Wikipedia:WikiProject Molecular and Cellular Biology/Style guidelines
From Wikipedia, the free encyclopedia
| This page will eventually contain a series of style guidelines for the Wikipedia:WikiProject Molecular and Cellular Biology.
It still has a long way to go. |
Contents |
[edit] Diagram guide
The guidelines for creating diagrams for the project can be found in the Molecular and Cellular Biology Diagram Guide.
[edit] Structures
[edit] Proteins
- Wikipedia articles about individual proteins or small protein families can be organized so as to look like Myoglobin, Gonadotropin-releasing hormone or Rubisco.
- Wikipedia articles about individual proteins or small protein families can each have a protein information box (see Myoglobin for an example).
- Each Wikipedia article about individual proteins or small protein families can be organized into one or more wikipedia category. See Whole proteome analysis for needed protein categories. See Cytoskeleton and Category:Cytoskeleton for an example.
- The main articles in each wikipedia protein category can be put into a navigation box (see the bottom of Cytoskeleton for an example).
[edit] Naming
[edit] Genes
The abbreviations of genes are according to HUGO Gene Nomenclature Committee and written in italic font style (the full names are also written in italic). It is recommended that we use abbreviations instead of the full name. Human gene names are written in capitals, for example ALDOA, INS, etc. For orthologs of human genes in other species, only the initial letter is capitalised, for example mouse Aldoa, bovine Ins, etc.
When we write about the genes this is correct - "the ALDOA gene is regulated...", "the rat gene for Aldoa is regulated..." or "ALDOA is regulated...", while this should not be allowed - "the gene ALDOA is regulated", b/c it's redundant. And if anyone starts arguing with you about it, say "Sorry, but we have a standart to follow" and redirect them to this section. -- Boris 15:32, 29 December 2005 (UTC)
[edit] Proteins
The same as with the genes, but not in italics. Thus human proteins are written like "THIS", whilst their orthologs in other species are written like "This". -- Boris 15:32, 29 December 2005 (UTC)
[edit] Templates
[edit] Infoboxes
| Myoglobin | |
|---|---|
 Model of helical domains in myoglobin. |
|
| Gene code: | HUGO code: MB |
| Structure: | molecular structure |
| Recent publications: | role in human pathologies, gene knockout |
| protein type: | Hemoprotein |
| Functions: | oxygen storage/transport |
| Domains: | globin |
| Diseases: | kidney disease, vasospasm |
| Taxa expressing: | many metazoan phyla, Archaea?, protozoan/eubacterial? |
| Cell types: | muscle cells |
| Subcellular localization: | cytoplasm |
| covalent modifications | glycation?, phosphorylation in whales? |
| Other names: | myoglobin-like proteins in microorganisms |
| Molecular interactions | oxygen, carbon monoxide, nitric oxide |
| related articles: | X-ray crystallography, Secondary structure |
[edit] Protein info box
Info box example for the protein myoblobin (to right).
Note: only the first (start) and last (finish) template are required. The middle three templates (function, location, other) are options.
{{Protbox start}} template:
- preferred name of the protein
- image for protein (might be structural diagram, cell localization, etc)
- caption for image
- link to gene(s) in database, which gene(s) code for it?
- link to database entry for protein structural info
- links to recent articles at Entrez PubMed.
(To support proteins that do not have an image, this template has been broken down into three components: Template:Protbox header, Template:Protbox image, and Template:Protbox topfields. An alternative to the topfields section is provided in Template:Protbox codes, and a simplified version is at Template:Protein.)
{{Protbox function}} template:
- categorization of the protein; what type of protein is it?
- functions of the protein
- structural domains in the protein
- disease conditions involving the protein
{{Protbox location}} template:
- taxonomic range of expression (wide? restricted?)
- which types of cells express it?
- Subcellular localization.
{{Protbox other}} template:
- covalent modifications with functional significance
- all names that have been applied to the protein
- what other molecules interact with it?
- links to wikipedia pages that discuss the protein
{{Protbox enzyme}} template:
- What reaction it catalyses
- The cofactors involved in the reaction
- Method enzyme is regulated
{{Protbox receptor}} template:
- Receptor actions, e.g. vasoconstriction, neuronal excitation, etc.
- Agonists
- Antagonists
{{Protbox finish}} template:
- This template simply marks the end of a protein information box. (required)
[edit] Cell type info box
This will be an information box for displaying basic information about individual cell types.
List of distinct cell types in the adult human body
Some useful references:
- open source cell type ontology project
- http://www.bioeng.auckland.ac.nz/anatml/anatml/database/cells/cells/index.html
- Cell types from Dorland's Medical Dictionary
Basic info could be, name(s), functions, what taxonomic groups has the cell type, etc.
Tissue type(s) that contain the cell type
The major types of proteins that are expressed and that provide the specialized functions of the cell type
I suggest we pick one cell type as an example and get started. I propose skeletal muscle.
[edit] Database templates
Templates like this ({{OMIM}}) for the Protein databases, Enzyme Number and PubMed. You'll find these very useful when citing your sources.
| Template Name | Usage | Renders As |
|---|---|---|
| Human genetics for a protein/gene: | {{OMIM|160000}} | Mendelian Inheritance in Man (OMIM) 160000 |
| Digital object identifier |
{{Doi|10.1038/437794a}} |
DOI:10.1038/437794a |
| Enzyme number: |
{{EC number|4.1.1.39}} |
EC 4.1.1.39 |
| Template for Protein Data Bank citations: | {{Protein Data Bank|9RUB}} | Protein Data Bank 9RUB |
| Template for PubMed Central full text articles |
{{PMC|137841}} | Full text at PMC: 137841 |
| Template for Entrez PubMed citations |
{{Entrez Pubmed|10336462}} | Entrez PubMed 10336462 |
| Template for Entrez gene citations |
{{EntrezGene|2695}} | EntrezGene 2695 |
| Template for RefSeq citations |
{{RefSeq|NM_004123}} | RefSeq NM_004123 |
| Template for UniProt citations |
{{UniProt|P09681}} | UniProt P09681 |
[edit] Protein topics navigation boxes
See User:Lilious for how to jazz up such navigation boxes.
Templates:
{{Protein topics}}
{{Protein methods}} Protein methods
{{Protein domains}}
| Protein domains: |
|---|
| BZIP | DED | Kringle | PH | SH2 | SH3 | zinc finger | coiled coil | helix bundle | globin fold | twisted open sheet | alpha/beta barrels | up and down barrel | greek key barrel | jelly roll barrel | greek key | leucine-rich repeat | beta propeller |
[edit] Research topic navigation boxes
Example: {{King's College DNA}}
 |
DNA structure research at King's College London 1947-1959 |
| Rosalind Franklin | Raymond Gosling | John Randall | Alec Stokes | Maurice Wilkins | Herbert Wilson |
[edit] What is a subtemplate?
- {{subst:template}}
- e.g.{{Infobox Molecular and Cellular Biology}}
{{Infobox Molecular and Cellular Biology }}
[edit] Stub templates
[edit] Add to existing categories
{{Molecular and Cellular Biology-category}}
 |
This category is of interest to the Molecular and Cellular Biology WikiProject. You can help improve and organize the articles in this category. |
[edit] Project banner template
{{Wikiproject MCB}} – A simple project banner template to mark articles that are part of this project. It serves, in part, as advertising for the project. It is to placed on the talk page of any atricles of interest to this wikiproject.
 |
This article is within the scope of the Molecular and Cellular Biology WikiProject. Please work to improve this article, or visit our project page to find other ways of helping. Thanks! | ||
|
Article Grading: The article has not been rated for quality and/or importance yet. Please rate the article and then leave comments here to explain the ratings and/or to identify the strengths and weaknesses of the article.. |
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[edit] Collaboration of the Month templates
| Template | What it makes | Where it goes | ||
|---|---|---|---|---|
| {{MCBnom}} |
|
The talk pages of articles nominated for the MCB Collaboration of the Month. | ||
| {{MCBcur | month=MONTH}} |
|
The talk pages of articles that are currently the MCB Collaboration of the Month. | ||
| {{MCBprev}} |
|
The talk pages of articles that were previously an MCB Collaboration of the Month. |
[edit] Protein structure templates
{{Protein quaternary structure}} under construction; suggestions welcome!
| Protein quaternary structure | ||
|---|---|---|
| General: | Globular protein | Fibrous protein | Membrane protein | Coiled coil | |
| Dimers: | Leucine zipper| Tryptophan repressor | Glutathione S-transferase | |
| Trimers: | Collagen | Hemagglutinin | Ornithine transcarbamylase | |
| Tetramers: | Hemoglobin | IgG | Avidin | Spectrin | |
| Hexamers: | DnaB helicase | Hemocyanin | Glutamate Dehydrogenase 1 | |
| Octamers: | Nucleosome | Hemerythrin | |
| Fibrils: | Actin | Tubulin | Flagellum | Pilus | |
| Complexes: | Preinitiation complex | Immunoglobulin M | |
| Machines: | Proteasome | Ribosome | ATP synthase | RNA polymerase | Spliceosome | |
| Virus: | Capsid | |
| Precipitates: | Salting out | Hofmeister series | |
| Methods: | Ultracentrifugation | Size exclusion chromatography | |
| ←Tertiary structure | Structure determination methods | |
{{Protein tertiary structure}}
| Protein tertiary structure | ||
|---|---|---|
| General: | Structural domain | Protein folding | |
| All-α folds: | Helix bundle | Globin fold | Homeodomain fold | Alpha solenoid | |
| All-β folds: | Immunoglobulin fold | Beta barrel | Beta-propeller domain | |
| α/β folds: | TIM barrel | Leucine-rich repeat | Flavodoxin fold | Thioredoxin fold | Trefoil knot fold | |
| α+β folds: | Ferredoxin fold | Ribonuclease A | SH2-like fold | |
| Irregular folds: | Conotoxin | |
| ←Secondary structure | Structure determination methods | Quaternary structure→ |
{{Protein structure determination}}
| Protein structure determination methods | ||
|---|---|---|
| High resolution: | X-ray crystallography | NMR | Electron crystallography | |
| Medium resolution: | Cryo-electron microscopy | Fiber diffraction | Mass spectrometry | |
| Spectroscopic: | NMR | Circular dichroism | Absorbance | Fluorescence | Fluorescence anisotropy | |
| Translational Diffusion: | Analytical ultracentrifugation | Size exclusion chromatography | Light scattering | NMR | |
| Rotational Diffusion: | Fluorescence anisotropy | Flow birefringence | Dielectric relaxation | NMR | |
| Chemical: | Hydrogen-deuterium exchange | Site-directed mutagenesis | Chemical modification | |
| Thermodynamic: | Equilibrium unfolding | |
| Computational: | Protein structure prediction | Molecular docking | |
| ←Tertiary structure | Quaternary structure→ | |
{{Protein secondary structure}}
| Protein secondary structure | ||
|---|---|---|
| Helices: | α-helix | 310 helix | π-helix | β-helix | Polyproline helix | Collagen helix | |
| Extended: | β-strand | Turn | Beta hairpin | Beta bulge | |
| Supersecondary: | Coiled coil | Helix-turn-helix | EF hand | |
| Secondary structure propensities of amino acids | ||
| Helix-favoring: | Methionine | Alanine | Leucine | Glutamic acid | Glutamine | Lysine | |
| Extended-favoring: | Threonine | Isoleucine | Valine | Phenylalanine | Tyrosine | Tryptophan | |
| Disorder-favoring: | Glycine | Serine | Proline | Asparagine | Aspartic acid | |
| No preference: | Cysteine | Histidine | Arginine | |
| ←Primary structure | Tertiary structure→ | |
{{Amino acids}}
| The 20 Common Amino Acids | ||
|---|---|---|
| Aliphatic: | Valine | Isoleucine | Leucine | Methionine | Alanine | Proline | Glycine | |
| Aromatic: | Phenylalanine | Tyrosine | Tryptophan | Histidine | |
| Polar, uncharged: | Asparagine | Glutamine | Serine | Threonine | |
| Positive charge (pKa): | Lysine (≈10.8) | Arginine (≈12.5) | Histidine (≈6.1) | |
| Negative charge (pKa): | Aspartic acid (≈3.9) | Glutamic acid (≈4.1) | Cysteine (≈8.3) | Tyrosine (≈10.1) | |
| Essential amino acid | Protein | Peptide | Genetic code | Primary structure→ | |
[edit] Templates for major families of biochemicals
{{Biochemical families}} under construction, overview template, fast cross-link
| Major Families of Biochemicals | ||
|---|---|---|
| Peptides | Amino acids | Nucleic acids | Carbohydrates | Lipids | Terpenoids | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | ||
{{AminoAcids}} under construction
| The 20 Common Amino Acids | ||
|---|---|---|
| Alanine (dp) | Arginine (dp) | Asparagine (dp) | Aspartic acid (dp) | Cysteine (dp) | Glutamic acid (dp) | Glutamine (dp) | Glycine (dp) | Histidine (dp) | Isoleucine (dp) | Leucine (dp) | Lysine (dp) | Methionine (dp) | Phenylalanine (dp) | Proline (dp) | Serine (dp) | Threonine (dp) | Tryptophan (dp) | Tyrosine (dp) | Valine (dp) | ||
| ←Peptides | Major families of biochemicals | Nucleic acids→ |
{{Nucleic acids}} under construction
| Nucleic acids and oligonucleotides edit | ||
|---|---|---|
| Nucleobases: | Adenine | Thymine | Uracil | Guanine | Cytosine | Purine | Pyrimidine | |
| Nucleosides: | Adenosine | Uridine | Guanosine | Cytidine | Deoxyadenosine | Thymidine | Deoxyguanosine | Deoxycytidine | |
| Nucleotides: | AMP | UMP | GMP | CMP | ADP | UDP | GDP | CDP | ATP | UTP | GTP | CTP | cAMP | cADPR | cGMP | |
| Deoxynucleotides: | dAMP | TMP | dGMP | dCMP | dADP | TDP | dGDP | dCDP | dATP | TTP | dGTP | dCTP | |
| Ribonucleic acids: | RNA | mRNA | tRNA | rRNA | ncRNA | sgRNA | shRNA | siRNA | snRNA | miRNA | snoRNA | LNA | |
| Deoxyribonucleic acids: | DNA | mtDNA | cDNA | plasmid | Cosmid | BAC | YAC | HAC | |
| Analogues of nucleic acids: | GNA | PNA | TNA| LNA | morpholino | |
| ←Amino acids | Major families of biochemicals | Carbohydrates→ |
{{Carbohydrates}} under construction
| Carbohydrates | ||
|---|---|---|
| General: | Aldose | Ketose | Pyranose | Furanose | |
| Geometry: | Pentose | Hexose | Heptose | Equatorial bond | Axial bond | Anomer | Mutarotation | |
| Small/Large: | Glyceraldehyde | Dihydroxyacetone | Erythrose | Threose | Erythrulose | Sedoheptulose | |
| Pentoses: | Ribose | Arabinose | Xylose | Lyxose | Ribulose | Xylulose | |
| Hexoses: | Glucose | Galactose | Mannose | Gulose | Idose | Talose | Allose | Altrose | Fructose | Sorbose | Tagatose | Psicose | Fucose | Rhamnose | |
| Disaccharides: | Sucrose | Lactose | Trehalose | Maltose | |
| Polymers: | Glycogen | Starch | Cellulose | Chitin | Amylose | Amylopectin | Stachyose | Inulin | Dextrin | |
| Glycosaminoglycans: | Heparin | Chondroitin sulfate | Hyaluronan | Heparan sulfate | Dermatan sulfate | Keratan sulfate | |
| Aminoglycosides: | Kanamycin | Streptomycin | Tobramycin | Neomycin | Paromomycin | Apramycin | Gentamicin | Netilmicin | Amikacin | |
| ←Nucleic acids | Major families of biochemicals | Lipids→ |
{{Lipids}} under construction
{{Terpenoids}} under construction
| Terpenes and Terpenoids | ||
|---|---|---|
| General: | ||
| Hemiterpenoids: | Isoprene | Prenol | Isovaleric acid | |
| Monoterpenoids: | Geranyl pyrophosphate | Eucalyptol | Limonene | Pinene | |
| Sesquiterpenoids: | Farnesyl pyrophosphate | Artemisinin | Bisabolol | |
| Diterpenoids: | Geranylgeranyl pyrophosphate | Retinol | Retinal | Phytol | Taxol | Forskolin | Aphidicolin | |
| Sesterterpenoids: | ||
| Triterpenoids: | Squalene | Lanosterol | |
| Tetraterpenoids: | Lycopene | Carotene | |
| Polyterpenoids: | ||
| ←Lipids | Major families of biochemicals | Carotenoids→ |
{{Carotenoids}} under construction
| Carotenoids | ||
|---|---|---|
| General: | ||
| Xanthophylls: | Lutein | Zeaxanthin | |
| Carotenes: | Lycopene | Carotene | |
| ←Terpenoids | Major families of biochemicals | Tetrapyrroles→ |
{{Tetrapyrroles}} under construction
| Tetrapyrroles | ||
|---|---|---|
| General: | Porphyrin | Corrin | Chlorin | Bacteriochlorin | |
| Hemes: | Bilirubin | Biliverdin | Urobilinogen | Urobilin | |
| Chlorophylls: | Protochlorophyllide | Chlorophyllide | |
| Phycobilins: | Phycoerythrin | Phycocyanin | |
| Corrins: | Vitamin B12 | |
| ←Carotenoids | Major families of biochemicals | Enzyme cofactors→ |
{{Enzyme cofactors}} under construction
| Enzyme Cofactors | ||
|---|---|---|
| General: | All B vitamins | All D vitamins | |
| Retinol (A) | ||
| Thiamine (B1) | Riboflavin (B2) | Niacin (B3) | Pantothenic acid (B5) | Pyridoxine (B6) | Biotin (B7) | Choline (vitamin-like) | Folic acid (B9) | Cyanocobalamin (B12) | ||
| Ascorbic acid (C) | ||
| Ergocalciferol (D2) | Cholecalciferol (D3) | Tocopherol (E) | Naphthoquinone (K) | ||
| Metals: | Iron | Copper | Magnesium | Manganese | Nickel | Zinc | |
| ←Tetrapyrroles | Major families of biochemicals | Steroids→ |
{{Steroids}} under construction
| Steroids | ||
|---|---|---|
| General: | ||
| Precursors: | Squalene | Lanosterol | |
| Common: | Cholesterol | Pregnenolone | 17-Hydroxypregnenolone | DHEA | Androstenedione | Androstanediol | |
| Estrogens: | Estradiol | Estriol | Estrone | |
| Androgens: | Testosterone | Dihydrotestosterone | Androsterone | |
| Progestagens: | Progesterone | 17-Hydroxyprogesterone | Progestins | |
| Glucocorticoids: | Prednisone | |
| Mineralocorticoids: | Aldosterone | |
| Phytosterols: | Stigmasterol | Brassicasterol | |
| Ergosterols: | Ergosterol | Ergocalciferol | |
| ←Enzyme cofactors | Major families of biochemicals | Flavonoids→ |
{{Flavonoids}} under construction
{{Alkaloids}} under construction
| Alkaloids | ||
|---|---|---|
| General: | ||
| Indole group: | 5-MeO-DMT | Dimethyltryptamine | Harmala alkaloids | Psilocin | Psilocybin | Reserpine | Serotonin | Tryptamine | Yohimbine | |
| Phenethylamine group: | Ephedrine | Mescaline | Phenethylamine | Tyramine | |
| Purine group: | Caffeine | Theobromine | Theophylline | |
| Pyridine group: | Coniine | |
| Pyrrolidine group: | Nicotine | |
| Quinoline group: | Quinine | |
| Isoquinoline group: | Codeine | Morphine | |
| Tropane group: | Cocaine | |
| Terpenoid group: | Aconitine | Solanine | |
| Betaines: | Choline | Muscarine | |
| Pyrazole group: | ||
| ←Flavonoids | Major families of biochemicals | Polyketides→ |
{{Polyketides}} under construction
| Polyketides | ||
|---|---|---|
| General: | ||
| Macrolides: | Erythromycin | Clarithromycin | Azithromycin | Tacrolimus | Picromycin | |
| Polyenes: | Amphotericin | |
| Tetracyclines: | ||
| Others: | Discodermolide | |
| ←Alkaloids | Major families of biochemicals | Peptides→ |
{{Peptides}} under construction, completing cycle of biochemicals
[edit] Other templates
[edit] Circulatory system
{{Blood}}
[edit] Human chromosomes
{{Chromosomes}}
| Human chromosomes |
|---|
|
{1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15} {16} {17} {18} {19} {20} {21} {22} {X} {Y} |
[edit] Vitamin-specific template
{{Vitamin}}
| Vitamins |
|---|
| Retinol (A) | B vitamins (Thiamine (B1), Riboflavin (B2), Niacin (B3), Pantothenic acid (B5), Pyridoxine (B6), Biotin (B7), Folic acid (B9), Cyanocobalamin (B12)) | Choline | Ascorbic acid (C) | Ergocalciferol and Cholecalciferol (D) | Tocopherol (E) | Naphthoquinone (K) |
[edit] Endocrinology template (hormones and glands)
{{hormones}}
| Hormones and endocrine glands - edit |
|---|
|
Hypothalamus: - TRH - CRH - GnRH - GHRH - somatostatin - dopamine | Posterior pituitary: vasopressin - oxytocin - lipotropin | Anterior pituitary: GH - ACTH - TSH - LH - FSH - prolactin - MSH - endorphins - lipotropin Thyroid: T3 and T4 - calcitonin | Parathyroid: PTH | Adrenal medulla: epinephrine - norepinephrine | Adrenal cortex: aldosterone - cortisol - DHEA | Pancreas: glucagon- insulin - somatostatin | Ovary: estradiol - progesterone - inhibin - activin | Testis: testosterone - AMH - inhibin | Pineal gland: melatonin | Kidney: renin - EPO - calcitriol - prostaglandin | Heart atrium: ANP Stomach: gastrin | Duodenum: CCK - GIP - secretin - motilin - VIP | Ileum: enteroglucagon | Liver: IGF-1 Placenta: hCG - HPL - estrogen - progesterone |
