1 - Lecture Guide

Review of Lecture 1: Structures you should know (be able to recognize and draw): General amino acid structure All standard amino acids: Ala A Alanine Arg R Arginine (GUANIDINIUM) Asn N Asparagine (AMINO GROUP) Asp D Aspartate (CARBOXYLATE) Glu E Glutamate (CARBOXYLATE) SIMILAR TO GAMA AMINOBUTYRATE Gln Q Glutamine (AMINO GROU) Gly G Glycine Cys C Cysteine (THIOL) His H Histidine (IMIDOZOLE) – SIMILAR TO HISTIMINE Ile I IsoleucineLeu L LeucineLys K Lysine Met M Methionine (HAS A THIOETHER) Phe F Phenylalanine (AROMATIC) Pro P Proline (HETROCYCLIC PYRIMIDINE RING) Ser S Serine (HYDROXYL) THIS IS A TYPICAL RESIDUE THAT BECOMES PHOSPHORYALTED ALONG WITH THE THREE OTHER HDROXYL GROUP AMINO ACIDS Thr T Threonine (HYDROXYL) Trp W Tryptophan (AROMATIC) Try Y Tyrosine (GIVES RISE TO THYROXINE AND EPINEPHRINE) Val V Valine For each amino acid, know the 1 and 3 letter code Be able to give the net charge of an amino acid or peptide at a specific pH. Be able to predict whether it will move towards the anode or the cathode in gel electrophoresis. If the protein is placed in a solution where: PH > PI It is a negative anion Move towards the anode (positive end) PI > PH It is a positive cation Move towards the cathode (negative end) PH = PI The particular molecule caries no net electrical charge Be able to calculate the pI values of peptides. PI = PKA + PKB / 2 ; WHERE PKA IS THE PK WHERE THE CHARGE IS ZERO AND WHERE PKB THE VALUE IN WHICH IS ADJACENT TO IT ON THE RIGHT. Know the general formulas of organic compounds: [IN NOTEBOOK] Alcohol Aldehyde (same as carbonyl) Ketone (same as carbonyl, but slightly different) Carboxylic acid Thiol (sulfhydryl) Amines (primary, secondary, tertiary) Know the general formulas of functional groups: Hydroxyl - OH Acyl - Carbonyl CarboxylateSulfhydryl (thiol) -SH Amino –NH2 Phosphate - OPOOH PhosphorylKnow the general formulas of linkages: Ester Ether R – O - R Amide FOUND IN PEPTIDE BONDS Phosphate ester TWO PHOSPHATES CONNECTED VIA A SINGLE OXYGEN PhosphoanhydrideBe able to recognize the structure for: [DRAWN IN BOOK] Histamine – histidine (imidazole group) JUST ADD CH2-NH3 TO THE END, JUST LIKE GAMA AMINOBUTYRATE. ?-aminobutyrate – glutamic acid/glutamate – rhymes with glumate: +NH3-CH2-CH2-CH2-COO- Epinephrine (adrenaline) - tyrosine thyroxine/triiodothyronine – Tyrosine (2 tyrosines connected via ester linkage) aspartame – aspartate and phenylalanine. For extra practice, do questions #28, 30, 33, 35 on page 181 of your text.