CHAPTER 4 PROTEIN STRUCTURE AND FUNCTION 2009 Garland Science Publishing The Shape and Structure of Proteins 4 1 Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right gene regulatory motor storage enzyme transport structural special purpose receptor signal A insulin B carboxylase C rhodopsin D hemoglobin E ferritin F myosin G green fluorescent protein H tubulin I homeodomain proteins 4 2 Indicate whether the following statements are true or false If a statement is false explain why it is false A Generally the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain B The polypeptide backbone refers to all atoms in a polypeptide chain except for those that form the peptide bonds C The chemical properties of amino acid side chains include charged uncharged polar and nonpolar D The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions which favor the clustering of nonpolar side chains in the interior 4 3 Fill in the blank spaces in the table below The first row has been completed for you 4 4 Fully folded proteins typically have polar side chains on their surfaces where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent In contrast some proteins have a polar side chain in their hydrophobic interior Which of following would not occur to help accommodate an internal polar side chain a A hydrogen bond forms between two polar side chains b A hydrogen bond forms between a polar side chain and protein backbone c A hydrogen bond forms between a polar side chain and an aromatic side chain d Hydrogen bonds form between polar side chains and a buried water molecule 4 5 To study how proteins fold scientists must be able to purify the protein of interest use solvents to denature the folded protein and observe the process of refolding at successive time points What is the effect of the solvents used in the denaturation process a The solvents break all covalent interactions b The solvents break all noncovalent interactions c The solvents break some of the noncovalent ineractions resulting in a misfolded protein d The solvents create a new protein conformation 4 6 Which of the following statements is true a Peptide bonds are the only covalent bonds that can link together two amino acids in proteins b The polypeptide backbone is free to rotate about each peptide bond c Nonpolar amino acids tend to be found in the interior of proteins d The sequence of the atoms in the polypeptide backbone varies between different proteins 4 7 For each of the following sentences fill in the blanks with the best word or phrase selected from the list below Not all words or phrases will be used each word or phrase should be used only once A newly synthesized protein generally folds up into a conformation All the information required to determine a protein s conformation is contained in its amino acid On being heated a protein molecule will become as a result of breakage of bonds On removal of urea an unfolded protein can become The final folded conformation adopted by a protein is that of energy composition covalent denatured highest irreversible lowest noncovalent renatured reversible sequence stable unstable 4 8 The correct folding of proteins is necessary to maintain healthy cells and tissues Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer s Huntington s and Creutzfeld Jacob disease the specific faulty protein is different for each disease What is the ultimate fate of these disease causing unfolded proteins a They are degraded b They bind a different target protein c They form structured filaments d They form protein aggregates 4 9 The three dimensional coordinates of atoms within a folded protein are determined experimentally After researchers obtain a protein s structural details they can use different techniques to highlight particular aspects of the structure What visual model best displays a protein s secondary structures helices and sheets a ribbon b space filling c backbone d wire 4 10 Typical folded proteins have a stability ranging from 7 to 15 kcal mol at 37 C Stability is a measure of the equilibrium between the folded F and unfolded U forms of the protein with the unfolded form having a greater free energy See Figure Q4 10 for a protein with a stability of 7 1 kcal mol calculate the fraction of protein that would be unfolded at equilibrium at 37 C The equilibrium constant Keq is related to the free energy G by the equation Keq 10 G 1 42 Figure Q4 10 4 11 Although all protein structures are unique there are common structural building blocks that are referred to as regular secondary structures Some have helices some have sheets and still others have a combination of both What makes it possible for proteins to have these common structural elements a specific amino acid sequences b side chain interactions c the hydrophobic core interactions d hydrogen bonds along the protein backbone 4 12 Which of the following is not a feature commonly observed in helices a left handedness b one helical turn every 3 6 amino acids c cylindrical shape d amino acid side chains that point outward 4 13 Which of the following is not a feature commonly observed in sheets a antiparallel regions b coiled coil patterns c extended polypeptide backbone d parallel regions 4 14 You wish to produce a human enzyme protein A by introducing its gene into bacteria The genetically engineered bacteria make large amounts of protein A but it is in the form of an insoluble aggregate with no enzymatic activity Which of the following procedures might help you to obtain soluble enzymatically active protein Explain your reasoning A Make the bacteria synthesize protein A in smaller amounts B Dissolve the protein aggregate in urea then dilute the solution and gradually remove the urea C Treat the insoluble aggregate with a protease D Make the bacteria overproduce chaperone proteins in addition to protein A E Heat the protein aggregate to denature all proteins then cool the mixture 4 15 Protein structures have several different levels of organization The primary structure of a protein is its amino acid sequence The secondary and tertiary structures are more complicated Consider the definitions below and select