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- 6) Proline is not commonly found in the middle of a-helices because its ring structure prevents it from adopting the proper value and because it disrupts the hydrogen-bonding pattern of the helix. Looking at the structure of proline in the amino acid sequence below, suggest how this residue would disrupt the hydrogen-bonding pattern of an a-helix. 'N H R N N H *** R6. Peptide bonds link many amino acids into chains of subunits that make polypeptides, or proteins. In the space below, or on a blank sheet of paper, draw the dehydration synthesis reaction showing the peptide bond that forms between two alanine (C3H;NO2) amino acids. Remember that all amino acids have an amino functional group at one end (N-terminal end) and a carboxyl functional group at the other end (C-terminal end). Also, alanine is an amino acid that has a CH3 off the middle ("R" group) carbon.1. Hydrogen bonds can form an alpha helix or beta sheet. The hydrogen atom has a partial positive because of the atom it is covalently bound to. Name the two most common atoms hydrogen bonds within biological systems that give hydrogen a partial positive charge. 2. Are the atoms named in the question above in the backbone of the protein or are they found in R groups? Which R groups? 3. Besides hydrogen, what other atom is involved in the hydrogen bonds in an alpha helix or beta sheet? In other words, hydrogen is interacting with what other atoms when it makes a hydrogen bond? 4. Write out, in order, the full names of the seven amino acids circled in the picture.
- 11. A polypeptide is making a short a-helix. A typical residue in an a-helix is involved in two H-bonds. At a minimum, how many residues this helix could have?4. Amino acids are linked together by peptide bonds to form polypeptides. (a) Draw the structure of a tripeptide (b) draw an asterisks (*) directly beside all alpha carbons and draw a square around all peptide bonds (c) Use arrows to identify and label the N-terminus and C-terminus (d) Draw a circle around the R group of each amino acid residue in the tripeptide and classify each R group as polar, non polar, acidic, or basic (e) Using the abbreviated names of the amino acids, provide the primary structure of the tripeptide you have drawn.2. Of the two sequences, which is more likely to have helical structure. Explain. a) -Glu-Asp-Glu-Glu-Asp-Leu- b) -Glu-Leu-Asp-Arg-Val-Lys-
- 3. Choose one of the following structures (a or b) to draw. a) Draw the basic structure of a nucleotide that is found only in RNA. Use 'P' for the phosphate (or try to draw this functional group if you wish). You must correctly draw the sugar/ribose, and include the appropriate nitrogenous base attached at the correct location. OR b) Draw the basic structure of the polysaccharide amylose (starch) - only include 3 monosaccharides within this chain. You do not need to draw the 'C' atoms within the ring, unless you want to. If you wish to leave the hydrogen atoms out that is fine, but make sure to include all functional groups and important bonds.3. Choose one of the following structures (a or b) to draw. a) Draw the basic structure of a nucleotide that is found only in RNA. Use 'P' for the phosphate (or try to draw this functional group if you wish). You must correctly draw the sugar/ribose, and include the appropriate nitrogenous base attached at the correct location. OR b) Draw the basic structure of the polysaccharide amylose (starch) - only include 3 monosaccharides within this chain. You do not need to draw the 'C' atoms within the ring, unless you want to. If you wish to leave the hydrogen atoms out that is fine, but make sure to include all functional groups and important bonds. 4. Illustrate with diagram(s) the process of competitive inhibition. Your labels and a brief description will be enough to summarize the process perfectly.4. Do the "Bond X" bonds in Figure 4 involve atoms in the amino acid R groups or in the polypeptide "backbone"/ "main chain" atoms? 5. Given Your Answer To “b," are each of the following statements True or False? Be able to explain your reasoning. o Only very specific primary sequences can form a-helices and B-sheets. o Many different primary sequences can form a-helices and B-sheets. Each arrow depicted in Figure 4D represents consecutive amino acids in the primary sequence of the polypeptide, while the different arrows may be formed from amino acids that are removed from each other in the primary sequence. Each arrow is referred to as a B-strand, and the structure formed through interaction of the B-strands is the B-sheet. In a complete protein, other segments of the protein would connect the different B-strands. 6. Do the "Bond X" bonds in the B-sheet connect atoms from the same B-strand or neighboring strands? TERTIARY STRUCTURE (A) (B) (C) Figure 4-17 Essential Cell Biology 3/e (o…
- 8) The figure shows an unfolded polypeptide consisting of six amino acids. Describe how cooperativity will drive protein folding of the polypeptide chain into an alpha-helixe- 10EEHOW is AG changed as each amino acid is incorporated into the secondary structure - s)? O H O H 3 H. H. 5 CH-C H. 6 -N-CH-C- OH O H,N CH-C -N CH C-N CH CH CH2 CH2 CH2 CH2 CH OH CH H;C CH316) Which of the following occurs when proteins fold? O The protein adopts Its lowest energy state form O Most of the non-polar and hydrophoblc residues are found burled in the proteln O The charged residues are found on the outside of the protelin O Secondary structural elements form O All of the above 17) Which of the following is NOT true about an a-helix? O The side chains extend radially outward from the helix axis DRis held together primarly by hydrogen bonds Ot usually involves multiple polypeptide chains O The peptide backbone is on the inside of the helix1. Draw the tripeptide: Val-Leu-Met at pH 7 with the N-terminus to the left and C-terminus to the right. On your drawing, do the following: a. Draw a triangle around the alpha carbons. b. Draw a box around the R-groups. c. Circle the atoms capable of hydrogen bonding. d. Highlight the peptide bond. Ma voy bludy 2. What specific atoms in your tripeptide (above) can participate in hydrogen bonding?