Chapter 5 Biochemistry – Flashcards

D) are usually transient.

D) permanently associated with the protein

B) one O2 molecule and one amino acid atom

A) hyperbolic

E) the larger the Ka, the smaller the KDd (dissociation constant)

E) very similar tertiary structures, but different primary structures

B) binding of a molecule to a binding site affects binding properties of another site on the protein.

C.) oxygen binding

C) it increases the affinity of hemoglobin for oxygen

C) it rarely occurs in enzymes

D) it binds to the Fe n hemoglobin and prevents the binding of O2

D) hydrophobic

C) hemoglobin

B) epitope

B) Fc

C) are synthesized by a population of identical, or "cloned," cells

A) They convert chemical energy into kinetic energy.

B) an alpha helix.

A) actin filament assembly.

B) conformation of myosin.

Ans: Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.

Ans: (a) Binding of free Fe2+ to oxygen would result in the formation of reactive oxygen species that can damage biological structures. Heme-bound iron is less reactive in this regard. (b) Binding of oxygen to free heme can result in irreversible oxidation of the Fe2+ to Fe3+ that does not bind oxygen. The environment of the heme group in proteins helps to prevent this from occurring.

Ans: An experiment would be carried out in which a fixed amount of the protein is incubated with varying amounts of ligand (long enough to reach equilibrium). The fraction of protein molecules that have a molecule of ligand bound is then determined. A plot of this fraction () vs. ligand concentration [L] should yield a hyperbola. The value of [L] when = 0.5 is equal to 1/Ka.

Ans: It binds to heme with a higher affinity than oxygen, and thus prevents oxygen from binding to hemoglobin.

Ans: Ka = 1/Kd. The larger the Ka (and hence the smaller the Kd), the higher the affinity of the protein for the ligand.

0= [L]/[L]+Kd thus = Kd/Kd+Kd = 1/2

Ans: The geometry of binding O2 and CO to heme is slightly different. In myoglobin there is a histidine residue that does not interact with the heme iron, but can interact with a ligand that is bound to the heme. It does not affect O2 binding but because of steric hindrance, it may prevent CO binding. As a result the relative affinity of protein-bound heme for CO and O2 is only 200, compared to 20,000 for free heme.

Ans: The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low partial pressures of O2 that occur in tissues. In contrast, the cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial pressures such as occur in the lungs, but lower affinity in the tissues. This permits hemoglobin to bind O2 in the lungs and release it in the tissues.

Ans: In the concerted model, binding of a ligand to one site on one subunit results in an allosteric effect that converts all of the remaining subunits to the high-affinity conformation. As a result, all of the subunits are either in the low- or high-affinity conformation. In the sequential model, each subunit is changed individually to the high affinity conformation. As a result, there are many possible combinations of low- and high-affinity subunits.

Ans: BPG binds to a cavity between the subunits. It binds preferentially to molecules in the low-affinity T state, thereby stabilizing that conformation.

Ans: (a) The affinity decreases with decreasing pH. (b) At lower pH (i.e., higher H+ concentration) there is increasing protonation of protein residues such as histidine, which stabilizes the low affinity conformation of the protein subunits.

Ans: In Hemoglobin S, the wild-type glutamate at residue 6 of the B-chain is replaced by valine. When oxygen is bound, both Hemoglobin A and Hemoglobin S are soluble, but in the deoxy- form. Hemoglobin S (but not Hemoglobin A) becomes very insoluble, due to exposure of the hydrophobic valine residue. This exposed "patch" causes aggregation of deoxy-Hemoglobin S into long insoluble fibrous aggregates, resulting in distorted shapes of the red blood cells (and leading to the symptoms of the disease). (See p. 168-169 and Fig. 5-20.)

Ans: As a result of genetic recombination mechanisms, antibody-producing B cells are capable of producing millions of different antibodies with different binding specificities.

Ans: An IgG protein contains two copies of a large polypeptide (heavy chain) and two copies of a small polypeptide (light chain). structure contributes significantly to the tertiary structure of domains of both chains. Disulfide bonds link the heavy chains to one another and to the light chains. The chains are arranged in a Y-shaped structure where the two arms are linked to the base by a protease sensitive ("hinge") region.

Ans: Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of the antigen and the antigen-binding site of the antibody.

Ans: The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as binding occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter binding.

Ans: The specific antibody is covalently attached to an inert supporting material, which is then packed into a chromatography column. The protein solution is passed through the column slowly; most proteins pass directly through, but those for which the antibody has specific affinity are adsorbed. They can subsequently be eluted by a buffer of low pH, a salt solution, or some other agent that breaks the antibody-antigen association.

Ans: The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association. These make possible immunoaffinity chromatography, immunocytochemistry, enzyme-linked immunosorbent assay (ELISA), and immunoblotting, all of which are described on pp. 173-175.

Ans: Myosin contains two copies of a large polypeptide (heavy chain) and four copies of a small polypeptide (light chain). The helix contributes significantly to the structure of the heavy chains. At their carboxyl termini, the heavy chains are wrapped around each other in a fibrous left-handed coil. At their amino termini, they each have a globular domain with which the light chains are associated.

Ans: G-actin is a monomeric protein that can polymerize to form a long polymeric filament known as F-actin.

Ans: ATP binding to myosin results in a conformational change that causes dissociation of actin from the myosin. ATP hydrolysis results in a change of orientation of the myosin relative to the actin filament, which allows movement to the next actin subunit. This is followed initially by release of the phosphate hydrolysis product and weak binding of the myosin to this actin subunit, and, subsequently, by tight binding and release of the ADP hydrolysis product.

Ans: First, ATP binds to myosin and a cleft in the myosin molecule opens, disrupting the actin-myosin interaction so that the bound actin is released. Second, ATP is hydrolyzed, causing a conformational change in the protein to a "high-energy" state that moves the myosin head and changes its orientation in relation to the actin thin filament. Myosin then binds weakly to an F-actin subunit closer to the Z disk than the one just released. Third, as the phosphate product of ATP hydrolysis is released from myosin, another conformational change occurs in which the myosin cleft closes, strengthening the myosin-actin binding. Fourth, this is followed quickly by a "power stroke" during which the conformation of the myosin head returns to the original resting state, its orientation relative to the bound actin changing so as to pull the tail of the myosin toward the Z disk. ADP is then released to complete the cycle. (See Fig. 5-31, p. 178.)

Ans: A given muscle consists of many bundled muscle fibers, each of which contains many myofibrils, each of which contains many thick and thin filaments. Furthermore when a muscle contracts, the myosin molecules move asynchronously. Thus, the individual steps of individual myosin molecules are masked by the millions of other myosin molecules taking steps at different times.