Biomolecules

Databases

Google:
PubMed:
PDB: Protein Data Bank (experimentally determined 3D structures)
PDBsum : Annotated summary of PDB entries
UniProt : Protein sequences
PubChem : Small molecule database
BMCD : Biological Macromolecule Crystallization Database (version 7.0)
GeneCards : Human Genes
MEROPS : Protease Data Bank
PDBbind : Experimentally measured binding affinity data for PDB entries
ASD : Allosteric Database
BioNumbers : Numbers in biology

Servers

Clustal Omega :Multiple Sequence Alignment
PISA :Proteins, Interfaces, Structures and Assemblies
ConSurf : Mapping conservation onto 3D structure from coordinates and multiple sequence alignment
What If : many helpful servers
PLIP : Protein-ligand interaction profiler
Proteins Plus :
Expasy : Bioinformatic tools
Playmolecules> : Servers for structural bioinformatics - Proteinprepare (PROPKA 3.1, PDB2PQR 2.1), Parameterize
Charmm : Simulation input generator
protein-sol pka : Calculate pKa for buried groups
PropKa : Calculate pKa
DelPhiPKa : Calculate pKa
Rosetta pKa Protocol : Calculate pKa

Small molecules
Standard (proteogenic) amino acids
Nucleic acids
Carbohydrates
Lipids
Reducing agents
Solvents
Elements
Ions/salts
Cofactors
Detergents
Chaotropic agents
Buffers
Drugs
Nomenclature

Proteins
Helices, strands/sheets, turns, motifs, domains
Enzymes
Transport proteins
Immune system proteins
Nucleic acid / protein complexes
Fibrous proteins
Viruses and viral proteins
Membrane proteins

History of Proteins
Equations

Small molecules related to biology

Standard (proteogenic) amino acids

Amino acids: Proteopedia wiki

Basic:

L-lysine (Lys, K): PDB wiki
L-arginine (Arg, R): PDB wiki
L-histidine (His, H): PDB wiki
Acidic:

L-aspartic acid (Asp, D): PDB wiki
L-glutamic acid (Glu, E): PDB wiki
Amides:

L-asparagine (Asn, N): PDB wiki
L-glutamine (Gln, Q): PDB wiki
Aliphatic:

L-alanine (Ala, A): PDB wiki
L-valine (Val, V): PDB wiki
L-leucine (Leu, L): PDB wiki
L-isoleucine (Ile, I): PDB wiki
Aromatic:

L-phenylalanine (Phe, F): PDB wiki
L-tyrosine (Try, Y): PDB wiki
L-tryptophan (Trp, W): PDB wiki
Hydroxyls:

L-serine (Ser, S): PDB wiki
L-threonine (Thr, T): PDB wiki
Sulfur containing:

L-cysteine (Cys, C): PDB wiki
L-methionine (Met, M): PDB wiki

Small:

glycine (Gly, G): PDB wiki
Cyclic:

L-proline (Pro, P): PDB wiki

Non-standard amino acids

pyrrolysine (Pyl, O):PDB wiki
selenocysteine (Sec, U):PDB wiki
N-formylmethionine (fMet):PDB wiki
4-hydroxy-L-proline (Hyp):PDB wiki
D-alanine (Dal):PDB wiki
L-ornithine (Orn):PDB wiki
Citrulline (Cir):PDB wiki

Nucleic acids

Nucleic acids: Proteopedia wiki
Nucleobase: wiki
Nucleoside: wiki
Nucleotide: wiki
Nucleic acid Structure: wiki

ATP (adenosine-5'-triphosphate): PDB wiki
TTP (thymidine-5'-triphosphate): PDB
CTP (cytidine-5p-triphosphate): PDB
GTP (guanosine-5p-triphosphate): PDB

DNA: PDB Proteopedia wiki
Transfer RNA (tRNA): PDB Proteopedia wiki
Ribosomal RNA (rRNA): PDB Proteopedia wiki
Messenger RNA (mRNA): PDB Proteopedia wiki

Carbohydrates

Ribose: PDB
Fructose: PDB
Alpha-D-glucose: PDB
D-glucose linear form: PDB
Sucrose: PDB
N-acetyl-d-glucosamine: PDB

Lipids

Phospholipids

Glycerophospholipids: wiki
phosphatidylethanolamine (PE): wiki
phosphatidylglycerol (PG): wiki
cardiolipin (CL): wiki
phosphatidylserine (PS): wiki
phosphatidic acid (PA): wiki
phosphatidylinositol (PI): wiki
phosphatidylcholine (PC): wiki

Sphingolipids

Sphingolipids: wiki
Sphingosine: wiki
Sphingomyelin: wiki

Glycolipids

Glycolipids: wiki

Sterols

Sterols: wiki
Cholesterol: wiki

Fatty acids and pronols

Fatty acids: wiki
Prenols: wiki

Reducing agents

Beta-mercaptoethanol (BME): PDB wiki
1,4-dithiothreitol (DTT): PDB wiki
Glutathione (GSH, L-gamma-glutamyl-L-cysteinylglycine): PDB wiki
tris(2-carboxyethyl)phosphine (TCEP): wiki

Solvents

Water: PDB wiki

Solvents for solubilizing peptides
Dimethyl sulfoxide (DMSO): PDB wiki
Dimethylformamide (DMF): PDB wiki
Acetonitrile: PDB wiki

Elements

Major/macro-minerals (macronutrients):

Structural elements:
Hydrogen, H: wiki
Oxygen, O: wiki
Carbon, C: wiki
Nitrogen, N: wiki

Sulfur, S: wiki
Phosphorus, P: wiki
Potassium, K: wiki
Calcium, Ca: wiki
Magnesium, Mg: wiki

Minor/micro-minerals (mircronutrients/trace elements):
Iron, Fe: wiki
Zinc, Zn: wiki
Chlorine, Cl: wiki
Sodium, Na: wiki
Iodine, I: wiki
Copper, Cu: wiki
Manganese, Mn: wiki
Cobolt, Co: wiki
Molybdenum, Mo: wiki
Selenium, Se: wiki
Valadium, V: wiki
Nickel, Ni: wiki

Ions/salts

Ion: wiki
Salts: wiki
Hofmeister series: wiki

Phosphate: PDB
Sulfate: PDB

Cofactors

I. Inorganic
II. Organics
1. Prosthetic groups (tightly bound)
2. cosubstrates (loosely bound)
Cofactors: wiki

Detergents

Surfactant: wiki
Micelle: wiki
Critical micelle concentration (CMC): wiki

Triton X-100: PDB wiki
Dodecyl-beta-D-maltoside (DDM): PDB
Beta-octylglucoside (BOG): PDB
Sodium dodecyl sulfate (SDS): PDB

Chaotropic agents

Chaotropic agents: wiki

Urea: PDB
Guanidine: PDB

Buffers

Buffer solutions: wiki

Tris (2-amino-2-hydroxymethyl-propane-1,3-diol): PDB wiki
Hepes (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid): PDB wiki
MES (2-(N-morpholino)ethanesulfonic acid): PDB wiki
Citrate: PDB wiki
Acetate: PDB wiki

Drugs

Aspirin (acetylsalicylic acid): PDB
Acetaminophen (Tylenol, Paracetamol, (n-(4-hydroxyphenyl)acetamide): PDB wiki
Ibuprofen (2-(4-isobutylphenyl)propionic acid): PDB
caffeine (3,7-dihydro-1,3,7-trimethyl-1h-purine-2,6-dione): PDB
penicillin G: PDB
penicillin G acyl-serine: PDB

Nomenclature

Greek letters: link

Amino acid atom names -
α (a) alpha
β (b) beta
γ (g) gamma
δ (d) delta
ε (e) epsilon
ζ (z) zeta
η (h) eta

Main chain angles -
φ (f) phi
ψ (y) psi
ω (w) omega

Side chain angles -
χ ( c ) chi

Proteins

Proteins:PDB Proteopedia wiki
Protein structure wiki
Protein superfamily wiki
Protein biosythesis wiki
Peptide synthesis wiki
Proteolysis wiki
Intrinsically disordered proteins wiki
Proteopathy wiki
Protein design wiki
Protein engineering wiki
Protein folding wiki
Protein dynamics wiki

Helices, strands/sheets, turns, motifs, domains

Peptide bond wiki
Disulfide bonds wiki
Non covalent interactions wiki
Peptides wiki
Ramachandran plot wiki
Dihedral angles wiki
Protein tertiary structure wiki
Protein domains wiki
Protein quaternary structure wiki
Secondary Structure: wiki
Helices - general geometrical features: wiki
π-helix: wiki
α-helix: wiki
Geometry: 360°/turn / 100°/residue = 3.6 residues/turn, there are 13 atoms in the H-bond chain ∴ another name for the alpha-helix is 13_3.6 , i + 4 → i
3₁₀-helix: wiki
β-sheet: wiki
Turns: wiki
β-turn: (4 residues involved, i + 3 → i) wiki
β-helix: wiki
Polyproline-helix: wiki
Collagen-helix: wiki
Motifs:
Coiled-coil wiki
Helix-turn-helix wiki
EF-hand wiki
β-hairpin wiki
Protein folds wiki

Enzymes

Hen-egg lysozyme: PDB Proteopedia wiki
T4 lysozyme: PDB Proteopedia wiki
Chymotrypsin: PDB Proteopedia wiki
Trypsin: PDB Proteopedia wiki
Trypsin inhibitor (Aprotinin, Bovine Pancreatic Trypsin Inhibitor (BPTI)): PDB Proteopedia wiki
Subtilisin: PDB Proteopedia wiki
Carboxypeptidase: PDB Proteopedia wiki
Pepsin: PDB Proteopedia wiki
Papain: PDB Proteopedia wiki
Lactate dehydrogenase: PDB Proteopedia wiki
Triose phosphate isomerase: PDB Proteopedia wiki
Ribonuclease A: PDB Proteopedia wiki
Staphylococcal nuclease: PDB Proteopedia wiki

Transport proteins

Myoglobin: PDB Proteopedia wiki
Hemoglobin: PDB Proteopedia wiki

Immune system proteins

Antibodies: PDB Proteopedia wiki

Nucleic acid / protein complexes

RNA polymerase: PDB Proteopedia wiki
DNA polymerase: PDB Proteopedia wiki
Catabolite Activator Protein/DNA complexes: PDB Proteopedia wiki
Lac repressor/DNA complexes: PDB Proteopedia wiki
Ribosome: PDB Proteopedia wiki
Restriction Enzymes: PDB Proteopedia wiki
DNA ligase: PDB Proteopedia wiki
Transcription factors (eg. Zinc Fingers): PDB Proteopedia wiki

Fibrous (structural) proteins

Collagen: PDB Proteopedia wiki
Keratin: Proteopedia wiki
Fibroin: Proteopedia wiki

Viruses and viral proteins

Picornaviruses (eg. Poliovirus and Rhinovirus): PDB Proteopedia wiki

Membrane proteins

Photosynthetic reaction center: PDB Proteopedia wiki
Potassium Channel: PDB Proteopedia wiki

Other interesting proteins

Crambin (storage protein, 46 residues, highest resolution structure, 0.48 Å): PDB Proteopedia wiki
Insulin: PDB Proteopedia wiki
Cytochrome c: PDB Proteopedia wiki
Calmodulin: PDB Proteopedia wiki
GFP-like Proteins: PDB Proteopedia wiki
Actin: PDB Proteopedia wiki
Myosin: PDB Proteopedia wiki

History of Proteins

Rene Just Hauy : (1784) Study of natural crystals
Justus von Liebig : (1830) Atomic makeup of proteins, Father of organic chemistry and modern teaching/research lab,
Jons Jacob Berzelius : (1836) Term and idea of catalysis, elemental analysis of molecules, isomers, name "protein"
Gerardus (Gerrit) Johannes Mulder : (1838) Atomic makeup of proteins (C,N,O,H,S)
Louis Pasteur : (1848) Demonstrated molecular chirality, and first explanation of isomerism
G. G. Stokes : (~1850) Fluid dynamics, fluorecence, light ...
Otto Funke : (1851) First scientist to successfully crystallize hemoglobin (other early studies of hemoglobin crystals by : Felix Hoppe-Seyler, Wilhelm Preyer, and E.T. Reichert + A.L. Brown)
August Kekule : (1857) Tetravalent carbon, (1858) C-C bonds, (1865) structure of benzene - aromatics
Heinrich Hlasiwetz : (~1869) Proteins are made up of amino acid residues, hydrolysis
Felix Hoppe-Seyler : (1877) Isolated hemoglobin in crystalline form, discovered Fe in hemoglobin
Wilhelm Rontgen : (1895) The discovery of X-rays
Eduard Buchner : (1897) Discovery of enzyme activity in the juice extract from yeast cells, atomic weights, elemental analysis
Albrecht Kossel : (1895) Chemical composition of proteins, polypeptide nature of protein molecules predicted, (1896) discovery of histidine
Michail S. Tswett (Tsvet) : (1900) Invention of chromatography
Franz Hofmeister : (1902) The peptide bond, the solubility of proteins in various salts
Hermann Emil Fischer : (1902) The peptide bond, discovery of many amino acids, lock and key hypothesis
S.P.L. Sorensen : (1909) Invention of the pH scale
William Lawrence Bragg (Son), William Henry Bragg (Dad) : (1912) The Bragg equation (when to expect a diffraction spot)
Leonor Michaelis, Maud Menten : (1913) Enzyme kinetic theory
G.N. Lewis : (1916) The covalent bond
Irving Langmuir : (1917) The hydrophobic effect - surfaces
Wendell Latimer, Worth Rodebush Hydrogen Bonding : (1920) The hydrogen bond
Theodor Svedberg : (~1920) Hydrodynamic studies of proteins: (analytical centrifuge)
James B. Sumner : (1926) Crystallization of urease , Enzymes are proteins
John Northrop : (1929) The crystallization of proteases (pepsin, pepsinogen, trypsin, chymotrypsin, bacteriophage)
Arne Tiselius : (1930) Electrophoresis, separation of blood serum proteins
William Astbury : (1931) First to propose mainchain-mainchain (backbone) hydrogen bonding, Keratin structure (X-ray fiber diffraction studies)
J.D. (John Desmond) Bernal : (1934) Diffraction of protein crystals
Dorothy Crowfoot Hodgkin : (1934) Diffraction of protein crystals, (1969) Crystal structure of insulin
Linus Pauling : (1930's) "The Nature of the Chemical Bond" Peptide bond resonance/geometry, (1951) alpha-helix, beta-sheet, (1949) molecular cause of sickle cell anemia
Edwin Cohn, John Edsall : (~1943) Blood protein fractionation, the hydrophobic effect, salting out of proteins
A.J.P.Martin, R.L.M. Synge : (~1948) Partition chromatography, Gas-Liquid Chromatography
Kaj Ulrik Linderstrom-Lang : (1951) Levels of protein structure (primary, secondary, tertiary, quaternary), hydrogen-deuterium exchange
Frederick Sanger : (1952) Protein (insulin) sequencing
Arthur Kornberg : (1956) DNA polymerase
Max Perutz : (1959) The crystal structure of haemoglobin, (1953) the "phase-problem" MIR
John Kendrew : (6Å 1957, 2Å 1959) The crystal structure of myoglobin
William Stein, Stanford Moore : (1958) First automated amino acid analyzer, structure and catalysis of ribonuclease
Francis Crick : (~1958) Central Dogma, structure of DNA (1953), packing of helices in Keratin, Collagen
Jacques Monod : (1965) Allosteric proteins

Equations - Some equations that are fundamental to biochemistry and protein structure

Bragg's law: nλ = 2dsinΘ Wiki :

Henderson-Hasselbalch equation: pH = pK_a + log[A-]/[HA] Wiki :

Beer-Lambert Law: A = log I_o/I = εlc ChemWiki :
A = absorbance (unitless)
ε = molar absorptivity or molar extinction coefficient (M^-1 cm^-1)
l = path length of cuvette (cm)
c = concentration (M)

Michaelis-Menten equation: v_o = V_max [S] / K_M + [S] Wiki :
v_o = initial velocity of the reaction
V_max = maximum velocity of the reaction
[S] = substrate concentration
K_M = 1/2 V_max (the Michaelis constant)

Gibbs free energy equation: ΔG = ΔH - TΔS Wiki :

Law of Mass Action - General expression of equilibrium constant: aA + bB ⇔ cC + dD , K_eq = [C]^c[D]^d / [A]^a[B]^b Discussion :