Amino Acids

Amino Acid Structure Know the parts of an amino acid 1. Amino group 2. Carboxylic Acid (Carboxylate) 3. R-Group

R-Groups Amino acids are classified by their R-groups and the groups interaction with water 1.Hydrophobic-The majority of R-groups 2. Polar Uncharged 3. Polar Charged

Hydrophobic R-Groups R-groups composed of only Hydrogen and Carbons One exception- Methionine contains sulfur, bound only to Carbon Phenylalanine Methionine

Polar uncharged and charged Look for Oxygens and Nitrogens Charged groups will be charged or have a primary amine or carboxylic acid part. Primary amines are written NH2 and Carboxylic acids COOH

Acid Base Properties Amino acids can be proton donors The pH at which the Carboxylate group gives up its proton is the pK1 and the Amino group is pK2 pK1 is the point where 50% of the carboxylate groups are unprotonated, and pK2 is where 50% of the amino groups are unprotonated Amino acids are good buffers at these points Add them together and divide by 2 to get the isoelectric point (pI) This is the point where all amino acids in a solution have zero net charge Amino acids are bad buffers at this point

Amino acids can form polypeptides Peptide Linkages: C-N bond Different order equals different peptides Ex: Gly-Ala-Pro isn’t the same as Pro-Ala-Gly Number of possible combinations using each AA once: (Number of Amino Acid)! Ex: tetrapeptide is 4! (4x3x2x1=24) Number of possible combinations using each AA as many times as we want: (number of AA)number in polypeptide Ex: 4 amino acids in a tetrapeptide =44

Amide planes An amide plane forms around the peptide linkage C,N,O,H are involved in the formation The double bonded O electrons resonate to the C-N bond, giving the peptide linkage a partial double bonded characteristic.

Protein Substructures Primary Order of the amino acids Ex: ala-gly-asp-leu-lys-phe Main type of interaction: covalent between amino acids, called peptide bond Secondary Alpha helix Main type of interaction: hydrogen bonds between amide planes

Protein substructure Tertiary Quaternary Main type of interactions: between R-groups H-bonds, Electrostatic, Hydrophobic, Covalent (disulfide bonds) Specifically, covalent bond called disulfide Between 2 cysteines’ sulfhydryl R-groups Quaternary Large molecular weights

Collagen Predominate AA: proline and glycine Gly- small R-group for rope-like structure Pro- Oxidizable R-group Requires Vitamin C; deficiency=scurvy Steps in formation Immature collagen is hydroxylated (-OH groups added) becoming procollagen Need Vitamin C as reducing agent in this step. If deficient, the person has scurvy Procollagen is glycolyslated (carbohydrate moeities added) making tropocollagen Mature collagen formed by crosslinks between hydroxylated prolines

Hemoglobin and Gas Exchange Bohr Effect

Gas exchange driven by pH HHb (protonated Hemoglobin) enters lungs Lungs are more basic, so HHb more likely to give up proton Oxygen (O2) binds to hemoglobin and it gives up the H+ HHb+ O2+HCO3- HbO2+H2O+CO2 The bicarbonate is the form that carbon dioxide goes to the lungs as. It travels in the blood plasma. All of the reactions occur inside the red blood cell

Gas Exchange Oxygenated hemoglobin travels to the tissues where it encounters an acidic enviroment. The acidity is the result of increase carbon dioxide, which is a metabolic byproduct In an acidic environment, hemoglobin tends to give up oxygen and bind the protons that are in the tissues Extra protons are there as the result of the acid CO2 Bicarbonate is moved out of the RBC, exchanged with Chloride (Cl-).

Gas Exchange Know that pH and Gas Pressures drive respiration Know which direction the equation is going H2O + HbO2- + CO2 HHb + O2 + HCO3- Which one occurs in the lungs? Which one occurs in the peripheral tissues?