2. State the four types of attractive interactions that give rise to tertiary protein structure. 3. Can more than one type of secondary structure be present in the same protein molecule? Explain your answer.
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- 3. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?2. a. In the following diagram of a portion of a protein, label the types of interactions that are shown. b. What level of protein structure are these interactions producing? b. CH CH3 CH3 Polypeptide backbone CH2 H3C H3Ç 10 CH С—ОН - CH,-S-S-CH,- а. CH2 с. -CH,-CH,-CH2-CH2-NH 0-C-CH2- d.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. Draw (or insert) the general formula of an amino acid and label the four components. Which one gives the molecule its functional role? 2. What determines the three-dimensional structure a protein will have in the cell? 3. How is the structure of a protein related to its function in the cell? Be specific and give an example.4. Tertiary structure of a protein describes: A. Sequence of amino acids B. Location of disulphide bonds C. Amino terminal end amino acid D. The nature of protein folding 5. Study of linear sequence of amino acids is done by all techniques listed except: A. End group analysis B. Hydrolysis by proteolytic enzymes C. Analyzing the content of each aminOacid D. Denaturing the protein 6. Primary structure decides: A. Rate of synthesis of protein B. Biological activity of the protein C. Rate of degradation of the protein D. Effect of proteolytic enzymes on protein4. In the following diagram of a portion of a protein, label the types of interactions that are shown. CH H;Ć `CH, | H;C _CH3 ! CH - Polypeptide backbone c=OH CH2 -CH5–S}-CH,-- -CH;-CH-CH;-CH, NH," 0-C-CH, d. What level of protein structure are these interactions producing?
- 2. The following bonds help to hold together protein tertiary structure. Which order below reflects their relative strength (with the weakest on the left and the strongest on the right) A. Hydrogen bond - ionic bond - covalent bond - hydrophobic interactions. B. Hydrophobic interactions - hydrogen bond - disulfide bridge - ionic bond. C. Ionic bond- disulfide bridge - hydrophobic interaction - hydrogen bond. D. Ionic bond – hydrophobic interactions - hydrogen bonc disulfide bridge.8. The following proteins represent a wide range of molecular weights and isoelectric points. Mr is the molecular weight of a single protein chain. • Protein 1: Mr 68,544; pl 6.11 (monomer) • Protein 2: Mr 29,041; pl 5.32 (dimer) • Protein 3: Mr 15,805; pl 5.7 (dimer) • Protein 4: Mr 12,165; pl 4.74 a. Which protein is the most acidic? Explain your answer. b. Which protein will migrate the slowest in an SDS-PAGE? Explain your answer. c. In what order will these proteins elute from a cation exchanger at pH 8? Explain your answer. d. In what order will these proteins salt out from a pH 7 solution by the dropwise addition of saturated ammonium sulfate? Explain your answer. 83°F 立3. Proteins are important for numerous functions in a cell and their activity/function is dependent on their structure. Each protein folds into its respective structure and ionic bonds between ions in side chains of proteins drives protein folding as shown by the oppositely charged ions in the figure below. 15 H .O H N Protein Draw a picture similar to the one shown above to show what will happen to such interactions when the pH increases. Show how this impacts protein structure. (Hint: Is the hydrogen ion concentration high or low? Note that hydrogen ions can be added or lost into molecules depending on the pH and that the NH3* is affected in this case.) Draw a picture similar to the one shown above to show what will happen to such interactions when the pH decreases. Show how this impacts protein structure. (Hint: Is the hydrogen ion concentration high or low? Note that hydrogen ions can be added or lost into molecules depending on the pH and that the COO is affected in this case.)…
- 4. The interactions on the backbone (not the side chains) contribute to the (circle one): primary/secondary/ tertiary/quaternary structure of the protein. On your drawing for #3_ indicated the partial charges on the atoms near the new covalent bond. For alpha-helix, these atoms of opposite partial charges that are four amino acids away are interacting to form bonds. 5. The interactions between side chains contribute to the primary/secondary/tertiary/quaternary (circle one or more) structure(s) of the protein. 6. What happens when you denature a protein with heat or pH changes? Which bonds are most likely broken?5. Bread contains mixture of polypeptides known as gluten. This polypeptide has two types which are gliadins and glutenins. If both polypeptides have presence of short a-helix sections because of high proline content, what level of protein structure is being depicted? 5a. If intermolecular bonds form between glutenin and gliadin, what level of protein structure is being depicted? 5b. During analysis, hydrophobic amino acids (i.e., glutamine and proline) were not found on gluten protein surfaces. In this case, what level of protein structure is being shown?1. An intrinsically disordered protein (IDP) is a protein that lacks a fixed three- dimensional structure. Estimate the size of an IDP of 100 amino acids by calculating the most probable end-to-end length of the protein. Assume the protein is a freely-joined chain with the length of each segment (amino acid) b = 3Å.