-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.html
155 lines (146 loc) · 9.41 KB
/
README.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>1. Metabolism pathway</title>
<style>
</style>
<link rel="stylesheet"
href="https://cdn.jsdelivr.net/gh/Microsoft/vscode/extensions/markdown-language-features/media/markdown.css">
<link rel="stylesheet"
href="https://cdn.jsdelivr.net/gh/Microsoft/vscode/extensions/markdown-language-features/media/highlight.css">
<style>
body {
font-family: -apple-system, BlinkMacSystemFont, 'Segoe WPC', 'Segoe UI', system-ui, 'Ubuntu', 'Droid Sans', sans-serif;
font-size: 14px;
line-height: 1.6;
}
</style>
<style>
.task-list-item {
list-style-type: none;
}
.task-list-item-checkbox {
margin-left: -20px;
vertical-align: middle;
}
</style>
</head>
<body class="vscode-body vscode-light">
<h1 id="1-metabolism-pathway">1. Metabolism pathway</h1>
<p><strong>Provided by Gao Senquan(2019013224), Chen Shurui(2019013222), Diao Tongxin(2019013240) and Lu
Minsi(2019080058) in THU. We've also push it to <code>Github</code> repository
(Available at <a
href="https://github.com/maxwell-gao/CH_metabolism_path">https://github.com/maxwell-gao/CH_metabolism_path</a>)</strong>
</p>
<h2 id="11-preface">1.1. <strong>Preface</strong></h2>
<p>The majority of our figures are generated by [<code>Escher</code>] (<a
href="https://github.com/zakandrewking/escher/">https://github.com/zakandrewking/escher/</a>),
[<code>COBRApy</code>] (<a href="https://opencobra.github.io/cobrapy/">https://opencobra.github.io/cobrapy/</a>)
and models in [<code>Jupyter Lab</code>] (<a href="https://jupyter.org/">https://jupyter.org/</a>). The
<code>BioRender</code> is also used for figure creating.</p>
<p>We use <code>COBRA</code> as an analyzing tool based on omics data flux to reveal how the metabolism flux
actually works in the living body.</p>
<p>This comprehensive homework is composed of three major parts: the source code we use, the figures we draw with
various tools (we believe that you may find them so different from each other soon😂), and the document you are
reading now (in the HTML form and the markdown form).</p>
<p>We aim to provide a creative form for biochemistry reviewing and understanding though we know that’s a hard work.
</p>
<ul>
<li><a href="#1-metabolism-pathway">1. Metabolism pathway</a>
<ul>
<li><a href="#11-preface">1.1. <strong>Preface</strong></a></li>
<li><a href="#12-metabolism-overview">1.2. <strong>Metabolism Overview</strong></a>
<ul>
<li><a href="#121-the-core-metabolism">1.2.1. The core metabolism</a></li>
</ul>
</li>
<li><a href="#13-central-carbon-metabolism">1.3. <strong>Central carbon Metabolism</strong></a>
<ul>
<li><a href="#131-flux-of-central-carbon">1.3.1. Flux of central carbon</a></li>
<li><a href="#132-emp-tca-and-ppp">1.3.2. EMP, TCA and PPP</a></li>
<li><a href="#133-glycolysis-and-glycolytic-enzymes">1.3.3. Glycolysis and Glycolytic
Enzymes</a></li>
<li><a href="#134-glycogen-degradation">1.3.4. Glycogen Degradation</a></li>
<li><a href="#135-krebs-cycle">1.3.5. Krebs Cycle</a></li>
<li><a href="#136-pentose-phosphate-pathway">1.3.6. Pentose Phosphate Pathway</a></li>
<li><a href="#137-oxidative-phosphorylation">1.3.7. Oxidative Phosphorylation</a></li>
<li><a href="#138-warburg-effect">1.3.8. Warburg Effect</a></li>
<li><a href="#139-the-cori-cyle-an-anaerobic-metabolic-method-for-glucogenesis">1.3.9. The Cori
Cyle: An Anaerobic Metabolic Method for Glucogenesis</a></li>
</ul>
</li>
<li><a href="#14-fatty-acid-metabolism">1.4. <strong>Fatty acid Metabolism</strong></a>
<ul>
<li><a href="#141-fatty-acid">1.4.1. Fatty Acid</a></li>
</ul>
</li>
<li><a href="#15-amino-acid-metabolism">1.5. <strong>Amino acid Metabolism</strong></a>
<ul>
<li><a href="#151-amino-acid-catabolism-and-urea-cycle">1.5.1. Amino Acid Catabolism and Urea
Cycle</a></li>
<li><a href="#152-metabolism-of-amino-acid-carbon-skeletons">1.5.2. Metabolism of Amino Acid
Carbon Skeletons</a></li>
</ul>
</li>
<li><a href="#16-nucleotide-metabolism">1.6. <strong>Nucleotide Metabolism</strong></a>
<ul>
<li><a href="#161-nucleotide-metabolism">1.6.1. Nucleotide Metabolism</a></li>
</ul>
</li>
<li><a href="#17-reference">1.7. <strong>Reference</strong></a></li>
</ul>
</li>
</ul>
<h2 id="12-metabolism-overview">1.2. <strong>Metabolism Overview</strong></h2>
<h3 id="121-the-core-metabolism">1.2.1. The core metabolism</h3>
<p><img src="GIF/core.gif" alt=""></p>
<p><object width="75%" height="800px" data="Core.html"></object></p>
<h2 id="13-central-carbon-metabolism">1.3. <strong>Central carbon Metabolism</strong></h2>
<h3 id="131-flux-of-central-carbon">1.3.1. Flux of central carbon</h3>
<p><object width="75%" height="1000px" data="CarbonMeta.html"></object></p>
<h3 id="132-emp-tca-and-ppp">1.3.2. EMP, TCA and PPP</h3>
<p><object width="75%" height="500px" data="EMP_TCA_PPP.html"></object></p>
<h3 id="133-glycolysis-and-glycolytic-enzymes">1.3.3. Glycolysis and Glycolytic Enzymes</h3>
<p><img src="Figures/Glycolysis%20and%20Glycolytic%20Enzymes.png" alt="Glycolysis and Glycolytic Enzymes"></p>
<h3 id="134-glycogen-degradation">1.3.4. Glycogen Degradation</h3>
<p><img src="Figures/Glycogen%20degradation.png" alt="Glycogen Degradation"></p>
<h3 id="135-krebs-cycle">1.3.5. Krebs Cycle</h3>
<p><img src="Figures/Krebs%20Cycle.png" alt="Krebs Cycle"></p>
<h3 id="136-pentose-phosphate-pathway">1.3.6. Pentose Phosphate Pathway</h3>
<p><img src="Figures/Pentose%20Phosphate%20Pathway.png" alt="Pentose Phosphate Pathway"></p>
<h3 id="137-oxidative-phosphorylation">1.3.7. Oxidative Phosphorylation</h3>
<p><img src="Figures/Oxidative%20Phosphorylation.png" alt="Oxidative Phosphorylation"></p>
<h3 id="138-warburg-effect">1.3.8. Warburg Effect</h3>
<p><img src="Figures/Warburg%20Effect.png" alt="Warburg Effect"></p>
<h3 id="139-the-cori-cyle-an-anaerobic-metabolic-method-for-glucogenesis">1.3.9. The Cori Cyle: An Anaerobic
Metabolic Method for Glucogenesis</h3>
<p><img src="Figures/The%20Cori%20Cycle_%20An%20Anaerobic%20Metabolic%20Method%20for%20Gluconeogenesis.png"
alt="The Cori Cycle: An Anaerobic Metabolic Method for Gluconeogenesis"></p>
<h2 id="14-fatty-acid-metabolism">1.4. <strong>Fatty acid Metabolism</strong></h2>
<h3 id="141-fatty-acid">1.4.1. Fatty Acid</h3>
<p><img src="GIF/FattyAcid.gif" alt=""></p>
<p><object width="75%" height="1000px" data="FAS.html"></object></p>
<p><object width="75%" height="1000px" data="FattyAcid.html"></object></p>
<p><img src="Figures/Fatty%20Acid.svg" alt="Fatty Acid" title="Fatty Acid"></p>
<h2 id="15-amino-acid-metabolism">1.5. <strong>Amino acid Metabolism</strong></h2>
<p><object width="75%" height="1000px" data="AA.html"></object></p>
<h3 id="151-amino-acid-catabolism-and-urea-cycle">1.5.1. Amino Acid Catabolism and Urea Cycle</h3>
<p><img src="Figures/Amino%20Acid%20Catabolism%20and%20Urea%20Cycle.png" alt="Amino Acid Catabolism and Urea Cycle"
title="Amino Acid Catabolism and Urea Cycle"></p>
<h3 id="152-metabolism-of-amino-acid-carbon-skeletons">1.5.2. Metabolism of Amino Acid Carbon Skeletons</h3>
<p><img src="Figures/Metabolism%20of%20Amino%20Acid%20Carbon%20Skeletons.png"
alt="Metabolism of Amino Acid Carbon Skeletons"></p>
<h2 id="16-nucleotide-metabolism">1.6. <strong>Nucleotide Metabolism</strong></h2>
<p><object width="75%" height="1000px" data="Nucleotide.html"></object></p>
<h3 id="161-nucleotide-metabolism">1.6.1. Nucleotide Metabolism</h3>
<p><img src="Figures/Nucleotide%20Metabolism.png" alt="Nucleotide Metabolism"></p>
<h2 id="17-reference">1.7. <strong>Reference</strong></h2>
<pre><code><code><div>Heirendt L, Arreckx S, Pfau T, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0[J]. Nature protocols, 2019, 14(3): 639-702.
Rowe E, Palsson B O, King Z A. Escher-FBA: a web application for interactive flux balance analysis[J]. BMC systems biology, 2018, 12(1): 84.
Brunk E, Sahoo S, Zielinski D C, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism[J]. Nature biotechnology, 2018, 36(3): 272.
Nelson D L, Lehninger A L, Cox M M. Lehninger principles of biochemistry[M]. Macmillan, 2008.
Nelson D L, Cox M M. Lehninger Principles of Biochemistry Lecture Notebook[M]. Macmillan, 2004.
</div></code></code></pre>
</body>
</html>