BCH 3125 Lecture Notes - Lecture 7: Protein Structure, Filter Paper, Equilibrium Constant

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24 Sep 2017

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Function of proteins: thermodynamics of binding: binding: thermodynamics of ligand binding. Ligand: a(cid:374)(cid:455) (cid:373)ole(cid:272)ule that (cid:271)i(cid:374)ds to a(cid:374)othe(cid:396) (cid:373)ole(cid:272)ule. I(cid:374) (cid:271)io(cid:272)he(cid:373)ist(cid:396)(cid:455), (cid:862)liga(cid:374)d(cid:863) usuall(cid:455) (cid:396)efe(cid:396) to a small molecule such which binds to a macro molecule. The macromolecule is often referred to as the receptor for the ligand. In protein-protein interactions, proteins themselves can be thought of as ligands. Ligands and their receptors bind in various manners, but the most common one is that they created something called a non-covalent complex. This means that the molecular components are held together by non-covalent interactions (such as ionic interactions, hydrogen bonds, van der waals, etc. ) So far, we talked about the equilibrium/thermodynamic view of binding. We can also think of binding from a kinetic perspective. Where there is an association energy barrier to the formation of our complex, and when the complex is bound there is the reverse reaction where it comes apparent.

Related Questions

16.Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form

multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large

distances within the cell and in the extracellular space. Which protein is not classified as a fibrous protein?

(a)elastase (b)collagen (c)keratin (d)elastin

17.You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a

single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through

the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely

to explain this result?

(a)the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers

(b)a change that results in the mutant proteinâs acquiring an overall positive instead of a negative charge

(c)a change that results in the mutant proteinâs being larger than the wild-type protein

(d)a change that results in the mutant proteinâs having a slightly different shape from the wild-type protein

18.Which of the following statements is true?

(a)Disulfide bonds are formed by the cross-linking of methionine residues.

(b)Disulfide bonds are formed mainly in proteins that are retained within the cytosol.

(c)Disulfide bonds stabilize but do not change a proteinâs final conformation.

(d)Agents such as mercaptoethanol can break disulfide bonds through oxidation.

19.Proteins bind selectively to small molecule targets called ligands. The selection of one ligand out of a mixture of

possible ligands depends on the number of weak, noncovalent interactions in the proteinâs ligand-binding site. Where

is the binding site typically located in the protein structure?

(a)on the surface of the protein (b)inside a cavity on the protein surface

(c)buried in the interior of the protein (d)forms on the surface of the protein in the presence of ligand

thanks

An allosteric interaction between a ligand and a protein is one in which: 74. changes in Km are negligible, so Km can be treated as a constant. C. binding of a molecule to a binding site affects binding of additional molecules to the same site. binding of a molecule to a binding site affects binding properties of another site on the protein. binding of the ligand to the protein is covalent. multiple molecules of the same ligand can bind to the same binding site. A. D. VO Vmax. E. varying [S] has no effect on Vo. 78. The steady state assumption, as applied to B. enzyme kinetics, implies: Km = Ks. the enzyme is regulated the ES complex is formed and broken down at equivalent rates. the Km is equivalent to the cellular substrate concentration A. B. C. C. D. D. E. the mximum velocity occurs when two different ligands can bind to the same binding site. E. the enzyme is saturated. The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: 79. 75. One of the enzymes involved in glycolysis aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the: Substrate added vo COmol/min) (mmol/L) A. apoenzyme. B. coenzyme. C. holoenzyme. D. prosthetic group. E. substrate 0.8 217 325 488 647 76. 1,000 The role of an enzyme in an enzyme- catalyzed reaction is to: bind a transition state intermediate, such that it cannot be converted back to substrate. ensure that all of the substrate is converted to product ensure that the product is more stable than the substrate. increase the rate at which substrate is converted into product. make the free-energy change for the reaction more favorable. A. The Km for this enzyme is approximately: B. C. D. E. A. 1 mM B. 1,000 mM. C. 2 mM D. 4 mM E. 6 mM 80. In competitive inhibition, an inhibitor: binds at several different sites on an enzyme. binds covalently to the enzyme. binds only to the ES complex. binds reversibly at the active site. lowers the characteristic Vmax of the enzyme A. B. C. D. E. 77. The benefit of measuring the initial rate of a reaction VO is that at the beginning of a reaction: A. [ES] can be measured accurately. B. changes in [S] are negligible, so [S can be treated as a constant

BCH 3125 Lecture Notes - Lecture 7: Protein Structure, Filter Paper, Equilibrium Constant

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