Essential Cell Biology 5th edition

170 CHAPTER 4 Protein Structure and Function
KEY TERMS
active site fibrous protein protein
allosteric globular protein protein domain
α helix GTP-binding protein protein family
amino acid sequence helix protein kinase
antibody intracellular condensate protein machine
antigen intrinsically disordered sequence protein phosphatase
β sheet ligand protein phosphorylation
binding site lysozyme quaternary structure
C-terminus mass spectrometry scaffold protein
chromatography Michaelis constant (K M ) secondary structure
coenzyme motor protein side chain
coiled-coil N-terminus substrate
conformation nuclear magnetic resonance subunit
cryoelectron microscopy (cryo-EM) (NMR) spectroscopy tertiary structure
disulfide bond peptide bond transition state
electrophoresis polypeptide, polypeptide chain turnover number
enzyme polypeptide backbone V max
feedback inhibition primary structure x-ray crystallography
QUESTIONS
QUESTION 4–9
Look at the models of the protein in Figure 4−11. Is the
red α helix right- or left-handed? Are the three strands that
form the large β sheet parallel or antiparallel? Starting at
the N-terminus (the purple end), trace your finger along the
peptide backbone. Are there any knots? Why, or why not?
QUESTION 4–10
Which of the following statements are correct? Explain your
answers.
A. The active site of an enzyme usually occupies only a
small fraction of the enzyme surface.
B. Catalysis by some enzymes involves the formation of
a covalent bond between an amino acid side chain and a
substrate molecule.
C. A β sheet can contain up to five strands, but no more.
D. The specificity of an antibody molecule is contained
exclusively in loops on the surface of the folded light-chain
domain.
E. The possible linear arrangements of amino acids are so
vast that new proteins almost never evolve by alteration of
old ones.
F. Allosteric enzymes have two or more binding sites.
G. Noncovalent bonds are too weak to influence the threedimensional
structure of macromolecules.
H. Affinity chromatography separates molecules according
to their intrinsic charge.
I. Upon centrifugation of a cell homogenate, smaller
organelles experience less friction and thereby sediment
faster than larger ones.
QUESTION 4–11
What common feature of α helices and β sheets makes them
universal building blocks for proteins?
QUESTION 4–12
Protein structure is determined solely by a protein’s amino
acid sequence. Should a genetically engineered protein in
which the original order of all amino acids is reversed have
the same structure as the original protein?
QUESTION 4–13
Consider the following protein sequence as an α helix:
Leu-Lys-Arg-Ile-Val-Asp-Ile-Leu-Ser-Arg-Leu-Phe-Lys-Val.
How many turns does this helix make? Do you find anything
remarkable about the arrangement of the amino acids in
this sequence when folded into an α helix? (Hint: consult the
properties of the amino acids in Figure 4−3.)
QUESTION 4–14
Simple enzyme reactions often conform to the equation:
E + S ↔ ES → EP ↔ E + P
where E, S, and P are enzyme, substrate, and product,
respectively.
A. What does ES represent in this equation?
B. Why is the first step shown with bidirectional arrows and
the second step as a unidirectional arrow?
C. Why does E appear at both ends of the equation?
D. One often finds that high concentrations of P inhibit the
enzyme. Suggest why this might occur.
E. If compound X resembles S and binds to the active site