Biomolecules
Databases
:
:
: Protein Data Bank (experimentally determined 3D structures)
: Annotated summary of PDB entries
: Protein sequences
: Small molecule database
: Biological Macromolecule Crystallization Database (version 7.0)
: Human Genes
: Protease Data Bank
: Experimentally measured binding affinity data for PDB entries
: Allosteric Database
: Numbers in biology
Servers
:Multiple Sequence Alignment
:Proteins, Interfaces, Structures and Assemblies
: Mapping conservation onto 3D structure from coordinates and multiple sequence alignment
: many helpful servers
: Protein-ligand interaction profiler
:
: Bioinformatic tools
: Servers for structural bioinformatics - Proteinprepare (PROPKA 3.1, PDB2PQR 2.1), Parameterize
: Simulation input generator
: Calculate pKa for buried groups
: Calculate pKa
: Calculate pKa
: 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:
Basic: 
L-lysine (Lys, K):
L-arginine (Arg, R):
L-histidine (His, H):
Acidic: 
L-aspartic acid (Asp, D):
L-glutamic acid (Glu, E):
Amides: 
L-asparagine (Asn, N):
L-glutamine (Gln, Q):
Aliphatic: 
L-alanine (Ala, A):
L-valine (Val, V):
L-leucine (Leu, L):
L-isoleucine (Ile, I):
Aromatic: 
L-phenylalanine (Phe, F):
L-tyrosine (Try, Y):
L-tryptophan (Trp, W):
Hydroxyls: 
L-serine (Ser, S):
L-threonine (Thr, T):
Sulfur containing: 
L-cysteine (Cys, C):
L-methionine (Met, M):
Small: 
glycine (Gly, G):
Cyclic: 
L-proline (Pro, P):
Non-standard amino acids
pyrrolysine (Pyl, O):
selenocysteine (Sec, U):
N-formylmethionine (fMet):
4-hydroxy-L-proline (Hyp):
D-alanine (Dal):
L-ornithine (Orn):
Citrulline (Cir):
Nucleic acids
Nucleic acids:
Nucleobase:
Nucleoside:
Nucleotide:
Nucleic acid Structure:
ATP (adenosine-5'-triphosphate):
TTP (thymidine-5'-triphosphate):
CTP (cytidine-5p-triphosphate):
GTP (guanosine-5p-triphosphate):
DNA:
Transfer RNA (tRNA):
Ribosomal RNA (rRNA):
Messenger RNA (mRNA):
Carbohydrates
Ribose:
Fructose:
Alpha-D-glucose:
D-glucose linear form:
Sucrose:
N-acetyl-d-glucosamine:
Lipids
Phospholipids
Glycerophospholipids:
phosphatidylethanolamine (PE):
phosphatidylglycerol (PG):
cardiolipin (CL):
phosphatidylserine (PS):
phosphatidic acid (PA):
phosphatidylinositol (PI):
phosphatidylcholine (PC):
Sphingolipids
Sphingolipids:
Sphingosine:
Sphingomyelin:
Glycolipids
Glycolipids:
Sterols
Sterols:
Cholesterol:
Fatty acids and pronols
Fatty acids:
Prenols:
Reducing agents
Beta-mercaptoethanol (BME):
1,4-dithiothreitol (DTT):
Glutathione (GSH, L-gamma-glutamyl-L-cysteinylglycine):
tris(2-carboxyethyl)phosphine (TCEP):
Solvents
Water:
Solvents for solubilizing peptides
Dimethyl sulfoxide (DMSO):
Dimethylformamide (DMF):
Acetonitrile:
Elements
Major/macro-minerals (macronutrients):
Structural elements:
Hydrogen, H:
Oxygen, O:
Carbon, C:
Nitrogen, N:
Sulfur, S:
Phosphorus, P:
Potassium, K:
Calcium, Ca:
Magnesium, Mg:
Minor/micro-minerals (mircronutrients/trace elements):
Iron, Fe:
Zinc, Zn:
Chlorine, Cl:
Sodium, Na:
Iodine, I:
Copper, Cu:
Manganese, Mn:
Cobolt, Co:
Molybdenum, Mo:
Selenium, Se:
Valadium, V:
Nickel, Ni:
Ions/salts
Ion:
Salts:
Hofmeister series:
Phosphate:
Sulfate:
Cofactors
I. Inorganic
II. Organics
1. Prosthetic groups (tightly bound)
2. cosubstrates (loosely bound)
Cofactors:
Detergents
Surfactant:
Micelle:
Critical micelle concentration (CMC):
Triton X-100:
Dodecyl-beta-D-maltoside (DDM):
Beta-octylglucoside (BOG):
Sodium dodecyl sulfate (SDS):
Chaotropic agents
Chaotropic agents:
Urea:
Guanidine:
Buffers
Buffer solutions:
Tris (2-amino-2-hydroxymethyl-propane-1,3-diol):
Hepes (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid):
MES (2-(N-morpholino)ethanesulfonic acid):
Citrate:
Acetate:
Drugs
Aspirin (acetylsalicylic acid):
Acetaminophen (Tylenol, Paracetamol, (n-(4-hydroxyphenyl)acetamide):
Ibuprofen (2-(4-isobutylphenyl)propionic acid):
caffeine (3,7-dihydro-1,3,7-trimethyl-1h-purine-2,6-dione):
penicillin G:
penicillin G acyl-serine:
Nomenclature
Greek letters:
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:
Protein structure
Protein superfamily
Protein biosythesis
Peptide synthesis
Proteolysis
Intrinsically disordered proteins
Proteopathy
Protein design
Protein engineering
Protein folding
Protein dynamics
Helices, strands/sheets, turns, motifs, domains
Peptide bond
Disulfide bonds
Non covalent interactions
Peptides
Ramachandran plot
Dihedral angles
Protein tertiary structure
Protein domains
Protein quaternary structure
Secondary Structure:
Helices - general geometrical features:
π-helix:
α-helix:
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 133.6 , i + 4 → i
310-helix:
β-sheet:
Turns:
β-turn: (4 residues involved, i + 3 → i)
β-helix:
Polyproline-helix:
Collagen-helix:
Motifs:
Coiled-coil
Helix-turn-helix
EF-hand
β-hairpin
Protein folds
Enzymes
Hen-egg lysozyme:
T4 lysozyme:
Chymotrypsin:
Trypsin:
Trypsin inhibitor (Aprotinin, Bovine Pancreatic Trypsin Inhibitor (BPTI)):
Subtilisin:
Carboxypeptidase:
Pepsin:
Papain:
Lactate dehydrogenase:
Triose phosphate isomerase:
Ribonuclease A:
Staphylococcal nuclease:
Transport proteins
Myoglobin:
Hemoglobin:
Immune system proteins
Antibodies:
Nucleic acid / protein complexes
RNA polymerase:
DNA polymerase:
Catabolite Activator Protein/DNA complexes:
Lac repressor/DNA complexes:
Ribosome:
Restriction Enzymes:
DNA ligase:
Transcription factors (eg. Zinc Fingers):
Fibrous (structural) proteins
Collagen:
Keratin:
Fibroin:
Viruses and viral proteins
Picornaviruses (eg. Poliovirus and Rhinovirus):
Membrane proteins
Photosynthetic reaction center:
Potassium Channel:
Other interesting proteins
Crambin (storage protein, 46 residues, highest resolution structure, 0.48 Å):
Insulin:
Cytochrome c:
Calmodulin:
GFP-like Proteins:
Actin:
Myosin:
History of Proteins
: (1784) Study of natural crystals
: (1830) Atomic makeup of proteins, Father of organic chemistry and modern teaching/research lab,
: (1836) Term and idea of catalysis, elemental analysis of molecules, isomers, name "protein"
: (1838) Atomic makeup of proteins (C,N,O,H,S)
: (1848) Demonstrated molecular chirality, and first explanation of isomerism
: (~1850) Fluid dynamics, fluorecence, light ...
: (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)
: (1857) Tetravalent carbon, (1858) C-C bonds, (1865) structure of benzene - aromatics
: (~1869) Proteins are made up of amino acid residues, hydrolysis
: (1877) Isolated hemoglobin in crystalline form, discovered Fe in hemoglobin
: (1895) The discovery of X-rays
: (1897) Discovery of enzyme activity in the juice extract from yeast cells, atomic weights, elemental analysis
: (1895) Chemical composition of proteins, polypeptide nature of protein molecules predicted, (1896) discovery of histidine
: (1900) Invention of chromatography
: (1902) The peptide bond, the solubility of proteins in various salts
: (1902) The peptide bond, discovery of many amino acids, lock and key hypothesis
: (1909) Invention of the pH scale
: (1912) The Bragg equation (when to expect a diffraction spot)
: (1913) Enzyme kinetic theory
: (1916) The covalent bond
: (1917) The hydrophobic effect - surfaces
: (1920) The hydrogen bond
: (~1920) Hydrodynamic studies of proteins: (analytical centrifuge)
: (1926) Crystallization of urease , Enzymes are proteins
: (1929) The crystallization of proteases (pepsin, pepsinogen, trypsin, chymotrypsin, bacteriophage)
: (1930) Electrophoresis, separation of blood serum proteins
: (1931) First to propose mainchain-mainchain (backbone) hydrogen bonding, Keratin structure (X-ray fiber diffraction studies)
: (1934) Diffraction of protein crystals
: (1934) Diffraction of protein crystals, (1969) Crystal structure of insulin
: (1930's) "The Nature of the Chemical Bond" Peptide bond resonance/geometry, (1951) alpha-helix, beta-sheet, (1949) molecular cause of sickle cell anemia
: (~1943) Blood protein fractionation, the hydrophobic effect, salting out of proteins
: (~1948) Partition chromatography, Gas-Liquid Chromatography
: (1951) Levels of protein structure (primary, secondary, tertiary, quaternary), hydrogen-deuterium exchange
: (1952) Protein (insulin) sequencing
: (1956) DNA polymerase
: (1959) The crystal structure of haemoglobin, (1953) the "phase-problem" MIR
: (6Å 1957, 2Å 1959) The crystal structure of myoglobin
: (1958) First automated amino acid analyzer, structure and catalysis of ribonuclease
: (~1958) Central Dogma, structure of DNA (1953), packing of helices in Keratin, Collagen
: (1965) Allosteric proteins
Equations - Some equations that are fundamental to biochemistry and protein structure
Bragg's law: nλ = 2dsinΘ :
Henderson-Hasselbalch equation: pH = pKa + log[A-]/[HA] :
Beer-Lambert Law: A = log Io/I = εlc :
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: vo = Vmax [S] / KM + [S] :
vo = initial velocity of the reaction
Vmax = maximum velocity of the reaction
[S] = substrate concentration
KM = 1/2 Vmax (the Michaelis constant)
Gibbs free energy equation: ΔG = ΔH - TΔS :
Law of Mass Action - General expression of equilibrium constant: aA + bB ⇔ cC + dD , Keq = [C]c[D]d / [A]a[B]b :