Cheat Sheet - Final Biochem Part III

Capitulo ¾ 1- α-Keratin is an intermediate filament with a basic structural unit of two α helices in a coiled coil. Each helix has a seven-residue repeating unit (heptad repeat). A representation of the α helices of a coiled coil dimer is shown. Each letter represents a different amino acid residue. 2- The terms motif (fold) and domain  describe levels of protein organization more complicated than primary or secondary structure. Differentiate between motifs and domains by matching each phrase to the appropriate term. 3- A small generic section of the primary structure of an α helix is given by 4- When performing site-directed mutagenesis to test predictions about which residues are essential for protein function, which amino acid substitution would disrupt protein structure the most. 5- Classify the words or phrases as descriptions or examples of fibrous proteins, globular proteins, or both. 6- Based on the chemical properties of the residues, determine which sequences would exhibit which structural properties. 7- The development of two procedures to ionize peptides, ESI and MALDI, allowed the use of mass spectrometry in peptide sequencing and proteomics. This contribution to biochemistry won the developers a Nobel Prize in Chemistry in 2002. 8- Consider the partial sequence of a peptide. 9- Consider the mass spectrum. Determine the sequence of the peptide from the mass spectrum. Notice that two of the residues, L and R, are already identified for you. Assume that any residues with mass around 113 are leucine. 10- Tertiary structures of proteins can be very complex. Analyzing and recognizing common structural patterns is the first step in understanding how proteins form higher-order structures. Two terms, domain and motif (also called fold), describe protein structural patterns. 11- The carbon–nitrogen peptide bond is rigid, but rotation can take place about the N−C   and α the C  α −C bonds in a protein (C  α is the α carbon atom). These bond angles define the conformation of the peptide chain. 12- Classify each phrase as a description of alpha helices, beta sheets, beta turns, or all. 13- Classify each protein example according to its highest level of protein structure. 14- Alpha helices are a type of secondary structure in proteins. What is the length of a 35.0   kDa single-stranded α-helical protein segment? Assume a mean residue mass of 110 Da . 15- Beta (𝛽) sheets are a type of secondary structure in proteins. A segment of a single chain in   . How many residues are in this segment? an antiparallel 𝛽  sheet has a length of 116 Å 16- The Merrifield peptide synthesis takes place on a solid support. This process simplifies purification of intermediates by attaching the growing peptide chain to a polymer resin. The black ball represents one of the polystyrene beads that make up the polymer resin. 17- Classify the descriptions of keratin, collagen, and fibroin. Some phrases may apply to more than one protein. 18- Classify each peptide chain as part of a parallel β sheet, part of an antiparallel β sheet, either type of β sheet, or not part of a β sheet. 19- Polylysine and polyglutamate are two examples of synthetic polypeptides that can assume an α-helical structure under appropriate conditions. 20- The hydrogen bonding responsible for the secondary structure of a protein generally takes place between backbone carbonyl oxygen atoms and amide hydrogen atoms. In contrast, the hydrogen bonding that contributes to the tertiary structure generally occurs between amino acid side chains. 21- A protein has the amino acid sequence 22- A protein biochemist attempted to determine the amino acid sequence of a decapeptide. Use the results from the trypsin, chymotrypsin, and cyanogen bromide treatments to suggest the amino acid sequence of this decapeptide. 23- The image shows the tertiary structure of a protein segment. Tertiary structure results from different interactions, or forces, between groups. Move the example of each force to the appropriate description on the protein. Then, identify the major force controlling tertiary structure. 24- Categorize the given phrases as descriptions of α-keratin, collagen, or fibroin. 25- A sample (426 mg) of an oligomeric protein of 𝑀r 177,000 was treated with an excess of 1-fluoro-2,4-dinitrobenzene (Sanger's reagent) under slightly alkaline conditions until the chemical reaction was complete. The peptide bonds of the protein were then completely hydrolyzed by heating it with concentrated HCl.   The hydrolysate was found to contain 4.09 mg of DNP-Val. 2,4-Dinitrophenyl derivatives of the α-amino groups of other amino acids could not be found.