Amino Acids, Peptides, and Proteins - PDF

image-15 (00-03-06)  Activity Let’s make Alanine or Valine with Ball and Sticks Take photo and send to [email protected] due : this Sunday image-22 (00-04-37) image-25 (00-05-16) A  Homework 4-ch3) homework8 Dr...

image-15 (00-03-06)  Activity Let’s make Alanine or Valine with Ball and Sticks Take photo and send to [email protected] due : this Sunday image-22 (00-04-37) image-25 (00-05-16) A  Homework 4-ch3) homework8 Draw 10 amino acids: Aromatic ring 3 Amino acids + charged 3 amino acids - charged 2 amino acids Glycine and Alanine image-35 (00-07-26) image-44 (00-09-23) Red circle= ionizable Side Chain image-55 (00-11-46) H+ H+ Hydrophobic /nonpolar Hydrophilic = polar  Titration of Amino Acids Amino acids with Non-ionizable Side Chain Amino acids with ionizable Side Chain Identify Amino acids Non-Charged Amino Acids Charged Amino Acids lysine  Recitation Watch the posted Video in 4-Ch3 Amino Acid Recitation How we study protein ? image-20 (00-02-17) image-67 (00-07-46) SDS-PAGE denaturation 03 SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) from youtube image-89 (00-10-20)  Topic Question 4-ch3 Explain SDS-PAGE and address what methods/how are used for measuring the size of proteins in SDS PAGE.  Topic Question 4-ch3 Illustrate the procedure of ion exchange, size exclusion, affinity chromatography image-92 (00-10-41) image-98 (00-11-23) Ms = determines mass-to-charge ratio (m/z) of its ion. Ions are generated by inducing either the loss or gain of a charge from a neutral species. Once formed, ions are electrostatically directed into a mass analyzer where they are separated according to m/z and finally detected. The result of molecular ionization, ion separation, and ion detection is a spectrum that can provide molecular mass and even structural information. Tandem MS  Topic Question 4-ch3 You are performing Protein sequencing. Explain how Edman degradation and MS for protein sequencing work. 1) logic 2) procedure  Topic Question 4-ch3 Explain two MSs : MALDI MS and Tandem MS  Discussion Discussion/Group Activity Homework 4-ch3) homework9 Draw a peptide : serine - glycine- tyrosine-alanine- leucine  QUESTION Which amino acid has three pKa values? A. leucine B. proline C. glycine D. threonine E. cysteine Which amino acid has three pKa values? E. cysteine Cysteine has three pKa values: pK1 (—COOH): 1.96 pK2 (—NH3+): 10.28 pK3 (R group): 8.18 Which amino acid would MOST frequently be found in the interior of a globular protein? A. Ala B. Lys C. glutamate D. cysteine Which amino acid would MOST likely be found in the interior of a globular protein? A. Alanine (Ala) Alanine has a nonpolar, aliphatic R group, —CH3. Nonpolar, hydrophobic side chains tend to cluster together within proteins, stabilizing protein structure through the hydrophobic effect.  Question Which statement is correct about peptides? A. Peptides have no α-carboxyl groups. B. Peptides have their amino acid sequences written from the N-terminus. C. Peptides do not have isoelectric points. D. Peptides are not biologically active. E. Peptide bonds are broken through condensation reactions.  Question , Response Which statement is correct about peptides? B. Peptides have their amino acid sequences written from the N-terminus. Peptides are named beginning with the amino-termi nal (N-terminal) residue.  Question 8 Which component is absolutely necessary for the purific ation of a protein? A. column chromatography B. the gene sequence of the protein C. a means of detecting the protein D. a centrifuge  Question 8, Response Which component is absolutely necessary for the purific ation of a protein? C. a means of detecting the protein To study a protein in detail, researchers must be abl e to separate it from other proteins in pure form and must have the techniques to determine its propertie s.  Question 9 Which protein would elute first from a gel filtration colum n? A. protein A, with Mr = 27,000 B. protein B, with Mr = 58,400 C. protein C, a homodimer with protomer Mr = 11,300 D. protein D, with Mr = 15,600  Clicker Question 9, Response Which protein would elute first from a gel filtratio n column? B. protein B, with Mr = 58,400 Size-exclusion chromatography, also called g el filtration, separates proteins according to size. In this method, large proteins emerge fr om the column sooner than small ones do.  Question 10 A new protein resembling myosin was reported. Unlike m yosin, it binds calcium. Its isoelectric point and molecular weight are very similar to those of myosin. Which method would BEST separate the new protein from myosin if thos e two proteins were in the same buffer solution? A. ion-exchange chromatography B. size-exclusion chromatography C. affinity chromatography D. dialysis E. fractionation  Question 10, Response Which method would BEST separate the new protein fro m myosin if those two proteins were in the same buffer s olution? C. affinity chromatography Attaching calcium to the beads in the column would creat e an affinity matrix that could help purify the protein. Prot eins that do not bind to calcium would flow more rapidly t hrough the column than the new protein, which does bin d calcium.  Question 12 Denaturing gel electrophoresis separates proteins base d on differences in: A. size and shape. B. molecular mass. C. charge. D. amino acid content.  Question 12, Response Denaturing gel electrophoresis separates proteins base d on differences in: A. size and shape. μ = electrophoretic mobility V = velocity V Z μ= = E = electrical potential E f Z = net charge f = frictional coefficient Thus, the migration of a protein in a gel during elect rophoresis is a function of its size and its shape.  Question 16 Which statement is true about mass spectrometry? A. Mass spectrometry can be performed on analytes in the liquid phase. B. Mass spectrometry can obtain the sequences of multiple polypeptide segments of 100 residues each. C. The mass (m) of an analyte is used to deduce the mass-to-charge ratio, m/z, with high precision. D. MALDI MS requires treatment of proteins with a protease before injection into a mass spectrometer. E. Mass spectrometry can monitor changes in the cellular proteome as a function of metabolic state.  , Response Which statement is true about mass spectrometry? A. C. E.  Question 18 Which statement is false? A. protein structure is commonly defined at four levels. between organisms. B. The function of a protein is a result of its amino acid sequence. C. Orthologs are homologs found in the same species. D. It is possible to change the amino acid sequence of a protein and have no effect on its function.  , Response Which statement is false? C. Orthologs are homologs found in the same species. Homologs from different species are called ortholog s.