Chapter 3 Vocabulary amino acids amino group carboxyl group functional group side chain backbone R group hydrophobic hydrophilic polar nonpolar monomer dimer trimer tetramer oligomer polymer oligopeptide polymerization macromolecule polypeptide protein condensation reaction dehydration reaction hydrolysis peptide bond N terminus C terminus primary structure secondary structure helix pleated sheet tertiary structure disulfide bonds Van der Waals interactions quaternary structure denaturation renaturation catalyst enzymes active site activation energy transition state substrate induced fit competitive inhibition allosteric regulation reaction rate Chapter 3 Expectations have a working understanding of The meanings and use of words on Vocabulary list Classify amino acid side chains by functional groups and chemical nature charged polar or nonpolar Polymerization into polypeptides and key features of peptide bond Levels of protein structure from primary to secondary tertiary and quaternary Interactions that stabilize folded proteins How enzymes accelerate the rates of chemical reactions How enzyme rates depend on temperature and concentrations of substrate and enzyme How competitive inhibitors differ from allosteric ligands How change in protein structure alters protein function Review the material at the end of the chapter Chapter 3 Sample Exam Questions 1 Using the amino acid table pick a polar uncharged a hydrophobic and a polar positively charged amino acid and reason out why they are hydrophobic and polar 2 An alpha helix is an example of what level of protein structure 3 What is a disulfide bond and how does it stabilize protein structure 4 What is the difference in binding site between a competitive and an allosteric inhibitor of an enzyme 5 An enzyme has a total of four active sites When you denature the molecule and study its composition you find that each active site occurs on a different polypeptide Which of the following hypotheses does this observation support A The enzyme is subject to allosteric regulation B The enzyme requires a cofactor to function normally C The protein s structure is affected by temperature and pH D The protein has quaternary structure 6 Which of the following observations is the strongest argument in favor of the hypothesis that protein structure and function are correlated A Proteins function best at certain temperatures B Proteins have four distinct levels of structure and many functions C Enzymes tend to be globular in shape D Denatured unfolded proteins do not function normally 7 What type of interaction is directly responsible for the formation of secondary structure A peptide bonds between adjacent amino acids B peptide bonds between nonadjacent amino acids C hydrogen bonds between sections of the polypeptide backbone D hydrogen bonds between side chains of amino acids 8 Which of the following is not true when comparing an uncatalyzed reaction to the same reaction with a catalyst A The catalyzed reaction will be faster B The catalyzed reaction will have a different G C The catalyzed reaction will have lower activation energy D The catalyzed reaction will not consume any of the catalyst 9 You ve discovered an enzyme that can catalyze two different chemical reactions Which of the following is most likely to be correct A The enzyme contains both alpha helices and beta pleated sheets B The enzyme is subject to both competitive inhibition and allosteric regulation C Two types of allosteric regulation occur The binding of one molecule activates the enzyme while the binding of a different molecule inhibits it D Either the enzyme has two distinct active sites or the reactants involved in the two reactions are very similar in size and shape 10 Enzymes accelerate reactions by preferentially binding to which state Why does this accelerate the reaction 11 At saturating substrate concentration what limits the rate of an enzymecatalyzed reaction Key 1 see text 2 secondary 3 a covalent bond joining the two sulfur atoms of two Cys residues it cross links the peptide chain and prevents the two parts from moving apart 4 competitive binds at active site and competes with substrate allosteric binds at some other site and influences the behavior of the protein by inducing a change in shape 5 D 6 D 7 C 8 B 9 D 10 transition state because binding to the TS lowers the energy barrier 11 the rate that the enzyme substrate complex can convert to product
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