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1、1 List three geometric features distinguishing atoms connected by a covalent bond versus those connected by a weak bond. How might these differences come into play when two macromolecules interact?(1) The strength of the bond ( covalent H:H 0.74, H-H in van der Waals bond 1.2)(2) Bond angle: covalen
2、t bond angles are fixed (a carbon atom with four covalent bonds, tetrahedral 109, weak bond angels are more variable(3) Freedom of rotation: single covalent band permits free rotation, double or triple are rigid, weaker bonds are less rigid (ionic bonds have no restriction on the relative orientatio
3、ns of bonded atoms)(4)directionalweak bond:In aqueous solutions, the average energy of a secondary bond is strong enough to make the secondary bond with other molecules ( the free energy equation)Organic molecules tending to form hydrogen bonds are water solubleHydrophobic “bonds” stabilize macromol
4、eculesWeak bonds attach enzymes to substratesWeak bonds mediate most protein-DNA and protein-protein interactionscovalent bond: primary Structure2Which is more likely to involve the most significant loss of free energy: the hybridization of two 100 base-pair stretches of single-stranded DNA to form
5、a double helix, an enzyme binding to its substrate, or an antibody binding to an antigen? Explain your answer.This process to form hydrogen bonds, more energy is required.The hybridization of the two strands of DNA would involve the greatest loss of free energy. Enzyme-substrate interactions involve
6、 many fewer weak bonds, which makes sense because this interaction is transitory短暂的 by nature. Antibody-antigen interactions are typically more extensive, and thus stronger, but still involve only a handful of specific interactions. Hybridization of two DNA molecules yields the most free energy, as
7、energy is provided by at least two hydrogen bonds formed per base pair as well as by the stacking interactions between adjacent bases.3What happens to the level of free energy during a spontaneous reaction? When free energy is lost during a reaction, what becomes of the energy? What occurs when a co
8、llection of atoms reaches its lowest energy state?Free energy is decrease. Free energy, lost as the equilibrium is approached, either transformed into heat or used to increase the amount of entropy. When a collection of atoms reaches its lowest state, it is in a state of equilibrium. 4 The (G associ
9、ated with a protein binding to an identical protein to form a homodimer（同源二聚体） is -2 kcal/mol. What is the Keq of this interaction at 25C? What does this say about the binding of these proteins at this temperature?G = -RT ln Keq Keq= e -G /RT R=1.987 cal/deg-mol T=298 e=2.718 Keq=29.30 This Keq mean
10、s that at equilibrium, the ratio of the bound proteins to the unbound proteins is nearly 30:1, meaning that virtually all of the proteins will bind to each other if present at molar concentrations. 5Describe and compare the three main types of weak chemical bonds that exist in biological systems.Van
11、 der Waals forces are produced from random fluctuations in the distribution of electrons within molecules. Because of these fluctuations, individual atoms experience temporary partial charges, and these partial charges can induce an opposite charge in neighboring atoms. These opposite charges then c
12、ause the atoms to be somewhat attracted to each other. Van der Waals attractions are very weak, typically about 1 kcal/mol, which is just slightly greater than the average thermal energy of molecules at room temperature. Van der Waals forces usually involve nonpolar atoms and can only work over a ve
13、ry small range of distances, as the atoms strongly repel抵抗 each other if too close and the van der Waals attractions rapidly fall to insignificant levels with increasing distance. Hydrogen bonds involve an interaction between a hydrogen with a partial positive charge and a nearby, negatively-charged
14、 atom. Such bonds typically arise where a hydrogen is covalently bound to a strongly electronegative atom, such as oxygen or nitrogen, and thus acquires a partial positive charge. Such partially charged hydrogens can then interact with neighboring groups with a negative charge, such as an oxygen or
15、nitrogen that is covalently bound toand which has obtained a partial negative charge froma less electronegative atom such as hydrogen or carbon. Hydrogen bonds are stronger than van der Waals forces, on the order of 3 to 7 kcal/mol. Ionic bonds can form between any two adjacent atoms having opposite
16、 charges of at least one unit. Sometimes, such bonds can involve hydrogen bonds, such as an interaction between a negatively charged oxygen within a COO- group and a positively-charged hydrogen within an NH3+ group. Ionic bonds are relatively strong, with energies of about 5 kcal/mol. 6 Describe the importance of distance to van der Waals interactions. How do
