1. Why a peptide bond can't rotate freely? 6%. 2. The and are two amino acids usually will break an a helix. 4% 3. The main force to keep a helices or B pleated sheets in their conformation is 4%.
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- 6. b. Draw a box around the disulfide bridge in oxytocin, if present, or write "none". 7. Mark each peptide bond in oxytocin by making the corresponding line in the structure thicker or marking it with a different color. The first one is shown for you as an example (in dark orange). 8. Number the central carbon of each amino acid in oxytocin by pointing a small arrow to it or by circling the corresponding vertex in the image. Numbers 1 and 2 indicate the central carbons of the first and second amino acids of oxytocin, and are shown for you as an example. 9. Fill out the following table, listing amino acids that make up oxytocin in order, from the N terminus to the C terminus, characterizing each amino acid by the properties of its R group (side chains), and briefly indicating the reasoning for the characterization. You may consult amino acid groupings by category in the slides (or the textbook, p.49), but you must explain the reasoning for each in your own words. CO 1 AA# Abbre- Full…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 CH3I. II. III. IV. V. O HƠN-CH-CANH-CH-C-NH-CH-CO alanyl CH3 2. Types of protein structures: What is the type of protein structure that contains a single strand and bound by disulfide bond. glycyl OH serine The structure containing an alpha- helix CH, 0 || H₂N-C-C-OH H O The structure contains beta pleated sheets The structure is made up of subunit What is the difference between a tertiary structure and a quaternary structure? CH₂OH 3. Indicate which structure is at low pH (acidic, basic or neutral (zwitterion) protein structures? H R H₂N-C-COO™ 4. What are five factors that affects 5.Indicate the amino acid as polar or nonpolar OH CH, O ! H₂N-C-C-OH H CH: 0 H₂N-C-C-0 H CH3 CH3 CH CH, O H₂N-C-C-0 H 6) Acids and bases denature a protein by disrupting A) peptide bonds and ionic bonds. B) amide bonds and alkene bonds. C) hydrophobic interactions and peptide bonds. D) ionic bonds and hydrophobic interactions. E) ionic bonds and hydrogen bonds. 5) Heat denatures a protein by disrupting A)…
- Select the properties that apply to the secondary structure alpha helices (select all that apply). U 0 can be Antiparallel can be Parallel are typically right handed are typically left handed obeys n+4 rule are formed by the pattern of hydrogen bonding the backbone makes with itself are formed by the pattern of covalent bonds the backbone makes with itself are formed by the pattern of electrostatic attractions the backbone makes with itself4. Below is data obtained for an unknown protein's dihedral angles. Each dot represents the dihedral angles of each amino acid. i. psi ii. 180 120 60 C -60 -120 0.0005 0.02 0.02- -1880 -120 What secondary structure(s) are present in the unknown protein? -60 phi 60 120 0.0005 Why is there a lot of white space? 1802. Two amino acids are shown below. Name them in the blanks, and then draw the structure of the dipeptide they would form if a peptide bond connected them (in the order shown.) Draw the dipeptide as a Zwitterion, and name it in the blank. H3N-CH- CH-C-O CH3 + + H3N-CH₂-C O
- Oligopeptide 1 Oligopeptide 2 N. N- H. N-H H Give the three-letter and one-letter names of the amino acids in each oligopeptide starting from the amino terminal to the carboxyl terminal. Make sure that the amino acid names are arranged in CORRECT order for both oligopeptides.-100 100 8. This is a helical wheel projection. The following amino acids of your protein were predicted to participate in an alpha helix: DRMVEHACKSI. a. Plot these amino acids in the helical wheel projection below. b. Is the alpha helix in your protein hydrophobic, amphipathic or hydrophobic? c. Would you expect this helix to be on the interior of the protein, exposed, or partially exposed?Which of the following is true of the molecule below? nucleotide 5' 3′ H₂C H₂C TNHNA O. HN CNH…NG NH O NH O HNU NH O CNHNG OHN nucleoside CH₂ CH₂ a purine pairs with a pyrimidine base the bases are held together by covalent bonds a nucleoside is made of the same components as a nucleotide The bases make up the backbone on the sides of the molecule
- 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.1. what do you think a “peptide”means? 2. Proteins are extremely long, folded chains of amino acids, containing between 150-1000 amino acids linked together in a straight chain. A protein will have a long repeating chain of-N-C-C- as its backbone, with different R groups sticking out. How long could a protein be? be specific. 3. Add the C’s and H’s into their structural formulas. picture includedBelow is the primary structure of a protein. A R 1 I I H H || O H 1 Psi bond [Select] Phi bond [Select] N-terminus [Select] B C D H O I || C-terminus [Select] NC-C-N-C-C-N-C-C-N-C-C-N-C-C - N... I 1 H H I R R H I 11 O HO I || R R I I H a. For each part of the question, select the letter associated the with appropriate component of the structure. Peptide bond [Select] I H U MO b. Which letter represents a bond without 360-degree rotation? [Select] H |