conformation of a protein
- </p>
- </div>
-</li>
-<li>
-<a name="NMR" id="NMR"></a><em>NMR</em>:
- <div class="term">NMR</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>nuclear magnetic resonance</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Nuclear magnetic resonance is a method of spectroscopy. It uses the magnetic
-resonance of covalent bonds for imaging, with clinical use for imaging living
-tissue.
- </p>
- </div>
-</li>
-<li>
-<a name="nucleoside" id="nucleoside"></a><em>nucleoside</em>:
- <div class="term">nucleoside</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The four bases of DNA are referred to as nucleosides when combined with thri
-corresponding sugar (ribose or deoxy-ribose). Thus nucleosides are nucleotides
-without phosphate.
- </p>
- </div>
-</li>
-<li>
-<a name="nucleotide" id="nucleotide"></a><em>nucleotide</em>:
- <div class="term">nucleotide</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nucleotide is a subunit of DNA or RNA consisting of purines and pyrimidines
-(adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or
-cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA
-and ribose in RNA). Triplets of nucleotides form codons.
- </p>
- </div>
-</li>
-<li>
-<a name="nucleus" id="nucleus"></a><em>nucleus</em>:
- <div class="term">nucleus</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Membrane-bound organelle that makes a cell an eukaryote. Contains DNA organized
-into chromosomes and the enzymes which are involved in DNA replication and
-transcription.
- </p>
- </div>
-</li>
-<li>
-<a name="omega" id="omega"></a><em>omega</em>:
- <div class="term">omega</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Angle of rotation of the bond between the nitrogen and the carbonyl carbon
-in an peptide bond. The angle is usually 180 degrees for a trans peptide
-bond.
- </p>
- </div>
-</li>
-<li>
-<a name="orf" id="orf"></a><em>orf</em>:
- <div class="term">orf</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>open reading frame</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The sequence of bases in DNA with no stop codons that may be a
-coding sequence for proteins.
- </p>
- </div>
-</li>
-<li>
-<a name="organelle" id="organelle"></a><em>organelle</em>:
- <div class="term">organelle</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A membrane bounded compartment of a eukaryotic cell with a specialized function.
- </p>
- </div>
-</li>
-<li>
-<a name="phosphorylation" id="phosphorylation"></a><em>phosphorylation</em>:
- <div class="term">oxidative phosphorylation</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Process of energy generation in bacteria and mitochondria where electrons are
-transferred from nutrients to oxygen, thereby generating ATP. Involves the
-intermediate generation of a pH gradient across a membrane.
- </p>
- </div>
-</li>
-<li>
-<a name="oxidoreductase" id="oxidoreductase"></a><em>oxidoreductase</em>:
- <div class="term">oxidoreductase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that catalyzes a process involved in oxidation, reduction, and
-electron or proton transfer reactions. Oxidoreductases form the 1st class of
-enzymes in the International Classification (EC.1).
- </p>
- </div>
-</li>
-<li>
-<a name="PCR" id="PCR"></a><em>PCR</em>:
- <div class="term">PCR</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>Polymerase Chain Reaction</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Method of amplifying fragments of DNA using a thermostable polymerase.
- </p>
- </div>
-</li>
-<li>
-<a name="peptidase" id="peptidase"></a><em>peptidase</em>:
- <div class="term">peptidase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Peptidase is any enzyme that catalyzes a process involving hydrolysis of peptide
-bonds. Usually, peptidases catalyze degradation of peptides into their amino
-acids.They mostly include enzymes in EC 3.4 class.
- </p>
- </div>
-</li>
-<li>
-<a name="peptideBond" id="peptideBond"></a><em>peptideBond</em>:
- <div class="term">peptide bond</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-An amide bond linking amino acids between their COOH and NH2 groups. This
-is essentially a planar bond having some double bond character, so free
-rotation is not possible.
- </p>
- </div>
-</li>
-<li>
-<a name="periplasm" id="periplasm"></a><em>periplasm</em>:
- <div class="term">periplasm</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-In bacteria, the space between inner and outer membrane.
- </p>
- </div>
-</li>
-<li>
-<a name="PEST" id="PEST"></a><em>PEST</em>:
- <div class="term">PEST</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Sequence of amino acids in any order (P,E,S,T) that signals cell machinery to
-degrade that protein.
- </p>
- </div>
-</li>
-<li>
-<a name="phi" id="phi"></a><em>phi</em>:
- <div class="term">phi</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The torsion angle of the C(alpha)-N bond of each amino acid. limited in
-angles of rotations as described by Ramachandran plots.
- </p>
- </div>
-</li>
-<li>
-<a name="phosphatase" id="phosphatase"></a><em>phosphatase</em>:
- <div class="term">phosphatase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A generic name for enzymes that cleave a phosphate from a protein, that has
-previously been attached by a kinase. These enzymes are important metabolic
-regulators.
- </p>
- </div>
-</li>
-<li>
-<a name="phosphate" id="phosphate"></a><em>phosphate</em>:
- <div class="term">phosphate</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-(PO4)3- is the anion of phosphoric acid. Inorganic phosphate can be transferred
-to many biochemically important molecules. It is transferred as a phosphoric
-acid anhydride (e.g. in ATP) usually for short term energy storage, or as an
-ester (with serine, threonine or tyrosine in proteins) for regulatory or
-structural purposes.
- </p>
- </div>
-</li>
-<li>
-<a name="phosphorylate" id="phosphorylate"></a><em>phosphorylate</em>:
- <div class="term">phosphorylate</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-To covalently attach a phosphoryl (PO3--) ion to a hydroxyl group, usually on an
-amino-acid residue within a protein, or on a sugar.Phosphorylation is a key
-activity of biochemical processes such as enzyme activity control. Kinases
-perform phosphorylation, and phosphatases perform dephosphorylation.
- </p>
- </div>
-</li>
-<li>
-<a name="PIR" id="PIR"></a><em>PIR</em>:
- <div class="term">PIR</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>Protein Identification Resource</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Protein sequence database, provided by the
-National Institute of Health. It cross references Genbank, PDB and other
-sequence databases.
- </p>
- </div>
-</li>
-<li>
-<a name="polypeptide" id="polypeptide"></a><em>polypeptide</em>:
- <div class="term">polypeptide</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A linear polymer of amino acids linked via peptide bonds. May be as short
-as 2 amino acids to virtually any length.
- </p>
- </div>
-</li>
-<li>
-<a name="primaryStructure" id="primaryStructure"></a><em>primaryStructure</em>:
- <div class="term">primary structure</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The amino acid sequence of a polypeptide chain.
- </p>
- </div>
-</li>
-<li>
-<a name="prochiral" id="prochiral"></a><em>prochiral</em>:
- <div class="term">prochiral</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-There are two different prochiral systems. Two chemically identical substituents
-on an otherwise chiral tetrahedral centre are prochiral. Secondly, sp2
-hybridised planar systems with three different substituents are also prochiral.
- </p>
- </div>
-</li>
-<li>
-<a name="prokaryote" id="prokaryote"></a><em>prokaryote</em>:
- <div class="term">prokaryote</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any organism made of simple cells without a DNA-containing nucleus.
-A prokaryote can either be a bacterium, archebacterium or cyanobacterium.
- </p>
- </div>
-</li>
-<li>
-<a name="prosthetic" id="prosthetic"></a><em>prosthetic</em>:
- <div class="term">prosthetic</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A non-protein substance when combined with a protein. Examples
-include a heme group in hemoglobin/ myoglobin/cytochromes, nucleic acids in
-nucleoproteins.
- </p>
- </div>
-</li>
-<li>
-<a name="protease" id="protease"></a><em>protease</em>:
- <div class="term">protease</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that degrades a protein by hydrolyzing peptide bonds. The distinction
-between proteases and peptidases is blurred, reflecting the difference between
-proteins and peptides. Proteases are in the class EC.3.4.21-24.
- </p>
- </div>
-</li>
-<li>
-<a name="ProteinDataBank" id="ProteinDataBank"></a><em>ProteinDataBank</em>:
- <div class="term">Protein Data Bank</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>PDB</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-An archival computer database of 3-D structures of biomolecules. It is
-maintained by Brookhaven National Laboratory (BNL). PDB also means a
-particular file format as well as the archive.
- </p>
- </div>
-</li>
-<li>
-<a name="proteolysis" id="proteolysis"></a><em>proteolysis</em>:
- <div class="term">proteolysis</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-To hydrolyze the peptide bond in proteins or peptides.<br>
--CONH- + H20 ----> -CO2H + H2N- <br>
-This is an exergonic reaction yielding an acid and an amine.
- </p>
- </div>
-</li>
-<li>
-<a name="psi" id="psi"></a><em>psi</em>:
- <div class="term">psi</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The torsion angle of the C(alpha)-C bond of each amino acid. Limited in
-angles of rotations as described by Ramachandran plots.
- </p>
- </div>
-</li>
-<li>
-<a name="pyruvate" id="pyruvate"></a><em>pyruvate</em>:
- <div class="term">pyruvate</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Part of the flow of phosphate groups from high energy phosphate donors to low
-energy acceptors via the ATP-ADP system. Pyruvate serves as an acceptor of
-electrons in glycolysis. It also mobilises acetyl CoA when carbohydrates are
-used in respiration, prior to the Krebs cycle. Its formula is CH3-C(=O)-CO2H.
- </p>
- </div>
-</li>
-<li>
-<a name="quaternaryStructure" id="quaternaryStructure"></a><em>quaternaryStructure</em>:
- <div class="term">quaternary structure</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The spatial relationship between polypeptide chains in a protein with
-several subunits.
- </p>
- </div>
-</li>
-<li>
-<a name="RamachandranPlot" id="RamachandranPlot"></a><em>RamachandranPlot</em>:
- <div class="term">Ramachandran plot</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A diagramatic representation of rotational angles, phi and psi, possibly
-occuring in a polypeptide, considering steric constraints from van der Waals
-radii of each atom.
- </p>
- </div>
-</li>
-<li>
-<a name="RasMOL" id="RasMOL"></a><em>RasMOL</em>:
- <div class="term">RasMOL</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A molecular graphics program for the visualisation of proteins, nucleic acids,
-and small molecules. The program is aimed at display, teaching, and generation
-of publication quality images. The program reads in a molecule co-ordinate file
-then interactively displays the molecule.
- </p>
- </div>
-</li>
-<li>
-<a name="receptor" id="receptor"></a><em>receptor</em>:
- <div class="term">receptor</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Receptors allow the interaction between messengers and the messaging process.
-They cover a wide range of biological processes.
- </p>
- </div>
-</li>
-<li>
-<a name="reverseTurn" id="reverseTurn"></a><em>reverseTurn</em>:
- <div class="term">reverse turn</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Reverse turns are the turns most often found in peptides and proteins.About one
-third of all residues in globular proteins are contained in turns that reverse
-the direction of the polypeptide chain.
- </p>
- </div>
-</li>
-<li>
-<a name="ribosome" id="ribosome"></a><em>ribosome</em>:
- <div class="term">ribosome</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Particle composed of ribosomal RNAs and proteins. Catalyzes translation of mRNAs
-to proteins.
- </p>
- </div>
-</li>
-<li>
-<a name="RNA" id="RNA"></a><em>RNA</em>:
- <div class="term">RNA</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>ribonucleic acid</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A macromolecule composed of ribonucleotides linked by phosphodiester bonds. RNA
-occurs in cells mainly as tRNA, mRNA and
-rRNA.
- </p>
- </div>
-</li>
-<li>
-<a name="RNAse" id="RNAse"></a><em>RNAse</em>:
- <div class="term">RNAse</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that catalyzes hydrolysis of phosphodiester bonds in RNA. The
-specificities as well as the structures of different ribonucleases are very
-different.
- </p>
- </div>
-</li>
-<li>
-<a name="RossmannFold" id="RossmannFold"></a><em>RossmannFold</em>:
- <div class="term">Rossmann fold</div>
-<div class="synonym">
-<em><strong>synonym:</strong></em>dinucleotide binding fold</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A super secondary structure most often comprised of two
-beta-alpha-beta-alpha-beta units that can bind dinucleotides.
- </p>
- </div>
-</li>
-<li>
-<a name="rotamer" id="rotamer"></a><em>rotamer</em>:
- <div class="term">rotamer</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A conformer describable by rotation about a (sungle) bond. For an amino acid side chain,
-the positions of atoms are defined by the chi angles. Amino acids have chi angle
-preferences caused by differing shapes of their side chains. Thus a set of
-commonly observed chi angle combinations (each combination represents a
-rotamer), may be assigned to each amino acid.
- </p>
- </div>
-</li>
-<li>
-<a name="rRNA" id="rRNA"></a><em>rRNA</em>:
- <div class="term">rRNA</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>ribosomal RNA</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Ribosomal RNA; forms part of the structure of ribosomes and is mainly
-responsible for their translational activity. In prokaryotes, there are three
-kinds of rRNA; in eukaryotes, there are four.
- </p>
- </div>
-</li>
-<li>
-<a name="SCOP" id="SCOP"></a><em>SCOP</em>:
- <div class="term">SCOP</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-acronym of Structural Classification Of Proteins. Database developed by MRC
-Laboratory of Molecular Biology and Centre for Protein Engineering in Cambridge,
-UK. Consists of all proteins whose 3D structure is available, providing
-structural and evolutionary relationships where possible.
- </p>
- </div>
-</li>
-<li>
-<a name="secondaryStructure" id="secondaryStructure"></a><em>secondaryStructure</em>:
- <div class="term">secondary structure</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The local spatial arrangement of a polypeptide chain backbone without
-regard to side chain conformation. Often used to characterize structural
-entities such as helices, and beta structures.
- </p>
- </div>
-</li>
-<li>
-<a name="SEQNET" id="SEQNET"></a><em>SEQNET</em>:
- <div class="term">SEQNET</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A UK-based database and software service for sequence and structure
-based at Daresbury Laboratory, UK. Daresbury is also the UK node of
-EMBNET.
- </p>
- </div>
-</li>
-<li>
-<a name="sheet" id="sheet"></a><em>sheet</em>:
- <div class="term">sheet</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Sheets are a major class of secondary structure of polypeptide chains. They can
-be parallel, antiparallel, mixed, planar or twisted.
- </p>
- </div>
-</li>
-<li>
-<a name="subunit" id="subunit"></a><em>subunit</em>:
- <div class="term">subunit</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A single polypeptide chain of a protein comprised of two or more polypeptides.
- </p>
- </div>
-</li>
-<li>
-<a name="supersecondaryStructure" id="supersecondaryStructure"></a><em>supersecondaryStructure</em>:
- <div class="term">supersecondary structure</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-This merges with tertiary structures of proteins. It covers beta
-hairpin turns, beta- and alpha- corners, helix hairpins, and increasingly complex
-motifs.
- </p>
- </div>
-</li>
-<li>
-<a name="Swiss3D" id="Swiss3D"></a><em>Swiss3D</em>:
- <div class="term">swiss3d</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Database at ExPASy containing many different formats of images of proteins whose
-crystal structures are available.
- </p>
- </div>
-</li>
-<li>
-<a name="SwissProt" id="SwissProt"></a><em>SwissProt</em>:
- <div class="term">SwissProt</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Data base of protein sequences. Each entry contains bibliography, a short
-description of the protein, pointers to other data bases and the
-sequence.
- </p>
- </div>
-</li>
-<li>
-<a name="tertiaryStructure" id="tertiaryStructure"></a><em>tertiaryStructure</em>:
- <div class="term">tertiary structure</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The three dimensional structure of the entire polypeptide chain including
-side chains.
- </p>
- </div>
-</li>
-<li>
-<a name="thymine" id="thymine"></a><em>thymine</em>:
- <div class="term">thymine</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>T</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of
-DNA and RNA. It is one member of the base pair A-T (adenine-thymine).
- </p>
- </div>
-</li>
-<li>
-<a name="topoisomerase" id="topoisomerase"></a><em>topoisomerase</em>:
- <div class="term">topoisomerase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Enzymes EC.5.99.1.2 and 3 which cuts DNA and un/winds it. Topo I cuts one strand
-and topo II cuts at two phosphates, 4 base pairs apart (like a restriction enzyme).
- </p>
- </div>
-</li>
-<li>
-<a name="torsionAngle" id="torsionAngle"></a><em>torsionAngle</em>:
- <div class="term">torsion angle</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The spatial relationship of 4 atoms i,j,k and l is described by a torsion which
-is the angle that vector i-j must be turned clockwise to cover k-l when viewing
-along vector j-k. There are two main torsion angles of a protein the psi and
-phi angles that define the conformation of the polypeptide backbone.
- </p>
- </div>
-</li>
-<li>
-<a name="transcription" id="transcription"></a><em>transcription</em>:
- <div class="term">transcription</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The process of reading DNA and synthesizing a complementary strand of mRNA,
-performed by RNA polymerase. In eukaryotes, transcription occurs in the nucleus
-and is therefore spatially separated from translation.
- </p>
- </div>
-</li>
-<li>
-<a name="transferase" id="transferase"></a><em>transferase</em>:
- <div class="term">transferase</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Any enzyme that catalyzes a process catalysing reactions in which groups are
-transferred. Transferases form the 2nd class of enzymes in the International
-Classification (EC.2).
- </p>
- </div>
-</li>
-<li>
-<a name="translation" id="translation"></a><em>translation</em>:
- <div class="term">translation</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The process of reading mRNA and synthesizing a corresponding peptide, performed
-by the ribosome. Translation occurs in the cytoplasm.
- </p>
- </div>
-</li>
-<li>
-<a name="tRNA" id="tRNA"></a><em>tRNA</em>:
- <div class="term">tRNA</div>
-<div class="@type">
-<em><strong>fullForm:</strong></em>transfer RNA</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Transfer RNA is an adaptor molecule that carries amino acids the ribosome during
-protein synthesis. They contain about 75-90 mononucleotide units. Each of the
-20 amino acids has at least one corresponding tRNAs, and some have multiple
-tRNAs.
- </p>
- </div>
-</li>
-<li>
-<a name="urf" id="urf"></a><em>urf</em>:
- <div class="term">unidentified reading frame</div>
-<div class="abbreviation">
-<em><strong>abbreviation:</strong></em>urf</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-The sequence of bases in DNA with no stop codons that is a
-coding sequence for proteins. However, as yet there is doubt about which gene,
-if any, they belong to.
- </p>
- </div>
-</li>
-<li>
-<a name="vanDerWaals" id="vanDerWaals"></a><em>vanDerWaals</em>:
- <div class="term">van der Waals</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-Van der Waals are weak interactions, which play a major part in protein
-structure.
- </p>
- </div>
-</li>
-<li>
-<a name="zincFinger" id="zincFinger"></a><em>zincFinger</em>:
- <div class="term">zinc finger</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-A secondary structure motif that is coordinated with a Zn atom. Involved
-in binding DNA as a transcription factor. The zinc is coordinated with
-either cys or his residues.
- </p>
- </div>
-</li>
-<li>
-<a name="zipper" id="zipper"></a><em>zipper</em>:
- <div class="term">zipper</div>
-<div class="definition">
-<em><strong>definition:</strong></em>
- <p xmlns:xlink="http://www.w3.org/1999/xlink/namespace/">
-An example of protein super secondary structures. They look like zips, and can
-unzip and reform. They are a type of coiled coil structure.
- </p>
- </div>
-</li>
-</ul>
-</body>
-</html>
diff --git a/usermanual/doc-stuff/nucleic-acids.html b/usermanual/doc-stuff/nucleic-acids.html
deleted file mode 100644
index 9406b2e..0000000
--- a/usermanual/doc-stuff/nucleic-acids.html
+++ /dev/null
@@ -1,206 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>Biochemistry of Nucleic Acids
-</TITLE>
-</HEAD>
-<BODY background="sandston.jpg" text="000033" link="0000dd" vlink="009933">
-<H1><center><A NAME="top">Select From The Following for More Details</H1>
-</center></font>
-<center><TABLE border=4 cellpadding=10 bgcolor=white>
-<TR>
-<TD align=left>
-<UL type="none">
-<font size=5 face=arial>
-<LI><A HREF="nucleic-acids.html#intro">Introduction to Nucleic Acids</A>
-<LI><A HREF="nucleic-acids.html#nomenclature">Nucleic Acid Structure and Nomenclature</A>
-<LI><A HREF="nucleic-acids.html#adenosine">Adenosine Derivatives</A>
-<LI><A HREF="nucleic-acids.html#guanosine">Guanosine Derivatives</A>
-<LI><A HREF="nucleic-acids.html#analogs">Nucleotide Analogs</A>
-<LI><A HREF="nucleic-acids.html#poly">Polynucleotides</A>
-<LI><A HREF="nucleic-acids.html#dna">The Structure of DNA</A>
-<UL type="none"><LI><A HREF="nucleic-acids.html#thermal">Thermal Properties of the Double Helix</A></UL>
-<P><LI>Analytical Tools for DNA Study
-<UL type="none"><LI><A HREF="nucleic-acids.html#chromatography">Chromatography</A>
-<LI><A HREF="nucleic-acids.html#electrophoresis">Electrophoresis</A>
-</UL></UL></TD></TR></table>
-<BR>
-<A HREF="home.html"><font size = 4> Return to Medical Biochemistry Page</font></A>
-<HR></center>
-
-<A NAME="intro"><H1><B><center>Introduction</B></center></H1></A>
-<P><font size=+2><DD>As a class, the nucleotides may be considered one of the most important metabolites of the cell. Nucleotides are found primarily as the monomeric units comprising the major nucleic acids of the cell, RNA and DNA. However, they also are required for numerous other important functions within the cell. These functions include:
-<UL>
-<LI><B>1.</B> serving as energy stores for future use in phosphate transfer reactions. These reactions are predominantly carried out by ATP.
-<LI><B>2.</B> forming a portion of several important coenzymes such as NAD<sup>+</sup>, NADP<sup>+</sup>, FAD and coenzyme A.
-<LI><B>3.</B> serving as mediators of numerous important cellular processes such as <B><font color=red>second messengers</B></font> in signal transduction events. The predominant second messenger is cyclic-AMP (cAMP), a cyclic derivative of AMP formed from ATP.
-<LI><B>4.</B> controlling numerous enzymatic reactions through allosteric effects on enzyme activity.
-<LI><B>5.</B> serving as activated intermediates in numerous biosynthetic reactions. These activated intermediates include S-adenosylmethionine (S-AdoMet) involved in methyl transfer reactions as well as the many sugar coupled nucleotides involved in <A HREF="glycogen.html#synthesis">glycogen</A> and <A HREF="protein-modifications.html#glycoproteins">glycoprotein</A> synthesis.
-</UL></font><font size=3><A HREF="nucleic-acids.html"top">back to the top</A></font>
-<HR>
-<A NAME="nomenclature"><H1><B><center>Nucleoside and Nucleotide Structure and Nomenclature</B></center></H1></A>
-<P><font size=+2><DD>The nucleotides found in cells are derivatives of the heterocyclic highly basic, compounds, <B><font color=red>purine</B></font> and <B><font color=red>pyrimidine</B></font>.
-<P><center><center>
-<table cellpadding=5 border=4 bgcolor=white>
-<TR valign=middle><TD align=center><img src="purine.jpg"</TD><TD align=center><img src="pyrimidine.jpg"</TD>
-
-<TR valign=middle><TD align=center><font color=red><B><font size=+2>Purine</TD><TD align=center><font size=+2><font color=red><B>Pyrimidine</TD>
-</center></table></TR>
-<HR width=0></center>
-<P><DD>It is the chemical basicity of the nucleotides that has given them the common term "bases" as they are associated with nucleotides present in DNA and RNA. There are five major bases found in cells. The derivatives of purine are called <B><font color=red>adenine</B></font> and <B><font color=red>guanine</B></font>, and the derivatives of pyrimidine are called <B><font color=red>thymine</B></font>, <B><font color=red>cytosine</B></font> and <B><font color=red>uracil</B></font>. The common abbreviations used for these five bases are, <B><font color=red>A, G, T, C</B></font> and <B><font color=red>U</B></font>.
-
-<P><center>
-<table cellpadding=5 border=4 bgcolor=white>
-<TR valign=middle><TD align=center><font size=+2><font color=maroon><B>Base Formula</TD><TD align=center><font color=maroon><font size=+2><B>Base (X=H)</TD><TD align=center><font color=maroon><font size=+2><B>Nucleoside<BR>X=ribose or<br>deoxyribose</TD><TD align=center><font color=maroon><font size=+2><B>Nucleotide<br>X=ribose phosphate</TD>
-
-<TR valign=middle><TD align=center><img src="cytosine.jpg"></TD><TD align=center><font size=+2>Cytosine, C</TD><TD align=center><font size=+2>Cytidine, A</TD><TD align=center><font size=+2>Cytidine monophosphate<BR>CMP</TD>
-
-<TR valign=middle><TD align=center><img src="uracil.jpg"></TD><TD align=center><font size=+2>Uracil, U</TD><TD align=center><font size=+2>Uridine, U</TD><TD align=center><font size=+2>Uridine monophosphate<BR>UMP</TD>
-
-<TR valign=middle><TD align=center><img src="thymine.jpg"></TD><TD align=center><font size=+2>Thymine, T</TD><TD align=center><font size=+2>Thymidine, T</TD><TD align=center><font size=+2>Thymidine monophosphate<BR>TMP</TD>
-
-<TR valign=middle><TD align=center><img src="adenine.jpg"></TD><TD align=center><font size=+2>Adenine, A</TD><TD align=center><font size=+2>Adenosine, A</TD><TD align=center><font size=+2>Adenosine monophosphate<BR>AMP</TD>
-
-<TR valign=middle><TD align=center><img src="guanine.jpg"></TD><TD align=center><font size=+2>Guanine, G</TD><TD align=center><font size=+2>Guanosine, A</TD><TD align=center><font size=+2>Guanosine monophosphate<BR>GMP</TD>
-</table></center></TR>
-
-<P><DD>The purine and pyrimidine bases in cells are linked to carbohydrate and in this form are termed, <B><font color=red>nucleosides</B></font>. The nucleosides are coupled to D-ribose or 2'-deoxy-D-ribose through a <font face=symbol>b</font>-N-glycosidic bond between the anomeric carbon of the ribose and the N<sup>9</sup> of a purine or N<sup>1</sup> of a pyrimidine.
-<DD>The base can exist in 2 distinct orientations about the N-glycosidic bond. These conformations are identified as, <B><font color=red><I>syn</B></I></font> and <B><font color=red><I>anti</B></I></font>. It is the anti conformation that predominates in naturally occurring nucleotides.
-<P><center><center>
-<table cellpadding=5 border=4 bgcolor=white>
-<TR valign=middle><TD align=center><img src="syn-adenine.jpg"</TD><TD align=center><img src="anti-adenine.jpg"</TD>
-
-<TR valign=middle><TD align=center><font color=maroon><B><font size=+2><I>syn</I>-Adenosine</TD><TD align=center><font size=+2><font color=maroon><B><I>anti</I>-Adenosine</TD>
-</center></table></TR>
-<HR width=0></center>
-<P><DD>Nucleosides are found in the cell primarily in their phosphorylated form. These are termed <B><font color=red>nucleotides</B></font>. The most common site of phosphorylation of nucleotides found in cells is the hydroxyl group attached to the 5'-carbon of the ribose The carbon atoms of the ribose present in nucleotides are designated with a prime (<font color=red><B>'</B></font>) mark to distinguish them from the backbone numbering in the bases. Nucleotides can exist in the mono-, di-, or tri-phosphorylated forms.
-<DD>Nucleotides are given distinct abbreviations to allow easy identification of their structure and state of phosphorylation. The monophosphorylated form of adenosine (adenosine-5'-monophosphate) is written as, <B><font color=red>AMP</B></font>. The di- and tri-phosphorylated forms are written as, <B><font color=red>ADP</B></font> and <B><font color=red>ATP</B></font>, respectively. The use of these abbreviations assumes that the nucleotide is in the 5'-phosphorylated form. The di- and tri-phosphates of nucleotides are linked by acid anhydride bonds. Acid anhydride bonds have a high <font face=symbol>D</font>G<sup>0'</sup> for hydrolysis imparting upon them a high potential to transfer the phosphates to other molecules. It is this property of the nucleotides that results in their involvement in group transfer reactions in the cell.
-<DD>The nucleotides found in DNA are unique from those of RNA in that the ribose exists in the 2'-deoxy form and the abbreviations of the nucleotides contain a <B><font color=red>d</B></font> designation. The monophosphorylated form of adenosine found in DNA (deoxyadenosine-5'-monophosphate) is written as <B><font color=red>dAMP</B></font>.
-<DD>The nucleotide uridine is never found in DNA and thymine is almost exclusively found in DNA. Thymine is found in tRNAs but not rRNAs nor mRNAs. There are several less common bases found in DNA and RNA. The primary modified base in DNA is 5-methylcytosine. A variety of modified bases appear in the tRNAs. Many modified nucleotides are encountered outside of the context of DNA and RNA that serve important biological functions.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR>
-<A NAME="adenosine"><H1><B><center>Adenosine Derivatives</B></center></H1></A>
-<P><font size=+2><DD>The most common adenosine derivative is the cyclic form, <B><font color=red>3'-5'-cyclic adenosine monophosphate, cAMP</B></font>. This compound is a very powerful <B><font color=red>second messenger</B></font> involved in passing <A HREF="signal-transduction.html">signal transduction</A> events from the cell surface to internal proteins, e.g. <A HREF="pkacamp.html">cAMP-dependent protein kinase</A> (<B>PKA</B>). PKA phosphorylates a number of proteins, thereby, affecting their activity either positively or negatively. Cyclic-AMP is also involved in the regulation of ion channels by direct interaction with the channel proteins, e.g. in the activation of odorant receptors by odorant molecules.
-<DD>Formation of cAMP occurs in response to activation of receptor coupled <B><I>adenylate cyclase</B></I>. These receptors can be of any type, e.g. hormone receptors or odorant receptors.
-<DD><B><font color=red>S-adenosylmethionine</B></font> is a form of <B><I>activated</B></I> methionine which serves as a methyl donor in methylation reactions and as a source of propylamine in the synthesis of polyamines.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR>
-<A NAME="guanosine"><H1><B><center>Guanosine Derivatives</B></center></H1></A>
-<P><font size=+2><DD>A cyclic form of GMP (<B><font color=red>cGMP</B></font>) also is found in cells involved as a second messenger molecule. In many cases its' role is to antagonize the effects of cAMP. Formation of cGMP occurs in response to receptor mediated signals similar to those for activation of adenylate cyclase. However, in this case it is <B><I>guanylate cyclase</B></I> that is coupled to the receptor.
-<DD>The most important cGMP coupled signal transduction cascade is that <A HREF="vitamins.html#vision">photoreception</A>. However, in this case activation of <B><font color=red>rhodopsin</B></font> (in the rods) or other <B><font color=red>opsins</B></font> (in the cones) by the absorption of a photon of light (through 11-<I>cis</I>-retinal covalently associated with rhodopsin and opsins) activates transducin which in turn activates a cGMP specific phosphodiesterase that hydrolyzes cGMP to GMP. This lowers the effective concentration of cGMP bound to gated ion channels resulting in their closure and a concomitant hyperpolarization of the cell.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR>
-<A NAME="analogs"><H1><B><center>Synthetic Nucleotide Analogs</B></center></H1></A>
-<P><font size=+2><DD>Many nucleotide analogues are chemically synthesized and used for their therapeutic potential. The nucleotide analogues can be utilized to inhibit specific enzymatic activities. A large family of analogues are used as anti-tumor agents, for instance, because they interfere with the synthesis of DNA and thereby preferentially kill rapidly dividing cells such as tumor cells. Some of the nucleotide analogues commonly used in chemotherapy are 6-mercaptopurine, 5-fluorouracil, 5-iodo-2'-deoxyuridine and 6-thioguanine. Each of these compounds disrupts the normal replication process by interfering with the formation of correct Watson-Crick base-pairing.
-<DD>Nucleotide analogs also have been targeted for use as antiviral agents. Several analogs are used to interfere with the replication of HIV, such as <B><font color=red>AZT (azidothymidine)</B></font> and <B><font color=red>ddI (dideoxyinosine)</B></font>.
-<DD>Several purine analogs are used to treat gout. The most common is <B><font color=red>allopurinol</B></font>, which resembles hypoxanthine. Allopurinol inhibits the activity of <B><I>xanthine oxidase</B></I>, an enzyme involved in <I>de novo</I> <A HREF="nucleotide-metabolism.html#purine">purine biosynthesis</A>. Additionally, several nucleotide analogues are used after organ transplantation in order to suppress the immune system and reduce the likelihood of transplant rejection by the host.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR><A NAME="poly"><H1><B><center>Polynucleotides</B></H1></center></A>
-<P><font size=+2><DD>Polynucleotides are formed by the condensation of two or more nucleotides. The condensation most commonly occurs between the alcohol of a 5'-phosphate of one nucleotide and the 3'-hydroxyl of a second, with the elimination of H<sub>2</sub>O, forming a <B><font color=red>phosphodiester bond</B></font>. The formation of phosphodiester bonds in DNA and RNA exhibits directionality. The primary structure of DNA and RNA (the linear arrangement of the nucleotides) proceeds in the 5' ----> 3' direction. The common representation of the primary structure of DNA or RNA molecules is to write the nucleotide sequences from left to right synonymous with the 5' -----> 3' direction as shown:
-<P><B><center>5'-pGpApTpC-3'</B></center>
-<P></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR><A NAME="dna"><H1><B><center>Structure of DNA</B></H1></center></A>
-<P><font size=+2><DD>Utilizing X-ray diffraction data, obtained from crystals of DNA, James Watson and Francis Crick proposed a model for the structure of DNA. This model (subsequently verified by additional data) predicted that DNA would exist as a helix of two complementary antiparallel strands, wound around each other in a rightward direction and stabilized by H-bonding between bases in adjacent strands. In the <B><font color=red>Watson-Crick model</B></font>, the bases are in the interior of the helix aligned at a nearly 90 degree angle relative to the axis of the helix. Purine bases form hydrogen bonds with pyrimidines, in the crucial phenomenon of <font color=red><B>base pairing</B></font>. Experimental determination has shown that, in any given molecule of DNA, the concentration of adenine (A) is equal to thymine (T) and the concentration of cytidine (C) is equal to guanine (G). This means that A will only base-pair with T, and C with G. According to this pattern, known as <B><font color=red>Watson-Crick base-pairing</B></font>, the base-pairs composed of G and C contain three H-bonds, whereas those of A and T contain two H-bonds. This makes G-C base-pairs more stable than A-T base-pairs.
-
-<P><center>
-<table cellpadding=5 border=4 bgcolor=white>
-
-<TR valign=middle><TD align=center><img src="at-basepair.jpg"></TD><TD align=center><img src="gc-basepair.jpg"></TD>
-
-<TR valign=middle><TD align=center><font size=+2><font color=maroon><B>A-T Base Pair</B></TD><TD align=center><font color=maroon><font size=+2><B>G-C Base Pair</B></TD>
-</table></center></TR>
-
-<P><DD>The antiparallel nature of the helix stems from the orientation of the individual strands. From any fixed position in the helix, one strand is oriented in the 5' ---> 3' direction and the other in the 3' ---> 5' direction. On its exterior surface, the double helix of DNA contains two deep grooves between the ribose-phosphate chains. These two grooves are of unequal size and termed the <B><font color=red>major</B></font> and <B><font color=red>minor grooves</B></font>. The difference in their size is due to the asymmetry of the deoxyribose rings and the structurally distinct nature of the upper surface of a base-pair relative to the bottom surface.
-<DD>The double helix of DNA has been shown to exist in several different forms, depending upon sequence content and ionic conditions of crystal preparation. The <font color=red><B>B-form</B></font> of DNA prevails under physiological conditions of low ionic strength and a high degree of hydration. Regions of the helix that are rich in pCpG dinucleotides can exist in a novel left-handed helical conformation termed <font color=red><B>Z-DNA</B></font>. This conformation results from a 180 degree change in the orientation of the bases relative to that of the more common A- and B-DNA.
-<P><center><table width=60% cellpadding=10 bgcolor=white border=4><TR valign=middle><TD align=center><img src="bdna.gif"></TD><TD align=center><img src="zdna.gif"></TD>
-<TR valign=middle><TD align=center><B><font color=blue><font size=+2>Structure of B-DNA </TD><TD align=center><B><font color=blue><font size=+2>Structure of Z-DNA</TD>
-</table></TR></center>
-
-<P><B><center>Parameters of Major DNA Helices</B>
-<P><table border=4 width=90% bgcolor=white>
-<TR valign=middle><TD align=center><B><font size=5 font color=blue>Parameters</TD><TD align=center><B><font size=5 font color=blue>A Form</TD><TD align=center><B><font size=5 font color=blue>B Form</TD><TD align=center><B><font size=5 font color=blue>Z-Form</TD>
-
-<TR valign=middle><TD align=center><font size=4>Direction of helical rotation</TD><TD align=center><font size=4>Right</TD><TD align=center><font size=4>Right</TD><TD align=center><font size=4>Left</TD>
-
-<TR valign=middle><TD align=center><font size=4>Residues per turn of helix</TD><TD align=center><font size=4>11</TD><TD align=center><font size=4>10</TD><TD align=center><font size=4>12 base pairs</TD>
-
-<TR valign=middle><TD align=center><font size=4>Rotation of helix per residue (in degrees)</TD><TD align=center><font size=4>33</TD><TD align=center><font size=4>36</TD><TD align=center><font size=4>-30</TD>
-
-<TR valign=middle><TD align=center><font size=4>Base tilt relative to helix axis (in degrees)</TD><TD align=center><font size=4>20</TD><TD align=center><font size=4>6</TD><TD align=center><font size=4>7</TD>
-
-<TR valign=middle><TD align=center><font size=4>Major groove</TD><TD align=center><font size=4>narrow and deep</TD><TD align=center><font size=4>wide and deep</TD><TD align=center><font size=4>Flat</TD>
-
-<TR valign=middle><TD align=center><font size=4>Minor groove</TD><TD align=center><font size=4>wide and shallow</TD><TD align=center><font size=4>narrow and deep</TD><TD align=center><font size=4>narrow and deep</TD>
-
-<TR valign=middle><TD align=center><font size=4>Orientation of N-glycosidic Bond</TD><TD align=center><font size=4>Anti</TD><TD align=center><font size=4>Anti</TD><TD align=center><font size=4>Anti for Py, Syn for Pu</TD>
-
-<TR valign=middle><TD align=center><font size=4>Comments</TD><TD align=center> </TD><TD align=center><font size=4>most prevalent within cells</TD><TD align=center><font size=4>occurs in stretches of alternating purine-pyrimidine base pairs</TD>
-</table></center></center></TR>
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR><A NAME="thermal"><H1><B><center>Thermal Properties of DNA</B></H1></center></A>
-<P><font size=+2><DD>As cells divide it is a necessity that the DNA be copied (replicated), in such a way that each daughter cell acquires the same amount of genetic material. In order for this process to proceed the two strands of the helix must first be separated, in a process termed denaturation. This process can also be carried out in vitro. If a solution of DNA is subjected to high temperature, the H-bonds between bases become unstable and the strands of the helix separate in a process of <B><font color=red>thermal denaturation</B></font>.
-<DD>The base composition of DNA varies widely from molecule to molecule and even within different regions of the same molecule. Regions of the duplex that have predominantly A-T base-pairs will be less thermally stable than those rich in G-C base-pairs. In the process of thermal denaturation, a point is reached at which 50% of the DNA molecule exists as single strands. This point is the <B><font color=red>melting temperature (T<sub>M</sub>)</B></font>, and is characteristic of the base composition of that DNA molecule. The T<sub>M</sub> depends upon several factors in addition to the base composition. These include the chemical nature of the solvent and the identities and concentrations of ions in the solution.
-<DD>When thermally melted DNA is cooled, the complementary strands will again re-form the correct base pairs, in a process is termed <B><font color=red>annealing</B></font> or <B><font color=red>hybridization</B></font>. The rate of annealing is dependent upon the nucleotide sequence of the two strands of DNA.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR><H1><B><center>Analysis of DNA Structure</B></H1></center></A>
-<P><font size=+2><A NAME="chromatography"><B><font color=red>Chromatography:</B></font> Several of the chromatographic techniques available for the <A HREF="protein-structure.html#ion">characterization of proteins</A> can also be applied to the characterization of DNA. The most commonly used technique is HPLC (high performance liquid chromatography). Affinity chromatographic techniques also can be employed. One common affinity matrix is hydroxyapatite (a form of calcium phosphate), which binds double-stranded DNA with a higher affinity than single-stranded DNA.
-<BR></font><font size=3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR><H1><B><center>Analysis of DNA Structure</B></H1></center></A>
-<P><font size=+2><A NAME="electrophoresis"><B><font color=red>Electrophoresis:</B></font> This procedure can serve the same function with regard to DNA molecules as it does for the <A HREF="protein-structure.html#electrophoresis">analysis of proteins</A>. However, since DNA molecules have much higher molecular weights than proteins, the molecular sieve used in electrophoresis of DNA must be different as well. The material of choice is agarose, a carbohydrate polymer purified from a salt water algae. It is a copolymer of mannose and galactose that when melted and re-cooled forms a gel with pores sizes dependent upon the concentration of agarose. The phosphate backbone of DNA is highly negatively charged, therefore DNA will migrate in an electric field. The size of DNA fragments can then be determined by comparing their migration in the gel to known size standards. Extremely large molecules of DNA (in excess of 106 base pairs) are effectively separated in agarose gels using <B><font color=red>pulsed-field gel electrophoresis (PFGE)</B></font>. This technique employs two or more electrodes, placed orthogonally with respect to the gel, that receive short alternating pulses of current. PFGE allows whole chromosomes and large portions of chromosomes to be analyzed.
-<BR></font><font size = 3><A HREF="nucleic-acids.html#top">back to the top</A></font>
-<HR>
-<font size=4><A HREF="biomolecules.html">Return to Basic Chemistry of Biomolecules</A></font>
-
-<HR>
-<A HREF="home.html"><IMG border=0 SRC=home.gif></A></img> <font size = 4> Return to Medical Biochemistry Page</font>
-<BR><HR>
-<font size=3>
-<I> Michael W. King, Ph.D / IU School of Medicine /<A HREF="mailto:mking at medicine.indstate.edu">mking at medicine.indstate.edu</A></I></font>
-<HR>
-<font color=maroon size=3>Last modified:</font> <b><font color=black size=3>Thursday, 10-May-01 10:14:02
-</BODY>
-</HTML>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/usermanual/doc-stuff/nucleic.html b/usermanual/doc-stuff/nucleic.html
deleted file mode 100644
index bbdf21f..0000000
--- a/usermanual/doc-stuff/nucleic.html
+++ /dev/null
@@ -1,201 +0,0 @@
-<HTML>
-
-<HEAD>
-
-<TITLE>Nucleic Acid Structure and Function</TITLE>
-
-<META NAME="GENERATOR" CONTENT="Internet Assistant for Microsoft Word 2.0z">
-</HEAD>
-<BODY BACKGROUND="/class/ksmam00/texture.gif" BGCOLOR=white>
-
-<H1>Nucleic Acid Structure and Function <BR>
-<BR>
-</H1>
-
-<P>
-The two nucleic acids deoxyribonucleic acid (DNA) and ribonucleic
-acid (RNA) are the informational molecules of all living organisms.
-Besides storing and transmitting information, RNA forms structural
-and functional parts of units such as the ribosome and in some
-system has a catalytic function as ribozymes. Both DNA and RNA
-are long polymers assembled for repeating subunits, the nucleotides.
-The sequence of nucleotides in information nucleic acids molecules
-(mainly DNA) makes up a code that stores and transmits the direction
-required for assembling all types of proteins.<BR>
-
-<P>
-Individual nucleotides, in addition to providing the building
-blocks of nucleic acids, carry out a variety of biological functions.
-Many nucleotides are molecules built on nucleotides that transport
-chemical energy in the form of phosphate groups or electrons from
-one reaction system to another. Others carry metabolites such
-as acetyl groups between reactions. Still other nucleotides in
-cyclic form are important in cell regulation.<BR>
-
-<P>
-<B>Nucleotides</B>
-<P>
-A nucleotide consists of three covalently-linked parts:
-<UL>
-<LI>a nitrogen-containing base (Pyrimidines and Purines)
-<LI>a five carbon sugar (deoxyribose and ribose sugars)
-<LI>one or more phosphate groups. (-H<SUB>2</SUB>PO<SUB>5</SUB>)
-</UL>
-
-<P>
-The nitrogenous bases are pyrimidines and purines containing carbon
-and nitrogen atoms. Pyrimidines contain one ring and purines contain
-two rings. Three pyrimidine bases, uracil (U), thymine (T), and
-cytosine (C), and two purine bases, adenine (A) and guanine (G),
-are assembled into nucleic acids in cells. The nitrogenous bases
-link covalently to ribose or deoxyribose five-carbon sugars. The
-two five-carbon sugar differ only in the chemical group bound
-to the number 2-carbon position. Ribose has an -OH group at the
-number 2 position and deoxyribose has single hydrogen in the number
-2-carbon position. A chain of one, two, or three phosphates links
-to the ribose or deoxyribose sugar at its 5-carbon to complete
-the mono-, di, or triphosphate form of a nucleotide.
-<P>
-<IMG SRC="/cell/chapter7/nucleotide.gif" ALT="Nucleotide">
-<P>
-<IMG SRC="/cell/chapter7/amp.gif" ALT="AMP">
-<P>
-<IMG SRC="/cell/chapter7/atp.gif" ALT="ATP">
-<P>
-The names used for nucleotides can be confusing. the term nucleotide
-refers to a complete unit containing all three subunits: a nitrogenous
-base, a five carbon sugar, and one or more phosphates. A unit
-consisting of only the base and sugar without phosphates is called
-a nucleoside and is named according to its nitrogenous base. For
-example, the base-sugar complex containing adenine and ribose
-is called adenosine; if deoxyribose is the sugar in the complex,
-it is called deoxyadenosine. To number the phosphate groups, nucleosides
-with added phosphates. The adenine-ribose complex with one phosphate,
-for example, is called adenosine monophosphate (AMP); with two
-phosphates, adenosine diphosphate (ADP); with three, adenosine
-triphosphate (ATP).
-<P>
-<IMG SRC="/cell/chapter7/base-pairing.gif" ALT="Base-Pairing">
-<BR>
-
-<P>
-<B>DNA and RNA</B>
-<P>
-The two nucleic acids DNA and RNA consist of nucleotides held
-in chains by a bridging phosphate group that extends between the
-5'-carbon of one sugar and the 3'-carbon of the next sugar in
-line. This arrangement produces a backbone chain of alternating
-sugar and phosphate groups. <BR>
-
-<P>
-The nucleotides of DNA chains contain the sugar deoxyribose, and
-one of the four bases A, T, C, and G. The nucleotides of RNA chains
-contain the sugar ribose, and one of the four bases A, U, C, and
-G. Thymine and uracil differ only in a methyl group linked to
-the ring in thymine but absent in Uracil. The fully processed
-and finished forms of both DNA and RNA usually contain a number
-of modified bases formed by chemical alteration of the original
-nucleotides to other types. As many as 10 to 155 of the bases
-in RNA molecules may be modified to other forms.<BR>
-
-<P>
-DNA exists in cell as a double helix containing two intertwined
-chains of nucleotides. In the DNA double helix, discovered by
-J.D. Watson and F.H. Crick in 1953, sugar-phosphate backbones
-of the two chains twist together in a right-handed direction to
-form the double spiral. The backbone chains, which are located
-at the surface of the double helix, are separated across the helix
-by a regular space that is filled in by the nitrogenous bases.
-The bases extend inward from the sugars toward the axis of the
-helix as base pairs, which stack in flat planes roughly perpendicular
-to the long axis of the helix. Each complete turn of the double
-helix includes about 10 base pairs.<BR>
-
-<P>
-The space separating the sugar-phosphate backbones of a DNA double
-helix is just wide enough to accommodate a purine-pyrimidine base
-pair. Purine-purine pairs are too wide, and pyrimidine-pyrimidine
-pairs are too narrow to fit this space exactly. The shapes of
-the bases and the location of groups capable of forming stabilizing
-hydrogen bonds impose further restrictions on base pairing. Three
-hydrogen bonds can form between quanine and cytosine and two between
-adenine and thymine. <BR>
-
-<P>
-The pairing restriction also means that the sequence of one nucleotide
-chain fixes the sequence of it partner in the double helix as
-a complementary cop in which C on one side is paired with a B
-on the opposite side, and an A is paired with a T. This relationship
-is critical to the processes of DNA replication and RNA transcription,
-in which one nucleotide chain is used as a template for assembly
-of a complementary copy. The two chains of DNA are antiparallel
-and run in opposite directions. The phosphate linkages in the
-chain on the left runs (5' 3' topbottom) from the 5'-carbon on
-deoxyribose (top) to the 3'-carbon of the sugar (bottom). The
-right chain runs from top to bottom (3'5')<BR>
-<BR>
-
-<P>
-<IMG SRC="/cell/chapter7/dna-rna.gif" ALT="DNA and RNA">
-<P>
-Three primary intermolecular forces hold the DNA double helix
-together. One is hydrogen bonding between base pairs in the interior
-of the molecules. Cumulatively, the hydrogen bonds form a stable
-structure if the helix includes at least 10 base pairs. Attractive
-Van der Waals forces between the closely packed atoms of the double
-helix, particularly between atoms in the tightly stacked base
-pairs, provide the second stabilizing force. The third results
-from hydrophobic association among base pairs in the interior
-of the helix. The nitrogenous bases, which are primarily nonpolar,
-pack tightly enough to exclude water and form a stable, primarily
-nonpolar environment in the helix interior.<BR>
-
-<P>
-RNA exists largely as single rather than double nucleotide chains
-in living cells. However, segments of RNA molecules may pair temporarily
-in double-helical form or may fold back on themselves to set up
-extensive double-helical regions. These fold-back double helices
-and their arrangement are often more important to RNA functions
-than nucleotide sequence, particularly in noncoding RNAs such
-as those of ribosomes.<BR>
-
-<P>
-DNA and RNA are subject to denaturation. As temperature increases,
-the hydrogen bonds and other forces holding the backbones together
-are increasingly disturbed until the two chains come apart and
-unwind. This denaturation or melting takes place in most DNA molecules
-at temperatures of about 50<SUP>o</SUP>C to 60<SUP>o</SUP>C. In
-many cases, DNA or RNA molecules can wind back into native form
-if temperatures return to normal values. Unwinding and rewinding
-of DNA and RNA molecules are often used as experimental procedures.
-<P>
-<IMG SRC="/cell/chapter7/picture-dna.gif" ALT="DNA">
-<P>
-The arrangement of sugars, phosphate groups, and bases in the
-DNA double helix can be seen by these two models. The space-filling
-model of the DNA double show how the base pair lie flat in a plane.
-The edges can be seen
-<P>
-<IMG SRC="/cell/chapter7/stone-dna.gif" ALT="DNA">
-<P>
-<A HREF="/bio/DNA.mov">3-D structure of DNA</A> Video<BR>
-
-<HR>
-
-<H1><CENTER><FONT SIZE=6 COLOR=#0000D4>Return<BR>
-</FONT></CENTER></H1>
-
-<P>
-<CENTER><A HREF="http://www.tamuk.edu/artsci/"><IMG SRC="/bio/return-a&s.gif"> </A><A HREF="http://www.tamuk.edu/artsci/webuser/as/art_science/bio/biowp.html"><IMG SRC="/bio/return-bio.gif"> </A><A HREF="http://www.tamuk.edu/"><IMG SRC=" /bio/return-university.gif"> </A><A HREF="http://www.tamuk.edu/grad "><IMG SRC="/bio/return-graduate.gif"> </A>
-<BR>
-<A HREF="/homepage-ntri/perez-home/jperez.html "><IMG SRC="/bio/return-perez.gif"></A>
-<A HREF="/index.html"><IMG SRC="/bio/return-natural.gif"> </A><A HREF="/homepage-ntri/lectures/lectures-map.html "><IMG SRC="/bio/return-classnotes.gif "> </A>
-<BR>
-</CENTER>
-<P>
-This page is maintained by the Natural Toxins Research Center
-at Texas A&M University - Kingsville. <BR>
-
-</BODY>
-
-</HTML>
diff --git a/usermanual/doc-stuff/nucleic_acids.html b/usermanual/doc-stuff/nucleic_acids.html
deleted file mode 100644
index 77b6438..0000000
--- a/usermanual/doc-stuff/nucleic_acids.html
+++ /dev/null
@@ -1 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN">
<HTML>
<HEAD>
<TITLE>Nucleic Acids Structure</TITLE>
</HEAD>
<BODY BGCOLOR="#FDF5E6" LINK="#990000" VLINK="#996666">
<!-- A table to constrain the width of the web pages to 500 pixels -->
<TABLE WIDTH=500>
<TR>
<TD>
<CENTER><FONT SIZE="2">
<A HREF="default.html">Intro</A> |
<A HREF="aa.html">Amino Acids</A> |
<A HREF="protein.html">Proteins</A> |
<A HREF="cho.html">Carbohydrates</A> |
<A HREF="nucleic_acids.html">Nucleic Acids</A> |
<A HREF="lipid.html">Lipids</A>
<BR>
<A HREF="http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/large_molecules_problems.html" target="new">Large Molecule Problem Set</A> |
<a href="http://www.thelifewire.com/con_index.htm?03" target="new">Textbook Resources</a>
</FONT></CENTER>
<CENTER>
<H2><FONT COLOR="#990000" FACE="HELVETICA,ARIAL">Nucleotides, DNA, RNA</FONT></H2>
</CENTER>
<H2><FONT COLOR="#990000" FACE="HELVETICA,ARIAL">Nucleic Acids</FONT></H2>
<UL TYPE=DISC>
<LI>DNA and RNA are very long, informational polymers.</LI>
<LI>Monomers units are nucleotides, consisting of a pentose (ribose or deoxyribose), a phosphate group, and a nitrogen containing base.</LI>
<LI>DNA and RNA have "polarity". We describe polarity at either 5' to 3', or 3' to 5'.</LI>
</UL>
<H2><FONT COLOR="#990000" FACE="HELVETICA,ARIAL"><a NAME="Nucleotides">Nucleotides</a></FONT></H2>
<CENTER>
<A HREF="javascript:location='nucleic_acids.html#Nucleotides';window.open('js/figure_03-016.html','characters','height=250,width=700,scrollbars=yes')">
Purves: Figure 16, Nucleotides have three components</A>
</CENTER>
<br>
<TABLE CELLSPACING="8" WIDTH="500">
<TR>
<TD ALIGN=CENTER WIDTH="500">
<IMG SRC="dA.GIF" ALT="nucleotide" ALIGN=MIDDLE WIDTH="527" HEIGHT="245">
</TD>
</TR>
</TABLE>
<UL TYPE=DISC>
<LI>DNA and RNA are made from monomers called nucleotides, consisting of a pentose (ribose or deoxyribose), a phosphate group, and a nitrogenous pyrimidine or purine base.</LI>
<LI>In DNA the bases are adenine (A), cytosine (C), guanine (G), and Thymine (T).</LI>
<LI>In RNA, uracil (U) replaces the base T.</LI>
</UL>
<HR>
<H2><FONT COLOR="#990000" FACE="HELVETICA,ARIAL"><a NAME="DNA">DNA Structure</a></FONT></H2>
<CENTER>
<A HREF="javascript:location='nucleic_acids.html#DNA';window.open('js/figure_03-017b.html','characters','height=520,width=450,scrollbars=yes')">
Purves: Figure 17b, DNA Structure</A>
</CENTER>
<br>
<UL TYPE=DISC>
<LI>The phosphate at the 5'-position of one nucleotide is covalently linked to the -OH at the 3'-position of next nucleotide.</LI>
<LI>Polarity can be defined as either 5' to 3', or 3' to 5'. </LI>
<LI>In the model of DNA (left), the left strand has a polarity of 5' (top) to 3' (bottom), and the other DNA strand has the opposite polarity. </LI>
<LI>The two DNA strands are said to be "antiparallel". </LI>
</UL>
<TABLE CELLSPACING="8" WIDTH="500">
<TR>
<TD ALIGN=CENTER WIDTH="500">
<IMG SRC="graphics/DNA.gif" ALT="DNA structure" WIDTH="327" HEIGHT="394">
</TD>
</TR>
</TABLE>
<UL TYPE=DISC>
<LI>In DNA, Watson and Crick in 1953 proposed a structure for DNA that has two chains held together by base pairing. The original paper published in 1953 earned them the Nobel prize.</LI>
<LI>A is always paired with T, and C is always paired with G. Only these pairs can form stable hydrogen bonds. This is known as complementarity.</LI>
<TABLE CELLSPACING="8" WIDTH="500">
<TR>
<TD ALIGN=CENTER WIDTH="500">
<IMG SRC="dG-dC.GIF" ALT="Base Pair" WIDTH="400" HEIGHT="335">
</TD>
</TR>
</TABLE>
<LI>The important point is that knowing the sequence of bases in DNA on one strand allows you to predict the sequences on the opposite strand. </LI>
</UL>
<HR>
<H2><FONT COLOR="#990000" FACE="HELVETICA,ARIAL"><a NAME="RNA">RNA</a></FONT></H2>
<CENTER>
<A HREF="javascript:location='nucleic_acids.html#DNA';window.open('js/figure_03-017a.html','characters','height=520,width=400,scrollbars=yes')">
Purves: Figure 17a, RNA Structure</A>
</CENTER>
<br>
<TABLE CELLSPACING="8" WIDTH="500">
<TR>
<TD ALIGN=left WIDTH="250">
<P>
In the RNA model, note the extra -OH on the sugar ring, and the use of U rather than T. RNA also has polarity.
</P>
<HR>
<P>
Cellular RNA is normally single-stranded, in contrast to DNA which is normally base-paired and double stranded.
</P>
</TD>
<TD ALIGN=CENTER WIDTH="250">
<IMG SRC="graphics/RNA.gif" ALT="RNA" WIDTH="234" HEIGHT="343">
</TD>
</TR>
</TABLE>
<HR>
<CENTER>
<FONT SIZE="2">
<A HREF="default.html">Intro</A> |
<A HREF="aa.html">Amino Acids</A> |
<A HREF="protein.html">Proteins</A> |
<A HREF="cho.html">Carbohydrates</A> |
<A HREF="nucleic_acids.html">Nucleic Acids</A> |
<A HREF="lipid.html">Lipids</A>
<BR>
<A HREF="http://www.biology.arizona.edu">Biology Project</A> |
<A HREF="http://www.blc.arizona.edu/courses/181gh/">Course Home Page</A>
</FONT>
</CENTER>
<CENTER>
<FONT SIZE=2>
Richard B. Hallick
<BR>
The University of Arizona
<BR>
Revised: August 23, 2001
<BR>
<A HREF = "mailto:hallick at u.arizona.edu">hallick at u.arizona.edu</A>
<BR>
All contents copyright © 1997-2001. All rights reserved.
</FONT>
</CENTER>
<!-- Close table constraining page width -->
</TD>
</TR>
</TABLE>
</BODY>
</HTML>
\ No newline at end of file
--
massXpert mass spectrometry suite: debian packaging
More information about the debian-science-commits
mailing list