Lehninger ch3 bioschemistry
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| What are the two conventions to identify C in amino acids | Two conventions are used to identify the carbons in an amino acid—a practice that can be confusing. The additional carbons in an R group are commonly designated beta, gamma, sigma , Epsilon , and so forth, proceed- ing out from the alpha carbon. For most other organic mol- ecules, carbon atoms are simply numbered from one end, giving highest priority (C-1) to the carbon with the substituent containing the atom of highest atomic number. Within this latter convention, the carboxyl Carbon of an amino acid would be C-1 and the alpha carbon Would be C-2 |
| Why properties are different for various amino acids? | They differ from each other in their side chains, or R groups, which vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water. |
| What are the main post-translational modifications of amino acids? | Some amino acid residues in a protein may be modified transiently to alter the protein’s function. The addition of phosphoryl, methyl, acetyl, adenylyl, ADP- ribosyl, or other groups to particular amino acid residues can increase or decrease a protein’s activity |
| How amino acids are classified by R-groups? | Their polarity, or ten- dency to interact with water at biological pH from nonpolar and hydrophobic (water-insoluble) to highly polar and hydrophilic (water-soluble). Within each class there are grada- tions of polarity, size, and shape of the R groups. -, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and hydrophobic. -Aromatic R Groups Phenylalanine, tyrosine, and tryp- tophan, with their aromatic side chains, are relatively nonpolar (hydrophobic). -Polar, Uncharged R Groups The R groups of these amino acids are more soluble in water, or more hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen bonds -Positively Charged (Basic) R Groups The most hydrophilic R groups are those that are either positively or nega- tively charged. - Negatively Charged (Acidic) R Groups The two amino acids having R groups with a net negative charge at pH 7.0 are aspartate and glutamate, each of which has a second carboxyl group. |
| Explain the properties of amino acids (molecular weight, pK values, pI, Hydropathy index). | Molecular weight : the sum of the atomic weights of the constituent atoms pI: The characteristic pH at which the net electric charge is zero Hydropathy index: values reflect the free energy (DG ) of transfer of the amino acid side chain from a hydrophobic solvent to water. Pka: refers to the equilibrium between the protonated positive nitrogen and deprotonated neutral nitrogen. |
| What does the Chirality of amino acids Mean? | For all the common amino acids except glycine, the ? carbon is bonded to four different groups: a car- boxyl group, an amino group, an R group, and a hydro- gen atom (in glycine, the R group is another hydrogen atom). |
| What is the General structure of amino acids,(what are the exception).? | All 20 of the common amino acids are alpha-amino acids. They have a carboxyl group and an amino group bonded to the same carbon atom (the alpha carbon) They differ from each other in their side chains, or R groups, This structure is common to all but one of the alpha-amino acids. (Proline, a cyclic amino acid, is the exception.) |
| Explain Peptide bond formation? | Formed by removal of the elements of water (dehydration) from the alpha-carboxyl group of one amino acid and the alpha-amino group of another Peptide bond formation is an example of a condensation reaction, a common class of reactions in living cells. |
| What defines properties of peptides and proteins ? | - size - amino acid composition - charge - hydrophobicity - modification |
| How these properties of peptides and proteins define methods of purification | -Size (gel filtration) -Charge (ion exchange) -Hydrophobicity (reverse phase) -Specific interactions (affinity) |
| Types of chromatography and what are their principles | -column chromatography which takes advantage of differences in protein charge, size, binding affinity, and other properties -Ion-exchange chromatography exploits differ- ences in the sign and magnitude of the net electric charge of proteins at a given pH -cation-exchange chromatography the solid matrix has negatively charged groups. In the mobile phase, proteins with a net positive charge migrate through the matrix more slowly than those with a net negative charge, -Size-exclusion chromatography, separates proteins according to size. In this method, large proteins emerge from the column sooner than small ones -Affinity chromatography is based on binding affinity |
| What are the components of chromatographic system and their purpose.? | -pump -mobile phase/ A solution, the mobile phase, flows through the matrix, - stationary phase/a solid, porous material (matrix) supported inside a column, -fraction collector - detector - recorder - column |
| What are principles of analytic methods (electrophoresis, isoelectric focusing, 2-D electrophoresis). | -electrophoresis/ Another important technique for the separation of pro- teins is based on the migration of charged proteins in an electric field, proteins can be visual- ized as well as separated, permitting a researcher to estimate quickly the number of different proteins in a mixture or the degree of purity of a particular protein preparation. - isoelectric focusing/is a procedure used to determine the isoelectric point (pI) of a protein, A pH gradient is established by allowing a mixture of low molecular weight organic acids and bases (ampholytes) to distribute themselves in an electric field generated across the gel. When a protein mixture is applied, each protein migrates until it reaches the pH that matches its pI. Proteins with different isoelec- tric points are thus distributed differently throughout the gel. 2-D electrophoresis/ permits the resolution of complex mixtures of proteins, Two-dimensional electrophoresis sepa- rates proteins of identical molecular weight that differ in pI, or proteins with similar pI values but different molecular weights. |
| What are the principles of immunological techniques (Western blotting, immunoprecipitation, immunocytochemistry, ELISA). | -Western blotting(Immunoblot)/use antibodies (or other specific ligands in related techniques) to identify target proteins among a number of unrelated protein species. They involve identification of protein target via antigen-antibody (or protein-ligand) specific reactions. -immunoprecipitation/Allows isolation of the protein of interest from the cell of tissue lysate; Also isolates proteins that interact with protein of interest. -immunocytochemistry/can confirm the expression and location of target peptides or protein antigens in the cell via specific combination of antibodies and target molecules. These bound antibodies can then be detected using several different methods. -ELISA/an immunological assay commonly used to measure antibodies, antigens, proteins and glycoproteins in biological samples designed for detecting and quantifying peptides, proteins, antibodies, and hormones. In ELISA, an antigen must be immobilized to a solid surface and then complexed with an antibody that is linked to an enzyme. CHECK SLIDES |