Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products)
Page 11/10: Structural hierarchy
Proteins Phenotype of organism 3 Dimensional structure Function by interaction
THE PROTEIN DATA BANK http://www.rcsb.org/pdb/
Two-dimensional gel showing more than 1,000 different proteins from E. Coli - Page 95/91
The function of proteins depend on their ability to interact with other molecules Proteome: Entire complement of an organisms proteins: yeast 6,000 proteins human 32,000 proteins Proteins can bind to: Substrate Molecules (small molecules) Cell Receptors Nucleic Acids (DNA/RNA) Polysaccharides Lipids
The environment in the cell is crowded Protein interactions are highly specific (avoid non-productive interactions) Molecule that interacts with protein is called the LIGAND (or substrate) This can be another protein
Examples of Functions Structure Transport Storage Catalysis Receptors Antibodies Movement (contraction and motility)
Amino Acids (building block of proteins) (Amino group) NH 2 (Carboxyl group) COOH (alpha carbon) (side chain) Ampholytes molecules that contain both acidic and basic groups - and will exist mostly as zwitterions in a certain range of ph
Side Chains R R = H The simplest amino acid Glycine 20 common amino acids Differ in properties because of R Many ways to classify amino acids types based on properties
Hydrophobic-aliphatic Non-polar methyl- or methylene- groups Usually located on the interior of the protein All of these side chains except for alanine are bifurcated
Hydrophobic-aromatic Only phenylalanine is entirely non-polar Tyrosine's phenolic side chain has a hydroxyl substituent Tryptophan has a nitrogen atom in its indole ring system Mainly buried in the hydrophobic interior of the protein
Neutral-polar Contain small aliphatic side chains containing polar groups Cannot readily ionize
Acidic Have carboxyl side chains and are therefore negatively charged at physiological ph (around ~ ph 7) The strongly polar nature of these residues means that they are most often found on the surface of proteins
Basic Of the basic amino acid side chains, histidine has the lowest pka (around 6) Lysine and arginine are more strongly basic and are positively charged at physiological ph's
Conformationally important Glycine and proline are unique as they influence the conformation of the polypeptide chain. Glycine essentially lacks a side chain and therefore can adopt conformations which are sterically forbidden for other amino acids. Proline is the most rigid amino acids since its side chain is covalently linked with the main chain nitrogen.
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One and Three letter codes Alanine Ala A first amino acid (AA) alphabetically Cysteine Cys C only AA to start with C Aspartate Asp D aspardate (or if you prefer, aspardic acid) Glutamate Glu E gluetamate (or gluetamic acid) Phenylalanine Phe F Fenylalanine Glycine Gly G alphabetically first of the AAs starting with G Histidine His H only AA starting with H Isoleucine Ile I only AA starting with I Lysine Lys K (I don't have a good mnemonic for this one) Leucine Leu L alphabetically first of the AAs starting with L Methionine Met M only AA starting with M Asparagine Asn N asparagine Proline Pro P starts with P and is P-shaped (imino acid ring) Glutamine Gln Q Q-tamine Arginine Arg R R-ginine Serine Ser S only AA starting with S Threonine Thr T alphabetically first AA starting with T Valine Val V only AA starting with V Tryptophan Trp W twyptophan (Elmer Fudd's favorite amino acid) Tyrosine Tyr Y tyrosine
AMINO ACIDS Summary CODE THREE ONE LETTER CHARACTERISTICS Alanine Ala A hydrophobic Arginine Arg R free amino group makes it basic and hydrophilic Asparagine Asn N carbohydrate can be covalently linked ("N- linked) to its -NH Aspartic acid Asp D free carboxyl group makes it acidic and hydrophilic Cysteine Cys C oxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S) Glutamic acid Glu E free carboxyl group makes it acidic and hydrophilic Glutamine Gln Q moderately hydrophilic Glycine Gly G so small it is amphiphilic (can exist in any surroundings) Histidine His H base/acid and hydrophilic
Isoleucine Ile I hydrophobic Leucine Leu L hydrophobic Lysine Lys K strongly basic and hydrophilic Methionine Met M hydrophobic Phenylalanine Phe F very hydrophobic Proline Pro P causes kinks in the chain Serine Ser S carbohydrate can be covalently linked ("O-linked") to its -OH Threonine Thr T carbohydrate can be covalently linked ("O-linked") to its -OH Tryptophan Trp W scarce in most plant proteins Tyrosine Tyr Y -OH group makes it moderately hydrophilic Valine Val V hydrophobic